@article{lindsey_2024, title={A life in light - in honor of David Mauzerall on his 95th birthday}, volume={6}, ISSN={["1573-5079"]}, DOI={10.1007/s11120-024-01105-6}, journal={PHOTOSYNTHESIS RESEARCH}, author={Lindsey, Jonathan S.}, year={2024}, month={Jun} } @article{taniguchi_lindsey_2024, title={Acquisition of absorption and fluorescence spectral data using chatbots}, volume={12}, ISSN={["2635-098X"]}, url={https://doi.org/10.1039/D4DD00255E}, DOI={10.1039/D4DD00255E}, abstractNote={Spectra – the lifeblood of photochemistry – have been very difficult to find in the literature. Chatbots, remarkably, may enable their more efficient acquisition and prove to be generally powerful tools for searching the scientific literature.}, journal={DIGITAL DISCOVERY}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2024}, month={Dec} } @article{taniguchi_du_lindsey_2024, title={Appropriate handling of fluorescence spectra for accurate spectral overlap (J) values in Forster energy transfer (FRET) calculations}, volume={13083}, ISBN={["978-1-5106-7489-9"]}, ISSN={["1996-756X"]}, DOI={10.1117/12.3025086}, journal={SPIE FUTURE SENSING TECHNOLOGIES 2024}, author={Taniguchi, Masahiko and Du, Hai and Lindsey, Jonathan S.}, year={2024} } @article{cao_nguyen_nevzorov_jovanovic_nalaoh_lindsey_2025, title={Conformational Analysis of Swallowtail Motifs in Porphyrins}, url={https://doi.org/10.1021/acs.joc.4c02059}, DOI={10.1021/acs.joc.4c02059}, abstractNote={Aqueous solubilization of porphyrins, often accomplished with appended polar aryl groups, can also be achieved with symmetrically branched alkyl (i.e., swallowtail) groups terminated with polar moieties. Here, carboxylic acids are employed as termini (versus prior phosphono- or phosphoester termini) in designs of trans-AB-porphyrins bearing a single swallowtail group (A) or trans-A2-porphyrins bearing two swallowtail groups. Variable-temperature 1H NMR studies (−60 to 97 °C) revealed that the 4-heptanedioic acid group at the meso-position of the free base porphyrin rotates with rate constant 5 s–1 (310 K) and Arrhenius energy barrier Ea = 11.5 kcal/mol, whereas an isopropyl group undergoes rotation ∼1000-times faster (k = 5770 s–1). The interconversion is sufficiently fast that conformational diastereomers, as when two such swallowtail groups are present in a trans-A2-porphyrin, would not be isolable at room temperature (Class I atropisomers). DFT calculations (4 porphyrins containing the isopropyl or 4-heptanedioic acid groups) showed that the lowest energy conformer contains the swallowtail C–H unit in the plane of the porphyrin. The presence of one or two 4-heptanedioic acid moieties imparted solubility of the porphyrin in phosphate-buffered saline (PBS). The results suggest applications in the life sciences where compact, aqueous-soluble porphyrins are desired.}, journal={The Journal of Organic Chemistry}, author={Cao, Phuong-Lien Doan and Nguyen, Khiem Chau and Nevzorov, Alexander A. and Jovanovic, Milena and Nalaoh, Phattananawee and Lindsey, Jonathan S.}, year={2025}, month={Jan} } @article{govindjee_canaani_cellarius_diner_greenbaum_hou_kiang_lindsey_mauzerall_mauzerall_et al._2024, title={Contributions of David Mauzerall to photosynthesis research - celebrating his 95th th birthday}, volume={8}, ISSN={["1573-9058"]}, DOI={10.32615/ps.2024.029}, abstractNote={We honor here Professor David Mauzerall, a pioneer in the fields of photochemistry and photobiology of porphyrins and chlorophylls in vitro and in vivo, on the occasion of his 95th birthday. Throughout his career at The Rockefeller University, he refined our understanding of how chlorophyll converts light energy into chemical energy. He exploited top-of-the-line laser technology in developing photoacoustics and a variety of other innovative experimental approaches. His experimental work and conceptual insights contributed greatly to our understanding of photosynthesis and the possible role of photosynthesis in the origin of life. His contributions include many landmark single-authored and collaborative papers, and his legacy includes the training of others who have become authorities themselves. After providing a brief description of his research accomplishments, we include tributes from several of his coworkers and his daughters highlighting their valuable experiences with David Mauzerall on this milestone birthday.}, journal={PHOTOSYNTHETICA}, author={Govindjee, G. and Canaani, O. and Cellarius, R. A. and Diner, B. and Greenbaum, E. and Hou, H. J. M. and Kiang, N. Y. and Lindsey, J. S. and Mauzerall, D. L. and Mauzerall, M. E. and et al.}, year={2024}, month={Aug} } @article{houson_wu_cao_lindsey_lapi_2024, title={Customizable Porphyrin Platform Enables Folate Receptor PET Imaging Using Copper-64}, volume={4}, ISSN={["1543-8392"]}, DOI={10.1021/acs.molpharmaceut.4c00015}, abstractNote={Folate receptors including folate receptor α (FRα) are overexpressed in up to 90% of ovarian cancers. Ovarian cancers overexpressing FRα often exhibit high degrees of drug resistance and poor outcomes. A porphyrin chassis has been developed that is readily customizable according to the desired targeting properties. Thus, compound O5 includes a free base porphyrin, two water-solubilizing groups that project above and below the macrocycle plane, and a folate targeting moiety. Compound O5 was synthesized (>95% purity) and exhibited aqueous solubility of at least 0.48 mM (1 mg/mL). Radiolabeling of O5 with}, journal={MOLECULAR PHARMACEUTICS}, author={Houson, Hailey A. and Wu, Zhiyuan and Cao, Phuong-Lien Doan and Lindsey, Jonathan S. and Lapi, Suzanne E.}, year={2024}, month={Apr} } @article{siwawannapong_diers_magdaong_nalaoh_kirmaier_lindsey_holten_bocian_2024, title={Extension of nature's NIR-I chromophore into the NIR-II region}, volume={5}, ISSN={["1463-9084"]}, DOI={10.1039/d4cp00779d}, abstractNote={Two annulated bacteriochlorin isomers exhibit profoundly different spectral and photophysical features, which are attributed to the absence or presence of electronic (and vibronic) mixing of x - and y -polarized transitions/states.}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Siwawannapong, Kittipan and Diers, James R. and Magdaong, Nikki Cecil M. and Nalaoh, Phattananawee and Kirmaier, Christine and Lindsey, Jonathan S. and Holten, Dewey and Bocian, David F.}, year={2024}, month={May} } @article{liu_ntim_wu_houson_lapi_lindsey_2024, title={Molecular design for sub-micromolar enzyme-instructed self-assembly (EISA)}, volume={6}, ISSN={["1369-9261"]}, DOI={10.1039/d4nj01798f}, abstractNote={Enzyme-instructed self-assembly (EISA) has been explored for many applications in the life sciences including imaging and therapeutics.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Liu, Qihui and Ntim, Thomas and Wu, Zhiyuan and Houson, Hailey A. and Lapi, Suzanne E. and Lindsey, Jonathan S.}, year={2024}, month={Jun} } @article{cao_wu_nalaoh_lindsey_2024, title={Molecular designs with PEG groups for water-solubilization of sparsely substituted porphyrins}, volume={6}, ISSN={["1369-9261"]}, DOI={10.1039/d4nj01178c}, abstractNote={Two relatively short polyethylene glycol (PEG) groups suffice to impart aqueous solubility to an otherwise hydrophobic porphyrin.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Cao, Phuong-Lien Doan and Wu, Zhiyuan and Nalaoh, Phattananawee and Lindsey, Jonathan S.}, year={2024}, month={Jun} } @article{govindjee_stirbet_lindsey_scheer_2024, title={On the Pelletier and Caventou (1817,1818) papers on chlorophyll and beyond}, volume={3}, ISSN={["1573-5079"]}, DOI={10.1007/s11120-024-01081-x}, journal={PHOTOSYNTHESIS RESEARCH}, author={Govindjee, Govindjee and Stirbet, Alexandrina and Lindsey, Jonathan S. and Scheer, Hugo}, year={2024}, month={Mar} } @article{taniguchi_lindsey_2024, title={Performance of chatbots in queries concerning fundamental concepts in photochemistry}, volume={11}, ISSN={["1751-1097"]}, url={https://doi.org/10.1111/php.14037}, DOI={10.1111/php.14037}, abstractNote={Abstract The advent of chatbots raises the possibility of a paradigm shift across society including the most technical of fields with regard to access to information, generation of knowledge, and dissemination of education and training. Photochemistry is a scientific endeavor with roots in chemistry and physics and branches that encompass diverse disciplines ranging from astronomy to zoology. Here, five chatbots have each been challenged with 13 photochemically relevant queries. The chatbots included ChatGPT 3.5, ChatGPT 4.0, Copilot, Gemini Advanced, and Meta AI. The queries encompassed fundamental concepts (e.g., “Why is the fluorescence spectrum typically the mirror image of the absorption spectrum?”), practical matters (e.g., “What is the inner filter effect and how to avoid it?”), philosophical matters (“Please create the most important photochemistry questions.”), and specific molecular features (e.g., “Why are azo dyes non‐fluorescent?”). The chatbots were moderately effective in answering queries concerning fundamental concepts in photochemistry but were glaringly deficient in specialized queries for dyes and fluorophores. In some instances, a correct response was embedded in verbose scientific nonsense whereas in others the entire response, while grammatically correct, was utterly meaningless. The unreliable accuracy makes present chatbots poorly suited for unaided educational purposes and highlights the importance of domain experts.}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2024}, month={Nov} } @article{aravindu_taniguchi_bocian_lindsey_2024, title={Synthesis of (oxo)chlorin dimers chelated with thallium(III)}, volume={28}, ISSN={["1099-1409"]}, url={https://doi.org/10.1142/S1088424624500548}, DOI={10.1142/S1088424624500548}, abstractNote={Two target dimers have been prepared for fundamental studies of hole/electron transfer. Metalation with thallium(III) enables clocking of the rate of hole/electron transfer between the two macrocycles. Each dimer contains a diphenylethyne linker joining two identical hydroporphyrins (chlorin or oxochlorin). The linker is substituted at the 4,4′-positions whereas each (oxo)chlorin is joined at the 10-position. Each (oxo)chlorin is equipped with a gem-dimethyl group at the 18-position to stabilize the hydroporphyrin chromophore toward adventitious dehydrogenation and a 3,5-di-tert-butyl group at the 5-position to achieve increased solubilization in organic media. The dimers parallel a prior set of diphenylethyne-linked (oxo)chlorin constructs containing zinc-free base, zinc-zinc, and copper-copper metalation states that have been examined in studies of electronic communication. The building block (oxo)chlorins for preparing the thallium-containing dimers have been prepared in quantities of 32–404 mg, a scale up to 14-fold larger than previously. Thallation of the free base (oxo)chlorin dimers was achieved with excess TlCl 3 ⋅4H 2 O in CH 2 Cl 2 /CH 3 OH (3–4:1) upon overnight reaction at room temperature. The long-wavelength (Q[Formula: see text] absorption band of (oxo)chlorins lies between that of the zinc(II) and free base counterparts. Absorption spectral comparisons are provided of the thallium(III) and free base (oxo)chlorin monomers and dimers.}, number={08}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Aravindu, Kunche and Taniguchi, Masahiko and Bocian, David F. and Lindsey, Jonathan S.}, year={2024}, month={Aug}, pages={527–535} } @article{tran_wang_zhang_jovanovic_siewert_moser_lindsey_2024, title={Synthesis of a model phyllobilin bearing an optical marker}, volume={6}, ISSN={["1369-9261"]}, url={https://doi.org/10.1039/D4NJ01533A}, DOI={10.1039/d4nj01533a}, abstractNote={Phyllobilins – important natural products derived from chlorophylls – contain a characteristic conjugation in the southern rim, which is mimicked here in a synthetic analogue.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Tran, Anh Thu Nguyen and Wang, Pengzhi and Zhang, Shaofei and Jovanovic, Milena and Siewert, Bianka and Moser, Simone and Lindsey, Jonathan S.}, year={2024}, month={Jun} } @article{nguyen_chung_nalaoh_lindsey_2024, title={Synthesis of chiral hexynones for use as precursors to native photosynthetic hydroporphyrins}, volume={1}, ISSN={["1369-9261"]}, DOI={10.1039/d3nj03900e}, abstractNote={A planned total synthesis of photosynthetic tetrapyrrole macrocycles installs essential stereochemical features in early precursors via established asymmetric methodology.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Nguyen, Khiem Chau and Chung, Duy T. M. and Nalaoh, Phattananawee and Lindsey, Jonathan S.}, year={2024}, month={Jan} } @article{wang_taniguchi_bocian_lindsey_2024, title={Synthesis of porphyrin triads chelated with thallium(III) for studies of ground-state hole/electron transfer}, volume={28}, ISSN={["1099-1409"]}, url={https://doi.org/10.1142/S1088424624500524}, DOI={10.1142/S1088424624500524}, abstractNote={Four target all-porphyrin triads have been prepared for fundamental studies of ground-state hole/electron transfer. Each triad contains thallium(III) porphyrins as bookends, which bear mesityl groups at the three non-linking meso-positions. The central porphyrin is a free base or thallium(III) porphyrin bearing mesityl or pentafluorophenyl groups at the two non-linking meso-positions. The linker is a 4,4 ′ -diphenylethyne unit joined at the porphyrin meso-positions. The net spacer between the two bookend thallium(III) porphyrins thus consists of diphenylethyne–porphyrin–diphenylethyne and is designed as a superexchange element for through-bond hole/electron transfer. The energetics of the superexchange element are tunable given the nature of the substituents and metalation state of the central porphyrin. The synthesis entailed Sonogashira coupling of two building blocks, a free base bis(4-iodophenyl)porphyrin and a mono-ethynylporphinato thallium(III) chloride. Two benchmark porphyrins also were prepared. Absorption spectral comparisons are provided including of the all-thallium(III) monomer, dimer, and triad.}, number={08}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Wang, Jieqi and Taniguchi, Masahiko and Bocian, David F. and Lindsey, Jonathan S.}, year={2024}, month={Aug}, pages={515–526} } @article{taniguchi_lindsey_2023, title={Absorption and fluorescence spectra of open-chain tetrapyrrole pigments-bilirubins, biliverdins, phycobilins, and synthetic analogues}, volume={55}, ISSN={["1873-2739"]}, DOI={10.1016/j.jphotochemrev.2023.100585}, abstractNote={Open-chain tetrapyrroles are ubiquitous and abundant in living organisms (algae, animals, bacteria, and plants), including examples such as bilirubin, biliverdin, phycocyanobilin, phycoerythrobilin, and urobilin. The open-chain tetrapyrroles, collectively termed bilins, arise from biosynthesis or degradation of tetrapyrrole macrocycles. Bilins are now known to play a wide variety of biological roles encompassing light-harvesting (in phycobiliproteins), photomorphogenesis, signaling, and redox chemistry. The absorption spectra of bilins spans the ultraviolet (UV), visible, to near-infrared (NIR) regions depending on the degree of conjugation, thereby providing a wide range of colors from red/orange to blue/green. The fluorescence intensity of bilins is often quite low and hence fewer spectra are available, but can be increased substantially by structural rigidification, as evidenced by the wide use of biliproteins as fluorescent labels. The present article describes a database of absorption and fluorescence spectra of bilins from natural and synthetic origins for 220 compounds (270 absorption and 13 fluorescence spectral traces). Spectral traces of bilins published over the past ∼50 years have been digitized and assembled along with information concerning solvent, photochemical properties (molar absorption coefficient and fluorescence quantum yield), and literature references. The spectral traces (xy-coordinate data files) can be viewed, downloaded, and accessed at www.photochemcad.com. The accessibility of spectral traces in digital format should facilitate identification and quantitative calculations of interest in diverse scientific areas.}, journal={JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2023}, month={Jun} } @article{son_wu_dou_fujita_cao_liu_lindsey_2023, title={Article Tethered Indoxyl-Glucuronides for Enzymatically Triggered Cross-Linking}, volume={28}, ISSN={["1420-3049"]}, DOI={10.3390/molecules28104143}, abstractNote={Indoxyl-glucuronides, upon treatment with β-glucuronidase under physiological conditions, are well known to afford the corresponding indigoid dye via oxidative dimerization. Here, seven indoxyl-glucuronide target compounds have been prepared along with 22 intermediates. Of the target compounds, four contain a conjugatable handle (azido-PEG, hydroxy-PEG, or BCN) attached to the indoxyl moiety, while three are isomers that include a PEG-ethynyl group at the 5-, 6-, or 7-position. All seven target compounds have been examined in indigoid-forming reactions upon treatment with β-glucuronidase from two different sources and rat liver tritosomes. Taken together, the results suggest the utility of tethered indoxyl-glucuronides for use in bioconjugation chemistry with a chromogenic readout under physiological conditions.}, number={10}, journal={MOLECULES}, author={Son, Juno and Wu, Zhiyuan and Dou, Jinghuai and Fujita, Hikaru and Cao, Phuong-Lien Doan and Liu, Qihui and Lindsey, Jonathan S.}, year={2023}, month={May} } @article{tran_wang_matsumoto_liu_jing_nalaoh_nguyen_taniguchi_lindsey_2023, title={Bacteriochlorin syntheses - Status, problems, and exploration}, volume={8}, ISSN={["1099-1409"]}, url={https://doi.org/10.1142/S1088424623501171}, DOI={10.1142/S1088424623501171}, abstractNote={ Bacteriochlorins – Nature’s near-infrared (NIR) chromophores – are distinguished by an intense ([Formula: see text] ∼;105 M[Formula: see text]cm[Formula: see text] long-wavelength absorption band in the ∼;700–1000 nm. The development of routes to prepare synthetic, tailorable bacteriochlorins holds promise for multiple disciplines where NIR-light-promoted photoactivity is of interest. A de novo route to bacteriochlorins equipped with a stabilizing gem-dimethyl group in each pyrroline ring was discovered in 2003. Continued development in this arena over 20 years has led to additional routes as well as methods to install substituents at selected positions about the perimeter of the macrocycle. The present paper reports studies that highlight substantial limitations of existing synthetic routes, including stymied access to multi-bacteriochlorin arrays and the inability to install (in a rational way) distinct groups at opposite sides of the macrocycle. The origins of the limitations are traced to particular stages of the chemistry ranging from derivatizing pyrroles, creating pyrrolines, constructing and elaborating dihydrodipyrrins, coupling dihydrodipyrrins, and forming macrocycles. Through exploration of a dozen aspects of bacteriochlorin syntheses, 60 new compounds (and nine known compounds via improved syntheses) have been prepared and characterized; the data include 20 single-crystal X-ray diffraction analyses. The research taken together points to areas of focus to fulfill the promise of this fascinating class of compounds. }, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Tran, Vy-Phuong and Wang, Pengzhi and Matsumoto, Nobuyuki and Liu, Sijia and Jing, Haoyu and Nalaoh, Phattananawee and Nguyen, Khiem Chau and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2023}, month={Aug} } @inbook{lindsey_taniguchi_2023, place={London}, title={Core chromophores of native photosynthetic pigments}, volume={3}, url={http://dx.doi.org/10.1016/b978-0-323-98391-4.00021-6}, DOI={10.1016/b978-0-323-98391-4.00021-6}, abstractNote={The patina of pigments that envelops Earth and enables photosynthesis to power the biosphere is chiefly comprised of chlorophylls and bacteriochlorophylls. Such pigments, which contain a porphyrin, chlorin, or bacteriochlorin chromophore, underpin a rich collection of fundamental phenomena: absorption of ambient light, excited-state energy and electron transfer, and ground-state electron and hole transfer. The present chapter (1) outlines the chemical synthesis of naked porphyrin, chlorin, and bacteriochlorin macrocycles that are devoid of peripheral substituents, and (2) compares the absorption spectra of the naked chromophores with those of the native macrocycles. The synthetic and comparative spectral studies provide the basis for deep insight into the features of the native chlorophylls and bacteriochlorophylls, which are deservedly regarded as celestial molecules in the photosciences firmament.}, booktitle={Photosynthesis}, publisher={Elsevier}, author={Lindsey, Jonathan S. and Taniguchi, Masahiko}, editor={Hou, J.M.H. and Allakhverdiev, S.I.Editors}, year={2023}, pages={33–48} } @misc{taniguchi_larocca_bernat_lindsey_2023, title={Digital Database of Absorption Spectra of Diverse Flavonoids Enables Structural Comparisons and Quantitative Evaluations}, volume={86}, ISSN={["1520-6025"]}, url={https://doi.org/10.1021/acs.jnatprod.2c00720}, DOI={10.1021/acs.jnatprod.2c00720}, abstractNote={Flavonoids play diverse roles in plants, comprise a non-negligible fraction of net primary photosynthetic production, and impart beneficial effects in human health from a plant-based diet. Absorption spectroscopy is an essential tool for quantitation of flavonoids isolated from complex plant extracts. The absorption spectra of flavonoids typically consist of two major bands, band I (300-380 nm) and band II (240-295 nm), where the former engenders a yellow color; in some flavonoids the absorption tails to 400-450 nm. The absorption spectra of 177 flavonoids and analogues of natural or synthetic origin have been assembled, including molar absorption coefficients (109 from the literature, 68 measured here). The spectral data are in digital form and can be viewed and accessed at http://www.photochemcad.com. The database enables comparison of the absorption spectral features of 12 distinct types of flavonoids including flavan-3-ols (e.g., catechin, epigallocatechin), flavanones (e.g., hesperidin, naringin), 3-hydroxyflavanones (e.g., taxifolin, silybin), isoflavones (e.g., daidzein, genistein), flavones (e.g., diosmin, luteolin), and flavonols (e.g., fisetin, myricetin). The structural features that give rise to shifts in wavelength and intensity are delineated. The availability of digital absorption spectra for diverse flavonoids facilitates analysis and quantitation of these valuable plant secondary metabolites. Four examples are provided of calculations─multicomponent analysis, solar ultraviolet photoprotection, sun protection factor (SPF), and Förster resonance energy transfer (FRET)─for which the spectra and accompanying molar absorption coefficients are sine qua non.}, number={4}, journal={JOURNAL OF NATURAL PRODUCTS}, author={Taniguchi, Masahiko and LaRocca, Connor A. and Bernat, Jake D. and Lindsey, Jonathan S.}, year={2023}, month={Apr}, pages={1087–1119} } @article{taniguchi_wu_sterling_lindsey_raghavachari_berezin_2023, title={Digitization of print-based absorption and fluorescence spectra extracting clarity from clutter}, volume={12398}, ISBN={["978-1-5106-5901-8"]}, ISSN={["1605-7422"]}, DOI={10.1117/12.2651694}, abstractNote={Absorption and fluorescence spectra are central to the photosciences. The PhotochemCAD initiative, aimed at assembling digital databases of absorption and fluorescence spectra for use across the photosciences, now comprises <1000 absorption spectra and <500 fluorescence spectra for ~1000 compounds along with companion photophysical parameters (molar absorption coefficient, fluorescence quantum yield) and citations to the originating scientific literature. The spectral databases have chiefly been assembled by digitizing spectra from the vast print literature. The conversion of print spectra to digital form presents several technical challenges: (1) print spectra are plagued by line crossing from overlaid spectra, use of discontinuous lines, and interference from grids, tick marks, and the graph baseline; (2) the print spectrum in some cases lacks wavelength markers or is annotated with markers at odds with values in the accompanying text; and (3) the digitized spectra often are composed of data with uneven wavelength (x-axis) intervals. Here, manually assisted digitization – wherein the user steps through a print spectrum with hand-eye assistance to create the corresponding digital dataset – is compared with automated digitization. Graphical features that bear on use of each method are outlined. Two spreadsheet-based tools have been developed for application following digitization: (i) conversion of xy-coordinate data from uneven to uniform x-axis intervals, and (ii) calibration of the digitized spectrum with appropriate wavelength values. The two tools enable more accurate rendition of print spectra into digital form, as required for qualitative comparisons and quantitative calculations, and have been added to the PhotochemCAD website (http://www.photochemcad.com).}, journal={REPORTERS, MARKERS, DYES, NANOPARTICLES, AND MOLECULAR PROBES FOR BIOMEDICAL APPLICATIONS XIV}, author={Taniguchi, Masahiko and Wu, Zhiyuan and Sterling, Caitlin and Lindsey, Jonathan S. and Raghavachari, Ramesh and Berezin, Mikhail Y.}, year={2023} } @article{jing_magdaong_diers_kirmaier_bocian_holten_lindsey_2023, title={Dyads with tunable near-infrared donor-acceptor excited-state energy gaps: molecular design and Forster analysis for ultrafast energy transfer}, volume={1}, ISSN={["1463-9084"]}, url={https://doi.org/10.1039/D2CP04689J}, DOI={10.1039/d2cp04689j}, abstractNote={Nine dyads composed of bacteriochlorins were prepared to investigate excited-state energy transfer (FRET) processes.}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Jing, Haoyu and Magdaong, Nikki Cecil M. and Diers, James R. and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2023}, month={Jan} } @article{nguyen_tran_wang_zhang_wu_taniguchi_lindsey_2023, title={Four Routes to 3-(3-Methoxy-1,3-dioxopropyl)pyrrole, a Core Motif of Rings C and E in Photosynthetic Tetrapyrroles}, volume={28}, ISSN={["1420-3049"]}, url={https://doi.org/10.3390/molecules28031323}, DOI={10.3390/molecules28031323}, abstractNote={The photosynthetic tetrapyrroles share a common structural feature comprised of a β-ketoester motif embedded in an exocyclic ring (ring E). As part of a total synthesis program aimed at preparing native structures and analogues, 3-(3-methoxy-1,3-dioxopropyl)pyrrole was sought. The pyrrole is a precursor to analogues of ring C and the external framework of ring E. Four routes were developed. Routes 1–3 entail a Pd-mediated coupling process of a 3-iodopyrrole with potassium methyl malonate, whereas route 4 relies on electrophilic substitution of TIPS-pyrrole with methyl malonyl chloride. Together, the four routes afford considerable latitude. A long-term objective is to gain the capacity to create chlorophylls and bacteriochlorophylls and analogues thereof by facile de novo means for diverse studies across the photosynthetic sciences.}, number={3}, journal={MOLECULES}, author={Nguyen, Khiem Chau and Tran, Anh Thu Nguyen and Wang, Pengzhi and Zhang, Shaofei and Wu, Zhiyuan and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2023}, month={Feb} } @article{sato_wu_dou_son_lindsey_2023, title={Indoxyl-glucosides bearing tethers for enzymatically triggered cross-linking}, volume={47}, ISSN={["1369-9261"]}, DOI={10.1039/d2nj06267d}, abstractNote={Tethered indoxyl-glucosides upon treatment with β-glucosidase under physiological conditions afford the corresponding indigoid dye via oxidative dimerization.}, number={17}, journal={NEW JOURNAL OF CHEMISTRY}, author={Sato, Daisuke and Wu, Zhiyuan and Dou, Jinghuai and Son, Juno and Lindsey, Jonathan S. S.}, year={2023}, month={May}, pages={8223–8242} } @article{jing_magdaong_diers_kirmaier_bocian_holten_lindsey_2023, title={Investigation of a bacteriochlorin-containing pentad array for panchromatic light-harvesting and charge separation}, volume={1}, ISSN={["1463-9084"]}, DOI={10.1039/d2cp05400k}, abstractNote={A crossbar array composed of a panchromatic light-harvesting triad and charge-separation triad has been synthesized and examined in fundamental photophysical studies.}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, author={Jing, Haoyu and Magdaong, Nikki Cecil M. and Diers, James R. and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2023}, month={Jan} } @article{liu_taniguchi_goel_lindsey_2024, title={Rapid screening of dyes for self-aggregation, adsorption and metabolic integrity - Quantitative metrics as a prelude to biological studies}, volume={223}, ISSN={["1873-3743"]}, url={https://doi.org/10.1016/j.dyepig.2023.111914}, DOI={10.1016/j.dyepig.2023.111914}, abstractNote={The development of dyes for biological applications typically begins with synthesis, is followed by spectroscopic/photophysical characterization, and culminates in testing with cultured cells or in animals. The present work describes a set of facile, low-technology, in vitro, largely quantitative absorption spectrophotometric assays in aqueous solution as a prelude to biological studies. The assays include the following: (1) Self-aggregation in phosphate-buffered saline (PBS), with or without the presence of 3 % bovine serum albumin (BSA), via reciprocal change in concentration and pathlength; (2) Adsorption to solid materials as biomolecular surrogates, including cellulose, chitosan, polyethylene (PE), styrene-divinylbenzene beads (XAD-4), polyacrylic beads (XAD-7), anion exchange beads (IRA-67), cation exchange beads (CG-50), polytetrafluoroethylene (PTFE) membranes, and Nylon membranes; (3) Hydrophilicity/hydrophobicity assessment, by measurement (not calculation) of logP values; and (4) Metabolic integrity, by exposure to a rat liver homogenate. Twenty-two dyes were examined in the assays. The dyes represent diverse classes (acridine, anthraquinone, azo, benzimidazole, coumarin, cyanine, flavonoid, naphthalene, phthalocyanine, polyene, tetrapyrrole, triarylmethine, xanthene), polarity (anionic, cationic, nonionic, hydrophobic, amphipathic), and absorption (ultraviolet, visible, near-infrared). As one example, indocyanine green (ICG), an FDA-approved dye for in vivo use, (i) aggregates at the concentration of 5 μM but disaggregates in the presence of BSA; (ii) in PBS is very adsorptive (>80 % binding) to various materials (cellulose, chitosan, PE, IRA-67, CG-50, PTFE, Nylon) and quite adsorptive (50–80 % binding) to XAD-4 and XAD-7, (iii) exhibits only marginal preference for water versus 1-octanol (1.5:1), and (iv) is largely digested by rat liver homogenate. A single dye can be examined in the span of one day. The quantitative metrics should prove valuable for establishing biologically relevant features of diverse dyes by simple studies in aqueous solution.}, journal={DYES AND PIGMENTS}, author={Liu, Qihui and Taniguchi, Masahiko and Goel, Shreya and Lindsey, Jonathan S.}, year={2024}, month={Apr} } @article{nguyen_lindsey_2023, title={Synthesis of a BC-Dihydrodipyrrin Building Block of Bacteriochlorophyll a}, volume={7}, ISSN={["1520-6904"]}, url={https://doi.org/10.1021/acs.joc.3c01216}, DOI={10.1021/acs.joc.3c01216}, abstractNote={A strategy for the synthesis of bacteriochlorophyll a relies on joining AD and BC halves that contain the requisite stereochemical configurations of the target macrocycle. The BC half (1) is a dihydrodipyrrin bearing a dimethoxymethyl group at the 1-position, a β-ketoester at the 8-position, and (R)-2-methyl and (R)-3-ethyl substituents in the pyrroline ring. An established route to AD-dihydrodipyrrins (Pd-mediated coupling of a 2-halopyrrole with a chiral 4-pentynoic acid followed by Petasis methenylation, acidic hydrolysis, Paal-Knorr ring closure, and Riley oxidation) proved to be unviable for BC-dihydrodipyrrins given the presence of the β-ketoester unit. A route presented here entails Pd-mediated coupling of a 2-halopyrrole (2) with (3R,4R)-4-ethyl-1,1-dimethoxy-3-methylhex-5-yn-2-one (3), anti-Markovnikov hydration of the alkyne to give the 1,4-diketone, and Paal-Knorr ring closure. Compound 3 was prepared by Schreiber-modified Nicholas reaction beginning with (S)-4-isopropyl-3-propionyloxazolidin-2-one and the hexacarbonyldicobalt complex of (±) 3-methoxy-1-(trimethylsilyl)pentyne followed by transformation of the aldehyde derived therefrom to the 1,1-dimethoxymethylcarbonyl motif. The absolute stereochemical configuration of the Schreiber-Nicholas alkylation product was confirmed by single-crystal X-ray diffraction, whereas the BC half (1) by 1H NMR spectroscopy showed a J value of 2.9 Hz consistent with the trans-configuration. Taken together, the route provides a key chiral building block for the synthesis of photosynthetic tetrapyrroles and analogues.}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Nguyen, Khiem Chau and Lindsey, Jonathan S.}, year={2023}, month={Jul} } @article{nguyen tran_wu_chung_nalaoh_lindsey_2023, title={Synthesis of model southern rim structures of photosynthetic tetrapyrroles and phyllobilins}, volume={7}, ISSN={["1369-9261"]}, url={http://dx.doi.org/10.1039/d3nj02515b}, DOI={10.1039/d3nj02515b}, abstractNote={Two simple pyrroles react in two simple reactions to afford a dipyrromethane analogue of the southern rim of native tetrapyrroles and their catabolites.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Nguyen Tran, Anh Thu and Wu, Zhiyuan and Chung, Duy T. M. and Nalaoh, Phattananawee and Lindsey, Jonathan S.}, year={2023}, month={Jul} } @misc{nguyen_zhang_liu_zhang_jin_taniguchi_miller_lindsey_2023, title={Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review}, volume={28}, ISSN={["1420-3049"]}, url={https://doi.org/10.3390/molecules28166132}, DOI={10.3390/molecules28166132}, abstractNote={Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium–microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known—each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or –OH or –OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.}, number={16}, journal={MOLECULES}, author={Nguyen, Kathy-Uyen and Zhang, Yunlong and Liu, Qihui and Zhang, Ran and Jin, Xiaohe and Taniguchi, Masahiko and Miller, Eric S. and Lindsey, Jonathan S.}, year={2023}, month={Aug} } @article{roy_magdaong_jing_rong_diers_kang_niedzwiedzki_taniguchi_kirmaier_lindsey_et al._2022, title={Balancing Panchromatic Absorption and Multistep Charge Separation in a Compact Molecular Architecture br}, volume={12}, ISSN={["1520-5215"]}, url={https://doi.org/10.1021/acs.jpca.2c06040}, DOI={10.1021/acs.jpca.2c06040}, abstractNote={A panchromatic triad and a charge-separation unit are joined in a crossbar architecture to capture solar energy. The panchromatic-absorber triad (T) is comprised of a central free-base porphyrin that is strongly coupled via direct ethyne linkages to two perylene-monoimide (PMI) groups. The charge-separation unit incorporates a free-base or zinc chlorin (C or ZnC) as a hole acceptor (or electron donor) and a perylene-diimide (PDI) as an electron acceptor, both attached to the porphyrin via diphenylethyne linkers. The free-base porphyrin is common to both light-harvesting and charge-separation motifs. The chlorin and PDI also function as ancillary light absorbers, complementing direct excitation of the panchromatic triad to produce the discrete lowest excited state of the array (T*). Attainment of full charge separation across the pentad entails two steps: (1) an initial excited-state hole/electron-transfer process to oxidize the chlorin (and reduce the panchromatic triad) or reduce the PDI (and oxidize the panchromatic triad); and (2) subsequent ground-state electron/hole migration to produce oxidized chlorin and reduced PDI. Full charge separation for pentad ZnC-T-PDI to generate ZnC+-T-PDI- occurs with a quantum yield of ∼30% and mean lifetime ∼1 μs in dimethyl sulfoxide. For C-T-PDI, initial charge separation is followed by rapid charge recombination. The molecular designs and studies reported here reveal the challenges of balancing the demands for charge separation (linker length and composition, excited-state energies, redox potentials, and medium polarity) with the constraints for panchromatic absorption (strong electronic coupling of the porphyrin and two PMI units) for integrated function in solar-energy conversion.}, number={50}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Roy, Arpita and Magdaong, Nikki Cecil M. and Jing, Haoyu and Rong, Jie and Diers, James R. and Kang, Hyun Suk and Niedzwiedzki, Dariusz M. and Taniguchi, Masahiko and Kirmaier, Christine and Lindsey, Jonathan S. and et al.}, year={2022}, month={Dec} } @article{taniguchi_bocian_holten_lindsey_2022, title={Beyond green with synthetic chlorophylls - Connecting structural features with spectral properties}, volume={52}, ISSN={["1873-2739"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85131670645&partnerID=MN8TOARS}, DOI={10.1016/j.jphotochemrev.2022.100513}, abstractNote={The distinct features of chlorophylls in photosynthesis have led to the formation of numerous derivatives for applications encompassing solar energy conversion, molecular photonics, photodynamic therapy, and molecular imaging. Synthetic chlorins created de novo and bearing a geminal dimethyl group in the reduced ring have proved invaluable for fundamental studies. Four decades of research have led to accumulation of tabulated spectra for > 400 such synthetic chlorins with distinct structural frameworks (17-oxochlorins, 131-oxophorbines, chlorinimides) and substituents (alkyl, aryl, ethynyl, phenylethynyl, acetyl, formyl) located at specific (meso, β) positions. In this review, spectral traces (324 absorption, 247 fluorescence) are assembled along with photophysical data including the molar absorption coefficient (ε), fluorescence quantum yield (Φf) and singlet excited-state lifetime (τs). The review uses the accumulated spectral data derived from chlorins all containing a uniform molecular scaffold to (1) highlight the effects of molecular structure on spectral features, and (2) identify trends including how ε, Φf and τs vary with wavelength and other features. Use of a common geminal-dimethyl-substituted chlorin scaffold – beginning with no substituents, to one substituent at designated sites, and to 2 or more substituents – provides a systematic Aufbau approach for understanding the absorption spectra of chlorins on a path to and beyond the native chlorophylls. The review provides insights concerning the rational design of potent analogues of Nature’s preeminent red-region absorbers for potential utilization in diverse applications and is aimed at multiple audiences: those interested in spectral properties, tetrapyrrole photophysics, and the molecular design of new chromophores.}, journal={JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS}, author={Taniguchi, Masahiko and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2022}, month={Sep} } @article{taniguchi_taniguchi_zhang_goto_lindsey_2022, title={Chasing the green echiuran worm Bonellia in tidal pools of Okinawa}, volume={11979}, ISBN={["978-1-5106-4829-6"]}, ISSN={["1996-756X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85131381961&partnerID=MN8TOARS}, DOI={10.1117/12.2608722}, abstractNote={Bonellia viridis, a green marine echiuran worm known since the early 19th century in the Mediterranean Sea, typically lives in sediments or rock crevices at a depth underwater of 3–10 m, causing acquisition of samples to generally require diving. The size of the main body trunk of the female is about 8 cm, whereas the (dwarf) male is 1 to 3 mm long and lives inside the female. The green pigmentation of B. viridis stems from bonellin, a tetrapyrrole macrocycle containing a chlorin chromophore. Bonellin is believed to exert diverse physiological functions (masculinization and sex determination, chemical defense, cytotoxicity, and antimicrobial activity) but not photosynthesis as for the better known native chlorin, chlorophyll. The existence of bonellin poses physiological, biosynthetic, and evolutionary questions. Here, we report in-depth assessment of information concerning tides at a wide shallow beach in Okinawa, identifying narrowly restricted periods when acquisition of Bonellia specimens could be pursued without diving. Indeed, <15 specimens of B. sp. were collected from Odo beach, Itoman city, Okinawa prefecture, Japan [26°09' N, 127°71' E], at midnight on days when the tides were exceptionally low: March 6–12, 2016; December 22–27, 2018; and January 18–25, 2019. The specimens were acquired manually from small tidal pools upon walking near the outer reef flat (~300 m from the shore) during the extremely low tides. Reasonably facile access without diving to Bonellia in a region distant from the Mediterranean should expand study of the diversity of these unusual green worms.}, journal={FRONTIERS IN BIOLOGICAL DETECTION: FROM NANOSENSORS TO SYSTEMS XIV}, author={Taniguchi, Masahiko and Taniguchi, Minami and Zhang, Ran and Goto, Ryutaro and Lindsey, Jonathan S.}, year={2022} } @article{jing_liu_jiang_tran_rong_wang_lindsey_2022, title={Meso bromination and derivatization of synthetic bacteriochlorins}, volume={46}, ISSN={["1369-9261"]}, DOI={10.1039/d1nj05853c}, abstractNote={Twelve bacteriochlorin building blocks featuring meso-substitution have been prepared including a set with finely tuned long-wavelength absorption (725–757 nm) for studies in photonics.}, number={12}, journal={NEW JOURNAL OF CHEMISTRY}, author={Jing, Haoyu and Liu, Sijia and Jiang, Jianbing and Tran, Vy-Phuong and Rong, Jie and Wang, Pengzhi and Lindsey, Jonathan S.}, year={2022}, month={Mar}, pages={5556–5572} } @article{liu_rong_wu_taniguchi_bocian_holten_lindsey_2022, title={Panchromatic Absorbers Tethered for Bioconjugation or Surface Attachment}, volume={27}, ISSN={["1420-3049"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85139868890&partnerID=MN8TOARS}, DOI={10.3390/molecules27196501}, abstractNote={The syntheses of two triads are reported. Each triad is composed of two perylene-monoimides linked to a porphyrin via an ethyne unit, which bridges the perylene 9-position and a porphyrin 5- or 15-position. Each triad also contains a single tether composed of an alkynoic acid or an isophthalate unit. Each triad provides panchromatic absorption (350–700 nm) with fluorescence emission in the near-infrared region (733 or 743 nm; fluorescence quantum yield ~0.2). The syntheses rely on the preparation of trans-AB-porphyrins bearing one site for tether attachment (A), an aryl group (B), and two open meso-positions. The AB-porphyrins were prepared by the condensation of a 1,9-diformyldipyrromethane and a dipyrromethane. The installation of the two perylene-monoimide groups was achieved upon the 5,15-dibromination of the porphyrin and the subsequent copper-free Sonogashira coupling, which was accomplished before or after the attachment of the tether. The syntheses provide relatively straightforward access to a panchromatic absorber for use in bioconjugation or surface-attachment processes.}, number={19}, journal={MOLECULES}, author={Liu, Rui and Rong, Jie and Wu, Zhiyuan and Taniguchi, Masahiko and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2022}, month={Oct} } @misc{jing_rong_taniguchi_lindsey_2022, title={Phenylene-linked tetrapyrrole arrays containing free base and diverse metal chelate forms - Versatile synthetic architectures for catalysis and artificial photosynthesis}, volume={456}, ISSN={["1873-3840"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85122467651&partnerID=MN8TOARS}, DOI={10.1016/j.ccr.2021.214278}, abstractNote={Tetrapyrrole macrocycles are central to photosynthesis yet a single macrocycle does not carry out photosynthesis; rather, assemblies of tetrapyrrole macrocycles work in concert in antenna complexes, reaction centers, and electron-transport chains to harvest sunlight, funnel excited-state energy and separate charge for biological use. A longstanding theme in artificial photosynthesis has been to construct covalently linked “arrays” of metalated and free base tetrapyrrole macrocycles for fundamental studies of such processes, which entail excited-state and ground-state interactions. Among linkers in arrays chemistry, the 1,2-, 1,3-, or 1,4-disubstituted phenylene unit has proved very attractive owing to the resulting short distance, defined architecture, and appropriate extent of electronic coupling of adjacent macrocycles to give rapid electron and/or energy transfer while largely retaining desired spectral features. Eight distinct strategies to construct phenylene-linked tetrapyrrole arrays are identified in a review with comprehensive coverage since inception in the early 1970s through mid-year 2021. The arrays predominantly incorporate porphyrins with very few chlorins and bacteriochlorins, reflecting historic availability of synthetic methods for macrocycle formation. Of the eight strategies, only two appear applicable to (bacterio)chlorins. While studies in artificial photosynthesis have largely fueled this field, applications in catalysis have also been examined. Altogether >400 arrays are covered. The review delves into synthesis and molecular design, sketches photophysical properties, and suggests unrealized opportunities in arrays chemistry.}, journal={COORDINATION CHEMISTRY REVIEWS}, author={Jing, Haoyu and Rong, Jie and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2022}, month={Apr} } @article{karg_taniguchi_lindsey_moser_2022, title={Phyllobilins - Bioactive Natural Products Derived from Chlorophyll - Plant Origins, Structures, Absorption Spectra, and Biomedical Properties}, volume={12}, ISSN={["1439-0221"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85140841360&partnerID=MN8TOARS}, DOI={10.1055/a-1955-4624}, abstractNote={AbstractPhyllobilins are open-chain products of the biological degradation of chlorophyll a in higher plants. Recent studies reveal that phyllobilins exert anti-oxidative and anti-inflammatory properties, as well as activities against cancer cells, that contribute to the human health benefits of numerous plants. In general, phyllobilins have been overlooked in phytochemical analyses, and – more importantly – in the analyses of medicinal plant extracts. Nevertheless, over the past three decades, > 70 phyllobilins have been identified upon examination of more than 30 plant species. Eight distinct chromophoric classes of phyllobilins are known: phyllolumibilins (PluBs), phylloleucobilins (PleBs), phylloxanthobilins (PxBs), and phylloroseobilins (PrBs)–each in type-I or type-II groups. Here, we present a database of absorption and fluorescence spectra that has been compiled of 73 phyllobilins to facilitate identification in phytochemical analyses. The spectra are provided in digital form and can be viewed and downloaded at www.photochemcad.com. The present review describes the plant origin, molecular structure, and absorption and fluorescence features of the 73 phyllobilins, along with an overview of key medicinal properties. The review should provide an enabling tool for the community for the straightforward identification of phyllobilins in plant extracts, and the foundation for deeper understanding of these ubiquitous but underexamined plant-derived micronutrients for human health.}, journal={PLANTA MEDICA}, author={Karg, Cornelia A. and Taniguchi, Masahiko and Lindsey, Jonathan S. and Moser, Simone}, year={2022}, month={Dec} } @article{magdaong_jing_diers_kirmaier_lindsey_bocian_holten_2022, title={Probing the Effects of Electronic-Vibrational Resonance on the Rate of Excited-State Energy Transfer in Bacteriochlorin Dyads}, volume={13}, ISSN={["1948-7185"]}, DOI={10.1021/acs.jpclett.2c02154}, abstractNote={The impact of vibrational-electronic resonances on the rate of excited-state energy transfer is examined in a set of bacteriochlorin dyads that employ the same phenylethyne linker. The donor/acceptor excited-state energy gap is tuned from ∼200 to ∼1100 cm-1 using peripheral substituents on the donor and acceptor bacteriochlorin macrocycles. Ultrafast energy transfer is observed with rate constants of (0.3 ps)-1 to (1.7 ps)-1, which agree with those predicted by Förster theory to within a factor of 2. Furthermore, the measured rates follow a trend-line with only small deviations that do not correlate with the density of vibrations at the donor/acceptor excited-state energy gap. Thus, if vibrational-electronic resonances occur in any of these dyads, which seems likely, the impact on the rate of energy transfer is small.}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY LETTERS}, author={Magdaong, Nikki Cecil M. and Jing, Haoyu and Diers, James R. and Kirmaier, Christine and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2022}, month={Sep}, pages={7906–7910} } @article{siwawannapong_nemeth_melander_rong_davis_taniguchi_carpenter_lindsey_melander_2022, title={Simple Dipyrrin Analogues of Prodigiosin for Use as Colistin Adjuvants}, volume={7}, ISSN={["1860-7187"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85133558458&partnerID=MN8TOARS}, DOI={10.1002/cmdc.202200286}, abstractNote={AbstractMultidrug resistant (MDR) bacteria are an increasing public health problem. One promising alternative to the development of new antibiotics is the use of antibiotic adjuvants, which would allow the continued use of FDA‐approved antibiotics that have been rendered ineffective due to resistance. Herein, we report a series of dipyrrins and pyrrole derivatives designed as analogues of prodigiosin and obatoclax, several of which potentiate the activity of colistin against Klebsiella pneumoniae, with lead compounds also potentiating colistin against Acinetobacter baumannii and Pseudomonas aeruginosa.}, number={16}, journal={CHEMMEDCHEM}, author={Siwawannapong, Kittipan and Nemeth, Ansley M. and Melander, Roberta J. and Rong, Jie and Davis, Jonathan R. and Taniguchi, Masahiko and Carpenter, Morgan E. and Lindsey, Jonathan S. and Melander, Christian}, year={2022}, month={Jul} } @article{sun_liu_wang_qin_schnedermann_maher_zheng_liu_chen_zhang_et al._2022, title={Syntheses and Properties of Metalated Tetradehydrocorrins}, volume={61}, ISSN={["1520-510X"]}, DOI={10.1021/acs.inorgchem.2c01642}, abstractNote={The monoanionic tetrapyrrolic macrocycle B,C-tetradehydrocorrin (TDC) resides chemically between corroles and corrins. This chemical space remains largely unexplored due to a lack of reliable synthetic strategies. We now report the preparation and characterization of Co(II)- and Ni(II)-metalated TDC derivatives ([Co-TDC]+ and [Ni-TDC]+, respectively) with a combination of crystallographic, electrochemical, computational, and spectroscopic techniques. [Ni-TDC]+ was found to undergo primarily ligand-centered electrochemical reduction, leading to hydrogenation of the macrocycle under cathodic electrolysis in the presence of acid. Transient absorption (TA) spectroscopy reveals that [Ni-TDC]+ and the two-electron-reduced [Ni-TDC]- possess long-lived excited states, whereas the excited state of singly reduced [Ni-TDC] exhibits picosecond dynamics. The Co(I) compound [Co-TDC] is air stable, highlighting the notable property of the TDC ligand to stabilize low-valent metal centers in contradistinction to other tetrapyrroles such as corroles, which typically stabilize metals in higher oxidation states.}, number={31}, journal={INORGANIC CHEMISTRY}, author={Sun, Rui and Liu, Mengran and Wang, Pengzhi and Qin, Yangzhong and Schnedermann, Christoph and Maher, Andrew G. and Zheng, Shao-Liang and Liu, Sijia and Chen, Boyang and Zhang, Shaofei and et al.}, year={2022}, month={Aug}, pages={12308–12317} } @article{jing_wang_chen_jiang_vairaprakash_liu_rong_chen_nalaoh_lindsey_2022, title={Synthesis of bacteriochlorins bearing diverse beta-substituents}, volume={3}, ISSN={["1369-9261"]}, DOI={10.1039/d1nj05852e}, abstractNote={Eleven bacteriochlorins have been prepared for surface attachment, bioconjugation, water-solubilization, vibrational studies, and elaboration into multichromophore arrays.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Jing, Haoyu and Wang, Pengzhi and Chen, Boyang and Jiang, Jianbing and Vairaprakash, Pothiappan and Liu, Sijia and Rong, Jie and Chen, Chih-Yuan and Nalaoh, Phattananawee and Lindsey, Jonathan S.}, year={2022}, month={Mar} } @article{wu_dou_nguyen_eppley_siwawannapong_zhang_lindsey_2022, title={Tailoring the AIE Chromogen 2-(2-Hydroxyphenyl)benzothiazole for Use in Enzyme-Triggered Molecular Brachytherapy}, volume={27}, ISSN={["1420-3049"]}, DOI={10.3390/molecules27248682}, abstractNote={A targeted strategy for treating cancer is antibody-directed enzyme prodrug therapy, where the enzyme attached to the antibody causes conversion of an inactive small-molecule prodrug into an active drug. A limitation may be the diffusion of the active drug away from the antibody target site. A related strategy with radiotherapeutics entails enzymatically promoted conversion of a soluble to insoluble radiotherapeutic agent, thereby immobilizing the latter at the target site. Such a molecular brachytherapy has been scarcely investigated. In distinct research, the advent of molecular designs for aggregation-induced emission (AIE) suggests translational use in molecular brachytherapy. Here, several 2-(2-hydroxyphenyl)benzothiazole substrates that readily aggregate in aqueous solution (and afford AIE) were elaborated in this regard. In particular, (1) the 2-(2-hydroxyphenyl) unit was derivatized to bear a pegylated phosphodiester that imparts water solubility yet undergoes enzymatic cleavage, and (2) a p-phenol unit was attached to the benzo moiety to provide a reactive site for final-step iodination (here examined with natural abundance iodide). The pegylated phosphodiester-iodinated benzothiazole undergoes conversion from aqueous-soluble to aqueous-insoluble upon treatment with a phosphatase or phosphodiesterase. The aggregation is essential to molecular brachytherapy, whereas the induced emission of AIE is not essential but provides a convenient basis for research development. Altogether, 21 compounds were synthesized (18 new, 3 known via new routes). Taken together, blending biomedical strategies of enzyme prodrug therapy with materials chemistry concerning substances that undergo AIE may comprise a step forward on the long road toward molecular brachytherapy.}, number={24}, journal={MOLECULES}, author={Wu, Zhiyuan and Dou, Jinghuai and Nguyen, Kathy-Uyen and Eppley, Jayden C. and Siwawannapong, Kittipan and Zhang, Yunlong and Lindsey, Jonathan S.}, year={2022}, month={Dec} } @article{diers_kirmaier_taniguchi_lindsey_bocian_holten_2021, title={A perspective on the redox properties of tetrapyrrole macrocycles}, volume={9}, ISSN={["1463-9084"]}, url={https://doi.org/10.1039/D1CP01943K}, DOI={10.1039/d1cp01943k}, abstractNote={Understanding the redox properties of tetrapyrroles requires deep insights into how structural/electronic alterations affect all four frontier molecular orbitals.}, number={35}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, publisher={Royal Society of Chemistry (RSC)}, author={Diers, James R. and Kirmaier, Christine and Taniguchi, Masahiko and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2021}, month={Sep} } @misc{taniguchi_lindsey_bocian_holten_2021, title={Comprehensive review of photophysical parameters (epsilon, Phi(f), tau(s)) of tetraphenylporphyrin (H2TPP) and zinc tetraphenylporphyrin (ZnTPP) - Critical benchmark molecules in photochemistry and photosynthesis}, volume={46}, ISBN={1873-2739}, url={https://doi.org/10.1016/j.jphotochemrev.2020.100401}, DOI={10.1016/j.jphotochemrev.2020.100401}, abstractNote={Tetraphenylporphyrin (H2TPP) and zinc tetraphenylporphyrin (ZnTPP) are widely used benchmark molecules in diverse photochemical studies given facile synthetic access, rich visible-region spectra, and broad structural analogy to chlorophylls. Yet the literature values for each key photophysical parameter – the molar absorption coefficient (ε), fluorescence quantum yield (Φf), and also singlet excited-state lifetime (τS) – vary over an astonishing range. Here, a comprehensive literature review (∼1940–September 2020) encompassing 871 publications is reported for these essential parameters. Each parameter is determined by measurement with distinct instrumentation and suffers idiosyncratic sources of error. The best values for H2TPP are ε = 460,000 cm−1·M−1, Φf = 0.090, and τS = 12.8 ns in Ar- purged toluene (Φf = 0.070, τS = 9.9 ns in toluene in air); the best values for ZnTPP are ε = 560,000 cm−1·M−1, Φf = 0.030, and τS = 2.1 ns in Ar-purged toluene (Φf = 0.029, τS = 2.0 ns in toluene in air). The choice of values for such parameters has far-reaching consequences in photochemistry ranging from fluorescence (or Förster) resonance energy transfer (FRET) processes to assessments of molecular brightness.}, journal={JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS}, publisher={Elsevier BV}, author={Taniguchi, Masahiko and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2021}, month={Mar}, pages={100401} } @article{lindsey_2021, title={Considerations of the biosynthesis and molecular diversity of tolyporphins}, volume={6}, ISSN={["1369-9261"]}, DOI={10.1039/d1nj01761f}, abstractNote={Tolyporphins, relatively new members of the pigments of life family found in a cyanobacterium, differ in the chromophores, pyrroline substituents, and stereochemistry, yet likely all derive from uroporphyrinogen III.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Lindsey, Jonathan S.}, year={2021}, month={Jun} } @article{rong_magdaong_taniguchi_diers_niedzwiedzki_kirmaier_lindsey_bocian_holten_2021, title={Electronic Structure and Excited-State Dynamics of Rylene-Tetrapyrrole Panchromatic Absorbers}, volume={125}, ISSN={["1520-5215"]}, url={https://doi.org/10.1021/acs.jpca.1c05771}, DOI={10.1021/acs.jpca.1c05771}, abstractNote={Panchromatic absorbers have potential applications in molecular-based energy-conversion schemes. A prior porphyrin-perylene dyad (P-PMI, where "MI" denotes monoimide) coupled via an ethyne linker exhibits panchromatic absorption (350-700 nm) and a tetrapyrrole-like lowest singlet excited state with a relatively long singlet excited-state lifetime (τS) and increased fluorescence quantum yield (Φf) versus the parent porphyrin. To explore the extension of panchromaticity to longer wavelengths, three arrays have been synthesized: a chlorin-terrylene dyad (C-TMI), a bacteriochlorin-terrylene dyad (B-TMI), and a perylene-porphyrin-terrylene triad (PMI-P-TMI), where the terrylene, a π-extended homologue of perylene, is attached via an ethyne linker. Characterization of the spectra (absorption and fluorescence), excited-state properties (lifetime, yields, and rate constants of decay pathways), and molecular-orbital characteristics reveals unexpected subtleties. The wavelength of the red-region absorption band increases in the order C-TMI (705 nm) < PMI-P-TMI (749 nm) < B-TMI (774 nm), yet each array exhibits diminished Φf and shortened τS values. The PMI-P-TMI triad in toluene exhibits Φf = 0.038 and τS = 139 ps versus the all-perylene triad (PMI-P-PMI) for which Φf = 0.26 and τS = 2000 ps. The results highlight design constraints for auxiliary pigments with tetrapyrroles to achieve panchromatic absorption with retention of viable excited-state properties.}, number={36}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, publisher={American Chemical Society (ACS)}, author={Rong, Jie and Magdaong, Nikki Cecil M. and Taniguchi, Masahiko and Diers, James R. and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2021}, month={Sep}, pages={7900–7919} } @article{nguyen_zhang_taniguchi_lindsey_2021, title={Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts}, volume={7}, ISSN={["1751-1097"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85110167749&partnerID=MN8TOARS}, DOI={10.1111/php.13474}, abstractNote={AbstractTolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial‐microbial holobiont (termed HT‐58‐2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a, complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH2Cl2/2‐propanol, 1:1) of HT‐58‐2 cultures with NaBH4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17‐dioxobacteriochlorins) exhibit a bathochromic shift (λabs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 131‐oxochlorin) exhibits a hypsochromic shift (λabs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λem 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non‐axenic cultures at microscale quantities (2 mL, 2 μm), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT‐58‐2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.}, number={6}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Nguyen, Kathy-Uyen and Zhang, Ran and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2021}, month={Jul} } @article{jin_zhang_zhang_nguyen_lindsey_miller_2021, title={Identification of Putative Biosynthetic Gene Clusters for Tolyporphins in Multiple Filamentous Cyanobacteria}, volume={11}, ISSN={["2075-1729"]}, DOI={10.3390/life11080758}, abstractNote={Tolyporphins A–R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification of similar BGCs in seven other filamentous cyanobacteria, including strains Nostoc sp. 106C, Nostoc sp. RF31YmG, Nostoc sp. FACHB-892, Brasilonema octagenarum UFV-OR1, Brasilonema octagenarum UFV-E1, Brasilonema sennae CENA114 and Oculatella sp. LEGE 06141, suggesting their potential for tolyporphins production. A similar gene cluster (BGC-2) also was identified unexpectedly in HT-58-2. Tolyporphins BGCs were not identified in unicellular cyanobacteria. Phylogenetic analysis based on 16S rRNA and a common component of the BGCs, TolD, points to a close evolutionary history between each strain and their respective tolyporphins BGC. Though identified with putative tolyporphins BGCs, examination of pigments extracted from three cyanobacteria has not revealed the presence of tolyporphins. Overall, the identification of BGCs and potential producers of tolyporphins presents a collection of candidate cyanobacteria for genetic and biochemical analysis pertaining to these unusual tetrapyrrole macrocycles.}, number={8}, journal={LIFE-BASEL}, author={Jin, Xiaohe and Zhang, Yunlong and Zhang, Ran and Nguyen, Kathy-Uyen and Lindsey, Jonathan S. and Miller, Eric S.}, year={2021}, month={Aug} } @article{magdaong_buhrmaster_faries_liu_tira_lindsey_hanson_holten_laible_kirmaier_2021, title={In Situ, Protein-Mediated Generation of a Photochemically Active Chlorophyll Analogue in a Mutant Bacterial Photosynthetic Reaction Center}, volume={60}, ISSN={["0006-2960"]}, DOI={10.1021/acs.biochem.1c00137}, abstractNote={All possible natural amino acids have been substituted for the native LeuL185 positioned near the B-side bacteriopheophytin (HB) in the bacterial reaction center (RC) from Rhodobacter sphaeroides. Additional mutations that enhance electron transfer to the normally inactive B-side cofactors are present. Approximately half of the isolated RCs with Glu at L185 contain a magnesium chlorin (CB) in place of HB. The chlorin is not the common BChl a oxidation product 3-desvinyl-3-acetyl chlorophyll a with a C-C bond in ring D and a C═C bond in ring B but has properties consistent with reversal of these bond orders, giving 17,18-didehydro BChl a. In such RCs, charge-separated state P+CB- forms in ∼5% yield. The other half of the GluL185-containing RCs have a bacteriochlorophyll a (BChl a) denoted βB in place of HB. Residues His, Asp, Asn, and Gln at L185 yield RCs with ≥85% βB in the HB site, while most other amino acids result in RCs that retain HB (≥95%). To the best of our knowledge, neither bacterial RCs that harbor five BChl a molecules and one chlorophyll analogue nor those with six BChl a molecules have been reported previously. The finding that altering the local environment within a cofactor binding site of a transmembrane complex leads to in situ generation of a photoactive chlorin with an unusual ring oxidation pattern suggests new strategies for amino acid control over pigment type at specific sites in photosynthetic proteins.}, number={16}, journal={BIOCHEMISTRY}, author={Magdaong, Nikki Cecil M. and Buhrmaster, James C. and Faries, Kaitlyn M. and Liu, Haijun and Tira, Gregory A. and Lindsey, Jonathan S. and Hanson, Deborah K. and Holten, Dewey and Laible, Philip D. and Kirmaier, Christine}, year={2021}, month={Apr}, pages={1260–1275} } @article{jin_miller_lindsey_2021, title={Natural Product Gene Clusters in the Filamentous Nostocales Cyanobacterium HT-58-2}, volume={11}, ISSN={["2075-1729"]}, DOI={10.3390/life11040356}, abstractNote={Cyanobacteria are known as rich repositories of natural products. One cyanobacterial-microbial consortium (isolate HT-58-2) is known to produce two fundamentally new classes of natural products: the tetrapyrrole pigments tolyporphins A–R, and the diterpenoid compounds tolypodiol, 6-deoxytolypodiol, and 11-hydroxytolypodiol. The genome (7.85 Mbp) of the Nostocales cyanobacterium HT-58-2 was annotated previously for tetrapyrrole biosynthesis genes, which led to the identification of a putative biosynthetic gene cluster (BGC) for tolyporphins. Here, bioinformatics tools have been employed to annotate the genome more broadly in an effort to identify pathways for the biosynthesis of tolypodiols as well as other natural products. A putative BGC (15 genes) for tolypodiols has been identified. Four BGCs have been identified for the biosynthesis of other natural products. Two BGCs related to nitrogen fixation may be relevant, given the association of nitrogen stress with production of tolyporphins. The results point to the rich biosynthetic capacity of the HT-58-2 cyanobacterium beyond the production of tolyporphins and tolypodiols.}, number={4}, journal={LIFE-BASEL}, author={Jin, Xiaohe and Miller, Eric S. and Lindsey, Jonathan S.}, year={2021}, month={Apr} } @article{liu_rong_liu_lindsey_2021, title={Single-Fluorophore Single-Chain Nanoparticle Undergoes Fluorophore-Driven Assembly with Fluorescence Features Retained in Physiological Milieu}, volume={3}, ISSN={["2637-6105"]}, DOI={10.1021/acsapm.0c01313}, abstractNote={To address the longstanding problem of solubilization of hydrophobic fluorophores in aqueous solution, a recent design employed a single fluorophore attached to the terminus of a heterotelechelic, ...}, number={4}, journal={ACS APPLIED POLYMER MATERIALS}, author={Liu, Sijia and Rong, Jie and Liu, Rui and Lindsey, Jonathan S.}, year={2021}, month={Apr}, pages={1767–1776} } @article{wang_lindsey_2021, title={Synthesis of AD-Dihydrodipyrrins Equipped with Latent Substituents of Native Chlorophylls and Bacteriochlorophylls}, volume={86}, ISSN={["1520-6904"]}, url={http://dx.doi.org/10.1021/acs.joc.1c01239}, DOI={10.1021/acs.joc.1c01239}, abstractNote={Native chlorophylls and bacteriochlorophylls share a common trans-substituted pyrroline ring D (17-propionic acid, 18-methyl), whereas diversity occurs in ring A particularly at the 3-position. Two dihydrodipyrrins equipped with native-like D-ring substituents and tailorable A-ring substituents have been synthesized. The synthesis relies on a Schreiber-modified Nicholas reaction to construct the stereochemically defined precursor to ring D, a dialkyl-substituted pent-4-ynoic acid. The carboxylic acid group of the intact propionic acid proved unworkable, whereupon protected propionate (-CO2tBu) and several latent propyl ethers were examined. The tert-butyldiphenylsilyl-protected propanol substituent proved satisfactory for reaction of the chiral N-acylated oxazolidinone, affording (2S,3S)-2-(3-((tert-butyldiphenylsilyl)oxy)propyl)-3-methylpent-4-ynoic acid in ∼30% yield over 8 steps. Two variants for ring A, 2-tert-butoxycarbonyl-3-Br/H-5-iodo-4-methylpyrrole, were prepared via the Barton-Zard route. Dihydrodipyrrin formation from the pyrrole and pentynoic acid entailed Jacobi Pd-mediated lactone formation, Petasis methenylation, and Paal-Knorr-type pyrroline formation. The two AD-dihydrodipyrrins bear the D-ring methyl and protected propanol groups with a stereochemical configuration identical to that of native (bacterio)chlorophylls, and a bromine or no substitution in ring A corresponding to the 3-position of (bacterio)chlorophylls. The analogous β-position of a lactone-pyrrole intermediate on the path to the dihydrodipyrrin also was successfully brominated, opening opportunities for late-stage diversification in the synthesis of (bacterio)chlorophylls.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Wang, Pengzhi and Lindsey, Jonathan S.}, year={2021}, month={Sep}, pages={11794–11811} } @article{chung_tran_chau nguyen_wang_lindsey_2021, title={Synthesis of model bacteriochlorophylls containing substituents of native rings A, C and E}, volume={7}, ISSN={["1369-9261"]}, url={http://dx.doi.org/10.1039/d1nj02469h}, DOI={10.1039/d1nj02469h}, abstractNote={An established route to the bacteriochlorophyll skeleton from two dihydrodipyrrin halves has been extended to accommodate several substituents characteristic of the native bacteriochlorophyll a.}, journal={NEW JOURNAL OF CHEMISTRY}, author={Chung, Duy T. M. and Tran, Phuong Vy and Chau Nguyen, Khiem and Wang, Pengzhi and Lindsey, Jonathan S.}, year={2021}, month={Jul} } @article{timothy j. o'donnell_gurr_dai_taniguchi_williams_lindsey_2021, title={Tolyporphins A-R, unusual tetrapyrrole macrocycles in a cyanobacterium from Micronesia, assessed quantitatively from the culture HT-58-2}, volume={6}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85109210079&partnerID=MN8TOARS}, DOI={10.1039/d1nj02108g}, abstractNote={Tolyporphins A–R are the newest additions to the family of native tetrapyrroles. LC-MS-dMRM and absorption spectroscopy have been employed for analysis of mixtures containing the 18 distinctive natural products.}, number={26}, journal={NEW JOURNAL OF CHEMISTRY}, author={Timothy J. O'Donnell and Gurr, Joshua R. and Dai, Jingqiu and Taniguchi, Masahiko and Williams, Philip G. and Lindsey, Jonathan S.}, year={2021}, month={Jun} } @article{taniguchi_lindsey_2021, title={Absorption and Fluorescence Spectral Database of Chlorophylls and Analogues}, volume={97}, ISSN={["1751-1097"]}, url={https://doi.org/10.1111/php.13319}, DOI={10.1111/php.13319}, abstractNote={AbstractAbsorption spectra and fluorescence spectra are essential for use across the photosciences, yet such spectra along with the all‐important values for molar absorption coefficient (ε) and fluorescence quantum yield (Φf) often are found with great difficulty. Here, a literature survey concerning the vital class of chlorophyll compounds has led to identification of spectra for 150 members. Spectra in print form have been digitized (with baseline corrections) and assembled into a database along with literature references, solvent identity and values for ε and Φf (where available). The database encompasses photosynthetic tetrapyrroles wherein the chromophore is a porphyrin (e.g. chlorophyll c1, protochlorophyll a), chlorin (e.g. chlorophyll a, bacteriochlorophyll c) or bacteriochlorin (e.g. bacteriochlorophyll a). Altogether, the database contains 305 absorption spectra (from 19 porphyrins, 109 chlorins and 22 bacteriochlorins) and 72 fluorescence spectra (from 10 porphyrins, 30 chlorins and 4 bacteriochlorins). The spectral database should facilitate comparisons and quantitative calculations. All spectra are available in print form in the Supporting Information. The entire database in digital form is available with the PhotochemCAD program for free downloading and further use at http://www.photochemcad.com.}, number={1}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, publisher={Wiley}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2021}, month={Jan}, pages={136–165} } @article{taniguchi_lindsey_2020, title={Absorption and fluorescence spectra of organic compounds from 40 sources - archives, repositories, databases, and literature search engines}, volume={11256}, ISSN={["1996-756X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85084177636&partnerID=MN8TOARS}, DOI={10.1117/12.2542859}, abstractNote={Absorption and fluorescence spectra are foundational data for studies in photochemistry as well as any area of science or technology that entails electronic spectroscopy. The data of interest include the spectra (graphs of intensity as a function of wavelength or wavenumber), the respective quantitative photophysical parameters – molar absorption coefficient [ε(λ)] and the fluorescence quantum yield [Φf] – and the conditions under which the data were obtained. Yet such qualitative and quantitative data are scattered across a wide landscape. Modern search engines provide access to much of the world’s published scientific literature (<108 articles) spanning <100 years but are surprisingly ineffective at pinpointing spectra and companion photophysical parameters. Manual curation has led to valuable collections albeit of uneven contents: some include spectra, others include only listings of spectral data (e.g., positions of peak intensity [λmax]), and many are not available in digital form. Numerous calculations in photophysics, such as propensity for Förster resonance energy transfer (FRET), require spectra and cannot be carried out with tabular listings of values of λmax, ε(λ) and Φf. Here, we summarize the spectral data available in 27 printed archives (beginning in the early 20th century), in repositories or databases at a dozen dedicated websites, and via scholarly literature search tools. The websites and search tools include PubChem, ChemSpider, NIST Chemistry WebBook, SciFinder, Reaxys, Google Scholar, Microsoft Academic, and Web of Science. This work is part of a long-term project to organize and assemble the world of spectral data for the molecular photosciences.}, journal={REPORTERS, MARKERS, DYES, NANOPARTICLES, AND MOLECULAR PROBES FOR BIOMEDICAL APPLICATIONS XII}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2020} } @article{cao_mehta_norcross_taniguchi_lindsey_2020, title={Analysis of Wikipedia pageviews to identify popular chemicals}, volume={11256}, ISSN={["1996-756X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85084186656&partnerID=MN8TOARS}, DOI={10.1117/12.2542835}, abstractNote={A new approach to assess popularity relies on analysis of the number of times a web article is viewed. Here, a strategy is described to identify chemicals of widespread interest. The strategy makes use of Wikipedia, a rapidly growing publicly editable web encyclopedia that has become an influential knowledge base. While the total number of chemicals mentioned in Wikipedia is unknown, use of the Wikipedia Chemical Structure Explorer (WCSE) developed by Novartis enables identification of those that are described in an Infobox or Chembox along with a Simplified Molecular-Input Line-Entry system (SMILES) code. Using a Python script, all so-listed chemicals (16,243) in Wikipedia were identified and then sorted on the basis of their pageview rankings. Of the 16,243 chemicals, 846 (5.2%) belonged to controlled substances (United States Drug Enforcement Administration), WHO essential medicines, or the top 300 US drugs. These 846 chemicals received 220 million pageviews, which is 41.4% of the pageviews for all members of the Wikipedia chemical list. The number of chemicals described in the entire corpus of Wikipedia remains a tiny fraction of the <107 known chemicals. Much remains to be done to make the venerable literature and data of chemistry readily accessible. Regardless, identification of popular chemicals in this manner can be used to create selected databases, to tailor educational curricula, or to create targeted informational materials (such as safety brochures); such considerations of public demand are likely to engender corresponding widespread interest.}, journal={REPORTERS, MARKERS, DYES, NANOPARTICLES, AND MOLECULAR PROBES FOR BIOMEDICAL APPLICATIONS XII}, author={Cao, Yuru and Mehta, Hely and Norcross, Ann E. and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2020} } @article{fujita_zhang_wu_lindsey_2020, title={Chromogenic agents built around a multifunctional double-triazine framework for enzymatically triggered cross-linking under physiological conditions}, volume={44}, ISSN={["1369-9261"]}, DOI={10.1039/c9nj06187h}, abstractNote={A molecular architecture designed for bioconjugation and internal absorption ratiometry undergoes enzymatically triggered cleavage of glucosyl groups and subsequent oxidative dimerization in aqueous solution to yield indigoid-containing scaffolds.}, number={10}, journal={NEW JOURNAL OF CHEMISTRY}, author={Fujita, Hikaru and Zhang, Yunlong and Wu, Zhiyuan and Lindsey, Jonathan S.}, year={2020}, month={Mar}, pages={3856–3867} } @article{donal f. o'shea_sommer_taniguchi_lindsey_2020, title={Crystal Structure of 1,9-Dibromo-5-phenyldipyrrin, Tetrapyrrole Synthesis Derivative and Free Base Ligand of BODIPY Building Blocks}, volume={36}, ISSN={["1883-3578"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85089361305&partnerID=MN8TOARS}, DOI={10.2116/xraystruct.36.21}, abstractNote={A free base ligand of a BODIPY building block, 1,9-dibromo-5-phenyldipyrrin (2), was synthesized. The crystal structure was determined by the single crustal X-ray diffraction method at 293 K. The compound crystallizes in a monoclinic system and was characterized as follows: P21/c, a = 9.94150(10), b = 15.8691(3), c = 10.2160(2)Å, β = 118.8050(6), Z = 4, V = 1412.28(4)Å3, Dcalcd = 1.778 g/cm3, Z = 4. The R1 [I > 2σ(I)] and wR2 (all data) values are 0.0266 and 0.0653, respectively, for all 2896 independent reflections.}, journal={X-RAY STRUCTURE ANALYSIS ONLINE}, author={Donal F. O'shea and Sommer, Roger D. and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2020}, month={Jul}, pages={21–22} } @article{zhang_wu_takashima_nguyen_matsumoto_lindsey_2020, title={Engineering of an archaeal phosphodiesterase to trigger aggregation-induced emission (AIE) of synthetic substrates}, volume={44}, ISSN={["1369-9261"]}, DOI={10.1039/d0nj03208e}, abstractNote={Aggregation-induced emission (AIE) probes that can be triggered by enzymatic activity are valuable for applications across the life sciences.}, number={33}, journal={NEW JOURNAL OF CHEMISTRY}, author={Zhang, Yunlong and Wu, Zhiyuan and Takashima, Ippei and Nguyen, Kathy-Uyen and Matsumoto, Nobuyuki and Lindsey, Jonathan S.}, year={2020}, month={Sep}, pages={14266–14277} } @article{nalaoh_bureekaew_promaraka_lindsey_2020, title={Fourfold alkyl wrapping of a copper(II) porphyrin thwarts macrocycle pi-pi stacking in a compact supramolecular package}, volume={76}, ISSN={["2053-2296"]}, DOI={10.1107/S2053229620007172}, abstractNote={Porphyrins are valuable constituents in optoelectronic, catalytic, and other applications, yet control of intermolecular π–π stacking is invariably essential to attain the desired properties. Superstructures built onto the porphyrin, often via meso-aryl groups, can afford facial encumbrance that suppresses π–π stacking, although some molecular designs have provided insufficient facial coverage and many have entailed cumbersome syntheses. In this study, a copper(II) porphyrin bearing four meso substituents, namely, {10,20-bis[2,6-bis(octyloxy)phenyl]-5,15-dibromoporphinato}copper(II), [Cu(C64H82Br2N4O4)], was prepared by metalation of the corresponding free-base porphyrin and was characterized by single-crystal X-ray diffraction. The crystal structure reveals a dihedral angle of 111.1 (2)° for the plane of the meso-aryl group relative to the plane of the porphyrin, with both aryl groups tilted in the same direction. Each of the four octyloxy groups exhibits a gauche conformation for the –OCH2CH2– unit but is extended with four or five anti (–CH2CH2–/H) conformations thereafter, causing each octyl group to span the dimension of the macrocycle. In a global frame of reference where the two Br atoms define the north/south poles and the two aryl groups are at antipodes on the equator, two octyl groups of one aryl unit project over the northern hemisphere (covering pyrroles A and B), whereas those of the other aryl unit project over the southern hemisphere (covering pyrroles C and D). Together, the four octyl groups ensheath the two faces of the porphyrin in a self-wrapped assembly. The closest approach of the Cu atom to an octyl methylene C atom (position 6) is 3.5817 (18) Å, the mean separations of neighboring porphyrin planes are 8.059 (4) and 4.693 (8) Å along the a and c axes, respectively, and the center-to-center distances between the Cu atoms of neighboring porphyrins are 10.2725 (4), 12.2540 (6), and 12.7472 (6) Å along the a, b, and c axes, respectively. The Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots provide information concerning contact interactions in the supramolecular assembly of the solid crystal.}, journal={ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY}, author={Nalaoh, Phattananawee and Bureekaew, Sareeya and Promaraka, Vinich and Lindsey, Jonathan S.}, year={2020}, month={Jul}, pages={647-+} } @article{magdaong_taniguchi_diers_niedzwiedzki_kirmaier_lindsey_bocian_holten_2020, title={Photophysical Properties and Electronic Structure of Zinc(II) Porphyrins Bearing 0-4 meso-Phenyl Substituents: Zinc Porphine to Zinc Tetraphenylporphyrin (ZnTPP)}, volume={124}, ISSN={["1520-5215"]}, url={https://doi.org/10.1021/acs.jpca.0c06841}, DOI={10.1021/acs.jpca.0c06841}, abstractNote={Six zinc(II) porphyrins bearing 0-4 meso-phenyl substituents have been examined spectroscopically and theoretically. Comparisons with previously examined free base analogues afford a deep understanding of the electronic and photophysical effects of systematic addition of phenyl groups in porphyrins containing a central zinc(II) ion versus two hydrogen atoms. Trends in the wavelengths and relative intensities of the absorption bands are generally consistent with predictions from time-dependent density functional theory calculations and simulations from Gouterman's four-orbital model. These trends derive from a preferential effect of the meso-phenyl groups to raise the energy of the highest occupied molecular orbital. The calculations reveal additional insights, such as a progressive increase in oscillator strength in the violet-red (B-Q) absorption manifold with increasing number of phenyls. Progressive addition of 0-4 phenyl substituents to the zinc porphyrins in O2-free toluene engenders a reduction in the measured lifetime of the lowest singlet excited state (2.5-2.1 ns), an increase in the S1 → S0 fluorescence yield (0.022-0.030), a decrease in the yield of S1 → T1 intersystem crossing (0.93-0.88), and an increase in the yield of S1 → S0 internal conversion (0.048-0.090). The derived rate constants for S1 decay reveal significant differences in the photophysical properties of the zinc chelates versus free base forms. The unexpected finding of a larger rate constant for internal conversion for zinc chelates versus free bases is particularly exemplary. Collectively, the findings afford fundamental insights into the photophysical properties and electronic structure of meso-phenylporphyrins, which are widely used as benchmarks for tetrapyrrole-based architectures in solar energy and life sciences research.}, number={38}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, publisher={American Chemical Society (ACS)}, author={Magdaong, Nikki Cecil M. and Taniguchi, Masahiko and Diers, James R. and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2020}, month={Sep}, pages={7776–7794} } @misc{wang_lindsey_2020, title={Riley Oxidation of Heterocyclic Intermediates on Paths to Hydroporphyrins-A Review}, volume={25}, ISSN={["1420-3049"]}, DOI={10.3390/molecules25081858}, abstractNote={Riley oxidation of advanced heterocyclic intermediates (dihydrodipyrrins and tetrahydrodipyrrins) is pivotal in routes to synthetic hydroporphyrins including chlorins, bacteriochlorins, and model (bacterio)chlorophylls. Such macrocycles find wide use in studies ranging from energy sciences to photomedicine. The key transformation (–CH3 → –CHO) is often inefficient, however, thereby crimping the synthesis of hydroporphyrins. The first part of the review summarizes 12 representative conditions for Riley oxidation across diverse (non-hydrodipyrrin) substrates. An interlude summarizes the proposed mechanisms and provides context concerning the nature of various selenium species other than SeO2. The second part of the review comprehensively reports the conditions and results upon Riley oxidation of 45 1-methyltetrahydrodipyrrins and 1-methyldihydrodipyrrins. A comparison of the results provides insights into the tolerable structural features for Riley oxidation of hydrodipyrrins. In general, Riley oxidation of dihydrodipyrrins has a broad scope toward substituents, but proceeds in only modest yield. Too few tetrahydrodipyrrins have been examined to draw conclusions concerning scope. New reaction conditions or approaches will be required to achieve high yields for this critical transformation in the synthesis of hydroporphyrins.}, number={8}, journal={MOLECULES}, author={Wang, Pengzhi and Lindsey, Jonathan S.}, year={2020}, month={Apr} } @article{nguyen_wang_lindsey_2021, title={Study of conditions for streamlined assembly of a model bacteriochlorophyll from two dihydrodipyrrin halves}, volume={45}, ISSN={["1369-9261"]}, url={http://dx.doi.org/10.1039/d0nj04855k}, DOI={10.1039/d0nj04855k}, abstractNote={Knoevenagel condensation followed by double-ring closure (Nazarov cyclization, electrophilic aromatic substitution, elimination of methanol) and optional zinc insertion smoothly afford models of the native bacteriochlorophylls.}, number={2}, journal={NEW JOURNAL OF CHEMISTRY}, author={Nguyen, Khiem Chau and Wang, Pengzhi and Lindsey, Jonathan S.}, year={2021}, month={Jan}, pages={569–581} } @article{fujita_jing_krayer_allu_veeraraghavaiah_wu_jiang_diers_magdaong_mandal_et al._2019, title={Annulated bacteriochlorins for near- infrared photophysical studies}, volume={43}, ISSN={["1369-9261"]}, DOI={10.1039/c9nj01113g}, abstractNote={Bacteriochlorins with phenaleno or benzo annulation absorb at 913 or 1033 nm and exhibit excited-state lifetimes of 150 or 7 ps, suggesting applications in photoacoustic imaging.}, number={19}, journal={NEW JOURNAL OF CHEMISTRY}, author={Fujita, Hikaru and Jing, Haoyu and Krayer, Michael and Allu, Srinivasarao and Veeraraghavaiah, Gorre and Wu, Zhiyuan and Jiang, Jianbing and Diers, James R. and Magdaong, Nikki Cecil M. and Mandal, Amit K. and et al.}, year={2019}, month={May}, pages={7209–7232} } @article{ballatore_milanesio_fujita_lindsey_durantini_2020, title={Bacteriochlorin-bis(spermine) conjugate affords an effective photodynamic action to eradicate microorganisms}, volume={13}, ISSN={["1864-0648"]}, DOI={10.1002/jbio.201960061}, abstractNote={AbstractA novel bacteriochlorin bearing two spermine units (BCS) was synthesized from 3,13‐dibromo‐8,8,18,18‐tetramethylbacteriochlorin (BC‐Br 3,13). The synthesis involved the Suzuki coupling of BC‐Br 3,13 to obtain a bacteriochlorin‐dibenzaldehyde (BCA), which was subjected to reductive amination with spermine. The resulting bacteriochlorin BCS presents a strong near‐infrared absorption band at 747 nm, emits at 750 nm with fluorescence quantum yield of 0.14, and generates singlet molecular oxygen, O2(1Δg), with a quantum yield of 0.27. Photokilling capacities mediated by BCS were evaluated in microbial cells. The viability of Staphylococcus aureus decreased 7 logs when cells were incubated with 1 μM BCS and irradiated for 15 minutes. Comparable photocytotoxic effect was obtained with Escherichia coli, when cells were treated for 30 minutes with visible light. BCS was also an effective photosensitizer to inactivate Candida albicans. In addition, this bacteriochlorin was able to eradicate bacteria at short incubation times. The structure of BCS contains eight basic amino groups that, when protonated in water, increase the binding to the cell envelope. In summary, the readily accessible bacteriochlorin BCS was highly effective at low concentrations as a broad‐spectrum antimicrobial photosensitizer.}, number={2}, journal={JOURNAL OF BIOPHOTONICS}, author={Ballatore, Maria B. and Milanesio, Maria E. and Fujita, Hikaru and Lindsey, Jonathan S. and Durantini, Edgardo N.}, year={2020}, month={Feb} } @article{matsumoto_taniguchi_lindsey_2020, title={Bioconjugatable synthetic chlorins rendered water-soluble with three PEG-12 groups via click chemistry}, volume={24}, ISSN={["1099-1409"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85072584806&partnerID=MN8TOARS}, DOI={10.1142/S1088424619501219}, abstractNote={ Chlorins provide many ideal features for use as red-region fluorophores but require molecular tailoring for solubilization in aqueous solution. A chlorin building-block bearing 18,18-dimethyl, 15-bromo and 10-[2,4,6-tris(propargyloxy)phenyl] substituents has been transformed via click chemistry with CH3(OCH2CH[Formula: see text]-N3 followed by Suzuki coupling with 3-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)propanoic acid, thereby installing a water-solubilization motif and a bioconjugatable handle, respectively. In toluene, [Formula: see text]-dimethylformamide (DMF) or water, the resulting facially encumbered free base chlorin exhibits characteristic chlorin absorption ([Formula: see text] [Formula: see text]412, 643 nm) and fluorescence ([Formula: see text] [Formula: see text]645 nm) spectra with only modest variation in fluorescence quantum yield ([Formula: see text] values (0.24, 0.25 and 0.19, respectively). The zinc chlorin derived therefrom exhibits similar spectral constancy ([Formula: see text] [Formula: see text]414 and 613 nm, [Formula: see text] [Formula: see text]616 nm) and [Formula: see text] 0.094, 0.10 and 0.086 in the three solvents. The results together indicate the viability of the molecular design and synthetic methodology to create red-region fluorophores for use in diverse applications. }, number={1-3}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Matsumoto, Nobuyuki and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2020}, pages={362–378} } @article{barnhart-dailey_zhang_zhang_anthony_aaron_miller_lindsey_timlin_2019, title={Cellular localization of tolyporphins, unusual tetrapyrroles, in a microbial photosynthetic community determined using hyperspectral confocal fluorescence microscopy}, volume={141}, ISSN={0166-8595 1573-5079}, url={http://dx.doi.org/10.1007/s11120-019-00625-w}, DOI={10.1007/s11120-019-00625-w}, abstractNote={The cyanobacterial culture HT-58-2, composed of a filamentous cyanobacterium and accompanying community bacteria, produces chlorophyll a as well as the tetrapyrrole macrocycles known as tolyporphins. Almost all known tolyporphins (A-M except K) contain a dioxobacteriochlorin chromophore and exhibit an absorption spectrum somewhat similar to that of chlorophyll a. Here, hyperspectral confocal fluorescence microscopy was employed to noninvasively probe the locale of tolyporphins within live cells under various growth conditions (media, illumination, culture age). Cultures grown in nitrate-depleted media (BG-11 0 vs. nitrate-rich, BG-11) are known to increase the production of tolyporphins by orders of magnitude (rivaling that of chlorophyll a) over a period of 30-45 days. Multivariate curve resolution (MCR) was applied to an image set containing images from each condition to obtain pure component spectra of the endogenous pigments. The relative abundances of these components were then calculated for individual pixels in each image in the entire set, and 3D-volume renderings were obtained. At 30 days in media with or without nitrate, the chlorophyll a and phycobilisomes (combined phycocyanin and phycobilin components) co-localize in the filament outer cytoplasmic region. Tolyporphins localize in a distinct peripheral pattern in cells grown in BG-11 0 versus a diffuse pattern (mimicking the chlorophyll a localization) upon growth in BG-11. In BG-11 0 , distinct puncta of tolyporphins were commonly found at the septa between cells and at the end of filaments. This work quantifies the relative abundance and envelope localization of tolyporphins in single cells, and illustrates the ability to identify novel tetrapyrroles in the presence of chlorophyll a in a photosynthetic microorganism within a non-axenic culture.}, number={3}, journal={Photosynthesis Research}, publisher={Springer Science and Business Media LLC}, author={Barnhart-Dailey, Meghan and Zhang, Yunlong and Zhang, Ran and Anthony, Stephen M. and Aaron, Jesse S. and Miller, Eric S. and Lindsey, Jonathan S. and Timlin, Jerilyn A.}, year={2019}, month={Mar}, pages={259–271} } @article{guo_xu_norcross_taniguchi_lindsey_2019, title={Developing a user community in the photosciences: a website for spectral data and access to PhotochemCAD}, volume={10893}, ISSN={["1996-756X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85073786008&partnerID=MN8TOARS}, DOI={10.1117/12.2508077}, abstractNote={A new website, centered on absorption and fluorescence spectra, has been designed for the broad community of members in the photosciences. Spectral data lie at the heart of the vast field of the photosciences, yet collections of such data are sparse, scattered and often in print rather than digital form. Because many if not most searches for photochemical data begin with individual spectra, the website should constitute a photosciences nexus. The database of <500 spectra can be accessed via text or by viewing molecular structures. The spectral data on the website are identical with those in the database associated with the software program PhotochemCAD, but only the latter contains the rich trove of companion references to the originating scientific literature. PhotochemCAD, which contains modules for diverse calculations germane to the photosciences, can be freely downloaded from the new website. To develop a community of users in the photosciences, a curated and validated set of email addresses of photoscientists has been generated from the primary photochemistry literature since 2004. The literature surveyed (19 journals, <45,000 articles) encompasses the flagship publications of 15 scholarly societies. The present work represents a step toward fulfilling the long-term ambition of assembling all known spectral data worldwide, from print and digital sources, in one carefully curated collection of digital data in a readily accessible site. The advances should broaden awareness and increase availability of spectra for diverse studies in the field of photosciences, which encompasses art, astrobiology, biology, chemistry, ecology, engineering, medicine, physics, textiles, and zoochromy.}, journal={REPORTERS, MARKERS, DYES, NANOPARTICLES, AND MOLECULAR PROBES FOR BIOMEDICAL APPLICATIONS XI}, publisher={SPIE}, author={Guo, Yaxue and Xu, Zhen and Norcross, Ann Elizabeth and Taniguchi, Masahiko and Lindsey, Jonathan S.}, editor={Achilefu, Samuel and Raghavachari, RameshEditors}, year={2019} } @article{fujita_dou_matsumoto_wu_lindsey_2020, title={Enzymatically triggered chromogenic cross-linking agents under physiological conditions}, volume={44}, ISSN={["1369-9261"]}, DOI={10.1039/c9nj04126e}, abstractNote={Oxidative dimerization of an indoxyl moiety, released by glycosidase action in aqueous solution, yields an indigoid dye in formats that enable bioconjugation and molecular cross-linking.}, number={3}, journal={NEW JOURNAL OF CHEMISTRY}, author={Fujita, Hikaru and Dou, Jinghuai and Matsumoto, Nobuyuki and Wu, Zhiyuan and Lindsey, Jonathan S.}, year={2020}, month={Jan}, pages={719–743} } @article{qi_taniguchi_lindsey_2019, title={Heuristics from Modeling of Spectral Overlap in Forster Resonance Energy Transfer (FRET)}, volume={59}, ISSN={["1549-960X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85062087853&partnerID=MN8TOARS}, DOI={10.1021/acs.jcim.8b00753}, abstractNote={Among the photophysical parameters that underpin Förster resonance energy transfer (FRET), perhaps the least explored is the spectral overlap term ( J). While by definition J increases linearly with acceptor molar absorption coefficient (ε(A) in M-1 cm-1), is proportional to wavelength (λ4), and depends on the degree of overlap of the donor fluorescence and acceptor absorption spectra, the question arose as to the value of J for the case of perfect spectral overlap versus that for representative fluorophores with incomplete spectral overlap. Here, Gaussian distributions of absorption and fluorescent spectra have been modeled that encompass varying degrees of overlap, full-width-at-half-maximum (fwhm), and Stokes shift. For ε(A) = 105 M-1 cm-1 and perfect overlap, the J value (in M-1 cm-1 nm4) ranges from 1.15 × 1014 (200 nm) to 7.07 × 1016 (1000 nm), is almost linear with λ4 (average of λabs and λflu), and is nearly independent of fwhm. For visible-region fluorophores with perfectly overlapped Gaussian spectra, the resulting value of J ( JG-0) is ∼0.71 ε(A)λ4 (M-1 cm-1 nm4). The experimental J values for homotransfer, as occurs in light-harvesting antennas, were calculated with spectra from a static database of 60 representative compounds (12 groups, 5 compounds each) and found to range from 4.2 × 1010 ( o-xylene) to 5.3 × 1016 M-1 cm-1 nm4 (a naphthalocyanine). The degree of overlap, defined by the ratio of the experimental J to the model JG-0 for perfectly overlapped spectra, ranges from ∼0.5% (coumarin 151) to 77% (bacteriochlorophyll a). The results provide insights into how a variety of factors affect the resulting J values. The high degree of spectral overlap for (bacterio)chlorophylls prompts brief conjecture concerning the relevance of energy transfer to the question "why chlorophyll".}, number={2}, journal={JOURNAL OF CHEMICAL INFORMATION AND MODELING}, author={Qi, Qi and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2019}, month={Feb}, pages={652–667} } @article{wu_fujita_magdaong_diers_hood_allu_niedzwiedzki_kirmaier_bocian_holten_et al._2019, title={New molecular design for blue BODIPYs}, volume={43}, ISSN={["1369-9261"]}, DOI={10.1039/c9nj01114e}, abstractNote={Dihydro analogues of BODIPYs exhibit spectral features (Φf ∼ 0.4–0.9) resembling aminocoumarins and suggest applications for broad-band photosensitization or where large Stokes shifts are desired.}, number={19}, journal={NEW JOURNAL OF CHEMISTRY}, author={Wu, Zhiyuan and Fujita, Hikaru and Magdaong, Nikki Cecil M. and Diers, James R. and Hood, Don and Allu, Srinivasarao and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and et al.}, year={2019}, month={May}, pages={7233–7242} } @article{liu_vairaprakash_lindsey_2019, title={Self-assembly with fluorescence readout in a free base dipyrrin-polymer triggered by metal ion binding in aqueous solution}, volume={43}, ISSN={["1369-9261"]}, DOI={10.1039/c9nj01787a}, abstractNote={Profound morphological and fluorogenic changes ensue upon binding of a zinc ion by two polymers, each of which bears a single dipyrrin at one terminus, forming the bis(dipyrrinato)Zn(ii) complex.}, number={24}, journal={NEW JOURNAL OF CHEMISTRY}, author={Liu, Rui and Vairaprakash, Pothiappan and Lindsey, Jonathan S.}, year={2019}, month={Jun}, pages={9711–9724} } @article{wang_nguyen_lindsey_2019, title={Synthesis of the Ring C Pyrrole of Native Chlorophylls and Bacteriochlorophylls}, volume={84}, ISSN={["1520-6904"]}, DOI={10.1021/acs.joc.9b01650}, abstractNote={As part of a program to develop practical syntheses of members of the family of (bacterio)chlorophylls, two routes to 2-iodo-3-methyl-4-(3-methoxy-1,3-dioxopropyl)pyrrole, a precursor of the universal ring C, have been developed. The β-ketoester of ring C is expected to give rise to ring E upon Knoevenagel condensation and Nazarov cyclization with a ring D constituent as demonstrated in an analogue synthesis. Two viable routes were developed beginning with N-TIPS-pyrrole or with 4-oxo-2-pentene and TosMIC, affording multi-gram-quantities of this ostensibly simple pyrrole.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Wang, Pengzhi and Nguyen, Khiem Chau and Lindsey, Jonathan S.}, year={2019}, month={Sep}, pages={11286–11293} } @article{wang_lu_lindsey_2020, title={Use of the Nascent Isocyclic Ring to Anchor Assembly of the Full Skeleton of Model Chlorophylls}, volume={85}, ISSN={["1520-6904"]}, DOI={10.1021/acs.joc.9b02770}, abstractNote={The chlorophyll skeleton contains a chlorin macrocycle and an annulated fifth (or isocyclic) ring bearing 131-oxo and 132-carbomethoxy substituents. The isocyclic ring has traditionally been constructed by annulation of an intact tetrapyrrole macrocycle. Here, a complementary route employs reaction of a gem-dimethyl-substituted dihydrodipyrrin-carboxaldehyde (AD half) and a dipyrromethane bearing a 3-methoxy-1,3-dioxopropyl group (BC half). A McMurry-like reaction of a 2-(2-nitro-5-oxohexyl)pyrrole was employed to construct the second pyrrole ring in one of three BC halves, whereas the other two were prepared by known routes. An AD half and a BC half were joined by Knoevenagel condensation at room temperature, affording the AD,BC-substituted 2-methoxycarbonyl-2-propenone. The subsequent reaction of three AD, BC-propenones (mixture of Z,E-isomers) in CH3CN containing InCl3 and In(OTf)3 at 80 °C afforded the chlorophyll skeleton as the chloroindium(III) chelate; the reaction proceeds via Nazarov cyclization (to form the isocyclic ring), SEAr (to construct the macrocycle), and 2e-,2H+ oxidation (to give the aromatic chromophore). The absorption spectra of the complexes closely resemble that of chlorophyll a. The present work exploits the nascent isocyclic ring as an anchor for directed assembly of the AD and BC halves, forming both the chlorin macrocycle and the isocyclic ring in a single-flask transformation.}, number={2}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Wang, Pengzhi and Lu, Futai and Lindsey, Jonathan S.}, year={2020}, month={Jan}, pages={702–715} } @article{hood_sahin_parkes-loach_jiao_harris_dilbeck_niedzwiedzki_kirmaier_loach_bocian_et al._2018, title={Expanding Covalent Attachment Sites of Nonnative Chromophores to Encompass the C-Terminal Hydrophilic Domain in Biohybrid Light-Harvesting Architectures}, volume={2}, ISSN={["2367-0932"]}, DOI={10.1002/cptc.201700182}, abstractNote={AbstractIncreasing the solar spectral coverage of native photosynthetic antennas can be achieved using biohybrid light‐harvesting (LH) structures comprised of native‐like bacterial photosynthetic peptides and synthetic bacteriochlorins with strong near‐infrared absorption. Four such biohybrids have been prepared wherein synthetic maleimido‐bearing bacteriochlorin BC1‐mal is covalently attached to a Cys residue substituted at either the +1, +5 or +11 position (relative to His‐0) of the 48‐residue β‐peptide of Rb. sphaeroides LH1. In addition, a β‐peptide with Phe substituted for Tyr at the +4 position along with +1Cys was used to examine possible quenching of the excited BC1 by the Tyr. The β‐peptide analogs, as well as their peptide‐BC1 conjugates when combined with native α‐peptide, and bacteriochlorophyll a (BChl a) self‐assemble to form αβ‐dyads and therefrom LH1‐type cyclic (αβ)n oligomers. Static and time‐resolved optical studies show that all of the oligomeric assemblies transfer excitation energy from the appended BC1 to the BChl a array (B875) with an average efficiency of 85 %.}, number={3}, journal={CHEMPHOTOCHEM}, author={Hood, Don and Sahin, Tuba and Parkes-Loach, Pamela S. and Jiao, Jieying and Harris, Michelle A. and Dilbeck, Preston and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Loach, Paul A. and Bocian, David F. and et al.}, year={2018}, month={Mar}, pages={300–313} } @article{hughes_jin_zhang_zhang_tran_williams_lindsey_miller_2018, title={Genome sequence, metabolic properties and cyanobacterial attachment of Porphyrobacter sp. HT-58-2 isolated from a filamentous cyanobacterium–microbial consortium}, volume={164}, ISSN={1350-0872 1465-2080}, url={http://dx.doi.org/10.1099/mic.0.000706}, DOI={10.1099/mic.0.000706}, abstractNote={Tolyporphins are structurally diverse tetrapyrrole macrocycles produced by the cyanobacterial culture HT-58-2. Although tolyporphins were discovered over 25 years ago, little was known about the microbiology of the culture. The studies reported herein expand the description of the community of predominantly alphaproteobacteria associated with the filamentous HT-58-2 cyanobacterium and isolate a dominant bacterium, Porphyrobacter sp. HT-58-2, for which the complete genome is established and growth properties are examined. Fluorescence in situ hybridization (FISH) analysis of the cyanobacterium-microbial community with a probe targeting the 16S rRNA of Porphyrobacter sp. HT-58-2 showed fluorescence emanating from the cyanobacterial sheath. Although genes for the biosynthesis of bacteriochlorophyll a (BChl a) are present in the Porphyrobacter sp. HT-58-2 genome, the pigment was not detected under the conditions examined, implying the absence of phototrophic growth. Comparative analysis of four Porphyrobacter spp. genomes from worldwide collection sites showed significant collinear gene blocks, with two inversions and three deletion regions. Taken together, the results enrich our understanding of the HT-58-2 cyanobacterium-microbial culture.}, number={10}, journal={Microbiology}, publisher={Microbiology Society}, author={Hughes, Rebecca-Ayme and Jin, Xiaohe and Zhang, Yunlong and Zhang, Ran and Tran, Sabrina and Williams, Philip G. and Lindsey, Jonathan S. and Miller, Eric S.}, year={2018}, month={Oct}, pages={1229–1239} } @article{yuen_diers_alexy_roy_mandal_kang_niedzwiedzki_kirmaier_lindsey_bocian_et al._2018, title={Origin of Panchromaticity in Multichromophore-Tetrapyrrole Arrays}, volume={122}, ISSN={["1089-5639"]}, DOI={10.1021/acs.jpca.8b06815}, abstractNote={Panchromatic absorbers that have robust photophysical properties enable new designs for molecular-based light-harvesting systems. Herein, we report experimental and theoretical studies of the spectral, redox, and excited-state properties of a series of perylene-monoimide-ethyne-porphyrin arrays wherein the number of perylene-monoimide units is stepped from one to four. In the arrays, a profound shift of absorption intensity from the strong violet-blue (B y and B x) bands of typical porphyrins into the green, red, and near-infrared (Q x and Q y) regions stems from mixing of chromophore and tetrapyrrole molecular orbitals (MOs), which gives multiplets of MOs having electron density spread over the entire array. This reduces the extensive mixing between porphyrin excited-state configurations and the transition-dipole addition and subtraction that normally leads to intense B and weak Q bands. Reduced configurational mixing derives from moderate effects of the ethyne and perylene on the MO energies and a more substantial effect of electron-density delocalization to reduce the configuration-interaction energy. Quantitative oscillator-strength analysis shows that porphyrin intensity is also shifted into the perylene-like green-region absorption and that the ethyne linkers lend absorption intensity. The reduced porphyrin configurational mixing also endows the S1 state with bacteriochlorin-like properties, including a 1-5 ns lifetime.}, number={36}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Yuen, Jonathan M. and Diers, James R. and Alexy, Eric J. and Roy, Arpita and Mandal, Amit Kumar and Kang, Hyun Suk and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Lindsey, Jonathan S. and Bocian, David F. and et al.}, year={2018}, month={Sep}, pages={7181–7201} } @article{taniguchi_hu_liu_du_lindsey_2018, title={Red and near-infrared fluorophores inspired by chlorophylls. Consideration of practical brightness in multicolor flow cytometry and biomedical sciences}, volume={10508}, ISSN={["1996-756X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85047458937&partnerID=MN8TOARS}, DOI={10.1117/12.2302709}, abstractNote={Demands in flow cytometry for increased multiplexing (for detection of multiple antigens) and brightness (for detection of rare entities) require new fluorophores (i.e., “colors”) with spectrally distinct fluorescence outside the relatively congested visible spectral region. Flow cytometry fluorophores typically must function in aqueous solution upon bioconjugation and ideally should exhibit a host of photophysical features: (i) strong absorption, (ii) sizable Stokes shift, (iii) modest if not strong fluorescence, and (iv) narrow fluorescence band. Tandem dyes have long been pursued to achieve a large effective Stokes shift, increased brightness, and better control over the excitation and emission wavelengths. Here, the attractive photophysical features of chlorophylls and bacteriochlorophylls – Nature’s chosen photoactive pigments for photosynthesis – are described with regards to use in flow cytometry. A chlorophyll (or bacteriochlorophyll) constitutes an intrinsic tandem dye given the red (or near-infrared) fluorescence upon excitation in the higher energy ultraviolet (UV) or visible absorption bands (due to rapid internal conversion to the lowest energy state). Synthetic (bacterio)chlorins are available with strong absorption (near-UV molar absorption coefficient ε(λexc) ~105 M-1cm-1), modest fluorescence quantum yield (Φf = 0.05–0.30), and narrow fluorescence band (10–25 nm) tunable from 600–900 nm depending on synthetic design. The “relative practical brightness” is given by intrinsic brightness [ε(λexc) x Φf] times ηf, the fraction of the fluorescence band that is captured by an emission filter in a multicolor experiment. The spectroscopic features of (bacterio)chlorins are evaluated quantitatively to illustrate practical brightness for this novel class of fluorophores in a prospective 8-color panel.}, journal={REPORTERS, MARKERS, DYES, NANOPARTICLES, AND MOLECULAR PROBES FOR BIOMEDICAL APPLICATIONS X}, publisher={SPIE}, author={Taniguchi, Masahiko and Hu, Gongfang and Liu, Rui and Du, Hai and Lindsey, Jonathan S.}, editor={Achilefu, Samuel and Raghavachari, RameshEditors}, year={2018} } @article{liu_lindsey_2019, title={Single-Polymer-Single-Cargo Strategy Packages Hydrophobic Fluorophores in Aqueous Solution with Retention of Inherent Brightness}, volume={8}, ISSN={["2161-1653"]}, DOI={10.1021/acsmacrolett.8b00907}, abstractNote={A strategy for encapsulating hydrophobic organic entities in aqueous solution has been developed through use of a self-assembling heterotelechelic amphiphilic random copolymer. The polymer (∼40 kDa), prepared by living radical polymerization, contains orthogonally reactive terminal groups and pendant hydrophobic (dodecyl), nonionic hydrophilic (PEG9), and ionic hydrophilic (sulfonate-terminated) groups. Covalent conjugation of a hydrophobic entity to the polymer terminus has been demonstrated for 8 classes of organic fluorophores. The resulting "pod-fluorophore" architecture is unimeric (∼15 nm in diameter) in aqueous solution with spectral features and fluorescence brightness resembling those of the benchmark fluorophore in organic solution. This strategy separates the functional design of the packaged molecular entity ("cargo") from the often vexing challenge of water solubilization and in so doing creates a unitary (one-pod-one-cargo) platform architecture for potential applications in cytometry, biomedical imaging, environmental sensing, and supramolecular chemistry.}, number={1}, journal={ACS MACRO LETTERS}, author={Liu, Rui and Lindsey, Jonathan S.}, year={2019}, month={Jan}, pages={79–83} } @article{hu_kang_mandal_roy_kirmaier_bocian_holten_lindsey_2018, title={Synthesis of arrays containing porphyrin, chlorin, and perylene-imide constituents for panchromatic light-harvesting and charge separation}, volume={8}, ISSN={["2046-2069"]}, DOI={10.1039/c8ra04052d}, abstractNote={Twelve arrays containing porphyrin, chlorin, and/or perylene-imide units were synthesized to investigate panchromatic absorption integrated with charge separation.}, number={42}, journal={RSC ADVANCES}, author={Hu, Gongfang and Kang, Hyun Suk and Mandal, Amit Kumar and Roy, Arpita and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2018}, pages={23854–23874} } @misc{liu_zhang_lindsey_2018, title={Total synthesis campaigns toward chlorophylls and related natural hydroporphyrins - diverse macrocycles, unrealized opportunities}, volume={35}, ISSN={["1460-4752"]}, DOI={10.1039/c8np00020d}, abstractNote={Quantitative evaluation of reported routes toward bonellin, chlorophylla, and tolyporphin A suggests heuristics for practical syntheses of native hydroporphyrins.}, number={9}, journal={NATURAL PRODUCT REPORTS}, author={Liu, Yizhou and Zhang, Shaofei and Lindsey, Jonathan S.}, year={2018}, month={Sep}, pages={879–901} } @article{jiang_matula_swierk_romano_wu_batista_crabtree_lindsey_wang_brudvig_2018, title={Unusual Stability of a Bacteriochlorin Electrocatalyst under Reductive Conditions. A Case Study on CO2 Conversion to CO}, volume={8}, ISSN={["2155-5435"]}, DOI={10.1021/acscatal.8b02991}, abstractNote={Photosynthetic CO2 fixation is mediated by the enzyme RuBisCo, which employs a nonredox-active metal (Mg2+) to bind CO2 adjacent to an organic ligand that provides reducing equivalents for CO2 fixa...}, number={11}, journal={ACS CATALYSIS}, author={Jiang, Jianbing and Matula, Adam J. and Swierk, John R. and Romano, Neyen and Wu, Yueshen and Batista, Victor S. and Crabtree, Robert H. and Lindsey, Jonathan S. and Wang, Hailiang and Brudvig, Gary W.}, year={2018}, month={Nov}, pages={10131–10136} } @article{jiao_yu_holten_lindsey_bocian_2017, title={Characterization of Hydroporphyrins Covalently Attached to Si(100)}, volume={21}, ISSN={["1099-1409"]}, DOI={10.1142/s1088424617500547}, abstractNote={ Attachment of synthetic analogs of natural tetrapyrroles to electroactive surfaces enables physicochemical interrogation and may provide material for use in catalysis, diagnostics, and energy conversion. Six synthetic zinc chlorins and one free base bacteriochlorin, tailored analogs of chlorophyll and bacteriochlorophyll, respectively, have been attached to Si(100) via a high-temperature (400°C) baking method. The hydroporphyrins bear diverse functional groups that enable surface attachment (vinyl, acetyl, triisopropylsilylethynyl, pentafluorophenyl, and hydroxymethylphenyl) and a geminal dimethyl group in each reduced ring for stabilization toward adventitious dehydrogenation. The films were examined by cyclic voltammetry, FTIR spectroscopy, X-ray photoelectron spectroscopy, and ellipsometry. Monofunctionalized and difunctionalized hydroporphyrins gave monolayer and multilayer films, respectively, indicating robustness of the hydroporphyrin molecules, but in each case the film was more heterogeneous than observed with comparable porphyrins. The data suggest that some amount of unattached molecules remain intercalated with surface-attached molecules. Additional molecular designs will need to be examined to develop a deep understanding of the structure-activity relationship for formation of homogeneous monolayers and multilayers of synthetic hydroporphyrins. }, number={7-8}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Jiao, Jieying and Yu, Miao and Holten, Dewey and Lindsey, Jonathan S. and Bocian, David F.}, year={2017}, pages={453–464} } @article{zhang_lindsey_2017, title={Construction of the Bacteriochlorin Macrocycle with Concomitant Nazarov Cyclization To Form the Annulated Isocyclic Ring: Analogues of Bacteriochlorophyll a}, volume={82}, ISSN={["0022-3263"]}, DOI={10.1021/acs.joc.6b02878}, abstractNote={Bacteriochlorophylls contain a bacteriochlorin macrocycle bearing an annulated fifth ring. The fifth ring, termed the isocyclic ring or ring E, is equipped with 131-oxo and 132-carbomethoxy substituents. Herein, a general route to stable, synthetic bacteriochlorophyll analogues is described. Knoevenagel condensation (∼40 mM, rt, CH2Cl2, piperidine/AcOH/molecular sieves) of a dihydrodipyrrin-carboxaldehyde (AD half) and a dihydrodipyrrin substituted with a β-ketoester (BC half) forms a propenone bearing the two halves (a hydrobilin analogue). Subsequent treatment (0.2 mM) with acid (Yb(OTf)3, CH3CN, 80 °C) promotes a double ring-closure process: (i) condensation between the α-position of pyrrole ring A and the α-acetal unit attached to pyrroline ring B forms the bacteriochlorin macrocycle, and (ii) Nazarov cyclization of the β-(propenoyl)-substituted ring C forms the isocyclic ring (E). Five new bacteriochlorins bearing various substituents (alkyl/alkyl, aryl, and alkyl/ester) at positions 2 and 3 (β-pyrrole sites, ring A) and 132 carboalkoxy groups (R = Me or Et) were constructed in 37-61% yield from the hydrobilin analogues. The BC half and AD half are available in five and eight steps, respectively, from the corresponding pyrrole-2-carboxaldehyde and unsaturated ketone. The bacteriochlorins exhibit absorption spectra typical of bacteriopheophytins (free base bacteriochlorophylls), with a strong near-infrared absorption band (707-751 nm).}, number={5}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Zhang, Shaofei and Lindsey, Jonathan S.}, year={2017}, month={Mar}, pages={2489–2504} } @article{taniguchi_lindsey_2018, title={Database of Absorption and Fluorescence Spectra of > 300 Common Compounds for use in PhotochemCAD}, volume={94}, ISSN={["1751-1097"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85041842097&partnerID=MN8TOARS}, DOI={10.1111/php.12860}, abstractNote={AbstractThe design of new molecules for photochemical studies typically requires knowledge of spectral features of pertinent chromophores beginning with the absorption spectrum (λabs) and accompanying molar absorption coefficient (ε, m−1 cm−1) and often extending to the fluorescence spectrum (λem) and fluorescence quantum yield (Φf), where the fluorescence properties may be of direct relevance or useful as proxies to gain insight into the nature of the first excited singlet state. PhotochemCAD databases, developed over a period of 30 years, are described here. The previous databases for 150 compounds have been expanded to encompass 339 compounds for which absorption spectra (including ε values), fluorescence spectra (including Φf values) and references to the primary literature have been included where available (552 spectra altogether). The compounds exhibit spectra in the ultraviolet, visible and/or near‐infrared spectral regions. The compound classes and number of members include acridines (21), aromatic hydrocarbons (41), arylmethane dyes (11), azo dyes (18), biomolecules (18), chlorins/bacteriochlorins (16), coumarins (14), cyanine dyes (19), dipyrrins (7), heterocycles (26), miscellaneous dyes (13), oligophenylenes (13), oligopyrroles (6), perylenes (5), phthalocyanines (11), polycyclic aromatic hydrocarbons (16), polyenes/polyynes (10), porphyrins (34), quinones (24) and xanthenes (15). A database of 31 solar spectra also is included.}, number={2}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, publisher={Wiley}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2018}, pages={290–327} } @article{hughes_zhang_zhang_williams_lindsey_miller_2017, title={Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01068-17}, abstractNote={ABSTRACT The cyanobacterial culture HT-58-2 was originally described as a strain of Tolypothrix nodosa with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a nonextant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Here, HT-58-2 was shown by 16S rRNA analysis to closely align with Brasilonema strains and not with Tolypothrix isolates. Light, fluorescence, and scanning electron microscopy revealed cyanobacterium filaments that are decorated with attached bacteria and associated with free bacteria. Metagenomic surveys of HT-58-2 cultures revealed a diversity of bacteria dominated by Erythrobacteraceae , 97% of which are Porphyrobacter species. A dimethyl sulfoxide washing procedure was found to yield enriched cyanobacterial DNA (presumably by removing community bacteria) and sequence data sufficient for genome assembly. The finished, closed HT-58-2Cyano genome consists of 7.85 Mbp (42.6% G+C) and contains 6,581 genes. All genes for biosynthesis of tetrapyrroles (e.g., heme, chlorophyll a , and phycocyanobilin) and almost all for cobalamin were identified dispersed throughout the chromosome. Among the 6,177 protein-encoding genes, coding sequences (CDSs) for all but two of the eight enzymes for conversion of glutamic acid to protoporphyrinogen IX also were found within one major gene cluster. The cluster also includes 10 putative genes (and one hypothetical gene) encoding proteins with domains for a glycosyltransferase, two cytochrome P450 enzymes, and a flavin adenine dinucleotide (FAD)-binding protein. The composition of the gene cluster suggests a possible role in tolyporphin biosynthesis. IMPORTANCE A worldwide search more than 25 years ago for cyanobacterial natural products with anticancer activity identified a culture (HT-58-2) from Micronesia that produces tolyporphins. Tolyporphins are tetrapyrroles, like chlorophylls, but have several profound structural differences that reside outside the bounds of known biosynthetic pathways. To begin probing the biosynthetic origin and biological function of tolyporphins, our research has focused on studying the cyanobacterial strain, about which almost nothing has been previously reported. We find that the HT-58-2 culture is composed of the cyanobacterium and a community of associated bacteria, complicating the question of which organisms make tolyporphins. Elucidation of the cyanobacterial genome revealed an intriguing gene cluster that contains tetrapyrrole biosynthesis genes and a collection of unknown genes, suggesting that the cluster may be responsible for tolyporphin production. Knowledge of the genome and the gene cluster sharply focuses research to identify related cyanobacterial producers of tolyporphins and delineate the tolyporphin biosynthetic pathway. }, number={19}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Hughes, Rebecca-Ayme and Zhang, Yunlong and Zhang, Ran and Williams, Philip G. and Lindsey, Jonathan S. and Miller, Eric S.}, year={2017}, month={Oct} } @article{maher_passard_dogutan_halbach_anderson_gagliardi_taniguchi_lindsey_nocera_2017, title={Hydrogen Evolution Catalysis by a Sparsely Substituted Cobalt Chlorin}, volume={7}, ISSN={["2155-5435"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85021076592&partnerID=MN8TOARS}, DOI={10.1021/acscatal.7b00969}, abstractNote={A sparsely substituted chlorin macrocycle containing a Co(II) center (1-Co) has been synthesized and structurally characterized. The Co(II) atom resides in a square planar coordination environment and induces significant out-of-plane distortion of the chlorin macrocycle. The paramagnetic Co(II) center resides in the macrocycle in a S = 1/2 spin state, which displays an axial doublet signal (g⊥ ≈ 2.3 and g∥ ≈ 2.03) in the X-band EPR spectrum. The open-shell d-orbital configuration is manifest in the transient absorption spectrum, which reveals an excited-state lifetime of 8.6 ± 0.2 ps for 1-Co. The Co(II) chlorin exhibits a rich oxidation–reduction chemistry with five reversible one-electron waves (three oxidative processes and two reductive processes) observed in the cyclic voltammogram. The reduction processes of 1-Co drive hydrogen evolution catalysis. Electrochemical kinetics analysis of HER by 1-Co in trifluoroacetic acid reveals a hydrogen evolution mechanism that proceeds by an ECEC mechanism. Bench...}, number={5}, journal={ACS CATALYSIS}, publisher={American Chemical Society (ACS)}, author={Maher, Andrew G. and Passard, Guillaume and Dogutan, Dilek K. and Halbach, Robert L. and Anderson, Bryce L. and Gagliardi, Christopher J. and Taniguchi, Masahiko and Lindsey, Jonathan S. and Nocera, Daniel G.}, year={2017}, month={May}, pages={3597–3606} } @article{zhang_zhang_nazari_bagley_miller_williams_muddiman_lindsey_2017, title={Mass spectrometric detection of chlorophyll a and the tetrapyrrole secondary metabolite tolyporphin A in the filamentous cyanobacterium HT-58-2. Approaches to high-throughput screening of intact cyanobacteria}, volume={21}, ISSN={["1099-1409"]}, DOI={10.1142/s108842461750078x}, abstractNote={ Tolyporphins are unusual tetrapyrrole macrocycles produced by the filamentous cyanobacterium–microbial community HT-58-2, the only known source to date. Numerous cyanobacterial samples have been collected worldwide but most have not been screened for secondary metabolites. Identification of tolyporphins typically has entailed lipophilic extraction followed by chromatographic fractionation and spectroscopic and/or mass spectrometric analysis. For quantitation, lengthy lipophilic extraction, sample processing and HPLC separation are needed. Examination by MALDI-TOF-MS (with the matrix 1,5-diaminonaphthalene) of lipophilic crude extracts of small-scale HT-58-2 samples (2 mL) without chromatographic fractionation enabled semi-quantitation of tolyporphin A over a 41-day growth period. Screening for tolyporphin A in intact or slightly sheared and vortexed HT-58-2 samples (no lipophilic extraction), and confirmation of identity by tandem MS, were carried out by IR-MALDESI-FTMS. Tolyporphin A was identified by the molecular ion and four characteristic fragments. The molecular ion of chlorophyll [Formula: see text] also was observed. The sheared and vortexed sample contained substantial numbers of intact cells as demonstrated by regrowth of the filamentous cyanobacterium–microbial culture. The semi-quantitative and rapid qualitative methods developed herein should facilitate examination of other tolyporphin-producing organisms among the vast worldwide strains of cyanobacteria as well as investigation of the biosynthesis of tolyporphins. }, number={11}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Zhang, Yunlong and Zhang, Ran and Nazari, Milad and Bagley, Michael C. and Miller, Eric S. and Williams, Philip G. and Muddiman, David C. and Lindsey, Jonathan S.}, year={2017}, month={Nov}, pages={759–768} } @article{taniguchi_du_lindsey_2018, title={PhotochemCAD 3: Diverse Modules for Photophysical Calculations with Multiple Spectral Databases}, volume={94}, ISSN={["1751-1097"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85041847837&partnerID=MN8TOARS}, DOI={10.1111/php.12862}, abstractNote={AbstractThe PhotochemCAD program, developed over 30 years, is described comprehensively with focus on features of the most recent version (PhotochemCAD 3). The program is equipped with a streamlined user interface and provisions for handling multiple spectral databases. Eight modules enable calculations to be performed on the basis of the spectra in the databases. The calculational modules provide results concerning properties of individual compounds (oscillator strength, transition dipole moment, natural radiative lifetime), interactions of multiple compounds (Förster energy transfer, Dexter energy transfer, analysis of energy transfer among an array of chromophores) and composition of mixtures (multicomponent analysis). Synthetic spectra (blackbody radiator, Gaussian and Lorentzian curves, delta functions) also can be generated. For comparison and calculation, synthetic and experimental spectra can be shifted along both coordinate axes and combined by addition, subtraction and use of multiplicative factors. The core databases (described in the companion paper) have been expanded to 339 compounds for which absorption spectra (including molar absorption coefficient, ε), fluorescence spectra (including fluorescence quantum yield, Φf) and references to the primary literature have been included where available (552 spectra altogether). A database of 31 solar spectra also is included. Each calculational module is described along with illustrative examples.}, number={2}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, publisher={Wiley}, author={Taniguchi, Masahiko and Du, Hai and Lindsey, Jonathan S.}, year={2018}, pages={277–289} } @article{zhang_zhang_hughes_dai_gurr_williams_miller_lindsey_2017, title={Quantitation of Tolyporphins, Diverse Tetrapyrrole Secondary Metabolites with Chlorophyll-Like Absorption, from a Filamentous Cyanobacterium-Microbial Community}, volume={29}, ISSN={0958-0344}, url={http://dx.doi.org/10.1002/pca.2735}, DOI={10.1002/pca.2735}, abstractNote={AbstractIntroductionTolyporphins are unusual tetrapyrrole macrocycles produced by a non‐axenic filamentous cyanobacterium (HT‐58‐2). Tolyporphins A–J, L, and M share a common dioxobacteriochlorin core, differ in peripheral substituents, and exhibit absorption spectra that overlap that of the dominant cyanobacterial pigment, chlorophyll a. Identification and accurate quantitation of the various tolyporphins in these chlorophyll‐rich samples presents challenges.ObjectiveTo develop methods for the quantitative determination of tolyporphins produced under various growth conditions relative to that of chlorophyll a.MethodologyChromatographic fractionation of large‐scale (440 L) cultures afforded isolated individual tolyporphins. Lipophilic extraction of small‐scale (25 mL) cultures, HPLC separation with an internal standard, and absorption detection enabled quantitation of tolyporphin A and chlorophyll a, and by inference the amounts of tolyporphins A–M. Absorption spectroscopy with multicomponent analysis of lipophilic extracts (2 mL cultures) afforded the ratio of all tolyporphins to chlorophyll a. The reported absorption spectral data for the various tolyporphins required re‐evaluation for quantitative purposes.Results and DiscussionThe amount of tolyporphin A after 50 days of illumination ranged from 0.13 nmol/mg dry cells (media containing nitrate) to 1.12 nmol/mg (without nitrate), with maximum 0.23 times that of chlorophyll a. Under soluble‐nitrogen deprivation after 35–50 days, tolyporphin A represents 1/3–1/2 of the total tolyporphins, and the total amount of tolyporphins is up to 1.8‐fold that of chlorophyll a.ConclusionsThe quantitative methods developed herein should facilitate investigation of the biosynthesis of tolyporphins (and other tetrapyrroles) as well as examination of other strains for production of tolyporphins. Copyright © 2017 John Wiley & Sons, Ltd.}, number={2}, journal={Phytochemical Analysis}, publisher={Wiley}, author={Zhang, Yunlong and Zhang, Ran and Hughes, Rebecca-Ayme and Dai, Jingqiu and Gurr, Joshua R. and Williams, Philip G. and Miller, Eric S. and Lindsey, Jonathan S.}, year={2017}, month={Nov}, pages={205–216} } @article{liu_allu_reddy_hood_diers_bocian_holten_lindsey_2017, title={Synthesis and photophysical characterization of bacteriochlorins equipped with integral swallowtail substituents}, volume={41}, ISSN={["1369-9261"]}, DOI={10.1039/c7nj00499k}, abstractNote={The two pyrroline units of bacteriochlorins can now bear gem-dialkyl or diaryl groups (L), which project above and below the macrocycle plane, whereas dimethyl groups generally have been accessible previously.}, number={11}, journal={NEW JOURNAL OF CHEMISTRY}, author={Liu, Yizhou and Allu, Srinivasarao and Reddy, Muthyala Nagarjuna and Hood, Don and Diers, James R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2017}, month={Jun}, pages={4360–4376} } @article{zhang_reddy_mass_kim_hu_lindsey_2017, title={Synthesis of tailored hydrodipyrrins and their examination in directed routes to bacteriochlorins and tetradehydrocorrins}, volume={41}, DOI={10.1039/c7nj01892d}, abstractNote={18 gem-dimethyl stabilized hydrodipyrrins with diverse α-substituents have been prepared and examined in directed syntheses of unsymmetrically substituted hydroporphyrins.}, number={19}, journal={New Journal of Chemistry}, author={Zhang, S. F. and Reddy, M. N. and Mass, O. and Kim, H. J. and Hu, G. F. and Lindsey, Jonathan}, year={2017}, pages={11170–11189} } @article{liu_chen_hood_taniguchi_diers_bocian_holten_lindsey_2017, title={Synthesis, photophysics and electronic structure of oxobacteriochlorins}, volume={41}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85022033561&partnerID=MN8TOARS}, DOI={10.1039/c6nj04135c}, abstractNote={Synthetic oxobacteriochlorins exhibit strong absorption in the deep-red window flanked by chlorins to the red and bacteriochlorins to the near-infrared.}, number={10}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Liu, Mengran and Chen, Chih-Yuan and Hood, Don and Taniguchi, Masahiko and Diers, James R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2017}, month={May}, pages={3732–3744} } @article{mandal_diers_niedzwiedzki_hu_liu_alexy_lindsey_bocian_holten_2017, title={Tailoring Panchromatic Absorption and Excited-State Dynamics of Tetrapyrrole–Chromophore (Bodipy, Rylene) Arrays—Interplay of Orbital Mixing and Configuration Interaction}, volume={139}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/JACS.7B09548}, DOI={10.1021/JACS.7B09548}, abstractNote={Three sets of tetrapyrrole-chromophore arrays have been examined that exhibit panchromatic absorption across large portions of the near-ultraviolet (NUV) to near-infrared (NIR) spectrum along with favorable excited-state properties for use in solar-energy conversion. The arrays vary the tetrapyrrole (porphyrin, chlorin, bacteriochlorin), chromophore (boron-dipyrrin, perylene, terrylene), and attachment sites (meso-position, β-pyrrole position). In all, seven dyads, one triad, and nine benchmarks in toluene and benzonitrile were studied using steady-state and time-resolved absorption and fluorescence spectroscopy. The results were analyzed with the aid of density functional theory (DFT) and time-dependent DFT calculations. Natural transition orbitals (NTOs) were constructed to assess the net change in electron density associated with each NUV-NIR absorption transition. The porphyrin-perylene dyad P-PMI displays the most even spectral coverage from 400 to 700 nm, with an average ε ∼ 43 000 M-1 cm-1. A significant contributor is a chromophore-induced reduction in the configuration interaction involving the four frontier molecular orbitals of benchmark porphyrins and associated constructive/destructive transition-dipole interference that results in intense (ε ∼ 400 000 M-1 cm-1) NUV and weak (<20 000 M-1 cm-1) visible features. P-PMI has an S1 lifetime (τS) of 4.7 ns in toluene and 1.3 ns in benzonitrile. Bacteriochlorin analogue BC-PMI has more extended spectral coverage (350-750 nm) and τS = 2.8 ns in toluene and 30 ps in benzonitrile. Terrylene analogue P-TMI has intermediate optical characteristics with τS = 310 ps in toluene and 150 ps in benzonitrile. The NTOs for most arrays show that S0 → S1 primarily involves the tetrapyrrole, but for P-TMI the NTOs have electron density delocalized over the two units as a result of extensive orbital mixing. Collectively, the insights obtained should aid the design of tetrapyrrole-based architectures for panchromatic light-harvesting systems for solar-energy conversion.}, number={48}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Mandal, Amit Kumar and Diers, James R. and Niedzwiedzki, Dariusz M. and Hu, Gongfang and Liu, Rui and Alexy, Eric J. and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2017}, month={Nov}, pages={17547–17564} } @article{zhang_jiang_liu_taniguchi_mandal_evans-storms_pitner_bocian_holten_lindsey_2016, title={Bioconjugatable, PEGylated hydroporphyrins for photochemistry and photomedicine. Narrow-band, near-infrared-emitting bacteriochlorins}, volume={40}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84984904482&partnerID=MN8TOARS}, DOI={10.1039/c6nj01155a}, abstractNote={PEGylated bacteriochlorins are soluble in water, can be excited in the ultraviolet, and exhibit a narrow fluorescence band in the NIR spectral region.}, number={9}, journal={NEW JOURNAL OF CHEMISTRY}, author={Zhang, Nuonuo and Jiang, Jianbing and Liu, Mengran and Taniguchi, Masahiko and Mandal, Amit Kumar and Evans-Storms, Rosemary B. and Pitner, J. Bruce and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2016}, pages={7750–7767} } @article{liu_chen_mandal_chandrashaker_evans-storms_pitner_bocian_holten_lindsey_2016, title={Bioconjugatable, PEGylated hydroporphyrins for photochemistry and photomedicine. Narrow-band, red-emitting chlorins}, volume={40}, ISSN={["1369-9261"]}, DOI={10.1039/c6nj01154c}, abstractNote={PEGylated chlorins are soluble in water, can be excited in the near-ultraviolet, and exhibit a relatively narrow fluorescence band in the red spectral region.}, number={9}, journal={NEW JOURNAL OF CHEMISTRY}, author={Liu, Mengran and Chen, Chih-Yuan and Mandal, Amit Kumar and Chandrashaker, Vanampally and Evans-Storms, Rosemary B. and Pitner, J. Bruce and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2016}, pages={7721–7740} } @article{deans_taniguchi_chandrashaker_ptaszek_lindsey_2016, title={Complexity in structure-directed prebiotic chemistry. Reaction bifurcation from a beta-diketone in tetrapyrrole formation}, volume={40}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84979074707&partnerID=MN8TOARS}, DOI={10.1039/c6nj00545d}, abstractNote={An unsymmetrical β-diketone with δ-aminolevulinic acid affords both a “defective” and a “normal” pyrrole; upon combinatorial reaction the former terminates chain-growth of the latter on the path to tetrapyrrole macrocycles.}, number={7}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Deans, Richard M. and Taniguchi, Masahiko and Chandrashaker, Vanampally and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2016}, month={Jul}, pages={6434–6440} } @article{deans_taniguchi_chandrashaker_ptaszek_chambers_soares_lindsey_2016, title={Complexity in structure-directed prebiotic chemistry. Unexpected compositional richness from competing reactants in tetrapyrrole formation}, volume={40}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84979079544&partnerID=MN8TOARS}, DOI={10.1039/c6nj00543h}, abstractNote={Acyclic reactants afford “partially defective” pyrroles that interfere with chain growth of “normal” pyrroles on the path to tetrapyrrole macrocycles.}, number={7}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Deans, Richard M. and Taniguchi, Masahiko and Chandrashaker, Vanampally and Ptaszek, Marcin and Chambers, Dana R. and Soares, Ana R. M. and Lindsey, Jonathan S.}, year={2016}, month={Jul}, pages={6421–6433} } @article{liu_lindsey_2016, title={Northern-Southern Route to Synthetic Bacteriochlorins}, volume={81}, ISSN={["1520-6904"]}, DOI={10.1021/acs.joc.6b02334}, abstractNote={A new route to bacteriochlorins via Northern-Southern (N-S) self-condensation of a dihydrodipyrrin-acetal complements a prior Eastern-Western (E-W) route. Each bacteriochlorin was prepared in five steps from an α-halopyrrole and a 2,2-dimethylpent-4-ynoic acid. The first three steps follow Jacobi's synthesis of dihydrodipyrrins: Pd-mediated coupling to form a lactone-pyrrole, Petasis reagent treatment for methenylation, and Paal-Knorr type ring closure to form the 1,2,2-trimethyl-substituted dihydrodipyrrin. Subsequent steps entail conversion of the 1-methyl group to the 1-(dimethoxymethyl) unit and acid-catalyzed self-condensation of the resulting dihydrodipyrrin-acetal. The essential differences between the N-S and E-W routes lie in (1) the location of the gem-dimethyl group (with respect to the 1-acetal unit) at the 2- versus 3-position in the dihydrodipyrrin-acetals, respectively, (2) the method of synthesis of the dihydrodipyrrins, and consequently (3) access to diverse substituted bacteriochlorins including those with substituents at the meso-positions. Ten new bacteriochlorins bearing 0-6 total aryl, alkyl, and carboethoxy substituents at the β-pyrrole and/or meso-positions have been prepared, with yields of macrocycle formation of up to 39%. Four single-crystal X-ray structures (two intermediates, two bacteriochlorins) were determined. The bacteriochlorins exhibit characteristic bacteriochlorophyll-like absorption spectra, including a Qy band in the region 713-760 nm.}, number={23}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Liu, Yizhou and Lindsey, Jonathan S.}, year={2016}, month={Dec}, pages={11882–11897} } @article{hu_liu_alexy_mandal_bocian_holten_lindsey_2016, title={Panchromatic chromophore–tetrapyrrole light-harvesting arrays constructed from Bodipy, perylene, terrylene, porphyrin, chlorin, and bacteriochlorin building blocks}, volume={40}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/C6NJ01782G}, DOI={10.1039/C6NJ01782G}, abstractNote={Five new chromophore–tetrapyrrole arrays bearing an ethynyl linker have been synthesized to explore the effects of chromophore nature and tetrapyrrole attachment site on panchromatic spectral properties.}, number={9}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Hu, Gongfang and Liu, Rui and Alexy, Eric J. and Mandal, Amit Kumar and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2016}, pages={8032–8052} } @article{mandal_taniguchi_diers_niedzwiedzki_kirmaier_lindsey_bocian_holten_2016, title={Photophysical Properties and Electronic Structure of Porphyrins Bearing Zero to Four meso-Phenyl Substituents: New Insights into Seemingly Well Understood Tetrapyrroles}, volume={120}, ISSN={["1089-5639"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85021654881&partnerID=MN8TOARS}, DOI={10.1021/acs.jpca.6b09483}, abstractNote={Six free base porphyrins bearing 0-4 meso substituents have been examined by steady-state and time-resolved absorption and fluorescence spectroscopy in both toluene and N,N-dimethylformamide (DMF). The lifetime of the lowest singlet excited state (S1) decreases with an increase in the number of meso-phenyl groups; the values in toluene are H2P-0 (15.5 ns) > H2P-1 (14.9 ns) > H2P-2c (14.4 ns) > H2P-2t (13.8 ns) ∼ H2P-3 (13.8 ns) > H2P-4 (12.8 ns), where "H2P" refers to the core free base porphyrin, the numerical suffix indicates the number of meso-phenyl groups, and "c" and "t" refer to cis and trans, respectively. The opposite trend is found for the fluorescence quantum yield; the values in toluene are H2P-0 (0.049) < H2P-1 (0.063) ∼ H2P-2c (0.063) < H2P-2t (0.071) < H2P-3 (0.073) < H2P-4 (0.090). Similar trends occur in DMF. All radiative and nonradiative (internal conversion and intersystem crossing) rate constants for S1 decay increase with the increasing number of meso-phenyl groups. The increase in the rate constant for fluorescence parallels an increase in oscillator strength of the S0 → S1 absorption manifold. The trend is reproduced by time-dependent density functional theory calculations. The calculations within the context of the four-orbital model reveal that the enhanced S0 ↔ S1 radiative probabilities derive from a preferential effect of the meso-phenyl groups to raise the energy of the highest occupied molecular orbital, which underpins a parallel bathochromic shift in the S0 → S1 absorption wavelength. Polarizations of the S1 and S2 excited states with respect to molecular structural features (e.g., the central proton axis) are analyzed in the context of historical conventions for porphyrins versus chlorins and bacteriochlorins, where some ambiguity exists, including for porphine, one of the simplest tetrapyrroles. Collectively, the study affords fundamental insights into the photophysical properties and electronic structure of meso-phenylporphyrins that should aid their continued widespread use as benchmarks for tetrapyrrole-based architectures in chemical, solar-energy, and life-sciences research.}, number={49}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Mandal, Amit Kumar and Taniguchi, Masahiko and Diers, James R. and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2016}, month={Dec}, pages={9719–9731} } @article{mandal_sahin_liu_lindsey_bocian_holten_2016, title={Photophysical comparisons of PEGylated porphyrins, chlorins and bacteriochlorins in water}, volume={40}, ISSN={["1369-9261"]}, DOI={10.1039/c6nj02091g}, abstractNote={Synthesis of a bioconjugatable water-soluble (PEGylated) trans-AB-porphyrin enables photophysical comparisons (τS, kf, kic, kisc, Φf, Φic, Φisc) with analogous chlorins and bacteriochlorins in DMF and water.}, number={11}, journal={NEW JOURNAL OF CHEMISTRY}, author={Mandal, Amit Kumar and Sahin, Tuba and Liu, Mengran and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2016}, pages={9648–9656} } @article{taniguchi_deans_chandrashaker_ptaszek_lindsey_2016, title={Scope and limitations of two model prebiotic routes to tetrapyrrole macrocycles}, volume={40}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84984911595&partnerID=MN8TOARS}, DOI={10.1039/c6nj01423b}, abstractNote={Aqueous reaction (35 °C, 72 h) of two acyclic compounds, an α-aminoketone + β-ketoester or β-diketone (not shown), affords a pyrrole that self-condenses to give the porphyrinogen.}, number={9}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Taniguchi, Masahiko and Deans, Richard M. and Chandrashaker, Vanampally and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2016}, pages={7445–7455} } @article{zhang_kim_tang_yang_bocian_holten_lindsey_2016, title={Synthesis and photophysical characteristics of 2,3,12,13-tetraalkylbacteriochlorins}, volume={40}, ISSN={["1369-9261"]}, DOI={10.1039/c6nj00517a}, abstractNote={Tetraalkylbacteriochlorins, available upon acid-mediated self-condensation of α-ester stabilized dihydrodipyrrin-carboxaldehydes, provide valuable models of the naturally occurring bacteriochlorophylls.}, number={7}, journal={NEW JOURNAL OF CHEMISTRY}, author={Zhang, Shaofei and Kim, Han-Je and Tang, Qun and Yang, Eunkyung and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2016}, month={Jul}, pages={5942–5956} } @article{chandrashaker_ptaszek_taniguchi_lindsey_2016, title={Synthesis of diverse acyclic precursors to pyrroles for studies of prebiotic routes to tetrapyrrole macrocycles}, volume={40}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84990050463&partnerID=MN8TOARS}, DOI={10.1039/c6nj02048h}, abstractNote={Some 50 ketones, β-diketones, β-ketoesters and α-aminoketones have been prepared for studies of the formation of trisubstituted pyrroles equipped for self-condensation leading to tetrapyrrole macrocycles.}, number={10}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Chandrashaker, Vanampally and Ptaszek, Marcin and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2016}, pages={8786–8808} } @misc{taniguchi_lindsey_2017, title={Synthetic Chlorins, Possible Surrogates for Chlorophylls, Prepared by Derivatization of Porphyrins}, volume={117}, ISSN={["1520-6890"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85010748506&partnerID=MN8TOARS}, DOI={10.1021/acs.chemrev.5b00696}, abstractNote={Chlorophylls make Earth green, are the central constituents in the engine of photosynthesis, and not surprisingly have garnered immense attention. A chlorin, the core chromophore of a chlorophyll, is a dihydroporphyrin macrocycle that contains one pyrroline ring and three pyrrole rings. The dominant method for the synthesis of chlorins has entailed the derivatization of porphyrins. The present review covers the ostensibly simple conversion of porphyrins, regardless of synthetic or biological origin, to chlorins. The period covered encompasses the entire history since the beginnings of chlorin synthetic chemistry in the early 20th century through 2015. Representative transformations include hydrogenation, cycloaddition, annulation, and diverse "breaking and mending" approaches. Altogether, the synthesis of >1000 chlorins or chlorin-like compounds (containing >50 distinct pyrroline motifs) is described. Such diversity animates the question "what structural features are essential for a chlorin to resemble chlorophyll?" To begin to address the structure-spectrum relationship, > 250 absorption spectra are provided for representative structures. The synthesis and spectral properties of the vast collection of compounds described herein are expected to illuminate the scope to which synthetic chlorins can serve as surrogates for chlorophylls and be exploited in diverse ways.}, number={2}, journal={CHEMICAL REVIEWS}, publisher={American Chemical Society (ACS)}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2017}, month={Jan}, pages={344–535} } @article{taniguchi_ptaszek_chandrashaker_lindsey_2017, title={The Porphobilinogen Conundrum in Prebiotic Routes to Tetrapyrrole Macrocycles}, volume={47}, ISSN={["1573-0875"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84969780645&partnerID=MN8TOARS}, DOI={10.1007/s11084-016-9506-1}, abstractNote={Attempts to develop a credible prebiotic route to tetrapyrroles have relied on enzyme-free recapitulation of the extant biosynthesis, but this process has foundered from the inability to form the pyrrole porphobilinogen (PBG) in good yield by self-condensation of the precursor δ-aminolevulinic acid (ALA). PBG undergoes robust oligomerization in aqueous solution to give uroporphyrinogen (4 isomers) in good yield. ALA, PBG, and uroporphyrinogen III are universal precursors to all known tetrapyrrole macrocycles. The enzymic formation of PBG entails carbon-carbon bond formation between the less stable enolate/enamine of one ALA molecule (3-position) and the carbonyl/imine (4-position) of the second ALA molecule; without enzymes, the first ALA reacts at the more stable enolate/enamine (5-position) and gives the pyrrole pseudo-PBG. pseudo-PBG cannot self-condense, yet has one open α-pyrrole position and is proposed to be a terminator of oligopyrromethane chain-growth from PBG. Here, 23 analogues of ALA have been subjected to density functional theoretical (DFT) calculations, but no motif has been identified that directs reaction at the 3-position. Deuteriation experiments suggested 5-(phosphonooxy)levulinic acid would react preferentially at the 3- versus 5-position, but a hybrid condensation with ALA gave no observable uroporphyrin. The results suggest efforts toward a biomimetic, enzyme-free route to tetrapyrroles from ALA should turn away from structure-directed reactions and focus on catalysts that orient the two aminoketones to form PBG in a kinetically controlled process, thereby avoiding formation of pseudo-PBG.}, number={1}, journal={ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES}, publisher={Springer Nature}, author={Taniguchi, Masahiko and Ptaszek, Marcin and Chandrashaker, Vanampally and Lindsey, Jonathan S.}, year={2017}, month={Mar}, pages={93–119} } @article{amanpour_hu_alexy_mandal_kang_yuen_diers_bocian_lindsey_holten_2016, title={Tuning the Electronic Structure and Properties of Perylene-Porphyrin-Perylene Panchromatic Absorbers}, volume={120}, ISSN={["1089-5639"]}, DOI={10.1021/acs.jpca.6b06857}, abstractNote={Light-harvesting architectures that afford strong absorption across the near-ultraviolet to near-infrared region, namely, panchromatic absorptivity, are potentially valuable for capturing the broad spectral distribution of sunlight. One previously reported triad consisting of two perylene monoimides strongly coupled to a free base porphyrin via ethyne linkers (FbT) shows panchromatic absorption together with a porphyrin-like S1 excited state albeit at lower energy than that of a typical monomeric porphyrin. Here, two new porphyrin-bis(perylene) triads have been prepared wherein the porphyrin bears two pentafluorophenyl substituents. The porphyrin is in the free base (FbT-F) or zinc chelate (ZnT-F) forms. The zinc chelate (ZnT) of the original triad bearing nonfluorinated aryl rings also was prepared. The triads were characterized using static and time-resolved optical spectroscopy. The results were analyzed with the aid of molecular-orbital characteristics obtained using density functional theory calculations. Of the four triads, FbT is the most panchromatic in affording the most even distribution of absorption spectral intensity as well as exhibiting the largest wavelength span (380-750 nm). The triads exhibit fluorescence yields (0.35 for FbT-F in toluene) that are substantially greater than for the porphyrin benchmarks (0.049 for FbP-F). The singlet excited-state lifetimes (τS) for the triads in toluene decrease in the order FbT-F (2.7 ns) > FbT (2.0 ns) > ZnT (1.2 ns) ∼ ZnT-F (1.1 ns). The τS values in benzonitrile are FbT (1.3 ns) > FbT-F (1.2 ns) > ZnT-F (0.6 ns) > ZnT (0.2 ns). Thus, the free base triads exhibit relatively long (1.2-2.7 ns) excited-state lifetimes in both polar and nonpolar media. The combined photophysical characteristics indicate that FbT and FbT-F are the best choices for panchromatic light-harvesting systems. Collectively, the findings afford insights into the effects of electronic structure on the panchromatic behavior of ethynyl-linked porphyrin-perylene architectures that can help guide next-generation designs and utilization of these systems.}, number={38}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Amanpour, Javad and Hu, Gongfang and Alexy, Eric J. and Mandal, Amit Kumar and Kang, Hyun Suk and Yuen, Jonathan M. and Diers, James R. and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2016}, month={Sep}, pages={7434–7450} } @article{deans_chandrashaker_taniguchi_lindsey_2015, title={Complexity in structure-directed prebiotic chemistry. Effect of a defective competing reactant in tetrapyrrole formation}, volume={39}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84945937304&partnerID=MN8TOARS}, DOI={10.1039/c5nj01474c}, abstractNote={A reactive but defective pyrrole, derived from the simple β-diketone acetylacetone, terminates chain-growth in a quantitative combinatorial manner in tetrapyrrole formation.}, number={11}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Deans, Richard M. and Chandrashaker, Vanampally and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2015}, pages={8273–8281} } @misc{lindsey_2015, title={De Novo Synthesis of Gem-Dialkyl Chlorophyll Analogues for Probing and Emulating Our Green World}, volume={115}, ISSN={["1520-6890"]}, DOI={10.1021/acs.chemrev.5b00065}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTDe Novo Synthesis of Gem-Dialkyl Chlorophyll Analogues for Probing and Emulating Our Green WorldJonathan S. Lindsey*View Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, United States*Phone: 919-515-6406. Fax: 919-513-2830. E-mail: [email protected]Cite this: Chem. Rev. 2015, 115, 13, 6534–6620Publication Date (Web):June 12, 2015Publication History Received2 February 2015Published online12 June 2015Published inissue 8 July 2015https://pubs.acs.org/doi/10.1021/acs.chemrev.5b00065https://doi.org/10.1021/acs.chemrev.5b00065review-articleACS PublicationsCopyright © 2015 American Chemical SocietyRequest reuse permissionsArticle Views2790Altmetric-Citations141LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Halogenation,Macrocycles,Organic compounds,Pyrroles,Substituents Get e-Alerts}, number={13}, journal={CHEMICAL REVIEWS}, author={Lindsey, Jonathan S.}, year={2015}, month={Jul}, pages={6534–6620} } @article{zhang_reddy_jiang_taniguchi_sommer_lindsey_2015, title={Elaboration of an unexplored substitution site in synthetic bacteriochlorins}, volume={19}, ISSN={["1099-1409"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84937975805&partnerID=MN8TOARS}, DOI={10.1142/s1088424615500534}, abstractNote={ The ability to introduce substituents at designated sites about the perimeter of synthetic bacteriochlorins – analogs of bacteriochlorophylls of bacterial photosynthesis – remains a subject of ongoing study. Here, the self-condensation of a dihydrodipyrrin-dioxolane affords a 5-[2-(trimethylsiloxy)ethoxy]bacteriochlorin. Like a 5-methoxybacteriochlorin, the latter undergoes regioselective bromination at the 15-position, directed by the distal 5-alkoxy group. On the other hand, attempted bromination of a bacteriochlorin bearing a 5-(2-hydroxyethoxy) group resulted in intramolecular ether formation with the adjacent β-pyrroline position to give an annulated dioxepine ring (confirmed by single-crystal X-ray structural analysis). The hydroxyethoxy group at the 5-position can be derivatized by acylation. In addition, the installation of auxochromes (methoxycarbonyl, phenylethynyl) at the β-pyrrole rings causes a substantial bathochromic shift of the long-wavelength absorption band (812 nm) and companion fluorescence emission band (821 nm). Taken together, the modification of the 5-substituent complements existing methods for installing a single substituent on the bacteriochlorin macrocycle. }, number={7}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, publisher={World Scientific Pub Co Pte Lt}, author={Zhang, Nuonuo and Reddy, Kanumuri Ramesh and Jiang, Jianbing and Taniguchi, Masahiko and Sommer, Roger D. and Lindsey, Jonathan S.}, year={2015}, month={Jul}, pages={887–902} } @article{vairaprakash_yang_sahin_taniguchi_krayer_diers_wang_niedzwiedzki_kirmaier_lindsey_et al._2015, title={Extending the Short and Long Wavelength Limits of Bacteriochlorin Near-Infrared Absorption via Dioxo- and Bisimide-Functionalization}, volume={119}, ISSN={["1520-6106"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84925935682&partnerID=MN8TOARS}, DOI={10.1021/jp512818g}, abstractNote={Six new bacteriochlorins expanding the range of the strong near-infrared (NIR) absorption (Qy band) to both shorter and longer wavelengths (∼690 to ∼900 nm) have been synthesized and characterized. The architectures include bacteriochlorin-bisimides that have six-membered imide rings spanning the 3,5- and 13,15-macrocycle positions or five-membered imide rings spanning the β-pyrrolic 2,3- and 12,13-positions. Both bisimide types absorb at significantly longer wavelength than the bacteriochlorin precursors (no fused rings), whereas oxo-groups at the 7- or 7,17-positions shift the Qy band to a new short wavelength limit. Surprisingly, bacteriochlorin-bisimides with five-membered β-pyrrolic-centered imide rings have a Qy band closer to that of six-membered bacteriochlorin-monoimides. However, the five-membered bisimides (versus the six-membered bacteriochlorin-monoimides) have significantly enhanced absorption intensity that is paralleled by an ∼2-fold higher fluorescence yield (∼0.16 vs ∼0.07) and longer singlet excited-state lifetime (∼4 ns vs ∼2 ns). The photophysical enhancements derive in part from mixing of the lowest unoccupied frontier molecular orbitals of the five-membered imide ring with those of the bacteriochlorin framework. In general, all of the new bacteriochlorins have excited-state lifetimes (1-4 ns) that are sufficiently long for use in molecular-based systems for photochemical applications.}, number={12}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Vairaprakash, Pothiappan and Yang, Eunkyung and Sahin, Tuba and Taniguchi, Masahiko and Krayer, Michael and Diers, James R. and Wang, Alfred and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Lindsey, Jonathan S. and et al.}, year={2015}, month={Mar}, pages={4382–4395} } @article{sahin_vairaprakash_borbas_balasubramanian_lindsey_2015, title={Hydrophilic bioconjugatable trans-AB-porphyrins and peptide conjugates}, volume={19}, ISSN={["1099-1409"]}, DOI={10.1142/s1088424615500121}, abstractNote={ Porphyrins bearing a single bioconjugatable group and a single water-solubilization motif in a trans-AB-architecture (with no other substituents) provide a compact design of value for studies in diverse disciplines. Established synthetic methods have been employed to prepare four new free base porphyrins and one Mn ( III ) chelate. The hydrophilic motif includes 4-N-methylpyridinium, 2,4,6-tris(carboxymethoxy)phenyl, 2,6-bis(phosphonomethoxy)phenyl, and carboxy; the bioconjugatable unit includes carboxy, maleimido, and N-hydroxysuccinimido (NHS) ester. Bioconjugation experiments with a protected porphyrin-diphosphate or unprotected porphyrin-diphosphonate were examined in organic solution or water, respectively. Both approaches were employed to conjugate to the ε-amino group of Lys11 in AcKPV- NH 2, a tripeptide fragment [ Ac -α-MSH(11-13)- NH 2] of melanocyte stimulating hormone, yielding porphyrin-peptide conjugates. }, number={5}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Sahin, Tuba and Vairaprakash, Pothiappan and Borbas, K. Eszter and Balasubramanian, Thiagarajan and Lindsey, Jonathan S.}, year={2015}, month={May}, pages={663–678} } @article{jiang_taniguchi_lindsey_2015, title={Near-infrared tunable bacteriochlorins equipped for bioorthogonal labeling}, volume={39}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84930627951&partnerID=MN8TOARS}, DOI={10.1039/c5nj00209e}, abstractNote={Nine new near-infrared absorbing (729–820 nm) synthetic bacteriochlorins are equipped with one of four reactive groups for bioorthogonal conjugation.}, number={6}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Jiang, Jianbing and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2015}, pages={4534–4550} } @article{alexy_hintz_hughes_taniguchi_lindsey_2015, title={Paley's watchmaker analogy and prebiotic synthetic chemistry in surfactant assemblies. Formaldehyde scavenging by pyrroles leading to porphyrins as a case study}, volume={13}, ISSN={["1477-0539"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84942899459&partnerID=MN8TOARS}, DOI={10.1039/c5ob01409c}, abstractNote={Facile exchange of micromolar dialkylpyrrolic constituents among a Poisson distribution of aqueous micelles overcomes immense statistical odds against reaction.}, number={39}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Alexy, Eric J. and Hintz, Carl W. and Hughes, Hubert M. and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2015}, pages={10025–10031} } @article{faries_diers_springer_yang_ptaszek_lahaye_krayer_taniguchi_kirmaier_lindsey_et al._2015, title={Photophysical Properties and Electronic Structure of Chlorin-Imides: Bridging the Gap between Chlorins and Bacteriochlorins}, volume={119}, ISSN={["1520-5207"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84934319596&partnerID=MN8TOARS}, DOI={10.1021/jp511257w}, abstractNote={Efficient light harvesting for molecular-based solar-conversion systems requires absorbers that span the photon-rich red and near-infrared (NIR) regions of the solar spectrum. Reported herein are the photophysical properties of a set of six chlorin-imides and nine synthetic chlorin analogues that extend the absorption deeper (624-714 nm) into these key spectral regions. These absorbers help bridge the gap between typical chlorins and bacteriochlorins. The new compounds have high fluorescence quantum yields (0.15-0.34) and long singlet excited-state lifetimes (4.2-10.9 ns). The bathochromic shift in Qy absorption is driven by substituent-based stabilization of the lowest unoccupied molecular orbital, with the largest shifts for chlorins that bear an electron-withdrawing, conjugative group at the 3-position in combination with a 13,15-imide ring.}, number={24}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Faries, Kaitlm M. and Diers, James R. and Springer, Joseph W. and Yang, Eunkyung and Ptaszek, Marcin and Lahaye, Dorothee and Krayer, Michael and Taniguchi, Masahiko and Kirmaier, Christine and Lindsey, Jonathan S. and et al.}, year={2015}, month={Jun}, pages={7503–7515} } @article{ra_gauger_muthukumaran_balasubramanian_chandrashaker_taniguchi_yu_talley_ehudin_ptaszek_et al._2015, title={Progress towards synthetic chlorins with graded polarity, conjugatable substituents, and wavelength tunability}, volume={19}, ISSN={["1099-1409"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85027922166&partnerID=MN8TOARS}, DOI={10.1142/s1088424615500042}, abstractNote={ Advances in chlorin synthetic chemistry now enable the de novo preparation of diverse chlorin-containing molecular architectures. Five distinct molecular designs have been explored here, including hydrophobic bioconjugatable (oxo)chlorins; a hydrophilic bioconjugatable chlorin; a trans-ethynyl/iodochlorin building block; a set of chlorins bearing electron-rich (methoxy, dimethylamino, methylthio) groups at the 3-position; and a set of ten 3,13-disubstituted chlorins chiefly bearing groups with extended π-moieties. Altogether 23 new chlorins (17 targets, 6 intermediates) have been prepared. The challenge associated with molecular designs that encompass the combination of "hydrophilic, bioconjugatable and wavelength-tunable" chiefly resides in the nature of the hydrophilic unit. }, number={4}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, publisher={World Scientific Pub Co Pte Lt}, author={Ra, Doyoung and Gauger, Kelly A. and Muthukumaran, Kannan and Balasubramanian, Thiagarajan and Chandrashaker, Vanampally and Taniguchi, Masahiko and Yu, Zhanqian and Talley, Daniel C. and Ehudin, Melanie and Ptaszek, Marcin and et al.}, year={2015}, month={Apr}, pages={547–572} } @article{sahin_harris_vairaprakash_niedzwiedzki_subramanian_shreve_bocian_holten_lindsey_2015, title={Self-Assembled Light-Harvesting System from Chromophores in Lipid Vesicles}, volume={119}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.5b04841}, abstractNote={Lipid vesicles are used as the organizational structure of self-assembled light-harvesting systems. Following analysis of 17 chromophores, six were selected for inclusion in vesicle-based antennas. The complementary absorption features of the chromophores span the near-ultraviolet, visible, and near-infrared region. Although the overall concentration of the pigments is low (~1 μM for quantitative spectroscopic studies) in a cuvette, the lipid-vesicle system affords high concentration (≥10 mM) in the bilayer for efficient energy flow from donor to acceptor. Energy transfer was characterized in 13 representative binary mixtures using static techniques (fluorescence-excitation versus absorptance spectra, quenching of donor fluorescence, modeling emission spectra of a mixture versus components) and time-resolved spectroscopy (fluorescence, ultrafast absorption). Binary donor-acceptor systems that employ a boron-dipyrrin donor (S0 ↔ S1 absorption/emission in the blue-green) and a chlorin or bacteriochlorin acceptor (S0 ↔ S1 absorption/emission in the red or near-infrared) have an average excitation-energy-transfer efficiency (ΦEET) of ~50%. Binary systems with a chlorin donor and a chlorin or bacteriochlorin acceptor have ΦEET ∼ 85%. The differences in ΦEET generally track the donor-fluorescence/acceptor-absorption spectral overlap within a dipole-dipole coupling (Förster) mechanism. Substantial deviation from single-exponential decay of the excited donor (due to the dispersion of donor-acceptor distances) is expected and observed. The time profiles and resulting ΦEET are modeled on the basis of (Förster) energy transfer between chromophores relatively densely packed in a two-dimensional compartment. Initial studies of two ternary and one quaternary combination of chromophores show the enhanced spectral coverage and energy-transfer efficacy expected on the basis of the binary systems. Collectively, this approach may provide one of the simplest designs for self-assembled light-harvesting systems that afford broad solar collection and efficient energy transfer.}, number={32}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Sahin, Tuba and Harris, Michelle A. and Vairaprakash, Pothiappan and Niedzwiedzki, Dariusz M. and Subramanian, Vijaya and Shreve, Andrew P. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2015}, month={Aug}, pages={10231–10243} } @article{jiang_yang_reddy_niedzwiedzki_kirmaier_bocian_holten_lindsey_2015, title={Synthetic bacteriochlorins bearing polar motifs (carboxylate, phosphonate, ammonium and a short PEG). Water-solubilization, bioconjugation, and photophysical properties}, volume={39}, ISSN={["1369-9261"]}, DOI={10.1039/c5nj00759c}, abstractNote={A bacteriochlorin scaffold has been derivatized for life sciences applications.}, number={7}, journal={NEW JOURNAL OF CHEMISTRY}, author={Jiang, Jianbing and Yang, Eunkyung and Reddy, Kanumuri Ramesh and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2015}, pages={5694–5714} } @article{jiang_reddy_pavan_lubian_harris_jiao_niedzwiedzki_kirmaier_parkes-loach_loach_et al._2014, title={Amphiphilic, hydrophilic, or hydrophobic synthetic bacteriochlorins in biohybrid light-harvesting architectures: consideration of molecular designs}, volume={122}, ISSN={["1573-5079"]}, DOI={10.1007/s11120-014-0021-9}, abstractNote={Biohybrid light-harvesting architectures can be constructed that employ native-like bacterial photosynthetic antenna peptides as a scaffold to which synthetic chromophores are attached to augment overall spectral coverage. Synthetic bacteriochlorins are attractive to enhance capture of solar radiation in the photon-rich near-infrared spectral region. The effect of the polarity of the bacteriochlorin substituents on the antenna self-assembly process was explored by the preparation of a bacteriochlorin-peptide conjugate using a synthetic amphiphilic bacteriochlorin (B1) to complement prior studies using hydrophilic (B2, four carboxylic acids) or hydrophobic (B3) bacteriochlorins. The amphiphilic bioconjugatable bacteriochlorin B1 with a polar ammonium-terminated tail was synthesized by sequential Pd-mediated reactions of a 3,13-dibromo-5-methoxybacteriochlorin. Each bacteriochlorin bears a maleimido-terminated tether for attachment to a cysteine-containing analog of the Rhodobacter sphaeroides antenna β-peptide to give conjugates β-B1, β-B2, and β-B3. Given the hydrophobic nature of the β-peptide, the polarity of B1 and B2 facilitated purification of the respective conjugate compared to the hydrophobic B3. Bacteriochlorophyll a (BChl a) associates with each conjugate in aqueous micellar media to form a dyad containing two β-peptides, two covalently attached synthetic bacteriochlorins, and a datively bonded BChl-a pair, albeit to a limited extent for β-B2. The reversible assembly/disassembly of dyad (β-B2/BChl)2 was examined in aqueous detergent (octyl glucoside) solution by temperature variation (15-35 °C). The energy-transfer efficiency from the synthetic bacteriochlorin to the BChl-a dimer was found to be 0.85 for (β-B1/BChl)2, 0.40 for (β-B2/BChl)2, and 0.85 for (β-B3/BChl)2. Thus, in terms of handling, assembly and energy-transfer efficiency taken together, the amphiphilic design examined herein is more attractive than the prior hydrophilic or hydrophobic designs.}, number={2}, journal={PHOTOSYNTHESIS RESEARCH}, author={Jiang, Jianbing and Reddy, Kanumuri Ramesh and Pavan, M. Phani and Lubian, Elisa and Harris, Michelle A. and Jiao, Jieying and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Parkes-Loach, Pamela S. and Loach, Paul A. and et al.}, year={2014}, month={Nov}, pages={187–202} } @article{yuen_harris_liu_diers_kirmaier_bocian_lindsey_holten_2015, title={Effects of Substituents on Synthetic Analogs of Chlorophylls. Part 4: How Formyl Group Location Dictates the Spectral Properties of Chlorophylls b, d and f}, volume={91}, ISSN={["1751-1097"]}, DOI={10.1111/php.12401}, abstractNote={AbstractPhotosynthetic organisms are adapted to light characteristics in their habitat in part via the spectral characteristics of the associated chlorophyll pigments, which differ in the position of a formyl group around the chlorin macrocycle (chlorophylls b, d, f) or no formyl group (chlorophyll a). To probe the origin of this spectral tuning, the photophysical and electronic structural properties of a new set of synthetic chlorins are reported. The zinc and free base chlorins have a formyl group at either the 2‐ or 3‐position. The four compounds have fluorescence yields in the range 0.19–0.28 and singlet excited‐state lifetimes of ca 4 ns for zinc chelates and ca 8 ns for the free base forms. The photophysical properties of the 2‐ and 3‐formyl zinc chlorins are similar to those observed previously for 13‐formyl or 3,13‐diformyl chlorins, but differ markedly from those for 7‐formyl analogs. Molecular‐orbital characteristics obtained from density functional theory (DFT) calculations were used as input to spectral simulations employing the four‐orbital model. The analysis has uncovered the key changes in electronic structure engendered by the presence/location of a formyl group at various macrocycle positions, which is relevant to understanding the distinct spectral properties of the natural chlorophylls a, b, d and f.}, number={2}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Yuen, Jonathan M. and Harris, Michelle A. and Liu, Mengran and Diers, James R. and Kirmaier, Christine and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2015}, pages={331–342} } @article{harris_sahin_jiang_vairaprakash_parkes-loach_niedzwiedzki_kirmaier_loach_bocian_holten_et al._2014, title={Enhanced Light-Harvesting Capacity by Micellar Assembly of Free Accessory Chromophores and LH1-like Antennas}, volume={90}, ISSN={["1751-1097"]}, DOI={10.1111/php.12319}, abstractNote={AbstractBiohybrid light‐harvesting antennas are an emerging platform technology with versatile tailorability for solar‐energy conversion. These systems combine the proven peptide scaffold unit utilized for light harvesting by purple photosynthetic bacteria with attached synthetic chromophores to extend solar coverage beyond that of the natural systems. Herein, synthetic unattached chromophores are employed that partition into the organized milieu (e.g. detergent micelles) that house the LH1‐like biohybrid architectures. The synthetic chromophores include a hydrophobic boron‐dipyrrin dye (A1) and an amphiphilic bacteriochlorin (A2), which transfer energy with reasonable efficiency to the bacteriochlorophyll acceptor array (B875) of the LH1‐like cyclic oligomers. The energy‐transfer efficiencies are markedly increased upon covalent attachment of a bacteriochlorin (B1 or B2) to the peptide scaffold, where the latter likely acts as an energy‐transfer relay site for the (potentially diffusing) free chromophores. The efficiencies are consistent with a Förster (through‐space) mechanism for energy transfer. The overall energy‐transfer efficiency from the free chromophores via the relay to the target site can approach those obtained previously by relay‐assisted energy transfer from chromophores attached at distant sites on the peptides. Thus, the use of free accessory chromophores affords a simple design to enhance the overall light‐harvesting capacity of biohybrid LH1‐like architectures.}, number={6}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Harris, Michelle A. and Sahin, Tuba and Jiang, Jianbing and Vairaprakash, Pothiappan and Parkes-Loach, Pamela S. and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Loach, Paul A. and Bocian, David F. and Holten, Dewey and et al.}, year={2014}, pages={1264–1276} } @article{chen_taniguchi_lindsey_2014, title={NMR spectral properties of 16 synthetic bacteriochlorins with site-specific C-13 or N-15 substitution}, volume={18}, ISSN={["1099-1409"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84903791617&partnerID=MN8TOARS}, DOI={10.1142/s1088424614500199}, abstractNote={ The 1 H , 13 C , and 15 N nuclear magnetic resonance (NMR) spectral properties have been examined of a family of synthetic bacteriochlorins wherein each member incorporates a pair of 13 C or 15 N atoms. The atom locations span the inner core of the macrocycle: (1) 15 N at the 21,23- or 22,24-positions; (2) 13 C at the meso- (5,15- or 10,20-) positions; (3) 13 C at the pyrrole α-positions (1,11- or 4,14-positions); and (4) 13 C at the pyrroline α-positions (6,16- or 9,19-positions). Each bacteriochlorin lacks peripheral substituents other than a geminal dimethyl group at the 8- and 18-positions to preclude adventitious dehydrogenation. In total, eight free base and eight zinc bacteriochlorin isotopologs were examined to directly assign 1 H , 13 C and 15 N resonances of the macrocycle skeleton. Complete and unambiguous assignments, including those for all tertiary and quaternary carbons, were accomplished chiefly by direct inspection of 1D NMR spectra of each isotopolog. Coupling constants (1 H –1 H , 13 C –1 H , 15 N –1 H , 13 C –13 C and 15 N –13 C ), which are rarely reported for tetrapyrroles, also were extracted. The 1 H and 13 C chemical shifts were then compared to those of unsaturated analogs (chlorin, porphyrin) and natural bacteriochlorophylls. The comprehensive set of NMR spectroscopic properties of sparsely substituted bacteriochlorins provides valuable information for understanding substitution effects and aromaticity in structurally more elaborate counterparts. }, number={6}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, publisher={World Scientific Pub Co Pte Lt}, author={Chen, Chih-Yuan and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2014}, month={Jun}, pages={433–456} } @article{alexy_yuen_chandrashaker_diers_kirmaier_bocian_holten_lindsey_2014, title={Panchromatic absorbers for solar light-harvesting}, volume={50}, ISSN={["1364-548X"]}, DOI={10.1039/c4cc06853j}, abstractNote={A set of panchromatic absorbers exhibiting long excited-state lifetimes in both polar and nonpolar media has been prepared. The architectures are based on a porphyrin strongly coupled electronically to 1-4 perylene-monoimides via ethyne linkers. The constructs should find utility in molecular solar-conversion systems.}, number={93}, journal={CHEMICAL COMMUNICATIONS}, author={Alexy, Eric J. and Yuen, Jonathan M. and Chandrashaker, Vanampally and Diers, James R. and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2014}, pages={14512–14515} } @article{springer_taniguchi_krayer_ruzié_diers_niedzwiedzki_bocian_lindsey_holten_2014, title={Photophysical properties and electronic structure of retinylidene–chlorin–chalcones and analogues}, volume={13}, ISSN={1474-905X 1474-9092}, url={http://dx.doi.org/10.1039/C3PP50421B}, DOI={10.1039/C3PP50421B}, abstractNote={Synthetic chlorins can accommodate diverse substituents about the macrocycle perimeter. Simple auxochromes ( e.g. , vinyl, acetyl, phenyl) allow systematic tuning of spectral and photophysical features. More extensive spectral tailoring may be achieved by using more potent, highly conjugated substituents that themselves bring new absorption into a target spectral region, if deleterious excited-state quenching processes can be avoided. To explore such an expanded substituent space, herein the spectral and photophysical properties of four chlorin–chalcones are reported. The molecules are free base and zinc chlorins with substituents at the 13-position that include a chalcone and an extended chalcone derived by reaction of the 13-acetylchlorin with benzaldehyde and all- trans -retinal, respectively. Measurements of the spectral and photophysical properties ( Φ _f, τ _s, k _f, k _ic, k _isc) are accompanied by density functional calculations that examine the characteristics of the frontier molecular orbitals. The chlorin–chalcones in nonpolar (toluene) and polar (dimethylsulfoxide) media exhibit bathochromically shifted (and intense) Q _y absorption bands. The presence of the retinylidene group adds new absorption in the blue-green region where the chlorins are typically transparent; excitation in this region leads to quantitative formation of the chlorin Q _y excited state. The spectral properties generally correlate with substituent effects on the frontier MOs. The four chlorin–chalcones in the solvent toluene have high fluorescence yields (0.24–0.30) and multi-nanosecond singlet excited-state lifetimes (3.7–8.4 ns), in addition to the added absorption imparted by the chalcone moiety. Collectively, the studies reported herein provide insight into the fundamental properties of chlorins and illustrate the utility of chalcones as a means of both tuning and augmenting the spectral properties of these chromophores.}, number={4}, journal={Photochemical & Photobiological Sciences}, publisher={Royal Society of Chemistry (RSC)}, author={Springer, Joseph W. and Taniguchi, Masahiko and Krayer, Michael and Ruzié, Christian and Diers, James R. and Niedzwiedzki, Dariusz M. and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2014}, pages={634} } @article{jiang_chen_zhang_vairaprakash_lindsey_2015, title={Polarity-tunable and wavelength-tunable bacteriochlorins bearing a single carboxylic acid or NHS ester. Use in a protein bioconjugation model system}, volume={39}, ISSN={["1369-9261"]}, DOI={10.1039/c4nj01340a}, abstractNote={10 new near-infrared absorbing bacteriochlorins (soluble in aqueous or membranous media) are equipped for protein bioconjugation.}, number={1}, journal={NEW JOURNAL OF CHEMISTRY}, author={Jiang, Jianbing and Chen, Chih-Yuan and Zhang, Nuonuo and Vairaprakash, Pothiappan and Lindsey, Jonathan S.}, year={2015}, month={Jan}, pages={403–419} } @article{yang_wang_diers_niedzwiedzki_kirmaier_bocian_lindsey_holten_2014, title={Probing Electronic Communication for Efficient Light-Harvesting Functionality: Dyads Containing a Common Perylene and a Porphyrin, Chlorin, or Bacteriochlorin}, volume={118}, ISSN={["1520-5207"]}, DOI={10.1021/jp411629m}, abstractNote={The synthesis, photophysical, redox, and molecular-orbital characteristics of three perylene-tetrapyrrole dyads were investigated to probe the efficacy of the arrays for use as light-harvesting constituents. Each dyad contains a common perylene-monoimide that is linked at the N-imide position via an arylethynyl group to the meso-position of the tetrapyrrole. The tetrapyrroles include a porphyrin, chlorin, and bacteriochlorin, which have zero, one, and two reduced pyrrole rings, respectively. The increased pyrrole-ring reduction results in a progressive red shift and intensification of the lowest-energy absorption band, as exemplified by benchmark monomers. The arylethyne linkage affords moderate perylene-tetrapyrrole electronic coupling in the dyads as evidenced by the optical, molecular-orbital, and redox properties of the components of the dyads versus the constituent parts. All three dyads in nonpolar solvents exhibit relatively fast (subpicosecond) energy transfer from the perylene to the tetrapyrrole. Competing charge-transfer processes are also absent in nonpolar solvents, but become active for both the chlorin and bacteriochlorin-containing dyads in polar solvents. Calculations of energy-transfer rates via the Förster, through-space mechanism reveal that these rates are, on average, 3-fold slower than the observed rates. Thus, the Dexter through-bond mechanism contributes more substantially than the through-space mechanism to energy transfer in the dyads. The electronic communication between the perylene and tetrapyrrole falls in a regime intermediate between those operative in other classes of perylene-tetrapyrrole dyads that have previously been studied.}, number={6}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Yang, Eunkyung and Wang, Jieqi and Diers, James R. and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2014}, month={Feb}, pages={1630–1647} } @article{liu_ptaszek_mass_minkler_sommer_bhaumik_lindsey_2014, title={Regioselective β-pyrrolic electrophilic substitution of hydrodipyrrin–dialkylboron complexes facilitates access to synthetic models for chlorophyll f}, volume={38}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/C3NJ01508D}, DOI={10.1039/C3NJ01508D}, abstractNote={Substituents in ring A of chlorophylls can exert profound effects on spectral properties. A de novo route to synthetic chlorins employs a tetrahydrodipyrrin reactant containing pyrrole and pyrroline rings. Complexation of the tetrahydrodipyrrin with a dialkylboron motif caused electrophilic substitution (bromination, formylation) to proceed predominantly at the β7- rather than α-position of the pyrrole ring, whereas an analogous dihydrodipyrrin underwent substitution equally at the 7- and 8-positions. The fully unsaturated dipyrrin–difluoroboron complex is known to undergo electrophilic substitution at the 8-position. The 7-position of the hydrodipyrrin ultimately gives rise to substituents at the chlorin 2-position (ring A), which heretofore has been little accessed. The position of substitution was confirmed by four single-crystal X-ray structures. Two isomeric formylchlorins were prepared by Pd-mediated carbonylation of the corresponding bromochlorins. Access to a 2-formylchlorin relied on bromination of the tetrahydrodipyrrin–dibutylboron complex, whereas a 3-formylchlorin was prepared by installation of the bromo group in the earliest precursor, pyrrole-2-carboxaldehyde. The two formylchlorins differ in absorption spectral properties: the Qy absorption maximum is 654 or 664 nm for the 2- or 3-formylchlorin, respectively. The synthetic formylchlorins provide initial models for understanding the strong red absorption of native 2- or 3-formylchlorophylls (f and d).}, number={4}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Liu, Mengran and Ptaszek, Marcin and Mass, Olga and Minkler, Daniel F. and Sommer, Roger D. and Bhaumik, Jayeeta and Lindsey, Jonathan S.}, year={2014}, pages={1717} } @article{huang_krayer_roubil_huang_holten_lindsey_hamblin_2014, title={Stable synthetic mono-substituted cationic bacteriochlorins mediate selective broad-spectrum photoinactivation of drug-resistant pathogens at nanomolar concentrations}, volume={141}, ISSN={["1873-2682"]}, DOI={10.1016/j.jphotobiol.2014.09.016}, abstractNote={Three stable synthetic mono-substituted cationic bacteriochlorins (BC37, BC38 and BC39) were recently reported to show exceptional activity (low nanomolar) in mediating photodynamic killing of human cancer cells after a 24h incubation upon excitation with near-infrared light (730 nm). The presence of cationic quaternary ammonium groups in each compound suggested likely activity as antimicrobial photosensitizers. Herein this hypothesis was tested against a panel of pathogenic microorganisms that have all recently drawn attention due to increased drug-resistance (Gram-positive bacteria, Staphylococcus aureus and Enterococcus faecalis; Gram-negative bacteria, Escherichia coli and Acinetobacter baumannii; and fungal yeasts, Candida albicans and Cryptococcus neoformans). All three bacteriochlorins were highly effective against both Gram-positive species (>6 logs of eradication at ⩽ 200 nM and 10 J/cm(2)). The dicationic bacteriochlorin (BC38) was best against the Gram-negative species (>6 logs at 1-2 μM) whereas the lipophilic monocationic bacteriochlorin (BC39) was best against the fungi (>6 logs at 1 μM). The bacteriochlorins produced substantial singlet oxygen (and apparently less Type-1 reactive-oxygen species such as hydroxyl radical) as judged by activation of fluorescent probes and comparison with 1H-phenalen-1-one-2-sulfonic acid; the order of activity was BC37 > BC38 > BC39. A short incubation time (30 min) resulted in selectivity for microbial cells over HeLa human cells. The highly active photodynamic inactivation of microbial cells may stem from the amphiphilic and cationic features of the bacteriochlorins.}, journal={JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY}, author={Huang, Liyi and Krayer, Michael and Roubil, John G. S. and Huang, Ying-Ying and Holten, Dewey and Lindsey, Jonathan S. and Hamblin, Michael R.}, year={2014}, month={Dec}, pages={119–127} } @article{taniguchi_henry_cogdell_lindsey_2014, title={Statistical considerations on the formation of circular photosynthetic light-harvesting complexes from Rhodopseudomonas palustris}, volume={121}, ISSN={["1573-5079"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84902284652&partnerID=MN8TOARS}, DOI={10.1007/s11120-014-9975-x}, abstractNote={Depending on growth conditions, some species of purple photosynthetic bacteria contain peripheral light-harvesting (LH2) complexes that are heterogeneous owing to the presence of different protomers (containing different αβ-apoproteins). Recent spectroscopic studies of Rhodopseudomonas palustris grown under low-light conditions suggest the presence of a C 3-symmetric LH2 nonamer comprised of two distinct protomers. The software program Cyclaplex, which enables generation and data-mining of virtual libraries of molecular rings formed upon combinatorial reactions, has been used to delineate the possible number and type of distinct nonamers as a function of numbers of distinct protomers. The yield of the C 3-symmetric nonamer from two protomers (A and B in varying ratios) has been studied under the following conditions: (1) statistical, (2) enriched (preclusion of the B-B sequence), and (3) seeded (pre-formation of an A-B-A block). The yield of C 3-symmetric nonamer is at most 0.98 % under statistical conditions versus 5.6 % under enriched conditions, and can be dominant under conditions of pre-seeding with an A-B-A block. In summary, the formation of any one specific nonamer even from only two protomers is unlikely on statistical grounds but must stem from enhanced free energy of formation or a directed assembly process by as-yet unknown factors.}, number={1}, journal={PHOTOSYNTHESIS RESEARCH}, publisher={Springer Nature}, author={Taniguchi, Masahiko and Henry, Sarah and Cogdell, Richard J. and Lindsey, Jonathan S.}, year={2014}, month={Jul}, pages={49–60} } @article{chen_bocian_lindsey_2014, title={Synthesis of 24 Bacteriochlorin Isotopologues, Each Containing a Symmetrical Pair of C-13 or N-15 Atoms in the Inner Core of the Macrocycle}, volume={79}, ISSN={["0022-3263"]}, DOI={10.1021/jo402488n}, abstractNote={Synthetic bacteriochlorins containing site-specific isotopic substitution enable spectroscopic interrogation to delineate physicochemical features relevant to bacteriochlorophylls in photosynthesis but have been little explored. A de novo synthesis has been employed to prepare bacteriochlorins wherein each macrocycle contains a pair of (13)C or (15)N atoms yet lacks substituents other than a geminal dimethyl group in each pyrroline ring. Preparation of a dihydrodipyrrin–acetal with single-isotopic substitution gives rise to a bacteriochlorin that contains two isotopic substitutions symmetrically disposed by a 180° rotation about the normal to the plane of the macrocycle. Eight such isotopically substituted bacteriochlorins were prepared from commercially available reactants (bacteriochlorin sites): ((13)C)paraformaldehyde (1, 11); ((13)C)formamide (4, 14); triethyl ((13)C)orthoformate (5, 15); K(13)CN (6, 16); (13)CH3NO2 (9, 19); N,N-dimethyl((13)C)formamide (10, 20); ((15)N)pyrrole (21, 23); CH3(15)NO2 (22, 24). Some loss of (15)N upon TiCl3-mediated McMurry-type ring closure of a nitro((15)N)hexanone is attributed to a parallel sequence of three reactions (Nef, exchange with natural-abundance NH4OAc buffer, and Paal–Knorr ring closure) leading to the dihydrodipyrrin–acetal. Zinc and copper chelates of each bacteriochlorin also were prepared. Together, the 24 bacteriochlorin isotopologues should provide valuable benchmarks for understanding ground- and excited-state molecular physics of the macrocycles related to photosynthetic function of bacteriochlorophylls.}, number={3}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Chen, Chih-Yuan and Bocian, David F. and Lindsey, Jonathan S.}, year={2014}, month={Feb}, pages={1001–1016} } @article{harris_jiang_niedzwiedzki_jiao_taniguchi_kirmaier_loach_bocian_lindsey_holten_et al._2014, title={Versatile design of biohybrid light-harvesting architectures to tune location, density, and spectral coverage of attached synthetic chromophores for enhanced energy capture}, volume={121}, ISSN={["1573-5079"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84902249655&partnerID=MN8TOARS}, DOI={10.1007/s11120-014-9993-8}, abstractNote={Biohybrid antennas built upon chromophore-polypeptide conjugates show promise for the design of efficient light-capturing modules for specific purposes. Three new designs, each of which employs analogs of the β-polypeptide from Rhodobacter sphaeroides, have been investigated. In the first design, amino acids at seven different positions on the polypeptide were individually substituted with cysteine, to which a synthetic chromophore (bacteriochlorin or Oregon Green) was covalently attached. The polypeptide positions are at -2, -6, -10, -14, -17, -21, and -34 relative to the 0-position of the histidine that coordinates bacteriochlorophyll a (BChl a). All chromophore-polypeptides readily formed LH1-type complexes upon combination with the α-polypeptide and BChl a. Efficient energy transfer occurs from the attached chromophore to the circular array of 875 nm absorbing BChl a molecules (denoted B875). In the second design, use of two attachment sites (positions -10 and -21) on the polypeptide affords (1) double the density of chromophores per polypeptide and (2) a highly efficient energy-transfer relay from the chromophore at -21 to that at -10 and on to B875. In the third design, three spectrally distinct bacteriochlorin-polypeptides were prepared (each attached to cysteine at the -14 position) and combined in an ~1:1:1 mixture to form a heterogeneous mixture of LH1-type complexes with increased solar coverage and nearly quantitative energy transfer from each bacteriochlorin to B875. Collectively, the results illustrate the great latitude of the biohybrid approach for the design of diverse light-harvesting systems.}, number={1}, journal={PHOTOSYNTHESIS RESEARCH}, author={Harris, Michelle A. and Jiang, Jianbing and Niedzwiedzki, Dariusz M. and Jiao, Jieying and Taniguchi, Masahiko and Kirmaier, Christine and Loach, Paul A. and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey and et al.}, year={2014}, month={Jul}, pages={35–48} } @article{diers_tang_hondros_chen_holten_lindsey_bocian_2014, title={Vibronic Characteristics and Spin-Density Distributions in Bacteriochlorins as Revealed by Spectroscopic Studies of 16 Isotopologues. Implications for Energy- and Electron-Transfer in Natural Photosynthesis and Artificial Solar-Energy Conversion}, volume={118}, ISSN={["1520-5207"]}, DOI={10.1021/jp504286w}, abstractNote={Vibronic characteristics and spin-density distributions in the core bacteriochlorin macrocycle were revealed by spectroscopic and theoretical studies of 16 isotopologues. The vibrational modes in copper bacteriochlorin isotopologues were examined via resonance Raman and Fourier-transform infrared spectroscopy. The resonance Raman spectra exhibit an exceptional sparcity of vibronically active modes of the core macrocycle, in contrast with the rich spectra of the natural bacteriochlorophylls. The Qy-excitation resonance Raman spectrum is dominated by a single mode at 727 cm-1, which calculations suggest is due to a symmetrical accordion-like deformation of the five-atom Cm(CaNCa)pyrroleCm portion of the ring core. This deformation also dominates the vibronic features in the absorption and fluorescence spectra. The spin-density distributions in the π-cation radical of the zinc bacteriochlorin isotopologues were studied by electron paramagnetic resonance spectroscopy. The spectra indicate a significant electron/spin density (ρ ∼ 0.1) on each meso-carbon atom. This observation contradicts the predictions of early calculations that have been assumed to be correct for nearly four decades. Collectively, these findings have implications for how the structural features that characterize natural bacteriochlorophylls might influence energy- and electron-transfer processes in photosynthesis and alter the thinking on the design of synthetic, bacteriochlorin-based arrays for solar-energy conversion.}, number={27}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Diers, James R. and Tang, Qun and Hondros, Christopher J. and Chen, Chih-Yuan and Holten, Dewey and Lindsey, Jonathan S. and Bocian, David F.}, year={2014}, month={Jul}, pages={7520–7532} } @article{aravindu_mass_vairaprakash_springer_yang_niedzwiedzki_kirmaier_bocian_holten_lindsey_2013, title={Amphiphilic chlorins and bacteriochlorins in micellar environments. Molecular design, de novo synthesis, and photophysical properties}, volume={4}, ISSN={2041-6520 2041-6539}, url={http://dx.doi.org/10.1039/C3SC51335A}, DOI={10.1039/C3SC51335A}, abstractNote={The incorporation of amphiphilic tetrapyrrole macrocycles in organized media is of great value for a variety of fundamental photochemical studies, yet work to date has chiefly employed porphyrins rather than chlorins or bacteriochlorins. The latter absorb strongly in the red or near-infrared spectral region, respectively. Here, eight amphiphilic macrocycles (six chlorins and two bacteriochlorins) have been designed, synthesized and characterized; the compounds differ in long wavelength absorption (610–745 nm) and peripheral substituents (type of auxochrome, hydrophobic/hydrophilic groups). A methyl pyridinium or benzoic acid substituent at the 15-position provides a polar “tail” whereas a hydrophobic group distal thereto (in the chlorins) provides a lipophilic “head” for the spontaneous incorporation in organized media. The eight (bacterio)chlorins are characterized by static and time-resolved absorption and fluorescence spectroscopy in N,N-dimethylformamide (DMF) and three micellar environments (TX-100, CTAB, and SDS) as well as ultrafast transient absorption studies in DMF. In most cases, a long-lived excited singlet state was observed [free base chlorins (Φf = 0.14–0.20; τS = 7.9–12.1 ns; Φisc = 0.5), zinc chlorins (Φf = 0.08–0.19; τS = 2.0–3.4 ns; Φisc = 0.6–0.8) and free base bacteriochlorins (Φf = 0.06–0.16; τS = 1.8–4.6 ns; Φisc = 0.4)]. In the case of bacteriochlorins, minimal medium dependence was observed whereas changing the hydrophilic group from methyl pyridinium to benzoic acid increases the fluorescence yield and excited-state lifetime by 50%. In the case of chlorins, the zinc chelate with methyl pyridinium substitution exhibits substantial environmental dependence due to interaction of the solvent with the methyl pyridinium group and the central zinc metal. Collectively, the studies provide valuable information for the design of red or near-infrared absorbing chromophores for incorporation into amphiphilic environments such as micelles, membranes, or proteins.}, number={9}, journal={Chemical Science}, publisher={Royal Society of Chemistry (RSC)}, author={Aravindu, Kunche and Mass, Olga and Vairaprakash, Pothiappan and Springer, Joseph W. and Yang, Eunkyung and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2013}, pages={3459} } @article{soares_thanaiah_taniguchi_lindsey_2013, title={Aqueous–membrane partitioning of β-substituted porphyrins encompassing diverse polarity}, volume={37}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/c3nj41042k}, DOI={10.1039/c3nj41042k}, abstractNote={Understanding the partitioning of organic molecules between aqueous solution and lipid membranes is critical to problems in fields ranging from drug design to environmental science to studies of the origin of life. Here, six β-substituted porphyrins of diverse polarity were examined for partitioning between the membranes of phosphatidylcholine vesicles and aqueous solution. The porphyrins include uroporphyrin I (number of carboxylic acid substituents = 8), heptacarboxylic acid porphyrin I (7), hexacarboxylic acid porphyrin I (6), coproporphyrin I (4), mesoporphyrin IX (2) and etioporphyrin I (0). The porphyrins were examined individually and collectively. In each case, size-exclusion chromatography was used to separate a porphyrins/vesicles fraction and a porphyrins/aqueous fraction. Each fraction was analyzed quantitatively by reversed-phase HPLC with fluorescence detection or by UV-Visible absorption spectroscopy to give partition coefficients. The partition coefficients for the six porphyrins also were calculated (clog P) using seven software programs: ACD/Labs, ALOGPS 2.1, Chemdraw, Molinspiration, KowWin, MarvinSketch, and XLOGP3. For perspective, clog P values for seven other porphyrins and 18 non-porphyrins also were calculated. Wide variation among programs was observed for almost all of the porphyrins and non-porphyrins of similar molecular weight. The dearth of porphyrins with requisite substituent patterns for experimental examination and the unreliability of calculation preclude definitive predictions concerning partitioning of unknown porphyrins; however, the results afford heuristics to predict aqueous–membrane partitioning of diverse β-substituted porphyrins.}, number={4}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Soares, Ana R. M. and Thanaiah, Yugaananthy and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2013}, pages={1087} } @article{soares_anderson_chandrashaker_lindsey_2013, title={Catalytic diversification upon metal scavenging in a prebiotic model for formation of tetrapyrrole macrocycles}, volume={37}, ISSN={["1369-9261"]}, DOI={10.1039/c3nj00498h}, abstractNote={A prebiotic model for the formation of tetrapyrrole macrocycles was examined in aqueous solution containing representative Earth-available metals [Mg(II), Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II) and Pd(II)]. First, a hydrophilic porphyrin (uroporphyrin I) was found to undergo metalation with all metals examined except Mg(II). Second, a competition experiment among the eight metals with uroporphyrin in limiting quantity afforded preferential metalation with Mn(II), Co(II), Cu(II) and Ni(II). A multicomponent analysis method enabled absorption spectrophotometric detection of 8 distinct uroporphyrins (7 metallo-, 1 free base) in a single mixture. Third, a dione–aminoketone reaction was performed in aqueous solution containing the metals followed by photooxidation in the presence of a quinone. The reaction proceeds through multiple stages: (1) dione–aminoketone condensation to give a pyrrole equipped for self-condensation, (2) tetramerization of the pyrrole and cyclization to give uroporphyrinogens, (3) 6e−/6H+ dehydrogenation (e.g., photooxidation) to give the uroporphyrins, and (4) metalation of the uroporphyrins. The presence versus absence of metals resulted in lower yields, yet Mn(II), Fe(II), Co(II), Cu(II) and Zn(II) each individually gave the corresponding metallouroporphyrin [with trivalent metals observed in three cases: Mn(III), Fe(III), and Co(III)]. Analogous reaction in the presence of all eight metals together gave the free base, Mn(III), and Zn(II) chelates whereas other metal chelates could not be reliably detected by absorption spectroscopy or mass spectrometry. Such metalloporphyrins greatly broaden the accessible redox levels, catalytic avenues, and photochemical features versus those of the free base porphyrins. Taken together, scavenging of metals is expected to increase the functional diversity of tetrapyrroles on early Earth.}, number={9}, journal={NEW JOURNAL OF CHEMISTRY}, author={Soares, Ana R. M. and Anderson, Dana R. and Chandrashaker, Vanampally and Lindsey, Jonathan S.}, year={2013}, pages={2716–2732} } @article{wang_yang_diers_niedzwiedzki_kirmaier_bocian_lindsey_holten_2013, title={Distinct Photophysical and Electronic Characteristics of Strongly Coupled Dyads Containing a Perylene Accessory Pigment and a Porphyrin, Chlorin, or Bacteriochlorin}, volume={117}, ISSN={["1520-5207"]}, DOI={10.1021/jp405004d}, abstractNote={The synthesis, photophysical, redox, and molecular-orbital characteristics of three perylene-tetrapyrrole dyads were investigated to elucidate characteristics favorable for use in next-generation light-harvesting assemblies. Each dyad contains a common perylene-monoimide that is linked at the 9-position via an ethynyl group to the meso-position of the tetrapyrrole. The tetrapyrroles include a porphyrin, chlorin, and bacteriochlorin, which have zero, one, and two reduced pyrrole rings, respectively. The increased pyrrole-ring reduction results in a progressive red shift and intensification of the lowest-energy absorption band, as exemplified by benchmark monomers. The direct ethyne linkage and accompanying strong perylene-tetrapyrrole electronic coupling in the dyads is evident by significant differences in optical absorption versus the sum of the features of the constituents. The perturbations decrease for the tetrapyrrole constituent along the series porphyrin > chlorin > bacteriochlorin. This trend is explained by the relative configurational mixing in the tetrapyrrole excited states and how the configuration-interaction energy (and not simply the energies of the configurations) is affected by coupling to the perylene. The perylene-tetrapyrrole electronic coupling is further evidenced in the redox and MO characteristics of the three dyads. All three dyads in nonpolar solvents exhibit relatively long singlet excited-state lifetimes (3.3-6.5 ns) and relatively large fluorescence quantum yields (0.14-0.40). Collectively, the physicochemical characteristics of the strongly coupled perylene-tetrapyrrole dyads render these architectures excellent candidates for light-harvesting materials with significant, even panchromatic, near-ultraviolet to near-infrared absorption.}, number={31}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Wang, Jieqi and Yang, Eunkrung and Diers, James R. and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2013}, month={Aug}, pages={9288–9304} } @article{taniguchi_du_lindsey_2013, title={Enumeration of Virtual Libraries of Combinatorial Modular Macrocyclic (Bracelet, Necklace) Architectures and Their Linear Counterparts}, volume={53}, ISSN={["1549-960X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84883274376&partnerID=MN8TOARS}, DOI={10.1021/ci400175f}, abstractNote={A wide variety of cyclic molecular architectures are built of modular subunits and can be formed combinatorially. The mathematics for enumeration of such objects is well-developed yet lacks key features of importance in chemistry, such as specifying (i) the structures of individual members among a set of isomers, (ii) the distribution (i.e., relative amounts) of products, and (iii) the effect of nonequal ratios of reacting monomers on the product distribution. Here, a software program (Cyclaplex) has been developed to determine the number, identity (including isomers), and relative amounts of linear and cyclic architectures from a given number and ratio of reacting monomers. The program includes both mathematical formulas and generative algorithms for enumeration; the latter go beyond the former to provide desired molecular-relevant information and data-mining features. The program is equipped to enumerate four types of architectures: (i) linear architectures with directionality (macroscopic equivalent = electrical extension cords), (ii) linear architectures without directionality (batons), (iii) cyclic architectures with directionality (necklaces), and (iv) cyclic architectures without directionality (bracelets). The program can be applied to cyclic peptides, cycloveratrylenes, cyclens, calixarenes, cyclodextrins, crown ethers, cucurbiturils, annulenes, expanded meso-substituted porphyrin(ogen)s, and diverse supramolecular (e.g., protein) assemblies. The size of accessible architectures encompasses up to 12 modular subunits derived from 12 reacting monomers or larger architectures (e.g. 13-17 subunits) from fewer types of monomers (e.g. 2-4). A particular application concerns understanding the possible heterogeneity of (natural or biohybrid) photosynthetic light-harvesting oligomers (cyclic, linear) formed from distinct peptide subunits.}, number={9}, journal={JOURNAL OF CHEMICAL INFORMATION AND MODELING}, publisher={American Chemical Society (ACS)}, author={Taniguchi, Masahiko and Du, Hai and Lindsey, Jonathan S.}, year={2013}, month={Sep}, pages={2203–2216} } @article{soares_taniguchi_chandrashaker_lindsey_2013, title={Expanded combinatorial formation of porphyrin macrocycles in aqueous solution containing vesicles. A prebiotic model}, volume={37}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/c3nj41041b}, DOI={10.1039/c3nj41041b}, abstractNote={The role of combinatorial processes in the origin of life remains relatively unexplored. In a chemical model for the possible prebiogenesis of tetrapyrrole macrocycles reported previously, a tandem combinatorial reaction of two diones (substituents = methyl, acetic acid) and two aminoketones (substituents = ethyl, propanoic acid) afforded up to 538 porphyrins (upon oxidation of the corresponding porphyrinogens). The reaction was performed at a 1 : 1 ratio of hydrophobic and hydrophilic substituents in each pool of reactants, and the resulting porphyrins partitioned in ∼1 : 1 ratio between aqueous solution and phosphatidylcholine vesicle membranes. Here, a change in the ratio of hydrophobic and hydrophilic substituents of the [2 × 2] reaction gave corresponding changes in the polarity profile of the resulting porphyrins (3.5–9.0% yield). Reaction of four diones and four aminoketones (bearing hydrophilic or hydrophobic substituents) in the presence of lipid vesicles followed by photooxidation afforded porphyrins in 8.7% yield. The resulting porphyrins partitioned in ∼1 : 1 ratio between phosphatidylcholine vesicles and aqueous solution, as observed previously for the [2 × 2] reaction. Both the aqueous fraction and the vesicles fraction were photochemically active as evidenced by the fluorescence quantum yield (Φf ∼ 0.1). Software (PorphyrinViLiGe) for virtual library generation indicates that the [4 × 4] reaction affords up to 131 464 porphyrins. The relative insensitivity of physicochemical properties (partitioning, photoactivity) toward combinatorial expansion may be a valuable yet unappreciated attribute for prebiotic functionality.}, number={4}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Soares, Ana R. M. and Taniguchi, Masahiko and Chandrashaker, Vanampally and Lindsey, Jonathan S.}, year={2013}, pages={1073} } @article{jiang_vairaprakash_reddy_sahin_pavan_lubian_lindsey_2014, title={Hydrophilic tetracarboxy bacteriochlorins for photonics applications}, volume={12}, ISSN={["1477-0539"]}, DOI={10.1039/c3ob41791c}, abstractNote={Bacteriochlorins absorb strongly in the near-infrared (NIR, 700-900 nm) region and hence are well suited for photophysical studies and photomedical applications, yet such endeavors heretofore have been largely limited by the intrinsic lipophilicity of the bacteriochlorin macrocycle. Here, a new molecular design is investigated wherein 3,5-dicarboxyphenyl units are appended to the β-pyrrolic positions of the bacteriochlorin. Use of the 3,5-aryl substitution motif places the carboxylic acid groups, which are anionic at neutral pH, above and below the plane of the bacteriochlorin macrocycle. A de novo synthesis has been employed to create five such bacteriochlorins, which uses as intermediates two new 2,12-dibromobacteriochlorin building blocks and a known 3,13-dibromobacteriochlorin. The aryl groups with protected carboxylate moieties were introduced by Suzuki coupling; subsequent deprotection afforded the hydrophilic bacteriochlorins. The latter were characterized by absorption and fluorescence spectroscopy in DMF and in aqueous phosphate buffer (pH 7). In most cases, comparable sharp emission (FWHM of ∼25 nm) and modest fluorescence yields (0.060-0.11) were observed in aqueous phosphate buffer medium and in DMF. Aqueous solubility was examined by absorption spectral interrogation of samples over a 1000-fold concentration range with reciprocal change in pathlength (∼0.5, 5, 50, and 500 μM; 10, 1, 0.1, and 0.01 cm pathlength cuvettes). One hydrophilic bacteriochlorin was prepared that contains a single maleimido-terminated tether for bioconjugation; the tether was installed by the sequence of 15-bromination of the bacteriochlorin, Suzuki coupling, and DCC-mediated amide formation. The maleimido-bacteriochlorin was conjugated to a 48-residue cysteine-containing peptide analogue of a constituent from a bacterial photosynthetic light-harvesting complex. Taken together, the results show a new molecular design and facile de novo synthetic route for obtaining hydrophilic bacteriochlorins including a bioconjugatable group if desired.}, number={1}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Jiang, Jianbing and Vairaprakash, Pothiappan and Reddy, Kanumuri Ramesh and Sahin, Tuba and Pavan, M. Phani and Lubian, Elisa and Lindsey, Jonathan S.}, year={2014}, month={Jan}, pages={86–103} } @article{harris_parkes-loach_springer_jiang_martin_qian_jiao_niedzwiedzki_kirmaier_olsen_et al._2013, title={Integration of multiple chromophores with native photosynthetic antennas to enhance solar energy capture and delivery}, volume={4}, ISSN={2041-6520 2041-6539}, url={http://dx.doi.org/10.1039/C3SC51518D}, DOI={10.1039/C3SC51518D}, abstractNote={Native length bacterial light-harvesting peptides carrying covalently attached designer chromophores have been created that self-assemble with native bacteriochlorophyll a (BChl a) to afford stable antennas with enhanced spectral coverage. Native (or native-like) α- and β-peptides interact with each other and BChl a to form a heterodimeric (αβ-dyad) unit that can then oligomerize to form biohybrid analogs of the bacterial core light-harvesting complex (LH1). Pairs of distinct synthetic chromophores were incorporated in αβ-dyads at selected distances from the BChl a target site (position 0). Two designs were explored. One design used green-yellow absorbing/emitting Oregon Green at the −34 position (toward the N-terminus relative to the BChl a coordination site) of β and orange-red absorbing/emitting Rhodamine Red at the −20 position of α, which combine with BChl a to give homogeneous oligomers. A second design used two different β-peptide conjugates, one with Oregon Green at the −34 position and the second with a near-infrared absorbing/emitting synthetic bacteriochlorin at the −14 position, which combine with α and BChl a to give a heterogeneous mixture of oligomers. The designs afford antennas with ∼45 to ∼60 pigments, provide enhanced spectral coverage across the visible and near-infrared regions relative to native antennas, and accommodate pigments at remote sites that contribute to solar light harvesting via an energy-transfer cascade. The efficiencies of energy-transfer to the BChl a target in the biohybrid antennas are comparable to native antennas, as revealed by static and time-resolved absorption and emission studies. The results show that the biohybrid approach, where designer chromophores are integrated via semisynthesis with native-like scaffolding, constitutes a versatile platform technology for rapid prototyping of antennas for solar energy capture without the laborious synthesis typically required for creating artificial photosynthetic light-harvesting architectures.}, number={10}, journal={Chemical Science}, publisher={Royal Society of Chemistry (RSC)}, author={Harris, Michelle A. and Parkes-Loach, Pamela S. and Springer, Joseph W. and Jiang, Jianbing and Martin, Elizabeth C. and Qian, Pu and Jiao, Jieying and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Olsen, John D. and et al.}, year={2013}, pages={3924} } @article{reddy_jiang_krayer_harris_springer_yang_jiao_niedzwiedzki_pandithavidana_parkes-loach_et al._2013, title={Palette of lipophilic bioconjugatable bacteriochlorins for construction of biohybrid light-harvesting architectures}, volume={4}, ISSN={2041-6520 2041-6539}, url={http://dx.doi.org/10.1039/C3SC22317E}, DOI={10.1039/C3SC22317E}, abstractNote={The challenge of creating both pigment building blocks and scaffolding to organize a large number of such pigments has long constituted a central impediment to the construction of artificial light-harvesting architectures. Light-harvesting (LH) antennas in photosynthetic bacteria are formed in a two-tiered self-assembly process wherein (1) a peptide dyad containing two bacteriochlorophyll a molecules forms, and (2) the dyads associate to form cyclic oligomers composed of 8 or 9 dyads in LH2 and 15 or 16 in LH1 of purple photosynthetic bacteria. While such antenna systems generally have near-quantitative transfer of excitation energy among pigments, only a fraction of the solar spectrum is typically absorbed. A platform architecture for study of light-harvesting phenomena has been developed that employs native photosynthetic peptide analogs, native bacteriochlorophyll a, and synthetic near-infrared-absorbing bacteriochlorins. Herein, the syntheses of 10 lipophilic bacteriochlorins are reported, of which 7 contain bioconjugatable handles (maleimide, iodoacetamide, formyl, carboxylic acid) for attachment to the peptide chassis. The bioconjugatable bacteriochlorins typically exhibit a long-wavelength absorption band in the range 710 to 820 nm, fluorescence yield of 0.1–0.2, and lifetime of the lowest singlet excited state of 2–5 ns. The α-helical structure of the native-like peptide is retained upon conjugation with a synthetic bacteriochlorin, as judged by single-reflection infrared studies. Static and time-resolved optical studies of the oligomeric biohybrid architectures in aqueous detergent solution reveal efficient (∼90%) excitation energy transfer from the attached bacteriochlorin to the native-like bacteriochlorophyll a sites. The biohybrid light-harvesting architectures thus exploit the self-constituting features of the natural systems yet enable versatile incorporation of members from a palette of synthetic chromophores, thereby opening the door to a wide variety of studies in artificial photosynthesis.}, number={5}, journal={Chemical Science}, publisher={Royal Society of Chemistry (RSC)}, author={Reddy, Kanumuri Ramesh and Jiang, Jianbing and Krayer, Michael and Harris, Michelle A. and Springer, Joseph W. and Yang, Eunkyung and Jiao, Jieying and Niedzwiedzki, Dariusz M. and Pandithavidana, Dinesh and Parkes-Loach, Pamela S. and et al.}, year={2013}, pages={2036} } @article{yang_ruzie_krayer_diers_niedzwiedzki_kirmaier_lindsey_bocian_holten_2013, title={Photophysical Properties and Electronic Structure of Bacteriochlorin-Chalcones with Extended Near-Infrared Absorption}, volume={89}, ISSN={["1751-1097"]}, DOI={10.1111/php.12053}, abstractNote={AbstractSynthetic bacteriochlorins enable systematic tailoring of substituents about the bacteriochlorin chromophore and thereby provide insights concerning the native bacteriochlorophylls of bacterial photosynthesis. Nine free‐base bacteriochlorins (eight prepared previously and one prepared here) have been examined that bear diverse substituents at the 13‐ or 3,13‐positions. The substituents include chalcone (3‐phenylprop‐2‐en‐1‐onyl) derivatives with groups attached to the phenyl moiety, a “reverse chalcone” (3‐phenyl‐3‐oxo‐1‐enyl), and extended chalcones (5‐phenylpenta‐2,4‐dien‐1‐onyl, retinylidenonyl). The spectral and photophysical properties (τs, Φf, Φic, Φisc, τT, kf, kic, kisc) of the bacteriochlorins have been characterized. The bacteriochlorins absorb strongly in the 780–800 nm region and have fluorescence quantum yields (Φf) in the range 0.05–0.11 in toluene and dimethylsulfoxide. Light‐induced electron promotions between orbitals with predominantly substituent or macrocycle character or both may give rise to some net macrocycle ↔ substituent charge‐transfer character in the lowest and higher singlet excited states as indicated by density functional theory (DFT) and time‐dependent DFT calculations. Such calculations indicated significant participation of molecular orbitals beyond those (HOMO − 1 to LUMO + 1) in the Gouterman four‐orbital model. Taken together, the studies provide insight into the fundamental properties of bacteriochlorins and illustrate designs for tuning the spectral and photophysical features of these near‐infrared‐absorbing tetrapyrrole chromophores.}, number={3}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Yang, Eunkyung and Ruzie, Christian and Krayer, Michael and Diers, James R. and Niedzwiedzki, Dariusz M. and Kirmaier, Christine and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2013}, pages={586–604} } @article{aravindu_kim_taniguchi_dilbeck_diers_bocian_holten_lindsey_2013, title={Synthesis and photophysical properties of chlorins bearing 0–4 distinct meso-substituents}, volume={12}, ISSN={1474-905X 1474-9092}, url={http://dx.doi.org/10.1039/C3PP50240F}, DOI={10.1039/C3PP50240F}, abstractNote={The presence of substituents at designated sites about the chlorin macrocycle can alter the spectral properties, a phenomenon that can be probed through synthesis. Prior syntheses have provided access to chlorins bearing distinct aryl substituents (individually or collectively) at the 5, 10, and 15-positions, but not the 20-position. A new Western half (5-phenyl-2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin) has been employed in condensation with an Eastern half (9-bromodipyrromethane-1-carboxaldehyde) followed by oxidative cyclization to give (5% yield) the zinc(ii) 20-phenylchlorin. Condensation of the same Western half and a diaryl-substituted Eastern half provided (11% yield) the zinc(ii) 5,10,20-triarylchlorin; demetalation with TFA followed by 15-bromination and Suzuki coupling gave the free base 5,10,15,20-tetraarylchlorin. Altogether, 10 new synthetic chlorins have been prepared. The near-UV (B) absorption band of the free base chlorins shifts bathochromically from 389 to 429 nm and that for the zinc chlorins from 398 to 420 nm as the number of meso -aryl rings is increased stepwise from 0-4. The long-wavelength (Q_y) absorption band undergoes a bathochromic and hypochromic shift upon increase in number of meso -aryl groups. Regardless of the number and positions of the meso -aryl substituents (including “walking a phenyl group around the ring”), the respective fluorescence quantum yields (0.17 to 0.27) and singlet excited-state lifetimes (9.4 to 13.1 ns) are comparable among the free base chlorins and the same is true for the zinc chelates (0.057 to 0.080; 1.2 to 1.6 ns). Density functional theory calculations show that of the frontier molecular orbitals of the chlorin, the energy of the HOMO−1 is the most affected by meso -aryl substituents, undergoing progressive destabilization as the number of meso -aryl groups is increased. The availability of chlorins with 0-4 distinct meso -aryl substituents provides the individual stepping-stones to bridge the known unsubstituted chlorin and the meso -tetraarylchlorins.}, number={12}, journal={Photochemical & Photobiological Sciences}, publisher={Royal Society of Chemistry (RSC)}, author={Aravindu, Kunche and Kim, Han-Je and Taniguchi, Masahiko and Dilbeck, Preston L. and Diers, James R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2013}, pages={2089} } @article{reddy_lubian_pavan_kim_yang_holten_lindsey_2013, title={Synthetic bacteriochlorins with integral spiro-piperidine motifs}, volume={37}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/C3NJ41161C}, DOI={10.1039/C3NJ41161C}, abstractNote={A new molecular design incorporates a spiro-piperidine unit in each pyrroline ring of synthetic bacteriochlorins, thereby (1) replacing the previous geminal dimethyl group with a functionally equivalent motif to suppress adventitious dehydrogenation, (2) enabling tailoring of the bacteriochlorin by nitrogen derivatization, and (3) leaving the β-pyrrolic positions available for introduction of auxochromes to tune the spectral properties. Conversion of an N-protected 4-piperidone to the N-protected α,β-unsaturated ketone, Michael reaction with 4-(ethoxycarbonyl)-3-ethyl-2-(2-nitroethyl)pyrrole, and subsequent reductive cyclization provided the spiro-piperidine-1-methyldihydrodipyrrin. Treatment with SeO2 followed by trimethyl orthoformate under acid catalysis converted the 1-methyl group to a 1-(1,1-dimethoxymethyl) motif. Self-condensation of the resulting spiro-piperidine-dihydrodipyrrin-acetal afforded the 5-methoxy- or 5-unsubstituted bacteriochlorin, each bearing two spiro-piperidine units. The spiro-piperidine units were derivatized at the nitrogens by methylation, sulfonylation, acylation, or quaternization; the latter with methyl iodide afforded two dicationic, hydrophilic bacteriochlorins. Altogether, eight spiro-piperidine-bacteriochlorins were prepared. Spectroscopic characterization was carried out in DMF (and in water for the quaternized, 5-methoxybacteriochlorin). Compared to the 5-unsubstituted analogue, the quaternized, 5-methoxybacteriochlorin has in DMF a shorter wavelength of the intense near-infrared absorption band (733 vs. 752 nm) and fluorescence band (739 vs. 760 nm), modestly greater fluorescence yield (0.15 vs. 0.08) and modestly longer lifetime of the lowest singlet excited state (4.7 vs. 3.3 ns). In general, the spiro-piperidinyl moiety does not significantly alter the rate constants or yields of the decay pathways (fluorescence, intersystem crossing, internal conversion) of the lowest singlet excited state of the bacteriochlorin. Taken together, the results describe a new molecular design for tailoring the polarity of near-infrared absorbers.}, number={4}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Reddy, Kanumuri Ramesh and Lubian, Elisa and Pavan, M. Phani and Kim, Han-Je and Yang, Eunkyung and Holten, Dewey and Lindsey, Jonathan S.}, year={2013}, pages={1157} } @article{taniguchi_soares_chandrashaker_lindsey_2012, title={A tandem combinatorial model for the prebiogenesis of diverse tetrapyrrole macrocycles}, volume={36}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/c2nj21050a}, DOI={10.1039/c2nj21050a}, abstractNote={The extant biosynthesis of tetrapyrrole macrocycles has been considered a paradigm for the prebiotic formation of such molecules, yet only a few analogous non-enzymic reactions along the overall process have been demonstrated. In a prior study, the aqueous non-enzymic reaction of a dione and an aminoketone (δ-aminolevulinic acid) afforded uroporphyrinogen, Nature's last universal precursor to all extant tetrapyrroles. Here, in one flask the non-enzymic combinatorial reaction of two diones (substituents = acetic acid and methyl) and two aminoketones (substituents = propionic acid and ethyl) yields four pyrroles, which upon subsequent combinatorial reaction afford a distribution of porphyrinogens. A software program for virtual library generation predicts 538 porphyrinogens from this [2 × 2] reaction (owing to combinations and permutations) of which there are 25 sets of isomers based on condensed formulas of substituents. The collection spans the entire range of polarity enabled by the biosynthesis including uro- (number of carboxylic acids = 8), copro- (4), meso- (2), and etio-porphyrinogen (0). The first two are successive intermediates in the extant biosynthesis, the latter two resemble in polarity the advanced biosynthetic products protoporphyrin and chlorophyll. Upon consideration of substituent patterns, the porphyrins (obtained by oxidation of the porphyrinogens) can be grouped into one of four polarity categories (predicted percentage): hydrophilic (0.4%), uncertain (83.6%), amphiphilic (15.6%), and hydrophobic (0.4%). HPLC and mass spectrometry data are consistent with expectations to the limit of analytical capabilities. Thus, in terms of the polarity of the tetrapyrrole macrocycles formed, an all-at-once non-enzymic combinatorial process recapitulates features of the stepwise biosynthetic pathway.}, number={4}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Taniguchi, Masahiko and Soares, Ana R. M. and Chandrashaker, Vanampally and Lindsey, Jonathan S.}, year={2012}, pages={1057} } @article{springer_parkes-loach_reddy_krayer_jiao_lee_niedzwiedzki_harris_kirmaier_bocian_et al._2012, title={Biohybrid Photosynthetic Antenna Complexes for Enhanced Light-Harvesting}, volume={134}, ISSN={["1520-5126"]}, DOI={10.1021/ja207390y}, abstractNote={Biohybrid antenna systems have been constructed that contain synthetic chromophores attached to 31mer analogues of the bacterial photosynthetic core light-harvesting (LH1) β-polypeptide. The peptides are engineered with a Cys site for bioconjugation with maleimide-terminated chromophores, which include synthetic bacteriochlorins (BC1, BC2) with strong near-infrared absorption and commercial dyes Oregon green (OGR) and rhodamine red (RR) with strong absorption in the blue-green to yellow-orange regions. The peptides place the Cys 14 (or 6) residues before a native His site that binds bacteriochlorophyll a (BChl-a) and, like the native LH proteins, have high helical content as probed by single-reflection IR spectroscopy. The His residue associates with BChl-a as in the native LH1 β-polypeptide to form dimeric ββ-subunit complexes [31mer(-14Cys)X/BChl](2), where X is one of the synthetic chromophores. The native-like BChl-a dimer has Q(y) absorption at 820 nm and serves as the acceptor for energy from light absorbed by the appended synthetic chromophore. The energy-transfer characteristics of biohybrid complexes have been characterized by steady-state and time-resolved fluorescence and absorption measurements. The quantum yields of energy transfer from a synthetic chromophore located 14 residues from the BChl-coordinating His site are as follows: OGR (0.30) < RR (0.60) < BC2 (0.90). Oligomeric assemblies of the subunit complexes [31mer(-14Cys)X/BChl](n) are accompanied by a bathochromic shift of the Q(y) absorption of the BChl-a oligomer as far as the 850-nm position found in cyclic native photosynthetic LH2 complexes. Room-temperature stabilized oligomeric biohybrids have energy-transfer quantum yields comparable to those of the dimeric subunit complexes as follows: OGR (0.20) < RR (0.80) < BC1 (0.90). Thus, the new biohybrid antennas retain the energy-transfer and self-assembly characteristics of the native antenna complexes, offer enhanced coverage of the solar spectrum, and illustrate a versatile paradigm for the construction of artificial LH systems.}, number={10}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Springer, Joseph W. and Parkes-Loach, Pamela S. and Reddy, Kanumuri Ramesh and Krayer, Michael and Jiao, Jieying and Lee, Gregory M. and Niedzwiedzki, Dariusz M. and Harris, Michelle A. and Kirmaier, Christine and Bocian, David F. and et al.}, year={2012}, month={Mar}, pages={4589–4599} } @article{chandrashaker_taniguchi_ptaszek_lindsey_2012, title={Competing Knorr and Fischer-Fink pathways to pyrroles in neutral aqueous solution}, volume={68}, ISSN={["0040-4020"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84863630235&partnerID=MN8TOARS}, DOI={10.1016/j.tet.2012.05.080}, abstractNote={Abstract A proposed chemical model for the prebiogenesis of tetrapyrrole macrocycles relies on the condensation of a 3-alkyl-substituted 2,4-diketone and an α-aminoketone to form a pyrrole equipped for subsequent self-condensation leading to porphyrinogens. The condensation of acyclic reactants can proceed via competing Knorr (desired) and Fischer–Fink (undesired) pathways. Here, the Knorr and Fischer–Fink pathways are quantitated using (1) analogues of those in the proposed prebiotic route wherein the resulting pyrroles are blocked from subsequent condensation, and (2) a set of internal standards for quantitation of crude reaction mixtures by 1H NMR spectroscopy following extraction into CS2. The reaction of 1-amino-2-butanone and 3-methyl-2,4-pentanedione at 60 °C in aqueous solution at pH 7 for 24 h afforded the Knorr pyrrole and Fischer–Fink pyrrole in yields of 48% and 7%, respectively. The reaction in hot aqueous acid (pH 4.6, reflux, 30 min) afforded the Knorr pyrrole in diminished yield (22%) relative to that of the Fischer–Fink pyrrole (11%). The Knorr pyrrole (4-ethyl-2,3-dimethylpyrrole) is evanescent whereas the Fischer–Fink pyrrole (2,3,4-trimethyl-5-propanoylpyrrole) is quite stable; hence, rapid analysis of the reaction mixture (vs workup and isolation) is essential for accurate analysis.}, number={34}, journal={TETRAHEDRON}, publisher={Elsevier BV}, author={Chandrashaker, Vanampally and Taniguchi, Masahiko and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2012}, month={Aug}, pages={6957–6967} } @article{taniguchi_lindsey_2012, title={Diversity, isomer composition, and design of combinatorial libraries of tetrapyrrole macrocycles}, volume={16}, ISSN={["1088-4246"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84860487739&partnerID=MN8TOARS}, DOI={10.1142/s1088424612004628}, abstractNote={ Combinatorial libraries of substituted tetrapyrrole macrocycles, which can now be prepared via a variety of approaches, typically are rich in isomers. Terminology for describing such isomers (due to distinct patterns of peripheral substituents) is delineated in several illustrative examples. A hierarchical relationship exists of molecular formula, condensed formula(s) of substituents, set(s) of pyrrole collocates (conveying each pair of β-pyrrolic substituents), and isomers of substituted tetrapyrrole macrocycles. Isomers with identical pyrrole collocate sets can arise owing to distinct positions or orientations of the (homo- or hetero-substituted) pyrrolic units in a macrocycle. Consideration of a handful of virtual combinatorial libraries illustrates tradeoffs of library size, chemical richness, and isomeric content. As one example, octa-derivatization of a tetrapyrrole scaffold with eight reactants A–H affords 2,099,728 members (99.7% isomers, 82,251 pyrrole collocate sets, and 6,435 condensed formulas) whereas the reversible self-condensation of four pyrroles that bear the same eight entities (AB, CD, EF, GH) affords 538 members (93.5% isomers, 35 pyrrole collocate sets, and 35 condensed formulas). Derivatization affords all combinations and permutations whereas self-condensation of substituted pyrroles carries collocational restrictions. Understanding such tradeoffs and the structural origin of isomerism are important aspects in the design of tetrapyrrole combinatorial libraries. }, number={1}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, publisher={World Scientific Pub Co Pte Lt}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2012}, month={Jan}, pages={1–13} } @article{hondros_aravindu_diers_holten_lindsey_bocian_2012, title={Effects of Linker Torsional Constraints on the Rate of Ground-State Hole Transfer in Porphyrin Dyads}, volume={51}, ISSN={["0020-1669"]}, DOI={10.1021/ic301613k}, abstractNote={Understanding hole/electron-transfer processes among interacting constituents of multicomponent molecular architectures is central to the fields of artificial photosynthesis and molecular electronics. Herein, we utilize a recently demonstrated (203)Tl/(205)Tl hyperfine "clocking" strategy to probe the rate of hole/electron transfer in the monocations of a series of three thallium-chelated porphyrin dyads, designated Tl(2)-U, Tl(2)-M, and Tl(2)-B, that are linked via diarylethynes wherein the number of ortho-dimethyl substituents on the aryl group of the linker systematically increases (none, one, and two, respectively). Variable-temperature (160-340 K) EPR studies on the monocations of the three dyads were used to examine the thermal activation behavior of the hole/electron-transfer process and reveal the following: (1) Hole/electron transfer at room temperature (295 K) slows as torsional constraints are added to the diarylethyne linker [k(Tl(2)-U) > k(Tl(2)-M) > k(Tl(2)-B)], with rate constants that correspond to time constants in the 2-5 ns regime. (2) As the temperature decreases, the hole/electron-transfer rates for the monocations of the three types of dyads converge and then cross over. At the lowest temperatures examined (160-170 K), the trend in the hole/electron-transfer rates is essentially reversed [k(Tl(2)-B) > k(Tl(2)-M) ~ k(Tl(2)-U)]. The trends in the temperature dependence of hole/electron-transfer among the three dyads are consistent with torsional motions of the aryl rings of the linker providing for thermal activation of the process at higher temperatures in the case of the less torsionally constrained dyads, Tl(2)-U and Tl(2)-M. In the case of the most torsionally constrained dyad, Tl(2)-B, the hole/electron-transfer process is activationless at all temperatures studied. The reversal in rates of hole/electron transfer among the three dyads at low temperature is qualitatively explained by the results of density functional theory calculations, which predict that static electronic factors could dominate the hole/electron-transfer process when torsional dynamics are thermally diminished.}, number={20}, journal={INORGANIC CHEMISTRY}, author={Hondros, Christopher J. and Aravindu, Kunche and Diers, James R. and Holten, Dewey and Lindsey, Jonathan S. and Bocian, David F.}, year={2012}, month={Oct}, pages={11076–11086} } @article{springer_faries_diers_muthiah_mass_kee_kirmaier_lindsey_bocian_holten_2012, title={Effects of Substituents on Synthetic Analogs of Chlorophylls. Part 3: The Distinctive Impact of Auxochromes at the 7-versus 3-Positions}, volume={88}, ISSN={["1751-1097"]}, DOI={10.1111/j.1751-1097.2012.01083.x}, abstractNote={AbstractAssessing the effects of substituents on the spectra of chlorophylls is essential for gaining a deep understanding of photosynthetic processes. Chlorophyll a and b differ solely in the nature of the 7‐substituent (methyl versus formyl), whereas chlorophyll a and d differ solely in the 3‐substituent (vinyl versus formyl), yet have distinct long‐wavelength absorption maxima: 665 (a) 646 (b) and 692 nm (d). Herein, the spectra, singlet excited‐state decay characteristics, and results from DFT calculations are examined for synthetic chlorins and 131‐oxophorbines that contain ethynyl, acetyl, formyl and other groups at the 3‐, 7‐ and/or 13‐positions. Substituent effects on the absorption spectra are well accounted for using Gouterman’s four‐orbital model. Key findings are that (1) the dramatic difference in auxochromic effects of a given substituent at the 7‐ versus3‐ or 13‐positions primarily derives from relative effects on the LUMO+1 and LUMO; (2) formyl at the 7‐ or 8‐position effectively “porphyrinizes” the chlorin and (3) the substituent effect increases in the order of vinyl < ethynyl < acetyl < formyl. Thus, the spectral properties are governed by an intricate interplay of electronic effects of substituents at particular sites on the four frontier MOs of the chlorin macrocycle.}, number={3}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Springer, Joseph W. and Faries, Kaitlyn M. and Diers, James R. and Muthiah, Chinnasamy and Mass, Olga and Kee, Hooi Ling and Kirmaier, Christine and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2012}, pages={651–674} } @article{yang_diers_huang_hamblin_lindsey_bocian_holten_2013, title={Molecular Electronic Tuning of Photosensitizers to Enhance Photodynamic Therapy: Synthetic Dicyanobacteriochlorins as a Case Study}, volume={89}, ISSN={["1751-1097"]}, DOI={10.1111/php.12021}, abstractNote={AbstractPhotophysical, photostability, electrochemical and molecular‐orbital characteristics are analyzed for a set of stable dicyanobacteriochlorins that are promising photosensitizers for photodynamic therapy (PDT). The bacteriochlorins are the parent compound (BC), dicyano derivative (NC)2BC and corresponding zinc (NC)2BC‐Zn and palladium chelate (NC)2BC‐Pd. The order of PDT activity against HeLa human cancer cells in vitro is (NC)2BC‐Pd > (NC)2BC > (NC)2BC‐Zn ≈ BC. The near‐infrared absorption feature of each dicyanobacteriochlorin is bathochromically shifted 35–50 nm (748–763 nm) from that for BC (713 nm). Intersystem crossing to the PDT‐active triplet excited state is essentially quantitative for (NC)2BC‐Pd. Phosphorescence from (NC)2BC‐Pd occurs at 1122 nm (1.1 eV). This value and the measured ground‐state redox potentials fix the triplet excited‐state redox properties, which underpin PDT activity via Type‐1 (electron transfer) pathways. A perhaps counterintuitive (but readily explicable) result is that of the three dicyanobacteriochlorins, the photosensitizer with the shortest triplet lifetime (7 μs), (NC)2BC‐Pd has the highest activity. Photostabilities of the dicyanobacteriochlorins and other bacteriochlorins studied recently are investigated and discussed in terms of four phenomena: aggregation, reduction, oxidation and chemical reaction. Collectively, the results and analysis provide fundamental insights concerning the molecular design of PDT agents.}, number={3}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Yang, Eunkyung and Diers, James R. and Huang, Ying-Ying and Hamblin, Michael R. and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2013}, pages={605–618} } @article{soares_taniguchi_chandrashaker_lindsey_2012, title={Primordial oil slick and the formation of hydrophobic tetrapyrrole macrocycles}, volume={12}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84868383598&partnerID=MN8TOARS}, DOI={10.1089/ast.2012.0857}, abstractNote={The functional end products of the extant biosynthesis of tetrapyrrole macrocycles in photosynthetic organisms are hydrophobic: chlorophylls and bacteriochlorophylls. A model for the possible prebiogenesis of hydrophobic analogues of nature's photosynthetic pigments was investigated by reaction of acyclic reactants in five media: aqueous solution (pH 7, 60°C, 24 h); aqueous solution containing 0.1 M decanoic acid (which forms a turbid suspension of vesicles); or aqueous solution accompanied by dodecane, mesitylene, or a five-component organic mixture (each of which forms a phase-separated organic layer). The organic mixture was composed of equimolar quantities of decanoic acid, dodecane, mesitylene, naphthalene, and pentyl acetate. The reaction of 1,5-dimethoxy-3-methylpentan-2,4-dione and 1-aminobutan-2-one to give etioporphyrinogens was enhanced in the presence of decanoic acid, affording (following chemical oxidation) etioporphyrins (tetraethyltetramethylporphyrins) in yields of 1.4-10.8% across the concentration range of 3.75-120 mM. The yield of etioporphyrins was greater in the presence of the five-component organic mixture (6.6% at 120 mM) versus that with dodecane or mesitylene (2.1% or 2.9%, respectively). The reaction in aqueous solution with no added oil-slick constituents resulted in phase separation-where the organic reactants themselves form an upper organic layer-and the yield of etioporphyrins was 0.5-2.6%. Analogous reactions leading to uroporphyrins (hydrophilic, eight carboxylic acids) or coproporphyrins (four carboxylic acids) were unaffected by the presence of decanoic acid or dodecane, and all yields were at most ∼2% or ∼8%, respectively. Taken together, the results indicate a facile means for the formation of highly hydrophobic constituents of potential value for prebiotic photosynthesis.}, number={11}, journal={Astrobiology}, publisher={Mary Ann Liebert Inc}, author={Soares, A. R. M. and Taniguchi, M. and Chandrashaker, V. and Lindsey, Jonathan}, year={2012}, pages={1055–1068} } @article{soares_taniguchi_chandrashaker_lindsey_2012, title={Self-organization of tetrapyrrole constituents to give a photoactive protocell}, volume={3}, ISSN={2041-6520 2041-6539}, url={http://dx.doi.org/10.1039/c2sc01120d}, DOI={10.1039/c2sc01120d}, abstractNote={A tandem combinatorial reaction of four acyclic, colorless compounds (two α-aminoketones and two diones; one polar and one nonpolar for each) in aqueous solution (30 mM each, 60 °C, pH 7, 24 h) containing lipid vesicles and with or without quinones and solar illumination affords a distribution of up to 538 porphyrins in 1.6–3.9% overall yield. The reactions leading to the porphyrins can occur in either or both the aqueous phase and the hydrophobic membrane of the vesicles. The porphyrins encompass a broad range of polarity and partition in the aqueous-lipid medium. Two fractions obtained by size-exclusion chromatography include porphyrins associated with the lipid vesicles and porphyrins in the aqueous phase. The porphyrins in both phases are photoactive as demonstrated by fluorescence quantum yield measurements (Φf ∼ 0.07–0.08) and by the Krasnovsky reaction (a photosynthetic-like process). The constituents of the Krasnovsky reaction employed here are methyl red, ascorbic acid, and 2,6-dichlorophenolindophenol. Illumination of the two porphyrin-containing samples (aqueous phase or vesicles) in the presence of the Krasnovsky constituents results in the reduction of methyl red and oxidation of ascorbic acid. Thus, the overall process transforms a colorless aqueous suspension via four stages (two combinatorial reactions, oxidation, physical partitioning) to photoactive porphyrins in distinct venues. The process may provide a model for the origin of pigments that enable proto-photosynthesis.}, number={6}, journal={Chemical Science}, publisher={Royal Society of Chemistry (RSC)}, author={Soares, Ana R. M. and Taniguchi, Masahiko and Chandrashaker, Vanampally and Lindsey, Jonathan S.}, year={2012}, pages={1963} } @article{huang_balasubramanian_yang_luo_diers_bocian_lindsey_holten_hamblin_2012, title={Stable Synthetic Bacteriochlorins for Photodynamic Therapy: Role of Dicyano Peripheral Groups, Central Metal Substitution (2H, Zn, Pd), and Cremophor EL Delivery}, volume={7}, ISSN={1860-7179}, url={http://dx.doi.org/10.1002/cmdc.201200351}, DOI={10.1002/cmdc.201200351}, abstractNote={AbstractA series of four stable synthetic bacteriochlorins was tested in vitro in HeLa cells for their potential in photodynamic therapy (PDT). The parent bacteriochlorin (BC), dicyano derivative (NC)2BC and corresponding zinc chelate (NC)2BC–Zn and palladium chelate (NC)2BC–Pd were studied. Direct dilution of a solution of bacteriochlorin in an organic solvent (N,N‐dimethylacetamide) into serum‐containing medium was compared with the dilution of bacteriochlorin in Cremophor EL (CrEL; polyoxyethylene glycerol triricinoleate) micelles into the same medium. CrEL generally reduced aggregation (as indicated by absorption and fluorescence) and increased activity up to tenfold (depending on bacteriochlorin), although it decreased cellular uptake. The order of PDT activity against HeLa human cancer cells after 24 h incubation and illumination with 10 J cm−2 of near‐infrared (NIR) light is (NC)2BC–Pd (LD50=25 nM) > (NC)2BC > (NC)2BC–Zn ≈ BC. Subcellular localization was determined to be in the endoplasmic reticulum, mitochondria and lysosomes, depending on the bacteriochlorin. (NC)2BC–Pd showed PDT‐mediated damage to mitochondria and lysosomes, and the greatest production of hydroxyl radicals as determined using a hydroxyphenylfluorescein probe. The incorporation of cyano substituents provides an excellent motif for the enhancement of the photoactivity and photostability of bacteriochlorins as PDT photosensitizers.}, number={12}, journal={ChemMedChem}, publisher={Wiley}, author={Huang, Ying-Ying and Balasubramanian, Thiagarajan and Yang, Eunkyung and Luo, Dianzhong and Diers, James R. and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey and Hamblin, Michael R.}, year={2012}, month={Oct}, pages={2155–2167} } @article{chen_sun_fan_taniguchi_mcdowell_yang_diers_bocian_holten_lindsey_2012, title={Synthesis and Physicochemical Properties of Metallobacteriochlorins}, volume={51}, ISSN={["1520-510X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84865712494&partnerID=MN8TOARS}, DOI={10.1021/ic301262k}, abstractNote={Access to metallobacteriochlorins is essential for investigation of a wide variety of fundamental photochemical processes, yet relatively few synthetic metallobacteriochlorins have been prepared. Members of a set of synthetic bacteriochlorins bearing 0-4 carbonyl groups (1, 2, or 4 carboethoxy substituents, or an annulated imide moiety) were examined under two conditions: (i) standard conditions for zincation of porphyrins [Zn(OAc)(2)·2H(2)O in N,N-dimethylformamide (DMF) at 60-80 °C], and (ii) treatment in tetrahydrofuran (THF) with a strong base [e.g., NaH or lithium diisopropylamide (LDA)] followed by a metal reagent MX(n). Zincation of bacteriochlorins that bear 2-4 carbonyl groups proceeded under the former method whereas those with 0-2 carbonyl groups proceeded with NaH or LDA/THF followed by Zn(OTf)(2). The scope of metalation (via NaH or LDA in THF) is as follows: (a) for bacteriochlorins that bear two electron-releasing aryl groups, M = Cu, Zn, Pd, and InCl (but not Mg, Al, Ni, Sn, or Au); (b) for bacteriochlorins that bear two carboethoxy groups, M = Ni, Cu, Zn, Pd, Cd, InCl, and Sn (but not Mg, Al, or Au); and (c) a bacteriochlorin with four carboethoxy groups was metalated with Mg (other metals were not examined). Altogether, 15 metallobacteriochlorins were isolated and characterized. Single-crystal X-ray analysis of 8,8,18,18-tetramethylbacteriochlorin reveals the core geometry provided by the four nitrogen atoms is rectangular; the difference in length of the two sides is ∼0.08 Å. Electronic characteristics of (metal-free) bacteriochlorins were probed through electrochemical measurements along with density functional theory calculation of the energies of the frontier molecular orbitals. The photophysical properties (fluorescence yields, triplet yields, singlet and triplet excited-state lifetimes) of the zinc bacteriochlorins are generally similar to those of the metal-free analogues, and to those of the native chromophores bacteriochlorophyll a and bacteriopheophytin a. The availability of diverse metallobacteriochlorins should prove useful in a variety of fundamental photochemical studies and applications.}, number={17}, journal={INORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Chen, Chih-Yuan and Sun, Erjun and Fan, Dazhong and Taniguchi, Masahiko and McDowell, Brian E. and Yang, Eunkyung and Diers, James R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2012}, month={Sep}, pages={9443–9464} } @article{sharma_krayer_sperandio_huang_huang_holten_lindsey_hamblin_2013, title={Synthesis and evaluation of cationic bacteriochlorin amphiphiles with effective in vitro photodynamic activity against cancer cells at low nanomolar concentration}, volume={17}, ISSN={["1099-1409"]}, DOI={10.1142/s108842461250126x}, abstractNote={ Bacteriochlorins are attractive candidates as photosensitizers for photodynamic therapy (PDT) due to their intense absorption in the near-infrared (NIR) region of the spectrum where light transmission through tissue is maximal. Many naturally occurring bacteriochlorins are inherently unstable due to adventitious atmospheric oxidation. A de novo synthesis affords bacteriochlorins that contain a geminal dimethyl group in each reduced pyrrole ring to increase stability against oxidation. Here, three new synthetic bacteriochlorins, each bearing a single side-chain containing one or two positive charges, were investigated for their in vitro PDT activity against HeLa human cancer cells. All bacteriochlorins were active at low nanomolar concentration when activated with NIR light; those bearing a single positive charge exhibited faster uptake and higher activity. The bacteriochlorins were localized in mitochondria, lysosomes and endoplasmic reticulum as shown by organelle specific fluorescent probes. Cell death was via apoptosis as shown by cell morphology and nuclear condensation. Taken together, the results show the importance of appropriate peripheral groups about a photosensitizer for effective PDT applications. }, number={1-2}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Sharma, Sulbha K. and Krayer, Michael and Sperandio, Felipe F. and Huang, Liyi and Huang, Ying-Ying and Holten, Dewey and Lindsey, Jonathan S. and Hamblin, Michael R.}, year={2013}, pages={73–85} } @article{mass_lindsey_2011, title={A trans-AB-Bacteriochlorin Building Block}, volume={76}, ISSN={["1520-6904"]}, DOI={10.1021/jo201967k}, abstractNote={Synthetic bacteriochlorins are of interest for fundamental studies in photochemistry because of their strong absorption in the near-infrared spectral region and close similarity with natural bacteriochlorophylls. A de novo route to 5-methoxybacteriochlorins entails self-condensation of a dihydrodipyrrin-acetal, which in turn is prepared from a 2-(2-nitroethyl)pyrrole species and an α,β-unsaturated ketone-acetal (e.g., 1,1-dimethoxy-4-methylpent-3-en-2-one). Here, four new results are reported concerning the synthesis of substituted bacteriochlorins. First, a new, scalable route to 1,1-dimethoxy-4-methylpent-3-en-2-one removes a significant previous impediment to the overall route. Second, the new route was employed to gain access to new α,β-unsaturated ketones and corresponding dihydrodipyrrins bearing alternative substituents in place of the dimethoxy unit. Third, a dihydrodipyrrin bearing a 1,3-dioxolan-2-yl moiety afforded the bacteriochlorin (30% yield) containing a 2-hydroxyethoxy substituent at the 5-position. Fourth, subsequent bromination proceeded regioselectively at the 15-position to give a trans-(5,15)-AB-bacteriochlorin building block. The linear 5,15-substitution pattern is attractive for a number of molecular designs. The results taken together afford deeper understanding of the scope and limitations of the de novo route and also advance the capabilities for tailoring synthetic bacteriochlorins.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Mass, Olga and Lindsey, Jonathan S.}, year={2011}, month={Nov}, pages={9478–9487} } @article{krayer_yang_diers_bocian_holten_lindsey_2011, title={De novo synthesis and photophysical characterization of annulated bacteriochlorins. Mimicking and extending the properties of bacteriochlorophylls}, volume={35}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/c0nj00771d}, DOI={10.1039/c0nj00771d}, abstractNote={Bacteriochlorophylls contain the bacteriochlorin chromophore and a fifth, five-membered oxopentano ring that encompasses positions 13–15 known as the “isocyclic” ring E. Such bacterio-131-oxophorbines have heretofore only been available in the naturally occurring compounds, and analogues bearing six-membered rings have only been available by derivatization of bacteriochlorophylls. A de novo route to synthetic bacteriochlorins, which bear a geminal dimethyl group in each pyrroline ring, has been extended to gain access to a bacterio-131-oxophorbine and bacteriochlorin-13,15-dicarboximides. The route relies on acid-catalyzed condensation of a dihydrodipyrrin-acetal to form the bacteriochlorin, which then is subjected to regioselective 15-bromination. Pd-mediated cyclization of the 15-bromobacteriochlorin bearing a 13-acetyl group (intramolecular α-arylation) or 13-ethoxycarbonyl group (carbamoylation and intramolecular imidation) gives the bacterio-131-oxophorbine or bacteriochlorin-13,15-dicarboximide, respectively. The resulting macrocycles exhibit absorption in the near-infrared spectral region (733–818 nm), which extends the spectral coverage beyond that obtained previously with synthetic bacteriochlorins that lack a fifth ring. The macrocycles also exhibit excited singlet-state lifetimes (1.9–4.6 ns) comparable to or longer than those of natural photosynthetic pigments. Density functional theory calculations predict that the bathochromically shifted absorption is primarily due to lowering of the energy of the lowest unoccupied molecular orbital. The new route complements existing semisynthetic routes and should enable fundamental spectroscopic studies and diverse photochemical applications.}, number={3}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Krayer, Michael and Yang, Eunkyung and Diers, James R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2011}, pages={587} } @article{mass_pandithavidana_ptaszek_santiago_springer_jiao_tang_kirmaier_bocian_holten_et al._2011, title={De novo synthesis and properties of analogues of the self-assembling chlorosomal bacteriochlorophylls}, volume={35}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/c1nj20611g}, DOI={10.1039/c1nj20611g}, abstractNote={Natural photosynthetic pigments bacteriochlorophyllsc, d and e in green bacteria undergo self-assembly to create an organized antenna system known as the chlorosome, which collects photons and funnels the resulting excitation energy toward the reaction centers. Mimicry of chlorosome function is a central problem in supramolecular chemistry and artificial photosynthesis, and may have relevance for the design of photosynthesis-inspired solar cells. The main challenge in preparing artificial chlorosomes remains the synthesis of the appropriate pigment (chlorin) equipped with a set of functional groups suitable to direct the assembly and assure efficient energy transfer. Prior approaches have entailed derivatization of porphyrins or semisynthesis beginning with chlorophylls. This paper reports a third approach, the de novo synthesis of macrocycles that contain the same hydrocarbon skeleton as chlorosomal bacteriochlorophylls. The synthesis here of Zn(II) 3-(1-hydroxyethyl)-10-aryl-131-oxophorbines (the aryl group consists of phenyl, mesityl, or pentafluorophenyl) entails selective bromination of a 3,13-diacetyl-10-arylchlorin, palladium-catalyzed 131-oxophorbine formation, and selective reduction of the 3-acetyl group using BH3·tBuNH2. Each macrocycle contains a geminal dimethyl group in the pyrroline ring to provide stability toward adventitious dehydrogenation. A Zn(II) 7-(1-hydroxyethyl)-10-phenyl-17-oxochlorin also has been prepared. Altogether, 30 new hydroporphyrins were synthesized. The UV-Vis absorption spectra of the new chlorosomal bacteriochlorophyll mimics reveal a bathochromic shift of ∼1800 cm−1 of the Qy band in nonpolar solvent, indicating extensive assembly in solution. The Zn(II) 3-(1-hydroxyethyl)-10-aryl-131-oxophorbines differ in the propensity to form assemblies based on the 10-substituent in the following order: mesityl}, number={11}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Mass, Olga and Pandithavidana, Dinesh R. and Ptaszek, Marcin and Santiago, Koraliz and Springer, Joseph W. and Jiao, Jieying and Tang, Qun and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and et al.}, year={2011}, pages={2671} } @article{lindsey_thamyongkit_taniguchi_bocian_2011, title={Encoding isotopic watermarks in molecular electronic materials as an anti-counterfeiting strategy. Application to porphyrins for information storage}, volume={15}, ISSN={["1099-1409"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80051761959&partnerID=MN8TOARS}, DOI={10.1142/s1088424611003458}, abstractNote={An approach for information storage employs tetrapyrrole macrocycles as charge-storage elements attached to a (semi)conductor in hybrid chips. Anti-counterfeiting measures must cohere with the tiny amounts of such electroactive material and strict constraints on composition in chips; accordingly, the incorporation of typical anti-counterfeiting taggants or microcarriers is precluded. The provenance of the tetrapyrroles can be established through the use of isotopic substitution integral to the macrocycle. The isotopic substitution can be achieved by rational site-specific incorporation or by combinatorial procedures. The formation of a mixture of such macrocycles with various isotopic composition (isotopically unmodified, isotopologues, isotopomers) provides the molecular equivalent of an indelible printed watermark. Resonance Raman spectroscopic examination can reveal the watermark, but not the underlying molecular and isotopic composition; imaging mass spectrometry can reveal the presence of isotopologues but cannot discriminate among isotopomers. Hence, deciphering the code that encrypts the watermark in an attempt at forgery is expected to be prohibitive. A brief overview is provided of strategies for incorporating isotopes in meso-substituted tetrapyrrole macrocycles.}, number={7-8}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, publisher={World Scientific Pub Co Pte Lt}, author={Lindsey, Jonathan S. and Thamyongkit, Patchanita and Taniguchi, Masahiko and Bocian, David F.}, year={2011}, pages={505–516} } @article{aravindu_krayer_kim_lindsey_2011, title={Facile synthesis of a B,D-tetradehydrocorrin and rearrangement to bacteriochlorins}, volume={35}, ISSN={1144-0546 1369-9261}, url={http://dx.doi.org/10.1039/c1nj20027e}, DOI={10.1039/c1nj20027e}, abstractNote={Tetradehydrocorrins contain an A–D ring junction and a level of saturation intermediate between that of a corrin (characteristic of vitamin B12) and that of a corrole. Self-condensation of a p-tolyl-substituted dihydrodipyrrin-acetal (DHDPA-T) in CH2Cl2 containing Yb(OTf)3 at room temperature afforded the corresponding free base B,D-tetradehydrocorrin (TDC-T) as the sole macrocycle in 77% yield. The presence of a geminal dimethyl group in each of the reduced rings in TDC-T affords stability toward adventitious dehydrogenation. Treatment of TDC-T to acidic conditions results in rearrangement and loss of methanol to give a bacteriochlorin with or without a 5-methoxy substituent; the yield was 56% (5-methoxybacteriochlorin MeOBC-T), 35% (MeOBC-T) or 20% (5-unsubstituted bacteriochlorin HBC-T) with TMSOTf/CH2Cl2, BF3·OEt2/CH3CN or BF3·OEt2/CH2Cl2, respectively. TDC-T undergoes regioselective bromination with NBS to give the 10-bromotetradehydrocorrin in 22% yield. The conversion of the (non-aromatic) tetradehydrocorrin to the (aromatic) bacteriochlorin reflects the relative stability of the two macrocycles and indicates the former may be an intermediate—kinetically trapped or transient depending on catalysis conditions—upon dihydrodipyrrin-acetal self-condensation.}, number={7}, journal={New Journal of Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Aravindu, Kunche and Krayer, Michael and Kim, Han-Je and Lindsey, Jonathan S.}, year={2011}, pages={1376} } @misc{lindsey_bocian_2011, title={Molecules for Charge-Based Information Storage}, volume={44}, ISSN={["1520-4898"]}, DOI={10.1021/ar200107x}, abstractNote={The inexorable drive to miniaturize information storage and processing devices has fueled the dreams of scientists pursuing molecular electronics: researchers in the field envisage exquisitely tailored molecular materials fulfilling the functions now carried out by semiconductors. A bottom-up assembly of such all-molecular devices would complement, if not supplant, the present top-down lithographic procedures of modern semiconductor fabrication. Short of these grand aspirations, a more near-term objective is to construct hybrid architectures wherein molecules are incorporated in semiconductor-based devices. Such a combined approach exploits the advantages of molecules for selected device functions while retaining the well-developed lithographic approaches for fabrication of the overall chip. In this Account, we survey more than a decade of results from our research programs to employ porphyrin molecules as charge-storage elements in hybrid semiconductor-molecular dynamic random access memory. Porphyrins are attractive for a variety of reasons: they meet the stability criteria for use in real-world applications, they are readily prepared and tailored synthetically, they undergo read-write processes at low potential, and they store charge for extended periods (up to minutes) in the absence of applied potential. Porphyrins typically exhibit two cationic redox states. Molecular architectures with greater than two cationic redox states are achieved by combinations of porphyrins in a variety of structures (for example, dyads, wherein the porphyrins have distinct potentials, triple deckers, and dyads of triple deckers). The incorporation of porphyrins in hybrid architectures has also required diverse tethers (alkyl, alkenyl, alkynyl, aryl, and combinations thereof) and attachment groups (alcohol, thiol, selenol, phosphonate, and hydrocarbon) for linkage to a variety of surfaces (Au, Si, SiO(2), TiN, Ge, and so forth). The porphyrins as monolayers exhibit high charge density and are robust to high-temperature excursions (400 °C for 30 min) under inert atmosphere conditions. Even higher charge densities, which are invaluable for device applications, were achieved by in situ formation of porphyrin polymers or by stepwise growth of porphyrin-imide oligomers. The various molecular architectures have been investigated by diverse surface characterization methods, including ellipsometry, atomic force microscopy, FTIR spectroscopy, and X-ray photoelectron spectroscopy, as well as a variety of electrochemical methods. These studies have further revealed that the porphyrin layers are robust under conditions of deposition of a top metal contact. The results to date indicate the superior features of selected molecular architectures for molecular electronics applications. The near-term utilization of such materials depends on further work for appropriate integration in semiconductor-based devices, whereas ultimate adoption may depend on advances that remain far afield, such as the development of fully bottom-up assembly processes.}, number={8}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Lindsey, Jonathan S. and Bocian, David F.}, year={2011}, month={Aug}, pages={638–650} } @article{yang_kirmaier_krayer_taniguchi_kim_diers_bocian_lindsey_holten_2011, title={Photophysical Properties and Electronic Structure of Stable, Tunable Synthetic Bacteriochlorins: Extending the Features of Native Photosynthetic Pigments}, volume={115}, ISSN={["1520-5207"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80052828697&partnerID=MN8TOARS}, DOI={10.1021/jp205258s}, abstractNote={Bacteriochlorins, which are tetrapyrrole macrocycles with two reduced pyrrole rings, are Nature's near-infrared (NIR) absorbers (700-900 nm). The strong absorption in the NIR region renders bacteriochlorins excellent candidates for a variety of applications including solar light harvesting, flow cytometry, molecular imaging, and photodynamic therapy. Natural bacteriochlorins are inherently unstable due to oxidative conversion to the chlorin (one reduced pyrrole ring) or the porphyrin. The natural pigments are also only modestly amenable to synthetic manipulation, owing to a nearly full complement of substituents on the macrocycle. Recently, a new synthetic methodology has afforded access to stable synthetic bacteriochlorins wherein a wide variety of substituents can be appended to the macrocycle at preselected locations. Herein, the spectroscopic and photophysical properties of 33 synthetic bacteriochlorins are investigated. The NIR absorption bands of the chromophores range from ∼700 to ∼820 nm; the lifetimes of the lowest excited singlet state range from ∼2 to ∼6 ns; the fluorescence quantum yields range from ∼0.05 to ∼0.25; and the yield of the lowest triplet excited state is ∼0.5. The spectroscopic/photophysical studies of the bacteriochlorins are accompanied by density functional theory (DFT) calculations that probe the characteristics of the frontier molecular orbitals. The DFT calculations indicate that the impact of substituents on the spectral properties of the molecules derives primarily from effects on the lowest unoccupied molecular orbital. Collectively, the studies show how the palette of synthetic bacteriochlorins extends the properties of the native photosynthetic pigments (bacteriochlorophylls). The studies have also elucidated design principles for tuning the spectral and photophysical characteristics as required for a wide variety of photochemical applications.}, number={37}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, publisher={American Chemical Society (ACS)}, author={Yang, Eunkyung and Kirmaier, Christine and Krayer, Michael and Taniguchi, Masahiko and Kim, Han-Je and Diers, James R. and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2011}, month={Sep}, pages={10801–10816} } @article{krayer_yang_kim_kee_deans_sluder_diers_kirmaier_bocian_holten_et al._2011, title={Synthesis and Photophysical Characterization of Stable Indium Bacteriochlorins}, volume={50}, ISSN={["1520-510X"]}, DOI={10.1021/ic200325d}, abstractNote={Bacteriochlorins have wide potential in photochemistry because of their strong absorption of near-infrared light, yet metallobacteriochlorins traditionally have been accessed with difficulty. Established acid-catalysis conditions [BF(3)·OEt(2) in CH(3)CN or TMSOTf/2,6-di-tert-butylpyridine in CH(2)Cl(2)] for the self-condensation of dihydrodipyrrin-acetals (bearing a geminal dimethyl group in the pyrroline ring) afford stable free base bacteriochlorins. Here, InBr(3) in CH(3)CN at room temperature was found to give directly the corresponding indium bacteriochlorin. Application of the new acid catalysis conditions has afforded four indium bacteriochlorins bearing aryl, alkyl/ester, or no substituents at the β-pyrrolic positions. The indium bacteriochlorins exhibit (i) a long-wavelength absorption band in the 741-782 nm range, which is shifted bathochromically by 22-32 nm versus the analogous free base species, (ii) fluorescence quantum yields (0.011-0.026) and average singlet lifetime (270 ps) diminished by an order of magnitude versus that (0.13-0.25; 4.0 ns) for the free base analogues, and (iii) higher average yield (0.9 versus 0.5) yet shorter average lifetime (30 vs 105 μs) of the lowest triplet excited state compared to the free base compounds. The differences in the excited-state properties of the indium chelates versus free base bacteriochlorins derive primarily from a 30-fold greater rate constant for S(1) → T(1) intersystem crossing, which stems from the heavy-atom effect on spin-orbit coupling. The trends in optical properties of the indium bacteriochlorins versus free base analogues, and the effects of 5-OMe versus 5-H substituents, correlate well with frontier molecular-orbital energies and energy gaps derived from density functional theory calculations. Collectively the synthesis, photophysical properties, and electronic characteristics of the indium bacteriochlorins and free base analogues reported herein should aid in the further design of such chromophores for diverse applications.}, number={10}, journal={INORGANIC CHEMISTRY}, author={Krayer, Michael and Yang, Eunkyung and Kim, Han-Je and Kee, Hooi Ling and Deans, Richard M. and Sluder, Camille E. and Diers, James R. and Kirmaier, Christine and Bocian, David F. and Holten, Dewey and et al.}, year={2011}, month={May}, pages={4607–4618} } @article{lindsey_mass_chen_2011, title={Tapping the near-infrared spectral region with bacteriochlorin arrays}, volume={35}, ISSN={["1144-0546"]}, DOI={10.1039/c0nj00977f}, abstractNote={Bacteriochlorophylls—natural pigments for absorption of near-infrared (NIR) light—underlie light-absorption and energy transduction in photosynthetic bacteria. Capturing and utilizing NIR light is valuable in fields ranging from artificial photosynthesis to photomedicine (photodynamic therapy, imaging, and diagnostics). The desired photochemical features may be best elicited with multicomponent architectures that support efficient excited-state energy and/or electron transfer, yet few such arrays containing bacteriochlorins (the core chromophore of bacteriochlorophylls) are known. This review outlines three synthetic approaches toward bacteriochlorins, surveys all known bacteriochlorin arrays, and compares molecular design strategies for light-harvesting arrays containing bacteriochlorinsversus (the better known) porphyrins.}, number={3}, journal={NEW JOURNAL OF CHEMISTRY}, author={Lindsey, Jonathan S. and Mass, Olga and Chen, Chih-Yuan}, year={2011}, pages={511–516} } @article{taniguchi_du_lindsey_2011, title={Virtual Libraries of Tetrapyrrole Macrocycles. Combinatorics, Isomers, Product Distributions, and Data Mining}, volume={51}, ISSN={["1549-960X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-80053326969&partnerID=MN8TOARS}, DOI={10.1021/ci200240e}, abstractNote={A software program (PorphyrinViLiGe) has been developed to enumerate the type and relative amounts of substituted tetrapyrrole macrocycles in a virtual library formed by one of four different classes of reactions. The classes include (1) 4-fold reaction of n disubstituted heterocycles (e.g., pyrroles or diiminoisoindolines) to form β-substituted porphyrins, β-substituted tetraazaporphyrins, or α- or β-substituted phthalocyanines; (2) combination of m aminoketones and n diones to form m × n pyrroles, which upon 4-fold reaction give β-substituted porphyrins; (3) derivatization of an 8-point tetrapyrrole scaffold with n reagents, and (4) 4-fold reaction of n aldehydes and pyrrole to form meso-substituted porphyrins. The program accommodates variable ratios of reactants, reversible or irreversible reaction (reaction classes 1 and 2), and degenerate modes of formation. Pólya's theorem (for enumeration of cyclic entities) has also been implemented and provides validation for reaction classes 3 and 4. The output includes the number and identity of distinct reaction-accessible substituent combinations, the number and identity of isomers thereof, and the theoretical mass spectrum. Provisions for data mining enable assessment of the number of products having a chosen pattern of substituents. Examples include derivatization of an octa-substituted phthalocyanine with eight reagents to afford a library of 2,099,728 members (yet only 6435 distinct substituent combinations) and reversible reaction of six distinct disubstituted pyrroles to afford 2649 members (yet only 126 distinct substituent combinations). In general, libraries of substituted tetrapyrrole macrocycles occupy a synthetically accessible region of chemical space that is rich in isomers (>99% or 95% for the two examples, respectively).}, number={9}, journal={JOURNAL OF CHEMICAL INFORMATION AND MODELING}, publisher={American Chemical Society (ACS)}, author={Taniguchi, Masahiko and Du, Hai and Lindsey, Jonathan S.}, year={2011}, month={Sep}, pages={2233–2247} } @article{lindsey_chandrashaker_taniguchi_ptaszek_2011, title={Abiotic formation of uroporphyrinogen and coproporphyrinogen from acyclic reactants}, volume={35}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650436322&partnerID=MN8TOARS}, DOI={10.1039/c0nj00716a}, abstractNote={Tetrapyrrole macrocycles (e.g., porphyrins) have long been proposed as key ingredients in the emergence of life, yet plausible routes for forming their essential pyrrole precursor have previously not been identified. Here, the anaerobic reaction of δ-aminolevulinic acid (ALA, 5–240 mM) with 5-methoxy-3-(methoxyacetyl)levulinic acid (1-AcOH, 5–240 mM) in water (pH 5–7) at 25–85 °C for a few hours to a few days affords uroporphyrinogen, which upon chemical oxidation gives uroporphyrin in overall yield of up to 10%. The key intermediate is the α-methoxymethyl-substituted analogue of the pyrrole porphobilinogen (PBG). Reaction of ALA and the decarboxy analogue of 1-AcOH (1-Me) gave coproporphyrinogen (without its biosynthetic precursor uroporphyrinogen as an intermediate); oxidation gave the corresponding coproporphyrin in yields comparable to those for uroporphyrin. In each case a mixture of porphyrin isomers was obtained, consistent with reversible oligopyrromethane formation. The route investigated here differs from the universal extant biosynthetic pathway to tetrapyrrole macrocycles, where uroporphyrinogen (isomer III) – nature's last common precursor to corrins, heme, and chlorophylls – is derived from eight molecules of ALA (via four molecules of PBG). The demonstration of the spontaneous self-organization of eight acyclic molecules to form the porphyrinogen under simple conditions may open the door to the development of a chemical model for the prebiogenesis of tetrapyrrole macrocycles.}, number={1}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Lindsey, Jonathan S. and Chandrashaker, Vanampally and Taniguchi, Masahiko and Ptaszek, Marcin}, year={2011}, pages={65–75} } @article{jiao_taniguchi_lindsey_bocian_2010, title={Activation Energies for Oxidation of Porphyrin Monolayers Anchored to Au(111)}, volume={26}, ISSN={["0743-7463"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957909893&partnerID=MN8TOARS}, DOI={10.1021/la102802n}, abstractNote={The activation energy for the oxidation of porphyrin monolayers anchored to gold surfaces is determined via measurement of the temperature dependence of the electron-transfer rates. The activation energy (1) increases with increasing surface concentration of the porphyrin and (2) is significantly lower (8.1-17 versus 37-49 kJ mol(-1)) when smaller, more mobile counterions (Cl(-) versus PF(6)(-)) are used as the supporting electrolyte. Regardless, the lower activation energies do not result in radically different electron-transfer rates for the different types of counterions owing to compensating entropic effects.}, number={20}, journal={LANGMUIR}, publisher={American Chemical Society (ACS)}, author={Jiao, Jieying and Taniguchi, Masahiko and Lindsey, Jonathan S. and Bocian, David F.}, year={2010}, month={Oct}, pages={15718–15721} } @article{ptaszek_lahaye_krayer_muthiah_lindsey_2010, title={De Novo Synthesis of Long-Wavelength Absorbing Chlorin-13,15-dicarboximides}, volume={75}, ISSN={["1520-6904"]}, DOI={10.1021/jo902649d}, abstractNote={Chlorins bearing a six-membered imide ring spanning positions 13-15, commonly referred to as purpurinimides, exhibit long-wavelength absorption yet have heretofore only been available via semisynthesis from naturally occurring chlorophylls. A concise route to synthetic chlorins, which bear a geminal dimethyl group in the pyrroline ring, has been extended to provide access to chlorin-13,15-dicarboximides. The new route entails (i) synthesis of a 13-bromochlorin, (ii) palladium-catalyzed carbamoylation at the 13-position, (iii) regioselective 15-bromination under acidic conditions, and (iv) one-flask palladium-mediated carbonylation and ring closure to form the imide. In some cases the ring closure reaction afforded the isomeric (and readily separable) chlorin-isoimide in addition to the chlorin-imide. The resulting chlorin-imides and chlorin-isoimides exhibit long-wavelength absorption (679-715 nm) and emission (683-720 nm) in the far-red and near-infrared spectral region. The absorption of the chlorin-(iso)imides fills the spectral window between that of analogous synthetic chlorins and 13(1)-oxophorbines (603-687 nm) and bacteriochlorins (707-792 nm). The synthetic versatility of the de novo route complements the existing semisynthetic route from chlorophylls and should enable fundamental spectroscopic studies and photochemical applications.}, number={5}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Ptaszek, Marcin and Lahaye, Dorothee and Krayer, Michael and Muthiah, Chinnasamy and Lindsey, Jonathan S.}, year={2010}, month={Mar}, pages={1659–1673} } @article{kirmaier_song_yang_schwartz_hindin_diers_loewe_tomizaki_chevalier_ramos_et al._2010, title={Excited-State Photodynamics of Perylene-Porphyrin Dyads 5 Tuning Light-Harvesting Characteristics via Perylene Substituents, Connection Motif, and Three-Dimensional Architecture}, volume={114}, ISSN={["1520-5207"]}, DOI={10.1021/jp910705q}, abstractNote={Seven perylene-porphyrin dyads were examined with the goal of identifying those most suitable for components of light-harvesting systems. The ideal dyad should exhibit strong absorption by the perylene in the green, undergo rapid and efficient excited-state energy transfer from perylene to porphyrin, and avoid electron-transfer quenching of the porphyrin excited state by the perylene in the medium of interest. Four dyads have different perylenes at the p-position of the meso-aryl group on the zinc porphyrin. The most suitable perylene identified in that set was then incorporated at the m- or o-position of the zinc porphyrin, affording two other dyads. An analogue of the o-substituted architecture was prepared in which the zinc porphyrin was replaced with the free base porphyrin. The perylene in each dyad is a monoimide derivative; the perylenes differ in attachment of the linker (either via a diphenylethyne linker at the N-imide or an ethynylphenyl linker at the C9 position) and the number (0-3) of 4-tert-butylphenoxy groups (which increase solubility and slightly alter the electrochemical potentials). In the p-linked dyad, the monophenoxy perylene with an N-imide diphenylethyne linker is superior in providing rapid and essentially quantitative energy transfer from excited perylene to zinc porphyrin with minimal electron-transfer quenching in both toluene and benzonitrile. The dyads with the same perylene at the m- or o-position exhibited similar results except for one case, the o-linked dyad bearing the zinc porphyrin in benzonitrile, where significant excited-state quenching is observed; this phenomenon is facilitated by close spatial approach of the perylene and porphyrin and the associated thermodynamic/kinetic enhancement of the electron-transfer process. Such quenching does not occur with the free base porphyrin because electron transfer is thermodynamically unfavorable even in the polar medium. The p-linked dyad containing a zinc porphyrin attached to a bis(4-tert-butylphenoxy)perylene via an ethynylphenyl linker at the C9 position exhibits ultrafast and quantitative energy transfer in toluene; the same dyad in benzonitrile exhibits ultrafast (<0.5 ps) perylene-to-porphyrin energy transfer, rapid (∼5 ps) porphyrin-to-perylene electron transfer, and fast (∼25 ps) charge recombination to the ground state. Collectively, this study has identified suitable perylene-porphyrin constructs for use in light-harvesting applications.}, number={45}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Kirmaier, Christine and Song, Hee-eun and Yang, Eunkyung and Schwartz, Jennifer K. and Hindin, Eve and Diers, James R. and Loewe, Robert S. and Tomizaki, Kin-ya and Chevalier, Fabien and Ramos, Lavoisier and et al.}, year={2010}, month={Nov}, pages={14249–14264} } @article{krayer_ptaszek_kim_meneely_fan_secor_lindsey_2010, title={Expanded Scope of Synthetic Bacteriochlorins via Improved Acid Catalysis Conditions and Diverse Dihydrodipyrrin-Acetals}, volume={75}, ISSN={["0022-3263"]}, DOI={10.1021/jo9025572}, abstractNote={Bacteriochlorins are attractive candidates for a wide variety of photochemical studies owing to their strong absorption in the near-infrared spectral region. The prior acid-catalysis conditions [BF(3) x O(Et)(2) in CH(3)CN at room temperature] for self-condensation of a dihydrodipyrrin-acetal (bearing a geminal dimethyl group in the pyrroline ring) typically afforded a mixture of three macrocycles: the expected 5-methoxybacteriochlorin (MeOBC-type), a 5-unsubstituted bacteriochlorin (HBC-type), and a free base B,D-tetradehydrocorrin (TDC-type). Here, a broad survey of >20 acids identified four promising acid catalysis conditions of which TMSOTf/2,6-di-tert-butylpyridine in CH(2)Cl(2) at room temperature was most attractive owing to formation of the 5-methoxybacteriochlorin as the sole macrocycle regardless of the pyrrolic substituents in the dihydrodipyrrin-acetal (electron-withdrawing, electron-donating, or no substituent). Eleven new dihydrodipyrrin-acetals were prepared following standard routes. Application of the new acid catalysis conditions has afforded diverse bacteriochlorins (e.g., bearing alkyl/ester, aryl/ester, diester, and no substituents) in a few days from commercially available starting materials. Consideration of the synthetic steps and yields for formation of the dihydrodipyrrin-acetal and bacteriochlorin underpins evaluation of synthetic plans for early installation of bacteriochlorin substituents via the dihydrodipyrrin-acetal versus late installation via derivatization of beta-bromobacteriochlorins. Treatment of the 5-methoxybacteriochlorins with NBS gave regioselective 15-bromination when no pyrrolic substituents were present or when each pyrrole contained two substituents; on the other hand, the presence of a beta-ethoxycarbonyl group caused loss of regioselectivity. The 15 new bacteriochlorins prepared herein exhibit a long-wavelength absorption band in the range 707-759 nm, providing tunable access to the near-infrared region. Taken together, this study expands the scope of available bacteriochlorins for fundamental studies and diverse applications.}, number={4}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Krayer, Michael and Ptaszek, Marcin and Kim, Han-Je and Meneely, Kelly R. and Fan, Dazhong and Secor, Kristen and Lindsey, Jonathan S.}, year={2010}, month={Feb}, pages={1016–1039} } @article{huang_mroz_zhiyentayev_sharma_balasubramanian_ruzie_krayer_fan_borbas_yang_et al._2010, title={In Vitro Photodynamic Therapy and Quantitative Structure-Activity Relationship Studies with Stable Synthetic Near-Infrared-Absorbing Bacteriochlorin Photosensitizers}, volume={53}, ISSN={["1520-4804"]}, DOI={10.1021/jm901908s}, abstractNote={Photodynamic therapy (PDT) is a rapidly developing approach to treating cancer that combines harmless visible and near-infrared light with a nontoxic photoactivatable dye, which upon encounter with molecular oxygen generates the reactive oxygen species that are toxic to cancer cells. Bacteriochlorins are tetrapyrrole compounds with two reduced pyrrole rings in the macrocycle. These molecules are characterized by strong absorption features from 700 to >800 nm, which enable deep penetration into tissue. This report describes testing of 12 new stable synthetic bacteriochlorins for PDT activity. The 12 compounds possess a variety of peripheral substituents and are very potent in killing cancer cells in vitro after illumination. Quantitative structure-activity relationships were derived, and subcellular localization was determined. The most active compounds have both low dark toxicity and high phototoxicity. This combination together with near-infrared absorption gives these bacteriochlorins great potential as photosensitizers for treatment of cancer.}, number={10}, journal={JOURNAL OF MEDICINAL CHEMISTRY}, author={Huang, Ying-Ying and Mroz, Pawel and Zhiyentayev, Timur and Sharma, Sulbha K. and Balasubramanian, Thiagarajan and Ruzie, Christian and Krayer, Michael and Fan, Dazhong and Borbas, K. Eszter and Yang, Eunkyung and et al.}, year={2010}, month={May}, pages={4018–4027} } @article{diers_taniguchi_holten_lindsey_bocian_2010, title={Probing the Rate of Hole Transfer in Oxidized Porphyrin Dyads Using Thallium Hyperfine Clocks}, volume={132}, ISSN={["0002-7863"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77956074080&partnerID=MN8TOARS}, DOI={10.1021/ja105082d}, abstractNote={Understanding hole/electron-transfer processes among interacting constituents of multicomponent molecular architectures is central to the fields of artificial photosynthesis and molecular electronics. One strategy for examining ground-state hole/electron transfer in oxidized tetrapyrrolic arrays entails analysis of the hyperfine interactions observed in the electron paramagnetic resonance (EPR) spectrum of the pi-cation radical. Herein, it is demonstrated that (203)Tl/(205)Tl hyperfine "clocks" are greatly superior to those provided by (1)H, (14)N, or (13)C owing to the fact that the (203)Tl/(205)Tl hyperfine couplings are much larger (15-25 G) than those of the (1)H, (14)N, or (13)C nuclei (1-6 G). The large (203)Tl/(205)Tl hyperfine interactions permit accurate simulations of the EPR spectra and the extraction of specific rates of hole/electron transfer. The (203)Tl/(205)Tl hyperfine clock strategy is applied to a series of seven porphyrin dyads. All of the dyads are joined at a meso position of the porphyrin macrocycle via linkers of a range of lengths and composition (diphenylethyne, diphenylbutadiyne, and (p-phenylene)(n), where n = 1-4); substituents such as mesityl at the nonlinking meso positions are employed to provide organic solubility. The hole/electron-transfer time constants are in the hundreds of picoseconds to sub-10 ns regime, depending on the specific porphyrin and/or linker. Density functional theory calculations on the constituents of the dyads are consistent with the view that the relative energies of the porphyrin versus linker highest occupied molecular orbitals strongly influence the hole/electron-transfer rates. Variable-temperature EPR studies further demonstrate that the hole/electron-transfer process is at best weakly activated (12-15 kJ mol(-1)) at room temperature and somewhat below. At lower temperatures, the process is essentially activationless. The weak activation is attributed to restricted torsional motions of the phenyl rings of the linker. Collectively, the studies provide the physical basis for the rational design of multicomponent architectures for efficient hole/electron transfer.}, number={34}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, publisher={American Chemical Society (ACS)}, author={Diers, James R. and Taniguchi, Masahiko and Holten, Dewey and Lindsey, Jonathan S. and Bocian, David F.}, year={2010}, month={Sep}, pages={12121–12132} } @article{nieves-bernier_diers_taniguchi_holten_bocian_lindsey_2010, title={Probing the Rate of Hole Transfer in Oxidized Synthetic Chlorin Dyads via Site-Specific C-13-Labeling}, volume={75}, ISSN={["1520-6904"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77952494274&partnerID=MN8TOARS}, DOI={10.1021/jo100527h}, abstractNote={Understanding electronic communication among interacting constituents of multicomponent molecular architectures is important for rational design in diverse fields including artificial photosynthesis and molecular electronics. One strategy for examining ground-state hole/electron transfer in an oxidized tetrapyrrolic array relies on analysis of the hyperfine interactions observed in the EPR spectrum of the pi-cation radical. This strategy has been previously employed to probe the hole/electron-transfer process in oxidized multiporphyrin arrays of normal isotopic composition, wherein (1)H and (14)N serve as the hyperfine "clocks", and in arrays containing site-specific (13)C-labels, which serve as additional hyperfine clocks. Herein, the hyperfine-clock strategy is applied to dyads of dihydroporphyrins (chlorins). Chlorins are more closely related structurally to chlorophylls than are porphyrins. A de novo synthetic strategy has been employed to introduce a (13)C label at the 19-position of the chlorin macrocycle, which is a site of large electron/hole density and is accessible synthetically beginning with (13)C-nitromethane. The resulting singly (13)C-labeled chlorin was coupled with an unlabeled chlorin to give a dyad wherein a diphenylethyne linker spans the 10-positions of the two zinc chlorins. EPR studies of the monocations of both the natural abundance and (13)C-labeled zinc chlorin dyads and benchmark zinc chlorin monomers reveal that the time scale for hole/electron transfer is in the 4-7 ns range, which is 5-10-fold longer than that in analogous porphyrin arrays. The slower hole/electron transfer rate observed for the chlorin versus porphyrin dyads is attributed to the fact that the HOMO is a(1u)-like for the chlorins versus a(2u)-like for the porphyrins; the a(1u)-like orbital exhibits little (or no) electron/hole density at the site of linker attachment whereas the a(2u)-like orbital exhibits significant electron/hole density at this site. Collectively, the studies of the chlorin and porphyrin dyads provide insights into the structural features that influence the hole/electron-transfer process.}, number={10}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Nieves-Bernier, Elias J. and Diers, James R. and Taniguchi, Masahiko and Holten, Dewey and Bocian, David F. and Lindsey, Jonathan S.}, year={2010}, month={May}, pages={3193–3202} } @article{huang_huang_mroz_tegos_zhiyentayev_sharma_lu_balasubramanian_krayer_ruzie_et al._2010, title={Stable Synthetic Cationic Bacteriochlorins as Selective Antimicrobial Photosensitizers}, volume={54}, ISSN={["1098-6596"]}, DOI={10.1128/aac.00125-10}, abstractNote={ABSTRACT Photodynamic inactivation is a rapidly developing antimicrobial treatment that employs a nontoxic photoactivatable dye or photosensitizer in combination with harmless visible light to generate reactive oxygen species that are toxic to cells. Tetrapyrroles (e.g., porphyrins, chlorins, bacteriochlorins) are a class of photosensitizers that exhibit promising characteristics to serve as broad-spectrum antimicrobials. In order to bind to and efficiently penetrate into all classes of microbial cells, tetrapyrroles should have structures that contain (i) one or more cationic charge(s) or (ii) a basic group. In this report, we investigate the use of new stable synthetic bacteriochlorins that have a strong absorption band in the range 720 to 740 nm, which is in the near-infrared spectral region. Four bacteriochlorins with 2, 4, or 6 quaternized ammonium groups or 2 basic amine groups were compared for light-mediated killing against a Gram-positive bacterium ( Staphylococcus aureus ), a Gram-negative bacterium ( Escherichia coli ), and a dimorphic fungal yeast ( Candida albicans ). Selectivity was assessed by determining phototoxicity against human HeLa cancer cells under the same conditions. All four compounds were highly active (6 logs of killing at 1 μM or less) against S. aureus and showed selectivity for bacteria over human cells. Increasing the cationic charge increased activity against E. coli . Only the compound with basic groups was highly active against C. albicans. Supporting photochemical and theoretical characterization studies indicate that (i) the four bacteriochlorins have comparable photophysical features in homogeneous solution and (ii) the anticipated redox characteristics do not correlate with cell-killing ability. These results support the interpretation that the disparate biological activities observed stem from cellular binding and localization effects rather than intrinsic electronic properties. These findings further establish cationic bacteriochlorins as extremely active and selective near-infrared activated antimicrobial photosensitizers, and the results provide fundamental information on structure-activity relationships for antimicrobial photosensitizers. }, number={9}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Huang, Liyi and Huang, Ying-Ying and Mroz, Pawel and Tegos, George P. and Zhiyentayev, Timur and Sharma, Sulbha K. and Lu, Zongshun and Balasubramanian, Thiagarajan and Krayer, Michael and Ruzie, Christian and et al.}, year={2010}, month={Sep}, pages={3834–3841} } @article{mroz_huang_szokalska_zhiyentayev_janjua_nifli_sherwood_ruzie_borbas_fan_et al._2010, title={Stable synthetic bacteriochlorins overcome the resistance of melanoma to photodynamic therapy}, volume={24}, ISSN={["0892-6638"]}, DOI={10.1096/fj.09-152587}, abstractNote={Cutaneous malignant melanoma remains a therapeutic challenge, and patients with advanced disease have limited survival. Photodynamic therapy (PDT) has been successfully used to treat many malignancies, and it may show promise as an antimelanoma modality. However, high melanin levels in melanomas can adversely affect PDT effectiveness. Herein the extent of melanin contribution to melanoma resistance to PDT was investigated in a set of melanoma cell lines that markedly differ in the levels of pigmentation;3 new bacteriochlorins successfully overcame the resistance. Cell killing studies determined that bacteriochlorins are superior at (LD50≈0.1 µM) when compared with controls such as the FDA‐approved Photofrin (LD50≈10 µM) and clinically tested LuTex (LD50≈=1 µM). The melanin content affects PDT effectiveness, but the degree of reduction is significantly lower for bacteriochlorins than for Photofrin. Microscopy reveals that the least effective bacteriochlorin localizes predominantly in lysosomes, while the most effective one preferentially accumulates in mitochondria. Interestingly all bacteriochlorins accumulate in melanosomes, and subsequent illumination leads to melanosomal damage shown by electron microscopy. Fluorescent probes show that the most effective bacteriochlorin produces significantly higher levels of hydroxyl radicals, and this is consistent with the redox properties suggested by molecular‐orbital calculations. The best in vitro performing bacteriochlorin was tested in vivo in a mouse melanoma model using spectrally resolved fluorescence imaging and provided significant survival advantage with 20% of cures (P<0.01).—Mroz, P., Huang, Y.‐Y., Szokalska, A., Zhiyentayev, T., Janjua, S., Nifli, A.‐P., Sherwood, M. E., Ruzié, C., Borbas, K. E., Fan, D., Krayer, M., Balasubramanian, T., Yang, E., Kee, H. L., Kirmaier, C., Diers, J. R., Bocian, D. F., Holten, D., Lindsey, J. S., Hamblin, M. R. Stable synthetic bacteriochlorins overcome the resistance of melanoma to photodynamic therapy. FASEB J. 24, 3160–3170 (2010). www.fasebj.org}, number={9}, journal={FASEB JOURNAL}, author={Mroz, Pawel and Huang, Ying-Ying and Szokalska, Angelika and Zhiyentayev, Timur and Janjua, Sahar and Nifli, Artemissia-Phoebe and Sherwood, Margaret E. and Ruzie, Christian and Borbas, K. Eszter and Fan, Dazhong and et al.}, year={2010}, month={Sep}, pages={3160–3170} } @article{mass_taniguchi_ptaszek_springer_faries_diers_bocian_holten_lindsey_2011, title={Structural characteristics that make chlorophylls green: interplay of hydrocarbon skeleton and substituents}, volume={35}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78650499742&partnerID=MN8TOARS}, DOI={10.1039/c0nj00652a}, abstractNote={Understanding the effects of substituents on natural photosynthetic pigments is essential for gaining a deep understanding of why such pigments were selected over the course of evolution for use in photosynthetic systems. This knowledge should provide for a more thoughtful design of artificial light-harvesting systems. The hydrocarbon skeleton of all chlorophylls is phorbine, which contains an annulated five-membered (isocyclic) ring in addition to the reduced pyrrole ring characteristic of chlorins. A phorbine and a 131-oxophorbine (which bears an oxo group in the isocyclic ring) were synthesized as benchmark molecules for fundamental spectral and photophysical studies. The phorbine and 131-oxophorbine macrocycles lack peripheral substituents other than a geminal dimethyl group in the reduced ring to stabilize the chlorin chromophore. The spectral properties and electronic structure of the zinc or free base 131-oxophorbine closely resemble those of the corresponding analogues of chlorophyll a. Accordingly, the fundamental electronic properties of chlorophylls are primarily a consequence of the 131-oxophorbine base macrocycle.}, number={1}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Mass, Olga and Taniguchi, Masahiko and Ptaszek, Marcin and Springer, Joseph W. and Faries, Kaitlyn M. and Diers, James R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2011}, pages={76–88} } @article{taniguchi_mass_boyle_tang_diers_bocian_holten_lindsey_2010, title={Structural studies of sparsely substituted synthetic chlorins and phorbines establish benchmarks for changes in the ligand core and framework of chlorophyll macrocycles}, volume={979}, ISSN={["1872-8014"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77955427819&partnerID=MN8TOARS}, DOI={10.1016/j.molstruc.2010.05.035}, abstractNote={Understanding the changes in molecular structure of tetrapyrrole macrocycles upon derivatization of the organic framework is essential for diverse studies ranging from metal complexation to formation of supramolecular assemblies. New, sparsely substituted free base chlorin, 17-oxochlorin, phorbine and 131-oxophorbine macrocycles provide benchmarks for naturally occurring hydroporphyrins and have been examined here by X-ray crystallography, resonance Raman spectroscopy, and density functional theoretical (DFT) calculations. The macrocycles contain no substituents other than a geminal-dimethyl group attached to the reduced, pyrroline ring. The X-ray studies indicate that the benchmark compounds exhibit only slight distortion from planarity, which increases along the series porphine < chlorin < oxochlorin < phorbine < oxophorbine. The elongated CβCβ bond distance due to sp3 versus sp2 hybridization in the pyrroline ring (ring D) of the (oxo)chlorins and (oxo)phorbines (1.52–1.54 Å) versus that of porphine (1.35 Å) is accompanied by altered bond angles in ring D. Introduction of ring E (exocyclic ring) in a chlorin to give the phorbine or oxophorbine causes alteration of the bond angles at many sites in the framework of the macrocycle; for example, the bond angles of N3C14C15 in the (oxo)phorbine are widened by ∼11° compared to those of porphine or the analogous sparsely substituted chlorin. As a result, the shape of the macrocycle core changes along the series of porphine (nearly square), (oxo)chlorin (kite-shaped), and (oxo)phorbine (right-angled trapezoid), and the core size increases in the order porphine < phorbine ∼ oxophorbine < oxochlorin ∼ chlorin. Comparison of the bond distances and angles in ring E of the phorbine versus oxophorbine indicates that the shortening of the C13C131 bond owing to the presence of the oxo-group is quite small, only 0.024 Å; thus, the unsymmetrical structure of ring E does not appear to be due to conjugation with the C131O group but may be a characteristic feature of the (oxo)phorbine framework. The X-ray data further indicate that the lengths of the oxochlorin C17O and oxophorbine C131O groups are essentially identical, a result also predicted by DFT calculations. Regardless, the observed frequencies for the stretching vibrations of the C17O (1721 cm−1) and C131O (1701 cm−1) groups are different and suggest that conjugation of the latter group with the π-system of the macrocycle is greater than that of the former group. Collectively, the studies provide new insights into the individual factors that give rise to the overall structural characteristics of various macrocycles.}, number={1-3}, journal={JOURNAL OF MOLECULAR STRUCTURE}, publisher={Elsevier BV}, author={Taniguchi, Masahiko and Mass, Olga and Boyle, Paul D. and Tang, Qun and Diers, James R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2010}, month={Aug}, pages={27–45} } @article{taniguchi_lindsey_2010, title={Synthesis of oligo(p-phenylene)-linked dyads containing free base, zinc(II) or thallium(III) porphyrins for studies in artificial photosynthesis}, volume={66}, ISSN={["0040-4020"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77955918878&partnerID=MN8TOARS}, DOI={10.1016/j.tet.2010.05.059}, abstractNote={A series of (p-phenylene)n-linked meso-mesityl-substituted porphyrin dyads (n=2–4) was prepared via Suzuki coupling of zinc(II) and free base porphyrin building blocks. The resulting zinc(II)/free base porphyrin dyads were demetalated. The series of free base porphyrin dimers (n=1–4), four other porphyrin dimers (with p-phenylene, diphenylethyne or diphenylbutadiyne linkers; and aryl or tridec-7-yl meso substituents), and several benchmark monomers were converted to the thallium(III)chloride complexes under mild conditions. The collection of eight Tl(III)Cl/Tl(III)Cl dimers is designed for studies of ground-state hole-transfer processes and comparison with the excited-state energy- and hole-transfer processes of the corresponding Zn(II)/free base dyads. Altogether, 18 new porphyrin arrays and benchmark monomers have been prepared.}, number={30}, journal={TETRAHEDRON}, publisher={Elsevier BV}, author={Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2010}, month={Jul}, pages={5549–5565} } @article{kee_diers_ptaszek_muthiah_fan_lindsey_bocian_holten_2009, title={Chlorin-Bacteriochlorin Energy-transfer Dyads as Prototypes for Near-infrared Molecular Imaging Probes: Controlling Charge-transfer and Fluorescence Properties in Polar Media}, volume={85}, ISSN={["1751-1097"]}, DOI={10.1111/j.1751-1097.2008.00532.x}, abstractNote={AbstractThe photophysical properties of two energy‐transfer dyads that are potential candidates for near‐infrared (NIR) imaging probes are investigated as a function of solvent polarity. The dyads (FbC‐FbB and ZnC‐FbB) contain either a free base (Fb) or zinc (Zn) chlorin (C) as the energy donor and a free base bacteriochlorin (B) as the energy acceptor. The dyads were studied in toluene, chlorobenzene, 1,2‐dichlorobenzene, acetone, acetonitrile and dimethylsulfoxide (DMSO). In both dyads, energy transfer from the chlorin to bacteriochlorin occurs with a rate constant of ∼(5–10 ps)−1 and a yield of >99% in nonpolar and polar media. In toluene, the fluorescence yields (Φf = 0.19) and singlet excited‐state lifetimes (τ∼5.5 ns) are comparable to those of the benchmark bacteriochlorin. The fluorescence yield and excited‐state lifetime decrease as the solvent polarity increases, with quenching by intramolecular electron (or hole) transfer being greater for FbC‐FbB than for ZnC‐FbB in a given solvent. For example, the Φf and τ values for FbC‐FbB in acetone are 0.055 and 1.5 ns and in DMSO are 0.019 and 0.28 ns, whereas those for ZnC‐FbB in acetone are 0.12 and 4.5 ns and in DMSO are 0.072 and 2.4 ns. The difference in fluorescence properties of the two dyads in a given polar solvent is due to the relative energies of the lowest energy charge‐transfer states, as assessed by ground‐state redox potentials and supported by molecular‐orbital energies derived from density functional theory calculations. Controlling the extent of excited‐state quenching in polar media will allow the favorable photophysical properties of the chlorin–bacteriochlorin dyads to be exploited in vivo. These properties include very large Stokes shifts (85 nm for FbC‐FbB, 110 nm for ZnC‐FbB) between the red‐region absorption of the chlorin and the NIR fluorescence of the bacteriochlorin (λf = 760 nm), long bacteriochlorin excited‐state lifetime (∼5.5 ns), and narrow (≤20 nm) absorption and fluorescence bands. The latter will facilitate selective excitation/detection and multiprobe applications using both intensity‐ and lifetime‐imaging techniques.}, number={4}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Kee, Hooi Ling and Diers, James R. and Ptaszek, Marcin and Muthiah, Chinnasamy and Fan, Dazhong and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2009}, pages={909–920} } @article{song_taniguchi_speckbacher_yu_bocian_lindsey_holten_2009, title={Excited-State Energy Flow in Phenylene-Linked Multiporphyrin Arrays}, volume={113}, ISSN={["1520-6106"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-67649303381&partnerID=MN8TOARS}, DOI={10.1021/jp902183g}, abstractNote={The dynamics and pathways for excited-state energy transfer in three dyads and five triads composed of combinations of zinc, magnesium, and free base porphyrins (denoted Zn, Mg, Fb) connected by p-phenylene linkers have been investigated. The processes in the triads include energy transfer between adjacent nonequivalent porphyrins, between adjacent equivalent porphyrins, and between nonadjacent nonequivalent porphyrins using the intervening porphyrin as a superexchange mediator. In the case of the triad ZnZnFbPhi, excitation of the zinc porphyrin (to yield Zn) ultimately leads to production of the excited free base porphyrin (Fb) via the three processes with the derived rate constants as follows: (2.8 ps)(-1) for ZnZn Fb --> ZnZnFb, (4 ps)(-1) for Zn ZnFb left arrow over right arrow ZnZn Fb, and (14 ps)(-1) for Zn ZnFb --> ZnZnFb. These results and those obtained for the other four triads show that energy transfer between nonadjacent sites is significant and is only 5-7-fold slower than between adjacent sites. This same scaling was found previously for arrays joined via diphenylethyne linkers. Simulations of the energy-transfer properties of fictive dodecameric arrays based on the data reported herein show that nonadjacent transfer steps make a significant contribution to the observed performance of such larger molecular architectures. Collectively, these results indicate that energy transfer between nonadjacent sites has important implications for the design of multichromophore arrays for molecular-photonic and solar-energy applications.}, number={23}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, publisher={American Chemical Society (ACS)}, author={Song, Hee-eun and Taniguchi, Masahiko and Speckbacher, Markus and Yu, Lianhe and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2009}, month={Jun}, pages={8011–8019} } @article{ruzie_krayer_lindsey_2009, title={Fast and Robust Route to Hydroporphyrin-Chalcones with Extended Red or Near-Infrared Absorption}, volume={11}, ISSN={["1523-7052"]}, DOI={10.1021/ol900277m}, abstractNote={The reaction of an acetylchlorin or diacetylbacteriochlorin with an aldehyde under microwave conditions readily affords the corresponding hydroporphyrin-chalcone. The aldehydes include aryl aldehydes, cinnamaldehyde, and all-trans-retinal. The chalcone causes a bathochromic shift of the long-wavelength absorption band of the hydroporphyrin by up to 24 nm. The facile conjugation and wavelength tunability should make such constructs valuable for fundamental spectroscopic studies as well as diverse photochemical applications in the relatively unexplored red and near-infrared spectral regions.}, number={8}, journal={ORGANIC LETTERS}, author={Ruzie, Christian and Krayer, Michael and Lindsey, Jonathan S.}, year={2009}, month={Apr}, pages={1761–1764} } @article{mroz_bhaumik_dogutan_aly_kamal_khalid_kee_bocian_holten_lindsey_et al._2009, title={Imidazole metalloporphyrins as photosensitizers for photodynamic therapy: Role of molecular charge, central metal and hydroxyl radical production}, volume={282}, ISSN={["1872-7980"]}, DOI={10.1016/j.canlet.2009.02.054}, abstractNote={The in vitro photodynamic therapy activity of four imidazole-substituted metalloporphyrins has been studied using human (HeLa) and mouse (CT26) cancer cell lines: an anionic Zn porphyrin and a homologous series of three cationic Zn, Pd or InCl porphyrins. A dramatic difference in phototoxicity was found: Pd cationic>InCl cationic>Zn cationic>Zn anionic. HeLa cells were more susceptible than CT26 cells. Induction of apoptosis was demonstrated using a fluorescent caspase assay. The anionic Zn porphyrin localized in lysosomes while the cationic Zn porphyrin localized in lysosomes and mitochondria, as assessed by fluorescence microscopy. Studies using fluorescent probes suggested that the cationic Pd porphyrin produced more hydroxyl radicals as the reactive oxygen species. Thus, the cationic Pd porphyrin has high potential as a photosensitizer and gives insights into characteristics for improved molecular designs.}, number={1}, journal={CANCER LETTERS}, author={Mroz, Pawel and Bhaumik, Jayeeta and Dogutan, Dilek K. and Aly, Zarmeneh and Kamal, Zahra and Khalid, Laiqua and Kee, Hooi Ling and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S. and et al.}, year={2009}, month={Sep}, pages={63–76} } @article{song_taniguchi_diers_kirmaier_bocian_lindsey_holten_2009, title={Linker Dependence of Energy and Hole Transfer in Neutral and Oxidized Multiporphyrin Arrays}, volume={113}, ISSN={["1520-6106"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-73349086237&partnerID=MN8TOARS}, DOI={10.1021/jp9072558}, abstractNote={The excited-state photodynamics of the neutral and one-electron-oxidized forms of five porphyrin dyads were studied in benzonitrile containing tetrabutylammonium hexafluorophosphate as the supporting electrolyte. Each dyad contains a zinc porphyrin (Zn) and a free base porphyrin (Fb) joined by a linear biphenylene (Phi(2)), terphenylene (Phi(3)), quaterphenylene (Phi(4)), diphenylbutadiyne (L), or phenylethyne (E) linker (ZnFbPhi(2), ZnFbPhi(3), ZnFbPhi(4), ZnFbL, ZnFbE). The findings along with recent results on the neutral and oxidized forms of ZnFb dyads containing a diphenylethyne or phenylene linker (ZnFbU, ZnFbPhi) and steric hindrance to porphyrin-linker internal rotation at one or both ends of a diarylethyne linker (ZnFbD, ZnFbP, ZnFbB) give insights into the effects of linker characteristics (length, orbital energies, orbital overlap with the porphyrins) on the rate constants for excited-state energy transfer, excited-state hole transfer, and ground-state hole transfer. Analysis of the results is aided by density functional theory molecular orbital calculations and Forster energy-transfer calculations. Although the rate constants for linker-mediated through-bond excited-state energy transfer can be modulated significantly using a number of molecular design criteria (e.g., linker characteristics, interplay between porphyrin orbital characteristics, and linker attachment site), ground-state hole transfer, which also occurs via a linker-mediated through-bond electron-exchange mechanism, is primarily affected by the free-energy driving force for the process as dictated by the redox characteristics of the interacting porphyrins. The insights gained from this study should aid in the design of next-generation multichromophore arrays for solar energy applications.}, number={52}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, publisher={American Chemical Society (ACS)}, author={Song, Hee-eun and Taniguchi, Masahiko and Diers, James R. and Kirmaier, Christine and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2009}, month={Dec}, pages={16483–16493} } @article{krayer_balasubramanian_ruzie_ptaszek_cramer_taniguchi_lindsey_2009, title={Refined syntheses of hydrodipyrrin precursors to chlorin and bacteriochlorin building blocks}, volume={13}, ISSN={["1099-1409"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70450189510&partnerID=MN8TOARS}, DOI={10.1142/S1088424609001406}, abstractNote={ Bromo-substituted hydrodipyrrins are valuable precursors to synthetic bromo-chlorins and bromo-bacteriochlorins, which in turn are versatile substrates for derivatization in pursuit of diverse molecular designs. 8-bromo-2,3-dihydro-1-(1,1-dimethoxymethyl)-3,3-dimethyldipyrrin (1) is a crucial precursor in the rational synthesis of the bacteriochlorin building block 3,13-dibromo-8,8,18,18-tetramethylbacteriochlorin ( H2BC-Br3Br13) . 8-bromo-2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin (2) is a crucial precursor in the rational synthesis of the analogous 3,13-disubstituted chlorin building block (e.g. H2C-Br3M10Br13 ). The routes to 1 and 2 share a common precursor, namely 4-bromo-2-(2-nitroethyl)-1-N-tosylpyrrole (6-Ts), which is derived from pyrrole-2-carboxaldehyde. The prior seven-step synthesis of 1 from pyrrole-2-carboxaldehyde has limited access to H2BC-Br3Br13 given the large excesses of materials, extensive reliance on column chromatography, and low overall yield (1.4%). Refined procedures for synthesis of the common precursor 6-Ts as well as 1 and 2 afford the advantages of (1) diminished consumption of solvents and reagents, (2) limited or no use of chlorinated solvents, (3) limited or no chromatography, and (4) improved yields of most steps. Streamlined procedures enable the final two or three transformations to be performed without purification of intermediates. The new procedures facilitate the expedient preparation of 1 and 2 at the multigram scale. }, number={10}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, publisher={World Scientific Pub Co Pte Lt}, author={Krayer, Michael and Balasubramanian, Thiagarajan and Ruzie, Christian and Ptaszek, Marcin and Cramer, David L. and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2009}, month={Oct}, pages={1098–1110} } @article{muthiah_lahaye_taniguchi_ptaszek_lindsey_2009, title={Regioselective Bromination Tactics in the de Novo Synthesis of Chlorophyll b Analogues}, volume={74}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-66449131206&partnerID=MN8TOARS}, DOI={10.1021/jo9002954}, abstractNote={The ability to introduce substituents at designated sites about the perimeter of the chlorin or 13(1)-oxophorbine macrocycle is essential for fundamental studies related to chlorophylls. A chlorin is a dihydroporphyrin, whereas a 13(1)-oxophorbine is a chlorin containing an annulated oxopentano ring spanning positions 13 and 15. 13(1)-Oxophorbines bearing auxochromes at the 7-position of the macrocycle are valuable targets given their resemblance to chlorophyll a or b, which contains the 13(1)-oxophorbine skeleton and bears a 7-methyl or 7-formyl group, respectively. A rational route to 7-substituted 13(1)-oxophorbines was developed that relies on a new method for regioselective bromination. Under neutral conditions, a 13-acetyl-10-mesitylchlorin (FbC-M(10)A(13)) undergoes bromination (with 1 molar equiv of NBS in THF) both in ring B (7-position) and at the 15-position (42% versus 28% isolated yield), thereby thwarting installation of the isocyclic ring (ring E, spanning the 13-15 positions). Under acidic conditions (10% TFA in CH(2)Cl(2)), ring B is deactivated, and bromination occurs preferentially at the 15-position (87% yield). The capability for preferential 15-bromination is essential to install the isocyclic ring, after which bromination can be directed to the 7-position of ring B (neutral conditions, 86% yield). The ability to suppress bromination in ring B (under acidic media) has been exploited in syntheses of sparsely substituted analogues of chlorophyll b. The analogues contain a 7-substituent (acetyl, formyl, or TIPS-ethynyl), a 10-mesityl group, and the 18,18-dimethyl group as the only substituents in the 13(1)-oxophorbine skeleton. The three analogues exhibit absorption spectral features that closely resemble those of free base analogues of chlorophyll b. Taken together, the facile access to chlorins and 13(1)-oxophorbines bearing substituents at distinct sites should enable fundamental spectroscopic studies and diverse applications.}, number={9}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Muthiah, Chinnasamy and Lahaye, Dorothee and Taniguchi, Masahiko and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2009}, month={May}, pages={3237–3247} } @article{lindsey_ptaszek_taniguchi_2009, title={Simple Formation of an Abiotic Porphyrinogen in Aqueous Solution}, volume={39}, ISSN={["1573-0875"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77949775456&partnerID=MN8TOARS}, DOI={10.1007/s11084-009-9168-3}, abstractNote={Porphyrins have long been proposed as key ingredients in the emergence of life yet plausible routes for forming their essential pyrrole precursor have heretofore not been identified. Here we show that the anaerobic reaction of δ-aminolevulinic acid (ALA, 1-5 mM) with the β-ketoester methyl 4-methoxyacetoacetate (2-40 mM) in water (pH5-7) at 70-100°C for >6 h affords the porphyrinogen, which upon chemical oxidation gives the corresponding porphyrin in overall yield of up to 10%. The key intermediate is the α-methoxymethyl-substituted pyrrole, which undergoes tetramerization and macrocycle formation under kinetic control. The resulting type-I porphyrin bears four propionic acid and four carbomethoxy groups, is distinct from porphyrins (e.g., uroporphyrin or coproporphyrin) derivable from ALA alone via the extant universal biosynthetic path to tetrapyrroles, and is photoactive upon assembly into cationic micelles in aqueous solution. The simple self-organization of eight acyclic molecules into a tetrapyrrole macrocycle, from which a porphyrin is derived that is photoactive in lipid assemblies, augurs well for the spontaneous origin of catalysts and pigments essential for prebiotic metabolism and proto-photosynthesis.}, number={6}, journal={ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES}, publisher={Springer Nature}, author={Lindsey, Jonathan S. and Ptaszek, Marcin and Taniguchi, Masahiko}, year={2009}, month={Dec}, pages={495–515} } @article{mardis_sutton_zuo_lindsey_tiede_2009, title={Solution-State Conformational Ensemble of a Hexameric Porphyrin Array Characterized Using Molecular Dynamics and X-ray Scattering}, volume={113}, ISSN={["1520-5215"]}, DOI={10.1021/jp808318x}, abstractNote={Solution-phase X-ray scattering measurements in combination with coordinate-based modeling have been used to characterize the conformational ensemble of a hexameric, diphenylethyne-linked porphyrin array in solution. Configurationally broadened X-ray scattering patterns measured at room temperature for dilute toluene solutions of the porphyrin array were compared to scattering patterns calculated from structural ensembles in constant pressure and temperature molecular dynamics simulations. Thermal fluctuations sampled at picosecond intervals within nanosecond time scale dynamic simulations show large-amplitude motions that include porphyrin ring "tipping" around the porphyrin linkage axes and extended hexameric porphyrin array "breathing" motions involving torsional distortions collectively distributed along porphyrin and diphenylethyne groups. Each type of group motion produced characteristic, angle-dependent dampening of scattering features that are needed to reproduce dampening features in the experimental X-ray scattering. However, mismatches in the magnitudes of experimental and simulated dampening of high-angle X-ray scattering patterns show that large-amplitude hexamer array breathing-type motions are significantly under-represented in the simulated ensembles. This comparison between experiment and simulation provides a means not only to interpret scattering data in terms of an explicit atomic model but more generally demonstrates the use of solution X-ray scattering as an experimental benchmark for the development of simulation methods that more accurately predict configurational dynamics of supramolecular assemblies.}, number={11}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Mardis, Kristy L. and Sutton, Heather M. and Zuo, Xiaobing and Lindsey, Jonathan S. and Tiede, David M.}, year={2009}, month={Mar}, pages={2516–2523} } @article{mass_ptaszek_taniguchi_diers_kee_bocian_holten_lindsey_2009, title={Synthesis and Photochemical Properties of 12-Substituted versus 13-Substituted Chlorins}, volume={74}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-68049111576&partnerID=MN8TOARS}, DOI={10.1021/jo900706x}, abstractNote={Understanding the effects of substituents on natural photosynthetic pigments is essential for the rational design of artificial photosynthetic systems. The long-wavelength absorption of chlorins derives from a transition that encompasses rings A and C, which includes the 2,3- and 12,13-positions, respectively. Chlorophylls bear a 3-vinyl group and a 13-keto group, as well as a full complement of substituents at the other beta-pyrrole sites. Prior studies of sparsely substituted synthetic chlorins to probe the effects of substituents yielded 3,13-substituted chlorins that contain a geminal dimethyl group in the pyrroline ring (for stability) and a mesityl group at the 10-position. Attempts to prepare analogous chlorins lacking the 10-mesityl substituent encountered unexpected difficulties during construction of the Eastern half precursor (8,9-dibromo-1-formyldipyrromethane) to the 13-bromochlorin. Direct bromination of 1-formyldipyrromethane with 2 mol equiv of NBS at -78 degrees C led to an isomeric mixture of the desired 8,9-dibromodipyrromethane (minor) and the unexpected 7,9-dibromodipyrromethane (major). Hence, a new rational route was developed for the synthesis of 8,9-dibromo-1-formyldipyrromethane that entailed (i) InCl(3)-catalyzed condensation of 4-bromo-2-(hydroxymethyl)pyrrole and pyrrole to give the 8-bromodipyrromethane, (ii) 1-formylation, and (iii) 9-bromination. Two new substituted chlorins carrying auxochromes at the 3- and 13-positions were synthesized. The photophysical and redox properties of the 13-substituted chlorins were compared with those of isomeric 12-substituted chlorins, synthesized previously via a 7,9-dibromo-1-formyldipyrromethane. Such studies (static absorption and fluorescence spectroscopy, time-resolved fluorescence spectroscopy, electrochemistry of the zinc chelates, and density functional theoretical calculations) reveal only very slight differences between the isomeric 12- and 13-substituted chlorins.}, number={15}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Mass, Olga and Ptaszek, Marcin and Taniguchi, Masahiko and Diers, James R. and Kee, Hooi Ling and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2009}, month={Aug}, pages={5276–5289} } @article{laha_muthiah_taniguchi_mcdowell_ptaszek_lindsey_2009, title={Synthetic Chlorins Bearing Auxochromes at the 3- and 13-Positions}, volume={74}, ISSN={0022-3263 1520-6904}, url={http://dx.doi.org/10.1021/jo9010602}, DOI={10.1021/jo9010602}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionSynthetic Chlorins Bearing Auxochromes at the 3- and 13-PositionsJoydev K. Laha, Chinnasamy Muthiah, Masahiko Taniguchi, Brian E. McDowell, Marcin Ptaszek, and Jonathan S. Lindsey*Cite this: J. Org. Chem. 2009, 74, 14, 5122Publication Date (Web):June 15, 2009Publication History Published online15 June 2009Published inissue 17 July 2009https://pubs.acs.org/doi/10.1021/jo9010602https://doi.org/10.1021/jo9010602correctionACS PublicationsCopyright © 2009 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views746Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (33 KB) Get e-AlertscloseSUBJECTS:Bromine,Chemical structure,Molecular structure,Photochemical properties,Regiochemistry Get e-Alerts}, number={14}, journal={The Journal of Organic Chemistry}, publisher={American Chemical Society (ACS)}, author={Laha, Joydev K. and Muthiah, Chinnasamy and Taniguchi, Masahiko and McDowell, Brian E. and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2009}, month={Jul}, pages={5122–5122} } @misc{lindsey_2010, title={Synthetic Routes to meso-Patterned Porphyrins}, volume={43}, ISSN={["0001-4842"]}, DOI={10.1021/ar900212t}, abstractNote={Synthetic meso-substituted porphyrins offer significant attractions compared with naturally occurring beta-substituted porphyrins. The attractions include the rectilinear arrangement of the four meso substituents and potential synthetic amenability from pyrrole and simple acyl reactants, thereby avoiding the cumbersome syntheses of beta-substituted pyrroles. In practice, however, the classical methods for the synthesis of meso-substituted porphyrins were characterized by high-temperature reactions, limited scope of substituents, and statistical mixtures accompanied by laborious chromatography if porphyrins bearing two different types of substituents were sought. Such methods left unrealized the tremendous utility of meso-substituted porphyrins across the enormously broad field of porphyrin science, which touches pure chemistry; energy, life and materials sciences; and medicine. This Account surveys a set of strategies, developed over a generation, that provide rational access to porphyrins bearing up to four distinct meso substituents. A "2 + 2" route employs a dipyrromethane-1,9-dicarbinol and a dipyrromethane (bearing ABC- and D-substituents, respectively) in a two-step, one-flask process of acid-catalyzed condensation followed by oxidation at room temperature to form the free base "ABCD-porphyrin." A "bilane" route relies on the acid-catalyzed reaction of a 1-acyldipyrromethane (CD substituents) and a 9-bromodipyrromethane-1-carbinol (AB substituents) to form the corresponding 19-acyl-1-bromobilane. Reaction of the latter compound in the presence of MgBr(2), 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), and toluene at reflux exposed to air affords the corresponding magnesium(II) porphyrin. The two routes are complementary, both in scope and in implementation. A suite of methods also affords trans-A(2)B(2)-porphyrins by reaction of a dipyrromethane and an aldehyde, self-condensation of a dipyrromethane-1-carbinol, or self-condensation of a 1-acyldipyrromethane. These new routes are also useful for preparing sparsely substituted porphyrins, which bear fewer than four meso substituents (e.g., trans-AB-porphyrins, A-porphyrins). Because of their compact size and the ability to incorporate hydrophilic or amphipathic groups, such molecules are ideal for biological applications. The success of these new synthetic strategies has relied on a number of advances including (1) the development of simple yet efficient routes to dipyrromethanes, acyldipyrromethanes, and dipyrromethane-carbinols, (2) the identification of acid catalysts and reaction conditions for condensations of pyrromethane species without accompanying acidolysis (which underlies scrambling and formation of a mixture of porphyrin products), (3) the development of analytical methods to rapidly screen for scrambling and to characterize the distribution of oligopyrromethanes and macrocycles, (4) selection and refinement of synthetic methods to increase yields and to limit or avoid use of chromatography, thereby achieving scalability to multigram levels, and (5) exploitation of discoveries concerning the fundamental chemistry of pyrrolic species. With these developments, the prior era of porphyrin synthesis has been supplanted with rational routes that proceed under very mild conditions and afford a single porphyrin bearing up to four distinct meso substituents. The meso substituents encompass a very wide range of molecular complexity. The resulting porphyrins can serve as building blocks in the construction of model systems, as components of molecular materials, and as surrogates for naturally occurring tetrapyrrole macrocycles.}, number={2}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Lindsey, Jonathan S.}, year={2010}, month={Feb}, pages={300–311} } @article{schmidt_jiao_bocian_lindsey_2008, title={A Bipodal-Tethered Porphyrin for Attachment to Silicon Surfaces in Studies of Molecular Information Storage}, volume={8}, ISSN={["1533-4899"]}, DOI={10.1166/jnn.2008.IC85}, abstractNote={An approach for molecular information storage entails use of redox-active molecules attached to an electroactive surface. Understanding the structural features that give rise to robust molecular monolayers with high charge density is an essential objective. Toward this goal, a zinc-porphyrin bearing an all-carbon bipodal tether, 5-(1,6-heptadien-4-yl)-15-phenyl-10,20-di-p-tolylporphinatozinc(II), has been synthesized by the reaction of a dipyrromethane and a dipyrromethane-1,9-dicarbinol. The porphyrin was attached to Si(100) via a high temperature procedure. The resulting molecular monolayers exhibited surface coverages, adsorption geometries, electron-transfer rates, and stabilities under repeated electrochemical cycling that are similar to those obtained with monopodal carbon tethers. The observation that the bipodal anchor does not provide enhanced stability is surprising given that attachment is achieved via two versus one covalent linkage.}, number={9}, journal={JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY}, author={Schmidt, Izabela and Jiao, Jieying and Bocian, David F. and Lindsey, Jonathan S.}, year={2008}, month={Sep}, pages={4813–4817} } @article{taniguchi_cramer_bhise_kee_bocian_holten_lindsey_2008, title={Accessing the near-infrared spectral region with stable, synthetic, wavelength-tunable bacteriochlorins}, volume={32}, ISSN={["1369-9261"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-45149130353&partnerID=MN8TOARS}, DOI={10.1039/b717803d}, abstractNote={The near-infrared (NIR) spectral region has been comparatively under-utilized for diverse materials and medical applications owing to the lack of chromophores that afford stability, solubility, synthetic malleability, and tunable photophysical features. Bacteriochlorins are attractive candidates in this regard; however, preparation via modification of naturally occurring bacteriochlorophylls or reduction of porphyrins or chlorins has proved cumbersome. To overcome such limitations, a dibromobacteriochlorin (BC-Br3Br13) was prepared de novo by the acid-catalyzed condensation of an 8-bromodihydrodipyrrin-acetal. BC-Br3Br13 bears (1) a geminal dimethyl group in each reduced ring to block adventitious dehydrogenation, and (2) bromo groups at the 3- and 13-positions for further chemical modifications. BC-Br3Br13 was subjected to four types of Pd-mediated coupling reaction (Suzuki, Stille, Sonogashira, dehalogenation) to give bacteriochlorins bearing substituents at the 3- and 13-positions (phenyl, vinyl, acetyl, phenylethynyl), and a benchmark bacteriochlorin lacking such substituents. The 3,13-divinylbacteriochlorin was transformed to the 3,13-diformylbacteriochlorin. Depending on the substituents at the 3- and 13-positions, the position of the long-wavelength absorption maximum (Qy(0,0) band) lies between 713 and 771 nm, the fluorescence emission maximum lies between 717 and 777 nm, and the fluorescence quantum yield ranges from 0.15 to 0.070. The ability to introduce a wide variety of functional groups via Pd-mediated coupling reactions and the tunable absorption and emission spectral properties suggest that synthetic bacteriochlorins are viable candidates for a wide variety of photochemical applications.}, number={6}, journal={NEW JOURNAL OF CHEMISTRY}, publisher={Royal Society of Chemistry (RSC)}, author={Taniguchi, Masahiko and Cramer, David L. and Bhise, Anil D. and Kee, Hooi Ling and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2008}, pages={947–958} } @article{jiao_schmidt_taniguchi_lindsey_bocian_2008, title={Comparison of Electron-Transfer Rates for Metal- versus Ring-Centered Redox Processes of Porphyrins in Monolayers on Au(111)}, volume={24}, ISSN={["0743-7463"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-55549087896&partnerID=MN8TOARS}, DOI={10.1021/la8019843}, abstractNote={The standard electron-transfer rate constants ( k ( 0 )) are measured for redox processes of Fe versus Zn porphyrins in monolayers on Au(111); the former undergoes a metal-centered redox process (conversion between Fe (III) and Fe (II) oxidation states) whereas the latter undergoes a ring-centered redox process (conversion between the neutral porphyrin and the pi-cation radical). Each porphyrin contains three meso-mesityl groups and a benzyl thiol for surface attachment. Under identical solvent (propylene carbonate)/electrolyte (1.0 M Bu 4NCl) conditions, the Zn (II) center has a coordinated Cl (-) ion when the porphyrin is in either the neutral or oxidized state. In the case of the Fe porphyrin, two species are observed a low-potential form ( E l (0) approximately -0.6 V) wherein the metal center has a coordinated Cl (-) ion when it is in either the Fe (II) or Fe (III) state and a high-potential form ( E h (0) approximately +0.2 V) wherein the metal center undergoes ligand exchange upon conversion from the Fe (III) to Fe (II) states. The k ( 0 ) values observed for all of the porphyrins depend on surface concentration, with higher concentrations resulting in slower rates, consistent with previous studies on porphyrin monolayers. The k ( 0 ) values for the ring-centered redox process (Zn chelate) are 10-40 times larger than those for the metal-centered process (Fe chelate); the k ( 0 ) values for the two forms of the Fe porphyrin differ by a factor of 2-4 (depending on surface concentration), the Cl (-) exchanging form generally exhibiting a faster rate. The faster rates for the ring- versus metal-centered redox process are attributed to the participating molecular orbitals and their proximity to the surface (given that the porphyrins are relatively upright on the surface): a pi molecular orbital that has significant electron density at the meso-carbon atoms (one of which is the site of attachment of the linker to the surface anchoring thiol) versus a d-orbital that is relatively well localized on the metal center.}, number={20}, journal={LANGMUIR}, publisher={American Chemical Society (ACS)}, author={Jiao, Jieying and Schmidt, Izabela and Taniguchi, Masahiko and Lindsey, Jonathan S. and Bocian, David F.}, year={2008}, month={Oct}, pages={12047–12053} } @article{anariba_tiznado_diers_schmidt_muresan_lindsey_zaera_bocian_2008, title={Comprehensive characterization of hybrid junctions comprised of a porphyrin monolayer sandwiched between a coinage metal overlayer and a Si(100) substrate}, volume={112}, ISSN={["1932-7447"]}, DOI={10.1021/jp802428y}, abstractNote={The promise of molecular electronics has stimulated a variety of approaches for making hybrid junctions wherein molecules are sandwiched between two metal contacts or a metal and a semiconductor contact. However, the fate of molecules subsequent to deposition of a top metal contact has generally not been well characterized. Toward this goal, the interaction of evaporated Cu, Ag, and Au films deposited in varying thicknesses (3, 5, and 8 nm) on a series of monolayer-coverage porphyrins covalently attached to Si(100) substrates was investigated. Each porphyrin contains a triallyl tripod attached to the porphyrin via a p-phenylene unit, which anchors the porphyrin to the Si(100) substrate via hydrosilylation of the allyl groups. All of the porphyrins are Zn chelates bearing meso p-tolyl substituents orthogonal (lateral) to the tripodal surface anchor, but contain different substituents in the meso position opposite (distal) to the surface anchor, p-tolyl, α,α,α-trifluoro-p-tolyl, pentafluorophenyl, or p-cyan...}, number={25}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Anariba, Franklin and Tiznado, Hugo and Diers, James R. and Schmidt, Izabela and Muresan, Ana Z. and Lindsey, Jonathan S. and Zaera, Francisco and Bocian, David F.}, year={2008}, month={Jun}, pages={9474–9485} } @article{muresan_lindsey_2008, title={Design and synthesis of water-soluble bioconjugatable trans-AB-porphyrins}, volume={64}, ISSN={["1464-5416"]}, DOI={10.1016/j.tet.2008.08.096}, abstractNote={Three free base porphyrins have been prepared that bear a polar and facially encumbering 2,4,6-tris(carboxymethoxy)phenyl motif at one meso (5-) position. The only other substituent (15-position) comprises phenyl, formyl, or p-aminophenyl. The porphyrins exhibit solubility in water (or aqueous buffer solutions) at pH >/=7 and concentrations >1 mM at room temperature. The concise syntheses, water-solubility, and bioconjugatable handle make these porphyrin constructs suitable for biological applications.}, number={50}, journal={TETRAHEDRON}, author={Muresan, Ana Z. and Lindsey, Jonathan S.}, year={2008}, month={Dec}, pages={11440–11448} } @article{borbas_chandrashaker_muthiah_kee_holten_lindsey_2008, title={Design, synthesis, and photophysical characterization of water-soluble chlorins}, volume={73}, ISSN={["1520-6904"]}, DOI={10.1021/jo7026728}, abstractNote={The use of chlorins as photosensitizers or fluorophores in a range of biological applications requires facile provisions for imparting high water solubility. Two free base chlorins have been prepared wherein each chlorin bears a geminal dimethyl group in the reduced ring and a water-solubilizing unit at the chlorin 10-position. In one design (FbC1-PO3H2), the water-solubilizing unit is a 1,5-diphosphonopent-3-yl ("swallowtail") unit, which has previously been used to good effect with porphyrins. In the other design (FbC2-PO3H2), the water-solubilizing unit is a 2,6-bis(phosphonomethoxy)phenyl unit. Two complementary routes were developed for preparing FbC2-PO3H2 that entail introduction of the protected phosphonate moieties either in the Eastern-half precursor to the chlorin or by derivatization of an intact chlorin. Water-solubilization is achieved in the last step of each synthesis upon removal of the phosphonate protecting groups. The chlorins FbC1-PO3H2 and FbC2-PO3H2 are highly water-soluble (>10 mM) as shown by 1H NMR spectroscopy (D2O) and UV-vis absorption spectroscopy. The photophysical properties of the water-soluble chlorins in phosphate-buffered saline solution (pH 7.4) at room temperature were investigated using static and time-resolved absorption and fluorescence spectroscopic techniques. Each chlorin exhibits dominant absorption bands in the blue and the red region (lambda = 398, 626 nm), a modest fluorescence yield (Phi f approximately 0.11), a long singlet excited-state lifetime (tau = 7.5 ns), and a high yield of intersystem crossing to give the triplet state (Phi isc = 0.9). The properties of the water-soluble chlorins in aqueous media are comparable to those of hydrophobic chlorins in toluene. The high aqueous solubility combined with the attractive photophysical properties make these compounds suitable for a wide range of biomedical applications.}, number={8}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Borbas, K. Eszter and Chandrashaker, Vanampally and Muthiah, Chinnasamy and Kee, Hooi Ling and Holten, Dewey and Lindsey, Jonathan S.}, year={2008}, month={Apr}, pages={3145–3158} } @article{song_kirmaier_taniguchi_diers_bocian_lindsey_holten_2008, title={Determination of Ground-State Hole-Transfer Rates Between Equivalent Sites in Oxidized Multiporphyrin Arrays Using Time-Resolved Optical Spectroscopy}, volume={130}, ISSN={["0002-7863"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-56449089593&partnerID=MN8TOARS}, DOI={10.1021/ja805673m}, abstractNote={Excited-state charge separation in molecular architectures has been widely explored, yet ground-state hole (or electron) transfer, particularly involving equivalent pigments, has been far less studied, and direct quantitation of the rate of transfer often has proved difficult. Prior studies of ground-state hole transfer between equivalent zinc porphyrins using electron paramagnetic resonance techniques give a lower limit of approximately (50 ns)(-1) on the rates. Related transient optical studies of hole transfer between inequivalent sites [zinc porphyrin (Zn) and free base porphyrin (Fb)] give an upper limit of approximately (20 ps)(-1). Thus, a substantial window remains for the unknown rates of ground-state hole transfer between equivalent sites. Herein, the ground-state hole-transfer processes are probed in a series of oxidized porphyrin triads (ZnZnFb) with the focus being on determination of the rates between the nominally equivalent sites (Zn/Zn). The strategy builds upon recent time-resolved optical studies of the photodynamics of dyads wherein a zinc porphyrin is electrochemically oxidized and the attached free base porphyrin is photoexcited. The resulting energy- and hole-transfer processes in the oxidized ZnFb dyads are typically complete within 100 ps of excitation. Such processes are also present in the triads and serve as a starting point for determining the rates of ground-state hole transfer between equivalent sites in the triads. The rate constant of the Zn/Zn hole transfer is found to be (0.8 ns)(-1) for diphenylethyne-linked zinc porphyrins and increases only slightly to (0.6 ns)(-1) when a shorter phenylene linker is utilized. The rate decreases slightly to (1.1 ns)(-1) when steric constraints are introduced in the diarylethyne linker. In general, the rate constants for ground-state Zn/Zn hole transfer in oxidized arrays are a factor of 40 slower than those for Zn/Fb transfer. Collectively, the findings should aid the design of next-generation molecular architectures for applications in solar-energy conversion.}, number={46}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, publisher={American Chemical Society (ACS)}, author={Song, Hee-eun and Kirmaier, Christine and Taniguchi, Masahiko and Diers, James R. and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2008}, month={Nov}, pages={15636–15648} } @article{jiao_nordfund_lindsey_bocian_2008, title={Effects of counterion mobility, surface morphology, and charge screening on the electron-transfer rates of porphyrin monolayers}, volume={112}, ISSN={["1932-7447"]}, DOI={10.1021/jp800123u}, abstractNote={The standard electron-transfer rate constants (k0) for the oxidation of porphyrin monolayers are reported for a number of solvent/electrolyte systems and electroactive surfaces. The goal is to explain the inverse correlation between the electron-transfer rates and the porphyrin surface concentration (Roth et al., J. Phys. Chem. B 2002, 106, 8639−8648). Each porphyrin is a zinc chelate and contains three meso-mesityl groups and a benzyl alcohol or benzyl thiol for surface attachment. The solvent/electrolyte systems include (i) the organic solvent propylene carbonate containing electrolytes with a common cation and anions of different size/mobility (PF6-, ClO4-, and Cl-) and (ii) neat ionic liquids with a common cation and anions of different size/mobility [(CF3SO2)2N- and (NC)2N-]. The substrates include Si(100), Au(111), and TiN. The k0 values observed using electrolytes with PF6-, ClO4-, and (CF3SO2)2N- counterions are similar to one another, whereas those observed using electrolytes Cl- and (NC)2N- coun...}, number={15}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Jiao, Jieying and Nordfund, Eric and Lindsey, Jonathan S. and Bocian, David F.}, year={2008}, month={Apr}, pages={6173–6180} } @article{song_kirmaier_diers_lindsey_bocian_holten_2009, title={Energy- and Hole-Transfer Dynamics in Oxidized Porphyrin Dyads}, volume={113}, ISSN={["1520-6106"]}, DOI={10.1021/jp8060637}, abstractNote={The mechanisms and dynamics of quenching of a photoexcited free base porphyrin (Fb*) covalently linked to a nearby oxidized zinc porphyrin (Zn(+)) have been investigated in a set of five dyads using time-resolved absorption spectroscopy. The dyads include porphyrins joined at the meso-positions by a diphenylethyne linker or a diarylethyne linker with 2,6-dimethyl substitution on either one or both of the aryl rings. Another dyad is linked at the beta-pyrrole positions of the porphyrins via a diphenylethyne linker. The type of linker and attachment site modulate the interporphyrin through-bond electronic coupling via steric hindrance (porphyrin-linker orbital overlap) and attachment motif (porphyrin electron density at the connection site). For each ZnFb dyad, the zinc porphyrin is selectively electrochemically oxidized (to produce Zn(+)Fb), the free base porphyrin is selectively excited with a 130 fs flash (to produce Zn(+)Fb*), and the subsequent dynamics monitored. The Zn(+)Fb* excited state has a lifetime of approximately 3 to approximately 30 ps (depending on the linker steric hindrance and attachment site) and decays by parallel excited-state energy- and hole-transfer pathways. The relative yields of the two channels depend on a number of factors including the linker-mediated through-bond electronic coupling and a modest (< or =20%) Forster through-space contribution for the energy-transfer route. One product of Zn(+)Fb* decay is the metastable ground-state ZnFb(+), which decays to the Zn(+)Fb preflash state by ground-state hole transfer with a linker-dependent rate constant of (20 ps)(-1) to (150 ps)(-1). Collectively, these results provide a detailed understanding of the mechanism and dynamics of quenching of excited porphyrins by nearby oxidized sites, as well as the dynamics of ground-state hole transfer between nonequivalent porphyrins (Zn and Fb). The findings also lay the foundation for the study of ground-state hole transfer between identical porphyrins (e.g., Zn/Zn, Fb/Fb) in larger multiporphyrin arrays wherein a hole is selectively placed via electrochemical oxidation.}, number={1}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Song, Hee-eun and Kirmaier, Christine and Diers, James R. and Lindsey, Jonathan S. and Bocian, David F. and Holten, Dewey}, year={2009}, month={Jan}, pages={54–63} } @article{kee_nothdurft_muthiah_diers_fan_ptaszek_bocian_lindsey_culver_holten_2008, title={Examination of chlorin-bacteriochlorin energy-transfer dyads as prototypes for near-infrared molecular imaging probes}, volume={84}, ISSN={["1751-1097"]}, DOI={10.1111/j.1751-1097.2008.00409.x}, abstractNote={AbstractNew classes of synthetic chlorin and bacteriochlorin macrocycles are characterized by narrow spectral widths, tunable absorption and fluorescence features across the red and near‐infrared (NIR) regions, tunable excited‐state lifetimes (<1 to >10 ns) and chemical stability. Such properties make dyad constructs based on synthetic chlorin and bacteriochlorin units intriguing candidates for the development of NIR molecular imaging probes. In this study, two such dyads (FbC‐FbB and ZnC‐FbB) were investigated. The dyads contain either a free base (Fb) or zinc (Zn) chlorin (C) as the energy donor and a free base bacteriochlorin (B) as the energy acceptor. In both constructs, energy transfer from the chlorin to bacteriochlorin occurs with a rate constant of ∼(5 ps)−1 and a yield of >99%. Thus, each dyad effectively behaves as a single chromophore with an exceptionally large Stokes shift (85 nm for FbC‐FbB and 110 nm for ZnC‐FbB) between the red‐region absorption of the chlorin and the NIR fluorescence of the bacteriochlorin (λf = 760 nm, Φf = 0.19, τ ∼ 5.5 ns in toluene). The long‐wavelength transitions (absorption, emission) of each constituent of each dyad exhibit narrow (≤20 nm) spectral widths. The narrow spectral widths enabled excellent selectivity in excitation and detection of one chlorin–bacteriochlorin energy‐transfer dyad in the presence of the other upon diffuse optical tomography of solution‐phase phantoms.}, number={5}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Kee, Hooi Ling and Nothdurft, Ralph and Muthiah, Chinnasamy and Diers, James R. and Fan, Dazhong and Ptaszek, Marcin and Bocian, David F. and Lindsey, Jonathan S. and Culver, Joseph P. and Holten, Dewey}, year={2008}, pages={1061–1072} } @article{dogutan_lindsey_2008, title={Investigation of the scope of a new route to ABCD-bilanes and ABCD-porphyrins}, volume={73}, ISSN={["1520-6904"]}, DOI={10.1021/jo8010396}, abstractNote={A new route to bilanes and porphyrins bearing four distinct meso substituents has been studied to elucidate the scope and gain entry to previously inaccessible compounds. The route entails (i) synthesis of a 1-bromo-19-acylbilane by acid-catalyzed condensation of a 1-acyldipyrromethane and a 9-bromodipyrromethane-1-carbinol and (ii) intramolecular cyclization of the 1-bromo-19-acylbilane in the presence of a metal salt (MgBr2, 3 mol equiv) and a non-nucleophilic base (DBU, 10 mol equiv) in a noncoordinating solvent (toluene) at 115 degrees C exposed to air to afford the corresponding magnesium(II) porphyrin. In this study, two sets of bilanes were initially prepared to explore substituent effects. In the first set, all bilanes vary only in the nature of the substituent at the 10-position. In the second set, all bilanes vary only in the nature of the substituent attached to the acyl unit (the 20-position). The substituents examined at the 10- and 20-positions include alkyl, aryl (electron-rich, electron-deficient, hindered), heteroaryl, ester, or no substituent (-H). The bilanes were obtained in 35-87% yield, and the target porphyrins in up to 60% yield. Further study of the scope focused on bilanes and porphyrins bearing three heterocyclic substituents (o-, m-, p-pyridyl) or four alkyl groups (ethyl, propyl, butyl, pentyl), in which case microwave irradiation was used for the porphyrin-forming step. Altogether, 17 bilanes and 19 porphyrins were prepared and characterized. In summary, the new route provides access to meso-substituted bilanes and porphyrins for which access is limited via other methods.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Dogutan, Dilek Kiper and Lindsey, Jonathan S.}, year={2008}, month={Sep}, pages={6728–6742} } @article{anariba_schmidt_muresan_lindsey_bocian_2008, title={Metal-molecule interactions upon deposition of copper overlayers on reactively functionalized porphyrin monolayers on Si(100)}, volume={24}, ISSN={["0743-7463"]}, DOI={10.1021/la800472c}, abstractNote={The interaction of evaporated Cu deposited on a series of porphyrins in monolayers covalently attached to Si(100) substrates was investigated using cyclic voltammetry and FTIR spectroscopy. Each porphyrin contains a triallyl tripod attached to the porphyrin via a p-phenylene unit. The tripod anchors the porphyrin to the Si(100) substrate via hydrosilylation of the allyl groups. Two of the porphyrins are Zn chelates that possess meso p-cyanophenyl substituentsone, ZnP-CND, contains a single group opposite (distal) to the tripodal surface anchor, whereas the other, ZnP-CNL, contains two groups orthogonal (lateral) to the surface anchor. A third Zn porphyrin, ZnP, containing nonreactive p-tolyl groups at all three nonanchoring meso positions, was examined for comparison. The fourth porphyrin, FbP-HD, is a metal-free species (free base) that contains nonreactive phenyl (distal) and p-tolyl groups (lateral) at the three nonanchoring meso positions. The fifth porphyrin, CuP-HD, is the Cu chelate of FbP-HD, and serves as a reference complex for evaluating the effects of Cu metal deposition onto FbP-HD. The studies indicate that all of the porphyrin monolayers are robust under the conditions of Cu deposition, experiencing no noticeable degradation. In addition, the Cu metal does not penetrate through the monolayer to form electrically conductive filaments. For the ZnP-CND monolayers, the deposited Cu quantitatively reacts/complexes with the distal cyano group. In contrast, for the ZnP-CNL monolayers no reaction/complexation of the lateral cyano groups is observed. For the FbP-HD monolayers, Cu deposition results in quantitative insertion of Cu into the free base porphyrin. Collectively, the studies demonstrate that porphyrin monolayers are amenable to direct deposition of Cu overlayers and that functionalization of the porphyrins can be used to mediate the attributes of the metal-molecule junction.}, number={13}, journal={LANGMUIR}, author={Anariba, Franklin and Schmidt, Lzabela and Muresan, Ana Z. and Lindsey, Jonathan S. and Bocian, David F.}, year={2008}, month={Jul}, pages={6698–6704} } @article{kee_bhaumik_diers_mroz_hamblin_bocian_lindsey_holten_2008, title={Photophysical characterization of imidazolium-substituted Pd(II), In(III), and Zn(II) porphyrins as photosensitizers for photodynamic therapy}, volume={200}, ISSN={["1873-2666"]}, DOI={10.1016/j.jphotochem.2008.08.006}, abstractNote={The photophysical properties of four imidazolium-substituted metalloporphyrins have been assessed to gain insights into the relative efficacy of the compounds for photodynamic therapy (PDT). A set of zinc(II), palladium(II), and chloro-indium(III) porphyrins all bear a net positive charge owing to the diethylimidazolium unit; one zinc chelate bears a negative charge owing to a bis(sulfobutyl)imidazolium unit. The photophysical properties of the cationic and anionic zinc porphyrins are very similar to one another in organic solvents, phosphate-buffered saline, and in the presence of bovine serum albumin. The properties of the zinc and palladium porphyrins bearing charged peripheral groups are generally similar to those of neutral analogs in organic solvents. The palladium porphyrin shows an essentially quantitative yield (≥0.99) of the triplet excited state compared to the zinc porphyrins (∼0.9), and all are quantitatively quenched (at the diffusion limit) by molecular oxygen in air-saturated fluid solution. If the rate constant and yield of quenching of the triplet excited state by energy or electron transfer to molecular oxygen is the same in the cellular environment as in solution, then these processes combined with the triplet yield contribute only a factor of 1.3 to the higher PDT activity of analogous palladium versus zinc porphyrins, which is much smaller than what is observed. Therefore, other factors such as transient reduction of the excited porphyrin or delivery to the target site must predominantly underlie the difference in PDT efficacy of these sensitizers.}, number={2-3}, journal={JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY}, author={Kee, Hooi Ling and Bhaumik, Jayeeta and Diers, James R. and Mroz, Pawel and Hamblin, Michael R. and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2008}, month={Dec}, pages={346–355} } @article{song_taniguchi_kirmaier_bocian_lindsey_holten_2009, title={Probing Ground-state Hole Transfer Between Equivalent, Electrochemically Inaccessible States in Multiporphyrin Arrays Using Time-resolved Optical Spectroscopy}, volume={85}, ISSN={["1751-1097"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-65349190560&partnerID=MN8TOARS}, DOI={10.1111/j.1751-1097.2008.00471.x}, abstractNote={AbstractA new strategy is described and implemented for determining the rates of hole‐transfer between equivalent porphyrins in multiporphyrin architectures. The approach allows access to these rates between sites that are not the most easily oxidized components of the array. The specific architectures investigated with this new strategy are triads consisting of one zinc porphyrin (Zn) and two free base porphyrins (Fb). The triads employ a diphenylethyne linker (ZnFbFbU) and a phenylene linker (ZnFbFbΦ). The zinc porphyrin is selectively oxidized to produce Zn+FbFb, the free base porphyrins are excited to produce the excited‐state mixture Zn+Fb*Fb and Zn+FbFb*, and the subsequent dynamics are monitored by ultrafast absorption spectroscopy. The system evolves by a combination of energy‐ and hole‐transfer processes involving (adjacent and nonadjacent) zinc and free base porphyrin constituents that are complete within 100 ps of excitation; the rate constants of many of these processes are derived from prior studies of the oxidized forms of the benchmark dyads (ZnFbU and ZnFbΦ). One of the excited‐state decay channels produces the metastable state ZnFbFb+ that decays to a second metastable state ZnFb+Fb by the target hole‐transfer process, followed by rapid hole transfer to produce the Zn+FbFb thermodynamic ground state of the system. The rate constant for hole transfer between the free base porphyrins in the oxidized ZnFbFb triads is found to be (0.5 ns)−1 and (0.6 ns)−1 across phenylene and diphenylethyne linkers, respectively. These rate constants are comparable to those recently measured, using a related but distinct strategy, for ground‐state hole transfer between zinc porphyrins in oxidized ZnZnFb triads. The two complementary strategies provide unique approaches for probing hole transfer between equivalent sites in multiporphyrin arrays, with the choice of method being guided by the particular target process and the ease of synthesis of the necessary architectures.}, number={3}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, publisher={Wiley}, author={Song, Hee-eun and Taniguchi, Masahiko and Kirmaier, Christine and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2009}, pages={693–704} } @article{dogutan_ptaszek_lindsey_2008, title={Rational or statistical routes from 1-acyldipyrromethanes to meso-substituted porphyrins. Distinct patterns, multiple pyridyl substituents, and amphipathic architectures}, volume={73}, ISSN={["0022-3263"]}, DOI={10.1021/jo800588n}, abstractNote={New methodology is described for the synthesis of porphyrins bearing four (A 4, cis-A 2B 2, cis-ABC 2, trans-A 2B 2) or fewer (A, cis-AB, cis-A 2, trans-A 2) meso substituents. The method entails condensation of two 1-acyldipyrromethanes in the presence of a metal salt (MgBr 2, 3 mol equiv) and a noncoordinating base (DBU, 10 mol equiv) in a noncoordinating solvent (toluene) with heating (conventional or microwave irradiation) and exposure to air. The rational synthesis of trans-A 2B 2- or trans-A 2-porphyrins was achieved via condensation of two identical 1-acyldipyrromethanes. The statistical synthesis of various meso-substituted porphyrins was achieved via condensation of two nonidentical 1-acyldipyrromethanes. Both routes possess attractive features including (1) no scrambling, (2) good yield (up to 60%) at high concentration (100 mM) for the macrocycle-forming step, (3) reasonable scope (aryl, heteroaryl, alkyl, or no substituent), (4) short reaction time ( approximately 2 h) via microwave irradiation, (5) magnesium porphyrins as the products, which easily undergo demetalation, and (6) facile chromatographic purification. A key advantage of the statistical route is to obtain a cis-substituted porphyrin without the corresponding trans isomer. For example, reaction of an A/B-substituted 1-acyldipyrromethane and the fully unsubstituted 1-formyldipyrromethane gave the magnesium chelates of three porphyrins: the trans-A 2B 2-porphyrin, the "hybrid" cis-AB-porphyrin, and porphine (no trans-AB-porphyrin can form), which were readily demetalated and separated as the free base species. Altogether 26 1-acyldipyrromethanes and 26 target porphyrins have been prepared, including many with two different pyridyl substituents. One set of amphipathic porphyrins includes cis-A 2B 2- or cis-A 2BC-porphyrins wherein A = pentyl and B/C = pyridyl ( o-, m-, p-). Taken together, the rational and statistical routes enable facile conversion of readily available 1-acyldipyrromethanes to diverse porphyrins bearing 1-4 meso substituents for which access is limited via other methods.}, number={16}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Dogutan, Dilek Kiper and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2008}, month={Aug}, pages={6187–6201} } @article{muresan_thamyongkit_diers_holten_lindsey_bocian_2008, title={Regiospecifically alpha-C-13-labeled porphyrins for studies of ground-state hole transfer in multiporphyrin arrays}, volume={73}, ISSN={["0022-3263"]}, DOI={10.1021/jo8012836}, abstractNote={Insight into the electronic communication between the individual constituents of multicomponent molecular architectures is essential for the rational design of molecular electronic and/or photonic devices. To clock the ground-state hole/electron-transfer process in oxidized multiporphyrin architectures, a p-diphenylethyne-linked zinc porphyrin dyad was prepared wherein one porphyrin bears two (13)C atoms and the other porphyrin is unlabeled. The (13)C atoms are located at the 1- and 9-positions (alpha-carbons symmetrically disposed to the position of linker attachment), which are sites of electron/spin density in the a(1u) HOMO of the porphyrin. The (13)C labels were introduced by reaction of KS(13)CN with allyl bromide to give the allyl isothiocyanate, which upon Trofimov pyrrole synthesis followed by methylation gave 2-(methylthio)pyrrole-2-(13)C. Reaction of the latter with paraformaldehyde followed by hydrodesulfurization gave dipyrromethane-1,9-(13)C, which upon condensation with a dipyrromethane-1,9-dicarbinol bearing three pentafluorophenyl groups gave the tris(pentafluorophenyl)porphyrin bearing (13)C labels at the 1,9-positions and an unsubstituted meso (5-) position. Zinc insertion, bromination at the 5-position, and Suzuki coupling with an unlabeled porphyrin bearing a suitably functionalized diphenylethyne linker gave the regiospecifically labeled zinc porphyrin dyad. Examination of the monocation of the isotopically labeled dyad via electron paramagnetic resonance (EPR) spectroscopy (and comparison with the monocations of benchmark monomers, where hole transfer cannot occur) showed that the hole transfer between porphyrin constituents of the dyad is slow (<10(6) s(-1)) on the EPR time scale at room temperature. The slow rate stems from the a(1u) HOMO of the electron-deficient porphyrins, which has a node at the site of linker connection. In contrast, analogous dyads of electron-rich porphyrins (wherein the HOMO is a(2u) and has a lobe at the site of linker connection) studied previously exhibit rates of hole transfer that are fast (>5 x 10(7) s(-1)) on the EPR time scale at room temperature.}, number={18}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Muresan, Ana Z. and Thamyongkit, Patchanita and Diers, James R. and Holten, Dewey and Lindsey, Jonathan S. and Bocian, David F.}, year={2008}, month={Sep}, pages={6947–6959} } @article{borbas_ruzie_lindsey_2008, title={Swallowtail bacteriochlorins. Lipophilic absorbers for the near-infrared}, volume={10}, ISSN={["1523-7060"]}, DOI={10.1021/ol800436u}, abstractNote={Bacteriochlorins absorb strongly in the near-infrared spectral region and hence are ideally suited for diverse photomedical applications, yet naturally occurring bacteriochlorins have limited stability and synthetic malleability. A de novo route has been exploited to prepare synthetic bacteriochlorins that bear a geminal dimethyl group in each pyrroline ring for stability and a symmetrically branched 1,5-dimethoxypentyl group attached to each pyrrole ring for solubility in lipophilic media.}, number={10}, journal={ORGANIC LETTERS}, author={Borbas, K. Eszter and Ruzie, Christian and Lindsey, Jonathan S.}, year={2008}, month={May}, pages={1931–1934} } @article{muthiah_kee_diers_fan_ptaszek_bocian_holten_lindsey_2008, title={Synthesis and excited-state photodynamics of a chlorin-bacteriochlorin dyad-through-space versus through-bond energy transfer in tetrapyrrole arrays}, volume={84}, ISSN={["1751-1097"]}, DOI={10.1111/j.1751-1097.2007.00258.x}, abstractNote={AbstractUnderstanding energy transfer among hydroporphyrins is of fundamental interest and essential for a wide variety of photochemical applications. Toward this goal, a synthetic free base ethynylphenylchlorin has been coupled with a synthetic free base bromobacteriochlorin to give a phenylethyne‐linked chlorin–bacteriochlorin dyad (FbC‐pe‐FbB). The chlorin and bacteriochlorin are each stable toward adventitious oxidation because of the presence of a geminal dimethyl group in each reduced pyrrole ring. A combination of static and transient optical spectroscopic studies indicate that excitation into the Qy band of the chlorin constituent (675 nm) of FbC‐pe‐FbB in toluene results in rapid energy transfer to the bacteriochlorin constituent with a rate of ∼(5 ps)−1 and efficiency of >99%. The excited bacteriochlorin resulting from the energy‐transfer process in FbC‐pe‐FbB has essentially the same fluorescence characteristics as an isolated monomeric reference compound, namely a narrow (12 nm fwhm) fluorescence emission band at 760 nm and a long‐lived (5.4 ns) Qy excited state that exhibits a significant fluorescence quantum yield (Φf = 0.19). Förster calculations are consistent with energy transfer in FbC‐pe‐FbB occurring predominantly by a through‐space mechanism. The energy‐transfer characteristics of FbC‐pe‐FbB are compared with those previously obtained for analogous phenylethyne‐linked dyads consisting of two porphyrins or two oxochlorins. The comparisons among the sets of dyads are facilitated by density functional theory calculations that elucidate the molecular‐orbital characteristics of the energy donor and acceptor constituents. The electron‐density distributions in the frontier molecular orbitals provide insights into the through‐bond electronic interactions that can also contribute to the energy‐transfer process in the different types of dyads.}, number={3}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Muthiah, Chinnasamy and Kee, Hooi Ling and Diers, James R. and Fan, Dazhong and Ptaszek, Marcin and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S.}, year={2008}, pages={786–801} } @article{ruzie_krayer_balasubramanian_lindsey_2008, title={Tailoring a bacteriochlorin building block with cationic, amphipathic, or lipophilic substituents}, volume={73}, ISSN={["1520-6904"]}, DOI={10.1021/jo800736c}, abstractNote={Bacteriochlorins are attractive candidates for photodynamic therapy (PDT) of diverse medical indications owing to their strong absorption in the near-infrared (NIR) region, but their use has been stymied by lack of access to stable, synthetically malleable molecules. To overcome these limitations, a synthetic free base 3,13-dibromobacteriochlorin (BC-Br(3)Br(13)) has been exploited as a building block in the synthesis of diverse bacteriochlorins via Pd-mediated coupling reactions (Sonogashira, Suzuki, and reductive carbonylation). Each bacteriochlorin is stable to adventitious dehydrogenation by virtue of the presence of a geminal dimethyl group in each pyrroline ring. The target bacteriochlorins bear cationic, lipophilic, or amphipathic substituents at the 3- and 13- (beta-pyrrolic) positions. A dicarboxybacteriochlorin was converted to amide derivatives via the intermediate diacid chloride. A diformylbacteriochlorin was subjected to reductive amination to give aminomethyl derivatives. A set of 3,5-disubstituted aryl groups bearing lipophilic or amphipathic groups was introduced via Suzuki coupling. Altogether 22 free base bacteriochlorins have been prepared. Eight aminoalkylbacteriochlorins were quaternized with methyl iodide at two or four amine sites per molecule, which resulted in water solubility. Each bacteriochlorin exhibits a Q(y) absorption band in the range of 720-772 nm. The ability to introduce a wide variety of peripheral functional groups makes these bacteriochlorins attractive candidates for diverse applications in photomedicine including PDT in the NIR region.}, number={15}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Ruzie, Christian and Krayer, Michael and Balasubramanian, Thiagarajan and Lindsey, Jonathan S.}, year={2008}, month={Aug}, pages={5806–5820} } @article{rogers_krayer_lindsey_melander_2009, title={Tandem dispersion and killing of bacteria from a biofilm}, volume={7}, ISSN={["1477-0539"]}, DOI={10.1039/b817923a}, abstractNote={The combined effects of biofilm dispersion with a 2-aminoimidazole-triazole conjugate and bactericidal activity with a photodynamic inactivation agent suggest a novel combination therapy for treating diverse microbial infections.}, number={3}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Rogers, Steven A. and Krayer, Michael and Lindsey, Jonathan S. and Melander, Christian}, year={2009}, pages={603–606} } @article{borbas_kee_holten_lindsey_2008, title={A compact water-soluble porphyrin bearing an iodoacetamido bioconjugatable site}, volume={6}, ISSN={["1477-0539"]}, DOI={10.1039/b715072e}, abstractNote={A broad range of applications requires access to porphyrins that are compact, water-soluble, and bioconjugatable. A symmetrically branched hydrocarbon chain ('swallowtail') bearing polar end groups imparts high (>10 mM) aqueous solubility upon incorporation at one of the meso positions of a trans-AB-porphyrin. Two such swallowtail-porphyrins (1a, 1b) equipped with a conjugatable group (carboxylic acid, bromophenyl) have been prepared previously. The synthesis of three new water-soluble trans-AB-porphyrins is reported, where each porphyrin bears a diphosphonate-terminated swallowtail group and an amino (2a), acetamido (2b), or iodoacetamido (2c) group. The amine affords considerable versatility for functionalization. The iodoacetamide provides a sulfhydryl-reactive site for bioconjugation. Porphyrins were fully characterized in aqueous solution by 1H NMR spectroscopy (in D2O), ESI-MS, static absorption spectroscopy, and static and time-resolved fluorescence spectroscopy. Porphyrins 2a-2c exhibit characteristic porphyrin absorption and emission bands in aqueous solution, with a strong, sharp absorption band in the blue region (approximately 401 nm) and emission in the red region (approximately 624, 686 nm). Porphyrin 2b in aqueous phosphate buffer or phosphate-buffered saline solution exhibits a fluorescence quantum yield of approximately 0.04 and an excited singlet-state lifetime of approximately 11 ns. Collectively, the facile synthesis, amenability to bioconjugation, large spacing between the main absorption and fluorescence features, and long singlet excited-state lifetime make this molecular design quite attractive for a range of biomedical applications.}, number={1}, journal={ORGANIC & BIOMOLECULAR CHEMISTRY}, author={Borbas, K. Eszter and Kee, Hooi Ling and Holten, Dewey and Lindsey, Jonathan S.}, year={2008}, pages={187–194} } @article{jiao_thamyongkit_schmidt_lindsey_bocian_2007, title={Characterization of porphyrin surface orientation in monolayers on au(111) and si(100) using spectroscopically labeled molecules}, volume={111}, ISSN={["1932-7447"]}, DOI={10.1021/jp073824c}, abstractNote={The synthesis and surface IR characterization are reported for a series of porphyrins bearing vibrational spectroscopic labels that afford distinction of the two in-plane axes of the porphyrin ring. The labeled porphyrins include three different types of tethers for surface attachment, those containing either methylthio (−CH2S−) or benzylthio (−BzS−) for attachment to either Au or Si and a tripodal alkenyl group for attachment to Si. The spectroscopic labels are placed so as to enable distinction between the methyl group of a p-tolyl substituent that lies along the molecular axis distal to the tether versus the p-tolyl substituents that lie along the orthogonal in-plane axis lateral to the tether. The porphyrins include isotopically labeled species containing CD3 and species wherein a CF3 replaces CH3. The spectroscopically labeled molecules allow evaluation of both the tilt angle (θ) with respect to the surface normal and the rotation angle (φ) about the molecular axis. These two angles cannot be uniquel...}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Jiao, Jieying and Thamyongkit, Patchanita and Schmidt, Izabela and Lindsey, Jonathan S. and Bocian, David F.}, year={2007}, month={Aug}, pages={12693–12704} } @misc{lahaye_muthukumaran_hung_gryko_reboucas_spasojevic_batinic-haberle_lindsey_2007, title={Design and synthesis of manganese porphyrins with tailored lipophilicity: Investigation of redox properties and superoxide dismutase activity}, volume={15}, ISSN={["1464-3391"]}, DOI={10.1016/j.bmc.2007.07.015}, abstractNote={Thirteen new manganese porphyrins and two porphodimethenes bearing one to three different substituents at the meso positions in a variety of architectures have been synthesized. The substituents employed generally are (i) electron-withdrawing to tune the reduction potential to the desirable range (near +0.3V vs NHE), and/or (ii) lipophilic to target the interior of lipid bilayer membranes and/or the blood-brain barrier. The influence of the substituents on the Mn(III)/Mn(II) reduction potentials has been characterized, and the superoxide dismutase activity of the compounds has been examined.}, number={22}, journal={BIOORGANIC & MEDICINAL CHEMISTRY}, author={Lahaye, Dorothee and Muthukumaran, Kannan and Hung, Chen-Hsiung and Gryko, Dorota and Reboucas, Julio S. and Spasojevic, Ivan and Batinic-Haberle, Ines and Lindsey, Jonathan S.}, year={2007}, month={Nov}, pages={7066–7086} } @article{dogutan_ptaszek_lindsey_2007, title={Direct synthesis of magnesium porphine via 1-formyldipyrromethane}, volume={72}, ISSN={["0022-3263"]}, DOI={10.1021/jo070532z}, abstractNote={The reaction of 1-formyldipyrromethane (100 mM) in toluene at 115 degrees C containing DBU (10 mol equiv) and MgBr2 (3 mol equiv) in the presence of air affords the magnesium chelate Mg(II) porphine in 30-40% yield. The advantages of the new method include simplicity, high concentration, chromatography-free purification, gram-scale synthesis, and avoidance of the poorly soluble free base porphine. Mg(II) porphine exhibits good solubility in common organic solvents and is a valuable core scaffold for derivatization.}, number={13}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Dogutan, Dilek Kiper and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2007}, month={Jun}, pages={5008–5011} } @article{kee_kirmaier_tang_diers_muthiah_taniguchi_laha_ptaszek_lindsey_bocian_et al._2007, title={Effects of substituents on synthetic analogs of chlorophylls. Part 1: Synthesis, vibrational properties and excited-state decay characteristics}, volume={83}, ISSN={["1751-1097"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34548711333&partnerID=MN8TOARS}, DOI={10.1111/j.1751-1097.2007.00150.x}, abstractNote={AbstractUnderstanding the effects of substituents on the spectra of chlorins is essential for a wide variety of applications. Recent developments in synthetic methodology have made possible systematic studies of the properties of the chlorin macrocycle as a function of diverse types and patterns of substituents. In this paper, the spectral, vibrational and excited‐state decay characteristics are examined for a set of synthetic chlorins. The chlorins bear substituents at the 5,10,15 (meso) positions or the 3,13 (β) positions (plus 10‐mesityl in a series of compounds) and include 24 zinc chlorins, 18 free base (Fb) analogs and one Fb or zinc oxophorbine. The oxophorbine contains the keto‐bearing isocyclic ring present in the natural photosynthetic pigments (e.g. chlorophyll a). The substituents cause no significant perturbation to the structure of the chlorin macrocycle, as evidenced by the vibrational properties investigated using resonance Raman spectroscopy. In contrast, the fluorescence properties are significantly altered due to the electronic effects of substituents. For example, the fluorescence wavelength maximum, quantum yield and lifetime for a zinc chlorin bearing 3,13‐diacetyl and 10‐mesityl groups (662 nm, 0.28, 6.0 ns) differ substantially from those of the parent unsubstituted chlorin (602 nm, 0.062, 1.7 ns). Each of these properties of the lowest singlet excited state can be progressively stepped between these two extremes by incorporating different substituents. These perturbations are associated with significant changes in the rate constants of the decay pathways of the lowest excited singlet state. In this regard, the zinc chlorins with the red‐most fluorescence also have the greatest radiative decay rate constant and are expected to have the fastest nonradiative internal conversion to the ground state. Nonetheless, these complexes have the longest singlet excited‐state lifetime. The Fb chlorins bearing the same substituents exhibit similar fluorescence properties. Such combinations of factors render the chlorins suitable for a range of applications that require tunable coverage of the solar spectrum, long‐lived excited states and red‐region fluorescence.}, number={5}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Kee, Hooi Ling and Kirmaier, Christine and Tang, Quin and Diers, James R. and Muthiah, Chinnasamy and Taniguchi, Masahiko and Laha, Joydev K. and Ptaszek, Marcin and Lindsey, Jonathan S. and Bocian, David F. and et al.}, year={2007}, pages={1110–1124} } @article{kee_kirmaier_tang_diers_muthiah_taniguchi_laha_ptaszek_lindsey_bocian_et al._2007, title={Effects of substituents on synthetic analogs of chlorophylls. Part 2: Redox properties, optical spectra and electronic structure}, volume={83}, ISSN={["1751-1097"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34548759138&partnerID=MN8TOARS}, DOI={10.1111/j.1751-1097.2007.00151.x}, abstractNote={AbstractThe optical absorption spectra and redox properties are presented for 24 synthetic zinc chlorins and 18 free base analogs bearing a variety of 3,13 (β) and 5,10,15 (meso) substituents. Results are also given for a zinc and free base oxophorbine, which contain the keto‐bearing isocyclic ring present in the natural photosynthetic pigments such as chlorophyll a. Density functional theory calculations were carried out to probe the effects of the types and positions of substituents on the characteristics (energies, electron distributions) of the frontier molecular orbitals. A general finding is that the 3,13 positions are more sensitive to the effects of auxochromes than the 5,10,15 positions. The auxochromes investigated (acetyl > ethynyl > vinyl > aryl) cause a significant redshift and intensification of the Qy band upon placement at the 3,13 positions, whereas groups at the 5,10,15 positions result in much smaller redshifts that are accompanied by a decrease in relative Qy intensity. In addition, the substituent‐induced shifts in first oxidation and reduction potentials faithfully track the energies of the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO), respectively. The calculations show that the LUMO is shifted more by substituents than the HOMO, which derives from the differences in the electron densities of the two orbitals at the substituent sites. The trends in the substituent‐induced effects on the wavelengths and relative intensities of the major features (By, Bx, Qx, Qy) in the near‐UV to near‐IR absorption bands are well accounted for using Gouterman’s four‐orbital model, which incorporates the effects of the substituents on the HOMO−1 and LUMO+1 in addition to the HOMO and LUMO. Collectively, the results and analysis presented herein and in the companion paper provide insights into the effects of substituents on the optical absorption, redox and other photophysical properties of the chlorins. These insights form a framework that underpins the rational design of chlorins for applications encompassing photomedicine and solar‐energy conversion.}, number={5}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, publisher={Wiley}, author={Kee, Hooi Ling and Kirmaier, Christine and Tang, Gun and Diers, James R. and Muthiah, Chinnasamy and Taniguchi, Masahiko and Laha, Joydev K. and Ptaszek, Marcin and Lindsey, Jonathan S. and Bocian, David F. and et al.}, year={2007}, pages={1125–1143} } @article{stromberg_marton_kee_kirmaier_diers_muthiah_taniguchi_lindsey_bocian_meyer_et al._2007, title={Examination of tethered porphyrin, chlorin, and bacteriochlorin molecules in mesoporous metal-oxide solar cells}, volume={111}, ISSN={["1932-7447"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-35748969147&partnerID=MN8TOARS}, DOI={10.1021/jp0749928}, abstractNote={The performance of five tetrapyrrole molecules as sensitizers in regenerative solar cells was evaluated. The tetrapyrroles form two sets. One set contains three meso-substituted porphyrins that differ only in the nature of their surface-binding tether:  isophthalic acid, ethynylisophthalic acid, or cyanoacrylic acid. The other set includes the ethynylisophthalic acid tether attached to porphyrin, chlorin, and bacteriochlorin macrocycles, which contain zero, one, and two saturated pyrrole rings, respectively. Incident photon-to-current efficiency was measured for each sensitizer loaded onto a mesoporous TiO2 semitransparent electrode in a solar cell. The porphyrin bearing the cyanoacrylic acid tether gives the largest peak and integrated (350−900 nm) photocurrent density of the five tetrapyrrole molecules. For this sensitizer, a quasi-monochromatic power conversion efficiency of 21% was obtained at the Soret maximum (450 nm), along with a fill factor of 0.69. To elucidate the molecular origins of the effec...}, number={42}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, publisher={American Chemical Society (ACS)}, author={Stromberg, Jonathan R. and Marton, Andras and Kee, Hooi Ling and Kirmaier, Christine and Diers, James R. and Muthiah, Chinnasamy and Taniguchi, Masahiko and Lindsey, Jonathan S. and Bocian, David F. and Meyer, Gerald J. and et al.}, year={2007}, month={Oct}, pages={15464–15478} } @article{thamyongkit_muresan_diers_holten_bocian_lindsey_2007, title={Meso-C-13-labeled porphyrins for studies of ground-state hole transfer in multiporphyrin arrays}, volume={72}, ISSN={["0022-3263"]}, DOI={10.1021/jo070593x}, abstractNote={Understanding electronic communication among interacting chromophores provides the foundation for a variety of applications. The ground-state electronic communication in diphenylethyne-linked zinc-porphyrin dyads has been investigated by a novel molecular design strategy that entails introduction of a 13C-atom (*) at specific sites of the porphyrins where there is substantial electron density in the relevant frontier (highest occupied) molecular orbital. The site of 13C substitution is at a meso-position, either the site of attachment of the linker (proximal, "P") or the site trans to the linker (distal, "D"). The substituents (R) at the non-linking meso-positions are mesityl, tridec-7-yl ("swallowtail"), or p-tolyl groups. Altogether five isotopically labeled porphyrin dyads have been prepared. The hole/electron-transfer properties of one-electron oxidized dyads have been examined by electron paramagnetic resonance (EPR) spectroscopy. The introduction of the meso-13C label provides a "clock" (via the hyperfine interactions) that allows investigation of a time scale for hole transfer that is 3-4 times shorter than that provided by the natural abundance 14N nuclei of the pyrrole nitrogen atoms. The EPR studies indicate that the hole transfer, which has been previously shown to be fast on the time scale of the 14N hyperfine clock ( approximately 220 ns), remains fast on the time scale of the 13C hyperfine clock ( approximately 50 ns).}, number={14}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Thamyongkit, Patchanita and Muresan, Ana Z. and Diers, James R. and Holten, Dewey and Bocian, David F. and Lindsey, Jonathan S.}, year={2007}, month={Jul}, pages={5207–5217} } @article{dogutan_zaidi_thamyongkit_lindsey_2007, title={New route to ABCD-porphyrins via bilanes}, volume={72}, ISSN={["1520-6904"]}, DOI={10.1021/jo701294d}, abstractNote={A new strategy for preparing porphyrins that bear up to four different meso-substituents (ABCD-porphyrins) relies on two key reactions. One key reaction entails a directed synthesis of a 1-protected 19-acylbilane by acid-catalyzed condensation at high concentration (0.5 M) of a 1-acyldipyrromethane and a 9-protected dipyrromethane-1-carbinol (derived from a 9-protected 1-acyldipyrromethane). Three protecting groups (X) were examined, including thiocyanato, ethylthio, and bromo, of which bromo proved most effective. The bilanes were obtained in 72-80% yield, fully characterized, and examined by 15N NMR spectroscopy. The second key reaction entails a one-flask transformation of the 1-protected 19-acylbilane under basic, metal-templating conditions to give the corresponding metalloporphyrin. The reaction parameters investigated for cyclization of the bilane include solvent, metal salt, base, concentration, temperature, atmosphere, and time. The best conditions entailed the 1-bromo-19-acylbilane at 100 mM in toluene containing DBU (10 mol equiv) and MgBr2 (3 mol equiv) at 115 degrees C exposed to air for 2 h, which afforded the magnesium porphyrin in 65% yield. The magnesium porphyrin is readily demetalated to give the free base porphyrin. A stepwise procedure (which entailed treatment of the 1-(ethylthio)-19-acylbilane to oxidation, metal complexation, desulfurization, carbonyl reduction, and acid-catalyzed condensation) was developed but was much less efficient than the one-flask process. The new route to ABCD-porphyrins retains the desirable features of the existing "2 + 2" (dipyrromethane + dipyrromethane-1,9-dicarbinol) method, such as absence of scrambling, yet has significant advantages. The advantages include the absence of acid in the porphyrin-forming step, the use of a metal template for cyclization, the ability to carry out the reaction at high concentration, the lack of a quinone oxidant, avoidance of use of dichloromethane, and the increased yield of macrocycle formation to give the target ABCD-metalloporphyrin.}, number={20}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Dogutan, Dilek Kiper and Zaidi, Syeda Huma H. and Thamyongkit, Patchanita and Lindsey, Jonathan S.}, year={2007}, month={Sep}, pages={7701–7714} } @article{muthiah_bhaumik_lindsey_2007, title={Rational routes to formyl-substituted chlorins}, volume={72}, ISSN={["0022-3263"]}, DOI={10.1021/jo0707885}, abstractNote={Two distinct approaches have been developed for the synthesis of chlorins bearing formyl groups: (1) reaction of an acetal-substituted 1-acyldipyrromethane with 2,3,5,6-tetrahydro-1,3,3-trimethyldipyrrin to give upon hydrolysis a 5-formylchlorin and (2) Pd-mediated coupling of a bromochlorin with a one-carbon synthon (hydroxymethyl tributyltin or CO) to give a 13-, 15-, or 3,13-formylchlorin. The zinc chlorins exhibit long-wavelength peak absorption maxima ranging from 626 to 667 nm, indicating the wavelength tunability afforded by formyl substitution.}, number={15}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Muthiah, Chinnasamy and Bhaumik, Jayeeta and Lindsey, Jonathan S.}, year={2007}, month={Jul}, pages={5839–5842} } @article{fan_taniguchi_lindsey_2007, title={Regioselective 15-bromination and functionalization of a stable synthetic bacteriochlorin}, volume={72}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34447323851&partnerID=MN8TOARS}, DOI={10.1021/jo070785s}, abstractNote={5-Methoxy-8,8,18,18-tetramethyl-2,12-di-p-tolylbacteriochlorin (MeO-BC) undergoes regioselective electrophilic bromination with NBS to give the 15-bromo analogue (MeO-BC-Br15) in 85% yield. By contrast, the bacteriochlorin lacking the 5-methoxy group (8,8,18,18-tetramethyl-2,12-di-p-tolylbacteriochlorin, H-BC) gives a mixture of two monobromo- and two dibromobacteriochlorins. Deuterium exchange of both bacteriochlorins (H-BC and MeO-BC) in acidic media (TFA-d) occurs preferentially at the beta-pyrrole positions (3, 13) > unhindered meso-positions (5, 15 for H-BC; 15 for MeO-BC) > hindered meso-positions (10, 20). The 15-bromo-5-methoxybacteriochlorin MeO-BC-Br15 was subjected to three types of Pd-mediated coupling reactions (Suzuki, Sonogashira, Hartwig-Buchwald) to give six bacteriochlorins bearing functional groups at the 15-position (49% to 85% yield). The groups include 4-(tert-butoxycarbonylmethoxy)phenyl, 4-pyridyl, 3,5-diformylphenyl, phenylethynyl, TIPS-ethynyl, and N-benzamido. The presence of the 15-ethynyl moiety shifts the position of the long-wavelength Qy band from 732 nm to approximately 753 nm. The ability to introduce a range of groups at a specific site enables synthetic bacteriochlorins to be tailored for a variety of applications.}, number={14}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Fan, Dazhong and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2007}, month={Jul}, pages={5350–5357} } @article{yao_borbas_lindsey_2008, title={Soluble precipitable porphyrins for use in targeted molecular brachytherapy}, volume={32}, ISSN={["1369-9261"]}, DOI={10.1039/b714127k}, abstractNote={In a new therapy that aims to concentrate and immobilize therapeutic radionuclides in nanoscale assemblies within solid tumors, a soluble precipitable reagent (SPR) is administered as the radionuclide carrier and is converted to non-diffusible precipitate by an enzyme located in tumor tissues. To meet the objective of such an SPR, we have prepared and examined a class of porphyrin–alkyldiphosphates that are soluble in aqueous solution and that are rendered insoluble upon removal of the two phosphate groups. The porphyrins examined herein are of the trans-AB architecture wherein the substituents are a bis(dihydroxyphosphoryloxy)alkyl group and a phenyl (or p-bromophenyl) group. Provisions for later incorporation of radionuclides have been established by preparation of the analogous copper chelate or the meso-iodo free-base porphyrin. Altogether, four porphyrins bearing a bis(dihydroxyphosphoryloxy)alkyl group were examined and found to exhibit satisfactory solubility in water (>1 mM). Dephosphorylation reactions have been carried out in vitro using the enzyme shrimp alkaline phosphatase. In each case, enzyme-induced precipitation was observed. The soluble-to-insoluble conversion has been examined by visual inspection, absorption spectroscopy, electrospray ionization mass spectrometry, and nephelometry using non-radiolabeled porphyrins.}, number={3}, journal={NEW JOURNAL OF CHEMISTRY}, author={Yao, Zhen and Borbas, K. Eszter and Lindsey, Jonathan S.}, year={2008}, pages={436–451} } @misc{ptaszek_mcdowell_taniguchi_kim_lindsey_2007, title={Sparsely substituted chlorins as core constructs in chlorophyll analogue chemistry. Part 1: Synthesis}, volume={63}, ISSN={["0040-4020"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33947635677&partnerID=MN8TOARS}, DOI={10.1016/j.tet.2007.02.038}, abstractNote={Five routes to stable chlorins bearing 0 or 1 meso substituents have been investigated, among which reaction of a 9-bromo-1-formyldipyrromethane and 2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin proved most effective. Application of this route afforded metallochlorins [Cu(II), Zn(II), Pd(II)] including the chlorin lacking any beta-pyrrole and meso substituents.}, number={18}, journal={TETRAHEDRON}, publisher={Elsevier BV}, author={Ptaszek, Marcin and McDowell, Brian E. and Taniguchi, Masahiko and Kim, Han-Je and Lindsey, Jonathan S.}, year={2007}, month={Apr}, pages={3826–3839} } @article{taniguchi_ptaszek_mcdowell_lindsey_2007, title={Sparsely substituted chlorins as core constructs in chlorophyll analogue chemistry. Part 2: Derivatization}, volume={63}, ISSN={["0040-4020"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33947700461&partnerID=MN8TOARS}, DOI={10.1016/j.tet.2007.02.076}, abstractNote={Stable chlorins bearing few or no substituents have been subjected to a variety of reactions including demetalation, magnesium insertion, oxochlorin formation, and bromination followed by Suzuki coupling. The kinetics of deuteration also have been determined for two oxochlorins and a series of chlorins bearing 0, 1, 2, or 3 meso-aryl substituents.}, number={18}, journal={TETRAHEDRON}, publisher={Elsevier BV}, author={Taniguchi, Masahiko and Ptaszek, Marcin and McDowell, Brian E. and Lindsey, Jonathan S.}, year={2007}, month={Apr}, pages={3840–3849} } @article{taniguchi_ptaszek_mcdowell_boyle_lindsey_2007, title={Sparsely substituted chlorins as core constructs in chlorophyll analogue chemistry. Part 3: Spectral and structural properties}, volume={63}, ISSN={["0040-4020"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33947694765&partnerID=MN8TOARS}, DOI={10.1016/j.tet.2007.02.040}, abstractNote={The availability of stable chlorins bearing few or no substituents has enabled a variety of fundamental studies. The studies described herein report absorption spectra of diverse chlorins, comparative NMR features of chlorins bearing 0-3 meso-aryl substituents, and X-ray structures of the fully unsubstituted chlorin and the oxochlorin.}, number={18}, journal={TETRAHEDRON}, publisher={Elsevier BV}, author={Taniguchi, Masahiko and Ptaszek, Marcin and McDowell, Brian E. and Boyle, Paul D. and Lindsey, Jonathan S.}, year={2007}, month={Apr}, pages={3850–3863} } @article{muthiah_taniguchi_kim_schmidt_kee_holten_bocian_lindsey_2007, title={Synthesis and photophysical characterization of porphyrin, chlorin and bacteriochlorin molecules bearing tethers for surface attachment}, volume={83}, ISSN={["0031-8655"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-36248978026&partnerID=MN8TOARS}, DOI={10.1111/j.1751-1097.2007.00195.x}, abstractNote={AbstractThe ability to tailor synthetic porphyrin, chlorin and bacteriochlorin molecules holds promise for diverse studies in artificial photosynthesis. Toward this goal, the synthesis and photophysical characterization of five tetrapyrrole compounds is described. Each compound bears a surface attachment group. One set contains three meso‐substituted porphyrins that differ only in the nature of a surface‐binding tether—isophthalic acid, ethynylisophthalic acid or cyanoacrylic acid. The other set includes a porphyrin, chlorin and bacteriochlorin each of which bears an ethynylisophthalic acid tether. The ester derivative of each compound was prepared for solution photophysical characterization studies. The photophysical studies include determination (in toluene or acetonitrile) of the electronic absorption and fluorescence spectra, fluorescence yield and lifetime of the lowest excited singlet state. The excited‐state lifetimes range from 1 to 5.6 ns for the five compounds. The radiative rate constant for the excited‐state decay was estimated from the photophysical data (fluorescence yield and excited‐state lifetime) and from Strickler–Berg analysis of the absorption and fluorescence spectra. The synthesis and characterization of the tetrapyrrole compounds underpin their use as sensitizers in molecular‐based solar cells.}, number={6}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, publisher={Wiley}, author={Muthiah, Chinnasamy and Taniguchi, Masahiko and Kim, Han-Je and Schmidt, Izabela and Kee, Hooi Ling and Holten, Dewey and Bocian, David F. and Lindsey, Jonathan S.}, year={2007}, pages={1513–1528} } @article{ptaszek_yao_savithri_boyle_lindsey_2007, title={Synthesis and structural properties of porphyrin analogues of bacteriochlorophyll c}, volume={63}, ISSN={["0040-4020"]}, DOI={10.1016/j.tet.2007.10.023}, abstractNote={The self-assembling photosynthetic pigment bacteriochlorophyll c contains α-hydroxyethyl and keto groups on opposite sides of the macrocycle. A porphyrin has been synthesized that contains a 3-hydroxymethyl group and a 15-ethoxycarbonyl group (ZnP2-OH). X-ray analysis of ZnP2-OH and the related porphyrin containing 5-hydroxymethyl and 15-ethoxycarbonyl groups (ZnP1-OH) in each case revealed infinite coordination polymers wherein the zinc porphyrins are bound by Zn–O coordination and are cofacially offset in a staircase architecture.}, number={51}, journal={TETRAHEDRON}, author={Ptaszek, Marcin and Yao, Zhen and Savithri, Dhanalekshmi and Boyle, Paul D. and Lindsey, Jonathan S.}, year={2007}, month={Dec}, pages={12629–12638} } @article{yao_bhaumik_dhanalekshmi_ptaszek_rodriguez_lindsey_2007, title={Synthesis of porphyrins bearing 1-4 hydroxymethyl groups and other one-carbon oxygenic substituents in distinct patterns}, volume={63}, ISSN={["0040-4020"]}, DOI={10.1016/j.tet.2007.07.108}, abstractNote={Porphyrins that bear one-carbon oxygenic substituents (hydroxymethyl, formyl, ester) directly attached to the macrocycle afford a compact architecture that is attractive for diverse applications. Routes to 9 porphyrins bearing such groups in distinct architectures (A(4)-, trans-A(2)-, trans-A(2)B(2)-, trans-AB- and trans-AB(2)C-porphyrins) have been explored (A = hydroxymethyl), including porphyrins bearing two one-carbon units in different oxidation states (hydroxymethyl/ester, formyl/ester). The hydroxymethyl group was introduced via TBDMS-protected dipyrromethane precursors.}, number={43}, journal={TETRAHEDRON}, author={Yao, Zhen and Bhaumik, Jayeeta and Dhanalekshmi, Savithri and Ptaszek, Marcin and Rodriguez, Phillip A. and Lindsey, Jonathan S.}, year={2007}, month={Oct}, pages={10657–10670} } @article{kulikov_schmidt_muresan_lee_bocian_lindsey_2007, title={Synthesis of porphyrins for metal deposition studies in molecular information storage applications}, volume={11}, ISSN={["1099-1409"]}, DOI={10.1142/S1088424607000801}, abstractNote={ Porphyrins may serve as the active charge-storage medium in memory chips. A series of 14 porphyrins (trans-A2B2, trans-AB2C, or A4 type; free base, copper or zinc chelate) has been synthesized for investigation of metal deposition on porphyrin monolayers. Each trans-AB2C porphyrin is equipped with a surface attachment group and a distal functional group (or flanking functional groups). The surface attachment groups include S-acetylthiomethyl, hydroxymethyl, TMS-ethynyl, allyl, and triallylmethyl; the functional groups include amino, cyano, dipyrrin-5-yl, formyl, and nitro; all of which are attached to the p-position of a porphyrin meso-phenyl group. Two non-redox-active triallylmethyl-substituted arenes were also prepared for use as control compounds. }, number={10}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Kulikov, Oleg V. and Schmidt, Izabela and Muresan, Ana Z. and Lee, Marcia A. -P. and Bocian, David F. and Lindsey, Jonathan S.}, year={2007}, pages={699–712} } @article{chen_zhang_wasinger_attenkofer_jennings_muresan_lindsey_2007, title={Tracking electrons and atoms in a photoexcited metalloporphyrin by X-ray transient absorption spectroscopy}, volume={129}, ISSN={["0002-7863"]}, DOI={10.1021/ja072979v}, abstractNote={Simultaneously tracking electronic and molecular structures of a photoexcited metalloporphyrin, present for only 200 ps in a dilute solution, has been realized using X-ray transient absorption spectroscopy (XTA). Using laser pulses as excitation sources and delayed X-ray pulses as probes, we were able to identify the excited state electronic configuration of a nickel porphyrin as singly occupied 3dx2-y2 and 3dz2 molecular orbitals (MOs) with an energy gap of ∼2.2 eV, and energy shifts 4pz MOs to 1.5 eV higher relative to that of the ground state, and an expanded porphyrin ring characterized by lengthening of Ni−N and Ni−C bonds. Moreover, kinetic XTA signals at different X-ray photon energies demonstrate the capability for acquiring the correlation and coherence between different optically excited states with the same technique. These results provide guidance for theoretical calculations as well as insightful understanding of optically excited states that play important roles in photochemical processes.}, number={31}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Chen, Lin X. and Zhang, Xiaoyi and Wasinger, Erik C. and Attenkofer, Klaus and Jennings, Guy and Muresan, Ana Z. and Lindsey, Jonathan S.}, year={2007}, month={Aug}, pages={9616-+} } @article{muthiah_ptaszek_nguyen_flack_lindsey_2007, title={Two complementary routes to 7-substituted chlorins. Partial mimics of chlorophyll b}, volume={72}, ISSN={["1520-6904"]}, DOI={10.1021/jo701500d}, abstractNote={Chlorophyll a and chlorophyll b exhibit distinct spectra yet differ only in the nature of a single substituent (7-methyl versus 7-formyl, respectively). Two complementary approaches have been developed for the synthesis of 7-substituted chlorins. The first approach is a de novo route wherein 2,9-dibromo-5-p-tolyldipyrromethane (Eastern half) and 9-formyl-2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin (Western half) undergo acid-catalyzed condensation followed by metal-mediated oxidative cyclization. The resulting zinc chlorin is sterically uncongested and bears (1) a geminal dimethyl group in the reduced, pyrroline ring, (2) a bromo substituent at the 7-position, and (3) a p-tolyl group at the 10-position. The second approach entails regioselective 7-bromination of a 10,15-diarylchlorin that lacks a substituent at the 5-position. In an extension of this latter approach, a 5,15-diarylchlorin that lacks a substituent at the 10-position undergoes regioselective bromination at the 8-position. The introduction of a TIPS-ethynyl, acetyl, or formyl group at the 7-position was achieved using Pd-catalyzed reactions with the corresponding 7-bromochlorin. In the 10-p-tolyl-substituted zinc chlorins, the series of substituents (7-TIPS-ethynyl, 7-acetyl, 7-formyl) progressively causes (1) a bathochromic shift in the absorption maximum of the B band (405 to 426 nm) and (2) a hypsochromic shift in the position of the Qy band (605 to 598 nm). The trends mirror those for chlorophyll b versus chlorophyll a but are of lesser magnitude. Taken together, the facile access to chlorins that bear auxochromes at the 7-position enables wavelength tunability and provides the foundation for fundamental spectroscopic studies.}, number={20}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Muthiah, Chinnasamy and Ptaszek, Marcin and Nguyen, Tien M. and Flack, Kyle M. and Lindsey, Jonathan S.}, year={2007}, month={Sep}, pages={7736–7749} } @article{zhang_wasinger_muresan_attenkofer_jennings_lindsey_chen_2007, title={Ultrafast stimulated emission and structural dynamics in nickel porphyrins}, volume={111}, ISSN={["1089-5639"]}, DOI={10.1021/jp0751763}, abstractNote={The excited-state structural dynamics of nickel(II)tetrakis(2,4,6-trimethylphenyl)porphyrin (NiTMP) and nickel(II)tetrakis(tridec-7-yl)porphyrin (NiSWTP) in a toluene solution were investigated via ultrafast transient optical absorption spectroscopy. An ultrashort stimulated emission between 620 and 670 nm from the S1 state was observed in both nickel porphyrins only when this state was directly generated via Q-band excitation, whereas such a stimulated emission was absent under B (Soret)-band excitation. Because the stimulated emission in the spectral region occurs only from the S1 state, this photoexcitation-wavelength-dependent behavior of Ni(II) porphyrins is attributed to a faster intersystem crossing from the S2 state than the internal conversion S2 --> S1. The dynamics of the excited-state pathways involving the (pi, pi*) and (d, d) states varies with the meso-substituted peripheral groups, which is attributed to the nickel porphyrin macrocycle distortion from a planar configuration. Evidence for intramolecular vibrational relaxation within 2 ps and vibrational cooling in 6-20 ps of a (d, d) excited state has been established for NiTMP and NiSWTP. Finally, the lifetimes of the vibrationally relaxed (d, d) state also depend on the nature of the peripheral groups, decreasing from 200 ps for NiTMP to 100 ps for the bulkier NiSWTP.}, number={46}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Zhang, Xiaoyi and Wasinger, Erik C. and Muresan, Ana Z. and Attenkofer, Klaus and Jennings, Guy and Lindsey, Jonathan S. and Chen, Lin X.}, year={2007}, month={Nov}, pages={11736–11742} } @article{laha_muthiah_taniguchi_lindsey_2006, title={A new route for installing the isocyclic ring on chlorins yielding 13(1)-oxophorbines}, volume={71}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33750454076&partnerID=MN8TOARS}, DOI={10.1021/jo0608265}, abstractNote={A new route to 13(1)-oxophorbines, the parent macrocycle of chlorophylls, begins with the synthesis of a 13-bromochlorin. Pd-mediated coupling of the latter with tributyl(1-ethoxyvinyl)tin and subsequent acidic hydrolysis afforded the 13-acetylchlorin (1). Treatment of 1 with NBS afforded the 15-bromo analogue in 70% yield. Pd-mediated alpha-arylation closed the isocyclic ring to give the 13(1)-oxophorbine (2) in 85% yield. Facile access to 13(1)-oxophorbines should enable a variety of spectroscopic studies and diverse applications.}, number={18}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Laha, Joydev K. and Muthiah, Chinnasamy and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2006}, month={Sep}, pages={7049–7052} } @article{thamyongkit_bhise_taniguchi_lindsey_2006, title={Alkylthio unit as an alpha-pyrrole protecting group for use in dipyrromethane synthesis}, volume={71}, ISSN={["1520-6904"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-32144435067&partnerID=MN8TOARS}, DOI={10.1021/jo051806q}, abstractNote={The synthesis of porphyrin precursors requires the successive introduction of substituents at the pyrrole α- and α‘-positions (2- and 5-, respectively). An α-pyrrole substituent that serves as a temporary masking agent and is not deactivating would greatly facilitate such syntheses, particularly for β-(3,4)-unsubstituted pyrroles, but has heretofore not been available. A series of α-RS groups (R = Me, Et, n-decyl, Ph) have been investigated in this regard, including the determination of the kinetics of substitution at the pyrrolic 3-, 4-, and 5-positions and the application to dipyrromethane formation. The RS group was readily introduced into the pyrrole α-position by the reaction of 2-thiocyanatopyrrole (prepared from pyrrole, ammonium thiocyanate, and iodine) and the corresponding Grignard reagent RMgBr. Each 2-alkylthio group activated the pyrrole ring toward deuteration at the 3- or 5- (vs 4-) position. The dipyrromethane synthesis was carried out using a 2:1 ratio of 2-(RS)pyrrole/benzaldehyde with a...}, number={3}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Thamyongkit, P and Bhise, AD and Taniguchi, M and Lindsey, JS}, year={2006}, month={Feb}, pages={903–910} } @article{borbas_mroz_hamblin_lindsey_2006, title={Bioconjugatable porphyrins bearing a compact swallowtail motif for water solubility}, volume={17}, ISSN={["1043-1802"]}, DOI={10.1021/bc050337w}, abstractNote={A broad range of applications requires access to water-soluble, bioconjugatable porphyrins. Branched alkyl groups attached at the branching site to the porphyrin meso position are known to impart high organic solubility. Such "swallowtail" motifs bearing a polar group (hydroxy, dihydroxyphosphoryl, dihydroxyphosphoryloxy) at the terminus of each branch have now been incorporated at a meso site in trans-AB-porphyrins. The incorporation of the swallowtail motif relies on rational synthetic methods whereby a 1,9-bis(N-propylimino)dipyrromethane (bearing a bioconjugatable tether at the 5-position) is condensed with a dipyrromethane (bearing a protected 1,5-dihydroxypent-3-yl unit at the 5-position). The two hydroxy groups in the swallowtail motif of each of the resulting zinc porphyrins can be transformed to the corresponding diphosphate or diphosphonate product. A 4-(carboxymethyloxy)phenyl group provides the bioconjugatable tether. The six such porphyrins reported here are highly water-soluble (> or =20 mM at room temperature in water at pH 7) as determined by visual inspection, UV-vis absorption spectroscopy, or 1H NMR spectroscopy. Covalent attachment was carried out in aqueous solution with the unprotected porphyrin diphosphonate and a monoclonal antibody against the T-cell receptor CD3epsilon. The resulting conjugate performed comparably to a commercially available fluorescein isothiocyanate-labeled antibody with Jurkat cells in flow cytometry and fluorescence microscopy assays. Taken together, this work enables preparation of useful quantities of water-soluble, bioconjugatable porphyrins in a compact architecture for applications in the life sciences.}, number={3}, journal={BIOCONJUGATE CHEMISTRY}, author={Borbas, K. Eszter and Mroz, Pawel and Hamblin, Michael R. and Lindsey, Jonathan S.}, year={2006}, month={May}, pages={638–653} } @article{lysenko_thamyongkit_schmidt_diers_bocian_lindsey_2006, title={Diverse porphyrin dimers as candidates for high-density charge-storage molecules}, volume={10}, ISSN={["1099-1409"]}, DOI={10.1142/S1088424606000041}, abstractNote={ Porphyrinic molecules have been shown to be viable candidates for a molecular-based information storage medium on the basis of redox activity. An optimal redox-based information storage medium requires a large charge density in the molecular footprint on the anchoring substrate. The use of dimeric versus monomeric architectures affords one route to achieving increased charge density without sacrificing surface cross sectional area. Towards this goal, a series of zinc and cobalt containing porphyrin dimers has been prepared and characterized. The interporphyrin linkages in the dimers include p-phenylene, ethynyl, 1,4-butadiynyl, and ethynylphenylethynyl joining porphyrin meso-positions; Crossley-type fusion bridging porphyrin β-positions, and Osuka-type triple fusions bridging one meso- and two β-positions. The electrochemical features of each dimer have been evaluated. }, number={1}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Lysenko, Andrey B. and Thamyongkit, Patchanita and Schmidt, Izabela and Diers, James R. and Bocian, David F. and Lindsey, Jonathan S.}, year={2006}, pages={22–32} } @article{song_kirmaier_schwartz_hindin_yu_bocian_lindsey_holten_2006, title={Effects of multiple pathways on excited-state energy flow in self-assembled wheel-and-spoke light-harvesting architectures}, volume={110}, ISSN={["1520-6106"]}, DOI={10.1021/jp064001a}, abstractNote={Static and time-resolved optical measurements are reported for three cyclic hexameric porphyrin arrays and their self-assembled complexes with guest chromophores. The hexameric hosts contain zinc porphyrins and 0, 1, or 2 free base (Fb) porphyrins (denoted Zn(6), Zn(5)Fb, or Zn(4)Fb(2), respectively). The guest is a core-modified (O replacing one of the four N atoms) dipyridyl-substituted Fb porphyrin (DPFbO) that coordinates to zinc porphyrins of a host via pyridyl-zinc dative bonding. Each architecture is designed to have a gradient of excited-state energies for excitation funneling among the weakly coupled constituents of the host to the guest. Energy transfer to the lowest-energy chromophore(s) (coordinated zinc porphyrins or Fb porphyrins) within a hexameric host occurs primarily via a through-bond (TB) mechanism, is rapid ( approximately 40 ps), and is essentially quantitative (>or=98%). Energy transfer from a pyridyl-coordinated zinc porphyrin of the host to the guest in the Zn(6)*DPFbO complex has a yield of approximately 75%, a rate constant of approximately (0.7 ns)(-1), and significant Förster through-space (TS) character. In the case of Zn(5)Fb*DPFbO, which has an additional TS route via the Fb porphyrin with a rate constant of approximately (20 ns)(-1), the yield of energy transfer to the guest is somewhat lower ( approximately 50%) than that for Zn(6)*DPFbO. Complex Zn(4)Fb(2)*DPFbO has an identical TS pathway via the Fb porphyrin plus an additional TS pathway involving the second Fb porphyrin (closer to the guest) with a rate constant of approximately (0.5 ns)(-1). This complex exhibits an energy-transfer yield to the guest that is significantly enhanced over that for Zn(5)Fb*DPFbO and comparable to that for Zn(6)*DPFbO. Collectively, the results for the various arrays suggest designs for similar host-guest complexes that are expected to exhibit much more efficient light harvesting and excitation trapping at the central guest chromophore.}, number={39}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Song, Hee-eun and Kirmaier, Christine and Schwartz, Jennifer K. and Hindin, Eve and Yu, Lianhe and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2006}, month={Oct}, pages={19131–19139} } @article{schmidt_jiao_thamyongkit_sharada_bocian_lindsey_2006, title={Investigation of stepwise covalent synthesis on a surface yielding porphyrin-based multicomponent architectures}, volume={71}, ISSN={["0022-3263"]}, DOI={10.1021/jo052650x}, abstractNote={Porphyrins have been shown to be a viable medium for use in molecular-based information storage applications. The success of this application requires the construction of a stack of components ("electroactive surface/tether/charge-storage molecule/linker/electrolyte/top contact") that can withstand high-temperature conditions during fabrication (up to 400 degrees C) and operation (up to 140 degrees C). To identify suitable chemistry that enables in situ stepwise synthesis of covalently linked architectures on an electroactive surface, three sets of zinc porphyrins (22 altogether) have been prepared. In the set designed to form the base layer on a surface, each porphyrin incorporates a surface attachment group (triallyl tripod or vinyl monopod) and a distal functional group (e.g., pentafluorophenyl, amine, bromo, carboxy) for elaboration after surface attachment. A second set designed for in situ dyad construction incorporates a single functional group (alcohol, isothiocyanato) that is complementary to the functional group in the base porphyrins. A third set designed for in situ multad construction incorporates two identical functional groups (bromo, alcohol, active methylene, amine, isothiocyanato) in a trans configuration (5,15-positions in the porphyrin). Each porphyrin that bears a surface attachment group was found to form a good quality monolayer on Si(100) as evidenced by the voltammetric and vibrational signatures. One particularly successful chemistry identified for stepwise growth entailed reaction of a surface-tethered porphyrin-amine with a dianhydride (e.g., 3,3',4,4'-biphenyltetracarboxylic dianhydride), forming the monoimide/monoanhydride. Subsequent reaction with a diamine (e.g., 4,4'-methylene-bis(2,6-dimethylaniline)) gave the bis(imide) bearing a terminal amine. Repetition of this stepwise growth process afforded surface-bound oligo-imide architectures composed of alternating components without any reliance on protecting groups. Taken together, the ability to prepare covalently linked constructs on a surface without protecting groups in a stepwise manner augurs well for the systematic preparation of a wide variety of functional molecular devices.}, number={8}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Schmidt, I and Jiao, JY and Thamyongkit, P and Sharada, DS and Bocian, DF and Lindsey, JS}, year={2006}, month={Apr}, pages={3033–3050} } @article{bhaumik_yao_borbas_taniguchi_lindsey_2006, title={Masked imidazolyl-dipyrromethanes in the synthesis of imidazole-substituted porphyrins}, volume={71}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33750879603&partnerID=MN8TOARS}, DOI={10.1021/jo061461r}, abstractNote={Imidazole-substituted metalloporphyrins are valuable for studies of self-assembly and for applications where water solubility is required. Rational syntheses of porphyrins bearing one or two imidazol-2-yl or imidazol-4-yl groups at the meso positions have been developed. The syntheses employ dipyrromethanes, 1-acyldipyrromethanes, and 1,9-diacyldipyrromethanes bearing an imidazole group at the 5-position. The polar, reactive imidazole unit was successfully masked by use of (1) the 2-(trimethylsilyl)ethoxymethyl (SEM) group at the imidazole pyrrolic nitrogen, and (2) a dialkylboron motif bound to the pyrrole of the dipyrromethane and coordinated to the imidazole imino nitrogen. The nonpolar nature of such doubly masked imidazolyl-dipyrromethanes facilitated handling. Selected masked dipyrromethanes were characterized by 11B and 15N NMR spectroscopy. Five distinct methods were examined to obtain trans-A2B2-, trans-AB2C-, and trans-AB-porphyrins. Each porphyrin contained one or two SEM-protected imidazole units. The SEM group could be removed with TBAF or HCl. Two zinc(II) porphyrins and a palladium(II) porphyrin bearing a single imidazole moiety were prepared and subjected to alkylation (with ethyl iodide, 1,3-propane sultone, or 1,4-butane sultone) to give water-soluble imidazolium- porphyrins. This work establishes the foundation for the rational synthesis of a variety of porphyrins containing imidazole units.}, number={23}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Bhaumik, Jayeeta and Yao, Zhen and Borbas, K. Eszter and Taniguchi, Masahiko and Lindsey, Jonathan S.}, year={2006}, month={Nov}, pages={8807–8817} } @article{song_kirmaier_schwartz_hindin_yu_bocian_lindsey_holten_2006, title={Mechanisms, pathways, and dynamics of excited-state energy flow in self-assembled wheel-and-spoke light-harvesting architectures}, volume={110}, ISSN={["1520-6106"]}, DOI={10.1021/jp064000i}, abstractNote={Static and time-resolved optical measurements are reported for two cyclic hexameric porphyrin arrays and their self-assembled complexes with guest chromophores. The hexameric hosts contain zinc porphyrins and 0 or 3 free base (Fb) porphyrins (denoted Zn(6) or Zn(3)Fb(3), respectively). The guests are a tripyridyl arene (TP) and a dipyridyl-substituted free base porphyrin (DPFb), each of which coordinates to zinc porphyrins of a host via pyridyl-zinc dative bonding. Each architecture is designed to have an overall gradient of excited-state energies that affords excitation funneling within the host and ultimately to the guest. Collectively, the studies delineate the various pathways, mechanisms, and rate constants of energy flow among the weakly coupled constituents of the host-guest complexes. The pathways include downhill unidirectional energy transfer between adjacent chromophores, bidirectional energy migration between identical chromophores, and energy transfer between nonadjacent chromophores. The energy transfer to the lowest-energy chromophore(s) within the backbone of a hexameric host (Fb porphyrins in Zn(3)Fb(3) or pyridyl-coordinated zinc porphyrins in Zn(6)*TP and Zn(6)*DPFb) proceeds primarily via a through-bond mechanism; the transfer is rapid (approximately 40 ps depending on the array) and essentially quantitative (>or=98%). The energy transfer from a pyridyl-coordinated zinc porphyrin of the host to the Fb porphyrin guest in the Zn(6)*DPFb complex is almost exclusively Förster through-space in nature; this process is much slower ( approximately 1 ns) and has a lower yield (65%). These studies highlight the utility of cyclic architectures for efficient light harvesting and energy transfer to a designated trapping site.}, number={39}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Song, Hee-eun and Kirmaier, Christine and Schwartz, Jennifer K. and Hindin, Eve and Yu, Lianhe and Bocian, David F. and Lindsey, Jonathan S. and Holten, Dewey}, year={2006}, month={Oct}, pages={19121–19130} } @article{zaidi_loewe_clark_jacob_lindsey_2006, title={Nearly chromatography-free synthesis of the A(3)B-porphyrin 5-(4-hydroxymethylphenyl)-10,15,20-tri-p-tolylporphinatozinc(II)}, volume={10}, ISSN={["1520-586X"]}, DOI={10.1021/op0502553}, abstractNote={Rational routes to synthetic porphyrins bearing distinct meso-substituents have typically been implemented at modest scale ( 10:1 ratio (versus 4:1 using EtMgBr), (iii) isolation of the dibutyltin complex of the 1,9-diacyl...}, number={2}, journal={ORGANIC PROCESS RESEARCH & DEVELOPMENT}, author={Zaidi, SHH and Loewe, RS and Clark, BA and Jacob, MJ and Lindsey, JS}, year={2006}, pages={304–314} } @article{thamyongkit_yu_padmaja_jiao_bocian_lindsey_2006, title={Porphyrin dyads bearing carbon tethers for studies of high-density molecular charge storage on silicon surfaces}, volume={71}, ISSN={["1520-6904"]}, DOI={10.1021/jo0522761}, abstractNote={Redox-active molecules that afford high charge density upon attachment to an electroactive surface are of interest for use in molecular-based information-storage applications. One strategy for increasing charge density is to covalently link a second redox center to the first in an architecture that uses the vertical dimension in essentially the same molecular footprint. Toward this end, a set of four new porphyrin dyads have been prepared and characterized. Each dyad consists of two zinc porphyrins, an intervening linker (p-phenylene or 4,4'-diphenylethyne), and a surface attachment group (ethynyl or triallyl group). The porphyrin dyads were attached to an electroactive Si(100) surface and interrogated via electrochemical and FTIR techniques. The charge density obtainable for the ethynyl-functionalized porphyrin dyads is approximately double that observed for an analogously functionalized monomer, whereas that for the triallyl-functionalized dyads is at most 40% larger. These results indicate that the molecular footprint of the former dyads is similar to that of a monomer while that of the latter dyads is larger. For both the ethynyl- and triallyl-functionalized porphyrin dyads, higher charge densities (smaller molecular footprints) are obtained for the molecules containing the 4,4'-diphenylethyne versus the p-phenylene linker. This feature is attributed to the enhanced torsional flexibility of the former linker compared with that of the latter, which affords better packed monolayers. The FTIR studies indicate that the adsorption geometry of all the dyads is qualitatively similar and similar to that of monomers. However, the dyads containing the 4,4'-diphenylethyne linker sit somewhat more upright on the surface than those containing the p-phenylene linker, generally consistent with the smaller molecular footprint for the former dyads. Collectively, the high surface charge density (34-58 muC.cm(-)(2)) of the porphyrin dyads makes these constructs viable candidates for molecular-information-storage applications.}, number={3}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Thamyongkit, P and Yu, LH and Padmaja, K and Jiao, JY and Bocian, DF and Lindsey, JS}, year={2006}, month={Feb}, pages={1156–1171} } @article{jiao_anariba_tiznado_schmidt_lindsey_zaera_bocian_2006, title={Stepwise formation and characterization of covalently linked multiporphyrin-imide architectures on Si(100)}, volume={128}, ISSN={["1520-5126"]}, DOI={10.1021/ja060906q}, abstractNote={A major challenge in molecular electronics and related fields entails the fabrication of elaborate molecular architectures on electroactive surfaces to yield hybrid molecular/semiconductor systems. A method has been developed for the stepwise synthesis of oligomers of porphyrins linked covalently via imide units. A triallyl-porphyrin bearing an amino group serves as the base unit on Si(100), and the alternating use of a dianhydride (3,3',4,4'-biphenyltetracarboxylic dianhydride) and a porphyrin-diamine for reaction enables the rapid and simple buildup of oligomers composed of 2-5 porphyrins. The properties of these porphyrin "multad" films on Si(100) were interrogated using a variety of techniques. The charge densities of the redox-active porphyrin oligomers were determined via electrochemical methods. The stepwise growth was evaluated in detail via Fourier transform infrared (FTIR) spectroscopy and by selected X-ray photoelectron spectroscopic (XPS) studies. The morphology was probed via AFM methods. Finally, the thickness was evaluated by using a combination of ellipsometry and AFM height profiling, accompanied by selected XPS studies. Collectively, these studies demonstrate that high charge density, ultrathin, multiporphyrin films of relatively well-controlled thickness can be grown in a stepwise fashion using the imide-forming reaction. The increased charge densities afforded by the porphyrin multads may prove important for the fabrication of molecular-based information-storage devices. This bottom-up process for construction of surface-tethered molecular architectures complements the top-down lithographic approach for construction of functional devices with nanoscale dimensions.}, number={21}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Jiao, Jieying and Anariba, Franklin and Tiznado, Hugo and Schmidt, Izabela and Lindsey, Jonathan S. and Zaera, Francisco and Bocian, David F.}, year={2006}, month={May}, pages={6965–6974} } @article{ptaszek_mcdowell_lindsey_2006, title={Synthesis of 1-formyldipyrromethanes}, volume={71}, ISSN={["0022-3263"]}, DOI={10.1021/jo060119b}, abstractNote={1-Formyldipyrromethanes are versatile precursors to porphyrins and chlorins. Two methods of synthesis of 1-formyldipyrromethanes have been investigated: (1) Vilsmeier formylation followed by selective removal of the unwanted 1,9-diformyldipyrromethane by dialkyltin complexation and (2) reaction with mesitylmagnesium bromide (MesMgBr) followed by formylation with phenyl formate. The two approaches are complementary (acidic versus basic conditions; statistical versus selective formylation). The latter was found to be more efficient for the preparation of 1-formyldipyrromethanes.}, number={11}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Ptaszek, Marcin and McDowell, Brian E. and Lindsey, Jonathan S.}, year={2006}, month={May}, pages={4328–4331} } @article{kim_dogutan_ptaszek_lindsey_2007, title={Synthesis of hydrodipyrrins tailored for reactivity at the 1- and 9-positions}, volume={63}, ISSN={["0040-4020"]}, DOI={10.1016/j.tet.2006.10.027}, abstractNote={A collection of 33 hydrodipyrrins (9 targets, 21 intermediates, and 3 byproducts) has been prepared. The hydrodipyrrins (dihydrodipyrrins, tetrahydrodipyrrins, and hexahydrodipyrrins) contain a pyrrole ring and a geminal-dimethyl substituted 1-pyrroline (or pyrrolidine) ring. The alpha-substituents on the pyrrole ring (H, Br, CHO) and pyrroline ring (H, CH(3), CH(OR)(2), OMe, SMe) provide different reactivity combinations (Nu(-), E(+)) and 0, 1, or 2 carbon atoms (which can give rise to the bridging meso-carbons in hydroporphyrins). Straightforward access to various hydrodipyrrins should facilitate development of syntheses of diverse hydroporphyrins.}, number={1}, journal={TETRAHEDRON}, author={Kim, Han-Je and Dogutan, Dilek Kiper and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2007}, month={Jan}, pages={37–55} } @article{laha_muthiah_taniguchi_mcdowell_ptaszek_lindsey_2006, title={Synthetic chlorins bearing auxochromes at the 3- and 13-positions}, volume={71}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33646926396&partnerID=MN8TOARS}, DOI={10.1021/jo060208o}, abstractNote={Synthetic chlorins bearing diverse auxochromes at the 3- and 13-positions of the macrocycle are valuable targets given their resemblance to chlorophylls a and b, which bear 3-vinyl and 13-keto groups. A de novo route has been exploited to construct nine zinc chlorins bearing substituents at the 3- and 13-positions and two benchmark zinc chlorins lacking such substituents. The chlorins are sterically uncongested and bear (1) a geminal dimethyl group in the reduced pyrroline ring, (2) a H, an acetyl, a triisopropylsilylethynyl (TIPS-ethynyl), or a vinyl at the 3-position, (3) a H, an acetyl, or TIPS-ethynyl at the 13-position, and (4) a H or a mesityl at the 10-position. The synthesis of the 13-substituted chlorins relied on p-TsOH x H2O-catalyzed condensation of an 8,9-dibromo-1-formyldipyrromethane (eastern half) and 2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin (western half), followed by metal-mediated oxidative cyclization, affording the 13-bromochlorin. Similar use of a bromo- or TIPS-ethynyl-substituted western half provided access to 3-substituted chlorins. A 3-bromo, 13-bromo, or 3,13-dibromochlorin was further transformed by Pd-coupling to introduce the vinyl group (via tributylvinyltin), TIPS-ethynyl group (via TIPS-acetylene), or acetyl group (via tributyl(1-ethoxyvinyl)tin, followed by acidic hydrolysis). In the 10-mesityl-substituted zinc chlorins, the series of substituents, 3-vinyl, 13-TIPS-ethynyl, 3-TIPS-ethynyl, 13-acetyl, 3,13-bis(TIPS-ethynyl), 3-TIPS-ethynyl-13-acetyl, or 3,13-diacetyl, progressively causes (1) a redshift in the absorption maximum of the B band (405-436 nm) and the Q(y) band (606-662 nm), (2) a relative increase in the intensity of the Q(y) band (I(B)/I(Q) = 4.2-1.5), and (3) an increase in the fluorescence quantum yield phi(f) (0.059-0.29). The zinc chlorins bearing a 3-TIPS-ethynyl-13-acetyl or a 3,13-diacetyl group exhibit a number of spectral properties resembling those of chlorophyll a or its zinc analogue. Taken together, this study provides access to finely tuned chlorins for spectroscopic studies and diverse applications.}, number={11}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Laha, Joydev K. and Muthiah, Chinnasamy and Taniguchi, Masahiko and McDowell, Brian E. and Ptaszek, Marcin and Lindsey, Jonathan S.}, year={2006}, month={May}, pages={4092–4102} } @article{hasselman_watson_stromberg_bocian_holten_lindsey_meyer_2006, title={Theoretical solar-to-electrical energy-conversion efficiencies of perylene-porphyrin light-harvesting arrays}, volume={110}, ISSN={["1520-6106"]}, DOI={10.1021/jp064547x}, abstractNote={The efficiencies of organic solar cells that incorporate light-harvesting arrays of organic pigments were calculated under 1 sun of air mass 1.5 solar irradiation. In one set of calculations, photocurrent efficiencies were evaluated for porphyrin, phthalocyanine, chlorin, bacteriochlorin, and porphyrin-bis(perylene) pigment arrays of different length and packing densities under the assumption that each solar photon absorbed quantitatively yielded one electron in the external circuit. In another more realistic set of calculations, solar conversion efficiencies were evaluated for arrays comprising porphyrins or porphyrin-(perylene)2 units taking into account competitive excited-state relaxation pathways. A system of coupled differential equations for all reactions in the arrays was solved on the basis of previously published rate constants for (1) energy transfer between the perylene and porphyrin pigments, (2) excited-state relaxation of the perylene and porphyrin pigments, and (3) excited-state electron injection into the semiconductor. This formal analysis enables determination of the optimal number of pigments in an array for solar-to-electrical energy conversion. The optimal number of pigments depends on the molar absorption coefficient and the density at which the arrays can be packed on an electrode surface. Taken together, the ability to employ fundamental photophysical, kinetic, and structural parameters of modular molecular architectures in assessments of the efficiency of solar-to-electrical energy conversion should facilitate the design of molecular-based solar cells.}, number={50}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Hasselman, Georg M. and Watson, David F. and Stromberg, Jonathan R. and Bocian, David F. and Holten, Dewey and Lindsey, Jonathan S. and Meyer, Gerald J.}, year={2006}, month={Dec}, pages={25430–25440} } @article{padmaja_youngblood_wei_bocian_lindsey_2006, title={Triple-decker sandwich compounds bearing compact triallyl tripods for molecular information storage applications}, volume={45}, ISSN={["1520-510X"]}, DOI={10.1021/ic060387s}, abstractNote={The design of redox-active molecules that afford multistate operation and high charge density is essential for molecular information storage applications. Triple-decker sandwich compounds composed of two lanthanide metal ions and three porphyrinic ligands exhibit a large number of oxidation states within a relatively narrow electrochemical window. High charge density requires a small footprint upon tethering triple deckers to an electroactive surface. All triple deckers examined to date for information storage have been tethered via the terminal ligand and have exhibited large footprints (approximately 670 A2). Five new homonuclear (Eu or Ce) triple deckers have been prepared (via statistical or rational methods) to examine the effect of tether attachment site on molecular footprint. Three triple deckers are tethered via the terminal ligand (porphyrin) or central ligand (porphyrin or imidazophthalocyanine), whereas two triple deckers each bear two tethers, one at each terminal ligand. The tether is a compact triallyl tripod. Monolayers of the triple deckers on Si(100) were examined by electrochemical and FTIR techniques. Each triple decker exhibited the expected four resolved voltammetric waves, owing to formation of the mono-, di-, tri-, and tetracations. The electrochemical studies of surface coverage (gamma, obtained by integrating the voltammetric waves) reveal that coverages approaching 10(-10) mol cm(-2), corresponding to a molecular footprint of approximately 170 A2, are readily achieved for all five of the triple deckers. The surface coverage observed for the tripodal functionalized triple deckers is approximately 4-fold higher than that obtained for monopodal-functionalized triple deckers (carbon, oxygen, or sulfur anchor atoms) attached to either Si(100) or Au(111). The fact that similar, relatively high, surface coverages can be achieved regardless of the location (or number) of the tripodal tether indicates that the tripodal functionalization, rather than the location of the tether, is the primary determinant of the packing density.}, number={14}, journal={INORGANIC CHEMISTRY}, author={Padmaja, Kisari and Youngblood, W. Justin and Wei, Lingyun and Bocian, David F. and Lindsey, Jonathan S.}, year={2006}, month={Jul}, pages={5479–5492} } @article{fan_taniguchi_yao_dhanalekshmi_lindsey_2005, title={1,9-bis(N,N-dimethylaminomethyl)dipyrromethanes in the synthesis of porphyrins bearing one or two meso substituents}, volume={61}, ISSN={["0040-4020"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-25144489698&partnerID=MN8TOARS}, DOI={10.1016/j.tet.2005.08.028}, abstractNote={A synthesis of 5,15-disubstituted zinc-porphyrins has been developed that employs condensation of a 1,9-bis(N,N-dimethylaminomethyl)dipyrromethane+a dipyrromethane in refluxing ethanol containing zinc acetate followed by oxidation with DDQ. The N,N-dimethylaminomethylation of the dipyrromethane was achieved via Eschenmoser's reagent (N,N-dimethylmethyleneammonium iodide) in CH2Cl2 at room temperature. The synthesis is compatible with diverse substituents (e.g., alkyl, aryl, ester, acetal) and enables rapid synthesis of trans-AB-, A2-, and A-porphyrins. The synthesis of >40 zinc porphyrins has been surveyed; 13 zinc porphyrins were isolated in yields of 5–20% without detectable scrambling.}, number={43}, journal={TETRAHEDRON}, publisher={Elsevier BV}, author={Fan, DZ and Taniguchi, M and Yao, Z and Dhanalekshmi, S and Lindsey, JS}, year={2005}, month={Oct}, pages={10291–10302} } @article{padmaja_wei_lindsey_bocian_2005, title={A compact all-carbon tripodal tether affords high coverage of porphyrins on silicon surfaces}, volume={70}, ISSN={["0022-3263"]}, DOI={10.1021/jo0510078}, abstractNote={[Structure: See text] Redox-active molecules designed to give high charge density on electroactive surfaces are essential for applications in molecular information storage. To achieve a small molecular footprint and thereby high surface charge density, a compound consisting of a triallyl tripod attached via a p-phenylene unit to a porphyrin (1) has been synthesized. The zinc chelate of 1 (Zn-1) was attached to Si(100). Electrochemical measurements indicate that the molecular footprint (75 A) in the monolayer is only approximately 50% larger than the minimum achievable, indicating high surface coverage. IR spectroscopy indicates that the bands due to the nu(C=C) (1638 cm(-1)) and gamma(CH) (915 cm(-1)) vibrations present in the solid sample (KBr pellet) are absent from the spectra of the monolayers of Zn-1, consistent with saturation of the double bond in each of the three legs of the tripod upon the hydrosilylation process accompanying attachment. Comparison of the relative intensities of the in-plane (998 cm(-1)) versus out-of-plane (797 cm(-1)) porphyrin modes indicates the average tilt angle (alpha) of the porphyrin ring with respect to the surface normal is approximately 46 degrees , a value also observed for analogous porphyrins tethered to Si(100) via monopodal carbon linkers. Accordingly, the higher packing densities afforded by the compact tripodal linker are not due to a more upright orientation on the surface. The charge-retention half-lives (t1/2) for the first oxidation state of the Zn-1 monolayers increase from 10 to 50 s at low surface coverage (1-5 x 10(-11) mol.cm(-2)) to near 200 s at saturation coverage (approximately 2 x 10(-10) mol.cm(-2)). Taken together, the high surface charge density (despite the lack of upright orientation) of the triallyl-tripodal porphyrin makes this construct a viable candidate for molecular information storage applications.}, number={20}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Padmaja, K and Wei, LY and Lindsey, JS and Bocian, DF}, year={2005}, month={Sep}, pages={7972–7978} } @article{wei_tiznado_liu_padmaja_lindsey_zaera_bocian_2005, title={Adsorption characteristics of tripodal thiol-functionalized porphyrins on gold}, volume={109}, ISSN={["1520-6106"]}, DOI={10.1021/jp0537005}, abstractNote={X-ray photoelectron and Fourier transform infrared spectroscopy studies are reported for self-assembled monolayers (SAMs) of two tripodal thiol-functionalized metalloporphyrins (Zn and Cu) and three benchmark tripods on gold substrates. The tripodal unit common to all five molecules is 1-(phenyl)-1,1,1-tris(4-mercaptomethylphenyl)methane (Tpd). Both porphyrins contain S-acetyl-protected thiols and are linked to the 4-position of the phenyl ring of Tpd via a phenylethyne group. The benchmark molecules include (1) two tripods containing a bromine atom at the 4-position of the apical phenyl ring, one a free thiol and the other its S-acetyl-protected analogue, and (2) a S-acetyl-protected tripod containing a phenylethyne unit at the 4-position of the apical phenyl group. Together, the spectroscopic studies reveal that none of the five tripodal molecules bond to the gold surface via all three sulfur atoms. Instead, the average number of bound thiols ranges from 1.5 to 2, with the porphyrinic molecules generally falling at the middle to upper end of the range and the smallest benchmark tripods falling at the lower end. Similar surface binding is found for the S-acetyl-protected and free benchmark tripods, indicating that the presence of the protecting group does not influence binding. Furthermore, the surface binding characteristics of the SAMs are not sensitive to deposition conditions such as solvent type, deposition time, or temperature of the solution.}, number={50}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Wei, LY and Tiznado, H and Liu, GM and Padmaja, K and Lindsey, JS and Zaera, F and Bocian, DF}, year={2005}, month={Dec}, pages={23963–23971} } @article{kim_lindsey_2005, title={De novo synthesis of stable tetrahydroporphyrinic macrocycles: Bacteriochlorins and a tetradehydrocorrin}, volume={70}, ISSN={["0022-3263"]}, DOI={10.1021/jo050467y}, abstractNote={[structures: see text] Bacteriochlorins (tetrahydroporphyrins) are attractive for diverse photochemical applications owing to their strong absorption in the near-infrared spectral region, as exemplified by the bacterial photosynthetic pigment bacteriochlorophyll a, yet often are labile toward dehydrogenation to give the chlorin. Tetradehydrocorrins (ring-contracted tetrahydroporphyrins) are attractive for studies of catalysis analogous to that of vitamin B12. An eight-step synthesis toward such tetrahydroporphyrinic macrocycles begins with p-tolualdehyde and proceeds to a dihydrodipyrrin-acetal (1) bearing a geminal dimethyl group and a p-tolyl substituent. Self-condensation of 1 in CH3CN containing BF3 x OEt2 at room temperature afforded a readily separable mixture of two free base bacteriochlorins and a free base B,D-tetradehydrocorrin. Each bacteriochlorin contains two geminal dimethyl groups to lock-in the bacteriochlorin hydrogenation level, p-tolyl substituents at opposing (2,12) beta-positions, and the absence (H-BC) or presence (MeO-BC) of a methoxy group at the 5- (meso) position. The B,D-tetradehydrocorrin (TDC) lies equidistant between the hydrogenation levels of corrin and corrole, is enantiomeric, and contains two geminal dimethyl groups, 2,12-di-p-tolyl substituents, and an acetal group at the pyrroline-pyrrole junction. Examination of the effect of the concentrations of 1 (2.5-50 mM) and BF3 x OEt2 (10-500 mM) revealed a different response surface for each of H-BC, MeO-BC, and TDC, enabling relatively selective preparation of a given macrocycle. The highest isolated yield of each was 49, 30, and 66%, respectively. The macrocycles are stable to routine handling in light and air. The bacteriochlorins display characteristic spectral features; for example, H-BC exhibits near-IR absorption (lambda(Qy) = 737 nm, epsilon(Qy) = 130,000 M(-1) cm(-1)) and emission (lambda(em) = 744 nm, phi(f) = 0.14). In summary, this simple entry to stable bacteriochlorins and tetradehydrocorrins should facilitate a wide variety of applications.}, number={14}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Kim, HJ and Lindsey, JS}, year={2005}, month={Jul}, pages={5475–5486} } @article{sharada_muresan_muthukumaran_lindsey_2005, title={Direct synthesis of palladium porphyrins from acyldipyrromethanes}, volume={70}, ISSN={["1520-6904"]}, DOI={10.1021/jo050120v}, abstractNote={[reaction: see text] Palladium porphyrins are valuable photosensitizers and luminescent agents in biology and materials chemistry. New methodology is described wherein a 1-acyldipyrromethane is converted into the palladium chelate of a trans-A(2)B(2) porphyrin via a one-flask reaction. The reaction entails self-condensation of the 1-acyldipyrromethane in refluxing ethanol containing KOH (5-10 mol equiv) and Pd(CH(3)CN)(2)Cl(2) (0.6 mol equiv) exposed to air. This direct route to palladium porphyrins is more expedient than the four steps of the traditional synthesis: (1) reduction of the 1-acyldipyrromethane; (2) acid-catalyzed condensation; (3) oxidation of the porphyrinogen intermediate; and (4) metal insertion. The new synthesis requires neither acid nor DDQ and formally entails only a 2e(-) + 2H(+) oxidation overall versus the traditional multistep synthesis which requires a 2e(-) + 2H(+) reduction per each 1-acyldipyrromethane (4e(-) + 4H(+) overall) followed by a 6e(-) + 6H(+) oxidation. The analogous reaction of a 1,9-diacyldipyrromethane and a dipyrromethane also gives the palladium porphyrin. Seven palladium porphyrins have been prepared in yields of 25-57%. The direct route also can be used with Cu(OAc)(2).H(2)O to give the copper porphyrin albeit in low yield. In summary, this methodology readily affords palladium porphyrins directly from acyldipyrromethanes.}, number={9}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Sharada, DS and Muresan, AZ and Muthukumaran, K and Lindsey, JS}, year={2005}, month={Apr}, pages={3500–3510} } @article{taniguchi_balakumar_fan_mcdowell_lindsey_2005, title={Imine-substituted dipyrromethanes in the synthesis of porphyrins bearing one or two meso substituents}, volume={9}, ISSN={["1099-1409"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33244492173&partnerID=MN8TOARS}, DOI={10.1142/S1088424605000678}, abstractNote={ 5,15-substituted porphyrins are valuable compounds in bioorganic and materials chemistry. A new synthesis has been developed that employs 1,9-diformylation of a dipyrromethane, conversion of the diformyldipyrromethane to the bis(imino) derivative, and reaction of the bis(imino)dipyrromethane + a dipyrromethane to give the zinc-porphyrin bearing trans-AB-substituents. 1,9-diformylation was achieved via Vilsmeier reaction. Imination was achieved by treatment of the 1,9-diformyldipyrromethane with excess amine under neat conditions at room temperature. The porphyrin-forming reaction was carried out over 2 h in refluxing ethanol containing zinc acetate exposed to air. Oxidation of the intermediate porphyrinogen occurs aerobically. A complex composed of two bis(imino)dipyrromethanes and two zinc atoms was observed to form reversibly during the course of the reaction. A set of zinc-porphyrins with trans-AB-, A 2-, or A-substituents has been prepared in yields of ~30% (without detectable scrambling) with straightforward purification. The reaction is applicable to A/B substituent combinations of aryl/aryl, aryl/alkyl, and aryl/H. }, number={8}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, publisher={World Scientific Pub Co Pte Lt}, author={Taniguchi, M and Balakumar, A and Fan, DZ and McDowell, BE and Lindsey, JS}, year={2005}, pages={554–574} } @article{zaidi_fico_lindsey_2006, title={Investigation of streamlined syntheses of porphyrins bearing distinct meso substituents}, volume={10}, ISSN={["1520-586X"]}, DOI={10.1021/op050193g}, abstractNote={The use of porphyrins in fundamental studies and diverse applications requires facile access to ample quantities of material in pure form. The existing conditions for the condensation of a dipyrromethane plus a dipyrromethane−dicarbinol employ 2.5 mM reactants and afford ∼30% yields with no detectable scrambling. Large-scale syntheses require condensation and oxidation conditions that function at higher concentrations. Thirty-one acids (plus additives) have been examined for reactions at 25 mM reactants using the synthesis of a trans-A2B2-porphyrin as a model. The porphyrin was formed in ∼20% yield upon condensation in CH2Cl2 at room temperature using (1) Sc(OTf)3 (3.2 mM) + 2,6-di-tert-butylpyridine (32 mM), or (2) Zn(OTf)2 (10 mM). Nine porphyrins were prepared in this manner in yields of 15−22% with no detectable scrambling, whereas three other porphyrins afforded low levels of scrambling and/or lower yields (8−14%). Conditions for the oxidation also have been investigated. The reaction of 5-mesityldip...}, number={1}, journal={ORGANIC PROCESS RESEARCH & DEVELOPMENT}, author={Zaidi, SHH and Fico, FM and Lindsey, JS}, year={2006}, pages={118–134} } @article{lysenko_malinovskii_padmaja_wei_diers_bocian_lindsey_2005, title={Multistate molecular information storage using S-acetylthio-derivatized dyads of triple-decker sandwich coordination compounds}, volume={9}, ISSN={["1099-1409"]}, DOI={10.1142/S1088424605000617}, abstractNote={An approach toward molecular information storage employs redox-active molecules attached to an electroactive surface. The chief advantages of such molecular capacitors include higher charge density and more versatile synthetic design than is afforded by typical semiconductor charge-storage materials. An architecture containing two triple-decker sandwich coordination complexes and an S-acetylthiomethyl-terminated tether has been designed for multibit storage. Each triple decker is composed of two phthalocyanines, one porphyrin, and two europium atoms. The oxidation potentials of each triple decker are tuned through the use of different substituents on the phthalocyanines (t-butyl, methyl, H ) and porphyrins (pentyl, p-tolyl). Interleaving of the four cationic oxidation states of each triple decker potentially affords eight distinct oxidation states. Two dyads were examined in solution and in self-assembled monolayers (SAMs) on a Au surface. One dyad exhibited eight distinct states in solution and in the SAM, thus constituting a molecular octal counter. The potentials ranged from −0.1-+1.3 V in solution and +0.1-+1.6 V in the SAM. Taken together, this approach provides a viable means of achieving multibit information storage at relatively low potential.}, number={7}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Lysenko, AB and Malinovskii, VL and Padmaja, K and Wei, LY and Diers, JR and Bocian, DF and Lindsey, JS}, year={2005}, pages={491–508} } @article{dixon_taniguchi_lindsey_2005, title={PhotochemCAD 2: A Refined Program with Accompanying Spectral Databases for Photochemical Calculations}, volume={81}, ISSN={["1751-1097"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-14744278395&partnerID=MN8TOARS}, DOI={10.1562/2004-11-06-TSN-361.1}, abstractNote={Abstract The PhotochemCAD program has been revised extensively. Calculations can be performed using eight modules (oscillator strength, transition dipole moment and natural radiative lifetime, Förster energy transfer, multicomponent analysis, blackbody radiator, artificial spectrum creation, transmission calculation, and analysis of energy transfer among linear multichromophore arrays). The user interface has been streamlined to facilitate visual display, operation of the various modules, input of user data via a wizard and output of spectra and calculations. The database of absorption and fluorescence spectra has been expanded to 150 photochemically relevant compounds. A database of solar spectra has been added. The program runs under Windows and is equipped with extensive literature references and help features, including a tutorial section with video files.}, number={1}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, publisher={Wiley}, author={Dixon, JM and Taniguchi, M and Lindsey, JS}, year={2005}, pages={212–213} } @article{ptaszek_bhaumik_kim_taniguchi_lindsey_2005, title={Refined synthesis of 2,3,4,5-tetrahydro-1,3,3-trimethyidipyrrin, a deceptively simple precursor to hydroporphyrins}, volume={9}, ISSN={["1520-586X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-26444474619&partnerID=MN8TOARS}, DOI={10.1021/op050087e}, abstractNote={2,3,4,5-Tetrahydro-1,3,3-trimethyldipyrrin (1) is a crucial building block in the rational synthesis of chlorins and oxochlorins. The prior 5-step synthesis of 1 from pyrrole-2-carboxaldehyde (2) employed relatively simple and well-known reactions yet suffered from several drawbacks, including limited scale (>/= 0.5 g of 1 per run). A streamlined preparation of 1 has been developed that entails four steps: (i) nitro-aldol condensation of 2 and nitromethane under neat conditions to give 2-(2-nitrovinyl)pyrrole (3), (ii) reduction of 3 with NaBH(4) to give 2-(2-nitroethyl)pyrrole (4), (iii) Michael addition of 4 with mesityl oxide under neat conditions or at high concentration to give gamma-nitrohexanonepyrrole 5, and (iv) reductive cyclization of 5 with zinc/ammonium formate to give 1. Several multistep transformations have been established, including the direct conversion of 2 --> 1. The advantages of the new procedures include (1) fewer steps, (2) avoidance of several problematic reagents, (3) diminished consumption of solvents and reagents, (4) lessened reliance on chromatography, and (5) scalability. The new procedures facilitate the preparation of 1 at the multigram scale.}, number={5}, journal={ORGANIC PROCESS RESEARCH & DEVELOPMENT}, publisher={American Chemical Society (ACS)}, author={Ptaszek, M and Bhaumik, J and Kim, HJ and Taniguchi, M and Lindsey, JS}, year={2005}, pages={651–659} } @article{zou_wei_chen_liu_thamyongkit_loewe_lindsey_mohideen_bocian_2005, title={Solution STM images of porphyrins on HOPG reveal that subtle differences in molecular structure dramatically alter packing geometry}, volume={9}, ISSN={["1099-1409"]}, DOI={10.1142/S1088424605000484}, abstractNote={ Solution STM images are reported for free-base octaethylporphyrin ( H 2 OEP ) and the Cu ( II ) and Zn ( II ) chelates ( CuOEP and ZnOEP ) on HOPG in 1,2-dichlorobenzene solution under ambient conditions. H 2 OEP and CuOEP each form a quasi-square lattice, whereas ZnOEP forms a quasi-hexagonal lattice on the surface. The binary mixture of any two of the porphyrins forms a well-ordered two-layer structure on the HOPG surface, with one species occupying the bridge sites of the array of the other species. All of the mixed adlayers exhibit a quasi-hexagonal lattice with a higher packing density than the single-component adlayers. Collectively, these observations indicate that the structure of the adlayers is controlled by a complex interplay of substrate-molecule and molecule-molecule interactions. }, number={6}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Zou, ZQ and Wei, LY and Chen, F and Liu, ZM and Thamyongkit, P and Loewe, RS and Lindsey, JS and Mohideen, U and Bocian, DF}, year={2005}, pages={387–392} } @article{yasseri_syomin_loewe_lindsey_zaera_bocian_2005, title={Structural and Electron-Transfer Characteristics of O-, S-, and Se-Tethered Porphyrin Monolayers on Si(100) [J. Am. Chem. Soc.2004,126, 15603−15612].}, volume={127}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja053081d}, DOI={10.1021/ja053081d}, abstractNote={Monolayers of two classes of Zn porphyrins have been prepared and examined on Si(100). These molecules, designated as ZnPBzX- and ZnPCH2X-, contain either a benzyl (-Bz-) or a methylene (-CH2-) unit terminated with a Group VI atom (X = O, S, Se) appended to a meso-position of the porphyrin, with the nonlinking meso-substituents consisting of either mesityl (-Bz- class) or p-tolyl and phenyl (-CH2- class) units. The two series of ZnPBzX- and ZnPCH2X- monolayers on Si(100) were examined using a variety of techniques, including X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and various electrochemical methods. The studies reveal the following characteristics of the ZnPBzX- and ZnPCH2X- monolayers. (1) Surface binding can be readily achieved to Si(100) with both relatively short (-Bz-) and very short (-CH2-) tethers regardless of the nature of the Group VI anchoring atom (O, S, Se). (2) The longer -Bz- tether affords monolayers with the porphyrin ring in a somewhat more upright orientation with respect to the surface than the shorter -CH2- tether. The more upright adsorption geometry of the porphyrins bearing the former type of linker leads to a higher packing density and more homogeneous redox thermodynamics. (3) The kinetics of electron transfer does not depend on the type of Group VI atom used for anchoring to the Si(100) surface. On the other hand, the type of linker does affect the electron-transfer rates, with the monolayers bearing the -CH2- linker exhibiting systematically faster rates than those bearing the -Bz- linker. Collectively, the studies reported herein provide a detailed picture of how the anchor atom and the linker type influence the structural and electron-transfer characteristics of these general classes of monolayers.}, number={25}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Yasseri, Amir A. and Syomin, Dennis and Loewe, Robert S. and Lindsey, Jonathan S. and Zaera, Francisco and Bocian, David F.}, year={2005}, month={Jun}, pages={9308–9308} } @article{wei_syomin_loewe_lindsey_zaera_bocian_2005, title={Structural and electron-transfer characteristics of carbon-tethered porphyrin monolayers on Si(100)}, volume={109}, ISSN={["1520-6106"]}, DOI={10.1021/jp044558v}, abstractNote={Structural and electron-transfer characteristics are reported for two classes of zinc porphyrin monolayers attached to Si(100) surfaces via Si-C bonds. One class, designated ZnP(CH(2))(n)- (n = 2-4), contains an alkyl linker appended to the meso-position of the porphyrin, with the nonlinking substituents being p-tolyl groups. The other, designated ZnPPh(CH(2))(n)- (n = 0-3), contains a phenyl or phenylalkyl linker appended to the meso-position of the porphyrin, with the nonlinking substituents being mesityl groups. Both classes of zinc porphyrin monolayers on Si(100) were examined using Fourier transform infrared spectroscopy and various electrochemical methods. The studies reveal the following: (1) The structural and electron-transfer characteristics of the ZnP(CH(2))(n)- and ZnPPh(CH(2))(n)- monolayers are generally similar to those of monolayers formed from porphyrins with analogous linkers, but anchored with an O, a S, or a Se atom. (2) The ZnP(CH(2))(n)-, ZnPPh-, and ZnPPhCH(2)- monolayers exhibit lower saturation coverages and have their porphyrin ring more tilted with respect to the surface normal than the ZnPPh(CH(2))(2)- and ZnPPh(CH(2))(3)- monolayers. (3) The electron-transfer rates for both the ZnP(CH(2))(n)- and ZnPPh(CH(2))(n)- classes of monolayers monotonically decrease as the length of the linker increases. (4) For all the ZnP(CH(2))(n)- and ZnPPh(CH(2))(n)- monolayers, both electron-transfer rates and charge-dissipation rates decrease monotonically as the surface coverage increases. Collectively, the studies reported herein provide a detailed picture of how the linker type influences the structural and electron-transfer characteristics of these general classes of monolayers.}, number={13}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Wei, LY and Syomin, D and Loewe, RS and Lindsey, JS and Zaera, F and Bocian, DF}, year={2005}, month={Apr}, pages={6323–6330} } @article{kee_kirmaier_yu_thamyongkit_youngblood_calder_ramos_noll_bocian_scheidt_et al._2005, title={Structural control of the photodynamics of boron-dipyrrin complexes}, volume={109}, ISSN={["1520-5207"]}, DOI={10.1021/jp0525078}, abstractNote={Boron-dipyrrin chromophores containing a 5-aryl group with or without internal steric hindrance toward aryl rotation have been synthesized and then characterized via X-ray diffraction, static and time-resolved optical spectroscopy, and theory. Compounds with a 5-phenyl or 5-(4-tert-butylphenyl) group show low fluorescence yields (approximately 0.06) and short excited-singlet-state lifetimes (approximately 500 ps), and decay primarily (>90%) by nonradiative internal conversion to the ground state. In contrast, sterically hindered analogues having an o-tolyl or mesityl group at the 5-position exhibit high fluorescence yields (approximately 0.9) and long excited-state lifetimes (approximately 6 ns). The X-ray structures indicate that the phenyl or 4-tert-butylphenyl ring lies at an angle of approximately 60 degrees with respect to the dipyrrin framework whereas the angle is approximately 80 degrees for mesityl or o-tolyl groups. The calculated potential energy surface for the phenyl-substituted complex indicates that the excited state has a second, lower energy minimum in which the nonhindered aryl ring rotates closer to the mean plane of the dipyrrin, which itself undergoes some distortion. This relaxed, distorted excited-state conformation has low radiative probability as well as a reduced energy gap from the ground state supporting a favorable vibrational overlap factor for nonradiative deactivation. Such a distorted conformation is energetically inaccessible in a complex bearing the sterically hindered o-tolyl or mesityl group at the 5-position, leading to a high radiative probability involving conformations at or near the initial Franck-Condon form of the excited state. These combined results demonstrate the critical role of aryl-ring rotation in governing the excited-state dynamics of this class of widely used dyes.}, number={43}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Kee, HL and Kirmaier, C and Yu, LH and Thamyongkit, P and Youngblood, WJ and Calder, ME and Ramos, L and Noll, BC and Bocian, DF and Scheidt, WR and et al.}, year={2005}, month={Nov}, pages={20433–20443} } @article{liu_schmidt_thamyongkit_loewe_syomin_diers_zhao_misra_lindsey_bocian_2005, title={Synthesis and Film-Forming Properties of Ethynylporphyrins}, volume={17}, ISSN={0897-4756 1520-5002}, url={http://dx.doi.org/10.1021/cm047858y}, DOI={10.1021/cm047858y}, abstractNote={Thermal treatment of ethynyl porphyrin monomers on a surface has been found to yield robust porphyrin films. The scope of this in situ polymerization has been surveyed by the synthesis and characterization of a collection of 20 zinc porphyrins bearing diverse patterns of 1−4 ethyne (or protected ethyne) groups and a variety of nonlinking substituents. Films have been prepared on Si(100), SiO2, Au(111), and glass. The films prepared on Si(100) have been examined by electrochemical methods, which indicate that surface coverages 50-fold greater than those of saturation-coverage monolayers are achievable, although the coverage varies appreciably (10-fold) among the survey group of molecules under a controlled set of film-forming conditions. Variation in these conditions affords control over the number of layers in the film (from a few to tens or more). The electrochemical characteristics of the multilayer films further indicate that the redox thermodynamics are of comparable homogeneity to those of monolayers...}, number={14}, journal={Chemistry of Materials}, publisher={American Chemical Society (ACS)}, author={Liu, Zhiming and Schmidt, Izabela and Thamyongkit, Patchanita and Loewe, Robert S. and Syomin, Dennis and Diers, James R. and Zhao, Qian and Misra, Veena and Lindsey, Jonathan S. and Bocian, David F.}, year={2005}, month={Jul}, pages={3728–3742} } @article{muthukumaran_zaidi_yu_thamyongkit_calder_sharada_lindsey_2005, title={Synthesis of dipyrrin-containing architectures}, volume={9}, ISSN={["1099-1409"]}, DOI={10.1142/S108842460500085X}, abstractNote={ Dipyrrins are valuable precursors to dyes [dipyrrinatoboron difluoride, bis(dipyrrinato)-zinc(II) complexes] and serve as ligands in a variety of self-assembled materials. Six new dipyrrin-containing architectures have been synthesized. The architectures include bis(dipyrrinato) complexes containing copper(II) or palladium(II), a dipyrrin bearing a protected phosphonic acid unit, a porphyrin bearing two dipyrrins in a trans configuration, a linear diphenylethyne-linked dipyrromethane-dipyrrin building block, and a triad composed of two zinc porphyrins joined via an intervening bis(dipyrrinato)copper(II) complex. Two porphodimethenatozinc complexes were prepared and found to have Φ f ≤ 0.002 (in toluene at room temperature), which is substantially less than the analogous bis(dipyrrinato)zinc complexes. Taken together, the syntheses described herein should broaden access to dipyrrins for use as complexation motifs in supramolecular chemistry and as pigments in light-harvesting applications. }, number={10-11}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Muthukumaran, Kannan and Zaidi, Syeda Huma H. and Yu, Lianhe and Thamyongkit, Patchanita and Calder, Matthew E. and Sharada, Duddu S. and Lindsey, Jonathan S.}, year={2005}, pages={745–759} } @article{zaidi_muthukumaran_tamaru_lindsey_2004, title={9-Acylation of 1-acyldipyrromethanes containing a dialkylboron mask for the alpha-acylpyrrole motif}, volume={69}, ISSN={["0022-3263"]}, DOI={10.1021/jo048587d}, abstractNote={1,9-Diacyldipyrromethanes are important precursors to porphyrins, yet synthetic access remains limited owing to (1) poor conversion in the 9-acylation of 1-acyldipyrromethanes and (2) handling difficulties because acyldipyrromethanes typically streak upon chromatography and give amorphous powders upon attempted crystallization. A reliable means for converting a dipyrromethane to a 1-acyldipyrromethane−dialkylboron complex was recently developed, where the dialkylboron (BR2) unit renders the complex hydrophobic and thereby facilitates isolation. Herein a refined preparation of 1,9-diacyldipyrromethanes is presented that employs the 1-acyldipyrromethane−BR2 complex as a substrate for 9-acylation. The dialkylboron unit provides protection for the α-acylpyrrole unit. 9-Acylation requires formation of the pyrrolyl−MgBr reagent and the presence of 1 equiv of a nonnucleophilic base to quench the proton liberated upon α-acylation. Reaction of the 1-acyldipyrromethane−BR2 complex (1 equiv) with mesitylmagnesium br...}, number={24}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Zaidi, SHH and Muthukumaran, K and Tamaru, S and Lindsey, JS}, year={2004}, month={Nov}, pages={8356–8365} } @article{balakumar_muthukumaran_lindsey_2004, title={A new route to meso-formyl porphyrins}, volume={69}, ISSN={["0022-3263"]}, DOI={10.1021/jo049819b}, abstractNote={Prior syntheses of porphyrins bearing meso-formyl groups have generally employed the Vilsmeier formylation of an acid-resistant copper or nickel porphyrin. A new approach for the synthesis of free base porphyrins bearing one or two (cis or trans) meso-formyl substituents entails the use of a dipyrromethane bearing an acetal group at the 5-position, a dipyrromethane-1-carbinol bearing an acetal group at the 5-position or carbinol position, or a dipyrromethane-1,9-dicarbinol bearing an acetal group at a carbinol position. Treatment of the resulting meso-acetal-substituted free base porphyrin to gentle acidic hydrolysis yields the corresponding meso-formyl porphyrin.}, number={15}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Balakumar, A and Muthukumaran, K and Lindsey, JS}, year={2004}, month={Jul}, pages={5112–5115} } @article{tamaru_yu_youngblood_muthukumaran_taniguchi_lindsey_2004, title={A tin-complexation strategy for use with diverse acylation methods in the preparation of 1,9-diacyldipyrromethanes}, volume={69}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0842285782&partnerID=MN8TOARS}, DOI={10.1021/jo035622s}, abstractNote={The acylation of dipyrromethanes to form 1,9-diacyldipyrromethanes is an essential step in the rational synthesis of porphyrins. Although several methods for acylation are available, purification is difficult because 1,9-diacyldipyrromethanes typically streak extensively upon chromatography and give amorphous powders upon attempted crystallization. A solution to this problem has been achieved by reacting the 1,9-diacyldipyrromethane with Bu(2)SnCl(2) to give the corresponding dibutyl(5,10-dihydrodipyrrinato)tin(IV) complex. The reaction is selective for dipyrromethanes that bear acyl groups at both the 1- and 9-positions but otherwise is quite tolerant of diverse substituents. The diacyldipyrromethane-tin complexes are stable to air and water, are highly soluble in common organic solvents, crystallize readily, and chromatograph without streaking. Four methods (Friedel-Crafts, Grignard, Vilsmeier, benzoxathiolium salt) were examined for the direct 1,9-diacylation of a dipyrromethane or the 9-acylation of a 1-acyldipyrromethane. In each case, treatment of the crude reaction mixture with Bu(2)SnCl(2) and TEA at room temperature enabled facile isolation of multigram quantities of the 1,9-diacyldipyrromethane-tin complex. The diacyldipyrromethane-tin complexes could be decomplexed with TFA in nearly quantitative yield. Alternatively, use of a diacyldipyrromethane-tin complex in a porphyrin-forming reaction (reduction with NaBH(4), acid-catalyzed condensation with a dipyrromethane, DDQ oxidation) afforded the desired free base porphyrin in yield comparable to that obtained from the uncomplexed diacyldipyrromethane. The acylation/tin-complexation strategy has been applied to a bis(dipyrromethane) and a porphyrin-dipyrromethane. In summary, the tin-complexation strategy has broad scope, is compatible with diverse acylation methods, and greatly facilitates access to 1,9-diacyldipyrromethanes.}, number={3}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Tamaru, S and Yu, LH and Youngblood, WJ and Muthukumaran, K and Taniguchi, M and Lindsey, JS}, year={2004}, month={Feb}, pages={765–777} } @article{dixon_lindsey_2004, title={An experiment planner for parallel multidirectional searches using an automated chemistry workstation}, volume={9}, ISSN={1535-5535}, url={http://dx.doi.org/10.1016/j.jala.2004.08.001}, DOI={10.1016/j.jala.2004.08.001}, abstractNote={ Automated chemical workstations capable of parallel, adaptive experimentation are well suited for performing reaction optimization. A new method for simplex-based optimization has been developed that enables multiple multidirectional search (MDS) procedures to be implemented in parallel. The MDS method employs a simplex with n + 1 points, where n is the number of dimensions or variables of the optimization. After the initial simplex is evaluated, a new simplex is generated by reflection about the one best point, where n new points are projected and all but the one best point are discarded. The MDS movements continue in the same fashion until a termination criterion is satisfied. The parallel version (PMDS') enables multiple, distinct optimizations in parallel in a single search space to find the global optimum, or individual optimizations in parallel of multiple independent search spaces. The PMDS' method is complementary to the parallel Simplex search method, in which only one new point is projected to generate a new simplex in each cycle of experimentation. }, number={6}, journal={Journal of the Association for Laboratory Automation}, publisher={SAGE Publications}, author={Dixon, James M. and Lindsey, Jonathan S.}, year={2004}, month={Dec}, pages={355–363} } @article{yasseri_syomin_malinovskii_loewe_lindsey_zaera_bocian_2004, title={Characterization of self-assembled monolayers of porphyrins bearing multiple thiol-derivatized rigid-rod tethers}, volume={126}, ISSN={["0002-7863"]}, DOI={10.1021/ja047723t}, abstractNote={A series of multithiol-functionalized zinc porphyrins has been prepared and characterized as self-assembled monolayers (SAMs) on Au. The molecules, designated ZnPS(n) (n = 1-4), contain from one to four [(S-acetylthio)methyl]phenylethynylphenyl groups appended to the meso-position of the porphyrin; the other meso-substituents are phenyl groups. For the dithiol-functionalized molecules, both the cis- and the trans-appended structures were examined. The ZnPS(n) SAMs were investigated using X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and various electrochemical methods. The studies reveal the following characteristics of the ZnPS(n) SAMs. (1) The ZnPS(n) molecules bind to the Au surface via a single thiol regardless of the number of thiol appendages that are available per molecular unit. (2) The porphyrins in the ZnPS(3) and ZnPS(4) SAMs bind to the surface in a more upright orientation than the porphyrins in the ZnPS(1), cis-ZnPS(2), and trans-ZnPS(2) SAMs. The porphyrins in the ZnPS(3) and ZnPS(4) SAMs are also more densely packed than those in the cis-ZnPS(2) and trans-ZnPS(2) SAMs. The packing density of the ZnPS(3) and ZnPS(4) SAMs is similar to that of the ZnPS(1) SAMs, despite the larger size of the molecules in the former SAMs. (3) The thermodynamics and kinetics of electron transfer are generally similar for all of the ZnPS(n) SAMs. The general similarities in the electron-transfer characteristics for all of the SAMs are attributed to the similar binding motif.}, number={38}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Yasseri, AA and Syomin, D and Malinovskii, VL and Loewe, RS and Lindsey, JS and Zaera, F and Bocian, DF}, year={2004}, month={Sep}, pages={11944–11953} } @article{geier_lindsey_2004, title={Effects of aldehyde or dipyrromethane substituents on the reaction course leading to meso-substituted porphyrins}, volume={60}, ISSN={["0040-4020"]}, DOI={10.1016/j.tet.2004.09.081}, abstractNote={To better understand the effects of diverse substituents on reactions leading to porphyrins, pyrrole+aldehyde condensations and related reactions of dipyrromethanes were examined. The course of pyrrole+aldehyde condensations was investigated by monitoring the yield of porphyrin (by UV–Vis spectroscopy), reaction of aldehyde (by TLC), and changes in the composition of oligomers (by laser desorption mass spectrometry). Reaction reversibility was examined via exchange experiments. Reversibility of reactions leading to porphyrin was further probed with studies of dipyrromethanes. The reaction course was found to depend on the nature of the substituent and the acid catalyst. Alkyl or electron-donating substituents displayed levels of reversibility (exchange/scrambling) on par or greater than that of the phenyl substituent, whereas electron-withdrawing or sterically bulky substituents exhibited little to no reversibility. The results obtained provide insight into the electronic and steric effects of different substituents and should facilitate the design of synthetic plans for preparing porphyrinic macrocycles.}, number={50}, journal={TETRAHEDRON}, author={Geier, GR and Lindsey, JS}, year={2004}, month={Dec}, pages={11435–11444} } @article{hindin_forties_loewe_ambroise_kirmaier_bocian_lindsey_holten_knox_2004, title={Excited-state energy flow in covalently linked multiporphyrin arrays: The essential contribution of energy transfer between nonadjacent chromophores}, volume={108}, ISSN={["1520-6106"]}, DOI={10.1021/jp047803j}, abstractNote={A series of multiporphyrin arrays has been studied to probe the contribution of energy transfer between second-neighbor ("nonadjacent") porphyrins and to determine the rate of energy transfer between identical porphyrins at adjacent sites. The arrays, organized in linear or branched architectures, contain up to 21 constituents, domains of 2-5 zinc porphyrins, and a single energy trap. The study has involved iterative cycles of molecular design, synthesis, determination of rates via transient absorption spectroscopy, and kinetic analysis. A rate constant of (30 ′ 10 ps) - 1 is deduced for bidirectional energy transfer between adjacent zinc porphyrins joined by a diphenylethyne linker. The value is (50 ′ 10 ps) - 1 when the porphyrin-linker internal rotation is hindered by o,o'-methyl groups on one aryl ring of the linker. Rates of nonadjacent energy transfers are typically only 5-10-fold less than the rates of adjacent transfers. Thus, the nonadjacent pathway has a significant impact on the overall rate of energy flow to the trap, even in architectures as small as triads. These findings provide information that will be essential for the rational design of multichromophore arrays whose function is to transfer excitation energy efficiently over large distances to a trap site.}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Hindin, E and Forties, RA and Loewe, RS and Ambroise, A and Kirmaier, C and Bocian, DF and Lindsey, JS and Holten, D and Knox, RS}, year={2004}, month={Aug}, pages={12821–12832} } @article{taniguchi_kim_ra_lindsey_2005, title={Introduction of a third meso substituent into 5,10-diaryl chlorins and oxochlorins}, volume={70}, ISSN={["1520-6904"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-11844252011&partnerID=MN8TOARS}, DOI={10.1021/jo048440m}, abstractNote={Chlorins/oxochlorins bearing distinct patterns of substituents are valuable compounds in bioorganic and materials chemistry. Treatment of a 5,10-diaryl-substituted chlorin or oxochlorin with TFA-d(1) resulted in selective deuteriation of the remaining meso positions (15, 20) rather than any of the beta-pyrrolic positions. Electrophilic iodination or bromination of a 5,10-diaryl-substituted chlorin proceeded with high regioselectivity, affording the 5,10-diaryl-15-halo-substituted chlorin. Iodination or bromination of a free base 5,10-diaryloxochlorin gave a mixture of products arising through halogenation at the 15-, 20-, and beta-pyrrolic positions, while bromination of a zinc 5,10-diaryloxochlorin selectively gave the 5,10-diaryl-20-bromo-substituted oxochlorin. The Suzuki coupling reaction of a phenyl boronic acid derivative and a 5,10-diaryl-15-iodooxochlorin or 5,10-diaryl-20-bromooxochlorin gave the corresponding 5,10,15- or 5,10,20-triaryloxochlorin. The introduction of a third aryl substituent into the chlorin or oxochlorin causes an approximately 5-nm red shift of the long wavelength Q(y) absorption band. Two phenylethyne-linked oxochlorin-oxochlorin dyads in distinct metalation states (zinc/free base, free base/zinc) were prepared by Sonogashira coupling reactions of a 5,10-diaryl-20-bromooxochlorin and a 10-substituted ethynylphenyl oxochlorin. This study provides access to new chlorins/oxochlorins that can be utilized in diverse applications.}, number={1}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Taniguchi, M and Kim, MN and Ra, D and Lindsey, JS}, year={2005}, month={Jan}, pages={275–285} } @article{li_mathur_gowda_surthi_zhao_yu_lindsey_bocian_misra_2004, title={Multibit memory using self-assembly of mixed ferrocene/porphyrin monolayers on silicon}, volume={16}, ISSN={["1521-4095"]}, DOI={10.1002/adma.200305680}, abstractNote={An alternative strategy for achieving multi‐bit functionality, which uses mixed self‐assembled monolayers of a benzyl alcohol‐tethered ferrocene (Fc‐BzOH) and a benzyl alcohol‐tethered porphyrin (Por‐BzOH) on silicon surfaces to achieve a four‐state (2‐bit) memory element, is presented. The four states include the neutral state and three distinct cationic states obtained upon oxidation of Fc‐BzOH (monopositive) and Por‐BzOH (monopositive, dipositive) molecules. Conventional cyclic voltammetry, capacitance, and conductance methods have been used to characterize the mixed monolayer.}, number={2}, journal={ADVANCED MATERIALS}, author={Li, QL and Mathur, G and Gowda, S and Surthi, S and Zhao, Q and Yu, LH and Lindsey, JS and Bocian, DF and Misra, V}, year={2004}, month={Jan}, pages={133-+} } @article{li_surthi_mathur_gowda_zhao_sorenson_tenent_muthukumaran_lindsey_misra_2004, title={Multiple-bit storage properties of porphyrin monolayers on SiO2}, volume={85}, ISSN={["1077-3118"]}, DOI={10.1063/1.1782254}, abstractNote={Hybrid molecule-silicon capacitors have been fabricated by the self-assembly of a monolayer of porphyrin molecules on a silicon oxide surface. The porphyrin employed [5-(4-dihydroxyphosphorylphenyl)-10,15,20-trimesitylporphinatozinc(II)] attaches to silicon oxide via a phosphonate linkage. Cyclic voltammetry current and capacitance/conductance measurements have been used to characterize the capacitors. The presence of multiple distinct peaks in current density and capacitance/conductance measurements are associated with oxidation and reduction of the molecular monolayer. The charge-storage states of the capacitor indicate applicability for use in multiple-bit memory devices.}, number={10}, journal={APPLIED PHYSICS LETTERS}, author={Li, QL and Surthi, S and Mathur, G and Gowda, S and Zhao, Q and Sorenson, TA and Tenent, RC and Muthukumaran, K and Lindsey, JS and Misra, V}, year={2004}, month={Sep}, pages={1829–1831} } @article{dixon_lindsey_2004, title={Performance of search algorithms in the examination of chemical reaction spaces with an automated chemistry workstation}, volume={9}, ISSN={1535-5535}, url={http://dx.doi.org/10.1016/j.jala.2004.08.004}, DOI={10.1016/j.jala.2004.08.004}, abstractNote={ One of the challenges in applying automated chemistry workstations to problems of reaction optimization entails choosing an appropriate optimization algorithm. In the study described herein, 10 different algorithms have been examined for efficacy in searching reaction spaces using scenarios that explore effects of workstation parallelism and search space size. The algorithms differ in scheduling (serial vs. parallel), adaptive features (open loop vs. closed loop), and methods for stepping through the search space. Several two-tiered algorithms enable a breadth-first survey followed by an indepth optimization. For a workstation with modest parallel capacity, a parallel but nonadaptive algorithm is most effective in small or coarse-grained search spaces, whereas parallel adaptive algorithms are superior for examining large or fine-grained search spaces. The parallel adaptive algorithms become increasingly effective as the size of the search space increases. A serial algorithm is most attractive with a serial workstation, or when chemical resources are limited regardless of workstation or search space. The breadth-first survey of the twotiered algorithms significantly improves the efficiency of the subsequent in-depth optimization. The results obtained provide guidance in choosing optimization algorithms, designing more sophisticated algorithms, and developing workstations with parallel and/or adaptive features that use such algorithms. }, number={6}, journal={Journal of the Association for Laboratory Automation}, publisher={SAGE Publications}, author={Dixon, James M. and Lindsey, Jonathan S.}, year={2004}, month={Dec}, pages={364–374} } @article{hindin_kirmaier_diers_tomizaki_taniguchi_lindsey_bocian_holten_2004, title={Photophysical properties of phenylethyne-linked porphyrin and oxochlorin dyads}, volume={108}, ISSN={["1520-6106"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-3042636305&partnerID=MN8TOARS}, DOI={10.1021/jp037614l}, abstractNote={A set of porphyrin-porphyrin and oxochlorin-oxochlorin dyads has been prepared in which the constituent pigments are joined at the meso-positions by a phenylethyne linker. Attachment of an ethynyl substituent to the meso-position of a tetrapyrrolic macrocycle strongly perturbs the electronic properties of the ring. The inherent asymmetry of the phenylethyne linker affords the possibility of perturbing either end of the dyad. The porphyrin dyads include bis-Zn, Zn-free base (Fb), and bis-Zn species wherein 0, 1, or 2 of the three nonlinking aryl rings of one of the Zn porphyrins are perfluorinated. The two oxochlorin dyads are both ZnFb species in which the meso-ethyne substituent is located on either the Zn complex or the Fb. The dyads have been studied using static and time-resolved absorption and emission spectroscopy and electrochemical techniques. The optical and electrochemical properties of a series of monomeric reference compounds were also examined. The time-resolved optical studies reveal that energy transfer in the phenylethyne-linked dyads is faster by ∼10-fold or more than in analogous dyads joined by a diphenylethyne linker. In particular, energy transfer occurs with a rate constant of > (20 ps) - 1 between the phenylethyne-linked oxochlorins and an efficiency of >98%, to be compared with a rate of (140 ps) - 1 and an efficiency of 83% found previously for diphenylethyne-linked oxochlorins. Taken together, these results should be useful in the design of multipigment architectures that absorb in the red and undergo fast and efficient energy transfer, as required for light-harvesting applications.}, number={24}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, publisher={American Chemical Society (ACS)}, author={Hindin, E and Kirmaier, C and Diers, JR and Tomizaki, KY and Taniguchi, M and Lindsey, JS and Bocian, DF and Holten, D}, year={2004}, month={Jun}, pages={8190–8200} } @article{carcel_laha_loewe_thamyongkit_schweikart_misra_bocian_lindsey_2004, title={Porphyrin architectures tailored for studies of molecular information storage}, volume={69}, ISSN={["0022-3263"]}, DOI={10.1021/jo0498260}, abstractNote={A molecular approach to information storage employs redox-active molecules tethered to an electroactive surface. Zinc porphyrins tethered to Au(111) or Si(100) provide a benchmark for studies of information storage. Three sets of porphyrins have been synthesized for studies of the interplay of molecular design and charge-storage properties: (1) A set of porphyrins is described for probing the effect of surface attachment atom on electron-transfer kinetics. Each porphyrin bears a meso-CH2X group for surface attachment where X = OH, SAc, or SeAc. (2) A set of porphyrins is described for studying the effect of surface-charge density in monolayers. Each porphyrin bears a benzyl alcohol for surface attachment and three nonlinking meso substituents of a controlled degree of bulkiness. (3) A set of porphyrins is described that enables investigation of on-chip patterning of the electrolyte. Each porphyrin bears a formyl group distal to the surface attachment group for subsequent derivatization with a molecular entity that comprises the electrolyte. Taken together, this collection of molecules enables a variety of studies to elucidate design issues in molecular-based information storage.}, number={20}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Carcel, CM and Laha, JK and Loewe, RS and Thamyongkit, P and Schweikart, KH and Misra, V and Bocian, DF and Lindsey, JS}, year={2004}, month={Oct}, pages={6739–6750} } @article{yasseri_syomin_loewe_lindsey_zaera_bocian_2004, title={Structural and electron-transfer characteristics of O-, S-, and Se-tethered porphyrin monolayers on Si(100)}, volume={126}, ISSN={["0002-7863"]}, DOI={10.1021/ja045243w}, abstractNote={Monolayers of two classes of Zn porphyrins have been prepared and examined on Si(100). These molecules, designated as ZnPBzX− and ZnPCH2X−, contain either a benzyl (−Bz−) or a methylene (−CH2−) unit terminated with a Group VI atom (X = O, S, Se) appended to a meso-position of the porphyrin, with the nonlinking meso-substituents consisting of either mesityl (−Bz− class) or p-tolyl and phenyl (−CH2− class) units. The two series of ZnPBzX− and ZnPCH2X− monolayers on Si(100) were examined using a variety of techniques, including X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and various electrochemical methods. The studies reveal the following characteristics of the ZnPBzX− and ZnPCH2X− monolayers. (1) Surface binding can be readily achieved to Si(100) with both relatively short (−Bz−) and very short (−CH2−) tethers regardless of the nature of the Group VI anchoring atom (O, S, Se). (2) The longer −Bz− tether affords monolayers with the porphyrin ring in a somewhat more upright orientation with respect to the surface than the shorter −CH2− tether. The more upright adsorption geometry of the porphyrins bearing the former type of linker leads to a higher packing density and more homogeneous redox thermodynamics. (3) The kinetics of electron transfer does not depend on the type of Group VI atom used for anchoring to the Si(100) surface. On the other hand, the type of linker does affect the electron-transfer rates, with the monolayers bearing the −CH2− linker exhibiting systematically faster rates than those bearing the −Bz− linker. Collectively, the studies reported herein provide a detailed picture of how the anchor atom and the linker type influence the structural and electron-transfer characteristics of these general classes of monolayers.}, number={47}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Yasseri, AA and Syomin, D and Loewe, RS and Lindsey, JS and Zaera, F and Bocian, DF}, year={2004}, month={Dec}, pages={15603–15612} } @article{tiede_zhang_chen_yu_lindsey_2004, title={Structural characterization of modular supramolecular architectures in solution}, volume={126}, ISSN={["1520-5126"]}, DOI={10.1021/ja048209q}, abstractNote={Structures of modular supramolecular architectures consisting of a hexameric, diphenylethyne-linked porphyrin macrocyclic array and the corresponding host-guest complex formed by inclusion of a tripyridyl guest molecule were characterized in solution using high-angle X-ray scattering. Scattering measurements made to 6 A resolution coupled with pair distance function (PDF) analyses demonstrated that (1) the porphyrin architectures are not rigid but are distributed across a conformational ensemble with a mean diameter that is 1.5 A shorter than the diameter of a symmetric, energy-minimized model structure, (2) the conformational envelope has limits of 3 A positional dispersion and full rotational freedom for all six porphyrin groups, and (3) insertion of the tripyridyl guest molecule expands the diameter of the host conformer by 0.6 A and decreases the configurational dispersion by approximately 2-fold. These results validate the molecular design, provide a new measure of conformational ensembles in solution that cannot be obtained by other techniques, and establish a structural basis for understanding the photophysical and guest-hosting functions of the hexameric porphyrin architectures in liquids.}, number={43}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Tiede, DM and Zhang, RT and Chen, LX and Yu, LH and Lindsey, JS}, year={2004}, month={Nov}, pages={14054–14062} } @article{sazanovich_kirmaier_hindin_yu_bocian_lindsey_holten_2004, title={Structural control of the excited-state dynamics of bis(dipyrrinato)zinc complexes: Self-assembling chromophores for light-harvesting architectures}, volume={126}, ISSN={["1520-5126"]}, DOI={10.1021/ja038763k}, abstractNote={The replacement of the phenyl rings at the 5,5'-positions of a bis(dipyrrinato)zinc complex with mesityl groups transforms the molecule from a very weak emitter that deactivates rapidly after photoexcitation (Phif = 0.006; tau approximately 90 ps) to a highly fluorescent chromophore with a long-lived singlet excited state (Phif = 0.36; tau approximately 3 ns). The results demonstrate that steric constraints on aryl-ring internal rotation dramatically alter the excited-state properties of 5,5'-substituted bis(dipyrrinato)metal complexes. The insights establish the foundation for tuning the photophysical properties of these chromophores for use in diverse photochemical applications.}, number={9}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Sazanovich, IV and Kirmaier, C and Hindin, E and Yu, LH and Bocian, DF and Lindsey, JS and Holten, D}, year={2004}, month={Mar}, pages={2664–2665} } @article{thamyongkit_speckbacher_diers_kee_kirmaier_holten_bocian_lindsey_2004, title={Swallowtail porphyrins: Synthesis, characterization and incorporation into porphyrin dyads}, volume={69}, ISSN={["1520-6904"]}, DOI={10.1021/jo049860e}, abstractNote={The incorporation of symmetrically branched tridecyl ("swallowtail") substituents at the meso positions of porphyrins results in highly soluble building blocks. Synthetic routes have been investigated to obtain porphyrin building blocks bearing 1-4 swallowtail groups. Porphyrin dyads have been synthesized in which the zinc or free base (Fb) porphyrins are joined by a 4,4'-diphenylethyne linker and bear swallowtail (or n-pentyl) groups at the nonlinking meso positions. The swallowtail-substituted Zn(2)- and ZnFb-dyads are readily soluble in common organic solvents. Static absorption and fluorescence spectra and electrochemical data show that the presence of the swallowtail groups slightly raises the energy level of the filled a(2u)(pi) HOMO. EPR studies of the pi-cation radicals of the swallowtail porphyrins indicate that the torsional angle between the proton on the alkyl carbon and p-orbital on the meso carbon of the porphyrin is different from that of a porphyrin bearing linear pentyl groups. Regardless, the swallowtail substituents do not significantly affect the photophysical properties of the porphyrins or the electronic interactions between the porphyrins in the dyads. In particular, time-resolved spectroscopic studies indicate that facile excited-state energy transfer occurs in the ZnFb dyad, and EPR studies of the monocation radical of the Zn(2)-dyad show that interporphyrin ground-state hole transfer is rapid.}, number={11}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Thamyongkit, P and Speckbacher, M and Diers, JR and Kee, HL and Kirmaier, C and Holten, D and Bocian, DF and Lindsey, JS}, year={2004}, month={May}, pages={3700–3710} } @article{tomizaki_lysenko_taniguchi_lindsey_2004, title={Synthesis of phenylethyne-linked porphyrin dyads}, volume={60}, ISSN={["0040-4020"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-1042275557&partnerID=MN8TOARS}, DOI={10.1016/j.tet.2004.01.003}, abstractNote={Four new porphyrin dyads have been prepared for studies in artificial photosynthesis. The two porphyrins are joined at the meso positions via a phenylethyne linker and are present in zinc/zinc or zinc/free base metalation states. The porphyrin bearing the ethynyl unit incorporates zero, one, or two pentafluorophenyl groups at non-linking meso positions for tuning the porphyrin redox potentials. The synthetic approach entailed Pd-mediated coupling of porphyrin building blocks that bear a single ethynylphenyl or bromo/iodo substituent.}, number={9}, journal={TETRAHEDRON}, publisher={Elsevier BV}, author={Tomizaki, K and Lysenko, AB and Taniguchi, M and Lindsey, JS}, year={2004}, month={Feb}, pages={2011–2023} } @article{liu_yasseri_loewe_lysenko_malinovskii_zhao_surthi_li_misra_lindsey_et al._2004, title={Synthesis of porphyrins bearing hydrocarbon tethers and facile covalent attachment to Si(100)}, volume={69}, ISSN={["0022-3263"]}, DOI={10.1021/jo049439q}, abstractNote={The use of redox-active molecules as the active storage elements in memory chips requires the ability to attach the molecules to an electroactive surface in a reliable and robust manner. To explore the use of porphyrins tethered to silicon via carbosilane linkages, 17 porphyrins have been synthesized. Fourteen porphyrins bear a tether at a single meso site, and three porphyrins bear functional groups at two beta sites for possible two-point attachment. Two high-temperature processing methods (400 degrees C under inert atmosphere) have been developed for rapid (minutes), facile covalent attachment to Si platforms. The high-temperature processing conditions afford attachment either by direct deposition of a dilute solution (1 microM-1 mM) of the porphyrin sample onto the Si substrate or sublimation of a neat sample onto the Si substrate. The availability of this diverse collection of porphyrins enables an in-depth examination of the effects of the tether (length, composition, terminal functional group, number of tethers) and steric bulk of nonlinking substituents on the information-storage properties of the porphyrin monolayers obtained upon attachment to silicon. Attachment proceeds readily with a wide variety of hydrocarbon tethers, including 2-(trimethylsilyl)ethynyl, vinyl, allyl, or 3-butenyl directly appended to the porphyrin and iodo, bromomethyl, 2-(trimethylsilyl)ethynyl, ethynyl, vinyl, or allyl appended to the 4-position of a meso-phenyl ring. No attachment occurs with substituents such as phenyl, p-tolyl, mesityl, or ethyl. Collectively, the studies show that the high-temperature attachment procedure (1) has broad scope encompassing diverse functional groups, (2) tolerates a variety of arene substituents, and (3) does not afford indiscriminate attachment. The high-temperature processing conditions are ideally suited for use in fabrication of hybrid molecular/semiconductor circuitry.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Liu, ZM and Yasseri, AA and Loewe, RS and Lysenko, AB and Malinovskii, VL and Zhao, Q and Surthi, S and Li, QL and Misra, V and Lindsey, JS and et al.}, year={2004}, month={Aug}, pages={5568–5577} } @article{thamyongkit_lindsey_2004, title={Synthesis of swallowtail-substituted multiporphyrin rods}, volume={69}, ISSN={["0022-3263"]}, DOI={10.1021/jo049348t}, abstractNote={The availability of multiporphyrin arrays with defined architectures and good solubility in organic solvents is essential for a wide variety of physical studies. Herein the synthesis of linear multiporphyrin arrays (triads, tetrad, pentad) bearing solubilizing 7-tridecyl (swallowtail) groups is presented. The rodlike arrays are composed of zinc porphyrins at the termini and 1, 2, or 3 free base porphyrins at the core. The free base porphyrins in the tetrad and pentad are joined to each other via p-phenylene linkers whereas the zinc porphyrins in each array are attached to the core free base porphyrins via 1,4-diphenylethyne linkers. The arrays are designed for studies of interporphyrin electronic communication.}, number={17}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Thamyongkit, P and Lindsey, JS}, year={2004}, month={Aug}, pages={5796–5799} } @article{laha_dhanalekshmi_taniguchi_ambroise_lindsey_2003, title={A scalable synthesis of meso-substituted dipyrromethanes}, volume={7}, ISSN={["1520-586X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0346735296&partnerID=MN8TOARS}, DOI={10.1021/op034083q}, abstractNote={A one-flask synthesis of meso-substituted dipyrromethanes has been refined. The procedure entails reaction of an aldehyde in 100 equiv of pyrrole as the solvent containing a mild Lewis acid (e.g., InCl3) at room temperature. Following removal and recovery of excess pyrrole, the dipyrromethane is obtained by crystallization. The procedure generates minimal waste and does not require aqueous/organic extraction, chromatography, or distillation. The procedure has been scaled linearly to obtain >100 g of 5-phenyldipyrromethane. The utility of various analytical methods for characterizing dipyrromethanes has been investigated.}, number={6}, journal={ORGANIC PROCESS RESEARCH & DEVELOPMENT}, publisher={American Chemical Society (ACS)}, author={Laha, JK and Dhanalekshmi, S and Taniguchi, M and Ambroise, A and Lindsey, JS}, year={2003}, pages={799–812} } @article{taniguchi_ra_kirmaier_hindin_schwartz_diers_knox_bocian_lindsey_holten_2003, title={Comparison of excited-state energy transfer in arrays of hydroporphyrins (chlorins, oxochlorins) versus porphyrins: Rates, mechanisms, and design criteria}, volume={125}, ISSN={["0002-7863"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0242330789&partnerID=MN8TOARS}, DOI={10.1021/ja035987u}, abstractNote={A set of chlorin-chlorin and oxochlorin-oxochlorin dyads has been prepared with components in the same or different metalation states. In each case a 4,4'-diphenylethyne linker spans the respective 10-position of each macrocycle. The dyads have been studied using static and time-resolved absorption and emission spectroscopy, resonance Raman spectroscopy, and electrochemical techniques. Excited-state energy transfer from a zinc chlorin to a free-base (Fb) chlorin occurs with a rate constant of (110 ps)(-1) and an efficiency of 93%; similar values of (140 ps)(-1) and 83% are found for the corresponding oxochlorin dyad. Energy transfer in both dyads is slower and less efficient than found previously for the analogous porphyrin dyad, which displays a rate of (24 ps)(-1) and a yield of 99%. The slower rates and diminished efficiencies in the ZnFb chlorin and oxochlorin dyads versus the ZnFb porphyrin dyad are attributed to substantially weaker linker-mediated through-bond (TB) electron-exchange coupling (as indicated by resonance Raman data). Although the through-space (TS, i.e., dipole-dipole) coupling in the ZnFb-chlorin and -oxochlorin dyads is enhanced relative to the ZnFb porphyrin dyad (as indicated by Förster calculations), this enhancement is insufficient to compensate for the greatly diminished TB coupling. Taken together, the chlorin and oxochlorin dyads examined herein serve as benchmarks for elucidating the energy-transfer, electrochemical, and other properties of light-harvesting arrays containing multiple chlorins or oxochlorins.}, number={44}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Taniguchi, M and Ra, D and Kirmaier, C and Hindin, E and Schwartz, JK and Diers, JR and Knox, RS and Bocian, DF and Lindsey, JS and Holten, D}, year={2003}, month={Nov}, pages={13461–13470} } @article{balakumar_lysenko_carcel_malinovskii_gryko_schweikart_loewe_yasseri_liu_bocian_et al._2004, title={Diverse redox-active molecules bearing O-, S-, or Se-terminated tethers for attachment to silicon in studies of molecular information storage}, volume={69}, ISSN={["1520-6904"]}, DOI={10.1021/jo034944t}, abstractNote={A molecular approach to information storage employs redox-active molecules tethered to an electroactive surface. Attachment of the molecules to electroactive surfaces requires control over the nature of the tether (linker and surface attachment group). We have synthesized a collection of redox-active molecules bearing different linkers and surface anchor groups in free or protected form (hydroxy, mercapto, S-acetylthio, and Se-acetylseleno) for attachment to surfaces such as silicon, germanium, and gold. The molecules exhibit a number of cationic oxidation states, including one (ferrocene), two [zinc(II)porphyrin], three [cobalt(II)porphyrin], or four (lanthanide triple-decker sandwich compound). Electrochemical studies of monolayers of a variety of the redox-active molecules attached to Si(100) electrodes indicate that molecules exhibit a regular mode of attachment (via a Si-X bond, X = O, S, or Se), relatively homogeneous surface organization, and robust reversible electrochemical behavior. The acetyl protecting group undergoes cleavage during the surface deposition process, enabling attachment to silicon via thio or seleno groups without handling free thiols or selenols.}, number={5}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Balakumar, A and Lysenko, AB and Carcel, C and Malinovskii, VL and Gryko, DT and Schweikart, KH and Loewe, RS and Yasseri, AA and Liu, ZM and Bocian, DF and et al.}, year={2004}, month={Mar}, pages={1435–1443} } @article{wei_padmaja_youngblood_lysenko_lindsey_bocian_2004, title={Diverse redox-active molecules bearing identical thiol-terminated tripodal tethers for studies of molecular information storage}, volume={69}, ISSN={["0022-3263"]}, DOI={10.1021/jo0349476}, abstractNote={To examine the effects of molecular structure on charge storage in self-assembled monolayers (SAMs), a family of redox-active molecules has been prepared wherein each molecule bears a tether composed of a tripodal linker with three protected thiol groups for surface attachment. The redox-active molecules include ferrocene, zinc porphyrin, ferrocene-zinc porphyrin, magnesium phthalocyanine, and triple-decker lanthanide sandwich coordination compounds. The tripodal tether is based on a tris[4-(S-acetylthiomethyl)phenyl]-derivatized methane. Each redox-active unit is linked to the methane vertex by a 4,4'-diphenylethyne unit. The electrochemical characteristics of each compound were examined in solution and in SAMs on Au. Redox-kinetic measurements were also performed on the SAMs (with the exception of the magnesium phthalocyanine) to probe (1) the rate of electron transfer in the presence of an applied potential and (2) the rate of charge dissipation after the applied potential is disconnected. The electrochemical studies of the SAMs indicate that the tripodal tether provides a more robust anchor to the Au surface than does a tether with a single site of attachment. However, the electron-transfer and charge-dissipation characteristics of the two tethers are generally similar. These results suggest that the tripodal tether offers superior stability characteristics without sacrificing electrochemical performance.}, number={5}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Wei, LY and Padmaja, K and Youngblood, WJ and Lysenko, AB and Lindsey, JS and Bocian, DF}, year={2004}, month={Mar}, pages={1461–1469} } @article{li_surthi_mathur_gowda_misra_sorenson_tenent_kuhr_tamaru_lindsey_et al._2003, title={Electrical characterization of redox-active molecular monolayers on SiO2 for memory applications}, volume={83}, ISSN={["0003-6951"]}, DOI={10.1063/1.1584088}, abstractNote={Hybrid silicon capacitors have been successfully fabricated by attaching monolayers of redox-active molecules via self-assembly to ultrathin silicon dioxide layers. Capacitance, conductance, and cyclic voltammetric measurements have been used to characterize these capacitors. The presence of distinct capacitance and conductance peaks associated with oxidation and reduction of the monolayers at low gate voltages indicates discrete electron storage states for these capacitors, suggesting their feasibility in memory devices. The inherent molecular scalability and low-power operation coupled with existing silicon technology support the approach of hybrid molecule-silicon devices as a strong candidate for next generation electronic devices.}, number={1}, journal={APPLIED PHYSICS LETTERS}, author={Li, QL and Surthi, S and Mathur, G and Gowda, S and Misra, V and Sorenson, TA and Tenent, RC and Kuhr, WG and Tamaru, S and Lindsey, JS and et al.}, year={2003}, month={Jul}, pages={198–200} } @article{yu_muthukumaran_sazanovich_kirmaier_hindin_diers_boyle_bocian_holten_lindsey_2003, title={Excited-state energy-transfer dynamics in self-assembled triads composed of two porphyrins and an intervening bis(dipyrrinato)metal complex}, volume={42}, ISSN={["1520-510X"]}, DOI={10.1021/ic034559m}, abstractNote={The synthesis and characterization of various triads composed of a linear array of two zinc porphyrins joined via an intervening bis(dipyrrinato)metal(II) complex are reported. The preparation exploits the facile complexation of dipyrrins with divalent metal ions to give bis(dipyrrinato)metal(II) complexes [abbreviated (dp)(2)M]. Copper(II) and palladium(II) chelates of dipyrrins (available by oxidation of dipyrromethanes) were prepared in 50-80% yield. A one-flask synthesis of bis(dipyrrinato)zinc(II) complexes was developed by oxidation of a dipyrromethane with DDQ or p-chloranil in the presence of Zn(OAc)(2).2H(2)O in THF ( approximately 80% yield). Three routes were developed for preparing porphyrin-dipyrrins: (1). Suzuki coupling of a boronate-substituted zinc porphyrin (ZnP) and bis[5-(4-iodophenyl)dipyrrinato]Pd(II) to give the (ZnP-dp)(2)Pd triad (50% yield), followed by selective demetalation of the (dp)(2)Pd unit by treatment with 1,4-dithiothreitol under neutral conditions (71% yield); (2). oxidation of a porphyrin-dipyrromethane with p-chloranil in the presence of Zn(OAc)(2).2H(2)O followed by chromatography on silica gel (71% yield); and (3). condensation of a dipyrrin-dipyrromethane and a dipyrromethane-dicarbinol under InCl(3) catalysis followed by oxidation with DDQ (10-16% yield). Four triads of form (ZnP-dp)(2)Zn were prepared in 83-97% yield by treatment of a porphyrin-dipyrrin with Zn(OAc)(2).2H(2)O at room temperature. Free base dipyrrins typically absorb at 430-440 nm, while the bis(dipyrrinato)metal complexes absorb at 460-490 nm. The fluorescence spectra/yields and excited-state lifetimes of the (ZnP-dp)(2)Zn triad in toluene show (1). efficient energy transfer from the bis(dipyrrinato)zinc(II) chromophore to the zinc porphyrins (98.5% yield), and (2). little or no quenching of the resulting excited zinc porphyrin relative to the isolated chromophore. Taken together, these results indicate that bis(dipyrrinato)zinc(II) complexes can serve as self-assembling linkers that further function as secondary light-collection elements in porphyrin-based light-harvesting arrays.}, number={21}, journal={INORGANIC CHEMISTRY}, author={Yu, LH and Muthukumaran, K and Sazanovich, IV and Kirmaier, C and Hindin, E and Diers, JR and Boyle, PD and Bocian, DF and Holten, D and Lindsey, JS}, year={2003}, month={Oct}, pages={6629–6647} } @article{sazanovich_balakumar_muthukumaran_hindin_kirmaier_diers_lindsey_bocian_holten_2003, title={Excited-state energy-transfer dynamics of self-assembled imine-linked porphyrin dyads}, volume={42}, ISSN={["1520-510X"]}, DOI={10.1021/ic034558u}, abstractNote={Toward the development of new strategies for the synthesis of multiporphyrin arrays, we have prepared and characterized (electrochemistry and static/time-resolved optical spectroscopy) a series of dyads composed of a zinc porphyrin and a free base porphyrin joined via imine-based linkers. One dyad contains two zinc porphyrins. Imine formation occurs under gentle conditions without alteration of the porphyrin metalation state. Five imine linkers were investigated by combination of formyl, benzaldehyde, and salicylaldehyde groups with aniline and benzoic hydrazide groups. The imine-linked dyads are quite stable to routine handling. The excited-state energy-transfer rate from zinc to free base porphyrin ranges from (70 ps)(-)(1) to (13 ps)(-)(1) in toluene at room temperature depending on the linker employed. The energy-transfer yield is generally very high (>97%), with low yields of deleterious hole/electron transfer. Collectively, this work provides the foundation for the design of multiporphyrin arrays that self-assemble via stable imine linkages, have predictable electronic properties, and have comparable or even enhanced energy-transfer characteristics relative to those of other types of covalently linked systems.}, number={21}, journal={INORGANIC CHEMISTRY}, author={Sazanovich, IV and Balakumar, A and Muthukumaran, K and Hindin, E and Kirmaier, C and Diers, JR and Lindsey, JS and Bocian, DF and Holten, D}, year={2003}, month={Oct}, pages={6616–6628} } @article{speckbacher_yu_lindsey_2003, title={Formation of porphyrins in the presence of acid-labile metalloporphyrins: A new route to mixed-metal multiporphyrin arrays}, volume={42}, ISSN={["1520-510X"]}, DOI={10.1021/ic026206d}, abstractNote={The ability to incorporate distinct metalloporphyrins at designated sites in multiporphyrin arrays is essential for diverse applications in materials and biomimetic chemistry. The synthesis of such mixed-metal arrays via acid catalyzed reactions has largely been restricted to metalloporphyrins of stability class II (e.g., Cu, Co, Ni) or I. We describe routes for the rational synthesis of mixed-metal arrays via acid-catalyzed condensations that are compatible with metalloporphyrins of stability class III (e.g., Zn) and IV (e.g., Mg). The routes are demonstrated for p-phenylene-linked arrays. The key finding is that several mild Lewis acids [InCl(3), Sc(OTf)(3), Yb(OTf)(3), and Dy(OTf)(3)], which are known to catalyze the dipyrromethane + dipyrromethane-dicarbinol condensation in CH(2)Cl(2) at room temperature without acidolysis, do not demetalate zinc or magnesium porphyrins under the same conditions. Rational routes to porphyrin dyads and triads employ reaction of a (porphyrin)-dipyrromethane and a (porphyrin)-dipyrromethane-dicarbinol. The porphyrin-forming reactions (six examples) proceed in yields of 18-28%. The metalation states of the arrays prepared in this manner include Zn-free base (ZnFb), MgFb, ZnFbMg, ZnFbZn, and ZnFbFb. Studies of the catalysis process indicate that the dipyrromethane + dipyrromethane-dicarbinol condensation is catalyzed by both the Lewis acid and a Brønsted acid derived in situ from the Lewis acid. Taken together, the ability to employ otherwise "acid-labile" metalloporphyrins as precursors in condensation procedures should broaden the scope of accessible mixed-metal multiporphyrin arrays and motivate further studies of the application of mild Lewis acid catalysts in porphyrin chemistry.}, number={14}, journal={INORGANIC CHEMISTRY}, author={Speckbacher, M and Yu, LH and Lindsey, JS}, year={2003}, month={Jul}, pages={4322–4337} } @article{liu_yasseri_lindsey_bocian_2003, title={Molecular memories that survive silicon device processing and real-world operation}, volume={302}, ISSN={["1095-9203"]}, DOI={10.1126/science.1090677}, abstractNote={ If molecular components are to be used as functional elements in place of the semiconductor-based devices present in conventional microcircuitry, they must compete with semiconductors under the extreme conditions required for processing and operating a practical device. Herein, we demonstrate that porphyrin-based molecules bound to Si(100), which exhibit redox behavior useful for information storage, can meet this challenge. These molecular media in an inert atmosphere are stable under extremes of temperature (400°C) for extended periods (approaching 1 hour) and do not degrade under large numbers of read-write cycles (10 12 ). }, number={5650}, journal={SCIENCE}, author={Liu, ZM and Yasseri, AA and Lindsey, JS and Bocian, DF}, year={2003}, month={Nov}, pages={1543–1545} } @article{muthukumaran_loewe_ambroise_tamaru_li_mathur_bocian_misra_lindsey_2004, title={Porphyrins bearing arylphosphonic acid tethers for attachment to oxide surfaces}, volume={69}, ISSN={["0022-3263"]}, DOI={10.1021/jo034945l}, abstractNote={Synthetic molecules bearing phosphonic acid groups can be readily attached to oxide surfaces. As part of a program in molecular-based information storage, we have developed routes for the synthesis of diverse porphyrinic compounds bearing phenylphosphonic acid tethers. The routes enable (1) incorporation of masked phosphonic acid groups in precursors for use in the rational synthesis of porphyrinic compounds and (2) derivatization of porphyrins with masked phosphonic acid groups. The precursors include dipyrromethanes, monoacyldipyrromethanes, and diacyldipyrromethanes. The tert-butyl group has been used to mask the dihydroxyphosphoryl substituent. The di-tert-butyloxyphosphoryl unit is stable to the range of conditions employed in syntheses of porphyrins and multiporphyrin arrays yet can be deprotected under mild conditions (TMS-Cl/TEA or TMS-Br/TEA in refluxing CHCl(3)) that do not cause demetalation of zinc or magnesium porphyrins. The porphyrinic compounds that have been prepared include (1) A(3)B-, trans-AB(2)C-, and ABCD-porphyrins that bear a single phenylphosphonic acid group, (2) a trans-A(2)B(2)-porphyrin bearing two phenylphosphonic acid groups, (3) a chlorin that bears a single phenylphosphonic acid group, and (4) a porphyrin dyad bearing a single phenylphosphonic acid group. For selected porphyrin-phosphonic acids, the electrochemical characteristics have been investigated for molecules tethered to SiO(2) surfaces grown on doped Si. The voltammetric behavior indicates that the porphyrin-phosphonic acids form robust, electrically well-behaved monolayers on the oxide surface.}, number={5}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Muthukumaran, K and Loewe, RS and Ambroise, A and Tamaru, SI and Li, QL and Mathur, G and Bocian, DF and Misra, V and Lindsey, JS}, year={2004}, month={Mar}, pages={1444–1452} } @article{loewe_ambroise_muthukumaran_padmaja_lysenko_mathur_li_bocian_misra_lindsey_2004, title={Porphyrins bearing mono or tripodal benzylphosphonic acid tethers for attachment to oxide surfaces}, volume={69}, ISSN={["1520-6904"]}, DOI={10.1021/jo034946d}, abstractNote={The ability to attach redox-active molecules to oxide surfaces in controlled architectures (distance, orientation, packing density) is essential for the design of a variety of molecular-based information storage devices. We describe the synthesis of a series of redox-active molecules wherein each molecule bears a benzylphosphonic acid tether. The redox-active molecules include zinc porphyrins, a cobalt porphyrin, and a ferrocene-zinc porphyrin. An analogous tripodal tether has been prepared that is based on a tris[4-(dihydroxyphosphorylmethyl)phenyl]-derivatized methane. A zinc porphyrin is linked to the methane vertex by a 1,4-phenylene unit. The tripodal systems are designed to improve monolayer stability and ensure vertical orientation of the redox-active porphyrin on the electroactive surface. For comparison purposes, a zinc porphyrin bearing a hexylphosphonic acid tether also has been prepared. The synthetic approaches for introduction of the phosphonic acid group include derivatization of a bromoalkyl porphyrin or use of a dimethyl or diethyl phosphonate substituted precursor in a porphyrin-forming reaction. The latter approach makes use of dipyrromethane building blocks bearing mono or tripodal dialkyl phosphonate groups. The zinc porphyrin-tripodal compound bearing benzylphosphonic acid legs tethered to a SiO(2) surface (grown on doped Si) was electrically well-behaved and exhibited characteristic porphyrin oxidation/reduction waves. Collectively, a variety of porphyrinic molecules can now be prepared with tethers of different length, composition, and structure (mono or tripodal) for studies of molecular-based information storage on oxide surfaces.}, number={5}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Loewe, RS and Ambroise, A and Muthukumaran, K and Padmaja, K and Lysenko, AB and Mathur, G and Li, QL and Bocian, DF and Misra, V and Lindsey, JS}, year={2004}, month={Mar}, pages={1453–1460} } @article{tomizaki_thamyongkit_loewe_lindsey_2003, title={Practical synthesis of perylene-monoimide building blocks that possess features appropriate for use in porphyrin-based light-harvesting arrays}, volume={59}, ISSN={["0040-4020"]}, DOI={10.1016/S0040-4020(03)00020-6}, abstractNote={Perylene-monoimide dyes with solubilizing aryloxy substituents at the perylene perimeter and a synthetic handle on the N-aryl group are valuable building blocks for incorporation as accessory pigments in porphyrin-based light-harvesting arrays. A family of such dyes has been prepared by reaction of 1,6,9-tris(4-tert-butylphenoxy)perylene-3,4-dicarboxylic anhydride with a set of 4-iodo/ethynyl anilines (with or without 2,6-diisopropyl substituents) in the presence of Zn(OAc)2·2H2O in imidazole/mesitylene at 130°C. The workup procedures throughout the synthesis have been streamlined for scale-up purposes, minimizing chromatography. Two bis(perylene)porphyrin building blocks were prepared in a rational manner and examined in Sonogashira and Glaser polymerizations. The two isopropyl groups on the N-aryl group and the three 4-tert-butylphenoxy groups at the perylene perimeter are essential for high solubility of the bis(perylene)porphyrins and corresponding oligomers in organic solvents.}, number={8}, journal={TETRAHEDRON}, author={Tomizaki, KY and Thamyongkit, P and Loewe, RS and Lindsey, JS}, year={2003}, month={Feb}, pages={1191–1207} } @article{schweikart_malinovskii_yasseri_li_lysenko_bocian_lindsey_2003, title={Synthesis and characterization of bis(S-acetylthio)-derivatized europium triple-decker monomers and oligomers}, volume={42}, ISSN={["0020-1669"]}, DOI={10.1021/ic034730u}, abstractNote={We report the synthesis of monomers, dimers, trimers, and oligomers of triple-decker (TD) complexes bearing S-acetylthio groups at the termini: AcS-(TD)(n)()-SAc. Each TD was of type (Pc)Eu(Pc)Eu(Por), where H(2)Pc = tetra-tert-butylphthalocyanine and H(2)Por is a meso-tetraarylporphyrin bearing functional groups at the 4-aryl position such as ethynyl, TMS-ethynyl, TIPS-ethynyl, or iodo. The TD arrays were prepared by Sonogashira- and Glaser-type coupling reactions, affording 1,4-diphenylethyne or 1,4-diphenylbutadiyne linkers joining the TDs. Each TD array exhibited high solubility in organic solvents such as CHCl(3) or CH(2)Cl(2). Self-assembled monolayers (SAMs) of all the TDs were prepared on Au substrates and investigated via a variety of electrochemical techniques aimed at determining redox potentials, rates of electron transfer under applied potential, and rates of charge retention in the absence of applied potential. The electrochemical measurements were accompanied by ellipsometric studies aimed at determining SAM thickness and, hence, the orientation of the complexes with respect to the surface plane. All of the TD SAMs exhibit robust, reversible voltammetry yielding four well-resolved waves in the potential range of 0 to +1.6 V (corresponding to the mono-, di-, tri-, and tetracations). The electron-transfer rates for the various oxidation states of all of the TD SAMS are similar and in the 10(4)-10(5) s(-)(1) range. The charge-dissipation rates (measured in terms of a charge-retention half-life) are also similar and are in the 10-60 s range. These rates are influenced by both the packing density of the molecules and the orientation of the molecules on the surface. The full body of data supports the view that all of the dithio-derivatized TD complexes assume a similar geometry on the surface. In particular, the complexes are oriented with their linkers/macrocycle planes generally parallel with the surface, unlike monothio-derivatized analogues, which are in a more perpendicular geometry. The parallel geometry of the dithio-derivatized TDs is qualitatively consistent with covalent attachment to Au via both thiols.}, number={23}, journal={INORGANIC CHEMISTRY}, author={Schweikart, KH and Malinovskii, VL and Yasseri, AA and Li, JZ and Lysenko, AB and Bocian, DF and Lindsey, JS}, year={2003}, month={Nov}, pages={7431–7446} } @article{muthukumaran_loewe_kirmaier_hindin_schwartz_sazanovich_diers_bocian_holten_lindsey_2003, title={Synthesis and excited-state photodynamics of a perylene-monoimide-oxochlorin dyad. A light-harvesting array}, volume={107}, ISSN={["1520-6106"]}, DOI={10.1021/jp026941a}, abstractNote={A perylene-oxochlorin dyad has been prepared and characterized for potential use as a new light-harvesting motif. The dyad (PMI−ZnO) consists of a perylene-monoimide dye (PMI) joined at the 5-position of a zinc oxochlorin (ZnO) via a diphenylethyne linker. The dyad and its subunits have been studied in both polar and nonpolar media using static and time-resolved optical spectroscopy and electrochemical techniques. Energy flows very rapidly from both unrelaxed (vibrationally, conformationally, or electronically) and relaxed forms of the excited perylene (PMI*) to the ground-state oxochlorin with an effective time constant of ∼4 ps and an efficiency of 99% in both toluene and benzonitrile. Subsequently, there is little or no quenching of the excited oxochlorin (ZnO*) in either solvent. These findings are consistent with the expectation that all charge-separated states such as PMI- ZnO+ lie energetically above both PMI* and ZnO* in both polar and nonpolar media. Furthermore, light absorption by the perylene ...}, number={15}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Muthukumaran, K and Loewe, RS and Kirmaier, C and Hindin, E and Schwartz, JK and Sazanovich, IV and Diers, JR and Bocian, DF and Holten, D and Lindsey, JS}, year={2003}, month={Apr}, pages={3431–3442} } @article{kirmaier_hindin_schwartz_sazanovich_diers_muthukumaran_taniguchi_bocian_lindsey_holten_2003, title={Synthesis and excited-state photodynamics of perylene-bis(imide)-oxochlorin dyads. A charge-separation motif}, volume={107}, ISSN={["1520-6106"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0037452013&partnerID=MN8TOARS}, DOI={10.1021/jp0269423}, abstractNote={Three perylene-oxochlorin dyads have been prepared and characterized with the goal of identifying charge-injection or molecular-switching motifs for use in molecular photonics. Each dyad consists of a perylene-bis(imide) dye (PDI) joined at the 10-position of a magnesium, zinc, or free base (Fb) oxochlorin via a diphenylethyne linker. Each dyad has been studied in both polar and nonpolar media using static and time-resolved optical spectroscopy and electrochemical techniques. Dyad PDI−MgO is an excellent charge-separation unit in which the excited perylene (∼3.5 ps lifetime) or the excited oxochlorin (lifetimes of 0.5 ns in benzonitrile and 1.0 ns in toluene) give rise to state PDI- MgO+ in high overall yield (>90%); the charge-separated state has a lifetime of ≥1 ns in both toluene and benzonitrile. The pathway for generating PDI- MgO+ from the excited perylene (PDI*) involves both hole transfer and energy transfer to the oxochlorin followed by electron transfer from the resulting MgO* to PDI. Similar de...}, number={15}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, publisher={American Chemical Society (ACS)}, author={Kirmaier, C and Hindin, E and Schwartz, JK and Sazanovich, IV and Diers, JR and Muthukumaran, K and Taniguchi, M and Bocian, DF and Lindsey, JS and Holten, D}, year={2003}, month={Apr}, pages={3443–3454} } @article{tomizaki_yu_wei_bocian_lindsey_2003, title={Synthesis of cyclic hexameric porphyrin arrays. Anchors for surface immobilization and columnar self-assembly}, volume={68}, ISSN={["1520-6904"]}, DOI={10.1021/jo034861c}, abstractNote={To investigate new architectures for the self-assembly of multiporphyrin arrays, a one-flask synthesis of a shape-persistent cyclic hexameric array of porphyrins was exploited to prepare six derivatives bearing diverse pendant groups. The new arrays contain 6-12 carboxylic acid groups, 12 amidino groups, 6 thiol groups, or 6 thiol groups and 6 carboxylic acid groups in protected form (S-acetylthio, TMS-ethyl, TMS-ethoxycarbonyl). The arrays contain alternating Zn and free base (Fb) porphyrins or all Zn porphyrins. The one-flask synthesis entails a template-directed, Pd-mediated coupling of a p/p'-substituted diethynyl Zn porphyrin and a m/m'-substituted diiodo Fb porphyrin. The porphyrin building blocks (trans-A(2)B(2), trans-AB(2)C) contain the protected pendant groups at nonlinking meso positions. A self-assembled monolayer (SAM) of a Zn(3)Fb(3) cyclic hexamer containing one thiol group on each porphyrin was prepared on a gold electrode and the surface-immobilized architecture was examined electrochemically. Together, the work reported herein provides cyclic hexameric porphyrin arrays for studies of self-assembly in solution or on surfaces.}, number={21}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Tomizaki, KY and Yu, LH and Wei, LY and Bocian, DF and Lindsey, JS}, year={2003}, month={Oct}, pages={8199–8207} } @article{matsumoto_du_lindsey_2002, title={A parallel simplex search method for use with an automated chemistry workstation}, volume={62}, ISSN={["0169-7439"]}, DOI={10.1016/S0169-7439(02)00010-2}, abstractNote={The Simplex method, an inherently serial means of optimization, can be used to search for improved conditions for chemical reactions. We have developed an automated chemistry workstation equipped for parallel adaptive experimentation. To exploit the capabilities of the workstation and thereby optimize reaction conditions in a more expedient manner, we have developed an experiment-planning module for performing Simplex searches in parallel. The parallel Simplex search (PSS) module enables multiple composite modified Simplex (CMS) searches to be performed in a concurrent manner. Features have been incorporated for two applications. (1) Multiple concurrent simplex searches in one search space, enabling optimization of conditions for one reaction. The use of Simplex searches starting from several points in a search space reduces the possibility of falsely concluding that a local maximum is the global maximum. (2) Concurrent investigation of multiple search spaces with one Simplex search per space, enabling optimization of conditions for each member of a set of catalysts or set of reactants for a given reaction. This latter feature is useful for combinatorial chemistry applications. All individual Simplex searches in a PSS study must employ the same experimental template. The PSS module includes options to define conditions for simplex moves as well as specifying initial points in the search space. Provisions are included for stop criteria, termination of an individual Simplex search, and global termination of multiple Simplex searches. The PSS method provides a parallel yet adaptive means for identifying improved conditions for chemical reactions.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Matsumoto, T and Du, H and Lindsey, JS}, year={2002}, month={May}, pages={129–147} } @article{matsumoto_du_lindsey_2002, title={A two-tiered strategy for simplex and multidirectional optimization of reactions with an automated chemistry workstation}, volume={62}, ISSN={["0169-7439"]}, DOI={10.1016/S0169-7439(02)00011-4}, abstractNote={A two-tiered strategy for optimizing reaction conditions has been developed for use with an automated chemistry workstation capable of parallel adaptive experimentation. In tier one, a broad survey of conditions is performed in parallel. In tier two, the promising region identified in the first tier is used as the starting point for in-depth searches. The search strategies employed in tier two include the composite-modified Simplex (CMS), multidirectional search (MDS), and parallel Simplex search (PSS) methods. Accordingly, this two-tiered strategy has been integrated into the CMS, MDS, and PSS experiment-planning modules. Each of these methods requires an initial user-defined simplex to explore reaction conditions. The breadth-first survey avoids the lengthy experimentation that occurs when the initial simplex is located far from the optimal region, and also diminishes the possibility of trapping in local maxima. Thus, the two-tiered strategy (breadth-first, depth-second) enables the optimal region to be reached rapidly.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Matsumoto, T and Du, H and Lindsey, JS}, year={2002}, month={May}, pages={149–158} } @article{chevalier_geier_lindsey_2002, title={Acidolysis of intermediates used in the preparation of core-modified porphyrinic macrocycles}, volume={6}, ISSN={["1088-4246"]}, DOI={10.1142/S108842460200021X}, abstractNote={ The stability towards acidolysis of intermediates used in the preparation of core-modified porphyrinic macrocycles was examined. Experiments were performed using analogs of 5-phenyldipyrromethane in which one of the two pyrrole rings was modified (XPM). The XPMs utilized in these studies had X = 2-furyl (OPM), 2-thienyl (SPM), 2-selenyl (SePM), or 3-pyrrolyl (NCPPM). The XPMs possess a potentially labile linkage to a heteroatom-modified ring as well as a potentially labile linkage to a pyrrole ring. The stability of the two types of linkages was examined under acid catalysis conditions commonly used in the preparation of porphyrinic macrocycles. The methodology employed enabled characterization of the stability of the XPM (GC analysis), the yield of porphyrin (UV-vis absorption), and the composition of porphyrinic species (laser-desorption mass spectrometry, LD-MS) formed upon acidolysis of the XPM. These experiments showed that (1) the linkage to the heteroatom-modified ring is fairly stable in the presence of a linkage to pyrrole, and (2) the linkage to pyrrole is much more stable in the XPMs than is the case in 5-phenyldipyrromethane. Additional experiments with analogs of 5-phenyldipyrromethane having both rings modified ( X 2 M ), where X = 2- furyl ( O 2 M ), 2- thienyl ( S 2 M ), or 2- selenyl ( Se 2 M ) confirmed that linkages to furyl, thienyl, and selenyl rings are stable towards acidolysis. Taken together, the observations concerning stability of various linkages provide a foundation for understanding the types and yields of core-modified porphyrinic macrocycles formed in reactions with reactants that are not direct precursors to the isolated products. }, number={3}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Chevalier, F and Geier, GR and Lindsey, JS}, year={2002}, pages={186–197} } @article{du_lindsey_2002, title={An approach for parallel and adaptive screening of discrete compounds followed by reaction optimization using an automated chemistry workstation}, volume={62}, ISSN={["0169-7439"]}, DOI={10.1016/S0169-7439(02)00012-6}, abstractNote={The challenge of finding appropriate reagents, catalysts, or cocatalysts for chemical reactions is typically met with a strategy of surveying broadly to identify a good starting point (i.e., a hit) from which an in-depth optimization can be performed. We have developed an approach for experiment planning that enables this two-tiered strategy to be implemented on an automated chemistry workstation. One experiment-planning module (Parascreen) for screening discrete substances to identify hits is linked to a second module (Multidirectional search, MDS) for optimization of each hit compound. The screening module has been constructed through modification of an experiment-planning module for performing grid searches. Each candidate is examined over a range of concentrations. Two levels of decision-making are performed. (1) Local evaluation: Yield-versus-time data from a given reaction are examined in a pattern-matching procedure to assess whether monitoring should be continued or terminated. (2) Global evaluation: When a user-defined threshold (e.g., yield) is reached, the candidate is flagged as a hit; any experiments at higher concentration of the same candidate are deleted. Each of the hit compounds is subjected to identification of refined conditions by means of an MDS optimization. Each module alone enables parallel adaptive experimentation. Several issues for automated use of two different modules in succession have been addressed. This two-tiered approach of breadth-first screening followed by in-depth optimization of hits enables autonomous experimentation using an automated chemistry workstation.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Du, H and Lindsey, JS}, year={2002}, month={May}, pages={159–170} } @article{dixon_du_cork_lindsey_2002, title={An experiment planner for performing successive focused grid searches with an automated chemistry workstation}, volume={62}, ISSN={["1873-3239"]}, DOI={10.1016/S0169-7439(02)00009-6}, abstractNote={Automated chemistry workstations equipped for parallel and adaptive experimentation can provide a significant impact in chemistry research, particularly for exploring search spaces as part of optimization studies. A traditional method of investigating a search space involves generation of a response surface upon examination of a regular grid of points (e.g., as in a full factorial design). Such experimental approaches are compatible with parallel experimentation but are not adaptive in directing the search toward favorable regions of the search space. We have developed an algorithm wherein a succession of grid searches is performed in a search space. The location of the optimal response obtained in one search cycle constitutes the location about which a subsequent more fine-grained search is performed. In this manner, a sequential iterative optimization can be achieved: one cycle is comprised of a set of parallel reactions followed by data evaluation, and multiple cycles occur until one of several user-defined termination criteria is satisfied. In successive cycles, the number of levels on each dimension can be decremented and the range of each dimension can be decreased by a defined “shrinkage” factor. The resulting successive focused grid search (SFGS) affords a breadth-first then in-depth study. We have developed an experimental planner that enables the SFGS algorithm to be implemented on an automated chemistry workstation. Options are available for adjusting the scope of experimentation to conserve material resources (e.g., solvent, reagents, reactants) or to curtail the duration of experimentation. Collectively, the SFGS module enables parallel adaptive experimentation and affords a comprehensive response surface that is fine-grained in the region of optimal response.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Dixon, JM and Du, H and Cork, DG and Lindsey, JS}, year={2002}, month={May}, pages={115–128} } @article{li_mathur_homsi_surthi_misra_malinovskii_schweikart_yu_lindsey_liu_et al._2002, title={Capacitance and conductance characterization of ferrocene-containing self-assembled monolayers on silicon surfaces for memory applications}, volume={81}, ISSN={["0003-6951"]}, DOI={10.1063/1.1500781}, abstractNote={Self-assembled monolayers of 4-ferrocenylbenzyl alcohol attached to silicon provided the basis for electrolyte-molecule-silicon capacitors. Characterization by conventional capacitance and conductance techniques showed very high capacitance and conductance peaks near ∼0.6 V associated with charging and discharging of electrons into and from discrete levels in the monolayer owing to the presence of the redox-active ferrocenes. The reversible charge trapping of these molecules suggest their potential application in memory devices. Due to the molecular scalability and low-power operation, molecular-silicon hybrid devices may be strong candidates for next-generation electronic devices.}, number={8}, journal={APPLIED PHYSICS LETTERS}, author={Li, QL and Mathur, G and Homsi, M and Surthi, S and Misra, V and Malinovskii, V and Schweikart, KH and Yu, LH and Lindsey, JS and Liu, ZM and et al.}, year={2002}, month={Aug}, pages={1494–1496} } @article{roth_lindsey_bocian_kuhr_2002, title={Characterization of charge storage in redox-active self-assembled monolayers}, volume={18}, ISSN={["0743-7463"]}, DOI={10.1021/la025525e}, abstractNote={Self-assembled monolayers (SAMs) of thiol-derivatized alkyl ferrocenes and Zn tetraarylporphyrins on a gold surface have been characterized under open circuit conditions using fluorescence imaging microscopy and a varietyof electrochemical methods. The fluorescence of the neutral form of the Zn tetraarylporphyrin SAM and the electrode cell potential are monitored simultaneously after oxidation of the SAM and subsequent establishment of an open circuit condition. These experiments capitalize on the fact that the neutral Zn tetraarylporphyrin SAM is fluorescent whereas emission from the oxidized Zn tetraarylporphyrin SAM is quenched. Accordingly, the fluorescence recovery after disconnection from an oxidizing potential provides an independent measure of the change in oxidation state of the porphyrin SAM as a function of time after the cell is open-circuited. This measurement demonstrates that the porphyrin SAM remains oxidized for an extended period (hundreds of seconds) even though the electrochemical cell potential decays rapidly to the open circuit potential (OCP). Cyclic voltammetry was used to confirm the electrochemical properties of the redox SAMs and to determine the surface coverage of the redox-active molecules. A new method, designated open circuit potential amperometry, was used to read the charge of the oxidized SAM at the OCP after charging currents have decayed away. Additionally, open circuit potential voltammetry yields a sigmoidal response with a characteristic half-wave potential identical to that observed with cyclic voltammetry, indicative of a Nernstian process. Collectively, these studies show that the electrochemical cell discharges to the OCP quickly, that the SAM remains oxidized under these conditions, and that these methods can be used to quantitatively determine the amount of stored charge in the SAM.}, number={10}, journal={LANGMUIR}, author={Roth, KM and Lindsey, JS and Bocian, DF and Kuhr, WG}, year={2002}, month={May}, pages={4030–4040} } @article{roth_gryko_clausen_li_lindsey_kuhr_bocian_2002, title={Comparison of electron-transfer and charge-retention characteristics of porphyrin-containing self-assembled monolayers designed for molecular information storage}, volume={106}, ISSN={["1520-6106"]}, DOI={10.1021/jp025850a}, abstractNote={The redox kinetics for a variety of porphyrin-containing self-assembled monolayers (SAMs) on Au are reported. The measurements probe both the rate of electron-transfer (k0) for oxidation (in the presence of applied potential) and the rate of charge dissipation after the applied potential is disconnected (characterized by a charge-retention half-life (t1/2)). The porphyrins include (1) monomeric Zn complexes that contain phenylmethylene linkers wherein the number of methylene spacers varies from 0 to 3, (2) monomeric Zn complexes that contain different ethynylphenyl-derived linkers, and (3) a triple-decker lanthanide sandwich complex with a phenylethynylphenyl linker. The k0 values for all the porphyrin SAMs are in the range of 104−105 s-1. The k0 values for the monomeric ethynylphenyl-linked porphyrin SAMs are generally faster than those for the monomeric phenylmethylene-linked SAMs. The rates for the latter SAMs decrease as the number of methylene spacers increases. The rates for the triple-decker SAM ar...}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Roth, KM and Gryko, DT and Clausen, C and Li, JZ and Lindsey, JS and Kuhr, WG and Bocian, DF}, year={2002}, month={Aug}, pages={8639–8648} } @article{loewe_lammi_diers_kirmaier_bocian_holten_lindsey_2002, title={Design and synthesis of light-harvesting rods for intrinsic rectification of the migration of excited-state energy and ground-state holes}, volume={12}, ISSN={["0959-9428"]}, DOI={10.1039/b108168c}, abstractNote={We present the design of molecular materials for ultimate use in solid-state solar cells. The molecular materials are semi-rigid oligomeric rods of defined length with metalloporphyrins in the backbone and a carboxy group at one end for attachment to a surface. The rods are designed to absorb visible light, and then undergo excited-state energy transfer and ground-state hole transfer in opposite directions along the length of the rod. The rational synthesis of the multiporphyrin arrays relies on joining porphyrin building blocks in an efficient and controlled manner. Several porphyrin building blocks have been synthesized that bear bromophenyl, iodophenyl, trimethylsilylethynylphenyl and/or ethynylphenyl substituents for use in a copper-free Sonogashira reaction using Pd2(dba)3 and P(o-tol)3. Competition experiments performed on equimolar quantities of an iodo-porphyrin and a bromo-porphyrin with an ethynyl-porphyrin show iodo + ethyne coupling with a low amount (35 °C) or undetectable amount (22 °C) of bromo + ethyne coupling. Efficient coupling of bromo-porphyrins with ethynyl-porphyrins was achieved using the same copper-free Sonogashira reaction conditions at higher temperature (50 °C or 80 °C). These findings allow successive coupling reactions to be achieved using substrates bearing iodo and bromo synthetic handles. Thus, a porphyrin-based tetrad (or pentad) was synthesized with a final convergent coupling of a bromo-substituted dyad (or triad) and an ethynyl-substituted dyad. A porphyrin triad was prepared by sequential iodo + ethyne coupling reactions. The triad, tetrad, and pentad each are comprised of a terminal magnesium porphyrin bearing one carboxy group (for surface attachment) and two pentafluorophenyl groups; the remaining porphyrins in each array are present as the zinc chelate. Electrochemical characterization of benchmark porphyrins indicates the presence of the desired electrochemical gradient for hole hopping in the arrays. Static absorption data indicate that the arrays are weakly coupled, while static fluorescence data indicate that the excited-state energy flows in high yield to the terminal magnesium porphyrin. Time-resolved spectroscopic analysis leads to rate constants in THF of (9 ps)−1, (15 ps)−1, and (30 ps)−1 for ZnMg dyad 20, Zn2Mg triad 13, and Zn3Mg tetrad 15, respectively, and quantum efficiencies ≥99% for energy flow to the magnesium porphyrin in each case. These design and synthesis strategies should be useful for the construction of materials for molecular-based solar cells.}, number={5}, journal={JOURNAL OF MATERIALS CHEMISTRY}, author={Loewe, RS and Lammi, RK and Diers, JR and Kirmaier, C and Bocian, DF and Holten, D and Lindsey, JS}, year={2002}, pages={1530–1552} } @article{schweikart_malinovskii_diers_yasseri_bocian_kuhr_lindsey_2002, title={Design, synthesis, and characterization of prototypical multistate counters in three distinct architectures}, volume={12}, ISSN={["0959-9428"]}, DOI={10.1039/b108520d}, abstractNote={The storage of multiple bits of information in distinct molecular oxidation states is anticipated to afford extraordinarily high memory densities. Among redox-active molecules, lanthanide porphyrinic triple-decker complexes are attractive candidates for such molecular information storage elements because they provide at least four cationic states over a modest potential range. Our approach toward a molecular multistate counter involves covalently linking two triple deckers with interleaving oxidation potentials to achieve a commensurate increase in the number of oxidation states within a single dyad. We report the design and synthesis of five dyads comprised of triple-decker complexes of the form (Pc)Ln(Pc)Ln(Por) or (Por1)Ln(Pc)Ln(Por2), where Pc = phthalocyaninato, Por = porphyrinato, and Ln = Ce or Eu. The dyads were prepared in a modular building-block fashion by Pd-mediated coupling of an iodophenyl-triple decker and an ethynylphenyl-triple decker. The different dyad architectures examined include a vertical architecture with one linker (V1), a horizontal architecture with one linker (H1), and a horizontal architecture with two linkers (H2). In each dyad, one or two S-acetylthiomethyl groups incorporated on the porphyrinic moiety of the triple decker enables attachment to an electroactive surface viain situ cleavage of the protected thiol linker(s). Three dyads (Dyad1–3) have the V1 architecture but different compositions of triple deckers; three dyads (Dyad3–5) have identical composition but different architectures (V1, H1, H2) for comparison of the properties in self-assembled monolayers (SAMs) on gold. The SAM of each dyad exhibits robust reversible electrochemical behavior; the redox waves are essentially the sum of the waves of the component triple deckers. In contrast, mixtures of the component triple decker monomers form poor quality SAMs with inferior electrochemical characteristics. Accordingly, all three dyad architectures are viable constructs for assembling a multistate counter.}, number={4}, journal={JOURNAL OF MATERIALS CHEMISTRY}, author={Schweikart, KH and Malinovskii, VL and Diers, JR and Yasseri, AA and Bocian, DF and Kuhr, WG and Lindsey, JS}, year={2002}, pages={808–828} } @article{geier_lindsey_2002, title={Effects of diverse acid catalysts on the reaction course in the two-step one-flask synthesis of meso-tetraphenylporphyrin}, volume={6}, ISSN={["1088-4246"]}, DOI={10.1142/S1088424602000208}, abstractNote={ A set of 45 acids or acid combinations was examined in the condensation of pyrrole + benzaldehyde (10 mM each in CH 2 Cl 2) leading to meso-tetraphenylporphyrin (TPP). Initial screening experiments identified suitable acid catalysts and the optimal concentration (in terms of TPP formation) for each acid. Subsequent experiments followed the time course of reactions using the best conditions identified in the screening experiments. The reaction course was followed by monitoring reactions from 1 min to 24 h for the yield of TPP (by UV-vis and HPLC), the yields of N-confused tetraphenylporphyrin and tetraphenylsapphyrin (by HPLC), the quantity of unreacted benzaldehyde (by TLC), and the oligomer composition (by laser desorption mass spectrometry). Diverse acids (Brønsted or Lewis; soluble or insoluble) were found to provide yields of TPP ranging up to ~50%. Only 10 acids gave no TPP. In addition, N-confused tetraphenylporphyrin was found to be a ubiquitous byproduct, whereas tetraphenylsapphyrin was not widely observed. MgBr 2-etherate and CuCl 2 each catalyzed porphyrinogen formation and resulted in porphyrin metalation following oxidation and neutralization of the reaction mixture, thereby providing direct, one-flask syntheses of magnesium and copper porphyrins. Observations concerning the reaction course obtained from prior studies of TFA or BF 3-etherate catalysis have been found to be quite general across a broad range of acid catalysts. Collectively, these results show that many acids have potential utility in porphyrin syntheses. }, number={3}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Geier, GR and Lindsey, JS}, year={2002}, pages={159–185} } @article{kodis_liddell_garza_clausen_lindsey_moore_moore_gust_2002, title={Efficient energy transfer and electron transfer in an artificial photosynthetic antenna-reaction center complex}, volume={106}, ISSN={["1520-5215"]}, DOI={10.1021/jp012133s}, abstractNote={A highly efficient functional mimic of a photosynthetic antenna−reaction center complex has been designed, synthesized, and studied spectroscopically. The antenna, consisting of four covalently linked zinc tetraarylporphyrins, (PZP)3−PZC, has been coupled to a free-base porphyrin−fullerene artificial photosynthetic reaction center, P−C60, to form a (PZP)3−PZC−P−C60 hexad. As revealed by time-resolved absorption and emission studies in 2-methyltetrahydrofuran solution at ambient temperature, excitation of a peripheral zinc porphyrin moiety is followed by singlet−singlet energy transfer to the central zinc porphyrin to give (PZP)3−1PZC−P−C60 with a time constant of 50 ps. The excitation is passed on to the free-base porphyrin in 32 ps to produce (PZP)3−PZC−1P−C60, which decays by electron transfer to the fullerene with a time constant of 25 ps. The resulting (PZP)3−PZC−P•+−C60•- charge-separated state is generated with a quantum yield of 0.98 based on light absorbed by the porphyrin antenna. Direct excitati...}, number={10}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Kodis, G and Liddell, PA and Garza, L and Clausen, PC and Lindsey, JS and Moore, AL and Moore, TA and Gust, D}, year={2002}, month={Mar}, pages={2036–2048} } @article{youngblood_gryko_lammi_bocian_holten_lindsey_2002, title={Glaser-mediated synthesis and photophysical characterization of diphenylbutadiyne-linked porphyrin dyads}, volume={67}, ISSN={["1520-6904"]}, DOI={10.1021/jo016150p}, abstractNote={The Pd-mediated Glaser coupling of a zinc monoethynyl porphyrin and a magnesium monoethynyl porphyrin affords a mixture of three 4,4'-diphenylbutadiyne-linked dyads comprised of two zinc porphyrins (Zn-pbp-Zn), two magnesium porphyrins (Mg-pbp-Mg), and one metalloporphyrin of each type (Zn-pbp-Mg). The latter is easily isolated due to the greater polarity of the magnesium versus the zinc chelate. Exposure of Zn-pbp-Mg to silica gel results in selective demetalation, affording Zn-pbp-Fb where Fb = free base porphyrin. This synthesis route employs the magnesium porphyrin as a latent form of the Fb porphyrin, thereby avoiding copper insertion during the Glaser reaction, and as a polar entity facilitating separation. The absorption spectrum of Zn-pbp-Mg or Zn-pbp-Fb is the sum of the spectra of the component parts, while in each case the fluorescence spectrum upon illumination of the Zn porphyrin is dominated by emission from the Mg or Fb porphyrin. Time-resolved absorption spectroscopy shows that the energy-transfer rate constants are (11 ps)(-1) and (37 ps)(-1) for Zn-pbp-Mg and Zn-pbp-Fb, respectively, corresponding to energy-transfer quantum yields of 0.995 and 0.983, respectively. The calculated Förster through-space rates are (1900 ps)(-1) and (1100 ps)(-1) for Zn-pbp-Mg and Zn-pbp-Fb, respectively. Accordingly, the through-bond process dominates for both dyads with a through-bond:through-space energy-transfer ratio of > or =97:1. Collectively, the studies show that the 4,4'-diphenylbutadiynyl linker supports fast and efficient energy transfer between Zn and Mg or Fb porphyrins.}, number={7}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Youngblood, WJ and Gryko, DT and Lammi, RK and Bocian, DF and Holten, D and Lindsey, JS}, year={2002}, month={Apr}, pages={2111–2117} } @article{roth_yasseri_liu_dabke_malinovskii_schweikart_yu_tiznado_zaera_lindsey_et al._2003, title={Measurements of electron-transfer rates of charge-storage molecular monolayers on Si(100). Toward hybrid molecular/semiconductor information storage devices}, volume={125}, ISSN={["0002-7863"]}, DOI={10.1021/ja021169a}, abstractNote={Redox kinetics were measured for two electroactive molecules attached to Si(100) surfaces, a ferrocene (Fc-BzOH) and a Zn(II) trimesitylporphyrin (Por-BzOH). Each molecule was derivatized with a benzyl alcohol linker for attachment to the Si surface via the formation of a Si-O bond. A complete protocol was developed for the preparation of stable Si(100) surfaces derivatized with the electroactive molecules. The redox-kinetic measurements were performed on the resulting Fc-BzOH and Por-BzOH monolayers to probe (1) the rate of electron transfer (k0) for oxidation in the presence of applied potentials and (2) the rate of charge dissipation after the applied potential is disconnected (in the form of a charge-retention half-life t1/2). The k0 values for the two types of monolayers were found to be similar to one another as were the t1/2 values. Perhaps more importantly, the electron-transfer rates for both the Fc-BzOH and the Por-BzOH monolayers differ from the charge-dissipation rates by approximately 6 orders of magnitude and are strongly dependent on the surface concentration of the electroactive species. For the Por-BzOH monolayers on Si(100), the k0 and t1/2 values and their trends as a function of surface coverage were determined to be similar to those previously measured for the analogous thiol-derivatized molecule assembled on Au(111). In contrast, the Fc-BzOH monolayers on Si(100) were found to exhibit much slower electron-transfer and charge-dissipation rates than those in the corresponding thiol-Au(111) case. Two alternative hypotheses are advanced to explain both the diminution in rates with increased surface coverage and the contrasting behavior with the analogous thiols on Au, one based on space-charge effects at the monolayer-solution interface, and a second relying on changes in distance of the redox centers from the surface as modulated by the orientation of the linking chains. Collectively, the ability to prepare and study stable, electroactive molecular media on Si(100) is likely to be key in the development of hybrid molecular/semiconductor devices.}, number={2}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Roth, KM and Yasseri, AA and Liu, ZM and Dabke, RB and Malinovskii, V and Schweikart, KH and Yu, LH and Tiznado, H and Zaera, F and Lindsey, JS and et al.}, year={2003}, month={Jan}, pages={505–517} } @article{taniguchi_kim_ra_schwartz_kirmaier_hindin_diers_prathapan_bocian_holten_et al._2002, title={Synthesis and electronic properties of regioisomerically pure oxochlorins}, volume={67}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0037131292&partnerID=MN8TOARS}, DOI={10.1021/jo025843i}, abstractNote={We describe a two-step conversion of C-alkylated zinc chlorins to zinc oxochlorins wherein the keto group is located in the reduced ring (17-position) of the macrocycle. The transformation proceeds by hydroxylation upon exposure to alumina followed by dehydrogenation with DDQ. The reactions are compatible with ethyne, iodo, ester, trimethylsilyl, and pentafluorophenyl groups. A route to a spirohexyl-substituted chlorin/oxochlorin has also been developed. Representative chlorins and oxochlorins were characterized by static and time-resolved absorption spectroscopy and fluorescence spectroscopy, resonance Raman spectroscopy, and electrochemistry. The fluorescence quantum yields of the zinc oxochlorins (Phi(f) = 0.030-0.047) or free base (Fb) oxochlorins (Phi(f) = 0.13-0.16) are comparable to those of zinc tetraphenylporphyrin (ZnTPP) or free base tetraphenylporphyrin (FbTPP), respectively. The excited-state lifetimes of the zinc oxochlorins (tau = 0.5-0.7 ns) are on average 4-fold lower than that of ZnTPP, and the lifetimes of the Fb oxochlorins (tau = 7.4-8.9 ns) are approximately 40% shorter than that of FbTPP. Time-resolved absorption spectroscopy of a zinc oxochlorin indicates the yield of intersystem crossing is >70%. Resonance Raman spectroscopy of copper oxochlorins show strong resonance enhancement of the keto group upon Soret excitation but not with Q(y)()-band excitation, which is attributed to the location of the keto group in the reduced ring (rather than in the isocyclic ring as occurs in chlorophylls). The one-electron oxidation potential of the zinc oxochlorins is shifted to more positive potentials by approximately 240 mV compared with that of the zinc chlorin. Collectively, the fluorescence yields, excited-state lifetimes, oxidation potentials, and various spectral characteristics of the chlorin and oxochlorin building blocks provide the foundation for studies of photochemical processes in larger architectures based on these chromophores.}, number={21}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Taniguchi, M and Kim, HJ and Ra, DY and Schwartz, JK and Kirmaier, C and Hindin, E and Diers, JR and Prathapan, S and Bocian, DF and Holten, D and et al.}, year={2002}, month={Oct}, pages={7329–7342} } @misc{kirmaier_yang_prathapan_miller_diers_bocian_lindsey_holten_2002, title={Synthesis and excited-state photodynamics of perylene-porphyrin dyads. 4. Ultrafast charge separation and charge recombination between tightly coupled units in polar media}, volume={28}, ISSN={["0922-6168"]}, DOI={10.1163/15685670260469384}, abstractNote={New perylene-porphyrin dyads that have excellent light-harvesting and energy-utilization capabilities in nonpolar media are found to exhibit efficient, ultrafast and tunable charge-transfer activity in polar media. The dyads consist of a perylene-monoimide dye (PMI) connected to a porphyrin (Por) via an ethynylphenyl (ep) linker. The porphyrin constituent of the PMI-ep-Por arrays is either a zinc or magnesium complex (Por = Zn or Mg) or a free-base form (Por = Fb). Following excitation of the perylene in each array in acetonitrile, PMI* decays in ≤0.4 ps by a combination of energy transfer to the ground-state porphyrin (forming Por*) and hole transfer (forming PMI-Por+). The excited porphyrin formed by energy transfer (or via direct excitation) then undergoes effectively quantitative electron transfer back to the perylene (τ = 1, 1, 700 ps for Por = Mg, Zn, Fb). Subsequently, charge recombination within PMI- Por+ returns each dyad quantitatively to the ground state (τ = 2, 4, 8 ps for Por = Mg, Zn, Fb). The dynamics of the PMI Por* → PMI-Por+ and PMI- Por+ → PMI Por charge-transfer processes can be modulated by altering the type of polar solvent (acetonitrile, benzonitrile, tetrahydrofuran and 2,6-lutidine). The charge-separation times for PMI-ep-Zn are 1, 6, 9 and 22 ps in these solvents, while the charge-recombination times are 4, 24, 38 and 34 ps. The efficient, rapid and tunable nature of the charge-transfer processes in polar media makes the PMI-ep-Por dyads useful units for performing molecular-switching functions. These properties when combined with the excellent light-harvesting and energy-transfer capabilities of the same arrays in nonpolar media afford a robust perylene-porphyrin motif that can be tailored for a variety of functions in molecular optoelectronics.}, number={7-9}, journal={RESEARCH ON CHEMICAL INTERMEDIATES}, author={Kirmaier, C and Yang, SI and Prathapan, S and Miller, MA and Diers, JR and Bocian, DF and Lindsey, JS and Holten, D}, year={2002}, pages={719–740} } @article{tomizaki_loewe_kirmaier_schwartz_retsek_bocian_holten_lindsey_2002, title={Synthesis and photophysical properties of light-harvesting arrays comprised of a porphyrin bearing multiple perylene-monoimide accessory pigments}, volume={67}, ISSN={["1520-6904"]}, DOI={10.1021/jo0258002}, abstractNote={We present the synthesis and characterization of new light-harvesting arrays containing two, four, or eight perylene-monoimide accessory pigments attached to a zinc porphyrin. Each perylene is substituted with one or three 4-tert-butylphenoxy substituents. A 4,3'- or 4,2'-diarylethyne linker joins the perylene N-imide position and the porphyrin meso-position, affording divergent or convergent architectures, respectively. The architectures are designed to provide high solubility in organic media and facile perylene-to-porphyrin energy transfer, while avoiding charge-transfer quenching of the excited porphyrin product. For the array containing four perylenes per porphyrin in both nonpolar (toluene) and polar (benzonitrile) media and for the array containing eight perylenes per porphyrin in toluene, the photoexcited perylene-monoimide dye (PMI) decays rapidly ( approximately 3.5 ps) and predominantly (>or=90%) by energy transfer to the zinc porphyrin to form the excited zinc porphyrin (Zn), which has excited-state characteristics (lifetime, fluorescence yield) comparable (within approximately 10%) to those of the isolated chromophore. For the array containing eight perylenes in benzonitrile, PMI decays approximately 80% by energy transfer (forming Zn) and approximately 20% by hole transfer (forming PMI- Zn+); Zn subsequently decays approximately 20% by electron transfer (also forming PMI- Zn+) and approximately 80% by the normal routes open to the porphyrin monomer (intersystem crossing, internal conversion, fluorescence). In addition to rapid and efficient perylene-to-porphyrin energy transfer, the broad blue-green to yellow absorption of the perylene dyes complements the blue absorption of the porphyrin, resulting in excellent light harvesting across a significant spectral region. Collectively, the work described herein identifies multiperylene-porphyrin arrays that exhibit suitable photochemical properties for use as motifs in larger light-harvesting systems.}, number={18}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Tomizaki, K and Loewe, RS and Kirmaier, C and Schwartz, JK and Retsek, JL and Bocian, DF and Holten, D and Lindsey, JS}, year={2002}, month={Sep}, pages={6519–6534} } @article{loewe_tomizaki_youngblood_bo_lindsey_2002, title={Synthesis of perylene-porphyrin building blocks and rod-like oligomers for light-harvesting applications}, volume={12}, ISSN={["1364-5501"]}, DOI={10.1039/b205680a}, abstractNote={We present the synthesis of four perylene–porphyrin building blocks for use in Glaser, Sonogashira, or Suzuki polymerizations. The building blocks bear synthetic handles (4-ethynylphenyl, 4-iodophenyl, bromo) at the trans (5,15) meso-positions of a zinc porphyrin and contain two or four perylene-monoimide dyes attached at the 3,5-positions of the non-linking meso-aryl rings of the porphyrin. Each perylene-monoimide bears three 4-tert-butylphenoxy substituents (at the 1-, 6-, and 9-positions) and two isopropyl groups (on the N-aryl unit) for increased solubility. In each case the intervening linker is a diarylethyne unit that bridges the N-imide position of the perylene and the meso-position of the porphyrin. The perylene–porphyrin building blocks were prepared by (1) reaction of a diperylene-dipyrromethane with an aldehyde yielding a trans-A2B2-porphyrin, (2) reaction of a diperylene-aldehyde with a dipyrromethane yielding a trans-A2B2-porphyrin, and (3) reaction of a diperylene-dipyrromethane with a dipyrromethane-dicarbinol yielding a trans-AB2C-porphyrin or ABCD-porphyrin. The building blocks were subjected to Glaser, Sonogashira, or Suzuki coupling conditions in an effort to prepare oligomers containing porphyrins joined via 4,4′-diphenylbutadiyne (dpb), 4,4′-diphenylethyne (dpe), or 1,4-phenylene linkers (p), respectively. Each porphyrin in the backbone bears two or four pendant perylene-monoimide dyes. The Glaser and Sonogashira reactions afforded a distribution of oligomers, whereas the Suzuki reaction was unsuccessful. The oligomers were soluble in solvents such as toluene, THF, or CHCl3 enabling routine handling. The use of perylenes results in (1) increased light-harvesting efficiency particularly in the green spectral region where porphyrins are relatively transparent and (2) greater solubility than is achieved with the use of porphyrins alone. The soluble perylene–porphyrin oligomers are attractive for use as light-harvesting materials in molecular-based solar cells.}, number={12}, journal={JOURNAL OF MATERIALS CHEMISTRY}, author={Loewe, RS and Tomizaki, K and Youngblood, WJ and Bo, ZS and Lindsey, JS}, year={2002}, pages={3438–3451} } @article{loewe_tomizaki_chevalier_lindsey_2002, title={Synthesis of perylene-porphyrin dyads for light-harvesting studies}, volume={6}, ISSN={["1099-1409"]}, DOI={10.1142/S1088424602000774}, abstractNote={ The spectral coverage of porphyrin-based light-harvesting arrays can be enhanced through the use of suitable accessory pigments. Perylene-monoimide dyes can serve as valuable accessory pigments with porphyrins. To investigate the choice of perylene-monoimide and the effects of molecular architecture on light-harvesting efficacy, five perylene-porphyrin dyads were prepared. Each dyad employs a diphenylethyne linker that bridges the perylene N-imide site and the porphyrin meso-position. Three dyads incorporate a mono-phenoxy perylene at the o-, m-, or p-position of the meso-aryl group on the porphyrin. The two remaining dyads incorporate a perylene-monoimide (bearing zero or three phenoxy substituents) at the p-position of the meso-aryl group on the porphyrin. The introduction of phenoxy groups on the perylenes increases the solubility, a key requirement for use in light-harvesting arrays. The long-wavelength absorption band of the perylene shifts from 506 nm to 532 or 533 nm upon substitution with one or three phenoxy groups, respectively. The synthesis of the dyads entails Pd -mediated coupling of a bromo-perylene and an ethynyl porphyrin, or the mixed-aldehyde condensation with a perylene-aldehyde, mesitaldehyde, and pyrrole. Five perylene-monoimide dyes bearing an ethyne or bromo substituent at the p-position of the N-aryl unit were developed for this modular chemistry. Each perylene-porphyrin dyad exhibits efficient energy transfer from the excited perylene to the ground-state porphyrin. }, number={9-10}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Loewe, RS and Tomizaki, KY and Chevalier, F and Lindsey, JS}, year={2002}, pages={626–642} } @article{ambroise_kirmaier_wagner_loewe_bocian_holten_lindsey_2002, title={Weakly coupled molecular photonic wires: Synthesis and excited-state energy-transfer dynamics}, volume={67}, ISSN={["1520-6904"]}, DOI={10.1021/jo025561i}, abstractNote={Molecular photonic wires, which absorb light and undergo excited-state energy transfer, are of interest as biomimetic models for photosynthetic light-harvesting systems and as molecular devices with potential applications in materials chemistry. We describe the stepwise synthesis of four molecular photonic wires. Each wire consists of an input unit, transmission element, and output unit. The input unit consists of a boron-dipyrrin dye or a perylene-monoimide dye (linked either at the N-imide or the C9 position); the transmission element consists of one or three zinc porphyrins affording short or long wires, respectively; and the output unit consists of a free base (Fb) porphyrin. The components in the arrays are joined in a linear architecture via diarylethyne linkers (an ethynylphenyl linker is attached to the C9-linked perylene). The wires have been examined by static absorption, static fluorescence, and time-resolved absorption spectroscopy. Each wire (with the exception of the C9-linked perylene wire) exhibits a visible absorption spectrum that is the sum of the spectra of the component parts, indicating the relatively weak electronic coupling between the components. Excitation of each wire at the wavelength where the input unit absorbs preferentially (typically 480-520 nm) results in emission almost exclusively from the Fb porphyrin. The static emission and time-resolved data indicate that the overall rate constants and quantum efficiencies for end-to-end (i.e., input to output) energy transfer are as follows: perylene-(N-imide)-linked short wire, (33 ps)(-1) and >99%; perylene-(C9)-linked short wire, (26 ps)(-1) and >99%; boron-dipyrrin-based long wire, (190 ps)(-1) and 81%; perylene-(N-imide)-linked long wire, (175 ps)(-1) and 86%. Collectively, the studies provide valuable insight into the singlet-singlet excited-state energy-transfer properties in weakly coupled molecular photonic wires.}, number={11}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Ambroise, A and Kirmaier, C and Wagner, RW and Loewe, RS and Bocian, DF and Holten, D and Lindsey, JS}, year={2002}, month={May}, pages={3811–3826} } @article{geier_callinan_rao_lindsey_2001, title={A survey of acid catalysts in dipyrromethanecarbinol condensations leading to meso-substituted porphyrins}, volume={5}, ISSN={["1088-4246"]}, DOI={10.1002/jpp.387}, abstractNote={ The successful use of dipyrromethanecarbinols in rational routes to porphyrinic macrocycles requires catalysis conditions that enable irreversible condensation, thereby avoiding substituent scrambling and formation of undesired porphyrin products. Previously, successful conditions of trifluoroacetic acid (TFA) (30 mM) in acetonitrile were identified following a lengthy survey of TFA and BF3-etherate catalysis in diverse solvents. In this study, focus was placed on the acid catalyst by examining 17 acids in CH 2 Cl 2, the traditional solvent for two-step, one-flask porphyrin syntheses. In the self-condensation of the carbinol derived from 1-(4-methylbenzoyl)-5-phenyldipyrromethane, porphyrin yields of 9–55% were obtained from the various acids, compared to 20% under TFA catalysis in acetonitrile. A number of catalytic conditions that produce little to no porphyrin in reactions of pyrrole + benzaldehyde afforded good yields of porphyrin and the suppression of scrambling in reactions of dipyrromethanecarbinols. The four best acid catalysts ( InCl 3, Sc ( OTf )3, Yb ( OTf )3, and Dy ( OTf )3) initially identified were then examined with dipyrromethanecarbinols bearing challenging substituents (alkyl, pyridyl, or no substituent). The greatest improvement was obtained with the pyridyl substrates. Selected reactions performed on a preparative scale (115 to 460 mg of isolated porphyrin) verified the results of the analytical-scale experiments and revealed the more facile isolation of the porphyrin from reactions performed in CH 2 Cl 2 rather than acetonitrile. This study provides alternatives to the use of TFA/acetonitrile that offer advantages in terms of yield and isolation of the porphyrin without sacrificing suppression of scrambling. Furthermore, the finding that poor catalysts for the benzaldehyde + pyrrole reaction can be excellent catalysts for dipyrromethanecarbinols provides guidance for the identification of other catalysts for use with reactive precursors in porphyrin-forming reactions. }, number={12}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Geier, GR and Callinan, JB and Rao, PD and Lindsey, JS}, year={2001}, month={Dec}, pages={810–823} } @article{ambroise_wagner_rao_riggs_hascoat_diers_seth_lammi_bocian_holten_et al._2001, title={Design and synthesis of porphyrin-based optoelectronic gates}, volume={13}, ISSN={["1520-5002"]}, DOI={10.1021/cm000773m}, abstractNote={Two porphyrin-based optoelectronic gates and several prototypical redox-switching components of gates have been synthesized for studies in molecular photonics. Linear and T-shaped molecular optoelectronic gates contain a boron-dipyrrin (BDPY) dye as the input unit, a zinc (Zn) porphyrin as the transmission unit, a free base (Fb) porphyrin as the output unit, and a magnesium (Mg) porphyrin as the redox-switching unit. The linear gate and T gate were synthesized using a molecular building block approach. In the linear gate synthesis, a BDPY−Zn porphyrin dyad was coupled with a Fb porphyrin−Mg porphyrin dimer. The synthesis of the T gate utilized a Zn porphyrin bearing four different meso substituents:  mesityl, 4-iodophenyl, 4-[2-(trimethylsilyl)ethynyl]phenyl, and 4-[2-triisopropyl)ethynyl]phenyl. Attachment of the three different groups to the Zn porphyrin was accomplished using successive Pd-mediated coupling reactions in the following sequence:  Fb porphyrin (output unit), BDPY dye (input unit), and Mg ...}, number={3}, journal={CHEMISTRY OF MATERIALS}, author={Ambroise, A and Wagner, RW and Rao, PD and Riggs, JA and Hascoat, P and Diers, JR and Seth, J and Lammi, RK and Bocian, DF and Holten, D and et al.}, year={2001}, month={Mar}, pages={1023–1034} } @article{geier_riggs_lindsey_2001, title={Investigation of acid cocatalysis in syntheses of tetra-phenylporphyrin}, volume={5}, ISSN={["1088-4246"]}, DOI={10.1002/jpp.380.abs}, number={9}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Geier, GR and Riggs, JA and Lindsey, JS}, year={2001}, month={Sep}, pages={681–690} } @article{geier_lindsey_2001, title={Investigation of porphyrin-forming reactions. Part 1. Pyrrole plus aldehyde oligomerization in two-step, one-flask syntheses of meso-substituted porphyrins}, ISSN={["1472-779X"]}, DOI={10.1039/b009088n}, abstractNote={A deep understanding of the two-step, one-flask synthesis of meso-substituted porphyrins requires characterization of the acyclic oligomers, which typically constitute ≥50% of the products. We have employed laser desorption mass spectrometry (LD-MS) to obtain a qualitative yet high resolution view of the oligomer content of crude oxidized reaction mixtures. This methodology complements other analytical methods which provide information regarding yields of porphyrin, other macrocyclic products, and unreacted aldehyde. Our findings include the following. (1) Crude oxidized porphyrin reaction mixtures provided peaks in the LD-MS spectrum which were readily assigned to oligomers (m/z 100–2000) derived from pyrrole–aldehyde condensation. The oligomers comprised one of four series depending on the ratio of pyrrole and aldehyde units. (2) Quite disparate reaction conditions that gave good yields of porphyrin also afforded a similar oligomer composition. (3) The change in the nature of the oligomers over time was readily monitored. (4) The maximum yield of porphyrin and the maximum diversity of the oligomer composition were attained at similar times. (5) The decline in yield of porphyrin at long reaction time was accompanied by truncation, not elongation, of oligomers. (6) The onset of the truncation of oligomers and the decline in yield of porphyrin were accompanied by a decrease of the aldehyde to low levels. (7) Pyrrole was incorporated into the growing oligomers more rapidly than aldehyde. Taken together, these studies show how various conditions alter the course of the pyrrole–aldehyde condensation.}, number={5}, journal={JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2}, author={Geier, GR and Lindsey, JS}, year={2001}, pages={677–686} } @article{geier_lindsey_2001, title={Investigation of porphyrin-forming reactions. Part 2. Examination of the reaction course in two-step, one-flask syntheses of meso-substituted porphyrins}, ISSN={["1472-779X"]}, DOI={10.1039/b009092l}, abstractNote={The reaction course leading to meso-substituted porphyrins was examined for reversibility (formation of oligomers, formation of α- and β-pyrrole linkages), inactivation of the acid catalyst, homogeneity of the reaction medium, and the pathway of oligomer formation. The methodology employed enabled characterization of the oligomer composition (LD-MS), yield of porphyrin (UV–Vis), yield of N-confused porphyrin (HPLC), and level of unreacted aldehyde (TLC). Experiments were performed with benzaldehyde and pyrrole with catalysis by TFA or BF3–Et2O. Key observations include the following. (1) Reactions with BF3–Et2O exhibited reversible exchange of oligomers throughout the reaction. With TFA, the oligomer exchange processes were reversible at short reaction times, but became largely irreversible over the course of several hours. (2) The BF3–Et2O activity declined during the course of the reaction, whereas that of TFA was little changed. (3) The reaction medium remained homogeneous at 10 mM pyrrole + aldehyde. (4) Dipyrromethanes comprised of α- but not β-linkages underwent cleavage with either TFA or BF3–Et2O. (5) Condensations with carbinol intermediates (pyrrole-carbinol, dipyrromethane-monocarbinol, dipyrromethane-dicarbinol) provided rapid reactions, lower yields of porphyrin, and longer oligomers than typical in reactions of pyrrole + benzaldehyde. Higher porphyrin yields were obtained with BF3–Et2O than TFA, which is attributed to the more facile recovery from longer oligomers with the former versus the latter catalyst. Collectively, these and other observations lead to a model for the aldehyde + pyrrole condensation comprised of a combination of irreversible and reversible reactions in oligomer formation, irreversible side reactions (formation of dipyrrins, β-linkages), and slow inactivation of the catalyst (BF3–Et2O).}, number={5}, journal={JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2}, author={Geier, GR and Lindsey, JS}, year={2001}, pages={687–700} } @article{geier_littler_lindsey_2001, title={Investigation of porphyrin-forming reactions. Part 3. The origin of scrambling in dipyrromethane plus aldehyde condensations yielding trans-A(2)B(2)-tetraarylporphyrins}, ISSN={["1472-779X"]}, DOI={10.1039/b009098k}, abstractNote={The dipyrromethane + aldehyde condensation is a common method for the synthesis of trans-A2B2-porphyrins, but is often plagued by scrambling processes that lead to a mixture of porphyrins. The problem of scrambling is more pronounced with unhindered dipyrromethanes (e.g., 5-phenyldipyrromethane) than with hindered dipyrromethanes (e.g., 5-mesityldipyrromethane). We have characterized the oligomer composition (by LD-MS), yield of porphyrin (by UV–Vis), yield of N-confused porphyrin (by HPLC), and level of unreacted aldehyde (by TLC) in dipyrromethane + aldehyde condensations leading to trans-A2B2-porphyrins. Reaction conditions known to suppress scrambling in reactions involving 5-phenyldipyrromethane (PDPM) were compared to conditions known to provide extensive scrambling. The low-scrambling conditions were found to suppress scrambling by inhibiting reaction of oligomer fragments generated by acid-induced cleavage of the dipyrromethane, rather than by inhibiting acidolysis itself. However, such reaction conditions were also found to inhibit the condensation, leading to low yields (<10%) of porphyrin. The condensation of PDPM + aldehyde was also compared to reactions involving 5-mesityldipyrromethane (MDPM) to understand why trans-A2B2-porphyrins can be prepared in good yield devoid of scrambling from reactions using MDPM. The absence of scrambling in MDPM + aldehyde condensations was due to the resistance of MDPM to acidolysis. Taken together, these studies provide insight into the origin of scrambling with different types of substrates under different reaction conditions in the dipyrromethane + aldehyde route to trans-A2B2-porphyrins.}, number={5}, journal={JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2}, author={Geier, GR and Littler, BJ and Lindsey, JS}, year={2001}, pages={701–711} } @article{geier_littler_lindsey_2001, title={Investigation of porphyrin-forming reactions. Part 4. Examination of the reaction course in syntheses of porphyrins via dipyrromethanecarbinols}, ISSN={["1472-779X"]}, DOI={10.1039/b009101o}, abstractNote={The dipyrromethanecarbinol motif is a key component in rational routes to a wide variety of porphyrinic macrocycles. We have investigated the dipyrromethane-monocarbinol self-condensation and the dipyrromethane-dicarbinol + dipyrromethane condensation under four different acid-catalysis conditions and have characterized the oligomer composition (by LD-MS), yield of porphyrin (by UV–Vis), and yield of N-confused porphyrin (by HPLC). Under conditions giving “no-scrambling”, the condensations are rapid and afford an oligomer composition characterized by (1) absence of scrambling, (2) suppression of acidolysis, and (3) a disproportionate amount of long oligomers from which recovery does not occur. The irreversibility of the reaction and lack of recovery from the long oligomers may explain the lower yields of dipyrromethanecarbinol condensations (<30%) compared with reversible reactions of aldehyde + pyrrole (∼50%). Modest levels of acidolysis and scrambling with the dipyrromethanecarbinols are obtained under reaction conditions that cause extensive scrambling in dipyrromethane + aldehyde condensations. Because both reactions give the same porphyrinogen, the scrambling processes must primarily involve the dipyrromethane or oligomer intermediates rather than the porphyrinogen. The dipyrromethane-monocarbinol self-condensation and dipyrromethane-dicarbinol + dipyrromethane condensation afford quite similar oligomer compositions, suggesting that both follow similar pathways to the porphyrinogen. Reaction conditions that suppress scrambling in the dipyrromethanecarbinol condensations were found to dramatically suppress formation of the N-confused porphyrin. Taken together, these experiments show how the greater reactivity of the dipyrromethanecarbinol unit (compared with the pyrrole + aldehyde reaction) facilitates synthesis of meso-substituted porphyrins without scrambling.}, number={5}, journal={JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2}, author={Geier, GR and Littler, BJ and Lindsey, JS}, year={2001}, pages={712–718} } @article{gross_chevalier_lindsey_2001, title={Investigation of rational syntheses of heteroleptic porphyrinic lanthanide (europium, cerium) triple-decker sandwich complexes}, volume={40}, ISSN={["0020-1669"]}, DOI={10.1021/ic0101634}, abstractNote={The use of lanthanide triple-decker sandwich molecules containing porphyrins and phthalocyanines in molecular information storage applications requires the ability to attach monomeric triple deckers or arrays of triple deckers to electroactive surfaces. Such applications are limited by existing methods for preparing triple deckers. The reaction of a lanthanide porphyrin half-sandwich complex ((Por)M(acac)) with a dilithium phthalocyanine (PcLi2) in refluxing 1,2,4-trichlorobenzene (bp 214 degrees C) affords a mixture of triple deckers of composition (Pc)M(Pc)M(Por), (Por)M(Pc)M(Por), and (Pc)M(Por)M(Pc). We have investigated more directed methods for preparing triple deckers of a given type with distinct metals in each layer. Application of the method of Weiss, which employs reaction of a (Por)M(acac) species with a lanthanide double decker in refluxing 1,2,4-trichlorobenzene, afforded the desired triple decker in some cases but a mixture of triple deckers in others. The approach we developed employs in situ formation of the lanthanide reagent EuCl[N(SiMe3)2]2 or CeI[N(SiMe3)2]2, which upon reaction with a porphyrin affords the half-sandwich complex (Por)EuX or (Por)CeX' (X = Cl, N(SiMe3)2; X' = I, N(SiMe3)2). Subsequent reaction with PcLi2 gives the double decker (Por)M(Pc). The (Por(1))EuX half-sandwich complex gave the desired triple decker upon reaction with (Pc)Eu(Pc) but little of the desired product upon reaction with (Por(2))Eu(Pc). The (Por(1))CeX' half-sandwich complex reacted with europium double deckers (e.g., (tBPc)Eu(Por(2)), (tBPc)2Eu) to give the triple deckers (Por(1))Ce(tBPc)Eu(Por(2)) and (Por(1))Ce(tBPc)Eu(tBPc) in a rational manner (tB = tetra-tert-butyl). The reactions yielding the half-sandwich, double-decker, and triple-decker complexes were performed in refluxing bis(2-methoxyethyl) ether (bp 162 degrees C). The porphyrins incorporated in the various triple deckers include meso-tetrapentylporphyrin, meso-tetra-p-tolylporphyrin, octaethylporphyrin, and meso-tetraarylporphyrins bearing iodo, ethynyl, or iodo and ethynyl substituents. The triple deckers bearing iodo and/or ethynyl substituents constitute useful building blocks for information storage applications.}, number={18}, journal={INORGANIC CHEMISTRY}, author={Gross, T and Chevalier, F and Lindsey, JS}, year={2001}, month={Aug}, pages={4762–4774} } @article{yu_lindsey_2001, title={Investigation of two rational routes for preparing p-phenylene-linked porphyrin trimers}, volume={57}, ISSN={["0040-4020"]}, DOI={10.1016/S0040-4020(01)00928-0}, abstractNote={Multiporphyrin arrays with p-phenylene linkers, aryl groups at the non-linking meso positions, and no β-substituents are attractive constructs for light-harvesting applications. Condensation of a free base porphyrin-benzaldehyde and 5-mesityldipyrromethane (10 mM each) in CH2Cl2 containing 100 mM TFA at room temperature for 30–40 min followed by oxidation with DDQ afforded a p-phenylene-linked porphyrin trimer in 36% yield. Suzuki coupling of an iodo-porphyrin and a bis(dioxaborolane)-porphyrin (20 and 10 mM, respectively) in toluene/DMF (2:1) containing K2CO3 (8 equiv.) at 90–95°C for ∼20 h afforded the same trimer in 66% yield. The former route was used to prepare a diethynyl substituted p-phenylene-linked porphyrin trimer. While the two routes are somewhat complementary in scope, both are convergent and proceed in a rational manner.}, number={45}, journal={TETRAHEDRON}, author={Yu, LH and Lindsey, JS}, year={2001}, month={Nov}, pages={9285–9298} } @article{lammi_wagner_ambroise_diers_bocian_holten_lindsey_2001, title={Mechanisms of excited-state energy-transfer gating in linear versus branched multiporphyrin arrays}, volume={105}, ISSN={["1520-5207"]}, DOI={10.1021/jp010857y}, abstractNote={We have investigated electrochemical switching of excited-state electronic energy migration in two optoelectronic gates with different architectures. Each gate consists of diarylethyne-linked subunits:  a boron-dipyrrin (BDPY) input unit, a Zn-porphyrin transmission unit, a free-base-porphyrin (Fb-porphyrin) output unit, and a Mg-porphyrin redox-switched site connected either to the Fb porphyrin (linear gate) or to the Zn porphyrin (branched, T gate). Both the linear and branched architectures show Fb-porphyrin emission when the Mg porphyrin is neutral and nearly complete quenching when the Mg porphyrin is oxidized to the π-cation radical. To determine the mechanism of gating, we undertook a systematic photophysical study of the gates and their dyad and triad components in neutral and oxidized forms, using static and time-resolved optical spectroscopy. Two types of photoinduced energy-transfer (and/or charge-transfer) processes are involved in gate operation:  transfer between adjacent subunits and transf...}, number={22}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Lammi, RK and Wagner, RW and Ambroise, A and Diers, JR and Bocian, DF and Holten, D and Lindsey, JS}, year={2001}, month={Jun}, pages={5341–5352} } @misc{holten_bocian_lindsey_2002, title={Probing electronic communication in covalently linked multiporphyrin arrays. A guide to the rational design of molecular photonic devices}, volume={35}, ISSN={["1520-4898"]}, DOI={10.1021/ar970264z}, abstractNote={Understanding electronic communication among the constituents in multicomponent macromolecular architectures is essential for the rational design of molecular devices for photonic, electronic, or optoelectronic applications. This Account describes studies aimed at understanding the mechanisms of electronic communication in porphyrin-based architectures that undergo excited-state energy migration and ground-state hole/electron hopping. Porphyrins are ideal building blocks for such constructs owing to their attractive and versatile physical properties and amenability to synthetic control. These properties have permitted the creation of covalently linked multiporphyrin arrays wherein the rates of excited-state energy migration and ground-state hole/electron hopping can be tuned over a wide range.}, number={1}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Holten, D and Bocian, DF and Lindsey, JS}, year={2002}, month={Jan}, pages={57–69} } @article{lammi_ambroise_wagner_diers_bocian_holten_lindsey_2001, title={Quenching of porphyrin excited states by adjacent or distant porphyrin cation radicals in molecular arrays}, volume={341}, ISSN={["0009-2614"]}, DOI={10.1016/S0009-2614(01)00452-3}, abstractNote={The quenching of photoexcited porphyrins by porphyrin cation radicals at adjacent or distant sites in diphenylethyne-linked porphyrin dyads and triads has been studied using static and time-resolved optical spectroscopy. The excited-state quenching is highly efficient in all cases (>99%) and occurs in ⩽11 ps between adjacent sites (by through-bond energy/charge transfer) and in ⩽55 ps between distant sites (likely by superexchange-assisted energy transfer). The rates can be tuned using the porphyrin-linker connection motif. These results should prove useful in the design of arrays that use electro- or photo-chemically generated porphyrin cation radicals for molecular switching and other applications in molecular photonics.}, number={1-2}, journal={CHEMICAL PHYSICS LETTERS}, author={Lammi, RK and Ambroise, A and Wagner, RW and Diers, JR and Bocian, DF and Holten, D and Lindsey, JS}, year={2001}, month={Jun}, pages={35–44} } @article{yu_lindsey_2001, title={Rational syntheses of cyclic hexameric porphyrin arrays for studies of self-assembling light-harvesting systems}, volume={66}, ISSN={["0022-3263"]}, DOI={10.1021/jo010742q}, abstractNote={Two new cyclic hexameric arrays of porphyrins have been prepared in a rational, convergent manner. The porphyrins in each cyclic hexamer are joined by diphenylethyne linkers affording a wheel-like array with a diameter of approximately 35 A. One array is comprised of five zinc (Zn) porphyrins and one free base (Fb) porphyrin (cyclo-Zn(5)FbU) while the other is comprised of an alternating sequence of two Zn porphyrins and one Fb porphyrin (cyclo-Zn(2)FbZn(2)FbU). The prior synthesis employed a one-flask template-directed process and afforded alternating Zn and Fb porphyrins or all Zn porphyrins. More diverse metalation patterns are attractive for manipulating the flow of excited-state energy in the arrays. The rational synthesis of each array employed three Pd-mediated coupling reactions with four tetraarylporphyrin building blocks bearing diethynyl, diiodo, bromo/iodo, or iodo/ethynyl groups. The final ring closure yielding the cyclic hexamer was achieved by reaction of a porphyrin pentamer + porphyrin monomer or the joining of two porphyrin trimers. In the presence of a tripyridyl template, the yields of the 5 + 1 and 3 + 3 reactions ranged from 10 to 13%. The 5 + 1 reaction in the absence of the template proceeded in 3.5% yield, thereby establishing the structure-directed contribution to cyclic hexamer formation. The 3 + 3 route relied on successive ethyne + iodo/bromo coupling reactions. One template-directed route to cyclo-Zn(2)FbZn(2)FbU employed a magnesium porphyrin, affording cyclo-Zn(2)FbZn(2)MgU from which magnesium was selectively removed. The arrays exhibit absorption spectra that are nearly the sum of the spectra of the component parts, indicating weak electronic coupling. Fluorescence spectroscopy showed that the quantum yield of energy transfer in toluene at room temperature from the Zn porphyrins to the Fb porphyrin(s) was 60% in cyclo-Zn(5)FbU and 90% in cyclo-Zn(2)FbZn(2)FbU. Two dipyridyl-substituted porphyrins, a Zn tetraarylporphyrin and a Fb oxaporphyrin, have been synthesized for use as guests in the cyclic hexamers, affording self-assembled arrays for light-harvesting studies.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Yu, LH and Lindsey, JS}, year={2001}, month={Nov}, pages={7402–7419} } @article{gryko_li_diers_roth_bocian_kuhr_lindsey_2001, title={Studies related to the design and synthesis of a molecular octal counter}, volume={11}, ISSN={["0959-9428"]}, DOI={10.1039/b008224o}, abstractNote={An approach to the storage of multiple bits of information at the molecular level employs molecules with a large number of distinct oxidation states. Europium triple-decker sandwich molecules composed of porphyrins and phthalocyanines afford four cationic states and are very attractive for molecular information-storage applications. A larger number of states can be achieved by combinations of triple deckers that afford interleaved oxidation potentials. In order to identify suitable candidates for effective interleaving of oxidation potentials, a library of 19 new triple-decker complexes was prepared. Electron-donating groups have been attached to the porphyrin and/or phthalocyanine moieties in order to achieve oxidation states in the low potential regime. The triple deckers are of three different types: (Pc)Eu(Pc)Eu(Por), (Pc)Eu(Por)Eu(Pc), and (Por)Eu(Pc)Eu(Por). The solution electrochemistry of each member of the library was examined. These studies revealed suitable pairs of triple deckers that provide effective interleaving of oxidation potentials. Six triple deckers of type (Pc)Eu(Pc)Eu(Por) were derivatized with a thioacetyl or thiocyanate group on the porphyrin unit for attachment to an electroactive surface. Each of the S-(acetylthio)-derivatized triple deckers forms a self-assembled monolayer (SAM) on Au viain situ cleavage of the thiol protecting group. The SAM of each triple decker is electrochemically robust and exhibits four, well-resolved reversible oxidation waves. Upon disconnection from the source of applied potential, the triple-decker SAMs retain charge for tens to hundreds of seconds. The exact value of the charge-retention time depends on the specific porphyrin/phthalocyanine in the triple decker and the particular oxidation state of the molecules in the SAM (e.g., mono- vs. di- vs. tri- vs. tetracation). For all of the triple-decker SAMs, the charge-retention time monotonically increases as the oxidation state of the molecules in the SAM increases. Collectively, the studies suggest that the triple-decker complexes are excellent candidates for multibit molecular information storage elements.}, number={4}, journal={JOURNAL OF MATERIALS CHEMISTRY}, author={Gryko, D and Li, JZ and Diers, JR and Roth, KM and Bocian, DF and Kuhr, WG and Lindsey, JS}, year={2001}, pages={1162–1180} } @article{yang_prathapan_miller_seth_bocian_lindsey_holten_2001, title={Synthesis and excited-state photodynamics in perylene-porphyrin dyads 2. Effects of porphyrin metalation state on the energy-transfer, charge-transfer, and deactivation channels}, volume={105}, ISSN={["1089-5647"]}, DOI={10.1021/jp010336a}, abstractNote={The photophysical properties of two perylene−porphyrin dyads have been examined in detail with the aim of expanding the functional utility of these constructs for molecular optoelectronics applications. The dyads consist of a perylene-bis(imide) dye (PDI) connected to either a magnesium porphyrin (Mg) or a free base porphyrin (Fb) via a diphenylethyne (pep) linker. The photophysical behavior of these two dyads show both similarities and differences to one another and to the dyad containing a zinc porphyrin (Zn) that was examined in the previous paper in this series. In the case of both PDI−pep−Fb and PDI−pep−Mg in toluene, the excited perylene unit (PDI*) decays rapidly (Fb = 2.9 ps; Mg = 2.5 ps) by energy transfer to the porphyrin forming PDI−pep−Por* in relatively high yield (Fb ∼ 85%; Mg ∼ 50%) and hole transfer to the porphyrin forming PDI-−pep−Por+ (Fb ∼ 15%; Mg ∼ 50%). This behavior parallels that observed for PDI−pep−Zn, for which rapid (2.5 ps) decay of PDI* affords PDI−pep−Zn* and PDI-−pep−Por+ w...}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Yang, SI and Prathapan, S and Miller, MA and Seth, J and Bocian, DF and Lindsey, JS and Holten, D}, year={2001}, month={Aug}, pages={8249–8258} } @article{prathapan_yang_seth_miller_bocian_holten_lindsey_2001, title={Synthesis and excited-state photodynamics of perylene-porphyrin dyads. 1. Parallel energy and charge transfer via a diphenylethyne linker}, volume={105}, ISSN={["1089-5647"]}, DOI={10.1021/jp010335i}, abstractNote={The photophysical properties of a perylene−porphyrin dyad have been examined with the aim of using this construct for molecular photonics applications. The dyad consists of a perylene-bis(imide) dye (PDI) connected to a zinc porphyrin (Zn) via a diphenylethyne linker (pep). In both polar and nonpolar solvents, the photoexcited perylene unit (PDI*) decays very rapidly (lifetimes of 2.5 (toluene) and 2.4 ps (acetonitrile)) by energy transfer to the porphyrin, forming PDI−pep−Zn* in high yield (80%, toluene; 70% acetonitrile), and hole transfer to the porphyrin, forming PDI-−pep−Zn+ in lesser yield (20%, toluene; 30% acetonitrile). In both toluene and acetonitrile, the Zn* excited state subsequently decays with a lifetime of 0.4 ns primarily (80%) by electron transfer to the perylene (forming PDI-−pep−Zn+). In the nonpolar solvent (toluene), the PDI-−pep−Zn+ charge-transfer product has a lifetime of >10 ns and decays by charge recombination primarily to the ground state but also by thermal repopulation of th...}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Prathapan, S and Yang, SI and Seth, J and Miller, MA and Bocian, DF and Holten, D and Lindsey, JS}, year={2001}, month={Aug}, pages={8237–8248} } @article{yang_lammi_prathapan_miller_seth_diers_bocian_lindsey_holten_2001, title={Synthesis and excited-state photodynamics of perylene-porphyrindyads. Part 3, Effects of perylene, linker, and connectivity on ultrafast energy transfer}, volume={11}, DOI={10.1039/b102741g}, abstractNote={New perylene–porphyrin dyads have been designed that exhibit superior light-harvesting and energy-utilization activity compared with earlier generations of structurally related dyads. The new dyads consist of a perylene mono(imide) dye (PMI) connected to a porphyrin (Por) via an ethynylphenyl (ep) linker. The PMI–ep–Por arrays were prepared with the porphyrin as either a zinc or magnesium complex (Por = Zn or Mg) or a free-base form (Por = Fb). The absorption properties of the perylene complement those of the porphyrin. Following excitation of the perylene (forming PMI*) in toluene, each array exhibits ultrafast (kENT ≥ (0.5 ps)−1) and essentially quantitative energy transfer from PMI* to the ground-state porphyrin (forming Por*). In each of the arrays, the properties of the excited porphyrin (lifetime, fluorescence yield, etc.) are basically unperturbed from those of the isolated pigment. Thus, following energy transfer, the excited porphyrin is not quenched by deleterious reactions involving the perylene accessory unit that would otherwise limit the ability of Por* to emit light or transfer energy to another stage in a molecular photonic device. Collectively, the PMI–ep–Por dyads represent the successful result of a molecular design strategy to produce arrays with excellent properties for use as light-input and energy-transduction elements for applications in molecular optoelectronics.}, number={10}, journal={Journal of Materials Chemistry}, author={Yang, S. I. and Lammi, R. K. and Prathapan, S. and Miller, M. A. and Seth, J. and Diers, J. R. and Bocian, D. F. and Lindsey, Jonathan and Holten, D.}, year={2001}, pages={2420–2430} } @article{taniguchi_ra_mo_balasubramanian_lindsey_2001, title={Synthesis of meso-substituted chlorins via tetrahydrobilene-a intermediates}, volume={66}, ISSN={["0022-3263"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035798224&partnerID=MN8TOARS}, DOI={10.1021/jo0104835}, abstractNote={Chlorin building blocks incorporating a geminal dimethyl group in the reduced ring and synthetic handles in specific patterns at the perimeter of the macrocycle are expected to have utility in biomimetic and materials chemistry. A prior route employed condensation of a dihydrodipyrrin (Western half) and a bromodipyrromethane-monocarbinol (Eastern half), followed by oxidative cyclization of the putative dihydrobilene-a to form the meso-substituted zinc chlorin in yields of approximately 10%. The limited stability of the dihydrodipyrrin precluded study of the chlorin-forming process. We now have refined this methodology. A tetrahydrodipyrrin Western half (2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin) has been synthesized and found to be quite stable. The condensation of the Western half and an Eastern half (100 mM each) proceeded smoothly in CH(3)CN containing 100 mM TFA at room temperature for 30 min. The resulting linear tetrapyrrole, a 2,3,4,5-tetrahydrobilene-a, also is quite stable, enabling study of the conversion to chlorin. Refined conditions for the oxidative cyclization were found to include the following: the tetrahydrobilene-a (10 mM), AgTf (3-5 molar equiv), Zn(OAc)(2) (15 molar equiv), and 2,2,6,6-tetramethylpiperidine (15 molar equiv) in CH(3)CN at reflux exposed to air for 4-6 h, affording the zinc chlorin. The chlorin-forming process could be implemented in either a two-flask process or a one-flask process. The two-flask process was applied to form six zinc chlorins bearing substituents such as pentafluorophenyl, 3,5-di-tert-butylphenyl, TMS-ethyl benzoate, iodophenyl, or ethynylphenyl (deprotection of the TMS-ethynyl group occurred during the oxidative cyclization process). The stepwise yields (isolated) for the condensation and oxidative cyclization processes forming the tetrahydrobilene and zinc chlorin were 32-72% and 27-62%, respectively, giving overall yields of zinc chlorin from the Eastern and Western halves of 12-45%. Taken together, the refinements introduced enable 100-mg quantities of chlorin building blocks to be prepared in a facile and rational manner.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Taniguchi, M and Ra, D and Mo, G and Balasubramanian, T and Lindsey, JS}, year={2001}, month={Nov}, pages={7342–7354} } @article{ambroise_li_yu_lindsey_2000, title={A self-assembled light-harvesting array of seven porphyrins in a wheel and spoke architecture}, volume={2}, ISSN={["1523-7052"]}, DOI={10.1021/ol006036d}, abstractNote={[reaction: see text]A shape-persistent cyclic array of six zinc porphyrins provides an effective host for a dipyridyl-substituted free base porphyrin, yielding a self-assembled structure for studies of light harvesting. Energy transfer occurs essentially quantitatively from uncoordinated to pyridyl-coordinated zinc porphyrins in the cyclic array. Energy transfer from the coordinated zinc porphyrin to the guest free base porphyrin is less efficient (phitrans approximately 40%) and is attributed to a Förster through-space process.}, number={17}, journal={ORGANIC LETTERS}, author={Ambroise, A and Li, JZ and Yu, LH and Lindsey, JS}, year={2000}, month={Aug}, pages={2563–2566} } @article{geier_ciringh_li_haynes_lindsey_2000, title={A survey of acid catalysts for use in two-step, one-flask syntheses of meso-substituted porphyrinic macrocycles}, volume={2}, ISSN={["1523-7060"]}, DOI={10.1021/ol005917h}, abstractNote={[reaction: see text] Diverse Lewis acids and Bronsted acids were examined in the two-step, one-flask synthesis of meso-tetraphenylporphyrin, N-confused tetraphenylporphyrin, and tetraphenylsapphyrin. The scope of acid catalysis was found to be very broad, with 35 of 45 acids providing TPP in yields ranging from 5% to 58%. NC-TPP was also widely observed in yields of 1-40%, and TPS was infrequently observed in yields of <1%. Additionally, conditions were found for direct preparation of magnesium TPP and copper TPP.}, number={12}, journal={ORGANIC LETTERS}, author={Geier, GR and Ciringh, Y and Li, FR and Haynes, DM and Lindsey, JS}, year={2000}, month={Jun}, pages={1745–1748} } @article{miller_lammi_prathapan_holten_lindsey_2000, title={A tightly coupled linear array of perylene, bis(porphyrin), and phthalocyanine units that functions as a photoinduced energy-transfer cascade}, volume={65}, ISSN={["1520-6904"]}, DOI={10.1021/jo0007940}, abstractNote={We have prepared a linear array of chromophores consisting of a perylene input unit, a bis(free base porphyrin) transmission unit, and a free base phthalocyanine output unit for studies in artificial photosynthesis and molecular photonics. The synthesis involved four stages: (1) a rational synthesis of trans-AB2C-porphyrin building blocks each bearing one meso-unsubstituted position, (2) oxidative, meso,meso coupling of the zinc porphyrin monomers to afford a bis(zinc porphyrin) bearing one phthalonitrile group and one iodophenyl group, (3) preparation of a bis(porphyrin)-phthalocyanine array via a mixed cyclization involving the bis(free base porphyrin) and 4-tert-butylphthalonitrile, and (4) Pd-mediated coupling of an ethynylperylene to afford a perylene-bis(porphyrin)-phthalocyanine linear array. The perylene-bis(porphyrin)-phthalocyanine array absorbs strongly across the visible spectrum. Excitation at 490 nm, where the perylene absorbs preferentially, results in fluorescence almost exclusively from the phthalocyanine (phi(f) = 0.78). The excited phthalocyanine forms with time constants of 2 ps (90%) and 13 ps (10%). The observed time constants resemble those of corresponding phenylethyne-linked dyads, including a perylene-porphyrin (< or = 0.5 ps) and a porphyrin-phthalocyanine (1.1 ps (70%) and 8 ps (30%)). The perylene-bis(porphyrin)-phthalocyanine architecture exhibits efficient light-harvesting properties and rapid funneling of energy in a cascade from perylene to bis(porphyrin) to phthalocyanine.}, number={20}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Miller, MA and Lammi, RK and Prathapan, S and Holten, D and Lindsey, JS}, year={2000}, month={Oct}, pages={6634–6649} } @article{rao_littler_geier_lindsey_2000, title={Efficient synthesis of monoacyl dipyrromethanes and their use in the preparation of sterically unhindered trans-porphyrins}, volume={65}, ISSN={["0022-3263"]}, DOI={10.1021/jo9915473}, abstractNote={The condensation of an aldehyde with a dipyrromethane bearing a sterically unhindered aryl substituent at the 5-position typically results in low yield and a mixture of porphyrin products derived from acidolytic scrambling. We have developed a concise nonscrambling synthesis of such trans-porphyrins that takes advantage of the availability of multigram quantities of dipyrromethanes. This route involves the selective monoacylation of the dipyrromethanes with a pyridyl thioester, reduction of the monoacyl dipyrromethane to the corresponding carbinol, and self-condensation of the carbinol to form the porphyrin. The monoacylation procedure has wide scope as demonstrated by the preparation of a set of 15 diverse monoacyl dipyrromethanes in good yield at the multigram scale. The dipyrromethanecarbinol self-condensation reaction is extremely rapid (<3 min) under mild room-temperature conditions and affords the trans-porphyrin in 16−28% yield. Analysis by laser-desorption mass spectrometry (LD-MS) of samples from the crude reaction mixture revealed no scrambling within the limit of detection (1 part in 100). The self-condensation is compatible with a range of electron-withdrawing or -releasing substituents as well as substituents for building block applications (TMS-ethyne, ethyne, iodo, ester). The absence of any detectable scrambling in the self-condensation enables a simple purification. The synthesis readily affords gram quantities of pure, sterically unhindered trans-porphyrins in a process involving minimal chromatography.}, number={4}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Rao, PD and Littler, BJ and Geier, GR and Lindsey, JS}, year={2000}, month={Feb}, pages={1084–1092} } @article{clausen_gryko_yasseri_diers_bocian_kuhr_lindsey_2000, title={Investigation of tightly coupled porphyrin arrays comprised of identical monomers for multibit information storage}, volume={65}, ISSN={["1520-6904"]}, DOI={10.1021/jo000489e}, abstractNote={Our prior designs for molecular-based information storage devices have employed multiple redox-active units organized in weakly coupled, covalently linked arrays. To explore a simpler design, we report here the synthesis of porphyrin arrays where porphyrins with identical oxidation potentials are directly linked to one another instead of joined via a molecular linker. Oxidative coupling with AgPF(6) of zinc(II)-5,15-bis(4-tert-butylphenyl)-10-phenylporphyrin, obtained by a rational synthesis, afforded the expected dimer joined by a meso-meso linkage and an unexpected trimer joined by meso-meso linkages. For attachment to an electroactive surface we synthesized a meso-linked porphyrin dimer with a thiol-linker in one of the meso positions. The S-acetyl protecting group was used to avoid handling free thiol groups. Coupling of zinc(II)-5,10,15-tris(3, 5-di-tert-butylphenyl)porphyrin ("upper half") and zinc(II)-5-[4-(S-acetylthio)phenyl]-10,20-bis(3, 5-di-tert-butylphenyl)porphyrin ("lower half") afforded three different meso-linked dimers with the desired dimer as the main product. Electrochemical examination of the meso-linked dimer in solution shows that the first two oxidation potentials of the array differ by approximately 0.15 V and straddle the value exhibited by the monomeric constituents. The third and fourth oxidation potentials of the array are also split although to a lesser extent ( approximately 0.08 V) than the first and second. For the meso-linked trimer, the first three oxidation waves are also split; however, these waves are severely overlapped. The electrochemical behavior of the dimers and trimer is indicative of strong electronic interactions among the porphyrins. The thiol-derivatized meso-linked dimers form self-assembled monolayers (SAMs) on gold via in situ cleavage of the S-acetylthio protecting group. The porphyrin SAM exhibits four well-resolved oxidation waves. Regardless, the meso-meso linkage is relatively unstable upon formation of the pi-cation radical(s). This characteristic indicates that the structural motif is of limited utility for molecular information storage elements.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Clausen, C and Gryko, DT and Yasseri, AA and Diers, JR and Bocian, DF and Kuhr, WG and Lindsey, JS}, year={2000}, month={Nov}, pages={7371–7378} } @article{rao_dhanalekshmi_littler_lindsey_2000, title={Rational syntheses of porphyrins bearing up to four different meso substituents}, volume={65}, ISSN={["0022-3263"]}, DOI={10.1021/jo000882k}, abstractNote={Porphyrins bearing specific patterns of substituents are crucial building blocks in biomimetic and materials chemistry. We have developed methodology that avoids statistical reactions, employs minimal chromatography, and affords up to gram quantities of regioisomerically pure porphyrins bearing predesignated patterns of up to four different meso substituents. The methodology is based upon the availability of multigram quantities of dipyrromethanes. A procedure for the diacylation of dipyrromethanes using EtMgBr and an acid chloride has been refined. A new procedure for the preparation of unsymmetrical diacyl dipyrromethanes has been developed that involves (1) monoacylation with EtMgBr and a pyridyl benzothioate followed by (2) introduction of the second acyl unit upon reaction with EtMgBr and an acid chloride. The scope of these acylation methods has been examined by preparing multigram quantities of diacyl dipyrromethanes bearing a variety of substituents. Reduction of the diacyl dipyrromethane to the corresponding dipyrromethane-dicarbinol is achieved with NaBH(4) in methanolic THF. Porphyrin formation involves the acid-catalyzed condensation of a dipyrromethane-dicarbinol and a dipyrromethane followed by oxidation with DDQ. Optimal conditions for the condensation were identified after examining various reaction parameters (solvent, temperature, acid, concentration, time). The conditions identified (2.5 mM reactants in acetonitrile containing 30 mM TFA at room temperature for <7 min) provided reaction without detectable scrambling (LD-MS) for aryl-substituted dipyrromethanes, and trace scrambling for alkyl-substituted dipyrromethanes. The desired porphyrins were obtained in 14-40% yield. The synthesis is compatible with diverse functionalities: amide, aldehyde, carboxylic acid, ester, nitrile, ether, bromo, iodo, ethyne, TMS-ethyne, TIPS-ethyne, perfluoroarene. In total 30 porphyrins of the types A(3)B, trans-A(2)B(2), trans-AB(2)C, cis-A(2)B(2), cis-A(2)BC, and ABCD were prepared, including >1-g quantities of three porphyrins.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Rao, PD and Dhanalekshmi, S and Littler, BJ and Lindsey, JS}, year={2000}, month={Nov}, pages={7323–7344} } @article{balasubramanian_strachan_boyle_lindsey_2000, title={Rational synthesis of beta-substituted chlorin building blocks}, volume={65}, ISSN={["0022-3263"]}, DOI={10.1021/jo000913b}, abstractNote={Chlorins provide the basis for plant photosynthesis, but synthetic model systems have generally employed porphyrins as surrogates due to the unavailability of suitable chlorin building blocks. We have adapted a route pioneered by Battersby to gain access to chlorins that bear two meso substituents, a geminal dimethyl group to lock in the chlorin hydrogenation level, and no flanking meso and beta substituents. The synthesis involves convergent joining of an Eastern half and a Western half. A 3,3-dimethyl-2,3-dihydrodipyrrin (Western half) was synthesized in four steps from pyrrole-2-carboxaldehyde. A bromodipyrromethane carbinol (Eastern half) was prepared by sequential acylation and bromination of a 5-substituted dipyrromethane followed by reduction. Chlorin formation is achieved by a two-flask process of acid-catalyzed condensation followed by metal-mediated oxidative cyclization. The latter reaction has heretofore been performed with copper templates. Investigation of conditions for this multistep process led to copper-free conditions (zinc acetate, AgIO(3), and piperidine in toluene at 80 degrees C for 2 h). The zinc chlorin was obtained in yields of approximately 10% and could be easily demetalated to give the corresponding free base chlorin. The synthetic process is compatible with a range of meso substituents (p-tolyl, mesityl, pentafluorophenyl, 4-[2-(trimethylsilyl)ethynyl]phenyl, 4-iodophenyl). Altogether four free base and four zinc chlorins have been prepared. The chlorins exhibit typical absorption spectra, fluorescence spectra, and fluorescence quantum yields. The ease of synthetic access, presence of appropriate substituents, and characteristic spectral features make these types of chlorins well suited for incorporation in synthetic model systems.}, number={23}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Balasubramanian, T and Strachan, JP and Boyle, PD and Lindsey, JS}, year={2000}, month={Nov}, pages={7919–7929} } @article{strachan_df o'shea_balasubramanian_lindsey_2000, title={Rational synthesis of meso-substituted chlorin building blocks}, volume={65}, ISSN={["1520-6904"]}, DOI={10.1021/jo991942t}, abstractNote={Chlorins provide the basis for plant photosynthesis, but synthetic model systems have generally employed porphyrins as surrogates due to the unavailability of suitable chlorin building blocks. We have adapted a route pioneered by Battersby to gain access to chlorins that bear two meso substituents, a geminal dimethyl group to lock in the chlorin hydrogenation level, and no flanking meso and β substituents. The synthesis involves convergent joining of an Eastern half and a Western half. A 3,3-dimethyl-2,3-dihydrodipyrrin (Western half) was synthesized in four steps from pyrrole-2-carboxaldehyde. A bromodipyrromethane carbinol (Eastern half) was prepared by sequential acylation and bromination of a 5-substituted dipyrromethane followed by reduction. Chlorin formation is achieved by a two-flask process of acid-catalyzed condensation followed by metal-mediated oxidative cyclization. The latter reaction has heretofore been performed with copper templates. Investigation of conditions for this multistep process led to copper-free conditions (zinc acetate, AgIO3, and piperidine in toluene at 80 °C for 2 h). The zinc chlorin was obtained in yields of ∼10% and could be easily demetalated to give the corresponding free base chlorin. The synthetic process is compatible with a range of meso substituents (p-tolyl, mesityl, pentafluorophenyl, 4-[2-(trimethylsilyl)ethynyl]phenyl, 4-iodophenyl). Altogether four free base and four zinc chlorins have been prepared. The chlorins exhibit typical absorption spectra, fluorescence spectra, and fluorescence quantum yields. The ease of synthetic access, presence of appropriate substituents, and characteristic spectral features make these types of chlorins well suited for incorporation in synthetic model systems.}, number={10}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Strachan, JP and DF O'Shea and Balasubramanian, T and Lindsey, JS}, year={2000}, month={May}, pages={3160–3172} } @article{gryko_lindsey_2000, title={Rational synthesis of meso-substituted porphyrins bearing one nitrogen heterocyclic group}, volume={65}, ISSN={["1520-6904"]}, DOI={10.1021/jo9918100}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTRational Synthesis of Meso-Substituted Porphyrins Bearing One Nitrogen Heterocyclic GroupDorota Gryko and Jonathan S. LindseyView Author Information Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204 Cite this: J. Org. Chem. 2000, 65, 7, 2249–2252Publication Date (Web):March 15, 2000Publication History Received23 November 1999Published online15 March 2000Published inissue 1 April 2000https://pubs.acs.org/doi/10.1021/jo9918100https://doi.org/10.1021/jo9918100brief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views3643Altmetric-Citations78LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. 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Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aldehydes,Condensation,Nitrogen,Pyrroles,Substituents Get e-Alerts}, number={7}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Gryko, D and Lindsey, JS}, year={2000}, month={Apr}, pages={2249–2252} } @article{lammi_ambroise_balasubramanian_wagner_bocian_holten_lindsey_2000, title={Structural control of photoinduced energy transfer between adjacent and distant sites in multiporphyrin arrays}, volume={122}, ISSN={["0002-7863"]}, DOI={10.1021/ja001031x}, abstractNote={A family of diphenylethyne-linked porphyrin dimers and trimers has been prepared via a building block approach for studies of energy-transfer processes. The dimers contain Mg and Zn porphyrins (MgZnU); the trimers contain an additional free base porphyrin (MgZnFbU). In both the dimers and trimers, sites of attachment to the Mg porphyrin (at the meso- or β-position) and diphenylethyne linker (at the para- or meta-positions) were varied, producing four Mg porphyrin−Zn porphyrin arrangements with the following linker configurations:  meso-p/p-meso, meso-m/p-meso, β-p/p-meso, and β-m/p-meso. All four trimers employ a meso-p/p-meso Zn porphyrin−Fb porphyrin connection. The ground- and excited-state properties of the porphyrin dimers and trimers have been examined using static and time-resolved optical techniques. The rate of energy transfer from the photoexcited Zn porphyrin to the Mg porphyrin decreases according to the following trend:  meso-p/p-meso (9 ps)-1 > β-p/p-meso (14 ps)-1 > meso-m/p-meso (19 ps)-1 ...}, number={31}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Lammi, RK and Ambroise, A and Balasubramanian, T and Wagner, RW and Bocian, DF and Holten, D and Lindsey, JS}, year={2000}, month={Aug}, pages={7579–7591} } @article{yang_li_cho_kim_bocian_holten_lindsey_2000, title={Synthesis and excited-state photodynamics of phenylethyne- linked porphyrin-phthalocyanine dyads}, volume={10}, DOI={10.1039/a906273d}, abstractNote={Free base, zinc and magnesium mono-ethynyl phthalocyanines have been prepared as building blocks for constructing phthalocyanine-containing molecular devices. The phthalocyanine building blocks were prepared by the statistical reaction of 4,5-diheptylphthalonitrile and 4-(3-hydroxy-3-methylbut-1-ynyl)phthalonitrile, followed by chromatographic separation and subsequent deprotection. Seven porphyrin–phthalocyanine dyads in various metalation states have been prepared (M1PM2Pc; M1, M2 = Zn2+, Mg2+, or 2H+). ZnPH2Pc and ZnPZnPc were synthesized by Pd-coupling reactions of an ethynylphthalocyanine and an iodoporphyrin. Five other dyads (H2PH2Pc, MgPH2Pc, MgPMgPc, H2PMgPc, ZnPMgPc) were prepared by selective metalation and demetalation reactions starting from ZnPH2Pc, based on the stability differences of metalloporphyrins and metallophthalocyanines. Transient absorption and static emission experiments indicate the following: (1) Excited singlet-state intramolecular energy transfer from the porphyrin to the phthalocyanine moiety is very fast (≤10 ps). (2) The efficiency of the energy-transfer process is very high (typically ≥90%), and is greatest in dyads in which competing charge transfer is inhibited on energetic grounds (e.g. >98% for H2PH2Pc). (3) Charge transfer involving the excited phthalocyanine and the porphyrin occurs to a limited degree (typically <10%) depending on the redox characteristics of the chromophores. (4) The desirable strong emission properties of monomeric phthalocyanines are retained in most of the dyads (Φf = 0.37–0.75). This paper establishes the foundation for utilizing phthalocyanines as strong-red absorbers, energy-transfer acceptors, and bright emitters in conjunction with porphyrin-based molecular photonic devices.}, number={2}, journal={Journal of Materials Chemistry}, author={Yang, S. I. and Li, J. Z. and Cho, H. S. and Kim, D. and Bocian, D. F. and Holten, D. and Lindsey, Jonathan}, year={2000}, pages={283–296} } @article{gryko_clausen_roth_dontha_bocian_kuhr_lindsey_2000, title={Synthesis of "porphyrin-linker-thiol" molecules with diverse linkers for studies of molecular-based information storage}, volume={65}, ISSN={["0022-3263"]}, DOI={10.1021/jo000487u}, abstractNote={The attachment of redox-active molecules such as porphyrins to an electroactive surface provides an attractive approach for electrically addressable molecular-based information storage. Porphyrins are readily attached to a gold surface via thiol linkers. The rate of electron transfer between the electroactive surface and the porphyrin is one of the key factors that dictates suitability for molecular-based memory storage. This rate depends on the type and length of the linker connecting the thiol unit to the porphyrin. We have developed different routes for the preparation of thiol-derivatized porphyrins with eight different linkers. Two sets of linkers explore the effects of linker length and conjugation, with one set comprising phenylethyne units and one set comprising alkyl units. One electron-deficient linker has four fluorine atoms attached directly to a thiophenyl unit. To facilitate the synthesis of the porphyrins, convenient routes have been developed to a wide range of aldehydes possessing a protected S-acetylthio group. An efficient synthesis of 1-(S-acetylthio)-4-iodobenzene also has been developed. A set of porphyrins, each bearing one S-acetyl-derivatized linker at one meso position and mesityl moieties at the three remaining meso positions, has been synthesized. Altogether seven new aldehydes, eight free base porphyrins and eight zinc porphyrins have been prepared. The zinc porphyrins bearing the different linkers all form self-assembled monolayers (SAMs) on gold via in situ cleavage of the S-acetyl protecting group. The SAM of each porphyrin is electrochemically robust and exhibits two reversible oxidation waves.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Gryko, DT and Clausen, C and Roth, KM and Dontha, N and Bocian, DF and Kuhr, WG and Lindsey, JS}, year={2000}, month={Nov}, pages={7345–7355} } @article{li_gryko_dabke_diers_bocian_kuhr_lindsey_2000, title={Synthesis of thiol-derivatized europium porphyrinic triple-decker sandwich complexes for multibit molecular information storage}, volume={65}, ISSN={["0022-3263"]}, DOI={10.1021/jo000490d}, abstractNote={The storage of multiple bits of information at the molecular level requires molecules with a large number of distinct oxidation states. Lanthanide triple-decker sandwich molecules employing porphyrins and phthalocyanines afford four cationic states and are very attractive for molecular information storage applications. Five triple-decker building blocks have been prepared of the type (phthalocyanine)Eu(phthalocyanine)Eu(porphyrin), each bearing one iodo, one ethyne, or one iodo and one ethyne group attached to the porphyrin unit. Two triple-decker building blocks with different oxidation potentials were derivatized with an S-acetylthiophenyl unit for attachment to an electroactive surface. To explore the preparation of arrays comprised of triple deckers, which may lead to the storage of a larger number of bits, two types of dyads of triple deckers were prepared. An ethyne-linked dyad of triple deckers bearing one S-acetylthiophenyl unit was prepared via repetitive Sonogashira couplings, and a butadiyne-linked dyad was prepared via a modified Glaser coupling. The triple deckers were characterized by absorption spectroscopy, laser-desorption mass spectrometry, and (1)H NMR spectroscopy. The thiol-derivatized triple deckers form self-assembled monolayers (SAMs) on gold via in situ cleavage of the thiol protecting group. The SAM of each array is electrochemically robust and exhibits three well-resolved, reversible oxidation waves. These electrochemical characteristics indicate that these types of molecules are well suited for storing multiple bits of information.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Li, JZ and Gryko, D and Dabke, RB and Diers, JR and Bocian, DF and Kuhr, WG and Lindsey, JS}, year={2000}, month={Nov}, pages={7379–7390} } @article{gryko_zhao_yasseri_roth_bocian_kuhr_lindsey_2000, title={Synthesis of thiol-derivatized ferrocene-porphyrins for studies of multibit information storage}, volume={65}, ISSN={["0022-3263"]}, DOI={10.1021/jo0004862}, abstractNote={One approach toward storage of multiple bits of information at the molecular level requires the construction of molecular architectures comprised of multiple redox-active units. Four new ferrocene-porphyrins have been synthesized to investigate questions concerning (1) the scope of redox-active molecules that can be employed in molecular information-storage schemes and (2) writing/reading rates as well as retention of charge in redox-active units located at different sites in a molecular architecture. Three of the ferrocene-porphyrins have linkers of different lengths between the ferrocene and porphyrin. The fourth ferrocene-porphyrin has two ferrocenes positioned at the lateral sites on the porphyrin. The latter architecture is designed to provide a shorter distance between the electroactive surface and the ferrocene while maintaining an upright orientation of the porphyrin. Each ferrocene-porphyrin affords three cationic oxidation states (ferrocene monocation, porphyrin monocation, porphyrin dication) in addition to the neutral state, thereby affording the capability of storing two bits of information. Each ferrocene-porphyrin bears an S-acetyl or S-(N-ethyl)carbamoyl-protected thiol moiety, thereby avoiding handling of free thiols. Each ferrocene-porphyrin forms a self-assembled monolayer (SAM) on gold via in situ cleavage of the thiol protecting group. The SAM of each array is electrochemically robust and exhibits three well-resolved, reversible oxidation waves.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Gryko, DT and Zhao, F and Yasseri, AA and Roth, KM and Bocian, DF and Kuhr, WG and Lindsey, JS}, year={2000}, month={Nov}, pages={7356–7362} } @article{clausen_gryko_dabke_dontha_bocian_kuhr_lindsey_2000, title={Synthesis of thiol-derivatized porphyrin dimers and trimers for studies of architectural effects on multibit information storage}, volume={65}, ISSN={["0022-3263"]}, DOI={10.1021/jo000488m}, abstractNote={We present the rational design and synthesis of multiporphyrin arrays containing thiol-derivatized linkers for the purpose of multibit molecular information storage. Porphyrin dimers and trimers were synthesized by the Pd-mediated coupling of iodo-substituted and ethynyl-substituted porphyrin building blocks in 5-51% yields. Each porphyrin dimer bears one S-acetylthio group. The architecture of the trimers incorporates a trans-substituted porphyrin (central) bearing two S-acetylthio groups and two diphenylethyne-linked porphyrins (wings) in a trans geometry. The central porphyrin and the wing porphyrins bear distinct substituents and central metals, thereby affording different oxidation potentials. The S-acetylthio groups provide a means for attachment of the arrays to an electroactive surface. The dimers are designed for vertical orientation on an electroactive surface while the trimers are designed for horizontal orientation of the central porphyrin. Altogether seven different arrays were synthesized. Each array forms a self-assembled monolayer (SAM) on gold via in situ cleavage of the S-acetyl protecting group. The SAM of each array is electrochemically robust and exhibits multiple, reversible oxidation waves. In general, however, the trimeric arrays appear to form more highly ordered monolayers that exhibit sharper, better-defined redox features.}, number={22}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Clausen, C and Gryko, DT and Dabke, RB and Dontha, N and Bocian, DF and Kuhr, WG and Lindsey, JS}, year={2000}, month={Nov}, pages={7363–7370} } @article{kuo_du_corkan_yang_lindsey_1999, title={A planning module for performing grid search, factorial design, and related combinatorial studies on an automated chemistry workstation}, volume={48}, ISSN={["0169-7439"]}, DOI={10.1016/S0169-7439(99)00021-0}, abstractNote={The investigation of combinations of factors in a defined search space has broad application in chemistry experimentation. The factors can involve continuous variables such as concentration and temperature, or discrete variables such as chemical reactants or reagents. The number of data points rapidly becomes quite large in such factorial experimentation, which can be adequately handled through the use of an automated chemistry workstation. The automated chemistry workstation utilizes experiment templates for implementation of factorial designs. Experimental templates represent generic plans that are used repetitively with slight variation of designated parameters for the chemical system under investigation. A linkage is established between the dimensions of the search space and the variables in the experimental template. Various patterns of points can be selected, enabling the composition of full factorial or partial factorial designs. The search space points are inscribed in the experimental template, giving rise to one experimental plan per point in the search space. The experimental plans are assessed for resource availability and those for which resources are sufficient are then scheduled for parallel implementation on a microscale automated chemistry workstation. An adaptive feature allows unproductive experiments to be terminated early, de-allocating resources for use in other experiments. Experimental plans can be readily composed and implemented for fundamental studies of chemical reactions, generating response surfaces, performing parallel screening procedures, and creating indexed combinatorial chemical libraries.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Kuo, PY and Du, H and Corkan, LA and Yang, KX and Lindsey, JS}, year={1999}, month={Aug}, pages={219–234} } @article{kuciauskas_liddell_lin_johnson_weghorn_lindsey_moore_moore_gust_1999, title={An artificial photosynthetic antenna-reaction center complex}, volume={121}, ISSN={["1520-5126"]}, DOI={10.1021/ja991255j}, abstractNote={A model photosynthetic antenna consisting of four covalently linked zinc tetraarylporphyrins, (PZP)3−PZC, has been joined to a free base porphyrin-fullerene artificial photosynthetic reaction center, P−C60, to form a (PZP)3−PZC−PC60 hexad. As revealed by time-resolved absorption and emission studies, excitation of any peripheral zinc porphyrin moiety (PZP) in 2-methyltetrahydrofuran solution is followed by singlet−singlet energy transfer to the central zinc porphyrin to give (PZP)3−1PZC−P−C60 with a time constant of ∼50 ps. The excitation is passed on to the free base porphyrin in 240 ps to produce (PZP)3−PZC−1P−C60, which decays by electron transfer to the fullerene with a time constant of 3 ps. The (PZP)3−PZC−P•+−C60•- charge-separated state thus formed has a lifetime of 1330 ps, and is generated with a quantum yield of 0.70 based on light absorbed by the zinc porphyrin antenna. The complex thus mimics the basic functions of natural photosynthetic antenna systems and reaction center complexes.}, number={37}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Kuciauskas, D and Liddell, PA and Lin, S and Johnson, TE and Weghorn, SJ and Lindsey, JS and Moore, AL and Moore, TA and Gust, D}, year={1999}, month={Sep}, pages={8604–8614} } @article{du_corkan_yang_kuo_lindsey_1999, title={An automated microscale chemistry workstation capable of parallel, adaptive experimentation}, volume={48}, ISSN={["0169-7439"]}, DOI={10.1016/S0169-7439(99)00019-2}, abstractNote={We have designed and constructed a 3rd-generation chemistry workstation and accompanying software for automated experimentation in relatively clean domains of chemistry. The workstation is designed for flexible, high-throughput, microscale chemistry and includes a reaction station with 60 reaction vessels. The experiment manager software includes a large number of features to facilitate experiment planning and implementation. The significant advances in software from the 2nd-generation system include the following: (1) Five experiment-planning modules have been incorporated to match different types of scientific experimentation, including open-loop and closed-loop experiments. The five modules enable plans to be composed for general-purpose (GP), decision-tree (DT), factorial design (FD), composite modified Simplex (CMS) and multidirectional search (MDS) experiments. (2) Parallel experimentation and adaptive experimentation have been blended so that some decision-making can be done using objective functions or early-termination functions while multiple experiments are in progress. Some planning modules (CMS, MDS and DT) can cause new experiments to be spawned based on the chemistry data obtained. (3) Decision-making can involve the local course of individual experiments and/or the global course of sets of experiments. (4) Resource management features provide the capability to look-ahead at experiments in queue, assess resource (chemicals, containers) availability and designate suitability for implementation. (5) Intelligent reagent-handling features support the autodilution of reagents, autoselection of appropriate stock solutions, autoassignment of containers and control over reaction volumes. (6) Opportunistic rescheduling features have been provided so that pending experiments can be advanced in queue whenever possible, leading to compressed experimental timeframes. (7) Templates composed for FD, CMS and MDS experiments can be stored and reused with modifications as required for specific experiments. (8) The scheduling module contains both a rigid scheduler and a flexible scheduler. (9) The software is modular and runs under Windows 95. This workstation is especially designed for fundamental investigations of chemical reactions and optimization of experimental reaction conditions.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Du, H and Corkan, LA and Yang, KX and Kuo, PY and Lindsey, JS}, year={1999}, month={Aug}, pages={181–203} } @article{geier_haynes_lindsey_1999, title={An efficient one-flask synthesis of N-confused tetraphenylporphyrin}, volume={1}, ISSN={["1523-7060"]}, DOI={10.1021/ol9910114}, abstractNote={[formula: see text] N-Confused meso-substituted porphyrin is a porphyrin isomer previously available from one-flask porphyrin syntheses as a low-yield byproduct (< 7.5%). We have found that methanesulfonic acid catalyzed condensation of pyrrole and benzaldehyde followed by DDQ oxidation provides N-confused tetraphenylporphyrin (NC-TPP) in up to 39% yield in analytical scale experiments. Preparative synthesis provided an isolated yield of 35% (800 mg). This represents a > 5-fold yield improvement and makes significant quantities of NC-TPP readily available.}, number={9}, journal={ORGANIC LETTERS}, author={Geier, GR and Haynes, DM and Lindsey, JS}, year={1999}, month={Nov}, pages={1455–1458} } @article{du_shen_kuo_lindsey_1999, title={Decision-tree programs for an adaptive automated chemistry workstation. Application to catalyst screening experiments}, volume={48}, ISSN={["0169-7439"]}, DOI={10.1016/S0169-7439(99)00020-9}, abstractNote={Abstract Automated chemistry workstations with the capability of altering the course of experimentation based on acquired data are essential for performing strategic searches. Such adaptive experimentation requires the ability to compose experimental plans for initiating, monitoring, evaluating, and making decisions about experiments. We have developed a decision-tree (DT) experiment-planning module that includes a complete command set for adaptive operation of the workstation. Functions for dialog prompts are included, enabling generic programs to be tailored for specific applications by various users. The DT experiment-planning module is one component of an experiment planner for an automated microscale chemistry workstation. The DT functions are also used to compose early-termination programs and describe objective functions for use in the companion factorial design, composite-modified simplex, and multidirectional search experiment-planning modules. The features of the DT experiment-planning module are illustrated with a program that screens a list of candidate compounds for catalytic activity. A set of dialog boxes at the beginning of the program prompts the user for information. Based on this information, the candidates are examined automatically (in a serial process) in exhaustive or hill-climbing searching strategies. A yield vs. time pattern-matching procedure is performed dynamically in order to assess whether monitoring should be continued. Decisions also are made concerning examination of the candidate at higher or lower concentrations. Higher concentrations are achieved by addition of aliquots of the candidate to the ongoing reaction, while lower concentrations are achieved by spawning a new reaction. When a user-defined yield threshold is reached or the entire user-specified concentration range has been spanned, catalysts and their effective concentration ranges are identified. This experiment-planning module enables composition of flexible programs for adaptive experimentation that can be used as stand-alone programs or as decision-making components of other searching programs.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Du, H and Shen, W and Kuo, PY and Lindsey, JS}, year={1999}, month={Aug}, pages={205–217} } @article{hascoat_yang_lammi_alley_bocian_lindsey_holten_1999, title={Effects of metalation state (Free base, Mg, Zn, Cd) on excited-state energy transfer in diarylethyne-linked porphyrin dimers}, volume={38}, ISSN={["0020-1669"]}, DOI={10.1021/ic990469z}, abstractNote={The ground- and excited-state properties of two new porphyrin dimers have been examined using static and time-resolved optical techniques. One dimer consists of a zinc porphyrin and a magnesium porphyrin (ZnMgU), and the other dimer consists of a cadmium porphyrin and a free base (Fb) porphyrin (CdFbU). In both arrays, the porphyrins are joined by a diarylethyne linker at one meso position with mesityl groups at the nonlinking meso positions. The rates of photoinduced energy transfer are faster for ZnMgU ((9 ps)(-)(1)) and CdFbU ((15 ps)(-)(1)) than found previously for ZnFbU ((24 ps)(-)(1)) and MgFbU ((31 ps)(-)(1)). Only for CdFbU does the yield of excited-state energy transfer (87%) drop below the near-quantitative (>/=99%) level, and this effect derives solely from competition with a very short inherent lifetime ( approximately 100 ps) of the photoexcited Cd porphyrin. The results further illustrate (1) the efficacy of this dimeric architecture for ultrafast excited-state energy transfer, (2) how molecular/electronic properties can be manipulated to tune photoinduced energy flow in multiporphyrin arrays, and (3) key factors impacting effective inter-porphyrin electronic communication, including porphyrin orbital tuning.}, number={21}, journal={INORGANIC CHEMISTRY}, author={Hascoat, P and Yang, SI and Lammi, RK and Alley, J and Bocian, DF and Lindsey, JS and Holten, D}, year={1999}, month={Oct}, pages={4849–4853} } @article{li_lindsey_1999, title={Efficient synthesis of light-harvesting arrays composed of eight porphyrins and one phthalocyanine}, volume={64}, ISSN={["1520-6904"]}, DOI={10.1021/jo991102e}, abstractNote={Effective light-harvesting arrays require multiple photoactive energy donors that funnel energy to an energy acceptor. Porphyrins and phthalocyanines are attractive components for light-harvesting arrays due to their strong absorption in the blue and red regions, respectively, and because energy transfer can occur from porphyrin to phthalocyanine regardless of their respective metalation states. Star-shaped light-harvesting arrays comprised of eight peripheral porphyrins and one core phthalocyanine have been prepared by a streamlined synthesis involving minimal reliance on protecting groups, a high degree of convergence, and facile chromatographic purification. The synthesis involves three distinct stages of complementary chemistries (porphyrin formation, Pd-mediated porphyrin dimer formation, phthalocyanine formation). Statistical reaction of p-iodobenzaldehyde, a phthalonitrile-linked benzaldehyde, and 5-mesityldipyrromethane afforded the desired trans-iodo/phthalonitrile-substituted porphyrin, which un...}, number={25}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Li, JZ and Lindsey, JS}, year={1999}, month={Dec}, pages={9101–9108} } @article{cork_sugawara_lindsey_corkan_du_1999, title={Further development of a versatile microscale automated workstation for parallel adaptive experimentation}, volume={11}, DOI={10.1002/(SICI)1098-2728(1999)11:4<217::AID-LRA6>3.3.CO;2-3}, abstractNote={We have further developed our microscale automated chemistry workstation for investigating the optimization of reaction conditions. The workstation includes a Cartesian robot for solvent delivery and reagent/sample handling, a 60-vessel reaction block, a UV–Vis absorption spectrometer, and vial racks for compound storage. This article describes the following hardware additions that increase the scope and versatility of the workstation: (a) an analytical high performance liquid chromatography (HPLC) instrument and accompanying hardware interface (slide rail, autosampler); (b) three reactor blocks of 20 vessels each, with independent temperature control of each reactor block between ca. 0 and 80°C; (c) a shaker rack for mixing, dilution, or extraction of samples; (d) a rotary valve on the dispense line for complete isolation of 4 independent solvent lines; (e) sample workup features using disposable cartridges or filters; (f) provisions for dispensing inert gas, for example, for flushing through reactors or for storing solvents and performing transfer/dispense operations under. Using the new features, we are able to obtain useful analytical data from a wider range of reaction mixtures, perform parallel reactions at different temperatures, and handle solvents and sensitive reagents. © 1999 John Wiley & Sons, Inc. Lab Robotics and Automation 11: 217–223, 1999}, number={4}, journal={Laboratory Robotics and Automation}, author={Cork, D. G. and Sugawara, T. and Lindsey, Jonathan and Corkan, L. A. and Du, H.}, year={1999}, pages={217–223} } @article{yang_seth_strachan_gentemann_kim_holten_lindsey_bocian_1999, title={Ground and excited state electronic properties of halogenated tetraarylporphyrins. Tuning the building blocks for porphyrin- based photonic devices}, volume={3}, DOI={10.1002/(SICI)1099-1409(199902)3:2<117::AID-JPP110>3.0.CO;2-X}, abstractNote={ The rational design of molecular photonic devices relies on the ability to select components with predictable electronic structure, excited state lifetimes and redox chemistry. Electronic communication in multiporphyrin arrays depends critically on the relative energies and electron density distributions of the frontier molecular orbitals, especially the energetically close highest occupied molecular orbitals (a2u and a1u). To explore how these ground and excited state properties can be modulated, we have synthesized and characterized 40 free base ( Fb ), magnesium and zinc tetraarylporphyrins. The porphyrins bear meso-substituents with the following substitution patterns: (1) four identical substituents (phenyl, o-chlorophenyl, p-chlorophenyl, o,o'-difluorophenyl, pentafluorophenyl, mesityl); (2) one, two, three or four o,o'-dichlorophenyl substituents; (3) one p-ethynylphenyl group and three mesityl or pentafluorophenyl groups; (4) one p-ethynyl-o,o″-dichlorophenyl or p-ethynyl-o,o″-dimethylphenyl and three phenyl groups. For each neutral complex the ground state electronic properties were investigated using electrochemical methods and optical absorption spectroscopy. Similarly the absorption, emission, and relaxation properties of the lowest singlet excited state were probed by time-resolved absorption and fluorescence methods. Each oxidized complex was investigated by static absorption and liquid and frozen solution EPR spectroscopy. The collective results of these investigations have provided insights into the direct (orbital overlap) and indirect (inductive/conjugative) mechanisms by which halogenated phenyl rings influence the static and dynamic electronic properties of neutral and oxidized porphyrinic chromophores. Three key findings are as follows. (1) The effective electron-withdrawing strength of halogenated phenyl rings required to reverse the ordering of the a2u and a1u HOMOs in Mg versus Zn tetraarylporphyrins has been elucidated. (2) Appropriate halogenation can significantly increase the excited state lifetime of a Zn porphyrin relative to the unsubstituted complex. (3) Halogenation can be used to modulate redox potentials in a manner that complements the enhancement of other electronic properties. The insights gained from study of this library of porphyrins provide a foundation for tuning the electronic properties of monomeric porphyrins as building blocks for multichromophoric assemblies in optoelectronics and other applications. }, number={2}, journal={Journal of Porphyrins and Phthalocyanines}, author={Yang, S. I. and Seth, J. and Strachan, J. P. and Gentemann, S. and Kim, D. and Holten, D. and Lindsey, Jonathan and Bocian, D. F.}, year={1999}, pages={117–147} } @article{du_jindal_lindsey_1999, title={Implementation of the multidirectional search algorithm on an automated chemistry workstation. A parallel yet adaptive approach for reaction optimization}, volume={48}, ISSN={["0169-7439"]}, DOI={10.1016/S0169-7439(99)00022-2}, abstractNote={We have developed an experiment-planning module for applying a powerful new pattern search algorithm toward the problems of reaction investigation and optimization. The experiment planner works in conjunction with a closed-loop automated chemistry workstation equipped for parallel experimentation. The new algorithm, developed by Torczon for parallel computation of mathematical functions, achieves a focused yet parallel approach to finding regions of improved response. Like a full factorial design, the search space involves a regular grid of points. Like the Simplex algorithm, the multidirectional search (MDS) algorithm uses the movement of a simplex through a search space. However, with each movement all points except the single best are discarded, whereas the Simplex algorithm discards only the one worst point. Thus, in an n-dimensional space, the MDS algorithm projects n mandatory points at every cycle (beyond the initial). In addition, a larger number of exploratory points are identified by look-ahead projection of possible future simplices. Such exploratory points lie on multiple independent lines of search. The responses for the mandatory and exploratory points are acquired via parallel experimentation, with the latter points examined to the extent that the workstation has available capacity during the same schedule. The data from such exploratory points can be used in later cycles of experimentation, accelerating convergence on the region of optimal response. In the case of unlimited parallel experimentation capacity, all possible points in the space are projected, as in a full factorial design. The MDS algorithm thus adapts to the available parallel capacity of the workstation. The MDS planning module includes options for specifying initial points, stop criteria, and early-termination processes. Provisions are included for parallel scheduling of batches of experiments, convergence of the search, and movement at the boundaries of the search space. An MDS investigation can thus be implemented with global decision-making concerning movements through a search space, and local decision-making concerning termination of individual experiments. The MDS algorithm enables directed evolutionary searches in a parallel mode and is ideally suited for rapid optimization of chemical reactions using a microscale automated chemistry workstation.}, number={2}, journal={CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS}, author={Du, H and Jindal, S and Lindsey, JS}, year={1999}, month={Aug}, pages={235–256} } @article{yang_seth_balasubramanian_kim_lindsey_holten_bocian_1999, title={Interplay of orbital tuning and linker location in controlling electronic communication in porphyrin arrays}, volume={121}, ISSN={["0002-7863"]}, DOI={10.1021/ja9842060}, abstractNote={The β-diphenylethyne-linked porphyrin dimers ZnFbU-β (nonlinking meso-mesityl substituents) and F30ZnFbU-β (nonlinking meso-pentafluorophenyl substituents) and their bis-Zn analogues have been examined by static spectroscopic (absorption, fluorescence, electron paramagnetic resonance), time-resolved spectroscopic (absorption, fluorescence), and electrochemical (cyclic and square-wave voltammetry, coulometry) methods. The β-linked dimers were examined to test the hypothesis that the nature of the porphyrin HOMO (a1u versus a2u) in concert with the position of the linker (β-pyrrole or meso carbon) mediates electronic communication (excited-state energy transfer, ground-state hole-hopping). The major findings are as follows:  (1) The rate of energy transfer is (56 ps)-1 for ZnFbU-β and (24 ps)-1 for F30ZnFbU-β. (2) The rate of hole/electron hopping in the monooxidized bis-Zn complex [F30Zn2U-β]+ is in the fast-exchange limit and is at least comparable to that for [Zn2U-β]+. These findings indicate that the p...}, number={16}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Yang, SI and Seth, J and Balasubramanian, T and Kim, D and Lindsey, JS and Holten, D and Bocian, DF}, year={1999}, month={Apr}, pages={4008–4018} } @article{wagner_ciringh_clausen_lindsey_1999, title={Investigation and refinement of palladium-coupling conditions for the synthesis of diarylethyne-linked multiporphyrin arrays}, volume={11}, ISSN={["0897-4756"]}, DOI={10.1021/cm9903529}, abstractNote={The synthesis of diarylethyne-linked multiporphyrin arrays requires Pd-mediated coupling conditions that are performed in dilute solution in the absence of copper and that give reaction mixtures that are easily purified. We previously developed copper-free Pd-mediated coupling conditions (Pd2(dba)3 and AsPh3 in toluene/triethylamine (5:1) at 35 °C) but extensive chromatography was required to remove unidentified porphyrinic byproducts. We have used laser-desorption mass spectrometry (LD-MS) and analytical size-exclusion chromatography (SEC) to assay the products from the coupling reaction of a zinc(II) iodophenylporphyrin (ZnI) and a zinc(II) ethynylphenylporphyrin (ZnU‘). Analysis of the crude reaction mixture revealed the diphenylethyne-linked dimer (Zn2U) as the major product, byproducts plausibly derived from phenyl−aryl exchange processes (a phenylated derivative of ZnU‘, a Ph2As-substituted derivative of ZnI), byproducts believed to originate from direct phenylation processes (a phenylated derivativ...}, number={10}, journal={CHEMISTRY OF MATERIALS}, author={Wagner, RW and Ciringh, Y and Clausen, C and Lindsey, JS}, year={1999}, month={Oct}, pages={2974–2983} } @article{srinivasan_haney_lindsey_zhang_chait_1999, title={Investigation of MALDI-TOF mass spectrometry of diverse synthetic metalloporphyrins, phthalocyanines and multiporphyrin arrays}, volume={3}, ISSN={["1088-4246"]}, DOI={10.1002/(SICI)1099-1409(199904)3:4<283::AID-JPP132>3.0.CO;2-F}, abstractNote={ We investigated the utility of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for analyzing porphyrinic compounds using a variety of different synthetic porphyrins, azaporphyrins, phthalocyanines and multiporphyrin arrays. Comparisons of spectra obtained from these analytes deposited either as neat samples or codeposited with neutral or acidic matrices have been made with the goal of identifying conditions that yield minimal demetalation, transmetalation, adduct formation and fragmentation. It was found that the molecular masses of many porphyrins can be successfully measured from neat sample preparations and do not require a matrix to facilitate desorption and ionization, although the measurement of large multiporphyrin arrays was facilitated by the use of matrices. Demetalation of magnesium porphyrins occurred in the presence of acidic matrices, but not with neutral matrices such as 1,4-benzoquinone. Positive ion spectra were obtained for each compound and negative ion spectra were also collected for the azaporphyrins and phthalocyanines. Examination of selected samples (prepared neat, with 1,4-benzoquinone, 2,3,5,6-tetrachloro-1,4-benzoquinone or α-cyano-4-hydroxycinnamic acid) showed that the dominant process of ionization involved oxidation yielding the radical cation M+· rather than the protonated molecule [M+H]+. MALDI-TOF-MS is shown to be a powerful analytical tool for the characterization of diverse synthetic porphyrinic compounds. }, number={4}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Srinivasan, N and Haney, CA and Lindsey, JS and Zhang, WZ and Chait, BT}, year={1999}, month={Apr}, pages={283–291} } @article{littler_ciringh_lindsey_1999, title={Investigation of conditions giving minimal scrambling in the synthesis of trans-porphyrins from dipyrromethanes and aldehydes}, volume={64}, ISSN={["0022-3263"]}, DOI={10.1021/jo982452o}, abstractNote={A diverse range of reaction conditions for the MacDonald-type 2 + 2 condensation of a 5-substituted dipyrromethane and an aldehyde has been studied with the goal of eliminating acid-catalyzed polypyrrolic rearrangement reactions in the synthesis of trans-porphyrins. A rapid screening method based on laser desorption mass spectrometry has enabled the degree of rearrangement to be examined as a function of the acid catalyst, reagent concentration, reagent stoichiometry, solvent, salts, and temperature. For condensations involving 5-mesityldipyrromethane, we identified reaction at 10 mM concentration in CH(2)Cl(2) with 17.8 mM TFA as optimal conditions for suppression of the rearrangement reaction. A synthetic procedure based on these conditions allowed the expedient synthesis of multigram batches of eight trans-porphyrins in 48-14% yield from 5-mesityldipyrromethane, with minimal chromatography. The same conditions were also effective for the synthesis of two trans-porphyrins derived from 5-(2,6-dichlorophenyl)dipyrromethane. Application of the same conditions to condensations involving 5-phenyldipyrromethane showed extensive rearrangement. Examination of a wide range of conditions showed that slow reactions are associated with less rearrangement. Two sets of conditions were identified that gave little or no scrambling: (1) condensation at 10 mM in MeCN at 0 degrees C with BF(3).Et(2)O catalysis in the presence of NH(4)Cl followed by DDQ oxidation and (2) condensation at 0.1 M in DMSO at 100 degrees C in the presence of NH(4)Cl (with no added acid catalyst) with air oxidation. Although yields are typically less than 10%, the elimination of the need to perform tedious chromatography improves the methodology available for the preparation of trans-porphyrins, derived from sterically unhindered dipyrromethanes.}, number={8}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Littler, BJ and Ciringh, Y and Lindsey, JS}, year={1999}, month={Apr}, pages={2864–2872} } @article{geier_lindsey_1999, title={N-confused tetraphenylporphyrin and tetraphenylsapphyrin formation in one-flask syntheses of tetraphenylporphyrin}, volume={64}, ISSN={["0022-3263"]}, DOI={10.1021/jo982068r}, abstractNote={The yields of tetraphenylporphyrin (TPP), N-confused tetraphenylporphyrin (NC-TPP), and tetraphenylsapphyrin (TPS) were examined under diverse conditions in the one-flask room-temperature reaction of pyrrole and benzaldehyde. The conditions examined included TFA and BF(3)-etherate catalysis, acid concentrations, pyrrole and benzaldehyde concentrations, pyrrole:benzaldehyde ratios, the addition of salt, and reaction times. The quantities of TPP, NC-TPP, and TPS were determined by HPLC. The yield of NC-TPP mirrored that of TPP during systematic variation of reaction parameters but was consistently lower (90%) or eight (>85%) accessory pigments per porphyrin. Biphasic excited-state decay behavior is exhibited by the BDPY pigments in isol...}, number={39}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Li, FR and Yang, SI and Ciringh, YZ and Seth, J and Martin, CH and Singh, DL and Kim, DH and Birge, RR and Bocian, DF and Holten, D and et al.}, year={1998}, month={Oct}, pages={10001–10017} } @article{van patten_shreve_lindsey_donohoe_1998, title={Energy-transfer modeling for the rational design of multiporphyrin light-harvesting arrays}, volume={102}, ISSN={["1520-6106"]}, DOI={10.1021/jp972304m}, abstractNote={Excited-state energy migration among a collection of pigments forms the basis for natural light-harvesting processes and synthetic molecular photonic devices. The rational design of efficient energy-transfer devices requires the ability to analyze the expected performance characteristics of target molecular architectures comprised of various pigments. Toward that goal, we present a general tool for modeling the kinetics of energy migration in weakly coupled multipigment arrays. A matrix-formulated eigenvalue/eigenvector approach has been implemented, using empirical data from a small set of prototypical molecules, to predict the quantum efficiency (QE) of energy migration in a variety of arrays as a function of rate, competitive processes, and architecture. Trends in the results point to useful design strategies including the following:  (1) The QE for energy transfer to a terminal acceptor upon random excitation within a linear array of isoenergetic pigments decreases rapidly as the length of the array i...}, number={21}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Van Patten, PG and Shreve, AP and Lindsey, JS and Donohoe, RJ}, year={1998}, month={May}, pages={4209–4216} } @article{yang_lammi_seth_riggs_arai_kim_bocian_holten_lindsey_1998, title={Excited-state energy transfer and ground-state hole electron hopping in p-phenylene-linked porphyrin dimers}, volume={102}, ISSN={["1089-5647"]}, DOI={10.1021/jp982729o}, abstractNote={The ground- and excited-state properties of a series of p-phenylene-linked porphyrin dimers have been examined using a variety of static and time-resolved spectroscopic techniques. The dimers consist of a zinc porphyrin and a free base (Fb) porphyrin (ZnFbΦ), two zinc porphyrins (Zn2Φ), or two Fb porphyrins (Fb2Φ). In each array, the porphyrins are joined by the p-phenylene linker at one meso position, with the nonlinking meso positions bearing mesityl groups. Three analogous dimers in which the mesityl groups are replaced with pentafluorophenyl groups (F30ZnFbΦ, F30Zn2Φ, and F30Fb2Φ) were also synthesized and characterized. The excited-state energy-transfer rate from the photoexcited Zn porphyrin to the Fb porphyrin is (3.5 ps)-1 for ZnFbΦ and (10 ps)-1 for F30ZnFbΦ. The quantum yields of excited-state energy transfer are ≥99% for both complexes. The energy-transfer rates in the p-phenylene-linked dimers are considerably faster than those observed for the analogous dimers containing a diphenylethyne link...}, number={47}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Yang, SI and Lammi, RK and Seth, J and Riggs, JA and Arai, T and Kim, DH and Bocian, DF and Holten, D and Lindsey, JS}, year={1998}, month={Nov}, pages={9426–9436} } @article{wagner_li_du_lindsey_1999, title={Investigation of cocatalysis conditions using an automated microscale multireactor workstation: Synthesis of meso-tetramesitylporphypin}, volume={3}, ISSN={["1083-6160"]}, DOI={10.1021/op9800459}, abstractNote={Prior manual work has shown that the condensation of mesitaldehyde and pyrrole leading to tetramesitylporphyrin depends sensitively on concentration and requires cocatalysis involving BF3·O(Et)2 and ethanol or other protic species. We have applied an automated microscale chemistry workstation capable of parallel or adaptive experimentation to systematically investigate these cocatalysis conditions. Examination of experimental grids spanning a 1000-fold range of the concentrations of BF3·O(Et)2 and ethanol identified the best cocatalysis conditions for various mesitaldehyde and pyrrole concentrations. As the reaction concentration increased from 10 to 200 mM, the optimal yields were achieved with a parallel increase in BF3·O(Et)2 concentration (from 3.3 to 56 mM), but the amount of ethanol remained relatively constant. Catalysis conditions were identified that afforded ∼30% yields for reactants in the range of 10−73 mM, thereby enabling the reaction to be performed at increased concentration without loss i...}, number={1}, journal={ORGANIC PROCESS RESEARCH & DEVELOPMENT}, author={Wagner, RW and Li, FR and Du, H and Lindsey, JS}, year={1999}, pages={28–37} } @article{du_fuh_li_corkan_lindsey_1998, title={PhotochemCAD: A computer-aided design and research tool in photochemistry}, volume={68}, DOI={10.1562/0031-8655(1998)068<0141:PACADA>2.3.CO;2}, number={2}, journal={Photochemistry and Photobiology}, author={Du, H. and Fuh, R. C. A. and Li, J. Z. and Corkan, L. A. and Lindsey, Jonathan}, year={1998}, pages={141–142} } @article{strachan_gentemann_seth_kalsbeck_lindsey_holten_bocian_1998, title={Synthesis and characterization of tetrachlorodiarylethyne-linked porphyrin dimers. Effects of linker architecture on intradimer electronic communication}, volume={37}, ISSN={["0020-1669"]}, DOI={10.1021/ic970967c}, abstractNote={The effects of incorporating chloro groups at all ortho positions of a diphenylethyne linker that bridges the zinc and free base (Fb) components of a porphyrin dimer (ZnFbB(Cl(4))) have been investigated in detail via various static and time-resolved spectroscopic methods. The excited-state energy-transfer rate in ZnFbB(Cl(4)) ((134 ps)(-)(1)) is 5-fold slower than that in the corresponding dimer having an unsubstituted linker (ZnFbU, (24 ps)(-)(1)) but is only modestly slower than that in the dimer having o-methyl groups on the linker (ZnFbB(CH(3))(4), (115 ps)(-)(1)). The ground-state hole/electron-hopping rates in the oxidized bis-Zn analogues of all three dimers are much slower than the excited-state energy-transfer rates. There is no discernible difference between the hole/electron-hopping rates in the o-chloro- and o-methyl-substituted arrays. The similar ground- and excited-state dynamics observed for the o-chloro- and o-methyl-substituted arrays is attributed to the dominance of torsional constraints in mediating the extent of through-bond electronic communication. These constraints attenuate intradimer communication by restricting the rotation toward coplanarity of the phenyl rings of the linker and the porphyrin rings. Thus, the o-chloro groups on the linker decrease electronic communication via a steric, rather than purely electronic, mechanism.}, number={6}, journal={INORGANIC CHEMISTRY}, author={Strachan, JP and Gentemann, S and Seth, J and Kalsbeck, WA and Lindsey, JS and Holten, D and Bocian, DF}, year={1998}, month={Mar}, pages={1191–1201} } @article{wagner_seth_yang_kim_bocian_holten_lindsey_1998, title={Synthesis and excited-state photodynamics of a molecular square containing four mutually coplanar porphyrins}, volume={63}, ISSN={["0022-3263"]}, DOI={10.1021/jo9803683}, abstractNote={To examine the effect of restricted porphyrin−porphyrin rotation on energy transfer in diphenylethyne-linked porphyrin arrays, a square macrocyclic array of four porphyrins has been prepared that locks the porphyrins in a mutually coplanar architecture. The palladium-mediated coupling of Zn(II) 5,10-dimesityl-15,20-bis(4-ethynylphenyl)porphyrin and 5,10-dimesityl-15,20-bis(4-iodophenyl)porphyrin afforded the molecular square (cyclo-Zn2Fb2U) with zinc (Zn) and free base (Fb) porphyrins on alternating corners. The yield of cyclo-Zn2Fb2U is relatively insensitive to concentration with reactants at 5−0.5 mM but declines significantly at ≤0.05 mM. Transient absorption data from cyclo-Zn2Fb2U in toluene at room temperature indicate that the rate of energy transfer from the photoexcited Zn porphyrin to a neighboring Fb porphyrin is (26 ps)-1. A ZnFb porphyrin (ZnFbU) with an identical diphenylethyne linker but no constraints on rotation exhibits an identical energy-transfer rate. Resonance Raman spectroscopy sho...}, number={15}, journal={JOURNAL OF ORGANIC CHEMISTRY}, author={Wagner, RW and Seth, J and Yang, SI and Kim, D and Bocian, DF and Holten, D and Lindsey, JS}, year={1998}, month={Jul}, pages={5042–5049} } @article{ravikanth_strachan_li_lindsey_1998, title={Trans-substituted porphyrin building blocks bearing iodo and ethynyl groups for applications in bioorganic and materials chemistry}, volume={54}, ISSN={["0040-4020"]}, DOI={10.1016/S0040-4020(98)00408-6}, abstractNote={The modular synthesis of linear or cyclic multiporphyrin arrays relies on the availability of trans-substituted porphyrin building blocks with high solubility in organic solvents. Eleven porphyrin building blocks were synthesized bearing iodo, ethynyl, and 2-(trimethylsilyl)ethynyl groups at the 4-, 3-, or 3,5-positions of two meso-aryl units, and mesityl groups at the other two meso-positions. The synthesis involves condensation of 5-mesityldipyrromethane with one or two aryl aldehydes. Combinations of functional groups include di-iodo, tetra-iodo, bis[(2-(trimethylsilyl)ethynyl], iodo and 2-(trimethylsilyl)ethynyl, and ethynyl and 2-(trimethylsilyl)ethynyl. In addition, a porphyrin bearing one 4-iodophenyl group and one 3,5-bis(boron-dipyrrin)phenyl group was synthesized for applications in molecular photonic devices. The iodo and ethynyl groups are ideally-suited for Pd-mediated coupling reactions, allowing the porphyrin building blocks to be joined in the systematic construction of soluble multiporphyrin arrays.}, number={27}, journal={TETRAHEDRON}, author={Ravikanth, M and Strachan, JP and Li, FR and Lindsey, JS}, year={1998}, month={Jul}, pages={7721–7734} } @article{li_yang_tyhonas_maccrum_lindsey_1997, title={Beneficial effects of salts on an acid-catalyzed condensation leading to porphyrin formation}, volume={53}, ISSN={["0040-4020"]}, DOI={10.1016/S0040-4020(97)00770-9}, abstractNote={Addition of one of a variety of salts to the room temperature, two-step, one flask reaction at 0.1 M forming tetraphenylporphyrin (TPP) gave yield increases of up to 2-fold. Among 21 insoluble salts, 12 gave increased yields, 6 had no effect, and 3 gave diminished yields. The salts that gave increases encompassed diverse cations but were restricted to the anions Cl−, Br−, I−, and Ph4B− while SO42−, F−, or BF4− did not give improved yields. All 7 soluble tetraalkylammonium or tetraphenylphosphonium salts (F−, Cl−, Ph4B−, PF6−, or HSO4− counterions) that were surveyed gave yield increases of > 1.5 fold. Thus a 10−1 M pyrrole-benzaldehyde condensation catalyzed with 10−2 M BF3·O(Et)2 in CH2Cl2 containing 0.1 equiv of NaCl (5.85 mg/10 mL CH2Cl2) or 0.0031 equiv of benzyltributylammonium chloride (Bu3BzlNCl) (based on [benzaldehyde]) gave ∼50% yield compared with ∼25% in the reaction without salt. The pyrrole-aldehyde condensation is much faster in the presence of salt, as measured by the rate of disappearance of benzaldehyde and the rate of formation of the porphyrin. Yield increases in the presence of salt were observed with catalysis by BF3·O(Et)2, BF3·2H2O, and CF3CO2H. Significant salt effects also were observed with BF3·O(Et)2 or CF3CO2H in the solvent diethyl ether, but the maximum yield was 15%. A survey of nine aldehydes showed yield improvements of up to 2-fold in six cases in the presence of salt. During the pyrrole-aldehyde reaction in CH2Cl2 either in the presence or absence of soluble salts, the medium becomes heterogeneous (measured by nephelometry). The addition of water to BF3·O(Et)2 in CH2Cl2 also yields a heterogeneous medium; in the presence of salt this medium affords twice the yield of porphyrin as that formed in the absence of salt. 11B NMR and 19F NMR experiments failed to unveil any new species formed by interaction of chloride-containing salts with BF3·O(Et)2. The complexity of the reaction medium, as well as insufficient information about the nature of the pyrrole-aldehyde condensation, preclude an assignment of mechanisms underlying the salt effects. However, a rank ordering of salts in the porphyrin reaction does not correlate with their desiccative power, and the generality of the salt effects is at odds with the selective anion templating of tetrapyrrolic macrocycles. Irreversible features of the pyrrole-aldehyde condensation have been identified via exchange experiments during the course of the reaction and 13C NMR labeling experiments. The improved reaction conditions can be used for preparative-scale syntheses, as 720 mg tetraphenylporphyrin (47% yield) was obtained from a 100 mL-scale reaction with 0.1 M reactants at room temperature.}, number={37}, journal={TETRAHEDRON}, author={Li, FR and Yang, KX and Tyhonas, JS and MacCrum, KA and Lindsey, JS}, year={1997}, month={Sep}, pages={12339–12360} } @misc{li_gentemann_kalsbeck_seth_lindsey_holten_bocian_1997, title={Effects of central metal ion (Mg, Zn) and solvent on singlet excited-state energy flow in porphyrin-based nanostructures}, volume={7}, ISSN={["1364-5501"]}, DOI={10.1039/a700146k}, abstractNote={Zinc porphyrins have been widely used as surrogates for chlorophyll (which contains magnesium) in photosynthetic model systems and molecular photonic devices. In order to compare the photodynamic behaviour of Mg- and Zn-porphyrins, dimeric and star-shaped pentameric arrays comprised of free-base (Fb) and Mg- or Zn-porphyrins with intervening diarylethyne linkers have been prepared. A modular building block approach is used to couple ethynyl- or iodo-substituted porphyrins in defined metallation states (Fb, Mg or Zn)via a Pd-catalysed reaction in 2–6 h. The resulting arrays are purified in 45–80% overall yields by combinations of size exclusion chromatography and adsorption chromatography (≥95% purity). High solubility of the arrays in organic solvents facilitates chemical and spectroscopic characterization. The star-shaped Mg 4 Fb- and Zn 4 Fb-pentamers, where the Fb-porphyrin is at the core of the array, have pairwise interactions similar to those of dimeric MgFb- and ZnFb-arrays. The arrays have been investigated by static and time-resolved absorption and fluorescence spectroscopy, as well as resonance Raman spectroscopy. The major findings include the following. (1) The rate of singlet excited-state energy transfer from the Mg-porphyrin to the Fb-porphyrin [(31 ps) -1 ] is comparable to that from the Zn-porphyrin to the Fb-porphyrin [(26 ps) -1 ] in the dimeric arrays. Qualitatively similar results are obtained for the star-shaped pentamers. The similar rates of energy transfer for the Mg- and Zn-containing arrays are attributed to the fact that the electronic coupling between the metalloporphyrin and Fb-porphyrin is approximately the same for Mg- vs. Zn-containing arrays. (2) The quantum yield of energy transfer is slightly higher in the Mg-arrays (99.7%) than in the Zn-arrays (99.0%) due to the longer inherent lifetime of Mg-porphyrins (10 ns) compared with Zn-porphyrins (2.5 ns). (3) The rate of energy transfer and the magnitude of the electronic coupling are essentially independent of the solvent polarity and the coordination geometry of the metalloporphyrin (four- or five-coordinate for Zn-porphyrins, five- or six-coordinate for Mg-porphyrins). (4) Polar solvents diminish the fluorescence yield and lifetime of the excited Fb-porphyrin in arrays containing either Mg- or Zn-porphyrins. These effects are attributed to charge-transfer quenching of the Fb-porphyrin by the adjacent metalloporphyrin rather than to changes in electronic coupling. The magnitude of the diminution is greater for the Mg-containing arrays, which is due to the greater driving force for charge separation. (5) The Zn-containing arrays are quite robust while the Mg-containing arrays are slightly labile toward demetallation and photooxidation. Taken together, these results indicate that porphyrin-based nanostructures having high energy-transfer efficiencies can be constructed from either Mg- or Zn-porphyrins. However, Mg-containing arrays may be superior in situations where a succession of energy-transfer steps occurs (due to a slightly higher yield per step) or where charge transfer is a desirable feature. On the other hand, Zn-porphyrins are better suited when it is desirable to avoid charge transfer quenching reactions. Accordingly, the merits of constructing a device from Mg- vs. Zn-containing porphyrins will be determined by the interplay of all of the above factors.}, number={7}, journal={JOURNAL OF MATERIALS CHEMISTRY}, author={Li, FR and Gentemann, S and Kalsbeck, WA and Seth, J and Lindsey, JS and Holten, D and Bocian, DF}, year={1997}, month={Jul}, pages={1245–1262} } @article{strachan_gentemann_seth_kalsbeck_lindsey_holten_bocian_1997, title={Effects of orbital ordering on electronic communication in multiporphyrin arrays}, volume={119}, ISSN={["0002-7863"]}, DOI={10.1021/ja971678q}, abstractNote={The rational design of molecular photonic devices requires a thorough understanding of all factors affecting electronic communication among the various constituents. To explore how electronic factors mediate both excited- and ground-state electronic communication in multiporphyrin arrays, we have conducted a detailed static spectroscopic (absorption, fluorescence, resonance Raman, electron paramagnetic resonance), time-resolved spectroscopic (absorption, fluorescence), and electrochemical (cyclic and square-wave voltammetry, coulometry) study of tetraarylporphyrin dimers. The complexes investigated include both zinc-free base (ZnFb) and bis-Zn dimers in which the porphyrin constituents are linked via diphenylethyne groups at the meso positions. Comparison of dimeric arrays containing pentafluorophenyl groups at all nonlinking meso positions (F30ZnFbU and F30Zn2U) with nonfluorinated analogs (ZnFbU and Zn2U) directly probes the effects of electronic factors on intradimer communication. The major findings o...}, number={46}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Strachan, JP and Gentemann, S and Seth, J and Kalsbeck, WA and Lindsey, JS and Holten, D and Bocian, DF}, year={1997}, month={Nov}, pages={11191–11201} } @article{wagner_johnson_lindsey_1997, title={Investigation of the one-flask synthesis of porphyrins bearing meso-linked straps of variable length, rigidity, and redox activity}, volume={53}, ISSN={["0040-4020"]}, DOI={10.1016/S0040-4020(97)00327-X}, abstractNote={The reactions of 18 dialdehydes have been examined in the two-step one-flask room temperature porphyrin synthesis. Efficient alkylation methods were established for the reaction of diols and diacids with m-bromomethylbenzaldehyde. Dialdehydes linked at the o,o′-or m,m′-positions were converted to strapped porphyrins in yields up to 25%, while the one p,p′-linked dialdehyde that was examined failed to give porphyrin. The resulting porphyrins bear straps joining adjacent meso-positions rather than across the face of the porphyrin. Dialdehydes incorporating rigid groups provided improved yields in some but not all cases. The yield of strapped porphyrin exhibited a maximum at 10−2 M reactant concentrations. The o,o′-strapped porphyrins exist as atropisomers that are sufficiently stable to interconversion at room temperature to be separable chromatographically. No atropisomers of m,m′-strapped porphyrins could be separated, though some could be observed by 1H NMR spectroscopy. For two different m,m′-strapped porphyrins, the ΔG‡ values for interconversion of the atropisomers were found to be 66 and 68 kJ/mol. The outer rings in these strapped porphyrins range in size from 14 to 24 atoms. Five porphyrins with bridging redox-active groups (ferrocene or anthraquinone) have been prepared in one-flask reactions, including a porphyrin bearing one ferrocene and one anthraquinone in straps across adjacent meta-substituted phenyl sites.}, number={20}, journal={TETRAHEDRON}, author={Wagner, RW and Johnson, TE and Lindsey, JS}, year={1997}, month={May}, pages={6755–6790} } @article{wagner_lindsey_1996, title={Boron-dipyrromethene dyes for incorporation in synthetic multi-pigment light-harvesting arrays}, volume={68}, ISSN={["0033-4545"]}, DOI={10.1351/pac199668071373}, abstractNote={Abstract}, number={7}, journal={PURE AND APPLIED CHEMISTRY}, author={Wagner, RW and Lindsey, JS}, year={1996}, month={Jul}, pages={1373–1380} } @misc{wagner_johnson_lindsey_1996, title={Soluble synthetic multiporphyrin arrays .1. Modular design and synthesis}, volume={118}, ISSN={["0002-7863"]}, DOI={10.1021/ja961611n}, abstractNote={A set of porphyrin building blocks has been developed for the construction of light-harvesting model compounds and related molecular photonic devices. The porphyrins are facially encumbered to enhance solubility in organic solvents, are employed in a defined metalation state (free base (Fb) or zinc chelate), and bear peripheral functional groups such as iodo or ethyne for joining the porphyrins via covalent bonds. The coupling of an iodophenylporphyrin and an ethynylphenylporphyrin via mild Pd-mediated reactions (2−4 mM of each porphyrin in toluene/triethylamine (5:1) with Pd2(dba)3 and AsPh3 at 35 °C for 2 h) yields the corresponding diphenylethyne-linked multiporphyrin array in 70−80% yield. The arrays are easily purified by a sequence of flash silica chromatography, preparative size exclusion chromatography, and gravity elution silica chromatography. The diphenylethyne linkers give a center-to-center separation of the porphyrins of ∼20 A. Model light-harvesting compounds are easily prepared using Zn an...}, number={45}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Wagner, RW and Johnson, TE and Lindsey, JS}, year={1996}, month={Nov}, pages={11166–11180} } @article{hsiao_krueger_wagner_johnson_delaney_mauzerall_fleming_lindsey_bocian_donohoe_1996, title={Soluble synthetic multiporphyrin arrays .2. Photodynamics of energy-transfer processes}, volume={118}, ISSN={["0002-7863"]}, DOI={10.1021/ja961612f}, abstractNote={Soluble ethyne-linked tetraarylporphyrin arrays that mimic natural light-harvesting complexes by absorbing light and directing excited-state energy have been investigated by static and time-resolved absorption and fluorescence spectroscopies. Of particular interest is the role of the diarylethyne linkers in mediating energy transfer. The major conclusions from this study, which is limited to the examination of arrays containing Zn and free-base (Fb) porphyrins, include the following:  (1) Singlet excited-state energy transfer from the Zn porphyrin to the Fb porphyrin is extremely efficient (95−99%). Competitive electron-transfer reactions are not observed. (2) The rate of energy transfer is slowed up to 4-fold by the addition of groups to the linker that limit the ability of the linker and porphyrin to adopt geometries tending toward coplanarity. Thus, the mechanism of energy transfer predominantly involves through-bond communication via the linker. Consistent with this notion, the measured lifetimes of t...}, number={45}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Hsiao, JS and Krueger, BP and Wagner, RW and Johnson, TE and Delaney, JK and Mauzerall, DC and Fleming, GR and Lindsey, JS and Bocian, DF and Donohoe, RJ}, year={1996}, month={Nov}, pages={11181–11193} }