TY - JOUR TI - Light-activated metal complexes that covalently modify DNA AU - Glazer, E.C. T2 - Israel Journal of Chemistry AB - Abstract Many drugs in current clinical use rely on mechanisms of action that involve damage to nucleic acids. While this has been a successful therapeutic approach for many years, the major limitation of these agents is systemic cytotoxicity, resulting from damage caused to healthy cells. Photoactive metal complexes offer the possibility of combining two successful treatment modalities for cancer and other diseases by providing DNA damage similar to that obtained with cisplatin, but in a spatially and temporally controlled manner, as with phototherapy. Recent progress in the field has provided metal complexes that can be triggered to create covalent adducts with nucleic acids both in vitro and in cells. Furthermore, several of these agents have been shown to induce cytotoxicity in cancer cell lines, in vitro tumor models, and in vivo animal models. In the last year, new compounds have been reported that can be activated with low energy light within the “therapeutic window,” where light penetration through tissue is sufficient to access larger volume tumors. This review highlights the advances that demonstrate the potential of light‐activated metal complexes as therapeutics and research tools for biomedical applications. DA - 2013/// PY - 2013/// DO - 10.1002/ijch.201300019 VL - 53 IS - 6-7 SP - 391-400 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84879501715&partnerID=MN8TOARS ER - TY - JOUR TI - Thiol-containing polymeric embedding materials for nanoskiving AU - Mays, R.L. AU - Pourhossein, P. AU - Savithri, D. AU - Genzer, J. AU - Chiechi, R.C. AU - Dickey, M.D. T2 - Journal of Materials Chemistry C AB - This paper describes the characterization of new embedding resins for nanoskiving (ultramicrotomy) that contain thiols. Nanoskiving is a technique to produce nanoscale structures using an ultramicrotome to section thin films of materials (e.g., gold) embedded in polymer. Epoxies are used typically as embedding resins for microtomy. Epoxies, however, do not adhere well to gold or other smooth metallic structures that are used commonly for nanoskiving. Thiol–ene and thiol–epoxy polymers provide improved adhesion to gold due to the thiol functional group. In addition, the thiol–ene polymers can be prepared within minutes using photopolymerization, which allows for rapid prototyping. Two commercial thiol-containing adhesives were evaluated as resins in addition to several formulations of commercially available monomers. The important physical and mechanical properties for microtomy of these unconventional embedding resins were characterized and the properties were compared to commercial epoxy resins. Gold nanowires were fabricated using nanoskiving of gold films embedded in these unconventional resins. These studies show that a 3 : 4 mixture of thiol (pentaerythritol tetra(3-mercaptopropionate)) and ene (triallyl-1,3,5-triazine-2,4,6-trione) works very well as a resin for nanoskiving and provides improved adhesion and reduced preparation time relative to epoxies. DA - 2013/// PY - 2013/// DO - 10.1039/c2tc00030j VL - 1 IS - 1 SP - 121-130 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84879924924&partnerID=MN8TOARS ER - TY - JOUR TI - Novel carbazole-phenothiazine dyads for dye-sensitized solar cells: A combined experimental and theoretical study AU - Marotta, G. AU - Reddy, M.A. AU - Singh, S.P. AU - Islam, A. AU - Han, L. AU - De Angelis, F. AU - Pastore, M. AU - Chandrasekharam, M. T2 - ACS Applied Materials and Interfaces AB - We report a joint experimental and computational work on new organic donor-acceptor dye sensitizers in which a carbazole (CZ) and a phenothiazine (PTZ) units are linked together by an alkyl C6H13, while two different anchoring groups are employed: the cyanoacrylic acid (CS1A, CSORG1) and the rhodanine-3-acetic acid (CS4A, CSORG4). The CZ moiety has multiple roles of (i) acting as an extra-electron donor portion, providing more electron density on the PTZ; (ii) suppressing the back-electron transfer from TiO2 to the electrolyte by forming a compact insulating dye layer; (iii) modulating dye aggregation on the semiconductor surface; and (iv) acting as an antenna, collecting photons and, through long-range energy transfer, redirecting the captured energy to the dye sensitizer. We show that the introduction of the CZ donor remarkably enhances the photovoltaic performances of the rhodanine-based dye, compared to the corresponding simple PTZ dye, with more than a two-fold increase in the overall efficiencies, while it does not bring beneficial effects in the case of the cyanoacrylic-based sensitizer. Based on quantum mechanical calculations and experimental measurements, we show that, in addition to a favored long-range energy transfer, which increases the light absorption in the blue region of the spectrum, the presence of the CZ unit in the CSORG4 dye effectively induces a beneficial aggregation pattern on the semiconductor surface, yielding a broadened and red-shifted light absorption, accounting for the two-fold increase in the generated photocurrent. DA - 2013/// PY - 2013/// DO - 10.1021/am402675q VL - 5 IS - 19 SP - 9635-9647 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84885442171&partnerID=MN8TOARS ER - TY - JOUR TI - Optical properties and aggregation of phenothiazine-based dye-sensitizers for solar cells applications: A combined experimental and computational investigation AU - Agrawal, S. AU - Pastore, M. AU - Marotta, G. AU - Reddy, M.A. AU - Chandrasekharam, M. AU - De Angelis, F. T2 - Journal of Physical Chemistry C AB - Combining computational modeling and experimental optical analyses, we investigate two prototypical phenothiazine-based organic solar cell sensitizers with the aim to understand the individual effects of solvation and aggregation on the dyes optical properties. Dye solvation and aggregation play a crucial role in determining the photoelectrochemical properties of these systems and the interplay of these two factors can lead to a misinterpretation of the underlying phenomenology due to their similar spectroscopic signals. In particular, upon adsorption of the dye onto the metal oxide surface, the dye UV–vis absorption spectrum may attain either a blue or a red shift compared to the dye in solution, which can either be originated from aggregation of surface-adsorbed dye and solvatochromism in the initial dye solution. Understanding the origin of these spectral changes along with their possible effect on charge-transfer properties is important for the further improvement of dye-sensitized solar cells. Based on our results, we show that the optical properties of phenothiazine-based dyes are much more sensitive to the type of explicit interactions with the solvent than to aggregation on the TiO2 surface. Therefore, this study gets new insights into the understanding of these properties and may assist the molecular engineering of new and more efficient dyes sensitizers. DA - 2013/// PY - 2013/// DO - 10.1021/jp4026305 VL - 117 IS - 19 SP - 9613-9622 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84878072118&partnerID=MN8TOARS ER - TY - JOUR TI - Synthesis and anticancer and antiviral activities of new 2-pyrazoline-substituted 4-thiazolidinones AU - Havrylyuk, D. AU - Zimenkovsky, B. AU - Vasylenko, O. AU - Lesyk, R. T2 - Journal of Heterocyclic Chemistry AB - 2‐(4,5‐Dihydropyrazol‐1‐yl)‐thiazol‐4‐ones ( 2–5 ) have been synthesized starting from 3‐phenyl‐5‐aryl‐1‐thiocarbamoyl‐2‐pyrazolines via [2+3]‐cyclization with 2‐bromopropionic acid, maleic anhydride, N ‐arylmaleimides, and aroylacrylic acids. The in vitro anticancer activity of 2a , 3a , 4a , 5b , and 5c were tested by the National Cancer Institute. Compounds 4a , 5b , and 5c demonstrated selective inhibition of leukemia cell lines growth at a single concentration (10 −5 M). The screening of antiviral activity for a broad panel of viruses revealed that N ‐(4‐methoxyphenyl)‐2‐{2‐[5‐(4‐methoxyphenyl)‐3‐phenyl‐4,5‐dihydropyrazol‐1‐yl]‐4‐oxo‐4,5‐dihydrothiazol‐5‐yl}‐acetamide 4a was highly active against Tacaribe TRVL 11 573 virus strain (EC 50 = 0.71 μg/mL, selectivity index = 130). DA - 2013/// PY - 2013/// DO - 10.1002/jhet.1056 VL - 50 IS - SUPPL.1 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84876947896&partnerID=MN8TOARS ER - TY - JOUR TI - Synthesis of 3S-substituted triazino[5,6-b]indoles and 4-thiazolidinone-triazino[5,6-b]indole hybrids with antitumor activity AU - Harkov, S. AU - Havrylyuk, D. AU - Lesyk, R. T2 - Chemistry and Chemical Technology DA - 2013/// PY - 2013/// VL - 7 IS - 4 SP - 381-389 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84897827225&partnerID=MN8TOARS ER - TY - JOUR TI - Synthesis and biological activity of isatines bearing thiazolidinone and pyrazoline moieties AU - Harkov, S. AU - Havrylyuk, D. AU - Atamanyuk, V. AU - Zimenkovsky, B. AU - Lesyk, R. T2 - Pharmacia DA - 2013/// PY - 2013/// VL - 60 IS - 1 SP - 8-18 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84888407984&partnerID=MN8TOARS ER - TY - JOUR TI - Synthesis and biological activity evaluation of 5-pyrazoline substituted 4-thiazolidinones AU - Havrylyuk, D. AU - Zimenkovsky, B. AU - Vasylenko, O. AU - Day, C.W. AU - Smee, D.F. AU - Grellier, P. AU - Lesyk, R. T2 - European Journal of Medicinal Chemistry AB - A series of novel 5-pyrazoline substituted 4-thiazolidinones have been synthesized. Target compounds were evaluated for their anticancer activity in vitro within DTP NCI protocol. Among the tested compounds, the derivatives 4d and 4f were found to be the most active, which demonstrated certain sensitivity profile toward the leukemia subpanel cell lines with GI₅₀ value ranges of 2.12-4.58 μM (4d) and 1.64-3.20 μM (4f). The screening of antitrypanosomal and antiviral activities of 5-(3-naphthalen-2-yl-5-aryl-4,5-dihydropyrazol-1-yl)-thiazolidine-2,4-diones was carried out with the promising influence of the mentioned compounds on Trypanosoma brucei, but minimal effect on SARS coronavirus and influenza types A and B viruses. DA - 2013/// PY - 2013/// DO - 10.1016/j.ejmech.2013.05.044 VL - 66 SP - 228-237 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84879470955&partnerID=MN8TOARS KW - Synthesis KW - Pyrazolines KW - 4-Thiazolidinones KW - Anticancer activity KW - Antitrypanosomal activity KW - Antiviral activity ER - TY - JOUR TI - Modern plastic solar cells: materials, mechanisms and modeling AU - Chiechi, Ryan C. AU - Havenith, Remco W.A. AU - Hummelen, Jan C. AU - Koster, L. Jan Anton AU - Loi, Maria A. T2 - Materials Today AB - We provide a short review of modern ‘plastic’ solar cells, a broad topic that spans materials science, physics, and chemistry. The aim of this review is to provide a primer for non-experts or researchers in related fields who are curious about this rapidly growing field of interdisciplinary research. We introduce the basic concepts of plastic solar cells and design rules for maximizing their efficiency, including modern quantum chemical calculations that can aide in the design of new materials. We discuss the history of the materials and modern trends in polymeric donor materials and fullerene acceptors, and provide demonstrative data from hybrid polymer/quantum dot devices. DA - 2013/7// PY - 2013/7// DO - 10.1016/j.mattod.2013.07.003 VL - 16 IS - 7-8 SP - 281-289 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84883180390&partnerID=MN8TOARS ER - TY - JOUR TI - Influence of an Atom in EGaIn/Ga 2 O 3 Tunneling Junctions Comprising Self-Assembled Monolayers AU - Fracasso, Davide AU - Muglali, Mutlu Iskender AU - Rohwerder, Michael AU - Terfort, Andreas AU - Chiechi, Ryan C. T2 - J. Phys. Chem. C AB - We compared the electrical properties of self-assembled monolayers (SAMs) formed on template-stripped Au from two homologous series of five different oligo(phenylene)s bearing alkane thiol tails. The terminal phenyl ring is substituted by a 4-pyridyl ring in one series, thus the two differ only by the substitution of C–H for N. We formed tunneling junctions using the liquid metal eutectic Ga–In (EGaIn) as a nondamaging, conformal top contact that is insensitive to functional groups and measured the current-density, J, tunneling decay constants, β, and transition voltages, Vtrans. Conductance measurements alone did not sufficiently differentiate the two series of molecules. The length dependences of the two series of SAMs produced values of β of 0.44 and 0.42 Å–1 for pyridyl- and phenyl-terminated SAMs, respectively, which lie between the expected values for alkanethiolates and oligo(phenylene)s. The values of Vtrans were ∼0.3 V larger for the phenyl-terminated SAMs than for the pyridyl-terminated SAMs. A comparison of the values of J to highest occupied molecular orbital (HOMO) levels determined by density functional theory (DFT) calculations revealed an odd–even effect for the phenyl-terminated SAMs but not the pyridyl-terminated SAMs. Plots of Vtrans versus the measured shift in work function, measured with a Kelvin probe, reveal a roughly linear trend. Plots of the difference between HOMO and Fermi energies reveal a strong linear trend with two distinct series that clearly differentiate the two series of SAMs, even between SAMs with nearly identical HOMO levels, but only when the dipole-induced shift in vacuum level is considered. The influence of the electronic properties of the SAMs is clearly evident in the conductance data and highlights the importance of molecular dipoles in tunneling junctions comprising SAMs. Taken together, the data show that tunneling junctions incorporating EGaIn as a top contact are sensitive enough to differentiate SAMs that differ by the substitution of a single atom. DA - 2013/5// PY - 2013/5// DO - 10.1021/jp401703p VL - 117 IS - 21 SP - 11367-11376 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84878352585&partnerID=MN8TOARS ER - TY - JOUR TI - Fabricating Nanogaps by Nanoskiving AU - Pourhossein, Parisa AU - Chiechi, Ryan C. T2 - JoVE AB - There are several methods of fabricating nanogaps with controlled spacings, but the precise control over the sub-nanometer spacing between two electrodes-and generating them in practical quantities-is still challenging. The preparation of nanogap electrodes using nanoskiving, which is a form of edge lithography, is a fast, simple and powerful technique. This method is an entirely mechanical process which does not include any photo- or electron-beam lithographic steps and does not require any special equipment or infrastructure such as clean rooms. Nanoskiving is used to fabricate electrically addressable nanogaps with control over all three dimensions; the smallest dimension of these structures is defined by the thickness of the sacrificial layer (Al or Ag) or self-assembled monolayers. These wires can be manually positioned by transporting them on drops of water and are directly electrically-addressable; no further lithography is required to connect them to an electrometer. DA - 2013/// PY - 2013/// DO - 10.3791/50406 IS - 75 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84901730347&partnerID=MN8TOARS KW - Chemistry KW - Issue 75 KW - Materials Science KW - Chemical Engineering KW - Electrical Engineering KW - Physics KW - Nanotechnology KW - nanodevices (electronic) KW - Nanoskiving KW - nanogaps KW - nanofabrication KW - molecular electronics KW - nanowires KW - fabrication KW - etching KW - ultramicrotome KW - scanning electron microscopy KW - SEM ER - TY - CONF TI - Quantum interference in EGaIn based tunneling junctions AU - Fracasso, Davide AU - Chiechi, Ryan C. A2 - Banerji, Natalie A2 - Silva, Carlos AB - In this report we discuss the great potential of Eutectic Gallium Indium (EGaIn) as conformal soft top electrode. EGaIn is a liquid eutectic supporting a skin (∼ 1 nm-thick) of self-limiting oxide Ga2O3 as a non-damaging, conformal top-contact. In the last half of decade EGaIn has been used by several group to form molecular junctions and study charge transport properties in self-assembled monolayer (SAMs). We compared the current density (J) versus applied bias (V) for three different self-assembled monolayers (SAMs) of ethynylthiophenol- functionalized anthracene derivatives with approximately the same thickness and diverse conjugation: linear- conjugation (AC), cross-conjugation (AQ), and broken-conjugation (AH) by using liquid eutectic Ga-In (EGaIn). This skin imparts non-Newtonian rheological properties that distinguish EGaIn from other top-contacts, however it may also have limited the maximum values of J observed for AC. We measure values of J for AH and AQ which are not significantly different (J ≈ 10-1 A/cm2 at V = 0.4 V). For AC, however, J is one (using log-averages) or two (using Gaussian mean) orders of magnitude higher than both AH and AQ. Our results are also in good qualitative agreement with gDFTB calculations on single AC, AQ, and AH molecules transport calculation, based on chemisorbed between Au contacts which predict currents, I, that are two orders of magnitude higher for AC than AH at 0 < |V| < 0.4 V. We ascribe these observations to quantum-interference effects. The agreement between the theoretical predictions on single-molecules and the measurements on SAMs suggest that molecule-molecule interactions do not play a significant role in the transport properties of AC, AQ, and AH. C2 - 2013/9/11/ C3 - Physical Chemistry of Interfaces and Nanomaterials XII DA - 2013/9/11/ DO - 10.1117/12.2026174 VL - 8811 SP - 88110U PB - SPIE-Intl Soc Optical Eng UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84889049610&partnerID=MN8TOARS KW - EGaIn KW - Tunneling Junctions KW - Quantum Interference KW - Conjugation ER - TY - JOUR TI - ChemInform Abstract: Enumeration of Isomers of Substituted Tetrapyrrole Macrocycles: From Classical Problems in Biology to Modern Combinatorial Libraries AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. T2 - ChemInform AB - Abstract Review: 232 refs. DA - 2013/7/11/ PY - 2013/7/11/ DO - 10.1002/chin.201331277 VL - 44 IS - 31 SP - no-no ER - TY - CONF TI - Paper-based single-walled carbon nanotube thin film for catalytic detection of nicotinamide adenine dinucleotide in human blood AU - Xiao, Y. AU - Dai, J.Y. AU - Paudyal, J. AU - Guntupalli, B. AU - Liang, P.P. AU - Pubillones, F. AU - Yang, Y.H. AU - Li, W.Z. AU - Wang, X.T T2 - 89th Florida Annual Meeting and Exposition C2 - 2013/// CY - Palm Harbor, FL DA - 2013/// PY - 2013/5/9/ ER - TY - CONF TI - Ambient filtration method to prepare paper-based electroactive nanoporous gold thin film for detection of dopamine and serotonin AU - Guntupalli, B. AU - Liang, P.P. AU - Dai, J.Y. AU - Yang, Y.H. AU - He, J. AU - Li, W.Z. AU - Xiao, Y. T2 - 89th Florida Annual Meeting and Exposition C2 - 2013/// CY - Palm Harbor, FL DA - 2013/// PY - 2013/5/9/ ER - TY - SOUND TI - Bringing biosensors to the bedside AU - Xiao, Y. DA - 2013/// PY - 2013/// M3 - Recruitment talk ER - TY - CONF TI - The North Carolina State University Mass Spectrometry Facility at the Cutting Edge of Scientific Research AU - Kandhi, V. AU - Williams, T. Islam T2 - Workshop on Allergy and Inflammation C2 - 2013/// CY - North Carolina State University, Raleigh, NC DA - 2013/// PY - 2013/// ER - TY - JOUR TI - Free energies of (Co, Fe, Ni, Zn) Fe 2 O 4 spinels and oxides in water at high temperatures and pressure from density functional theory: results for stoichiometric NiO and NiFe2O4surfaces AU - O’Brien, C J AU - Rák, Z AU - Brenner, D W T2 - Journal of Physics: Condensed Matter AB - A set of effective chemical potentials (ECPs) are derived that connect energies of (Co, Fe, Ni, Zn)Fe2O4 spinels and oxides calculated at 0 K from density functional theory (DFT) to free energies in high temperature and pressure water. The ECPs are derived and validated by solving a system of linear equations that combine DFT and experimental free energies for NiO, ZnO, Fe2O3, Fe3O4, FeO(OH), CoFe2O4, ZnFe2O4, NiFe2O4 and H2O. To connect to solution phase chemistry, a set of ECPs are also derived for solvated Ni(2+), Zn(2+), Fe(2+) and Fe(3+) ions using an analogous set of linear equations and the solid ECPs. The ECPs are used to calculate free energies of low index stoichiometric surfaces of nickel oxide (NiO) and nickel ferrite (NiFe2O4) in water as a function of temperature from 300 to 600 K at a pressure of 155 bar. Surface denuding at high temperatures is predicted, the implications of which for the formation of oxide corrosion products on heat transfer surfaces in light-water nuclear reactors are discussed. DA - 2013/10/8/ PY - 2013/10/8/ DO - 10.1088/0953-8984/25/44/445008 VL - 25 IS - 44 SP - 445008 SN - 0953-8984 1361-648X UR - http://dx.doi.org/10.1088/0953-8984/25/44/445008 ER - TY - JOUR TI - In Vitro Selection of Shape-Changing DNA Nanostructures Capable of Binding-Induced Cargo Release AU - Oh, Seung Soo AU - Plakos, Kory AU - Xiao, Yi AU - Eisenstein, Michael AU - Soh, H. Tom T2 - ACS Nano AB - Many biological systems employ allosteric regulatory mechanisms, which offer a powerful means of directly linking a specific binding event to a wide spectrum of molecular functionalities. There is considerable interest in generating synthetic allosteric regulators that can perform useful molecular functions for applications in diagnostics, imaging and targeted therapies, but generating such molecules through either rational design or directed evolution has proven exceptionally challenging. To address this need, we present an in vitro selection strategy for generating conformation-switching DNA nanostructures that selectively release a small-molecule payload in response to binding of a specific trigger molecule. As an exemplar, we have generated a DNA nanostructure that hybridizes with a separate 'cargo strand' containing an abasic site. This abasic site stably sequesters a fluorescent cargo molecule in an inactive state until the DNA nanostructure encounters an ATP trigger molecule. This ATP trigger causes the nanostructure to release the cargo strand, thereby liberating the fluorescent payload and generating a detectable fluorescent readout. Our DNA nanostructure is highly sensitive, with an EC50 of 30 μM, and highly specific, releasing its payload in response to ATP but not to other chemically similar nucleotide triphosphates. We believe that this selection approach could be generalized to generate synthetic nanostructures capable of selective and controlled release of other small-molecule cargos in response to a variety of triggers, for both research and clinical applications. DA - 2013/11/4/ PY - 2013/11/4/ DO - 10.1021/nn404079v VL - 7 IS - 11 SP - 9675-9683 J2 - ACS Nano LA - en OP - SN - 1936-0851 1936-086X UR - http://dx.doi.org/10.1021/nn404079v DB - Crossref KW - allostery KW - microfluidics KW - in vitro selection KW - functional aptamer KW - ATP KW - ATMND KW - structure-switching ER - TY - JOUR TI - Controlling the function of DNA nanostructures with specific trigger sequences AU - Deborggraeve, Stijn AU - Dai, Jian Yuan AU - Xiao, Yi AU - Soh, Hyongsok Tom T2 - Chem. Commun. AB - We report a hybridization-based switching mechanism with single-base specificity that can be readily integrated with functional DNA nanostructures. As an exemplar, we have developed a switchable DNAzyme (SDZ) that only becomes activated in the presence of a perfectly matched trigger sequence and operates effectively at room temperature. DA - 2013/// PY - 2013/// DO - 10.1039/c2cc36878a VL - 49 IS - 4 SP - 397-399 J2 - Chem. Commun. LA - en OP - SN - 1359-7345 1364-548X UR - http://dx.doi.org/10.1039/c2cc36878a DB - Crossref ER - TY - JOUR TI - Self-Assembled DNA Monolayer Buffered Dynamic Ranges of Mercuric Electrochemical Sensor AU - Lou, Xinhui AU - Zhao, Tao AU - Liu, Ran AU - Ma, Jie AU - Xiao, Yi T2 - Analytical Chemistry AB - Sensors with wide dynamic ranges (DRs) are typically constructed by utilizing a set of ligands with varied affinities for the same target. We report here a novel buffer self-assembled monolayer (BSAM) strategy, to fabricate sensors with extraordinarily broad DRs using a single recognition ligand. We demonstrated the concept of BSAM by constructing the electrochemical mercuric sensors with different surface probe densities (SPD) on a gold electrode. These sensors are based on the coordination of Hg(2+) with a pair of thymine (T) formed between the two proximate poly(T) oligonucleotides on the electrode surface and Hg(2+) binding induced DNA strand displacement of ferrocene tagged poly(A). There are three types of T-Hg(2+)-T coordination: those formed between (a) two poly(T) strands where none are hybridized with poly(A) strands, thus contributing zero effect on releasing the signaling probe, (b) poly(A)/poly(T) hybridized and nonhybridized poly(T) strands, resulting in the release of a signaling probe from the surface; and (c) two poly(A)/poly(T) hybridized strands, causing the release of two signaling probes from the surface. The DRs from 10 pM to 0.1 mM at varied SPDs were observed, attributing to the tunable Hg(2+) storage capability of the poly(T) SAM formed on the surface due to the coordination mechanism of (a) and (b). The DR was able to be further extended to 1 mM by using the longer poly(T) strands. The ready-to-use sensor exhibited great selectivity against the common interferential metal ions. As demonstrated, the BSAM strategy is a facile way to fabricate sensors with tunable and wide DRs. DA - 2013/7/24/ PY - 2013/7/24/ DO - 10.1021/ac401680c VL - 85 IS - 15 SP - 7574-7580 J2 - Anal. Chem. LA - en OP - SN - 0003-2700 1520-6882 UR - http://dx.doi.org/10.1021/ac401680c DB - Crossref ER - TY - CONF TI - Preliminary Photophysical Studies on Metal Complexes of Catecholate Nitronyl-Nitroxides: Exploring the Effects of Tunable Exchange Couplings on Charge-Separated Excited States AU - Shultz, D. T2 - International Symposium on the Photophysics and Photochemistry of Coordination Compounds C2 - 2013/// DA - 2013/// PY - 2013/7/9/ ER - TY - JOUR TI - Dynamics of the Striped Bass (Morone saxatilis) Ovary Proteome Reveal a Complex Network of the Translasome AU - Reading, Benjamin J. AU - Williams, Valerie N. AU - Chapman, Robert W. AU - Williams, Taufika Islam AU - Sullivan, Craig V. T2 - Journal of Proteome Research AB - We evaluated changes in the striped bass (Morone saxatilis) ovary proteome during the annual reproductive cycle using label-free quantitative mass spectrometry and a novel machine learning analysis based on K-means clustering and support vector machines. Modulated modularity clustering was used to group co-variable proteins into expression modules and Gene Ontology (GO) biological process and KEGG pathway enrichment analyses were conducted for proteins within those modules. We discovered that components of the ribosome along with translation initiation and elongation factors generally decrease as the annual ovarian cycle progresses toward ovulation, concomitant with a slight increase in components of the 26S-proteasome. Co-variation within more than one expression module of components from these two multi-protein complexes suggests that they are not only co-regulated, but that co-regulation occurs through more than one sub-network. These components also co-vary with subunits of the TCP-1 chaperonin system and enzymes of intermediary metabolic pathways, suggesting that protein folding and cellular bioenergetic state play important roles in protein synthesis and degradation. We provide further evidence to suggest that protein synthesis and degradation are intimately linked, and our results support function of a proteasome–ribosome supercomplex known as the translasome. DA - 2013/3/4/ PY - 2013/3/4/ DO - 10.1021/pr3010293 VL - 12 IS - 4 SP - 1691-1699 J2 - J. Proteome Res. LA - en OP - SN - 1535-3893 1535-3907 UR - http://dx.doi.org/10.1021/PR3010293 DB - Crossref KW - ribosome KW - proteasome KW - translasome KW - ovary KW - reproduction KW - mass-spectrometry KW - support vector machines KW - teleost KW - fish ER - TY - JOUR TI - Excitonic states in a (Ti6O12)3 nanotube AU - Papas, B. N. AU - Whitten, J. L. T2 - The Journal of Chemical Physics AB - The low-lying excited electronic states of a (Ti6O12)3 nanotube are investigated using ab initio self-consistent field configuration interaction theory. The transition energies and moments are calculated and the nature of the orbitals involved is discussed. Transitions correspond to an excitation from an O2p to a nearby Ti3d orbital and singlet-singlet transitions vary in excitation energy from 2.1 eV to 4.3 eV, depending on the oxygen site and environment of the titanium site. Two different structures for the three stacked Ti6O12 rings are found. The occluded Ti structure is lower in energy than a staggered structure by 1.25 eV, only 0.02 eV/bond. Excited electronic states are found to correspond to highly localized holes on oxygen and a highly localized electron in a d orbital on a nearest neighbor titanium. The staggered structure has four absorptions that lie within the intense portion of the solar spectrum, at 585 nm, 472 nm, 471 nm, 423 nm; the occluded structure has one strong absorption, at 532 nm. DA - 2013/2/7/ PY - 2013/2/7/ DO - 10.1063/1.4789815 VL - 138 IS - 5 SP - 054312 J2 - The Journal of Chemical Physics LA - en OP - SN - 0021-9606 1089-7690 UR - http://dx.doi.org/10.1063/1.4789815 DB - Crossref ER - TY - JOUR TI - Spectroscopic Detection of Medium Range Order in Hydrogenated Amorphous Silicon, a-Si(H): Applications in Photovolatics, Thin Film Transistors and Si-based Microelectronics AU - Lucovsky, G. AU - Parsons, G. AU - Zeller, D. AU - Wu, K. AU - Papas, B. AU - Whitten, J. AU - Lujan, R. AU - Street, R.A. T2 - Physics Procedia AB - Hydrogenated amorphous silicon, a-Si1-xHx, with ~ at.10% or x ~0.1±0.02, is used in photovoltaics (PV), and thin film transistors (TFT's). Amorphous Si (a-Si) thin films, thought to be free of H, are used as precursors for polycrystalline gate electrodes in microelectronics. PV and TFT alloys has been deposited by the glow discharge method (GD), remote plasma-enhanced chemical vapor deposition (RPECVD, and reactive magnetron sputtering (RMS) with bonded-H determined by deposition precursors and substrate temperatures. Two conditions are required for low Si dangling bond densities ~0.5 to 1x1016 cm−3: (i) a bonded monohydride, Si-H, concentration of ~10 at. % H, and (ii) a deposition, and/or a post-deposition anneal at ~240 °C to 300 °C. These reduce strain by introducing medium range order (MRO) as nano-meter scale aperiodically-assembled clusters. Si L2,3 X-ray absorption spectroscopy (XAS) has been used to confirm MRO extending beyond short-range order (SRO) of continuous random networks (CRN) through observation of ligand-field split d-state features. These are associated with symmetry-adapted linear combinations (SALCs) of atomic states forming molecular orbital valence bands. XAS and photoelectron spectroscopy (PES) studies have confirmed that a-Si used for microelectronic applications also has MRO as well. This is associated with a H-transfer reaction from an Si-H bond of the cluster into a Si-H-Si bonding arrangement on near-neighbor sites. MRO has also identified by other spectroscopic techniques: spectroscopic ellipsomentry (SE), and ultra-violet or X-ray photoemission spectroscopy (UPS or XPS). The same H-atom motion induced by absorption of sun-light is responsible for the Staebler-Wronski Effect (SWE); the generation of Si-atom dangling bonds that degrade PV performance. DA - 2013/// PY - 2013/// DO - 10.1016/j.phpro.2013.04.012 VL - 44 SP - 91-98 J2 - Physics Procedia LA - en OP - SN - 1875-3892 UR - http://dx.doi.org/10.1016/j.phpro.2013.04.012 DB - Crossref KW - hydrogenated amorphous Si KW - a-Si-H KW - photovoltaic applications KW - thin film transistors KW - fine grain polycrystalline Si KW - medium range order KW - ligand field splittings KW - X-ray absorption spectroscopy KW - photemission spectroscopy KW - Staebler-Wronski Effect ER - TY - JOUR TI - Temporal Analysis of theMagnaporthe OryzaeProteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation AU - Franck, William L. AU - Gokce, Emine AU - Oh, Yeonyee AU - Muddiman, David C. AU - Dean, Ralph A. T2 - Molecular & Cellular Proteomics AB - Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity. DA - 2013/5/12/ PY - 2013/5/12/ DO - 10.1074/MCP.M112.025874 VL - 12 IS - 8 SP - 2249-2265 J2 - Mol Cell Proteomics LA - en OP - SN - 1535-9476 1535-9484 UR - http://dx.doi.org/10.1074/MCP.M112.025874 DB - Crossref ER - TY - JOUR TI - Storage of Hydrogen Spin Polarization in Long-Lived 13 C 2 Singlet Order and Implications for Hyperpolarized Magnetic Resonance Imaging AU - Feng, Yesu AU - Theis, Thomas AU - Liang, Xiaofei AU - Wang, Qiu AU - Zhou, Pei AU - Warren, Warren S. T2 - J. Am. Chem. Soc. AB - Hyperpolarized magnetic resonance imaging (MRI) is a powerful technique enabling real-time monitoring of metabolites at concentration levels not accessible by standard MRI techniques. A considerable challenge this technique faces is the T1 decay of the hyperpolarization upon injection into the system under study. Here we show that AnA′nXX′ spin systems such as 13C2-1,2-diphenylacetylene (13C2-DPA) sustain long-lived polarization for both 13C and 1H spins with decay constants of almost 4.5 min at high magnetic fields of up to 16.44 T without spin-locking; the T1 of proton polarization is only 3.8 s. Therefore, storage of the proton polarization in a 13C2-singlet state causes a 69-fold extension of the spin lifetime. Notably, this extension is demonstrated with proton-only pulse sequences, which can be readily implemented on standard clinical scanners. DA - 2013/7/3/ PY - 2013/7/3/ DO - 10.1021/ja404936p VL - 135 IS - 26 SP - 9632-9635 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84879771142&partnerID=MN8TOARS ER - TY - JOUR TI - Multiplets at zero magnetic field: The geometry of zero-field NMR AU - Butler, Mark C. AU - Ledbetter, Micah P. AU - Theis, Thomas AU - Blanchard, John W. AU - Budker, Dmitry AU - Pines, Alexander T2 - J. Chem. Phys. AB - For liquid samples at Earth's field or below, nuclear-spin motion within scalar-coupled networks yields multiplets as a spectroscopic signature. In weak fields, the structure of the multiplets depends on the magnitude of the Zeeman interaction relative to the scalar couplings; in Earth's field, for example, heteronuclear couplings are truncated by fast precession at distinct Larmor frequencies. At zero field, weak scalar couplings are truncated by the relatively fast evolution associated with strong scalar couplings, and the truncated interactions can be described geometrically. When the spin system contains a strongly coupled subsystem A, an average over the fast evolution occurring within the subsystem projects each strongly coupled spin onto FA, the summed angular momentum of the spins in A. Weakly coupled spins effectively interact with FA, and the coupling constants for the truncated interactions are found by evaluating projections. We provide a formal description of zero-field spin systems with truncated scalar couplings while also emphasizing visualization based on a geometric model. The theoretical results are in good agreement with experimental spectra that exhibit second-order shifts and splittings. DA - 2013/// PY - 2013/// DO - 10.1063/1.4803144 VL - 138 IS - 18 SP - 184202 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84877988199&partnerID=MN8TOARS ER - TY - JOUR TI - High-Resolution Zero-Field NMR J -Spectroscopy of Aromatic Compounds AU - Blanchard, John W. AU - Ledbetter, Micah P. AU - Theis, Thomas AU - Butler, Mark C. AU - Budker, Dmitry AU - Pines, Alexander T2 - J. Am. Chem. Soc. AB - We report the acquisition and interpretation of nuclear magnetic resonance (NMR) J-spectra at zero magnetic field for a series of benzene derivatives, demonstrating the analytical capabilities of zero-field NMR. The zeroth-order spectral patterns do not overlap, which allows for straightforward determination of the spin interactions of substituent functional groups. Higher-order effects cause additional line splittings, revealing additional molecular information. We demonstrate resonance linewidths as narrow as 11 mHz, permitting resolution of minute frequency differences and precise determination of long-range J-couplings. The measurement of J-couplings with the high precision offered by zero-field NMR may allow further refinements in the determination of molecular structure and conformation. DA - 2013/3/6/ PY - 2013/3/6/ DO - 10.1021/ja312239v VL - 135 IS - 9 SP - 3607-3612 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84874926140&partnerID=MN8TOARS ER - TY - JOUR TI - Chemical analysis using J-coupling multiplets in zero-field NMR AU - Theis, Thomas AU - Blanchard, John W. AU - Butler, Mark C. AU - Ledbetter, Micah P. AU - Budker, Dmitry AU - Pines, Alexander T2 - Chemical Physics Letters AB - Zero-field nuclear magnetic resonance (NMR) spectroscopy is emerging as a new, potentially portable, and cost-effective NMR modality with the ability to provide information-rich, high-resolution spectra. We present simple rules for analysis of zero-field NMR spectra based on first-order perturbation theory and the addition of angular momenta. These rules allow for the prediction of observed spectral lines without numerical simulation. Results are presented for a few small organic molecules with characteristic spin topologies, demonstrating unambiguous assignment of peaks, highlighting the potential of zero-field NMR as a tool for chemical identification. DA - 2013/8// PY - 2013/8// DO - 10.1016/j.cplett.2013.06.042 VL - 580 SP - 160-165 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84880924575&partnerID=MN8TOARS ER - TY - JOUR TI - Parahydrogen-induced polarization at zero magnetic field AU - Butler, Mark C. AU - Kervern, Gwendal AU - Theis, Thomas AU - Ledbetter, Micah P. AU - Ganssle, Paul J. AU - Blanchard, John W. AU - Budker, Dmitry AU - Pines, Alexander T2 - J. Chem. Phys. AB - We use symmetry arguments and simple model systems to describe the conversion of the singlet state of parahydrogen into an oscillating sample magnetization at zero magnetic field. During an initial period of free evolution governed by the scalar-coupling Hamiltonian HJ, the singlet state is converted into scalar spin order involving spins throughout the molecule. A short dc pulse along the z axis rotates the transverse spin components of nuclear species I and S through different angles, converting a portion of the scalar order into vector order. The development of vector order can be described analytically by means of single-transition operators, and it is found to be maximal when the transverse components of I are rotated by an angle of ±π∕2 relative to those of S. A period of free evolution follows the pulse, during which the vector order evolves as a set of oscillating coherences. The imaginary parts of the coherences represent spin order that is not directly detectable, while the real parts can be identified with oscillations in the z component of the molecular spin dipole. The dipole oscillations are due to a periodic exchange between Iz and Sz, which have different gyromagnetic ratios. The frequency components of the resulting spectrum are imaginary, since the pulse cannot directly induce magnetization in the sample; it is only during the evolution under HJ that the vector order present at the end of the pulse evolves into detectable magnetization. DA - 2013/// PY - 2013/// DO - 10.1063/1.4805062 VL - 138 IS - 23 SP - 234201 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84884502649&partnerID=MN8TOARS ER - TY - JOUR TI - Fundamental Aspects of Parahydrogen Enhanced Low-Field Nuclear Magnetic Resonance AU - Colell, Johannes AU - Türschmann, Pierre AU - Glöggler, Stefan AU - Schleker, Philipp AU - Theis, Thomas AU - Ledbetter, Micah AU - Budker, Dmitry AU - Pines, Alexander AU - Blümich, Bernhard AU - Appelt, Stephan T2 - Phys. Rev. Lett. AB - We report new phenomena in low-field $^{1}\mathrm{H}$ nuclear magnetic resonance (NMR) spectroscopy using parahydrogen induced polarization (PHIP), enabling determination of chemical shift differences, $\ensuremath{\delta}\ensuremath{\nu}$, and the scalar coupling constant $J$. NMR experiments performed with thermal polarization in millitesla magnetic fields do not allow the determination of scalar coupling constants for homonuclear coupled spins in the inverse weak coupling regime ($\ensuremath{\delta}\ensuremath{\nu}<J$). We show here that low-field PHIP experiments in the inverse weak coupling regime enable the precise determination of $\ensuremath{\delta}\ensuremath{\nu}$ and $J$. Furthermore we experimentally prove that observed splittings are related to $\ensuremath{\delta}\ensuremath{\nu}$ in a nonlinear way. Naturally abundant $^{13}\mathrm{C}$ and $^{29}\mathrm{Si}$ isotopes lead to heteronuclear $J$-coupled $^{1}\mathrm{H}$-multiplet lines with amplitudes significantly enhanced compared to the amplitudes for thermally prepolarized spins. PHIP-enhanced NMR in the millitesla regime allows us to measure characteristic NMR parameters in a single scan using samples containing rare spins in natural abundance. DA - 2013/3// PY - 2013/3// DO - 10.1103/physrevlett.110.137602 VL - 110 IS - 13 UR - http://dx.doi.org/10.1103/physrevlett.110.137602 ER - TY - JOUR TI - Reaction of HppE with Substrate Analogues: Evidence for Carbon–Phosphorus Bond Cleavage by a Carbocation Rearrangement AU - Chang, Wei-chen AU - Mansoorabadi, Steven O. AU - Liu, Hung-wen T2 - Journal of the American Chemical Society AB - (S)-2-Hydroxypropylphosphonic acid ((S)-2-HPP) epoxidase (HppE) is an unusual mononuclear non-heme iron enzyme that catalyzes the oxidative epoxidation of (S)-2-HPP in the biosynthesis of the antibiotic fosfomycin. Recently, HppE has been shown to accept (R)-1-hydroxypropylphosphonic acid as a substrate and convert it to an aldehyde product in a reaction involving a biologically unprecedented 1,2-phosphono migration. In this study, a series of substrate analogues were designed, synthesized, and used as mechanistic probes to study this novel enzymatic transformation. The resulting data, together with insights obtained from density functional theory calculations, are consistent with a mechanism of HppE-catalyzed phosphono group migration that involves the formation of a carbocation intermediate. As such, this reaction represents a new paradigm for biological C–P bond cleavage. DA - 2013/5/23/ PY - 2013/5/23/ DO - 10.1021/ja403441x VL - 135 IS - 22 SP - 8153-8156 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/JA403441X DB - Crossref ER - TY - JOUR TI - Substrate-Triggered Addition of Dioxygen to the Diferrous Cofactor of Aldehyde-Deformylating Oxygenase to Form a Diferric-Peroxide Intermediate AU - Pandelia, Maria E. AU - Li, Ning AU - Nørgaard, Hanne AU - Warui, Douglas M. AU - Rajakovich, Lauren J. AU - Chang, Wei-chen AU - Booker, Squire J. AU - Krebs, Carsten AU - Bollinger, J. Martin, Jr. T2 - Journal of the American Chemical Society AB - Cyanobacterial aldehyde-deformylating oxygenases (ADOs) belong to the ferritin-like diiron-carboxylate superfamily of dioxygen-activating proteins. They catalyze conversion of saturated or monounsaturated Cn fatty aldehydes to formate and the corresponding Cn–1 alkanes or alkenes, respectively. This unusual, apparently redox-neutral transformation actually requires four electrons per turnover to reduce the O2 cosubstrate to the oxidation state of water and incorporates one O-atom from O2 into the formate coproduct. We show here that the complex of the diiron(II/II) form of ADO from Nostoc punctiforme (Np) with an aldehyde substrate reacts with O2 to form a colored intermediate with spectroscopic properties suggestive of a Fe2III/III complex with a bound peroxide. Its Mössbauer spectra reveal that the intermediate possesses an antiferromagnetically (AF) coupled Fe2III/III center with resolved subsites. The intermediate is long-lived in the absence of a reducing system, decaying slowly (t1/2 ∼ 400 s at 5 °C) to produce a very modest yield of formate (<0.15 enzyme equivalents), but reacts rapidly with the fully reduced form of 1-methoxy-5-methylphenazinium methylsulfate (MeOPMS) to yield product, albeit at only ∼50% of the maximum theoretical yield (owing to competition from one or more unproductive pathway). The results represent the most definitive evidence to date that ADO can use a diiron cofactor (rather than a homo- or heterodinuclear cluster involving another transition metal) and provide support for a mechanism involving attack on the carbonyl of the bound substrate by the reduced O2 moiety to form a Fe2III/III-peroxyhemiacetal complex, which undergoes reductive O–O-bond cleavage, leading to C1–C2 radical fragmentation and formation of the alk(a/e)ne and formate products. DA - 2013/10/9/ PY - 2013/10/9/ DO - 10.1021/ja405047b VL - 135 IS - 42 SP - 15801-15812 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/JA405047B DB - Crossref ER - TY - JOUR TI - Mechanistic studies of an unprecedented enzyme-catalysed 1,2-phosphono-migration reaction AU - Chang, Wei-chen AU - Dey, Mishtu AU - Liu, Pinghua AU - Mansoorabadi, Steven O. AU - Moon, Sung-Ju AU - Zhao, Zongbao K. AU - Drennan, Catherine L. AU - Liu, Hung-wen T2 - Nature AB - (S)-2-hydroxypropylphosphonate ((S)-2-HPP) epoxidase (HppE) is a mononuclear non-haem-iron-dependent enzyme responsible for the final step in the biosynthesis of the clinically useful antibiotic fosfomycin. Enzymes of this class typically catalyse oxygenation reactions that proceed via the formation of substrate radical intermediates. By contrast, HppE catalyses an unusual dehydrogenation reaction while converting the secondary alcohol of (S)-2-HPP to the epoxide ring of fosfomycin. Here we show that HppE also catalyses a biologically unprecedented 1,2-phosphono migration with the alternative substrate (R)-1-HPP. This transformation probably involves an intermediary carbocation, based on observations with additional substrate analogues, such as (1R)-1-hydroxyl-2-aminopropylphosphonate, and model reactions for both radical- and carbocation-mediated migration. The ability of HppE to catalyse distinct reactions depending on the regio- and stereochemical properties of the substrate is given a structural basis using X-ray crystallography. These results provide compelling evidence for the formation of a substrate-derived cation intermediate in the catalytic cycle of a mononuclear non-haem-iron-dependent enzyme. The underlying chemistry of this unusual phosphono migration may represent a new paradigm for the in vivo construction of phosphonate-containing natural products that can be exploited for the preparation of new phosphonate derivatives. DA - 2013/4// PY - 2013/4// DO - 10.1038/nature11998 VL - 496 IS - 7443 SP - 114-118 J2 - Nature LA - en OP - SN - 0028-0836 1476-4687 UR - http://dx.doi.org/10.1038/NATURE11998 DB - Crossref ER - TY - JOUR TI - Evidence that the fosfomycin-producing epoxidase, HppE, is a non-heme-iron peroxidase T2 - Science AB - The iron-dependent epoxidase HppE converts (S)-2-hydroxypropyl-1-phosphonate (S-HPP) to the antibiotic fosfomycin [(1R,2S)-epoxypropylphosphonate] in an unusual 1,3-dehydrogenation of a secondary alcohol to an epoxide. HppE has been classified as an oxidase, with proposed mechanisms differing primarily in the identity of the O2-derived iron complex that abstracts hydrogen (H•) from C1 of S-HPP to initiate epoxide ring closure. We show here that the preferred cosubstrate is actually H2O2 and that HppE therefore almost certainly uses an iron(IV)-oxo complex as the H• abstractor. Reaction with H2O2 is accelerated by bound substrate and produces fosfomycin catalytically with a stoichiometry of unity. The ability of catalase to suppress the HppE activity previously attributed to its direct utilization of O2 implies that reduction of O2 and utilization of the resultant H2O2 were actually operant. DA - 2013/// PY - 2013/// DO - 10.1126/science.1240373 VL - 342 IS - 6161 SP - 991-995 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84888026754&partnerID=MN8TOARS ER - TY - BOOK TI - Methylerythritol phosphate pathway of isoprenoid biosynthesis AU - Zhao, L. AU - Chang, W.-C. AU - Xiao, Y. AU - Liu, H.-W. AU - Liu, P. AB - Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway–based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations. DA - 2013/// PY - 2013/// DO - 10.1146/annurev-biochem-052010-100934 VL - 82 SE - 497-530 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84878950920&partnerID=MN8TOARS KW - isoprenoids KW - biosynthesis KW - enzyme mechanism KW - metabolic engineering KW - synthetic biology KW - methylerythritol phosphate pathway KW - mevalonic acid pathway KW - MVA KW - MEP ER - TY - JOUR TI - Current development in isoprenoid precursor biosynthesis and regulation AU - Chang, Wei-chen AU - Song, Heng AU - Liu, Hung-wen AU - Liu, Pinghua T2 - Current Opinion in Chemical Biology AB - Isoprenoids are one of the largest classes of natural products and all of them are constructed from two precursors, isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). For decades, the mevalonic acid (MVA) pathway was proposed to be the only IPP and DMAPP biosynthetic pathway. This review summarizes the newly discovered IPP and DMAPP production pathways since late 1990s, their distribution among different kingdoms, and their roles in secondary metabolite production. These new IPP and DMAPP production pathways include the methylerythritol phosphate (MEP) pathway, a modified MVA pathway, and the 5-methylthioadenosine shunt pathway. Relative to the studies on the MVA pathway, information on the MEP pathway regulation is limited and the mechanistic details of several of its novel transformations remain to be addressed. Current status on both MEP pathway regulation and mechanistic issues is also presented. DA - 2013/8// PY - 2013/8// DO - 10.1016/j.cbpa.2013.06.020 VL - 17 IS - 4 SP - 571-579 J2 - Current Opinion in Chemical Biology LA - en OP - SN - 1367-5931 UR - http://dx.doi.org/10.1016/J.CBPA.2013.06.020 DB - Crossref ER - TY - JOUR TI - Development and Characterization of a Novel Plug and Play Liquid Chromatography-Mass Spectrometry (LC-MS) Source That Automates Connections between the Capillary Trap, Column, and Emitter AU - Bereman, Michael S. AU - Hsieh, Edward J. AU - Corso, Thomas N. AU - Van Pelt, Colleen K. AU - MacCoss, Michael J. T2 - Molecular & Cellular Proteomics AB - We report the development and characterization of a novel, vendor-neutral ultra-high pressure-compatible (~10,000 p.s.i.) LC-MS source. This device is the first to make automated connections with user-packed capillary traps, columns, and capillary emitters. The source uses plastic rectangular inserts (referred to here as cartridges) where individual components (i.e. trap, column, or emitter) can be exchanged independent of one another in a plug and play manner. Automated robotic connections are made between the three cartridges using linear translation powered by stepper motors to axially compress each cartridge by applying a well controlled constant compression force to each commercial LC fitting. The user has the versatility to tailor the separation (e.g. the length of the column, type of stationary phase, and mode of separation) to the experimental design of interest in a cost-effective manner. The source is described in detail, and several experiments are performed to evaluate the robustness of both the system and the exchange of the individual trap and emitter cartridges. The standard deviation in the retention time of four targeted peptides from a standard digest interlaced with a soluble Caenorhabditis elegans lysate ranged between 3.1 and 5.3 s over 3 days of analyses. Exchange of the emitter cartridge was found to have an insignificant effect on the abundance of various peptides. In addition, the trap cartridge can be replaced with minimal effects on retention time (<20 s). DA - 2013/2/19/ PY - 2013/2/19/ DO - 10.1074/MCP.O112.024893 VL - 12 IS - 6 SP - 1701-1708 J2 - Mol Cell Proteomics LA - en OP - SN - 1535-9476 1535-9484 UR - http://dx.doi.org/10.1074/MCP.O112.024893 DB - Crossref ER - TY - JOUR TI - Crystals: The Formation of Pd Nanocrystals from Pd2(dba)3Microcrystals (Part. Part. Syst. Charact. 3/2013) AU - Chung, Sungwook AU - Leonard, Donovan N. AU - Altoe, Virginia AU - Aloni, Shaul AU - De Yoreo, James J. AU - Franzen, Stefan T2 - Particle & Particle Systems Characterization AB - The image shows hexagonal Pd nanocrystals formed from hexagonal Pd2(dba)3 microcrystals. As-grown hexagonal platelets formed from a Pd2(dba)3 precursor are shown to be disordered microcrystals containing 1–2 nm Pd clusters, which grow and transform into Pd nanocrystals under an electron beam or through thermal annealing. In-depth investigation of the crystal structure and transformation process are presented by James J. De Yoreo, Stefan Franzen and co-workers on page 280. DA - 2013/3// PY - 2013/3// DO - 10.1002/PPSC.201370010 VL - 30 IS - 3 SP - 298-298 J2 - Particle Particle Systems Characterization LA - en OP - SN - 0934-0866 UR - http://dx.doi.org/10.1002/PPSC.201370010 DB - Crossref ER - TY - JOUR TI - The Formation of Pd Nanocrystals from Pd2(dba)3Microcrystals AU - Chung, Sungwook AU - Leonard, Donovan N. AU - Altoe, Virginia AU - Aloni, Shaul AU - De Yoreo, James J. AU - Franzen, Stefan T2 - Particle & Particle Systems Characterization AB - As‐grown platelets formed from tris‐(dibenzylideneacetone) dipalladium(0) [Pd 2 (dba) 3 ] precursor in the presence of Pd17 RNA are investigated before and after thermal annealing. Results show that as‐grown platelets are disordered crystals of Pd 2 (dba) 3 containing 1−2 nm Pd clusters and platelets grown in the absence of RNA are morphologically and structurally similar to those formed with RNA. The initially formed crystals are so sensitive to environmental variables that the degree of crystallinity can not be determined accurately by electron diffraction. X‐ray crystallography on as‐grown platelets gives a crystal structure consistent with Pd 2 (dba) 3 , but reveals a composition of ≈Pd 1.07 (dba) 3 , indicating one Pd atom in Pd 2 (dba) 3 is lost from the structure. Both electron beam and thermally induced decomposition of as‐grown Pd 2 (dba) 3 platelets having a hexagonal habit on the micrometer scale produces elemental Pd platelets having a hexagonal habit on the nanometer scale. These hexagonal platelets are composed of a partially sparse form of Pd 2 (dba) 3 that is initially crystalline but rapidly degrades due to the loss of Pd atoms from organic ligand cages. Once released, Pd atoms aggregate to form Pd clusters, which grow and transform into well‐formed Pd nanocrystals under electron‐beam irradiation or through thermal annealing. DA - 2013/2/7/ PY - 2013/2/7/ DO - 10.1002/ppsc.201200114 VL - 30 IS - 3 SP - 280-286 J2 - Particle Particle Systems Characterization LA - en OP - SN - 0934-0866 UR - http://dx.doi.org/10.1002/ppsc.201200114 DB - Crossref KW - palladium KW - microcrystals KW - nanocrystals KW - transmission electron microscopy KW - thermal annealing ER - TY - CHAP TI - Reprogramming the Biosynthesis of Natural Products by Directed Evolution AU - Williams, Gavin AU - Koryakina, Irina AU - McArthur, John AU - Draelos, Matthew AU - Randal, Shan AU - Muddimanl, David T2 - Developments in Biotechnology and Bioprocessing A2 - Kantardjieff, Anne A2 - Asuri, Prashanth A2 - Coffman, Jonathan L. A2 - Jayapal, Karthik T3 - ACS Symposium Series AB - Directed evolution is a powerful biochemical tool used to alter the function and properties of enzymes. Modification of the activity of key enzymes responsible for the biosynthesis of complex, biologically active natural products may provide routes to increase the diversity of natural products or generate novel and more potent analogues. Here we describe our combined efforts aimed to utilize and improve upon combinatorial biosynthesis techniques to reprogram the biosynthesis of polyketide natural products. We describe a synthetic biology approach that uses directed enzyme evolution to broaden the substrate specificities of enzymes used in natural product biosynthesis. These engineered mutant enzymes will be used to construct artificial biosynthetic pathways for the synthesis and installation of a broad array of natural and non-natural building blocks into polyketides. PY - 2013/1// DO - 10.1021/bk-2013-1125.ch009 SP - 147–163 PB - American Chemical Society SN - 0841229104 0841229112 SV - 1125 UR - http://dx.doi.org/10.1021/bk-2013-1125.ch009 ER - TY - JOUR TI - Bis[N-alkyl-NN-di(2-pyridylmethyl)amine]zinc(II) perchlorates display cis-facial stereochemistry in solid state and solution AU - Simmons, J. Tyler AU - Yuan, Zhao AU - Daykin, Kirsten L. AU - Nguyen, Brian T. AU - Clark, Ronald J. AU - Shatruk, Michael AU - Zhu, Lei T2 - Supramolecular Chemistry AB - N-Alkyl-N,N-di(2-pyridylmethyl)amines are ligands commonly used by supramolecular chemists in molecular recognition and sensing applications. The metal coordination complexes of these ligands, in particular those with 2:1 (ligand:metal) molar ratio, have not been sufficiently characterised in solution. In this work, bis[N-alkyl-N,N-di(2-pyridylmethyl)amine]zinc(II) perchlorates are characterised in both solid and solution phases, using X-ray crystallography and NMR spectroscopy, respectively. Only the cis-facial stereoisomer is observed. Density functional theory calculations support the thermodynamic preference for this stereochemistry, as in one representative case the gas phase energy of the cis-facial configuration is lower than those of the trans-facial and meridional configurations by 4.0 and 4.5 kcal/mol, respectively. DA - 2013/11/12/ PY - 2013/11/12/ DO - 10.1080/10610278.2013.844816 VL - 26 IS - 3-4 SP - 214-222 J2 - Supramolecular Chemistry LA - en OP - SN - 1061-0278 1029-0478 UR - http://dx.doi.org/10.1080/10610278.2013.844816 DB - Crossref KW - cis-facial KW - di(2-pyridylmethyl)amine KW - zinc KW - HMBC KW - DFT ER - TY - RPRT TI - LOW POWER UPCONVERSION FOR SOLAR FUELS PHOTOCHEMISTRY AU - Castellano, Felix A3 - Office of Scientific and Technical Information (OSTI) AB - Earth abundant copper(I) diimine complexes represent a renewable and economically feasible alternative to commonly used heavy metal containing chromophores. In the metal-to-ligand charge transfer (MLCT) excited state, copper(I) diimine complexes typically undergo a significant structural rearrangement, leading to molecules with large Stokes shifts and very short excited state lifetimes, thereby limiting their usefulness as sensitizers in bimolecular electron and triplet energy transfer reactions. Strategically placed bulky substituents on the coordinating phenanthroline ligands have proven useful in restricting the transiently produced excited state Jahn-Teller distortion, leading to longer-lived excited states. By combining bulky sec-butyl groups in the 2- and 9- positions with methyl groups in the 3-,4-, 7-, and 8- positions, a remarkably long-lived (2.8 μs in DCM) copper(I) bis-phenanthroline complex, [Cu(dsbtmp)2]+, has been synthesized and characterized. Unlike other copper(I) diimine complexes, [Cu(dsbtmp)2]+ also retains a μs lifetime in coordinating solvents such as acetonitrile and water as a result of the cooperative sterics inherent in the molecular design. Preliminary results on the use of this complex in hydrogen-forming homogeneous photocatalysis is presented. Photon upconversion based on sensitized triplet-triplet annihilation (TTA) represents a photochemical means to generate high-energy photons (or high-energy chemical products) from low-energy excitation, having potential applications in solar energy conversion and solar fuels producing devices. For the first time, synthetically facile and earth abundant Cu(I) MLCT sensitizers have been successfully incorporated into two distinct photochemical upconversion schemes, affording both red-to-green and orange-to-blue wavelength conversions. Preliminary results on aqueous-based photochemical upconversion as well as intramolecular Sn(IV) porphyrins containing axially coordinated aromatic hydrocarbon chromophores poised for upconversion photochemistry are also presented. DA - 2013/8/5/ PY - 2013/8/5/ DO - 10.2172/1089302 PB - Office of Scientific and Technical Information (OSTI) ER - TY - CHAP TI - Stereoselective Formation of Amines by Nucleophilic Addition to Azomethine Derivatives T2 - Stereoselective Formation of Amines AB - This chapter describes state-of-the-art methods to prepare α-chiral amines by the addition of nonstabilized nucleophiles to imine derivatives. The first part of the chapter illustrates the most effective diastereoselective addition reaction (substrate controlled and chiral auxiliary based methods) whereas the second part focuses on catalytic asymmetric methods. PY - 2013/// DO - 10.1007/128_2013_492 UR - http://dx.doi.org/10.1007/128_2013_492 KW - Azomethine KW - Chiral amines KW - Chiral auxiliaries KW - Chiral catalysts KW - Chiral ligands KW - Nucleophilic addition ER - TY - ENCYC TI - α-Diazo-4-methoxy-β-oxobenzenepropanenitrile T2 - Encyclopedia of Reagents for Organic Synthesis AB - [126893-72-9] C10H7N3O2 (MW 201.18) InChI = 1S/C10H7N3O2/c1-15-8-4-2-7(3-5-8)10(14)9(6-11)13-12/h2-5H,1H3 InChIKey = SSRJRWKNAOEFFT-UHFFFAOYSA-N (used as a carbene precursor for Rh(II)-catalyzed cyclopropanation of alkenes to form α-cyano-cyclopropylketones, and for the formation of 5-halo-1,2,3-triazoles) Alternative Name: none. Physical Data: mp 62 °C, yellow solid. Solubility: soluble in CH2Cl2, CHCl3, THF, DMF, MeCN. Slightly soluble in Et2O. Form Supplied in: not commercially available. Purification: silica gel chromatography, using 80% CHCl3 in hexane as eluent. Handling, Storage, and Precautions: the compound is potentially explosive and should be stored neat at −20 °C, at which it is stable for at least 12 months. DA - 2013/4/22/ PY - 2013/4/22/ DO - 10.1002/047084289x.rn01541 UR - http://dx.doi.org/10.1002/047084289x.rn01541 ER - TY - JOUR TI - Stereoselective Rh2 (S-IBAZ) 4-Catalyzed Cyclopropanation of Alkenes, Alkynes, and Allenes: Asymmetric Synthesis of Diacceptor Cyclopropylphosphonates and Alkylidenecyclopropanes AU - Lindsay, Vincent N. G. AU - Fiset, Dominic AU - Gritsch, Philipp J. AU - Azzi, Soula AU - Charette, André B. T2 - Journal of the American Chemical Society AB - A mild and highly stereoselective rhodium(II)-catalyzed cyclopropanation of alkenes, alkynes, and allenes with diacceptor diazo compounds is reported. Using the phosphonate moiety as an efficient trans-directing group, the first catalytic asymmetric route to diacceptor cycloprop(en)ylphosphonates was developed by employing an α-cyano diazophosphonate and Rh2(S-IBAZ)4 as chiral catalyst. The isosteric character of phosphonic and carboxylic acid derivatives allowed the alternative use of an α-cyano diazo ester in the process, leading to α-cyano cycloprop(en)ylcarboxylates in high yields and stereoselectivities. Taking advantage of the particular reactivity of the cyanocarbene intermediates involved in this system, the scope of compatible substrates could be extended to substituted allenes, leading to the development of the first catalytic enantioselective method for the synthesis of diacceptor alkylidenecyclopropanes. DA - 2013/1/15/ PY - 2013/1/15/ DO - 10.1021/ja3099728 VL - 135 IS - 4 SP - 1463–1470 SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja3099728 ER - TY - ENCYC TI - Methyl α-diazo-4-methoxy-β-oxo-benzenepropanoate T2 - Encyclopedia of Reagents for Organic Synthesis AB - [1198573-66-8] C11H10N2O4 (MW 234.21) InChI = 1S/C11H10N2O4/c1-16-8-5-3-7(4-6-8)10(14)9(13-12)11(15)17-2/h3-6H,1-2H3 InChIKey = VNNIUPQLCJJRGZ-UHFFFAOYSA-N (used as a carbene precursor for Rh(II)-catalyzed cyclopropanation of alkenes to form β-keto-cyclopropanecarboxylates, and for the formation of 2-aminofurans via a carbenoid-mediated formal [3+2] cycloaddition with enamines) Alternative Name: none. Physical Data: yellow oil. Solubility: soluble in most organic solvents. Form Supplied in: not commercially available. Purification: silica gel chromatography, using 25% EtOAc in hexane as eluent. Handling, Storage, and Precautions: potentially explosive compound. The title compound should be stored neat at −20 °C, at which temperature it is stable for at least 12 months. DA - 2013/4/22/ PY - 2013/4/22/ DO - 10.1002/047084289x.rn01540 UR - http://dx.doi.org/10.1002/047084289x.rn01540 ER - TY - ENCYC TI - 2-Diazo-1-(4-methoxyphenyl)-2-nitroethanone T2 - Encyclopedia of Reagents for Organic Synthesis AB - [1196665-69-6] C9H7N3O4 (MW 221.17) InChI = 1S/C9H7N3O4/c1-16-7-4-2-6(3-5-7)8(13)9(11-10)12(14)15/h2-5H,1H3 InChIKey = WOIHPWWKNSZJKD-UHFFFAOYSA-N (used as a carbene precursor for Rh(II)-catalyzed cyclopropanation of alkenes, leading to the corresponding α-nitro-cyclopropylketones) Alternative Name: none. Physical Data: mp 75–76 °C, yellow solid. Solubility: soluble in CH2Cl2, CHCl3, THF, DMF, and MeCN. Slightly soluble in Et2O. Insoluble in H2O. Form Supplied in: not commercially available. Purification: silica gel chromatography, using 100% CHCl3 as eluent. Handling, Storage, and Precautions: explosive compound (shock and heat sensitive). The title compound should be stored neat at −20 °C, at which it is stable for at least 12 months. It can be stored at room temperature for 1 d without decomposition. DA - 2013/4/22/ PY - 2013/4/22/ DO - 10.1002/047084289x.rn01542 UR - http://dx.doi.org/10.1002/047084289x.rn01542 ER - TY - JOUR TI - Theoretical Investigations of CO2and H2Sorption in an Interpenetrated Square-Pillared Metal–Organic Material AU - Pham, Tony AU - Forrest, Katherine A. AU - McLaughlin, Keith AU - Tudor, Brant AU - Nugent, Patrick AU - Hogan, Adam AU - Mullen, Ashley AU - Cioce, Christian R. AU - Zaworotko, Michael J. AU - Space, Brian T2 - The Journal of Physical Chemistry C AB - Simulations of CO2 and H2 sorption and separation were performed in [Cu(dpa)2SiF6-i], a metal–organic material (MOM) consisting of an interpenetrated square grid of Cu2+ ions coordinated to 4,4′-dipyridylacetylene (dpa) rings and pillars of SiF62– ions. This class of water stable MOMs shows great promise in practical gas sorption/separation with especially high selectivity for CO2 and variable selectivity for other energy related gases. Simulated CO2 sorption isotherms and isosteric heats of adsorption, Qst, at ambient temperatures were in excellent agreement with the experimental measurements at all pressures considered. Further, it was observed that the Qst for CO2 increases as a function of uptake in [Cu(dpa)2SiF6-i]. This suggests that nascently sorbed CO2 molecules within a channel contribute to a more energetically favorable site for additional CO2 molecules, i.e., in stark contrast to typical behavior, sorbate intermolecular interactions enhance sorption energetics with increased loading. The simulated structure at CO2 saturation shows a loading with tight packing of 8 CO2 molecules per unit cell. The CO2 molecules can be seen alternating between a vertical and horizontal alignment within a channel, with each CO2 molecule coordinating to an equatorial fluorine MOM atom. Calculated H2 sorption isotherms and Qst values were also in good agreement with the experimental measurements in [Cu(dpa)2SiF6-i]. H2 saturation corresponds to 10 H2 molecules per unit cell for the studied structure. Moreover, there were two observed binding sites for hydrogen sorption in [Cu(dpa)2SiF6-i]. Simulations of a 30:70 CO2/H2 mixture, typical of syngas, in [Cu(dpa)2SiF6-i] showed that the MOM exhibited a high uptake and selectivity for CO2. In addition, it was observed that the presence of H2O had a negligible effect on the CO2 uptake and selectivity in [Cu(dpa)2SiF6-i], as simulations of a mixture containing CO2, H2, and small amounts of CO, N2, and H2O produced comparable results to the binary mixture simulations. DA - 2013/5/6/ PY - 2013/5/6/ DO - 10.1021/jp402764s VL - 117 IS - 19 SP - 9970-9982 J2 - J. Phys. Chem. C LA - en OP - SN - 1932-7447 1932-7455 UR - http://dx.doi.org/10.1021/jp402764s DB - Crossref ER - TY - JOUR TI - Computational Studies of CO2Sorption and Separation in an Ultramicroporous Metal–Organic Material AU - Forrest, Katherine A. AU - Pham, Tony AU - Hogan, Adam AU - McLaughlin, Keith AU - Tudor, Brant AU - Nugent, Patrick AU - Burd, Stephen D. AU - Mullen, Ashley AU - Cioce, Christian R. AU - Wojtas, Lukasz AU - Zaworotko, Michael J. AU - Space, Brian T2 - The Journal of Physical Chemistry C AB - Grand canonical Monte Carlo (GCMC) simulations of CO2 sorption and separation were performed in [Zn(pyz)2SiF6], a metal–organic material (MOM) consisting of a square grid of Zn2+ ions coordinated to pyrazine (pyz) linkers and pillars of SiF62– ions. This MOM was recently shown to have an unprecedented selectivity for CO2 over N2, CH4, and H2 under industrially relevant conditions. The simulated CO2 sorption isotherms and calculated isosteric heat of adsorption, Qst, values were in excellent agreement with the experimental data for all the state points considered. CO2 saturation in [Zn(pyz)2SiF6] was achieved at near-ambient temperatures and pressures lower than 1.0 atm. Moreover, the sorbed CO2 molecules were representative of a liquid/fluid under such conditions as confirmed through calculating the isothermal compressibility, βT, values. The simulated CO2 uptakes within CO2/N2 (10:90), CO2/CH4 (50:50), and CO2/H2 (30:70) mixture compositions, characteristic of flue gas, biogas, and syngas, respectively, were comparable to those that were produced in the single-component CO2 sorption simulations. The modeled structure at saturation revealed a loading of 1 CO2 molecule per unit cell. The favored CO2 sorption site was identified as the attraction of the carbon atoms of CO2 molecules to four equatorial fluorine atoms of SiF62– anions simultaneously, resulting in CO2 molecules localized at the center of the channel. Furthermore, experimental studies have shown that [Zn(pyz)2SiF6] sorbed minimal amounts of CO2 and N2 at their respective liquid temperatures. Analysis of the crystal structure at 100 K revealed that the unit cell undergoes a slight contraction in all dimensions and contains pyrazine rings that are mildly slanted with an angle of 13.9°. Additionally, molecular dynamics (MD) simulations revealed that the sorbate molecules are anchored to the framework at low temperatures, which inhibits diffusion. Thus, it is hypothesized that the sorbed molecules become trapped in the pores and block other sorbate molecules from entering the MOM at low temperatures. DA - 2013/8/14/ PY - 2013/8/14/ DO - 10.1021/jp405781c VL - 117 IS - 34 SP - 17687-17698 J2 - J. Phys. Chem. C LA - en OP - SN - 1932-7447 1932-7455 UR - http://dx.doi.org/10.1021/jp405781c DB - Crossref ER - TY - JOUR TI - Examining the Effects of Different Ring Configurations and Equatorial Fluorine Atom Positions on CO2Sorption in [Cu(bpy)2SiF6] AU - Forrest, Katherine A. AU - Pham, Tony AU - Nugent, Patrick AU - Burd, Stephen D. AU - Mullen, Ashley AU - Wojtas, Lukasz AU - Zaworotko, Michael J. AU - Space, Brian T2 - Crystal Growth & Design AB - Simulations of CO2 sorption were performed in a metal–organic material (MOM) that is part of a “SIFSIX” family of compounds that has remarkable carbon dioxide capture and separation properties. The MOM considered here has the formula [Cu(bpy)2SiF6] (bpy = 4,4′-bipyridine). This hydrophobic MOM is both water-stable and CO2-specific with significant sorption capacity under ambient conditions. The crystal structure reveals bpy rings and equatorial fluorine atoms in multiple possible orientations; the static disorder has been modeled based on single-crystal X-ray diffraction data revealing several possible relatives of atoms in the crystal structure. With regards to the bpy rings, the structure can be interpreted as two pyridyl rings with coplanar configurations within a unit cell (configuration 1), a twisted bpy ring conformation in which orthogonal pyridyl rings have C4 symmetry about the Cu2+ ion (configuration 2), and a twisted bpy ring conformation in which the two orthogonal pyridyl rings are facing one another within a unit cell (configuration 3). Further, the equatorial fluorine atoms can be positioned such that all atoms are eclipsed with the square grid (position A), oriented at a 21.3° angle with respect to the square grid (position B), and oriented at a 45° angle with respect to the square grid (position C). It was observed that experimental data for CO2 sorption were only consistent with sorption into configurations 1 and 3 with any of the possible equatorial fluorine atom positions at ambient temperatures, although simulations using position A produced slightly higher uptakes in these bpy ring configurations. It is demonstrated that the orientation of the bpy rings in configurations 1 and 3 allows more space for the sorbate molecules and thus promotes favorable MOM–sorbate interactions, resulting in isotherms in line with the experimental results. The results from this study suggests that [Cu(bpy)2SiF6] in either configuration 1 or 3 with CO2 present in the pores at ambient temperatures is consistent with experimental sorption measurements and crystal structure data. DA - 2013/9/10/ PY - 2013/9/10/ DO - 10.1021/cg401034s VL - 13 IS - 10 SP - 4542-4548 J2 - Crystal Growth & Design LA - en OP - SN - 1528-7483 1528-7505 UR - http://dx.doi.org/10.1021/cg401034s DB - Crossref ER - TY - JOUR TI - A Polarizable and Transferable PHAST N2Potential for Use in Materials Simulation AU - Cioce, Christian R. AU - McLaughlin, Keith AU - Belof, Jonathan L. AU - Space, Brian T2 - Journal of Chemical Theory and Computation AB - A polarizable and transferable intermolecular potential energy function, potentials with high accuracy, speed, and transferability (PHAST), has been developed from first principles for molecular nitrogen to be used in the modeling of heterogeneous processes such as materials sorption and separations. A five-site (van der Waals and point charge) anisotropic model, that includes many-body polarization, is proposed. It is parametrized to reproduce high-level electronic structure calculations (CCSD(T) using Dunning-type basis sets extrapolated to the CBS limit) for a representative set of dimer potential energy curves. Thus it provides a relatively simple yet robust and broadly applicable representation of nitrogen. Two versions are developed, differing by the type of mixing rules applied to unlike Lennard-Jones potential sites. It is shown that the Waldman–Hagler mixing rules are more accurate than Lorentz–Berthelot. The resulting potentials are demonstrated to be effective in modeling neat nitrogen but are designed to also be useful in modeling N2 interactions in a large array of environments such as metal–organic frameworks and zeolites and at interfaces. In such settings, capturing anisotropic forces and interactions with (open and coordinated) metals and charged/polar environments is essential. In developing the potential, it was found that adding a seemingly redundant dimer orientation, slip-parallel (S), improved the transferability of the potential energy surface (PES). Notably, one of the solid phases of nitrogen was not as accurately represented energetically without including S in the representative set. Liquid simulations, however, were unaffected and worked equally well for both potentials. This suggests that accounting for a wide variety of configurations is critical in designing a potential that is intended for use in heterogeneous environments where many orientations, including those not commonly explored in the bulk, are possible. Testing and validation of the potential are achieved via simulations of a thermal distribution of trimer geometries compared to analogous high level electronic structure calculations and molecular simulations of bulk pressure–density isotherms across the vapor, supercritical, and liquid phases. Crystal lattice parameters and energetics of the α-N2 and γ-N2 solid phases are also evaluated and determined to be in good agreement with experiment. Thus the proposed potential is shown to be efficacious for gas, liquid, and solid use, representing both disordered and ordered configurations. DA - 2013/11/22/ PY - 2013/11/22/ DO - 10.1021/ct400526a VL - 9 IS - 12 SP - 5550-5557 J2 - J. Chem. Theory Comput. LA - en OP - SN - 1549-9618 1549-9626 UR - http://dx.doi.org/10.1021/ct400526a DB - Crossref ER - TY - JOUR TI - Investigating the Gas Sorption Mechanism in an rht-Metal–Organic Framework through Computational Studies AU - Pham, Tony AU - Forrest, Katherine A. AU - Eckert, Juergen AU - Georgiev, Peter A. AU - Mullen, Ashley AU - Luebke, Ryan AU - Cairns, Amy J. AU - Belmabkhout, Youssef AU - Eubank, Jarrod F. AU - McLaughlin, Keith AU - Lohstroh, Wiebke AU - Eddaoudi, Mohamed AU - Space, Brian T2 - The Journal of Physical Chemistry C AB - Grand canonical Monte Carlo (GCMC) simulations were performed to investigate CO2 and H2 sorption in an rht-metal–organic framework (MOF) that was synthesized with a ligand having a nitrogen-rich trigonal core through trisubstituted triazine groups and amine functional groups. This MOF was synthesized by two different groups, each reporting their own distinct gas sorption measurements and crystal structure. Electronic structure calculations demonstrated that the small differences in the atomic positions between each group’s crystal structure resulted in different electrostatic parameters about the Cu2+ ions for the respective unit cells. Simulations of CO2 sorption were performed with and without many-body polarization effects and using our recently developed CO2 potentials, in addition to a well-known bulk CO2 model, in both crystallographic unit cells. Simulated CO2 sorption isotherms and calculated isosteric heats of adsorption, Qst, values were in excellent agreement with the results reported previously by Eddaoudi et al. for both structures using the polarizable CO2 potential. For both crystal structures, the initial site for CO2 sorption were the Cu2+ ions that had the higher positive charge in the unit cell, although the identity of this electropositive Cu2+ ion was different in each case. Simulations of H2 sorption were performed with three different hydrogen potentials of increasing anisotropy in both crystal structures and the results, especially with the highest fidelity model, agreed well with Eddaoudi et al.’s experimental data. The preferred site of H2 sorption at low loading was between two Cu2+ ions of neighboring paddlewheels. The calculation of the normalized hydrogen dipole distribution for the polarizable model in both crystal structures aided in the identification of four distinct sorption sites in the MOF, which is consistent to what was observed in the experimental inelastic neutron scattering (INS) spectra. Lastly, while the experimental results for the two groups are quantitatively different, the sorption mechanisms (for both crystal structures and sorbates) are broadly similar and not inconsistent with either set of experimental data; the theoretical sorption isotherms themselves resemble those by Eddaoudi et al. DA - 2013/12/27/ PY - 2013/12/27/ DO - 10.1021/jp409950r VL - 118 IS - 1 SP - 439–456 SN - 1932-7447 1932-7455 UR - http://dx.doi.org/10.1021/jp409950r ER - TY - JOUR TI - Enhancement of CO2 selectivity in a pillared pcu MOM platform through pillar substitution AU - Nugent, Patrick AU - Rhodus, Vanessah AU - Pham, Tony AU - Tudor, Brant AU - Forrest, Katherine AU - Wojtas, Lukasz AU - Space, Brian AU - Zaworotko, Michael T2 - Chemical Communications AB - Pillar substitution in a long-known metal–organic material with saturated metal centres, [Cu(bipy)2(SiF6)]n, has afforded the first crystallographically characterized porous materials based upon TiF62− and SnF62− anions as pillars. Gas adsorption studies revealed similar surface areas and adsorption isotherms but enhanced selectivity towards CO2vs. CH4 and N2. DA - 2013/// PY - 2013/// DO - 10.1039/c3cc37695h VL - 49 IS - 16 SP - 1606 J2 - Chem. Commun. LA - en OP - SN - 1359-7345 1364-548X UR - http://dx.doi.org/10.1039/c3cc37695h DB - Crossref ER - TY - JOUR TI - Understanding Hydrogen Sorption in a Metal–Organic Framework with Open-Metal Sites and Amide Functional Groups AU - Pham, Tony AU - Forrest, Katherine A. AU - Nugent, Patrick AU - Belmabkhout, Youssef AU - Luebke, Ryan AU - Eddaoudi, Mohamed AU - Zaworotko, Michael J. AU - Space, Brian T2 - The Journal of Physical Chemistry C AB - Grand canonical Monte Carlo (GCMC) studies of the mechanism of hydrogen sorption in an rht-MOF known as Cu-TPBTM are presented. The MOF is a decorated/substituted isostructural analogue to the unembellished rht-MOF, PCN-61, that was studied previously [Forrest, K. A.J. Phys. Chem. C 2012, 116, 15538−15549.]. The simulations were performed using three different hydrogen potentials of increasing complexity. Simulated hydrogen sorption isotherms and calculated isosteric heat of adsorption, Qst, values were in excellent agreement with the reported experimental data for only a polarizable model in one of four experimentally observed crystal structure configurations. The study demonstrates the ability of modeling to distinguish the differential sorption of distinct strucures; one configuration is found to be dominant due to favorable interactions with substrates. In addition, it was discovered that the presence of polar amide groups had a significant effect on the electrostatics of the Cu2+ ions and directs the low-pressure physisorption of hydrogen in the MOF. This is in contrast to what was observed in PCN-61, where an exterior copper ion had a higher relative charge and was the favored loading site. This tunability of the electrostatics of the copper ions via chemical substitution on the MOF framework can be explained by the presence of the negatively charged oxygen atom of the amide group that causes the interior Cu2+ ion to exhibit a higher positive charge through an inductive effect. Further, control simulations, taking advantage of the flexibility afforded by theoretical modeling, include artificially modified charges for both Cu2+ ions chosen equal to or with a higher charge on the exterior Cu2+ ion. This choice resulted in distinctly different hydrogen sorption characteristics in Cu-TPBTM with no direct sorption on the open-metal sites. Thus, this study demonstrates both the tunable nature of MOF platforms and the possibility for rational design of sorption/catalytic sites and characteristics through the active interplay of theory and experiment. The ability of accurate, carefully parametrized and transferable force fields to model and predict small molecule sorption in MOFs, even including open-metal sites, is demonstrated. DA - 2013/4/25/ PY - 2013/4/25/ DO - 10.1021/jp402304a VL - 117 IS - 18 SP - 9340-9354 J2 - J. Phys. Chem. C LA - en OP - SN - 1932-7447 1932-7455 UR - http://dx.doi.org/10.1021/jp402304a DB - Crossref ER - TY - JOUR TI - Pillar substitution modulates CO2 affinity in “mmo” topology networks AU - Mohamed, Mona H. AU - Elsaidi, Sameh K. AU - Pham, Tony AU - Forrest, Katherine A. AU - Tudor, Brant AU - Wojtas, Lukasz AU - Space, Brian AU - Zaworotko, Michael J. T2 - Chemical Communications AB - The use of WO4(2-) instead of CrO4(2-) or MoO4(2-) as an angular pillar in topology nets has afforded two isostructural porous nets of formula [M(bpe)2WO4] (M = Co or Ni, bpe = 1,2-(4-pyridyl)ethene). The Ni variant, WOFOUR-1-Ni, is highly selective towards CO2 thanks to its exceptionally high isosteric heat of adsorption (Qst) of -65.5 kJ mol(-1) at zero loading. DA - 2013/// PY - 2013/// DO - 10.1039/c3cc44745f VL - 49 IS - 84 SP - 9809 J2 - Chem. Commun. LA - en OP - SN - 1359-7345 1364-548X UR - http://dx.doi.org/10.1039/c3cc44745f DB - Crossref ER - TY - JOUR TI - Solving the Many-Body Polarization Problem on GPUs: Application to MOFs AU - Tudor, Brant AU - Space, Brian T2 - The Journal of Computational Science Education DA - 2013/11// PY - 2013/11// DO - 10.22369/issn.2153-4136/4/1/5 VL - 4 IS - 1 SP - 30-34 J2 - JOCSE OP - SN - 2153-4136 UR - http://dx.doi.org/10.22369/issn.2153-4136/4/1/5 DB - Crossref ER - TY - JOUR TI - A Polarizable and Transferable PHAST CO2 Potential for Materials Simulation AU - Mullen, Ashley L. AU - Pham, Tony AU - Forrest, Katherine A. AU - Cioce, Christian R. AU - McLaughlin, Keith AU - Space, Brian T2 - Journal of Chemical Theory and Computation AB - Reliable PHAST (Potentials with High Accuracy Speed and Transferability) intermolecular potential energy functions for CO2 have been developed from first principles for use in heterogeneous systems, including one with explicit polarization. The intermolecular potentials have been expressed in a transferable form and parametrized from nearly exact electronic structure calculations. Models with and without explicit many-body polarization effects, known to be important in simulation of interfacial processes, are constructed. The models have been validated on pressure-density isotherms of bulk CO2 and adsorption in three metal-organic framework (MOF) materials. The present models appear to offer advantages over high quality fluid/liquid state potentials in describing CO2 interactions in interfacial environments where sorbates adopt orientations not commonly explored in bulk fluids. Thus, the nonpolar CO2-PHAST and polarizable CO2-PHAST* potentials are recommended for materials/interfacial simulations. DA - 2013/11/22/ PY - 2013/11/22/ DO - 10.1021/ct400549q VL - 9 IS - 12 SP - 5421-5429 J2 - J. Chem. Theory Comput. LA - en OP - SN - 1549-9618 1549-9626 UR - http://dx.doi.org/10.1021/ct400549q DB - Crossref ER - TY - JOUR TI - Efficient calculation of many-body induced electrostatics in molecular systems AU - McLaughlin, Keith AU - Cioce, Christian R. AU - Pham, Tony AU - Belof, Jonathan L. AU - Space, Brian T2 - The Journal of Chemical Physics AB - Potential energy functions including many-body polarization are in widespread use in simulations of aqueous and biological systems, metal-organics, molecular clusters, and other systems where electronically induced redistribution of charge among local atomic sites is of importance. The polarization interactions, treated here via the methods of Thole and Applequist, while long-ranged, can be computed for moderate-sized periodic systems with extremely high accuracy by extending Ewald summation to the induced fields as demonstrated by Nymand, Sala, and others. These full Ewald polarization calculations, however, are expensive and often limited to very small systems, particularly in Monte Carlo simulations, which may require energy evaluation over several hundred-thousand configurations. For such situations, it shall be shown that sufficiently accurate computation of the polarization energy can be produced in a fraction of the central processing unit (CPU) time by neglecting the long-range extension to the induced fields while applying the long-range treatments of Ewald or Wolf to the static fields; these methods, denoted Ewald E-Static and Wolf E-Static (WES), respectively, provide an effective means to obtain polarization energies for intermediate and large systems including those with several thousand polarizable sites in a fraction of the CPU time. Furthermore, we shall demonstrate a means to optimize the damping for WES calculations via extrapolation from smaller trial systems. DA - 2013/11/14/ PY - 2013/11/14/ DO - 10.1063/1.4829144 VL - 139 IS - 18 SP - 184112 J2 - The Journal of Chemical Physics LA - en OP - SN - 0021-9606 1089-7690 UR - http://dx.doi.org/10.1063/1.4829144 DB - Crossref ER - TY - JOUR TI - A Robust Molecular Porous Material with High CO2 Uptake and Selectivity AU - Nugent, Patrick S. AU - Rhodus, Vanessah Lou AU - Pham, Tony AU - Forrest, Katherine AU - Wojtas, Lukasz AU - Space, Brian AU - Zaworotko, Michael J. T2 - Journal of the American Chemical Society AB - We report MPM-1-TIFSIX, a molecular porous material (MPM) based upon the neutral metal complex [Cu2(adenine)4(TiF6)2], that self-assembles through a hydrogen-bonding network. This MPM is amenable to room-temperature synthesis and activation. Gas adsorption measurements and ideal adsorbed solution theory selectivity predictions at 298 K revealed enhanced CO2 separation performance relative to a previously known variant as well as the highest CO2 uptake and isosteric heat of adsorption yet reported for an MPM. MPM-1-TIFSIX is thermally stable to 568 K and retains porosity and capacity even after immersion in water for 24 h. DA - 2013/7/22/ PY - 2013/7/22/ DO - 10.1021/ja4054948 VL - 135 IS - 30 SP - 10950-10953 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/ja4054948 DB - Crossref ER - TY - JOUR TI - Porous materials with optimal adsorption thermodynamics and kinetics for CO2 separation AU - Nugent, Patrick AU - Belmabkhout, Youssef AU - Burd, Stephen D. AU - Cairns, Amy J. AU - Luebke, Ryan AU - Forrest, Katherine AU - Pham, Tony AU - Ma, Shengqian AU - Space, Brian AU - Wojtas, Lukasz AU - Eddaoudi, Mohamed AU - Zaworotko, Michael J. T2 - Nature DA - 2013/2/27/ PY - 2013/2/27/ DO - 10.1038/nature11893 VL - 495 IS - 7439 SP - 80-84 J2 - Nature LA - en OP - SN - 0028-0836 1476-4687 UR - http://dx.doi.org/10.1038/nature11893 DB - Crossref ER - TY - JOUR TI - Synthetic bacteriochlorins with integral spiro-piperidine motifs AU - Reddy, Kanumuri Ramesh AU - Lubian, Elisa AU - Pavan, M. Phani AU - Kim, Han-Je AU - Yang, Eunkyung AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/C3NJ41161C VL - 37 IS - 4 SP - 1157 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/C3NJ41161C DB - Crossref ER - TY - JOUR TI - Serendipitous synthetic entrée to tetradehydro analogues of cobalamins AU - Deans, Richard M. AU - Mass, Olga AU - Diers, James R. AU - Bocian, David F. AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - Tetradehydrocorrin macrocycles occupy a saturation level halfway between that of octadehydrocorrins and corrins (e.g., cyanocobalamin). While octadehydrocorrin chemistry is relatively well understood, few studies have been done on more reduced macrocycles owing to synthetic limitations. The reaction of a 2,3-dihydro-1,3,3-trimethyldipyrrin (Western half) bearing a 7-(4-iodophenyl) group and a 1-(dimethoxymethyl)-9-bromo-2,3-dihydro-3,3-dimethyldipyrrin (Eastern half) bearing a 7-p-tolyl group in the presence of Ga(OTf)3 afforded the corresponding B,D-tetradehydrocorrin (1) in 24% yield. Use of a Western half bearing a 7-(4-ethylphenyl) group afforded the B,D-tetradehydrocorrin (2) in 29% yield. Each tetradehydrocorrin bears a 1-methyl group at the A–D ring junction (and hence is enantiomeric), a geminal dimethyl group in each pyrroline ring, and distinct substituents at the 7- and 17-positions; characterization included 1H and 13C NMR spectroscopies, absorption spectroscopy, mass spectrometry, and X-ray crystallography (2 only). Treatment of 1 or 2 with CoCl2 afforded the cobalt chelate as a mixture of stereoisomers containing an apical methoxide or hydroxide ligand. The cobalt-tetradehydrocorrin was characterized by absorption spectroscopy, mass spectrometry, infrared spectroscopy and electrochemistry. The cobalt chelate was smoothly titrated with THF, pyridine, and KCN or Bu4NCN. While the assignment of the oxidation state of the cobalt remains provisional, the use of natural abundance versus isotopically substituted solvents or titrants (CD3OD, K13CN) enabled clear identification of the apical ligands. The facile access to stable, synthetically tailored B,D-tetradehydrocorrins should open the door to fundamental studies of simple surrogates of cyanocobalamin. DA - 2013/// PY - 2013/// DO - 10.1039/C3NJ00574G VL - 37 IS - 12 SP - 3964 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/C3NJ00574G DB - Crossref ER - TY - JOUR TI - Integrative Chemical–Biological Read-Across Approach for Chemical Hazard Classification AU - Low, Yen AU - Sedykh, Alexander AU - Fourches, Denis AU - Golbraikh, Alexander AU - Whelan, Maurice AU - Rusyn, Ivan AU - Tropsha, Alexander T2 - Chemical Research in Toxicology AB - Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here, we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (“biological” similarity). The Chemical–Biological Read-Across (CBRA) approach infers each compound’s toxicity from both chemical and biological analogues whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models. DA - 2013/8/5/ PY - 2013/8/5/ DO - 10.1021/TX400110F VL - 26 IS - 8 SP - 1199-1208 J2 - Chem. Res. Toxicol. LA - en OP - SN - 0893-228X 1520-5010 UR - http://dx.doi.org/10.1021/TX400110F DB - Crossref ER - TY - JOUR TI - Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches AU - Fourches, Denis AU - Muratov, Eugene AU - Ding, Feng AU - Dokholyan, Nikolay V. AU - Tropsha, Alexander T2 - Journal of Chemical Information and Modeling AB - We report on the prediction accuracy of ligand-based (2D QSAR) and structure-based (MedusaDock) methods used both independently and in consensus for ranking the congeneric series of ligands binding to three protein targets (UK, ERK2, and CHK1) from the CSAR 2011 benchmark exercise. An ensemble of predictive QSAR models was developed using known binders of these three targets extracted from the publicly available ChEMBL database. Selected models were used to predict the binding affinity of CSAR compounds toward the corresponding targets and rank them accordingly; the overall ranking accuracy evaluated by Spearman correlation was as high as 0.78 for UK, 0.60 for ERK2, and 0.56 for CHK1, placing our predictions in the top 10% among all the participants. In parallel, MedusaDock, designed to predict reliable docking poses, was also used for ranking the CSAR ligands according to their docking scores; the resulting accuracy (Spearman correlation) for UK, ERK2, and CHK1 were 0.76, 0.31, and 0.26, respectively. In addition, performance of several consensus approaches combining MedusaDock- and QSAR-predicted ranks altogether has been explored; the best approach yielded Spearman correlation coefficients for UK, ERK2, and CHK1 of 0.82, 0.50, and 0.45, respectively. This study shows that (i) externally validated 2D QSAR models were capable of ranking CSAR ligands at least as accurately as more computationally intensive structure-based approaches used both by us and by other groups and (ii) ligand-based QSAR models can complement structure-based approaches by boosting the prediction performances when used in consensus. DA - 2013/7/17/ PY - 2013/7/17/ DO - 10.1021/CI400216Q VL - 53 IS - 8 SP - 1915-1922 J2 - J. Chem. Inf. Model. LA - en OP - SN - 1549-9596 1549-960X UR - http://dx.doi.org/10.1021/CI400216Q DB - Crossref ER - TY - JOUR TI - Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening AU - Zhang, Liying AU - Fourches, Denis AU - Sedykh, Alexander AU - Zhu, Hao AU - Golbraikh, Alexander AU - Ekins, Sean AU - Clark, Julie AU - Connelly, Michele C. AU - Sigal, Martina AU - Hodges, Dena AU - Guiguemde, Armand AU - Guy, R. Kiplin AU - Tropsha, Alexander T2 - Journal of Chemical Information and Modeling AB - Quantitative structure–activity relationship (QSAR) models have been developed for a data set of 3133 compounds defined as either active or inactive against P. falciparum. Because the data set was strongly biased toward inactive compounds, different sampling approaches were employed to balance the ratio of actives versus inactives, and models were rigorously validated using both internal and external validation approaches. The balanced accuracy for assessing the antimalarial activities of 70 external compounds was between 87% and 100% depending on the approach used to balance the data set. Virtual screening of the ChemBridge database using QSAR models identified 176 putative antimalarial compounds that were submitted for experimental validation, along with 42 putative inactives as negative controls. Twenty five (14.2%) computational hits were found to have antimalarial activities with minimal cytotoxicity to mammalian cells, while all 42 putative inactives were confirmed experimentally. Structural inspection of confirmed active hits revealed novel chemical scaffolds, which could be employed as starting points to discover novel antimalarial agents. DA - 2013/1/23/ PY - 2013/1/23/ DO - 10.1021/ci300421n VL - 53 IS - 2 SP - 475-492 J2 - J. Chem. Inf. Model. LA - en OP - SN - 1549-9596 1549-960X UR - http://dx.doi.org/10.1021/ci300421n DB - Crossref ER - TY - JOUR TI - Using Graph Indices for the Analysis and Comparison of Chemical Datasets AU - Fourches, Denis AU - Tropsha, Alexander T2 - Molecular Informatics AB - In cheminformatics, compounds are represented as points in multidimensional space of chemical descriptors. When all pairs of points found within certain distance threshold in the original high dimensional chemistry space are connected by distance-labeled edges, the resulting data structure can be defined as Dataset Graph (DG). We show that, similarly to the conventional description of organic molecules, many graph indices can be computed for DGs as well. We demonstrate that chemical datasets can be effectively characterized and compared by computing simple graph indices such as the average vertex degree or Randic connectivity index. This approach is used to characterize and quantify the similarity between different datasets or subsets of the same dataset (e.g., training, test, and external validation sets used in QSAR modeling). The freely available ADDAGRA program has been implemented to build and visualize DGs. The approach proposed and discussed in this report could be further explored and utilized for different cheminformatics applications such as dataset diversification by acquiring external compounds, dataset processing prior to QSAR modeling, or (dis)similarity modeling of multiple datasets studied in chemical genomics applications. DA - 2013/9/9/ PY - 2013/9/9/ DO - 10.1002/MINF.201300076 VL - 32 IS - 9-10 SP - 827-842 J2 - Mol. Inf. LA - en OP - SN - 1868-1743 UR - http://dx.doi.org/10.1002/MINF.201300076 DB - Crossref KW - Chemical dataset graph KW - Graph indices KW - QSAR KW - ADDAGRA ER - TY - JOUR TI - Catalytic proton reduction with transition metal complexes of the redox-active ligand bpy2PYMe AU - Nippe, Michael AU - Khnayzer, Rony S. AU - Panetier, Julien A. AU - Zee, David Z. AU - Olaiya, Babatunde S. AU - Head-Gordon, Martin AU - Chang, Christopher J. AU - Castellano, Felix N. AU - Long, Jeffrey R. T2 - Chemical Science AB - A new pentadentate, redox-active ligand bpy2PYMe has been synthesized and its corresponding transition metal complexes of Fe2+ (1), Co2+ (2), Ni2+ (3), Cu2+ (4), and Zn2+ (5) have been investigated for electro- and photo-catalytic proton reduction in acetonitrile and water, respectively. Under weak acid conditions, the Co complex displays catalytic onset at potentials similar to those of the ligand centered reductions in the absence of acid. Related Co complexes devoid of ligand redox activity catalyze H2 evolution under similar conditions at significantly higher overpotentials, showcasing the beneficial effect of combining ligand-centered redox activity with a redox-active Co center. Furthermore, turnover numbers as high as 1630 could be obtained under aqueous photocatalytic conditions using [Ru(bpy)3]2+ as a photosensitizer. Under those conditions catalytic hydrogen production was solely limited by photosensitizer stability. Introduction of an electron withdrawing CF3 group into the pyridine moiety of the ligand as in bpy2PYMe-CF3 renders its corresponding Co complex 6 less active for proton reduction in electro- and photocatalytic experiments. This surprising effect of ligand substitution was investigated by means of density functional theory calculations which suggest the importance of electronic communication between Co1+ and the redox-active ligand. Taken together, the results provide a path forward in the design of robust molecular catalysts in aqueous media with minimized overpotential by exploiting the synergy between redox-active metal and ligand components. DA - 2013/// PY - 2013/// DO - 10.1039/C3SC51660A VL - 4 IS - 10 SP - 3934 J2 - Chem. Sci. LA - en OP - SN - 2041-6520 2041-6539 UR - http://dx.doi.org/10.1039/C3SC51660A DB - Crossref ER - TY - JOUR TI - Near-IR phosphorescent metalloporphyrin as a photochemical upconversion sensitizer AU - Deng, Fan AU - Sommer, Jonathan R. AU - Myahkostupov, Mykhaylo AU - Schanze, Kirk S. AU - Castellano, Felix N. T2 - Chemical Communications AB - The phosphorescent metalloporphyrin sensitizer PtTPTNP (TPTNP = tetraphenyltetranaphtho[2,3]porphyrin) has been successfully coupled with perylenediimide (PDI) or rubrene utilized as triplet acceptors/annihilators to upconvert 690 nm incident photons into yellow fluorescence through sensitized triplet–triplet annihilation at overall efficiencies in the 6–7% range while exhibiting exceptional photostability. DA - 2013/// PY - 2013/// DO - 10.1039/C3CC44479A VL - 49 IS - 67 SP - 7406 J2 - Chem. Commun. LA - en OP - SN - 1359-7345 1364-548X UR - http://dx.doi.org/10.1039/C3CC44479A DB - Crossref ER - TY - JOUR TI - Orange-to-blue and red-to-green photon upconversion with a broadband absorbing copper(i) MLCT sensitizer AU - McCusker, Catherine E. AU - Castellano, Felix N. T2 - Chemical Communications AB - A synthetically facile and earth abundant Cu(I) metal-to-ligand charge transfer sensitizer was successfully incorporated into two distinct photochemical upconversion schemes, affording red-to-green and orange-to-blue wavelength conversions. DA - 2013/// PY - 2013/// DO - 10.1039/C3CC40778K VL - 49 IS - 34 SP - 3537 J2 - Chem. Commun. LA - en OP - SN - 1359-7345 1364-548X UR - http://dx.doi.org/10.1039/C3CC40778K DB - Crossref ER - TY - JOUR TI - Charge-Transfer and Ligand-Localized Photophysics in Luminescent Cyclometalated Pyrazolate-Bridged Dinuclear Platinum(II) Complexes AU - Chakraborty, Arnab AU - Deaton, Joseph C. AU - Haefele, Alexandre AU - Castellano, Felix N. T2 - Organometallics AB - We present the synthesis, photophysical characterization, and electrochemistry of three series of cyclometalated binuclear platinum(II) complexes, each bridged by two 3,5-disubstituted pyrazolate ligands (μ-R2pz). These neutral compounds have the general formula [C∧NPt(μ-R2pz)]2, where C∧N is a cyclometalating ligand corresponding to 2-(2′-thienyl)pyridine (thpy), 1-phenylisoquinoline (piq), or 7,8-benzoquinoline (bzq) with R = H, Me, iPr, Ph, corresponding to series I–III dimers, respectively. Systematic variation of the cyclometalating ligands in addition to the bridging pyrazolates renders colorful structures exhibiting a range of electrochemical and spectroscopic behavior with absorption and photoluminescence properties tuned over a wide portion of the visible spectrum. Steric bulk introduced into the 3,5-positions on the pz bridges readily modulates intramolecular d8–d8 metal–metal σ interactions strongly affecting the frontier orbitals’ electronic structure, manifested by changes in absorption and emission energy, excited-state lifetime, and photoluminescence quantum yield. Cyclic voltammetry revealed the presence of two very closely spaced reversible C∧N ligand-based reductions ranging between −1.97 and −2.56 V vs Fc+/Fc, and the first metal–metal-centered oxidation wave was found to be reversible in dichloromethane and irreversible in coordinating THF in most instances. All the complexes of series I displayed triplet ligand-localized excited states at all temperatures, while an increase of steric bulk in the pz bridge in the two other molecular series resulted in a variation of photophysical behavior ranging from charge transfer to ligand localized, including admixture behavior. DA - 2013/7/8/ PY - 2013/7/8/ DO - 10.1021/OM400276V VL - 32 IS - 14 SP - 3819-3829 J2 - Organometallics LA - en OP - SN - 0276-7333 1520-6041 UR - http://dx.doi.org/10.1021/OM400276V DB - Crossref ER - TY - JOUR TI - Improving the Catalytic Activity of Semiconductor Nanocrystals through Selective Domain Etching AU - Khon, Elena AU - Lambright, Kelly AU - Khnayzer, Rony S. AU - Moroz, Pavel AU - Perera, Dimuthu AU - Butaeva, Evgeniia AU - Lambright, Scott AU - Castellano, Felix N. AU - Zamkov, Mikhail T2 - Nano Letters AB - Colloidal chemistry offers an assortment of synthetic tools for tuning the shape of semiconductor nanocrystals. While many nanocrystal architectures can be obtained directly via colloidal growth, other nanoparticle morphologies require alternative processing strategies. Here, we show that chemical etching of colloidal nanoparticles can facilitate the realization of nanocrystal shapes that are topologically inaccessible by hot-injection techniques alone. The present methodology is demonstrated by synthesizing a two-component CdSe/CdS nanoparticle dimer, constructed in a way that both CdSe and CdS semiconductor domains are exposed to the external environment. This structural morphology is highly desirable for catalytic applications as it enables both reductive and oxidative reactions to occur simultaneously on dissimilar nanoparticle surfaces. Hydrogen production tests confirmed the improved catalytic activity of CdSe/CdS dimers, which was enhanced 3–4 times upon etching treatment. We expect that the demonstrated application of etching to shaping of colloidal heteronanocrystals can become a common methodology in the synthesis of charge-separating nanocrystals, leading to advanced nanoparticles architectures for applications in areas of photocatalysis, photovoltaics, and light detection. DA - 2013/4/3/ PY - 2013/4/3/ DO - 10.1021/NL400715N VL - 13 IS - 5 SP - 2016-2023 J2 - Nano Lett. LA - en OP - SN - 1530-6984 1530-6992 UR - http://dx.doi.org/10.1021/NL400715N DB - Crossref KW - Photovoltaics KW - catalysis KW - nanocrystals KW - etching KW - titanium dioxide ER - TY - JOUR TI - Annihilation Limit of a Visible-to-UV Photon Upconversion Composition Ascertained from Transient Absorption Kinetics AU - Deng, Fan AU - Blumhoff, Jörg AU - Castellano, Felix N. T2 - The Journal of Physical Chemistry A AB - Noncoherent sensitized green-to-near-visible upconversion has been achieved utilizing palladium(II) octaethylporphyrin (PdOEP) as the triplet sensitizer and anthracene as the energy acceptor/annihilator in vacuum degassed toluene. Selective 547 nm excitation of PdOEP with incident irradiance as low as 600 μW/cm(2) results in the observation of anthryl fluorescence at higher energy. Stern-Volmer analysis of the dynamic phosphorescence quenching of PdOEP by anthracene possesses an extremely large K(SV) of 810,000 M(-1), yielding a triplet-triplet energy transfer quenching constant of 3.3 × 10(9) M(-1) s(-1). Clear evidence for the subsequent triplet-triplet annihilation (TTA) of anthracene was afforded by numerous experiments, one of the most compelling was an excitation scan illustrating that the Q-band absorption features of PdOEP are solely responsible for sensitizing the anti-Stokes fluorescence. The upconverted emission intensity with respect to the excitation power was shown to vary between quadratic and linear using either coherent or noncoherent light sources, illustrating the expected kinetic limits for the light producing photochemistry under continuous wave illumination. Time-resolved experiments directly comparing the total integrated anthracene intensity/time fluorescence data produced through upconversion (λ(ex) = 547 nm, delayed signal) and with direct excitation (λ(ex) = 355 nm, prompt signal) under conditions where the laser pulse is completely absorbed by the sample reveal annihilation efficiencies of approximately 40%. Similarly, the delayed fluorescence kinetic analysis reported by Schmidt and co-workers (J. Phys. Chem. Lett. 2010, 1, 1795-1799) was used to reveal the maximum possible efficiency from a model red-to-yellow upconverting composition and this treatment was applied to the anthryl triplet absorption decay transients of anthracene measured for the PdOEP/anthracene composition at 430 nm. From this analysis approximately 50% of the anthryl triplets that decay by TTA produce singlet fluorescence, consistent with the notion that annihilation spin statistics does not impose efficiency limits on upconversion photochemistry. DA - 2013/5/15/ PY - 2013/5/15/ DO - 10.1021/JP4022618 VL - 117 IS - 21 SP - 4412-4419 J2 - J. Phys. Chem. A LA - en OP - SN - 1089-5639 1520-5215 UR - http://dx.doi.org/10.1021/JP4022618 DB - Crossref ER - TY - JOUR TI - Toward Organic Photohydrides: Excited-State Behavior of 10-Methyl-9-phenyl-9,10-dihydroacridine AU - Yang, Xin AU - Walpita, Janitha AU - Zhou, Dapeng AU - Luk, Hoi Ling AU - Vyas, Shubham AU - Khnayzer, Rony S. AU - Tiwari, Subodh C. AU - Diri, Kadir AU - Hadad, Christopher M. AU - Castellano, Felix N. AU - Krylov, Anna I. AU - Glusac, Ksenija D. T2 - The Journal of Physical Chemistry B AB - The excited-state hydride release from 10-methyl-9-phenyl-9,10-dihydroacridine (PhAcrH) was investigated using steady-state and time-resolved UV/vis absorption spectroscopy. Upon excitation, PhAcrH is oxidized to the corresponding iminium ion (PhAcr(+)), while the solvent (acetonitrile/water mixture) is reduced (52% of PhAcr(+) and 2.5% of hydrogen is formed). The hydride release occurs from the triplet excited state by a stepwise electron/hydrogen-atom transfer mechanism. To facilitate the search for improved organic photohydrides that exhibit a concerted mechanism, a computational methodology is presented that evaluates the thermodynamic parameters for the hydride ion, hydrogen atom, and electron release from organic hydrides. DA - 2013/5/23/ PY - 2013/5/23/ DO - 10.1021/JP401770E VL - 117 IS - 49 SP - 15290-15296 J2 - J. Phys. Chem. B LA - en OP - SN - 1520-6106 1520-5207 UR - http://dx.doi.org/10.1021/JP401770E DB - Crossref ER - TY - JOUR TI - Design of a Long-Lifetime, Earth-Abundant, Aqueous Compatible Cu(I) Photosensitizer Using Cooperative Steric Effects AU - McCusker, Catherine E. AU - Castellano, Felix N. T2 - Inorganic Chemistry AB - A new homoleptic Cu(I) photosensitizer, [Cu(dsbtmp)2](+) (dsbtmp = 2,9-di(sec-butyl)-3,4,7,8-tetramethyl-1,10-phenanthroline), designed to exhibit cooperative steric hindrance, unexpectedly produced strong photoluminescence (Φ = 1.9-6.3%) and long excited state lifetimes (τ = 1.2-2.8 μs) in a broad range of coordinating and noncoordinating solvents. The combination of the 2,9-sec-butyl substituents with the neighboring 3,8-methyl groups led to a Cu(I) complex with small degrees of ground and excited state distortion ultimately producing a molecule with robust metal-to-ligand charge transfer photophysics largely insulated from solvent interactions, reversible redox chemistry serving as a strong excited state reductant, along with impressive thermodynamic and photochemical stability in solution. DA - 2013/7/15/ PY - 2013/7/15/ DO - 10.1021/IC401213P VL - 52 IS - 14 SP - 8114-8120 J2 - Inorg. Chem. LA - en OP - SN - 0020-1669 1520-510X UR - http://dx.doi.org/10.1021/IC401213P DB - Crossref ER - TY - JOUR TI - Tracking of Tuning Effects in Bis-Cyclometalated Iridium Complexes: A Combined Time Resolved Infrared Spectroscopy, Electrochemical, and Computational Study AU - Chirdon, Danielle N. AU - McCusker, Catherine E. AU - Castellano, Felix N. AU - Bernhard, Stefan T2 - Inorganic Chemistry AB - Electronic structure and photophysical properties have been investigated for a new series of fluorinated iridium complexes with the parent [Ir(ppy)2(deeb)](PF6) (deeb is 4,4'-diethylester-2,2'-bipyridine). Time resolved infrared spectroscopy (TRIR) has been used to observe the long-lived triplet excited state of each complex confirming its mixed charge transfer character. Supplementary evidence of charge transfer in the triplet state is provided via emission spectroscopy, transient absorption spectroscopy, and density functional theory (DFT) calculations. Both computational and spectroscopic assignments reveal consistency in the first excitation throughout the series of complexes. Electrochemical measurements meanwhile show that increasing fluorination still induces expected shifting of frontier orbitals. Excited states beyond the lowest lying triplet are probed for the complexes via UV-vis spectroscopy which reveals three distinct features. These features are assigned via time-dependent DFT (TD-DFT) to build a broader understanding of electronic structure. DA - 2013/7/11/ PY - 2013/7/11/ DO - 10.1021/IC401009Q VL - 52 IS - 15 SP - 8795-8804 J2 - Inorg. Chem. LA - en OP - SN - 0020-1669 1520-510X UR - http://dx.doi.org/10.1021/IC401009Q DB - Crossref ER - TY - JOUR TI - Mono- and Dinuclear Cationic Iridium(III) Complexes Bearing a 2,5-Dipyridylpyrazine (2,5-dpp) Ligand AU - Donato, Loïc AU - McCusker, Catherine E. AU - Castellano, Felix N. AU - Zysman-Colman, Eli T2 - Inorganic Chemistry AB - The synthesis, X-ray structures, photophysical, and electrochemical characterization of mono- (1) and dinuclear (2) cationic iridium(III) complexes bearing a 2,5-dipyridylpyrazine (2,5-dpp) ancillary ligand are reported. Upon the complexation of a first equivalent of iridium, the photoluminescence shifts markedly into the deep red (λem = 710 nm, ΦPL = 0.9%) compared to other cationic iridium complexes such as [Ir(ppy)2(bpy)]PF6. With the coordination of a second equivalent of iridium, room temperature luminescence is completely quenched. Both 1 and 2 are luminescent at low temperatures but with distinct excited state decay kinetics; the emission of 2 is significantly red-shifted compared to 1. Emission both at 298 and 77 K results from a mixed charge-transfer state. Density functional theory (DFT) calculations and electrochemical behavior point to an electronic communication between the two iridium complexes. DA - 2013/7/18/ PY - 2013/7/18/ DO - 10.1021/IC400478D VL - 52 IS - 15 SP - 8495-8504 J2 - Inorg. Chem. LA - en OP - SN - 0020-1669 1520-510X UR - http://dx.doi.org/10.1021/IC400478D DB - Crossref ER - TY - JOUR TI - Photochemical Upconversion: A Physical or Inorganic Chemistry Experiment for Undergraduates Using a Conventional Fluorimeter AU - Wilke, Bryn M. AU - Castellano, Felix N. T2 - Journal of Chemical Education AB - Photochemical upconversion is a regenerative process that transforms lower-energy photons into higher-energy light through two sequential bimolecular reactions, triplet sensitization of an appropriate acceptor followed by singlet fluorescence producing triplet–triplet annihilation derived from two energized acceptors. This laboratory directly investigates this phenomenon using the facile photo-induced triplet–triplet energy-transfer reaction between the benchmark inorganic chromophore tris(2,2′-bipyridyl)ruthenium(II), [Ru(bpy)3]2+, and 9,10-diphenylanthracene (DPA). Selective green excitation of [Ru(bpy)3]2+ in the presence of DPA results in two observations, the (dynamic) quenching of the [Ru(bpy)3]2+ photoluminescence in the red and the production of upconverted DPA singlet fluorescence in the blue. The quadratic nature of the incident light power dependence for the latter process is easily realized by using the percent transmission characteristics of neutral density filters placed in the excitation beam prior to sample illumination. In a single laboratory period, students are able to directly visualize the upconverted fluorescence generated and gain experience in various aspects of fluorescence spectroscopy, triplet energy-transfer processes, quenching, and reaction molecularity. DA - 2013/4/10/ PY - 2013/4/10/ DO - 10.1021/ED300142Z VL - 90 IS - 6 SP - 786-789 J2 - J. Chem. Educ. LA - en OP - SN - 0021-9584 1938-1328 UR - http://dx.doi.org/10.1021/ED300142Z DB - Crossref KW - Upper-Division Undergraduate KW - Inorganic Chemistry KW - Physical Chemistry KW - Laboratory Instruction KW - Hands-On Learning/Manipulatives KW - Photochemistry KW - Fluorescence Spectroscopy KW - Kinetics KW - Rate Law KW - UV-Vis Spectroscopy ER - TY - JOUR TI - Ultrafast Photoinduced Electron Transfer in Viologen-Linked BODIPY Dyes AU - Frath, Denis AU - Yarnell, James E. AU - Ulrich, Gilles AU - Castellano, Felix N. AU - Ziessel, Raymond T2 - ChemPhysChem AB - Abstract New boron‐dipyrromethene (BODIPY) dyes linked to viologen are prepared and their photophysical and electrochemical properties are investigated. Both synthesized molecules have similar electronic absorption spectra with the absorption maximum localized at 517 and 501 nm for dye 1 and dye 2 , respectively. They exhibit well‐defined redox behavior, highlighting the presence of BODIPY and viologen subunits, with little perturbation of the redox potential of both subunits with respect to the parent compounds. Both dyes are heavily quenched by photoinduced electron transfer from the BODIPY to the viologen subunit. The transient absorption technique demonstrates that dye 2 forms the viologen radical within a timeframe of 7.1 ps, and that the charge‐separated species has a lifetime of 59 ps. Sustained irradiation of dye 2 in the presence of a tertiary amine allows for the accumulation of BODIPY–methyl‐4,4′‐bipyridinium (BODIPY–MV + ), as observed by its characteristic absorption at 396 and 603 nm. However, dye 2 does not generate catalytic amounts of hydrogen under standard conditions. DA - 2013/8/15/ PY - 2013/8/15/ DO - 10.1002/CPHC.201300547 VL - 14 IS - 14 SP - 3348-3354 J2 - ChemPhysChem LA - en OP - SN - 1439-4235 UR - http://dx.doi.org/10.1002/CPHC.201300547 DB - Crossref KW - absorption KW - dyes KW - pigments KW - electron transfer KW - fluorescent probes KW - photophysics ER - TY - JOUR TI - Ranking Solvent Interactions and Dielectric Constants with [Pt(mesBIAN)(tda)]: A Cautionary Tale for Polarity Determinations in Ionic Liquids AU - Baker, Gary A. AU - Rachford, Aaron A. AU - Castellano, Felix N. AU - Baker, Sheila N. T2 - ChemPhysChem AB - Abstract The solvatochromic properties of [Pt(mesBIAN)(tda)] are studied in traditional molecular solvents and ionic liquids and duly compared along established empirical solvent parameter scales. The charge‐transfer absorption band of [Pt(mesBIAN)(tda)] is determined to be primarily dependent upon solvent acidity and dipolarity. Notably, ionic liquids do not obey the same well‐behaved trend as molecular solvents, highlighting the complexity and domain (nano)segregation inherent to ionic liquids. DA - 2013/2/21/ PY - 2013/2/21/ DO - 10.1002/CPHC.201200981 VL - 14 IS - 5 SP - 1025-1030 J2 - ChemPhysChem LA - en OP - SN - 1439-4235 UR - http://dx.doi.org/10.1002/CPHC.201200981 DB - Crossref KW - charge-transfer absorption KW - dielectric constants KW - ionic liquids KW - nano(segregation) KW - polarity ER - TY - JOUR TI - Surface Electrostatics and Peptide Binding to Lipid Bilayer of Defined Curvature AU - Voinov, Maxim A. AU - Marek, Antonin AU - Kett, Peter AU - Smirnov, Alex I. T2 - Biophysical Journal AB - Many proteins are known to have strong binding preferences for curved lipid bilayer surfaces. This property of proteins to sense membrane curvature has a number of implications in cellular processes including endocytosis, exocytosis, and vesicle trafficking as well as pathogenic processes associated with viral infections or protein aggregation disorders. Here we employ small unilamellar vesicles (SUVs) that are sized by extrusion through nanoporous filters as a model of convex membranes with accessible outer surface. For concave structures we developed nanopore-confined tubular lipid bilayers with tunable curvature radii ranging from ca. 40 to 250 nm. The nanotubular bilayers are formed by lipid self-assembly inside cylindrical nanopores of anodic aluminum oxide (AAO). These systems impose essentially no restrictions on the lipid composition and have the inner surface of negative curvature accessible for solute molecules and peptide binding. Using these model structures we show that the surface electrostatic potential of lipid bilayers is affected by the curvature to a rather large degree. For example, for SUVs composed of negatively charged lipids the magnitude of the surface potential increased with bilayer bending from ca. −106 mV for 100 nm SUV to −166 mV for 30 nm SUVs. These measurements were carried out by spin probe EPR method using recently synthesized lipids having pH-reporting nitroxides covalently tethered to the lipid polar head. EPR titration experiments were followed by the measurement of the lipid vesicle electrophoretic mobility and peptide binding. Overall, the data indicate that the bilayer bending affects the local electrostatic potential in a rather large degree providing a likely biophysical mechanism for affecting protein binding to lipid membranes without adjusting lipid composition. Supported by U.S. DOE Contract DE-FG02-02ER15354. DA - 2013/1// PY - 2013/1// DO - 10.1016/j.bpj.2012.11.579 VL - 104 IS - 2 SP - 98a J2 - Biophysical Journal LA - en OP - SN - 0006-3495 UR - http://dx.doi.org/10.1016/j.bpj.2012.11.579 DB - Crossref ER - TY - JOUR TI - Iron(ii) spin crossover films on Au(111): scanning probe microscopy and photoelectron spectroscopy AU - Pronschinske, Alex AU - Bruce, Robert C. AU - Lewis, Geoff AU - Chen, Yifeng AU - Calzolari, Arrigo AU - Buongiorno-Nardelli, Marco AU - Shultz, David A. AU - You, Wei AU - Dougherty, Daniel B. T2 - Chemical Communications AB - The growth of films of [H2B(pz)2]Fe(II)(bpy) on Au(111) is characterized from the bilayer film to multilayer film regime. Scanning tunneling microscopy shows a transition from a well-ordered, uniform bilayer film to a poorly-ordered film at larger thicknesses. Previous local tunneling spectroscopy and conductance mapping in bilayer films permit the identification of coexisting molecular spin-states at all temperatures. New ultraviolet photoelectron spectroscopy is consistent with this picture and in agreement with the density of states calculated by density functional theory. In thicker films with a polycrystalline morphology, evidence for a more bulk-like change in spin composition as a function of temperature is obtained by observing the reduction in intensity of Fe 2p core level satellites in X-ray photoelectron spectra. DA - 2013/// PY - 2013/// DO - 10.1039/C3CC44904A VL - 49 IS - 89 SP - 10446 J2 - Chem. Commun. LA - en OP - SN - 1359-7345 1364-548X UR - http://dx.doi.org/10.1039/C3CC44904A DB - Crossref ER - TY - JOUR TI - Modification of Molecular Spin Crossover in Ultrathin Films AU - Pronschinske, Alex AU - Chen, Yifeng AU - Lewis, Geoffrey F. AU - Shultz, David A. AU - Calzolari, Arrigo AU - Buongiorno Nardelli, Marco AU - Dougherty, Daniel B. T2 - Nano Letters AB - Scanning tunneling microscopy and local conductance mapping show spin-state coexistence in bilayer films of Fe[(H2Bpz2)2bpy] on Au(111) that is independent of temperature between 131 and 300 K. This modification of bulk behavior is attributed in part to the unique packing constraints of the bilayer film that promote deviations from bulk behavior. The local density of states measured for different spin states shows that high-spin molecules have a smaller transport gap than low-spin molecules and are in agreement with density functional theory calculations. DA - 2013/3/27/ PY - 2013/3/27/ DO - 10.1021/nl304304e VL - 13 IS - 4 SP - 1429-1434 J2 - Nano Lett. LA - en OP - SN - 1530-6984 1530-6992 UR - http://dx.doi.org/10.1021/nl304304e DB - Crossref KW - Molecular spintronics KW - spin crossover KW - scanning tunneling microscopy KW - density functional theory ER - TY - JOUR TI - Transition metal complexes of donor–acceptor biradicals AU - Kirk, Martin L. AU - Shultz, David A. T2 - Coordination Chemistry Reviews AB - The nature of the electronic coupling in transition metal Donor–Acceptor and Donor–Bridge–Acceptor systems has become a subject of interest in the last decade due to the importance of electronic coupling in molecular electronics. Here we review the synthesis, structure, magnetism, and spectroscopy of donor–acceptor biradicals as they pertain to understanding the electronic origins and magnitude of the electronic coupling matrix element that figures prominently in electron transfer (transport). Stable D–A systems may be thought of as ground state analogues of charge separated states generated in photoinduced electron transfer processes and as model systems for understanding single molecule mediated electron transport between biased nanoelectrodes. The strong coupling (adiabatic) regime will be covered in this review as well as the methodology for probing the magnitude of the electronic coupling in this limit. D–A biradicals can facilitate long-range ferromagnetic exchange between localized spins mediated by delocalized electrons, and this is a new phenomenon in molecular systems. The use of the VBCI approach to develop a complete electronic structure description of strong electronic coupling in D–A and D–B–A biradicals, the origin of long-range biradical ferromagnetic exchange, and the relationship of these biradicals to molecular electronic materials will form the basis of the review. DA - 2013/1// PY - 2013/1// DO - 10.1016/J.CCR.2012.07.007 VL - 257 IS - 1 SP - 218-233 J2 - Coordination Chemistry Reviews LA - en OP - SN - 0010-8545 UR - http://dx.doi.org/10.1016/J.CCR.2012.07.007 DB - Crossref KW - Semiquinone KW - Nitronyl nitroxide KW - Biradical KW - Valence bond configuration interaction KW - Heterospin biradical KW - Donor-acceptor KW - Electron correlation KW - Electron transfer KW - Electron transport KW - Excited state KW - Magnetic coupling KW - Ferromagnetic exchange KW - Donor-bridge-acceptor KW - Electronic structure KW - Electron paramagnetic resonance KW - Resonance Raman KW - Molecular orbital KW - Spin-dependent delocalization KW - Molecular electronics KW - Photoinduced electron transfer ER - TY - JOUR TI - Comparison of the growth and degradation of poly(glycolic acid) and poly(ε-caprolactone) brushes AU - Hu, Xinfang AU - Hu, Gongfang AU - Crawford, Kaitlyn AU - Gorman, Christopher B. T2 - Journal of Polymer Science Part A: Polymer Chemistry AB - The growth and degradation of poly(glycolic acid) (PGA) and poly(ε-caprolactone) (PCL) brushes were compared. Using tin (octanoate) as the catalyst, optimal conditions were found for growth of each polyester brush from the hydroxy-terminated silicon surface via ring-opening polymerization. PCL brushes grew thicker at elevated temperatures but the thickest PGA brushes grew at room temperature. Unlike bulk polyesters that can degrade under both acidic and basic conditions, the confined surface polyester brushes only degraded under neutral or basic conditions. The degradation mechanism of grafted polyester brushes was probed through a blocking test. It was shown that the terminal hydroxy groups of these polyester brushes were essential to the degradation process indicating a preferential backbiting mechanism. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 4643–4649 DA - 2013/8// PY - 2013/8// DO - 10.1002/POLA.26885 SP - n/a-n/a J2 - J. Polym. Sci. Part A: Polym. Chem. LA - en OP - SN - 0887-624X UR - http://dx.doi.org/10.1002/POLA.26885 DB - Crossref KW - degradation KW - polyesters KW - ring-opening polymerization ER - TY - JOUR TI - Correction to Elucidating Band-Selective Sensitization in Iron(II) Polypyridine-TiO2 Assemblies AU - Bowman, David N. AU - Blew, James H. AU - Tsuchiya, Takashi AU - Jakubikova, Elena T2 - Inorganic Chemistry AB - ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to Elucidating Band-Selective Sensitization in Iron(II) Polypyridine-TiO2 AssembliesDavid N. Bowman, James H. Blew, Takashi Tsuchiya, and Elena Jakubikova*Cite this: Inorg. Chem. 2013, 52, 24, 14449Publication Date (Web):December 4, 2013Publication History Published online4 December 2013Published inissue 16 December 2013https://doi.org/10.1021/ic402856jCopyright © 2013 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views329Altmetric-Citations8LEARN 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 InReddit PDF (190 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts DA - 2013/12/4/ PY - 2013/12/4/ DO - 10.1021/IC402856J VL - 52 IS - 24 SP - 14449-14449 J2 - Inorg. Chem. LA - en OP - SN - 0020-1669 1520-510X UR - http://dx.doi.org/10.1021/IC402856J DB - Crossref ER - TY - JOUR TI - Tyrosyl Radicals in Dehaloperoxidase AU - Dumarieh, Rania AU - D'Antonio, Jennifer AU - Deliz-Liang, Alexandria AU - Smirnova, Tatyana AU - Svistunenko, Dimitri A. AU - Ghiladi, Reza A. T2 - Journal of Biological Chemistry AB - Dehaloperoxidase (DHP) from Amphitrite ornata, having been shown to catalyze the hydrogen peroxide-dependent oxidation of trihalophenols to dihaloquinones, is the first oxygen binding globin that possesses a biologically relevant peroxidase activity. The catalytically competent species in DHP appears to be Compound ES, a reactive intermediate that contains both a ferryl heme and a tyrosyl radical. By simulating the EPR spectra of DHP activated by H2O2, Thompson et al. (Thompson, M. K., Franzen, S., Ghiladi, R. A., Reeder, B. J., and Svistunenko, D. A. (2010) J. Am. Chem. Soc. 132, 17501–17510) proposed that two different radicals, depending on the pH, are formed, one located on either Tyr-34 or Tyr-28 and the other on Tyr-38. To provide additional support for these simulation-based assignments and to deduce the role(s) that tyrosyl radicals play in DHP, stopped-flow UV-visible and rapid-freeze-quench EPR spectroscopic methods were employed to study radical formation in DHP when three tyrosine residues, Tyr-28, Tyr-34, and Tyr-38, were replaced either individually or in combination with phenylalanines. The results indicate that radicals form on all three tyrosines in DHP. Evidence for the formation of DHP Compound I in several tyrosine mutants was obtained. Variants that formed Compound I showed an increase in the catalytic rate for substrate oxidation but also an increase in heme bleaching, suggesting that the tyrosines are necessary for protecting the enzyme from oxidizing itself. This protective role of tyrosines is likely an evolutionary adaptation allowing DHP to avoid self-inflicted damage in the oxidative environment. Dehaloperoxidase (DHP) from Amphitrite ornata, having been shown to catalyze the hydrogen peroxide-dependent oxidation of trihalophenols to dihaloquinones, is the first oxygen binding globin that possesses a biologically relevant peroxidase activity. The catalytically competent species in DHP appears to be Compound ES, a reactive intermediate that contains both a ferryl heme and a tyrosyl radical. By simulating the EPR spectra of DHP activated by H2O2, Thompson et al. (Thompson, M. K., Franzen, S., Ghiladi, R. A., Reeder, B. J., and Svistunenko, D. A. (2010) J. Am. Chem. Soc. 132, 17501–17510) proposed that two different radicals, depending on the pH, are formed, one located on either Tyr-34 or Tyr-28 and the other on Tyr-38. To provide additional support for these simulation-based assignments and to deduce the role(s) that tyrosyl radicals play in DHP, stopped-flow UV-visible and rapid-freeze-quench EPR spectroscopic methods were employed to study radical formation in DHP when three tyrosine residues, Tyr-28, Tyr-34, and Tyr-38, were replaced either individually or in combination with phenylalanines. The results indicate that radicals form on all three tyrosines in DHP. Evidence for the formation of DHP Compound I in several tyrosine mutants was obtained. Variants that formed Compound I showed an increase in the catalytic rate for substrate oxidation but also an increase in heme bleaching, suggesting that the tyrosines are necessary for protecting the enzyme from oxidizing itself. This protective role of tyrosines is likely an evolutionary adaptation allowing DHP to avoid self-inflicted damage in the oxidative environment. DA - 2013/10/6/ PY - 2013/10/6/ DO - 10.1074/JBC.M113.496497 VL - 288 IS - 46 SP - 33470-33482 J2 - J. Biol. Chem. LA - en OP - SN - 0021-9258 1083-351X UR - http://dx.doi.org/10.1074/JBC.M113.496497 DB - Crossref KW - Hemoglobin KW - Iron KW - Peroxidase KW - Radicals KW - Tyrosine KW - Compound ES KW - Compound I KW - Compound II KW - Dehaloperoxidase KW - Ferryl ER - TY - JOUR TI - Molecular pH Probes at a Protein-Lipid Interface: Assessment of Local Dielectric Environment for Transmembrane Peptide AU - Donohue, Matthew AU - Voynov, Maxim A. AU - Smirnov, Alex I. AU - Smirnova, Tatyana I. T2 - Biophysical Journal AB - Spin-labeling EPR spectroscopy has found many applications in studying structure and dynamics of proteins and biological membranes. Recently, there has been substantial interest in utilizing EPR to characterize local effects of polarity and hydrogen bonding in these systems. Here we report on employing an pH-sensitive EPR probe IMSTL (S-(1-oxyl-2,2,3,5,5-pentamethylimidazolidin-4-ylmethyl) ester) to profile heterogeneous dielectric environments along the α-helix of a WALP peptide integrated in a lipid bilayer. A series of symmetrically positioned double cysteine mutants were labeled with a pH-sensitive nitroxide and the protonation state of IMTSL was directly observed by EPR. Q-band DEER experiments with double-labeled WALPs were employed to derive nitroxide-nitroxide distances of nitroxides before and after the protonation and, therefore, the positions of pH probes with respect to lipid bialyer. Thus, for the first time measurements of local electrostatics at peptide-bilayer interface were based on direct distance measurements rather than on assumptions on the probe location. For double-labeled WALP consecutive protonation of symmetrically positioned nitroxide tags was observed. The difference in observable pKa values was interpreted in terms of electrostatic interaction energy between titratable probes allowing us to estimate effective dielectric constant. Supported by NSF-0843632 to TIS. DA - 2013/1// PY - 2013/1// DO - 10.1016/j.bpj.2012.11.2073 VL - 104 IS - 2 SP - 373a J2 - Biophysical Journal LA - en OP - SN - 0006-3495 UR - http://dx.doi.org/10.1016/j.bpj.2012.11.2073 DB - Crossref ER - TY - JOUR TI - Redox states of Desulfovibrio vulgaris DsrC, a key protein in dissimilatory sulfite reduction AU - Venceslau, Sofia S. AU - Cort, John R. AU - Baker, Erin S. AU - Chu, Rosalie K. AU - Robinson, Errol W. AU - Dahl, Christiane AU - Saraiva, Ligia M. AU - Pereira, Ines A. C. T2 - Biochemical and Biophysical Research Communications AB - Dissimilatory reduction of sulfite is carried out by the siroheme enzyme DsrAB, with the involvement of the protein DsrC, which has two conserved redox-active cysteines. DsrC was initially believed to be a third subunit of DsrAB. Here, we report a study of the distribution of DsrC in cell extracts to show that, in the model sulfate reducer Desulfovibrio vulgaris, the majority of DsrC is not associated with DsrAB and is thus free to interact with other proteins. In addition, we developed a cysteine-labelling gel-shift assay to monitor the DsrC redox state and behaviour, and procedures to produce the different redox forms. The oxidized state of DsrC with an intramolecular disulfide bond, which is proposed to be a key metabolic intermediate, could be successfully produced for the first time by treatment with arginine. DA - 2013/// PY - 2013/// DO - 10.1016/j.bbrc.2013.10.116 VL - 441 IS - 4 SP - 732-736 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000328434800007&KeyUID=WOS:000328434800007 KW - Dissimilatory sulfite reductase KW - Desulfovibrio KW - DsrC KW - MalPEG KW - Gel-shift assay ER - TY - JOUR TI - LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets AU - Crowell, Kevin L. AU - Slysz, Gordon W. AU - Baker, Erin S. AU - LaMarche, Brian L. AU - Monroe, Matthew E. AU - Ibrahim, Yehia M. AU - Payne, Samuel H. AU - Anderson, Gordon A. AU - Smith, Richard D. T2 - Bioinformatics AB - The addition of ion mobility spectrometry to liquid chromatography-mass spectrometry experiments requires new, or updated, software tools to facilitate data processing.We introduce a command line software application LC-IMS-MS Feature Finder that searches for molecular ion signatures in multidimensional liquid chromatography-ion mobility spectrometry-mass spectrometry (LC-IMS-MS) data by clustering deisotoped peaks with similar monoisotopic mass, charge state, LC elution time and ion mobility drift time values. The software application includes an algorithm for detecting and quantifying co-eluting chemical species, including species that exist in multiple conformations that may have been separated in the IMS dimension.LC-IMS-MS Feature Finder is available as a command-line tool for download at http://omics.pnl.gov/software/LC-IMS-MS_Feature_Finder.php. The Microsoft.NET Framework 4.0 is required to run the software. All other dependencies are included with the software package. Usage of this software is limited to non-profit research to use (see README).rds@pnnl.gov.Supplementary data are available at Bioinformatics online. DA - 2013/// PY - 2013/// DO - 10.1093/bioinformatics/btt465 VL - 29 IS - 21 SP - 2804-2805 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000325997500024&KeyUID=WOS:000325997500024 ER - TY - JOUR TI - Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking AU - Merkley, Eric D. AU - Baker, Erin S. AU - Crowell, Kevin L. AU - Orton, Daniel J. AU - Taverner, Thomas AU - Ansong, Charles AU - Ibrahim, Yehia M. AU - Burnet, Meagan C. AU - Cort, John R. AU - Anderson, Gordon A. AU - Smith, Richard D. AU - Adkins, Joshua N. T2 - Journal of the American Society For Mass Spectrometry AB - Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone. DA - 2013/// PY - 2013/// DO - 10.1007/s13361-012-0565-x VL - 24 IS - 3 SP - 444-449 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000315515700016&KeyUID=WOS:000315515700016 KW - Cross-linking KW - Proteins KW - Cross-linked peptides KW - Ionmobility spectrometry KW - Mass Spectrometry KW - Liquid chromatography KW - Drift time KW - Protein structure KW - Heavy isotope labeling ER - TY - JOUR TI - Increasing confidence of LC-MS identifications by utilizing ion mobility spectrometry AU - Crowell, Kevin L. AU - Baker, Erin S. AU - Payne, Samuel H. AU - Ibrahim, Yehia M. AU - Monroe, Matthew E. AU - Slysz, Gordon W. AU - LaMarche, Brian L. AU - Petyuk, Vladislav A. AU - Piehowski, Paul D. AU - Danielson, William F., III AU - Anderson, Gordon A. AU - Smith, Richard D. T2 - International Journal of Mass Spectrometry AB - Ion mobility spectrometry in conjunction with liquid chromatography separations and mass spectrometry offers a range of new possibilities for analyzing complex biological samples. To fully utilize the information obtained from these three measurement dimensions, informatics tools based on the accurate mass and time tag methodology were modified to incorporate ion mobility spectrometry drift times for peptides observed in human serum. In this work a reference human serum database was created for 12,139 peptides and populated with the monoisotopic mass, liquid chromatography normalized elution time, and ion mobility spectrometry drift time(s) for each. We demonstrate that the use of three dimensions for peak matching during the peptide identification process resulted in an increased numbers of identifications and a lower false discovery rate relative to only using the mass and normalized elution time dimensions. DA - 2013/// PY - 2013/// DO - 10.1016/j.ijms.2013.06.028 VL - 354 SP - 312-317 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000327809900044&KeyUID=WOS:000327809900044 KW - Ion mobility spectrometry KW - Mass spectrometry KW - Peptide identification KW - LC-MS KW - LC-IMS-MS KW - AMT tag KW - False discovery rate KW - Drift time ER - TY - JOUR TI - Combining heavy isotope labeling, chemical cross-linking, ion mobility spectrometry, and mass spectrometry to study the structure of homomultimeric protein complexes AU - Merkley, Eric D. AU - Baker, Erin S. AU - Crowell, Kevin L. AU - Orton, Daniel J. AU - Taverner, Thomas AU - Ansong, Charles AU - Ibrahim, Yehia M. AU - Burnett, Meagan C. AU - Sanchez, Octavio AU - Cort, John R. AU - Anderson, Gordon A. AU - Smith, Richard D. AU - Adkins, Joshua N. T2 - Abstracts of Papers of the American Chemical Society DA - 2013/// PY - 2013/// VL - 246 UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000329618401034&KeyUID=WOS:000329618401034 ER - TY - BOOK TI - Experimental biochemistry: Theory, experiment, analysis and reporting AU - Hardin, C. AU - Ascencio-Ibaanez, T. AU - Knopp, J. DA - 2013/// PY - 2013/// PB - Dubuque, Iowa: Kendall Hunt ER - TY - CONF TI - Ligand field splittings in core level transitions for transition metal (TM) oxides: Tanabe-Sugano diagrams and (TM) dangling bonds in vacated O-atom defects AU - Lucovsky, G. AU - Wu, K. AU - Pappas, B. AU - Whitten, J. C2 - 2013/// C3 - Xxist international symposium on the jahn-teller effect 2012 DA - 2013/// VL - 428 ER - TY - JOUR TI - Systematic Evaluation of 2,6-Linked Pyridine-Thiophene Oligomers AU - Rocha, Silvia V. AU - Finney, Nathaniel S. T2 - JOURNAL OF ORGANIC CHEMISTRY AB - An efficient synthesis of alternating 2,6-linked pyridine–thiophene (Py-Th) oligomers allows systematic evaluation of their optical and electrochemical properties. The six- and eight-ring oligomers are revealed to be brightly luminescent, even in the solid state. The oligomers are easily reduced but cannot be electrochemically oxidized. The longer oligomers have reduction potentials similar to those reported for pyridine–thiophene polymers of less defined structure. Protonation of the pyridine or substitution at C4 are shown to further modulate the electronic properties and, in combination with the low-lying absolute LUMO energies, these data suggest that the compounds are potential n-type materials worthy of further study. DA - 2013/11/15/ PY - 2013/11/15/ DO - 10.1021/jo401735g VL - 78 IS - 22 SP - 11255-11261 SN - 1520-6904 ER - TY - JOUR TI - Synthesis, characterization and structural investigation of novel meso-pyridyl BODIPY–cobaloxime complexes AU - Bartelmess, Juergen AU - Weare, Walter W. AU - Sommer, Roger D. T2 - Dalton Transactions AB - We report the synthesis of four boron–dipyrromethene (BODIPY) sensitized cobaloxime complexes as structural models of light-driven proton reduction catalysts. The BODIPY chromophore is covalently linked to the cobaloxime via a pyridine molecule in the meso-position of the BODIPY. Electron withdrawing or donating substituents on the pyridine (e.g. chloro- or methyl-groups) allow a comparison of the influence of these substituents on cobaloxime–BODIPY interactions. This includes altering the overall stability of the complexes and tuning the catalytically relevant CoII/III redox couple over a range of 220 mV, which will assist in the design of future cobaloxime–chromophore complexes. All complexes were characterized using electrochemistry, electronic absorption and fluorescence spectroscopy. Additionally, we present crystal structures of the four new BODIPY–cobaloxime complexes and elucidate the influence of the structural modifications. We found that these compounds produce sub-stoichiometric quantities of hydrogen under standard photon-driven hydrogen evolving conditions. DA - 2013/// PY - 2013/// DO - 10.1039/c3dt51849c VL - 42 IS - 41 SP - 14883 ER - TY - JOUR TI - Superexchange Contributions to Distance Dependence of Electron Transfer/Transport: Exchange and Electronic Coupling in Oligo(para-Phenylene)- and Oligo(2,5-Thiophene)-Bridged Donor–Bridge–Acceptor Biradical Complexes AU - Kirk, Martin L. AU - Shultz, David A. AU - Stasiw, Daniel E. AU - Lewis, Geoffrey F. AU - Wang, Guangbin AU - Brannen, Candice L. AU - Sommer, Roger D. AU - Boyle, Paul D. T2 - Journal of the American Chemical Society AB - The preparation and characterization of three new donor–bridge–acceptor biradical complexes are described. Using variable-temperature magnetic susceptibility, EPR hyperfine coupling constants, and the results of X-ray crystal structures, we evaluate both exchange and electronic couplings as a function of bridge length for two quintessential molecular bridges: oligo(para-phenylene), β = 0.39 Å–1 and oligo(2,5-thiophene), β = 0.22 Å–1. This report represents the first direct comparison of exchange/electronic couplings and distance attenuation parameters (β) for these bridges. The work provides a direct measurement of superexchange contributions to β, with no contribution from incoherent hopping. The different β values determined for oligo(para-phenylene) and oligo(2,5-thiophene) are due primarily to the D–B energy gap, Δ, rather than bridge–bridge electronic couplings, HBB. This is supported by the fact that the HBB values extracted from the experimental data for oligo(para-phenylene) (HBB = 11 400 cm–1) and oligo(2,5-thiophene) (12 300 cm–1) differ by <10%. The results presented here offer unique insight into the intrinsic molecular factors that govern HDA and β, which are important for understanding the electronic origin of electron transfer and electron transport mediated by molecular bridges. DA - 2013/11/4/ PY - 2013/11/4/ DO - 10.1021/JA4081887 VL - 135 IS - 45 SP - 17144-17154 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/JA4081887 DB - Crossref ER - TY - JOUR TI - Spin-Peierls distortions in TiPO4 AU - Bykov, Maxim AU - Zhang, Jian AU - Schoenleber, Andreas AU - Woelfel, Alexander AU - Ali, Sk Imran AU - Smaalen, Sander AU - Glaum, R. AU - Koo, H. -J. AU - Whangbo, M. -H. AU - Reuvekamp, P. G. AU - Law, J. M. AU - Hoch, C. AU - Kremer, R. K. T2 - PHYSICAL REVIEW B AB - On the basis of single-crystal x-ray diffraction we show that TiPO${}_{4}$ undergoes a spin-Peierls distortion below 74.5(5) K, with a dimerization of the Ti chains along the $\mathbf{c}$ axis. Between 74.5(5) and 111.6(3) K, TiPO${}_{4}$ develops an incommensurate (IC) phase with temperature-dependent $\mathbf{q}$ vector (${\ensuremath{\sigma}}_{1}$,0,0). Density functional calculations strongly suggest that the IC phase results from a frustration of the lock-in spin-Peierls transition due to the competition of three energetically almost degenerate crystal structures and elastic coupling of the Ti chains via the bridging PO${}_{4}$ units. The phase transition into the IC phase is of second order, but the lock-in transition into the spin-Peierls distortion below 74.5 K is of weak first order in nature. DA - 2013/11/19/ PY - 2013/11/19/ DO - 10.1103/physrevb.88.184420 VL - 88 IS - 18 SP - SN - 2469-9969 ER - TY - JOUR TI - Small-molecule inhibition of bacterial two-component systems to combat antibiotic resistance and virulence AU - Worthington, Roberta J. AU - Blackledge, Meghan S. AU - Melander, Christian T2 - FUTURE MEDICINAL CHEMISTRY AB - Infections caused by multidrug-resistant bacteria are a considerable and increasing global problem. The development of new antibiotics is not keeping pace with the rapid evolution of resistance to almost all clinically available drugs, and novel strategies are required to fight bacterial infections. One such strategy is the control of pathogenic behaviors, as opposed to simply killing bacteria. Bacterial two-component system (TCS) signal transduction pathways control many pathogenic bacterial behaviors, such as virulence, biofilm formation and antibiotic resistance and are, therefore, an attractive target for the development of new drugs. This review presents an overview of TCS that are potential targets for such a strategy, describes small-molecules inhibitors of TCS identified to date and discusses assays for the identification of novel inhibitors. The future perspective for the identification and use of inhibitors of TCS to potentially provide new therapeutic options for the treatment of drug-resistant bacterial infections is discussed. DA - 2013/7// PY - 2013/7// DO - 10.4155/fmc.13.58 VL - 5 IS - 11 SP - 1265-1284 SN - 1756-8927 ER - TY - JOUR TI - Interface kinetic diffusion reaction leading to fast and continuous generation of AgCl nanocubes in NaCl solution AU - Lou, Z. Z. AU - Huang, B. B. AU - Wang, Z. Y. AU - Qin, X. Y. AU - Zhang, X. Y. AU - Liu, Y. Y. AU - Zhang, R. AU - Dai, Y. AU - Whangbo, M. H. T2 - Dalton Transactions (Cambridge, England : 2003) DA - 2013/// PY - 2013/// VL - 42 IS - 42 SP - 15219-15225 ER - TY - JOUR TI - Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments AU - Loziuk, Philip L. AU - Wang, Jack AU - Li, Quanzi AU - Sederoff, Ronald R. AU - Chiang, Vincent L. AU - Muddiman, David C. T2 - JOURNAL OF PROTEOME RESEARCH AB - Workflows in bottom-up proteomics have traditionally implemented the use of proteolysis during sample preparation; enzymatic digestion is most commonly performed using trypsin. This results in the hydrolysis of peptide bonds forming tryptic peptides, which can then be subjected to LC–MS/MS analysis. While the structure, specificity, and kinetics of trypsin are well characterized, a lack of consensus and understanding has remained regarding fundamental parameters critical to obtaining optimal data from a proteomics experiment. These include the type of trypsin used, pH during digestion, incubation temperature as well as enzyme-to-substrate ratio. Through the use of design of experiments (DOE), we optimized these parameters, resulting in deeper proteome coverage and a greater dynamic range of measurement. The knowledge gained from optimization of a discovery-based proteomics experiment was applied to targeted LC–MS/MS experiments using protein cleavage-isotope dilution mass spectrometry for absolute quantification. We demonstrated the importance of these digest parameters with respect to our limit of detection as well as our ability to acquire more accurate quantitative measurements. Additionally, we were able to quantitatively account for peptide decay observed in previous studies, caused by nonspecific activity of trypsin. The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics. DA - 2013/12// PY - 2013/12// DO - 10.1021/pr4008442 VL - 12 IS - 12 SP - 5820-5829 SN - 1535-3907 KW - design of experiments KW - proteolytic digestion KW - LC-MS/MS KW - Populus trichocarpa ER - TY - JOUR TI - Tyrosyl radicals in dehaloperoxidase how nature deals with evolving an oxygen-binding globin to a biologically relevant peroxidase AU - Dumarieh, R. AU - D'Antonio, J. AU - Deliz-Liang, A. AU - Smirnova, T. AU - Svistunenko, D. A. AU - Ghiladi, R. A. T2 - Journal of Biological Chemistry DA - 2013/// PY - 2013/// VL - 288 IS - 46 SP - 33470-33482 ER - TY - JOUR TI - Synthesis, Structure, Photophysics, and a DFT Study of Phosphorescent C*(NN)-N-boolean AND- and (CNN)-N-boolean AND-N-boolean AND-Coordinated Platinum Complexes AU - Harris, Caleb F. AU - Vezzu, Dileep A. K. AU - Bartolotti, Libero AU - Boyle, Paul D. AU - Huo, Shouquan T2 - INORGANIC CHEMISTRY AB - The reaction of N,N-diphenyl-2,2′-bipyridin-6-amine (L1) and N,N-diphenyl-6-(1H-pyrazol-1-yl)pyridin-2-amine (L2) with K2PtCl4 produced C*N∧N-coordinated cycloplatinated compounds with a five–six fused metallacycle 1a and 2a, respectively, which were then converted into their phenylacetylide derivatives 1b and 2b, respectively. Similar reactions starting from 2-phenyl-6-(1H-pyrazol-1-yl)pyridine (L3) produced C∧N∧N-coordinated platinum complexes 3a and 3b with a five–five-fused metallacycle. The structures of 1a, 1b, 2b, 3a, and 3b were determined by X-ray crystallography. The C*N∧N-coordinated platinum complexes are closer to a square geometry, whereas the C∧N∧N-coordinated complexes display a nearly perfect planar geometry. The π···π interactions were revealed in the crystal packing for 1a, 2b, and 3a with a π···π contact of 3.450, 3.422, and 3.414 Å, respectively. Two conformers were revealed in the crystal structure of 2b, one with the phenyl ring of the phenylacetylide being approximately parallel with the coordination plane and the other with the phenyl ring being approximately perpendicular to the coordination plane. Both 1a and 1b are weakly emissive in the red region. Complexes 2a and 3a are also weakly emissive, but their acetylide derivatives 2b and 3b emitted strongly green light at room temperature with quantum yields of 43 and 62%, respectively. DFT/TDDFT calculations were performed to elucidate the nature of their electronic transitions. The calculations suggested that lowest singlet and triplet excited states are characteristic of a mixed state involving one or more charge-transfer transitions such as ILCT, MLCT, and LLCT. DA - 2013/10/21/ PY - 2013/10/21/ DO - 10.1021/ic400732g VL - 52 IS - 20 SP - 11711-11722 SN - 1520-510X ER - TY - JOUR TI - Synthesis and Optical Properties of Ag(I), Pb(II), and Bi(III) Tantalate-Based Photocatalysts AU - Boltersdorf, Jonathan AU - Wong, Tricia AU - Maggard, Paul A. T2 - ACS CATALYSIS AB - The Ag(I) and Bi(III) tantalates Ag2Ta4O11, BiTa7O19, and Bi7Ta3O18 were prepared by solid-state methods at 1000 °C for 24–48 h. The Pb(II)-containing tantalate PbTa2O6 was prepared at 1100 °C for 24 h, whereas Pb3Ta4O13 and PbTa4O11 were synthesized from a reaction of A2Ta4O11 (A = Na, Ag) precursors with a PbCl2 flux (at 1:1, 5:1, and 10:1 molar ratios) at 700 °C from 24 to 96 h. The PbTa2O6, Pb3Ta4O13, and Bi7Ta3O18 structures consist of TaO6 layers and TaO6 chains/rings with Pb(II) ions located within the cavities. The structures of Ag2Ta4O11, PbTa4O11, and BiTa7O19 consist of layers of TaO7 pentagonal bipyramids that alternate with Ag(I), Pb(II), and Bi(III) cations, respectively. UV–vis diffuse reflectance data were used to measure bandgap sizes for Ag2Ta4O11 (∼3.9 eV), PbTa4O11 (∼3.8–3.95 eV), Pb3Ta4O13 (∼3.0 eV), PbTa2O6 (∼3.6 eV), BiTa7O19 (∼3.6 eV), and Bi7Ta3O18 (∼2.75 eV). A decrease in the band gap was observed with an increase in the Pb(II) or Bi(III) content. Photocatalytic activities of the platinized samples in aqueous solutions under ultraviolet irradiation were found to range from ∼7 to ∼194 μmol H2·g–1·h–1 in aqueous methanol and from ∼42 to ∼213 μmol O2·g–1·h–1 in aqueous silver nitrate. Electronic-structure calculations based on density functional theory show the highest-energy valence band states consist of the respective Ag 4d orbital/Pb 6s orbital/Bi 6s orbital and O 2p orbital contributions, and the lowest-energy conduction band states arise from the Ta 5d orbital contributions. The latter are delocalized over the TaO7 pentagonal bipyramid layers within the A2Ta4O11 (A = Na, Ag), PbTa4O11, and BiTa7O19 structures. Nearly all of the tantalates exhibit significant water oxidation photocatalytic activity. However, higher activity for water reduction was found for tantalates consisting of TaO7 pentagonal bipyramid layers that can serve as charge-migration pathways. DA - 2013/12// PY - 2013/12// DO - 10.1021/cs400707x VL - 3 IS - 12 SP - 2943-2953 SN - 2155-5435 KW - photocatalysis KW - lead exchange KW - layered tantalate KW - solar energy KW - band engineering ER - TY - JOUR TI - Synthesis and Characterization of MnCrO4, a New Mixed-Valence Antiferromagnet AU - Nalbandyan, Vladimir B. AU - Zvereva, Elena A. AU - Yalovega, Galina E. AU - Shukaev, Igor L. AU - Ryzhakova, Anastasiya P. AU - Guda, Alexander A. AU - Stroppa, Alessandro AU - Picozzi, Silvia AU - Vasiliev, Alexander N. AU - Whangbo, Myung-Hwan T2 - INORGANIC CHEMISTRY AB - A new orthorhombic phase, MnCrO4, isostructural with MCrO4 (M = Mg, Co, Ni, Cu, Cd) was prepared by evaporation of an aqueous solution, (NH4)2Cr2O7 + 2 Mn(NO3)2, followed by calcination at 400 °C. It is characterized by redox titration, Rietveld analysis of the X-ray diffraction pattern, Cr K edge and Mn K edge XANES, ESR, magnetic susceptibility, specific heat and resistivity measurements. In contrast to the high-pressure MnCrO4 phase where both cations are octahedral, the new phase contains Cr in a tetrahedral environment suggesting the charge balance Mn2+Cr6+O4. However, the positions of both X-ray absorption K edges, the bond lengths and the ESR data suggest the occurrence of some mixed-valence character in which the mean oxidation state of Mn is higher than 2 and that of Cr is lower than 6. Both the magnetic susceptibility and the specific heat data indicate an onset of a three-dimensional antiferromagnetic order at TN ≈ 42 K, which was confirmed also by calculating the spin exchange interactions on the basis of first principles density functional calculations. Dynamic magnetic studies (ESR) corroborate this scenario and indicate appreciable short-range correlations at temperatures far above TN. MnCrO4 is a semiconductor with activation energy of 0.27 eV; it loses oxygen on heating above 400 °C to form first Cr2O3 plus Mn3O4 and then Mn1.5Cr1.5O4 spinel. DA - 2013/10/21/ PY - 2013/10/21/ DO - 10.1021/ic401391b VL - 52 IS - 20 SP - 11850-11858 SN - 1520-510X ER - TY - JOUR TI - Lengthening the Intersubunit Linker of Procaspase 3 Leads to Constitutive Activation AU - MacKenzie, Sarah H. AU - Schipper, Joshua L. AU - England, Erika J. AU - Thomas, Melvin E., III AU - Blackburn, Kevin AU - Swartz, Paul AU - Clark, A. Clay T2 - BIOCHEMISTRY AB - The conformational ensemble of procaspase 3, the primary executioner in apoptosis, contains two major forms, inactive and active, with the inactive state favored in the native ensemble. A region of the protein known as the intersubunit linker (IL) is cleaved during maturation, resulting in movement of the IL out of the dimer interface and subsequent active site formation (activation-by-cleavage mechanism). We examined two models for the role of the IL in maintaining the inactive conformer, an IL-extension model versus a hydrophobic cluster model, and we show that increasing the length of the IL by introducing 3-5 alanines results in constitutively active procaspases. Active site labeling and subsequent analyses by mass spectrometry show that the full-length zymogen is enzymatically active. We also show that minor populations of alternately cleaved procaspase result from processing at D169 when the normal cleavage site, D175, is unavailable. Importantly, the alternately cleaved proteins have little to no activity, but increased flexibility of the linker increases the exposure of D169. The data show that releasing the strain of the short IL, in and of itself, is not sufficient to populate the active conformer of the native ensemble. The IL must also allow for interactions that stabilize the active site, possibly from a combination of optimal length, flexibility in the IL, and specific contacts between the IL and interface. The results provide further evidence that substantial energy is required to shift the protein to the active conformer. As a result, the activation-by-cleavage mechanism dominates in the cell. DA - 2013/9/10/ PY - 2013/9/10/ DO - 10.1021/bi400793s VL - 52 IS - 36 SP - 6219-6231 SN - 0006-2960 ER - TY - JOUR TI - In Situ Electrode Calibration Strategy for Voltammetric Measurements In Vivo AU - Roberts, James G. AU - Toups, J. Vincent AU - Eyualem, Eyob AU - McCarty, Gregory S. AU - Sombers, Leslie A. T2 - ANALYTICAL CHEMISTRY AB - Technological advances have allowed background-subtracted fast-scan cyclic voltammetry to emerge as a powerful tool for monitoring molecular fluctuations in living brain tissue; however, there has been little progress to date in advancing electrode calibration procedures. Variability in the performance of these handmade electrodes renders calibration necessary for accurate quantification; however, experimental protocol makes standard postcalibration difficult or in some cases impossible. We have developed a model that utilizes information contained in the background charging current to predict electrode sensitivity to dopamine, ascorbic acid, hydrogen peroxide, and pH shifts at any point in an electrochemical experiment. Analysis determined a high correlation between predicted sensitivity and values obtained using the traditional postcalibration method, across all analytes. To validate this approach in vivo, calibration factors obtained with this model at electrodes in brain tissue were compared to values obtained at these electrodes using a traditional ex vivo calibration. Both demonstrated equal power of predictability for dopamine concentrations. This advance enables in situ electrode calibration, allowing researchers to track changes in electrode sensitivity over time and eliminating the need to generalize calibration factors between electrodes or across multiple days in an experiment. DA - 2013/12/3/ PY - 2013/12/3/ DO - 10.1021/ac402884n VL - 85 IS - 23 SP - 11568-11575 SN - 1520-6882 ER - TY - JOUR TI - Hydrogen Sensing under Ambient Conditions Using SnO2 Nanowires: Synergetic Effect of Pd/Sn Codeposition AU - Jeong, Seung Ho AU - Kim, Sol AU - Cha, Junho AU - Son, Min Soo AU - Park, Sang Han AU - Kim, Ha-Yeong AU - Cho, Man Ho AU - Whangbo, Myung-Hwan AU - Yoo, Kyung-Hwa AU - Kim, Sung-Jin T2 - NANO LETTERS AB - Semiconducting SnO2 nanowires deposited with Pd and Sn nanoparticles on their surface are shown to be a highly sensitive hydrogen sensor with fast response time at room temperature. Compared with the SnO2 nanowire deposited with Pd or Sn nanoparticles alone, the Pd/Sn-deposited SnO2 nanowire exhibits a significant improvement in the sensitivity and reversibility of sensing hydrogen gas in the air at room temperature. Our investigation indicates that two factors are responsible for the synergistic effect of Pd/Sn codeposition on SnO2 nanowires. One is that in the presence of Pd the oxidation of Sn nanoparticles on the surface of the SnO2 nanowire is incomplete leading only to suboxides SnOx (1 ≤ x < 2), and the other is that the surface of the Pd/Sn-deposited SnO2 nanowire is almost perfectly hydrophobic. DA - 2013/12// PY - 2013/12// DO - 10.1021/nl402998g VL - 13 IS - 12 SP - 5938-5943 SN - 1530-6992 KW - Room-temperature hydrogen sensor KW - SnO2 nanowire KW - synergetic effect of Pd/Sn codeposition ER - TY - JOUR TI - Highly Active Modulators of Indole Signaling Alter Pathogenic Behaviors in Gram-Negative and Gram-Positive Bacteria AU - Minvielle, Marine J. AU - Eguren, Kristen AU - Melander, Christian T2 - CHEMISTRY-A EUROPEAN JOURNAL AB - Abstract Indole is a universal signal that regulates various bacterial behaviors, such as biofilm formation and antibiotic resistance. To generate mechanistic probes of indole signaling and control indole‐mediated pathogenic phenotypes in both Gram‐positive and Gram‐negative bacteria, we have investigated the use of desformylflustrabromine (dFBr) derivatives to generate highly active indole mimetics. We have developed non‐microbicidal dFBr derivatives that are 27–2000 times more active than indole in modulating biofilm formation, motility, acid resistance, and antibiotic resistance. The activity of these analogues parallels indole, because they are dependent on temperature, the enzyme tryptophanase TnaA, and the transcriptional regulator SdiA. This investigation demonstrates that molecules based on the dFBr scaffold can alter pathogenic behaviors by mimicking indole‐signaling pathways. DA - 2013/12/16/ PY - 2013/12/16/ DO - 10.1002/chem.201303510 VL - 19 IS - 51 SP - 17595-17602 SN - 1521-3765 KW - desformylflustrabromine KW - mechanistic probes KW - natural products KW - phenotype control KW - structure-activity relationships ER - TY - JOUR TI - Functional Consequences of the Open Distal Pocket of Dehaloperoxidase-Hemoglobin Observed by Time-Resolved X-ray Crystallography AU - Zhao, Junjie AU - Srajer, Vukica AU - Franzen, Stefan T2 - BIOCHEMISTRY AB - Using time-resolved X-ray crystallography, we contrast a bifunctional dehaloperoxidase-hemoglobin (DHP) with previously studied examples of myoglobin and hemoglobin to understand the functional role of the distal pocket of globins. One key functional difference between DHP and other globins is the requirement that H2O2 enter the distal pocket of oxyferrous DHP to displace O2 from the heme Fe atom and thereby activate the heme for the peroxidase function. The open architecture of DHP permits more than one molecule to simultaneously enter the distal pocket of the protein above the heme to facilitate the unique peroxidase cycle starting from the oxyferrous state. The time-resolved X-ray data show that the distal pocket of DHP lacks a protein valve found in the two other globins that have been studied previously. The photolyzed CO ligand trajectory in DHP does not have a docking site; rather, the CO moves immediately to the Xe-binding site. From there, CO can escape but can also recombine an order of magnitude more rapidly than in other globins. The contrast with DHP dynamics and function more precisely defines the functional role of the multiple conformational states of myoglobin. Taken together with the high reduction potential of DHP, the open distal site helps to explain how a globin can also function as a peroxidase. DA - 2013/11/12/ PY - 2013/11/12/ DO - 10.1021/bi401118q VL - 52 IS - 45 SP - 7943-7950 SN - 0006-2960 ER - TY - JOUR TI - Experimental Determination of the Crystallization Phase-Boundary Velocity in the Halozeotype CZX-1 AU - Dill, Eric D. AU - Josey, Amanda A. AU - Folmer, Jacob C.W. AU - Hou, Feier AU - Martin, James D. T2 - Chemistry of Materials AB - Isothermal crystallization experiments were performed on the halozeotype CZX-1 with 2D temperature- and time-resolved synchrotron X-ray diffraction (TtXRD) and differential scanning calorimetry (DSC). These crystallization experiments demonstrate that the fundamental materials property, the velocity of the phase boundary of the crystallization front, vpb, can be recovered from the Kolmogorov Johnson and Mehl and Avrami (KJMA) model of phase-boundary controlled reactions by introducing the sample volume into the KJMA rate expression. An additional corrective term is required if the sample volume of the crystallization measurement is anisotropic. The concurrent disappearance of the melt and appearance of the crystalline phase demonstrate that no intermediates exist in the crystallization pathway. The velocity of the phase boundary approaches 0 as the glass transition (Tg ≈ 30 °C) is approached and at about 10° below melting point (Tm = 173 °C). The velocity of the phase boundary reaches a maximum of 30 μm s–1 at 135 °C. Single or near-single crystals are grown under conditions where the vpb is much greater than the rate of nucleation. DA - 2013/10/10/ PY - 2013/10/10/ DO - 10.1021/cm402745e VL - 25 IS - 20 SP - 3932-3940 J2 - Chem. Mater. LA - en OP - SN - 0897-4756 1520-5002 UR - http://dx.doi.org/10.1021/cm402745e DB - Crossref KW - crystallization kinetics KW - Avrami KW - DSC kinetics KW - XRD kinetics KW - phase-boundary velocity KW - time-resolved diffraction KW - synchrotron ER - TY - JOUR TI - Evidence of Entropy-Driven Bistability through N-15 NMR Analysis of a Temperature- and Solvent-Induced, Chiroptical Switching Polycarbodiimide AU - Reuther, James F. AU - Novak, Bruce M. T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - The thermo- and solvo-driven chiroptical switching process observed in specific polycarbodiimides occurs in a concerted fashion with large deviations in specific optical rotation (OR) and CD Cotton effect as a consequence of varying populations of two distinct polymer conformations. These two conformations are clearly visible in the 15N NMR and IR spectra of the 15N-labeled poly(15N-(1-naphthyl)-N′-octadecylcarbodiimide) (Poly-3) and poly(15N-(1-naphthyl)-15N′-octadecylcarbodiimide) (Poly-5). Using van’t Hoff analysis, the enthalpies and entropies of switching (ΔHswitching; ΔSswitching) were calculated for both Poly-3 and Poly-5 using the relative integrations of both peaks in the 15N NMR spectra at different temperatures to measure the populations of each state. The chiroptical switching (i.e., transitioning from state A to state B) was found to be an endothermic process (positive ΔHswitching) for both Poly-3 and Poly-5 in all solvents studied, meaning the conformation correlating with the downfield chemical shift (ca. 148 ppm, state B) is the higher enthalpy state. The compensating factor behind this phenomenon has been determined to be the large increase in entropy in CHCl3 as a result of the switching. Herein, we propose that the increased entropy in the system is a direct consequence of increased disorder in the solvent as the switching occurs. Specifically, the chloroform solvent molecules are very ordered around the polymer chains due to favorable solvent–polymer interactions, but as the switching occurs, these interactions become less favorable and disorder results. The same level of solvent disorder is not achieved in toluene, causing the chiroptical switching process to occur at higher temperatures. DA - 2013/12/25/ PY - 2013/12/25/ DO - 10.1021/ja4098803 VL - 135 IS - 51 SP - 19292-19303 SN - 0002-7863 ER - TY - JOUR TI - Efficient Separation of Photogenerated Electron-Hole Pairs by the Combination of a Heterolayered Structure and Internal Polar Field in Pyroelectric BiOIO3 Nanoplates AU - Wang, Wenjun AU - Huang, Baibiao AU - Ma, Xiangchao AU - Wang, Zeyan AU - Qin, Xiaoyan AU - Zhang, Xiaoyang AU - Dai, Ying AU - Whangbo, Myung-Hwan T2 - CHEMISTRY-A EUROPEAN JOURNAL AB - Electrify your chemistry! Pyroelectric heterolayered BiOIO3 nanoplates efficiently separate photogenerated electron-hole pairs due to the combined effect of their heterolayered structure and internal polar field (see scheme). Pyroelectric BiOIO3 nanoplates, synthesized by a simple hydrothermal method, were found to possess a superior photocatalytic activity under UV irradiation. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. DA - 2013/10/25/ PY - 2013/10/25/ DO - 10.1002/chem.201302884 VL - 19 IS - 44 SP - 14777-14780 SN - 1521-3765 KW - BiOIO3 KW - electron-hole separation KW - heterolayered structure KW - photocatalysts KW - polar field KW - semiconducters ER - TY - JOUR TI - Crystal Growth Simulations To Establish Physically Relevant Kinetic Parameters from the Empirical Kolmogorov–Johnson–Mehl–Avrami Model AU - Dill, Eric D. AU - Folmer, Jacob C. W. AU - Martin, James D. T2 - Chemistry of Materials AB - A series of simulations was performed to enable interpretation of the material and physical significance of the parameters defined in the Kolmogorov, Johnson and Mehl, and Avrami (KJMA) rate expression commonly used to describe phase boundary controlled reactions of condensed matter. The parameters k, n, and t0 are shown to be highly correlated, which if unaccounted for seriously challenge mechanistic interpretation. It is demonstrated that rate measurements exhibit an intrinsic uncertainty without precise knowledge of the location and orientation of nucleation with respect to the free volume into which it grows. More significantly, it is demonstrated that the KJMA rate constant k is highly dependent on sample size. However, under the simulated conditions of slow nucleation relative to crystal growth, sample volume and sample anisotropy correction affords a means to eliminate the experimental condition dependence of the KJMA rate constant, k, producing the material-specific parameter, the velocity of the phase boundary, vpb. DA - 2013/10/10/ PY - 2013/10/10/ DO - 10.1021/cm402751x VL - 25 IS - 20 SP - 3941-3951 J2 - Chem. Mater. LA - en OP - SN - 0897-4756 1520-5002 UR - http://dx.doi.org/10.1021/cm402751x DB - Crossref KW - crystallization simulation KW - nucleation rate KW - Avrami KW - crystallization kinetics KW - phase boundary velocity KW - size-effect KW - shape-effect ER - TY - JOUR TI - Cellular Delivery and Photochemical Activation of Antisense Agents through a Nucleobase Caging Strategy AU - Govan, Jeane M. AU - Uprety, Rajendra AU - Thomas, Meryl AU - Lusic, Hrvoje AU - Lively, Mark O. AU - Deiters, Alexander T2 - ACS CHEMICAL BIOLOGY AB - Antisense oligonucleotides are powerful tools to regulate gene expression in cells and model organisms. However, a transfection or microinjection is typically needed for efficient delivery of the antisense agent. We report the conjugation of multiple HIV TAT peptides to a hairpin-protected antisense agent through a light-cleavable nucleobase caging group. This conjugation allows for the facile delivery of the antisense agent without a transfection reagent, and photochemical activation offers precise control over gene expression. The developed approach is highly modular, as demonstrated by the conjugation of folic acid to the caged antisense agent. This enabled targeted cell delivery through cell-surface folate receptors followed by photochemical triggering of antisense activity. Importantly, the presented strategy delivers native oligonucleotides after light-activation, devoid of any delivery functionalities or modifications that could otherwise impair their antisense activity. DA - 2013/10// PY - 2013/10// DO - 10.1021/cb400293e VL - 8 IS - 10 SP - 2272-2282 SN - 1554-8937 ER - TY - JOUR TI - Biologically inspired strategies for combating bacterial biofilms AU - Blackledge, Meghan S. AU - Worthington, Roberta J. AU - Melander, Christian T2 - CURRENT OPINION IN PHARMACOLOGY AB - Infections caused by bacterial biofilms are a significant global health problem, causing considerable patient morbidity and mortality and contributing to the economic burden of infectious disease. This review describes diverse strategies to combat bacterial biofilms, focusing firstly on small molecule interference with bacterial communication and signaling pathways, including quorum sensing and two-component signal transduction systems. Secondly we discuss enzymatic approaches to the degradation of extracellular matrix components to effect biofilm dispersal. Both of these approaches are based upon non-microbicidal mechanisms of action, and thereby do not place a direct evolutionary pressure on the bacteria to develop resistance. Such approaches have the potential to, in combination with conventional antibiotics, play an important role in the eradication of biofilm based bacterial infections. DA - 2013/10// PY - 2013/10// DO - 10.1016/j.coph.2013.07.004 VL - 13 IS - 5 SP - 699-706 SN - 1471-4973 ER - TY - JOUR TI - The UDP-diacylglucosamine Pyrophosphohydrolase LpxH in Lipid A Biosynthesis Utilizes Mn2+ Cluster for Catalysis AU - Young, Hayley E. AU - Donohue, Matthew P. AU - Smirnova, Tatyana I. AU - Smirnov, Alex I. AU - Zhou, Pei T2 - JOURNAL OF BIOLOGICAL CHEMISTRY AB - In Escherichia coli and the majority of β- and γ-proteobacteria, the fourth step of lipid A biosynthesis, i.e. cleavage of the pyrophosphate group of UDP-2,3-diacyl-GlcN, is carried out by LpxH. LpxH has been previously suggested to contain signature motifs found in the calcineurin-like phosphoesterase (CLP) family of metalloenzymes; however, it cleaves a pyrophosphate bond instead of a phosphoester bond, and its substrate contains nucleoside diphosphate moieties more common to the Nudix family rather than to the CLP family. Furthermore, the extent of biochemical data fails to demonstrate a significant level of metal activation in enzymatic assays, which is inconsistent with the behavior of a metalloenzyme. Here, we report cloning, purification, and detailed enzymatic characterization of Haemophilus influenzae LpxH (HiLpxH). HiLpxH shows over 600-fold stimulation of hydrolase activity in the presence of Mn2+. EPR studies reveal the presence of a Mn2+ cluster in LpxH. Finally, point mutants of residues in the conserved metal-binding motifs of the CLP family greatly inhibit HiLpxH activity, highlighting their importance in enzyme function. Contrary to previous analyses of LpxH, we find HiLpxH does not obey surface dilution kinetics. Overall, our work unambiguously establishes LpxH as a calcineurin-like phosphoesterase containing a Mn2+ cluster coordinated by conserved residues. These results set the scene for further structural investigation of the enzyme and for design of novel antibiotics targeting lipid A biosynthesis.Background: LpxH is a novel pyrophosphate hydrolase in lipid A biosynthesis.Results: Enzymatic and EPR studies reveal a catalytically important Mn2+ cluster within LpxH.Conclusion: LpxH is a Mn2+-dependent lipid A enzyme with an active site similar to calcineurin-like phosphatases, not Nudix family hydrolases.Significance: Unmasking the true nature of LpxH catalysis represents an important step toward structural characterization and development of antibiotics. In Escherichia coli and the majority of β- and γ-proteobacteria, the fourth step of lipid A biosynthesis, i.e. cleavage of the pyrophosphate group of UDP-2,3-diacyl-GlcN, is carried out by LpxH. LpxH has been previously suggested to contain signature motifs found in the calcineurin-like phosphoesterase (CLP) family of metalloenzymes; however, it cleaves a pyrophosphate bond instead of a phosphoester bond, and its substrate contains nucleoside diphosphate moieties more common to the Nudix family rather than to the CLP family. Furthermore, the extent of biochemical data fails to demonstrate a significant level of metal activation in enzymatic assays, which is inconsistent with the behavior of a metalloenzyme. Here, we report cloning, purification, and detailed enzymatic characterization of Haemophilus influenzae LpxH (HiLpxH). HiLpxH shows over 600-fold stimulation of hydrolase activity in the presence of Mn2+. EPR studies reveal the presence of a Mn2+ cluster in LpxH. Finally, point mutants of residues in the conserved metal-binding motifs of the CLP family greatly inhibit HiLpxH activity, highlighting their importance in enzyme function. Contrary to previous analyses of LpxH, we find HiLpxH does not obey surface dilution kinetics. Overall, our work unambiguously establishes LpxH as a calcineurin-like phosphoesterase containing a Mn2+ cluster coordinated by conserved residues. These results set the scene for further structural investigation of the enzyme and for design of novel antibiotics targeting lipid A biosynthesis. Background: LpxH is a novel pyrophosphate hydrolase in lipid A biosynthesis. Results: Enzymatic and EPR studies reveal a catalytically important Mn2+ cluster within LpxH. Conclusion: LpxH is a Mn2+-dependent lipid A enzyme with an active site similar to calcineurin-like phosphatases, not Nudix family hydrolases. Significance: Unmasking the true nature of LpxH catalysis represents an important step toward structural characterization and development of antibiotics. DA - 2013/9/20/ PY - 2013/9/20/ DO - 10.1074/jbc.m113.497636 VL - 288 IS - 38 SP - 26987-27001 SN - 1083-351X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84884550173&partnerID=MN8TOARS ER - TY - JOUR TI - Structural Refinement of Ladder-Type Perylenediimide Dimers: A Classical Tale of Conformational Dynamics AU - Myahkostupov, Mykhaylo AU - Prusakova, Valentina AU - Oblinsky, Daniel G. AU - Scholes, Gregory D. AU - Castellano, Felix N. T2 - JOURNAL OF ORGANIC CHEMISTRY AB - We have synthesized and thoroughly characterized two representative ladder-type acetylene-bridged perylenediimide dimers bearing long alkyl chain solubilizing groups, bis[1-ethynyl-N,N′-bis(1-hexylheptyl)-perylene-3,4:9,10-tetracarboxylic diimide] ([PDICC]2, 1) and 1,1′-ethynyl-bis[N,N′-bis(1-hexylheptyl)-perylene-3,4:9,10-tetracarboxylic diimide] ([PDI]2CC, 2). In these dimeric PDI molecules, NMR-based structural characterization became nontrivial because severe 1H spectral broadening and greater than expected numbers of observed 13C resonances substantially complicated the interpretation of traditional 1-D spectra. However, rational two-dimensional NMR approaches based on both homo- and heteronuclear couplings (1H–1H COSY; 1H–13C HSQC), in conjunction with high-level structural DFT calculations (GIAO/B3LYP/6-31G(d,p)/PCM, chloroform), were readily applied to these structures, producing well-defined analytical characterization, and the associated methodology is described in detail. Furthermore, on the basis of dynamic NMR experiments, both 1 and 2 were found to exist in a perylene-centered conformational dynamic equilibrium (ΔG‡ = 13–17 kcal/mol), which primarily caused the observed ambiguities in conventional 1-D spectra. DA - 2013/9/6/ PY - 2013/9/6/ DO - 10.1021/jo401348w VL - 78 IS - 17 SP - 8634-8644 SN - 0022-3263 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84883763311&partnerID=MN8TOARS ER - TY - JOUR TI - Robust Cuprous Phenanthroline Sensitizer for Solar Hydrogen Photocatalysis AU - Khnayzer, Rony S. AU - McCusker, Catherine E. AU - Olaiya, Babatunde S. AU - Castellano, Felix N. T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - The Cu(I) metal-to-ligand charge-transfer complex, [Cu(dsbtmp)2](+) (dsbtmp = 2,9-di(sec-butyl)-3,4,7,8-tetramethyl-1,10-phenanthroline), exhibits outstanding stability as a visible-light-absorbing photosensitizer in hydrogen-evolving homogeneous photocatalysis. In concert with the Co(dmgH)2(py)Cl water reduction catalyst and N,N-dimethyl-p-toluidine sacrificial donor in 1:1 H2O:CH3CN, this Cu(I) sensitizer remains active even after 5 days of visible-light-pumped (λex = 452 ± 10 nm) hydrogen evolution catalysis. Deuteration studies illustrate that the hydrogen produced from this composition does indeed originate from aqueous protons. DA - 2013/9/25/ PY - 2013/9/25/ DO - 10.1021/ja407816f VL - 135 IS - 38 SP - 14068-14070 SN - 0002-7863 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84884875774&partnerID=MN8TOARS ER - TY - JOUR TI - Optochemical control of RNA interference in mammalian cells AU - Govan, Jeane M. AU - Young, Douglas D. AU - Lusic, Hrvoje AU - Liu, Qingyang AU - Lively, Mark O. AU - Deiters, Alexander T2 - NUCLEIC ACIDS RESEARCH AB - Short interfering RNAs (siRNAs) and microRNAs (miRNAs) have been widely used in mammalian tissue culture and model organisms to selectively silence genes of interest. One limitation of this technology is the lack of precise external control over the gene-silencing event. The use of photocleavable protecting groups installed on nucleobases is a promising strategy to circumvent this limitation, providing high spatial and temporal control over siRNA or miRNA activation. Here, we have designed, synthesized and site-specifically incorporated new photocaged guanosine and uridine RNA phosphoramidites into short RNA duplexes. We demonstrated the applicability of these photocaged siRNAs in the light-regulation of the expression of an exogenous green fluorescent protein reporter gene and an endogenous target gene, the mitosis motor protein, Eg5. Two different approaches were investigated with the caged RNA molecules: the light-regulation of catalytic RNA cleavage by RISC and the light-regulation of seed region recognition. The ability to regulate both functions with light enables the application of this optochemical methodology to a wide range of small regulatory RNA molecules. DA - 2013/12// PY - 2013/12// DO - 10.1093/nar/gkt806 VL - 41 IS - 22 SP - 10518-10528 SN - 1362-4962 ER - TY - JOUR TI - Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells AU - Hemphill, J. AU - Chou, C. J. AU - Chin, J. W. AU - Deiters, A. T2 - Journal of the American Chemical Society AB - Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference. DA - 2013/// PY - 2013/// DO - 10.1021/ja4051026 VL - 135 IS - 36 SP - 13433-13439 ER - TY - JOUR TI - Enhancing the Thermoelectric Properties of Layered Transition-Metal Dichalcogenides 2H-MQ(2) (M = Mo, W; Q = S, Se, Te) by Layer Mixing: Density Functional Investigation AU - Lee, Changhoon AU - Hong, Jisook AU - Whangbo, Myung-Hwan AU - Shim, Ji Hoon T2 - CHEMISTRY OF MATERIALS AB - We explored how to improve the thermoelectric properties of the layered transition-metal dichalcogenides 2H-MQ2 (M = Mo, W; Q = S, Se, Te) by comparing the thermoelectric properties of hypothetical mixed-layer systems 2H-MQ2/2H-MQ′2, in which two different layers 2H-MQ2 and 2H-MQ′2 (Q, Q′ = S, Se, Te) alternate, with those of their pure components on the basis of density functional calculations. Our study predicts that the mixed-layer compounds MS2/MTe2 (M = Mo, W) strongly enhance the thermoelectric properties as a consequence of reducing the band gap and the interlayer van der Waals interactions. The layer-mixing is predicted to be a promising way of improving the thermoelectric properties of 2H-MQ2. DA - 2013/9/24/ PY - 2013/9/24/ DO - 10.1021/cm402281n VL - 25 IS - 18 SP - 3745-3752 SN - 1520-5002 KW - thermoelectric property KW - layered transition-metal dichalcogenide KW - layer mixing KW - density functional calculation ER - TY - JOUR TI - Effect of Ligand Coordination on the Structures and Visible-Light Photocatalytic Activity of Manganese Vanadate Hybrids AU - Luo, Lan AU - Maggard, Paul A. T2 - CRYSTAL GROWTH & DESIGN AB - A new manganese–vanadate hybrid structure, Mn(H2O)(bpy)V2O6 (I; bpy = 2,2′-bipyridine), has been synthesized via hydrothermal methods and characterized by single crystal X-ray diffraction [P21/n, Z = 4, a = 6.8557(4) Å, b = 10.4900(6) Å, c = 19.7921(13) Å, β = 96.419(4)°], infrared spectroscopy, thermogravimetric analysis, magnetic susceptibility measurements, and UV–vis diffuse reflectance. The structure is comprised of manganese vanadate layers with 2,2’-bipyridine ligands coordinated to the Mn(II) cations. The water molecules coordinated to the manganese sites can be reversibly desorbed at ∼190 °C with the formation of a new hybrid structure before then further decomposing to MnV2O6 upon heating to 300 °C. Notably, I undergoes a reversible structural transformation to Mn(bpy)V4O11(bpy) (II) under hydrothermal conditions. This structural transformation results from additional bpy-ligand coordination to 1/4 of the vanadium sites. Magnetic data indicate Mn(II) cations in both I and II are high spin (S = 5/2). The optical bandgap sizes of I and II were measured to be ∼2.2 eV and ∼1.6 eV, respectively, and that are calculated by DFT methods to arise primarily from Mn-to-bpy and Mn-to-V electronic transitions between the valence and conduction bands. Visible-light irradiation of II in aqueous solutions leads to photocatalytic activities for total water splitting at rates of ∼92 μmol H2/1/2O2 g–1 h–1 and ∼21 μmol H2/1/2O2 g–1 h–1 for II, with and without a 1 wt % Pt surface cocatalyst, respectively, but no measurable activity for I. Rates for only H2 production using aqueous methanol solutions were significantly lower. Results from electronic structure calculations show that the change in ligand coordination from I to II causes the excited electrons to populate slightly lower-energy bpy ligand π* orbitals that are coordinated to V(V), and thus this structural change in II leads to a better excited-state charge separation within its hybrid structure. DA - 2013/12// PY - 2013/12// DO - 10.1021/cg401062f VL - 13 IS - 12 SP - 5282-5288 SN - 1528-7505 ER - TY - JOUR TI - Comment on 'Cooperativity between two selected RNA Pdases in the synthesis of Pd nanoparticles' by J. L. Rouge et al., J. Mater. Chem., 2010, 20, 8394-8398 AU - Franzen, Stefan T2 - JOURNAL OF MATERIALS CHEMISTRY B AB - A graphical abstract is available for this content DA - 2013/// PY - 2013/// DO - 10.1039/c3tb20820f VL - 1 IS - 45 SP - 6339-6341 SN - 2050-7518 ER - TY - JOUR TI - Challenges to marrying atomic and continuum modeling of materials AU - Brenner, Donald W. T2 - CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE AB - Abstract As the engineering and characterization of bulk materials has progressed down to the nanometer scale, atomic-level modeling has moved from the realm of chemistry and physics to become an important tool for mechanical and materials engineers. However, connecting even the largest atomic simulations currently carried out in three dimensions to full engineering scales is a major challenge. The purpose of this brief article is to comment on these challenges and on the future of approaches that marry atomic and continuum modeling with the goal of increasing the spatial domain accessible to molecular modeling of the mechanical properties of materials. DA - 2013/12// PY - 2013/12// DO - 10.1016/j.cossms.2013.07.005 VL - 17 IS - 6 SP - 257-262 SN - 1879-0348 KW - Multiscale modeling KW - Molecular modeling KW - Finite element analysis ER - TY - JOUR TI - Across the Structural Re-Entrant Transition in BaFe2(PO4)(2): Influence of the Two-Dimensional Ferromagnetism AU - David, Renald AU - Pautrat, Alain AU - Filimonov, Dmitry AU - Kabbour, Houria AU - Vezin, Herve AU - Whangbo, Myung-Hwan AU - Mentre, Olivier T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - BaFe2(PO4)2 was recently prepared by hydrothermal synthesis and identified as the first two-dimensional (2D) Ising ferromagnetic oxide, in which honeycomb layers made up of edge-sharing FeO6 octahedra containing high-spin Fe2+ ions (S = 2) are isolated by PO4 groups and Ba2+ cations. BaFe2(PO4)2 has a trigonal R-3 structure at room temperature but adopts a triclinic P-1 structure below 140 K due to the Jahn–Teller (JT) instability arising from the (t2g)4(eg)2 configuration. The triclinic crystal structure was refined to find significantly distorted Fe2+O6 octahedra in the honeycomb layers while the distortion amplitude QJT was estimated to 0.019 Å. The JT stabilization energy is estimated to be ∼7 meV per formula unit by DFT calculations. Below ∼70 K, very close to the ferromagnetic transition temperature Tc = 65.5 K, the structure of BaFe2(PO4)2 returns to a trigonal R-3 structure in the presence of significant ferromagnetic domains. This rare re-entrant structural transition is accompanied by a discontinuous change in the quadrupolar splitting of Fe2+, as determined by Mössbauer spectroscopy. EPR measurements show the presence of magnetic domains well above Tc , as expected for a ferromagnetic 2D Ising system, and support that the magnetism of BaFe2(PO4)2 is uniaxial (g⊥ = 0). DA - 2013/9/4/ PY - 2013/9/4/ DO - 10.1021/ja404697b VL - 135 IS - 35 SP - 13023-13029 SN - 0002-7863 ER - TY - JOUR TI - Up-Conversion Luminescence of Gold Nanospheres When Excited at Nonsurface Plasmon Resonance Wavelength by a Continuous Wave Laser AU - Neupane, Bhanu AU - Zhao, Luyang AU - Wang, Gufeng T2 - NANO LETTERS AB - We show that, when gold nanospheres are excited at the red side of the surface plasmon resonance (SPR) wavelength at 592 nm by a continuous wave (CW) laser, they give substantial up-converted luminescence in the SPR wavelength range. The luminescence intensity scales as a second-order function of the excitation power, with a quantum yield ∼1/50 of down-conversion luminescence when illuminated at a power of 30 MW/cm2. The luminescence spectrum is completely different than the SPR profile, indicating a new emission mechanism possibly involving interband transitions coupled with phonons or localized vibration of neighboring gold atoms. Such luminescence is also observed to be substantial for short gold nanorods with an aspect ratio of ∼2 but weak for bulk gold. This study provides new insight to the understanding of gold nanoparticle luminescence and opens a new detection scheme for gold nanoparticle-based biological imaging. DA - 2013/9// PY - 2013/9// DO - 10.1021/nl401505p VL - 13 IS - 9 SP - 4087-4092 SN - 1530-6992 KW - Up conversion KW - photoluminescence KW - gold nanospheres KW - gold nanorods KW - surface plasmon resonance (SPR) KW - interband transition ER - TY - JOUR TI - The Regulatory Implications of Hydroquinone for the Multifunctional Enzyme Dehaloperoxidase-Hemoglobin from Amphitrite ornata AU - Zhao, Jing AU - Zhao, Junjie AU - Franzen, Stefan T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - Hydroquinone (H2Q) has been observed to compete with the oxidation of substrates 2,4,6-tribromophenol (2,4,6-TBP) and 2,4,6-trichlorophenol (2,4,6-TCP) catalyzed by the dehaloperoxidase-hemoglobin (DHP) from Amphitrite ornata in the presence of H2O2. This competition is observed as a lag phase during which H2Q is preferentially oxidized to 1,4-benzoquinone (1,4-BQ) while totally inhibiting either 2,4,6-TBP or 2,4,6-TCP oxidation. The inhibition by H2Q is distinct from that of the native competitive inhibitor 4-bromophenol (4-BP) since H2Q is itself oxidized and its product 1,4-BQ is not an inhibitor. Thus, once H2Q is completely consumed, the inhibition is removed, and normal substrate turnover is initiated, which explains the lag phase. To probe the mechanism of lag phase, the reactions between H2Q and DHP were both studied both in the presence and in the absence of H2O2. The reversible reactions between ferric/oxyferrous DHP A and H2Q/1,4-BQ are shown to involve a proton-coupled electron transfer (PCET) mechanism, where the distal histidine His55 serves as the proton acceptor. The pKa of the distal histidine His55 has been determined by resonance Raman spectroscopy in order to corroborate its involvement in this mechanism. Consistent with the proposed mechanism, kinetic assays have shown that H2Q serves as a substrate for DHP that follows the Michaelis–Menten kinetics. Unlike H2Q, the product 1,4-BQ has a relatively large Ki value and therefore has negligible inhibition. This study sheds light on understanding the difference between substrate and inhibitor binding sites and regulatory implication for the peroxidase and oxygen-transporter functions in DHP. It also provides information on PCET in DHP, which is important for resolving the switching between the ferric peroxidase catalytic function and the ferrous oxygen transport function. DA - 2013/11/28/ PY - 2013/11/28/ DO - 10.1021/jp407663n VL - 117 IS - 47 SP - 14615-14624 SN - 1520-6106 ER - TY - JOUR TI - Synthesis and photophysical properties of chlorins bearing 0–4 distinct meso-substituents AU - Aravindu, Kunche AU - Kim, Han-Je AU - Taniguchi, Masahiko AU - Dilbeck, Preston L. AU - Diers, James R. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - Photochemical & Photobiological Sciences AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/C3PP50240F VL - 12 IS - 12 SP - 2089 J2 - Photochem. Photobiol. Sci. LA - en OP - SN - 1474-905X 1474-9092 UR - http://dx.doi.org/10.1039/C3PP50240F DB - Crossref ER - TY - JOUR TI - Silver Exchange of Layered Metal Oxides and Their Photocatalytic Activities AU - Boltersdorf, Jonathan AU - Maggard, Paul A. T2 - ACS Catalysis AB - Layered Dion–Jacobson phases RbLaNb2O7 and RbA2Nb3O10 (A = Ca, Sr) and the Ruddlesden–Popper phase Rb2La2Ti3O10 were prepared by solid-state methods at a reaction time of 50 h and a temperature of 1100 °C. The products were silver-exchanged within a AgNO3 flux at a reaction time of 24 h and a temperature of 250 °C. Substitution of silver cations into the interlayer spacing of the layered structures is found to decrease the optical bandgap sizes on average by ∼0.5 to ∼1.0 eV. The products were found by scanning electron microscopy (SEM) to exhibit irregularly shaped platelet morphologies with an average size of ∼1–5 μm across their lateral dimensions and stepped edges ranging from ∼20 to ∼300 nm in height. Significant increases in photocatalytic hydrogen production rates for all silver-exchanged products were observed. The silver-exchanged RbA2Nb3O10 layered structures exhibited the highest photocatalytic hydrogen formation rates under ultraviolet and visible irradiation (∼13,616 μmol H2·g–1·h–1). These rates were 10 times higher than prior to silver exchange (∼1,418 μmol H2·g–1·h–1). However, photocatalytic activity under only visible light irradiation is not observed. It is also found that the silver cations located at the surfaces are reduced to Ag(s) after prolonged UV and visible light exposure in solution, which functions to increase their activity under UV irradiation. Electronic-structure calculations based on density functional theory show that the highest-energy valence band states are composed of Ag 4d-orbital and O 2p-orbital contributions within the interlayer spacing of the structure. The lowest-energy conduction band states arise from the Nb/Ti d-orbital and O 2p-orbital contributions that are confined to the two-dimensional niobate/titanate sheets within the structures and along which the excited-electrons can preferentially migrate. DA - 2013/10/15/ PY - 2013/10/15/ DO - 10.1021/CS400466B VL - 3 IS - 11 SP - 2547-2555 J2 - ACS Catal. LA - en OP - SN - 2155-5435 2155-5435 UR - http://dx.doi.org/10.1021/CS400466B DB - Crossref KW - photocatalysis KW - flux synthesis KW - layered-niobate KW - solar energy KW - band engineering ER - TY - JOUR TI - Reversible cyclic peptide libraries for the discovery of affinity ligands AU - Menegatti, S. AU - Ward, K. L. AU - Naik, A. D. AU - Kish, W. S. AU - Blackburn, R. K. AU - Carbonell, R. G. T2 - Analytical Chemistry AB - A novel strategy is presented for the identification of cyclic peptide ligands from combinatorial libraries of reversible cyclic depsipeptides. A method for the solid-phase synthesis of individual cyclic depsipeptides and combinatorial libraries of these compounds is proposed, which employs lactic acid (Lact) and the dipeptide ester (Nα-Ac)-Ser(Ala)- as linkers for dilactonization. Upon alkaline treatment of the beads selected by screening a model library, the cyclic depsipeptides are linearized and released from the solid support to the liquid phase, to be sequenced via single-step tandem mass spectrometry (MS/MS). The protocol presented for library synthesis provides for wide structural diversity. Two model sequences, VVWVVK and AAWAAR, were chosen to present different structural examples for depsipeptide libraries and demonstrate the process of sequence determination by mass spectrometry. Further, a case study using the IgG binding cyclic depsipeptide cyclo[(Nα-Ac)-S(A)-RWHYFK-Lact-E] is presented to demonstrate the process of library screening and sequence determination on the selected beads. Finally, a method is shown for synthesis of the irreversible cyclic peptide corresponding to the proposed depsipeptide structure, to make the ligand stable to the aqueous acid and alkaline conditions encountered in affinity chromatographic applications. The cyclic peptide ligand was synthesized on a poly(methacrylate) resin and used for chromatographic binding of the target IgG. DA - 2013/// PY - 2013/// DO - 10.1021/ac401954k VL - 85 IS - 19 SP - 9229–9237 ER - TY - JOUR TI - Observation of Majorana quantum critical behaviour in a resonant level coupled to a dissipative environment AU - Mebrahtu, H. T. AU - Borzenets, I. V. AU - Zheng, H. AU - Bomze, Y. V. AU - Smirnov, A. I. AU - Florens, S. AU - Baranger, H. U. AU - Finkelstein, G. T2 - NATURE PHYSICS AB - A quantum phase transition is an abrupt change between two distinct ground states of a many-body system, driven by an external parameter. In the vicinity of the quantum critical point (QCP) where the transition occurs, a new phase may emerge that is determined by quantum fluctuations and is very different from either phase. In particular, a conducting system may exhibit non-Fermi-liquid behaviour. Although this scenario is well established theoretically, controllable experimental realizations are rare. Here, we experimentally investigate the nature of the QCP in a simple nanoscale system—a spin-polarized resonant level coupled to dissipative contacts. We fine-tune the system to the QCP, realized exactly on-resonance and when the coupling between the level and the two contacts is symmetric. Several anomalous transport scaling laws are demonstrated, including a striking non-Fermi-liquid scattering rate at the QCP, indicating fractionalization of the resonant level into two Majorana quasiparticles. A quantum critical point associated with a carbon nanotube quantum dot that is in contact with dissipative leads exhibits striking non-Fermi-liquid properties and anomalous scaling. The dissipative environment enables the comparison of the system under thermal- and non-equilibrium conditions. DA - 2013/11// PY - 2013/11// DO - 10.1038/nphys2735 VL - 9 IS - 11 SP - 732-737 SN - 1745-2481 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84887225371&partnerID=MN8TOARS ER - TY - JOUR TI - Enzyme-Modified Carbon-Fiber Microelectrode for the Quantification of Dynamic Fluctuations of Nonelectroactive Analytes Using Fast-Scan Cyclic Voltammetry AU - Lugo-Morales, Leyda Z. AU - Loziuk, Philip L. AU - Corder, Amanda K. AU - Toups, J. Vincent AU - Roberts, James G. AU - McCaffrey, Katherine A. AU - Sombers, Leslie A. T2 - ANALYTICAL CHEMISTRY AB - Neurotransmission occurs on a millisecond time scale, but conventional methods for monitoring nonelectroactive neurochemicals are limited by slow sampling rates. Despite a significant global market, a sensor capable of measuring the dynamics of rapidly fluctuating, nonelectroactive molecules at a single recording site with high sensitivity, electrochemical selectivity, and a subsecond response time is still lacking. To address this need, we have enabled the real-time detection of dynamic glucose fluctuations in live brain tissue using background-subtracted, fast-scan cyclic voltammetry. The novel microbiosensor consists of a simple carbon fiber surface modified with an electrodeposited chitosan hydrogel encapsulating glucose oxidase. The selectivity afforded by voltammetry enables quantitative and qualitative measurements of enzymatically generated H2O2 without the need for additional strategies to eliminate interfering agents. The microbiosensors possess a sensitivity and limit of detection for glucose of 19.4 ± 0.2 nA mM–1 and 13.1 ± 0.7 μM, respectively. They are stable, even under deviations from physiological normoxic conditions, and show minimal interference from endogenous electroactive substances. Using this approach, we have quantitatively and selectively monitored pharmacologically evoked glucose fluctuations with unprecedented chemical and spatial resolution. Furthermore, this novel biosensing strategy is widely applicable to the immobilization of any H2O2 producing enzyme, enabling rapid monitoring of many nonelectroactive enzyme substrates. DA - 2013/9/17/ PY - 2013/9/17/ DO - 10.1021/ac4017852 VL - 85 IS - 18 SP - 8780-8786 SN - 1520-6882 ER - TY - JOUR TI - Enumeration of Virtual Libraries of Combinatorial Modular Macrocyclic (Bracelet, Necklace) Architectures and Their Linear Counterparts AU - Taniguchi, Masahiko AU - Du, Hai AU - Lindsey, Jonathan S. T2 - JOURNAL OF CHEMICAL INFORMATION AND MODELING AB - 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. DA - 2013/9// PY - 2013/9// DO - 10.1021/ci400175f VL - 53 IS - 9 SP - 2203-2216 SN - 1549-960X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84883274376&partnerID=MN8TOARS ER - TY - JOUR TI - Electronic and Exchange Coupling in a Cross-Conjugated D–B–A Biradical: Mechanistic Implications for Quantum Interference Effects AU - Kirk, Martin L. AU - Shultz, David A. AU - Stasiw, Daniel E. AU - Habel-Rodriguez, Diana AU - Stein, Benjamin AU - Boyle, Paul D. T2 - Journal of the American Chemical Society AB - A combination of variable-temperature EPR spectroscopy, electronic absorption spectroscopy, and magnetic susceptibility measurements have been performed on Tp(Cum,Me)Zn(SQ-m-Ph-NN) (1-meta) a donor-bridge-acceptor (D-B-A) biradical that possesses a cross-conjugated meta-phenylene (m-Ph) bridge and a spin singlet ground state. The experimental results have been interpreted in the context of detailed bonding and excited-state computations in order to understand the excited-state electronic structure of 1-meta. The results reveal important excited-state contributions to the ground-state singlet-triplet splitting in this cross-conjugated D-B-A biradical that contribute to our understanding of electronic coupling in cross-conjugated molecules and specifically to quantum interference effects. In contrast to the conjugated isomer, which is a D-B-A biradical possessing a para-phenylene bridge, admixture of a single low-lying singly excited D → A type configuration into the cross-conjugated D-B-A biradical ground state makes a negligible contribution to the ground-state magnetic exchange interaction. Instead, an excited state formed by a Ph-NN (HOMO) → Ph-NN (LUMO) one-electron promotion configurationally mixes into the ground state of the m-Ph bridged D-A biradical. This results in a double (dynamic) spin polarization mechanism as the dominant contributor to ground-state antiferromagnetic exchange coupling between the SQ and NN spins. Thus, the dominant exchange mechanism is one that activates the bridge moiety via the spin polarization of a doubly occupied orbital with phenylene bridge character. This mechanism is important, as it enhances the electronic and magnetic communication in cross-conjugated D-B-A molecules where, in the case of 1-meta, the magnetic exchange in the active electron approximation is expected to be J ~ 0 cm(-1). We hypothesize that similar superexchange mechanisms are common to all cross-conjugated D-B-A triads. Our results are compared to quantum interference effects on electron transfer/transport when cross-conjugated molecules are employed as the bridge or molecular wire component and suggest a mechanism by which electronic coupling (and therefore electron transfer/transport) can be modulated. DA - 2013/9/23/ PY - 2013/9/23/ DO - 10.1021/JA405354X VL - 135 IS - 39 SP - 14713-14725 J2 - J. Am. Chem. Soc. LA - en OP - SN - 0002-7863 1520-5126 UR - http://dx.doi.org/10.1021/JA405354X DB - Crossref ER - TY - JOUR TI - Effect of Solvent and Ancillary Ligands on the Catalytic H/D Exchange Reactivity of Cp*Ir-III(L) Complexes AU - Lehman, Matthew C. AU - Gary, J. Brannon AU - Boyle, Paul D. AU - Sanford, Melanie S. AU - Ison, Elon A. T2 - ACS CATALYSIS AB - The reactivity of a series of Cp*IrIII(L) complexes that contain a diverse set of ancillary ligands, L, (L = PMe3, N-heterocyclic carbene, NHC = 1,3-dimethylimidazol-2-ylidene, aqua, 4-t-butylpyridine, and 4-(2,4,6-tris-(4-t-butylphenyl)pyridinium)pyridine tetrafluoroborate) has been examined in catalytic H/D exchange reactions between C6H6 and a series of deuterated solvents (methanol-d4, acetic acid-d4, and trifluoroacetic acid-d1). These studies demonstrate that (1) the mechanism of catalytic H/D exchange is significantly influenced by the nature of the solvent; (2) electron-donating ligands (PMe3, NHC) promote the formation of Ir hydrides in methanol-d4, and these are critical intermediates in catalytic H/D exchange processes; and (3) weak/poorly donating ligands (4-t-butylpyridine, 4-(2,4,6-tris-(4-t-butylphenyl)pyridinium)pyridine tetrafluoroborate and aqua) can support efficient H/D exchange catalysis in acetic acid-d4. DA - 2013/10// PY - 2013/10// DO - 10.1021/cs400420n VL - 3 IS - 10 SP - 2304-2310 SN - 2155-5435 KW - H/D exchange KW - C-H activation KW - C-H functionalization KW - Cp*Ir-III catalysts KW - kinetics KW - isotope effects ER - TY - JOUR TI - Dihydropyridine preparation and application in the synthesis of pyridine derivatives AU - Comins, D. L. AU - Higuchi, K. AU - Young, D. W. T2 - Advances in heterocyclic chemistry, vol 110 DA - 2013/// PY - 2013/// VL - 110 SP - 175-235 ER - TY - JOUR TI - Cp*Ir-III-Catalyzed Oxidative Coupling of Benzoic Acids with Alkynes AU - Frasco, Daniel A. AU - Lilly, Cassandra P. AU - Boyle, Paul D. AU - Ison, Elon A. T2 - ACS CATALYSIS AB - Cp*Ir(III) complexes have been shown to catalyze the oxidative coupling of benzoic acids with alkynes in methanol at 60 °C to form a variety of isocoumarins. The use of AgOAc as an oxidant was required to facilitate significant product formation. Alkyl alkynes were shown to be more reactive substrates than aryl alkynes, and a number of functional groups were tolerated on benzoic acid. Combined mechanistic and computational studies (BP86) revealed that (1) C–H activation occurs via an acetate-assisted mechanism; (2) C–H activation is not turnover limiting; and (3) the oxidant oxidizes the reduced form of the catalyst via an Ir(I)–Ir(II)–Ir(III) sequence. DA - 2013/10// PY - 2013/10// DO - 10.1021/cs400656q VL - 3 IS - 10 SP - 2421-2429 SN - 2155-5435 KW - C-H functionalization KW - oxidative coupling KW - C-H activation KW - Cp*Ir-III KW - annulation ER - TY - JOUR TI - Carbon Nanotube Yarn Electrodes for Enhanced Detection of Neurotransmitter Dynamics in Live Brain Tissue AU - Schmidt, Andreas C. AU - Wang, Xin AU - Zhu, Yuntian AU - Sombers, Leslie A. T2 - ACS NANO AB - This work demonstrates the potential of nanoscale carbon electrode materials for improved detection of electroactive neurotransmitter dynamics in the brain. Individual multiwalled carbon nanotubes were synthesized via chemical vapor deposition, spun into yarns, and used in the fabrication of disk microelectrodes that were subsequently characterized using scanning electron and atomic force microscopies. The carbon nanotube yarn electrodes were coupled with fast-scan cyclic voltammetry and used to discriminately detect rapid neurotransmitter fluctuations in acute brain slices. The results demonstrate that the distinct structural and electronic properties of the nanotubes result in improved selectivity, sensitivity, and spatial resolution, as well as faster apparent electron transfer kinetics when compared to the conventional carbon-fiber microelectrodes typically used in vivo. DA - 2013/9// PY - 2013/9// DO - 10.1021/nn402857u VL - 7 IS - 9 SP - 7864-7873 SN - 1936-086X KW - FSCV KW - carbon fiber KW - microelectrode KW - dopamine KW - voltammetry ER - TY - JOUR TI - A Crucial Role of Bond Covalency Competition in Determining the Bandgap and Photocatalytic Performance of Silver Oxosalts AU - Jin, Xiaoyan AU - Kim, In Young AU - Jo, Yun Kyung AU - Bettis, Jerry L., Jr. AU - Koo, Hyun-Joo AU - Whangbo, Myung-Hwan AU - Hwang, Seong-Ju T2 - JOURNAL OF PHYSICAL CHEMISTRY C AB - The optical bandgaps, the surface charges, and the photocatalytic activities of the silver oxosalts Ag3AsO4, Ag2CO3, Ag3PO4, Ag2SO4, and Ag2SeO4 are systematically investigated with several experimental techniques and first principles density functional theory calculations. The trends in the optical bandgaps and the surface charges of these silver oxosalts, Agx(XOy)z, are analyzed by considering how the X–O bond covalency affects the charge on the terminal oxygen atoms and the Ag–O bond covalency. The optical bandgaps of Agx(XOy)z are well-described by the bond-covalency competition in the Ag–O–X linkages because an increase in the overlap between the O 2s/2p and X ns/np orbitals decreases the overlap between the Ag 4d and O 2s/2p orbitals. The optical bandgap increases linearly with increasing the Z/r ratio of the atom X, a simple measure of the X–O bond covalency. In the photodegradation of charged molecules, the surface charge of Agx(XOy)z plays a prominent role and decreases with increasing the Z/r ratio. As expected from the present theoretical predictions, newly investigated Ag2SeO4 exhibits a promising photocatalytic activity under visible light. The Z/r ratio of the central atom X provides an effective measure for predicting the photocatalyst performance and the optical bandgap of silver oxosalts Agx(XOy)z. DA - 2013/12/19/ PY - 2013/12/19/ DO - 10.1021/jp4101784 VL - 117 IS - 50 SP - 26509-26516 SN - 1932-7455 ER - TY - JOUR TI - Unified model of ferroelectricity induced by spin order AU - Xiang, H. J. AU - Wang, P. S. AU - Whangbo, M. -H. AU - Gong, X. G. T2 - PHYSICAL REVIEW B AB - For spin-order-driven ferroelectricity, a general theory that includes both purely electronic and ion-displacement contributions simultaneously is lacking. Here we present a realistic method for describing the ion-displacement part of the ferroelectricity and combine it with the pure electronic description proposed earlier to formulate a unified model that can describe any spin order including an incommensurate one. This unified model reproduces first-principles results known for representative multiferroics and provides insight into the origin of ferroelectricity and magnetoelectric coupling. We find that multiferroicity in spiral magnets LiCuVO${}_{4}$ and TbMnO${}_{3}$ can be explained by our unified model, but not by previous spin current models. The magnetoelectric effect observed for BiFeO${}_{3}$ in the cycloidal spiral state is found to originate from the exchange striction. DA - 2013/8/8/ PY - 2013/8/8/ DO - 10.1103/physrevb.88.054404 VL - 88 IS - 5 SP - SN - 2469-9969 ER - TY - JOUR TI - Serendipitous synthetic entree to tetradehydro analogues of cobalamins AU - Deans, R. M. AU - Mass, O. AU - Diers, J. R. AU - Bocian, D. F. AU - Lindsey, J. S. T2 - New Journal of Chemistry DA - 2013/// PY - 2013/// VL - 37 IS - 12 SP - 3964-3975 ER - TY - JOUR TI - Promiscuity of a modular polyketide synthase towards natural and non-natural extender units AU - Koryakina, Irina AU - McArthur, John B. AU - Draelos, Matthew M. AU - Williams, Gavin J. T2 - Organic & Biomolecular Chemistry AB - Combinatorial biosynthesis approaches that involve modular type I polyketide synthases (PKSs) are proven strategies for the synthesis of polyketides. In general however, such strategies are usually limited in scope and utility due to the restricted substrate specificity of polyketide biosynthetic machinery. Herein, a panel of chemo-enzymatically synthesized acyl-CoA's was used to probe the promiscuity of a polyketide synthase. Promiscuity determinants were dissected, revealing that the KS is remarkably tolerant to a diverse array of extender units, while the AT likely discriminates between extender units that are native to the producing organism. Our data provides a clear blueprint for future enzyme engineering efforts, and sets the stage for harnessing extender unit promiscuity by employing various in vivo polyketide diversification strategies. DA - 2013/// PY - 2013/// DO - 10.1039/c3ob40633d VL - 11 IS - 27 SP - 4449 J2 - Org. Biomol. Chem. LA - en OP - SN - 1477-0520 1477-0539 UR - http://dx.doi.org/10.1039/c3ob40633d DB - Crossref ER - TY - JOUR TI - Novel Soft-Chemistry Route of Ag2Mo3O10 center dot 2H(2)O Nanowires and in Situ Photogeneration of a Ag@Ag2Mo3O10 center dot 2H(2)O Plasmonic Heterostructure AU - Hakouk, Khadija AU - Deniard, Philippe AU - Lajaunie, Luc AU - Guillot-Deudon, Catherine AU - Harel, Sylvie AU - Wang, Zeyan AU - Huang, Baibiao AU - Koo, Hyun-Joo AU - Whangbo, Myung-Hwan AU - Jobic, Stephane AU - Dessapt, Remi T2 - INORGANIC CHEMISTRY AB - Ultrathin Ag2Mo3O10·2H2O nanowires (NWs) were synthesized by soft chemistry under atmospheric pressure from a hybrid organic–inorganic polyoxometalate (CH3NH3)2[Mo7O22] and characterized by powder X-ray diffraction, DSC/TGA analyses, FT-IR and FT-Raman spectroscopies, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Their diameters are a few tens of nanometers and hence much thinner than that found for silver molybdates commonly obtained under hydrothermal conditions. The optical properties of Ag2Mo3O10·2H2O NWs before and after UV irradiation were investigated by UV–vis–NIR diffuse reflectance spectroscopy revealing, in addition to photoreduction of Mo6+ to Mo5+ cations, in situ photogeneration of well-dispersed silver Ag0 nanoparticles on the surface of the NWs. The resulting Ag@Ag2Mo3O10·2H2O heterostructure was confirmed by electron energy-loss spectroscopy (EELS), X-ray photoelectron spectroscopy (XPS), and Auger spectroscopy. Concomitant reduction of Mo6+ and Ag+ cations under UV excitation was discussed on the basis of electronic band structure calculations. The Ag@Ag2Mo3O10·2H2O nanocomposite is an efficient visible-light-driven plasmonic photocatalyst for degradation of Rhodamine B dye in aqueous solution. DA - 2013/6/3/ PY - 2013/6/3/ DO - 10.1021/ic400343v VL - 52 IS - 11 SP - 6440-6449 SN - 1520-510X ER - TY - JOUR TI - Nonlinear pressure dependence of T-N in almost multiferroic EuTiO3 AU - Guguchia, Z. AU - Caslin, K. AU - Kremer, R. K. AU - Keller, H. AU - Shengelaya, A. AU - Maisuradze, A. AU - Bettis, J. L. AU - Kohler, J. AU - Bussmann-Holder, A. AU - Whangbo, M. H. T2 - Journal of Physics. Condensed Matter DA - 2013/// PY - 2013/// VL - 25 IS - 37 ER - TY - JOUR TI - MicroRNA miR-122 as a therapeutic target for oligonucleotides and small molecules AU - Thomas, M. AU - Deiters, A. T2 - Current Medicinal Chemistry AB - The most abundant microRNA (miRNA) in the liver, miR-122, is regulated by specific, liver-enriched transcription factors and is responsible for proper proliferation and differentiation of hepatocytes and for the regulation of lipid and cholesterol metabolisms. miR-122 is also involved in several hepatic disorders, as downregulation of miR-122 is often associated with hepatocellular carcinoma (HCC) and miR-122 is a required component for the replication and proliferation of the hepatitis C virus (HCV). Various probes have been developed to promote a better understanding of the involvement of miR-122 in liver diseases, including modified antisense agents and small molecule inhibitors. These agents, capable of specifically modifying miR-122 activity, provide excellent tools to investigate the function and regulation of miR-122 and offer potential new lead compounds for drug discovery. Especially small molecule modifiers can display numerous advantages over nucleotide analogs, as discussed in this review. DA - 2013/// PY - 2013/// DO - 10.2174/0929867311320290009 VL - 20 IS - 29 SP - 3629-3640 ER - TY - JOUR TI - Mechanism of MTO-Catalyzed Deoxydehydration of Diols to Alkenes Using Sacrificial Alcohols AU - Liu, Shuo AU - Senocak, Aysegul AU - Smeltz, Jessica L. AU - Yang, Linan AU - Wegenhart, Benjamin AU - Yi, Jing AU - Kenttaemaa, Hilkka I. AU - Ison, Elon A. AU - Abu-Omar, Mandi M. T2 - ORGANOMETALLICS AB - Catalytic deoxydehydration (DODH) of vicinal diols is carried out employing methyltrioxorhenium (MTO) as the catalyst and a sacrificial alcohol as the reducing agent. The reaction kinetics feature an induction period when MTO is added last and show zero-order in [diol] and half-order dependence on [catalyst]. The rate-determining step involves reaction with alcohol, as evidenced by a KIE of 1.4 and a large negative entropy of activation (ΔS‡ = −154 ± 33 J mol–1 K–1). The active form of the catalyst is methyldioxorhenium(V) (MDO), which is formed by reduction of MTO by alcohol or via a novel C–C bond cleavage of an MTO-diolate complex. The majority of the MDO-diolate complex is present in dinuclear form, giving rise to the [Re]1/2 dependence. The MDO-diolate complex undergoes further reduction by alcohol in the rate-determining step to give rise to a putative rhenium(III) diolate. The latter is the active species in DODH extruding stereoselectively trans-stilbene from (R,R)-(+)-hydrobenzoin to regenerate MDO and complete the catalytic cycle. DA - 2013/6/10/ PY - 2013/6/10/ DO - 10.1021/om400127z VL - 32 IS - 11 SP - 3210-3219 SN - 1520-6041 ER - TY - JOUR TI - Mass Recalibration of FT-ICR Mass Spectrometry Imaging Data Using the Average Frequency Shift of Ambient Ions AU - Barry, Jeremy A. AU - Robichaud, Guillaume AU - Muddiman, David C. T2 - JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY AB - Achieving and maintaining high mass measurement accuracy (MMA) throughout a mass spectrometry imaging (MSI) experiment is vital to the identification of the observed ions. However, when using FTMS instruments, fluctuations in the total ion abundance at each pixel due to inherent biological variation in the tissue section can introduce space charge effects that systematically shift the observed mass. Herein we apply a recalibration based on the observed cyclotron frequency shift of ions found in the ambient laboratory environment, polydimethylcyclosiloxanes (PDMS). This calibration method is capable of achieving part per billion (ppb) mass accuracy with relatively high precision for an infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI dataset. Comparisons with previously published mass calibration approaches are also presented. DA - 2013/7// PY - 2013/7// DO - 10.1007/s13361-013-0659-0 VL - 24 IS - 7 SP - 1137-1145 SN - 1879-1123 KW - Mass spectrometry imaging KW - FT-ICR MS KW - Mass calibration KW - MALDESI KW - MMA ER - TY - JOUR TI - Intrinsic optical gain in thin films of a conjugated polymer under picosecond excitation AU - Lampert, Z. E. AU - Lappi, S. E. AU - Papanikolas, J. M. AU - Reynolds, C. L. T2 - Applied Physics Letters DA - 2013/// PY - 2013/// VL - 103 IS - 3 ER - TY - JOUR TI - Influence of laser irradiation and microwave plasma treatment on the thermal properties of graphene platelets AU - Zheng, H. AU - Jagannadham, K. T2 - Journal of Vacuum Science & Technology. A, Vacuum, Surfaces, and Films DA - 2013/// PY - 2013/// VL - 31 IS - 4 ER - TY - JOUR TI - Grid-free powder averages: On the applications of the Fokker-Planck equation to solid state NMR AU - Edwards, Luke J. AU - Savostyanov, D. V. AU - Nevzorov, A. A. AU - Concistre, M. AU - Pileio, G. AU - Kuprov, Ilya T2 - JOURNAL OF MAGNETIC RESONANCE AB - We demonstrate that Fokker-Planck equations in which spatial coordinates are treated on the same conceptual level as spin coordinates yield a convenient formalism for treating magic angle spinning NMR experiments. In particular, time dependence disappears from the background Hamiltonian (sample spinning is treated as an interaction), spherical quadrature grids are avoided completely (coordinate distributions are a part of the formalism) and relaxation theory with any linear diffusion operator is easily adopted from the Stochastic Liouville Equation theory. The proposed formalism contains Floquet theory as a special case. The elimination of the spherical averaging grid comes at the cost of increased matrix dimensions, but we show that this can be mitigated by the use of state space restriction and tensor train techniques. It is also demonstrated that low correlation order basis sets apparently give accurate answers in powder-averaged MAS simulations, meaning that polynomially scaling simulation algorithms do exist for a large class of solid state NMR experiments. DA - 2013/10// PY - 2013/10// DO - 10.1016/j.jmr.2013.07.011 VL - 235 SP - 121-129 SN - 1096-0856 KW - NMR KW - MAS KW - SLE KW - Fokker-Planck equation KW - State space restriction ER - TY - JOUR TI - Dimethylammonium copper formate [(CH3)(2)NH2]Cu(HCOO)(3): A metal-organic framework with quasi-one-dimensional antiferromagnetism and magnetostriction AU - Wang, Zhenxing AU - Jain, Prashant AU - Choi, Kwang-Yong AU - Tol, Johan AU - Cheetham, Anthony K. AU - Kroto, Harold W. AU - Koo, Hyun-Joo AU - Zhou, Haidong AU - Hwang, Jungmin AU - Choi, Eun Sang AU - Whangbo, Myung-Hwan AU - Dalal, Naresh S. T2 - PHYSICAL REVIEW B AB - Metal-organic frameworks (MOFs) can exhibit many interesting properties such as multiferroic behavior, dipolar glass, gas storage, and protonic conductivity. Here we report that dimethylammonium copper formate (DMACuF) [(CH${}_{3}$)${}_{2}$NH${}_{2}$]Cu(HCOO)${}_{3}$, a cation templated nonporous MOF with perovskite topology, exhibits strong one-dimensional (1D) antiferromagnetism with a N\'eel temperature, ${T}_{N}$, of 5.2 K. These conclusions are derived from detailed magnetic susceptibility, heat capacity, dielectric constant, and high-frequency electron paramagnetic resonance measurements as well as density functional theory (DFT) calculations. The magnetic susceptibility exhibits a broad maximum at \ensuremath{\sim}50 K, suggesting low-dimensional magnetism; heat capacity measurements show a N\'eel temperature of 5.2 K. The magnetization versus field data at 1.8 K shows a spin-flop transition at ${H}_{sf}$ \ensuremath{\sim} 1.7 T. The ratio ${T}_{N}$/$J=6.5\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}2}$, where $J$ is the near-neighbor exchange constant (77.4 K), and the small value (2 K) of the interchain coupling suggests that DMACuF is close to an ideal 1D magnet. In this three-dimensional crystal lattice, the 1D magnetic behavior is made possible by the Jahn-Teller distortion of the 3${d}^{9}$ Cu${}^{2+}$ ions. Temperature dependence of the electron paramagnetic resonance field and the linewidth exhibits critical broadening for temperatures below 50 K, following a behavior quite characteristic of 1D spin systems. DFT calculations show that [(CH${}_{3}$)${}_{2}$NH${}_{2}$]Cu(HCOO)${}_{3}$ has a magnetic structure in which 1D antiferromagnetic chains parallel to the $c$ direction are weakly coupled ferromagnetically, supporting the thermomagnetic and EPR results. Dielectric measurements under applied magnetic fields of 0\ensuremath{-}7 T reveal a kink at the ${T}_{N}$, a clear indication of magnetostriction behavior. DA - 2013/6/10/ PY - 2013/6/10/ DO - 10.1103/physrevb.87.224406 VL - 87 IS - 22 SP - SN - 1550-235X ER - TY - JOUR TI - Diarylpyrenes vs. diaryltetrahydropyrenes: Crystal structures, fluorescence, and upconversion photochemistry AU - El-Ballouli, Ala'a O. AU - Khnayzer, Rony S. AU - Khalife, Jihane C. AU - Fonari, Alexandr AU - Hallal, Kassem M. AU - Timofeeva, Tatiana V. AU - Patra, Digambara AU - Castellano, Felix N. AU - Wex, Brigitte AU - Kaafarani, Bilal R. T2 - JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY AB - Abstract The synthesis of two series of substituted 2,7-diaryl-4,5,9,10-tetrahydropyrenes ( 1a – c ) and 2,7-diarylpyrenes ( 2a – c ) is reported; the opposing phenyl tips being terminated with t Bu (a), OCH 3 (b), or F ( c ) to impart variation in electronic properties. X-ray crystallographic analysis of the six compounds revealed edge-to-face packing predominately due to van der Waals forces in the solid state in all instances. The photophysical properties of these compounds were investigated in solution and in solid state/thin films. Since the 2,7-bis(4- tert -butylphenyl)tetrahydropyrene 1a possesses unity fluorescence quantum efficiency, it was successfully employed as the emitter in a low power upconversion scheme featuring fac -Ir(ppy) 3 [ppy = 2-phenylpyridine] as the photosensitizer. DA - 2013/11/15/ PY - 2013/11/15/ DO - 10.1016/j.jphotochem.2013.07.018 VL - 272 SP - 49-57 SN - 1010-6030 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84884505475&partnerID=MN8TOARS KW - Pyrene KW - Tetrahydropyrene KW - OLED KW - Upconversion photochemistry ER - TY - JOUR TI - DNA Computation in Mammalian Cells: MicroRNA Logic Operations AU - Hemphill, James AU - Deiters, Alexander T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - DNA computation can utilize logic gates as modules to create molecular computers with biological inputs. Modular circuits that recognize nucleic acid inputs through strand hybridization activate computation cascades to produce controlled outputs. This allows for the construction of synthetic circuits that can be interfaced with cellular environments. We have engineered oligonucleotide AND gates to respond to specific microRNA (miRNA) inputs in live mammalian cells. Both single and dual-sensing miRNA-based computation devices were synthesized for the cell-specific identification of endogenous miR-21 and miR-122. A logic gate response was observed with miRNA expression regulators, exhibiting molecular recognition of miRNA profile changes. Nucleic acid logic gates that are functional in a cellular environment and recognize endogenous inputs significantly expand the potential of DNA computation to monitor, image, and respond to cell-specific markers. DA - 2013/7/17/ PY - 2013/7/17/ DO - 10.1021/ja404350s VL - 135 IS - 28 SP - 10512-10518 SN - 0002-7863 ER - TY - JOUR TI - A Contoured Network of Anionic Trimesic Acids on Au(111) and Its Host-Guest Chemistry AU - Kim, Jandee AU - Rhee, Choong K. AU - Koo, Hyun-J. AU - Kasapbasi, Emine E. AU - Whangbo, Myung-H. T2 - JOURNAL OF PHYSICAL CHEMISTRY C AB - This work describes a trimesic acid (TMA) network formed at the open-circuit potential (OCP, ∼0.13 V) on Au(111), which we investigate with electrochemical scanning tunneling microscopy (STM). The unit cell of the TMA network at the OCP was (5√3 × 5√3)R30°–4TMA, while that of a well-known honeycomb network of flat-lying TMAs at −0.1 V was (6 × 6)R30°–2TMA. The most significant difference between the two networks is the fraction of hydrogen bonds appearing as bright spots in the STM images: it is 1/3 in the former but 1 in the latter. Additional differences were the shapes and lengths of the STM spots and the packing density of TMAs. A contoured network composed of crownlike anionic TMA hexamers was proposed to explain all the differences. The TMAs in the crownlike hexamer were rotated along the molecular axis and were tilted up from the surface by ∼30° to have hydrogen bonds with reasonable O–H···O distance, and the hexamers were interconnected to a contoured network. The existence of the anionic TMA hexamer was evidenced by selective host–guest interaction of Cu2+ ions and 1-mercaptohexane with the contoured network. At a higher potential than the OCP, simple arrays of anionic TMA dimers with much higher packing densities were observed, depending on the availability of TMAs from solution. The potential dependence of the structure of the TMA adlayer is discussed in terms of a transition from molecular adsorption to anionic adsorption. DA - 2013/11/7/ PY - 2013/11/7/ DO - 10.1021/jp403203s VL - 117 IS - 44 SP - 22636-22643 SN - 1932-7455 ER - TY - JOUR TI - The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata AU - Jiang, Shu AU - Wright, Iain AU - Swartz, Paul AU - Franzen, Stefan T2 - BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS AB - The activation of dehaloperoxidase-hemoglobin (DHP) to form a ferryl intermediate requires the distal histidine, H55, to act as an acid base catalyst. The lack of ancillary amino acids in the distal pocket to assist in this process makes H55 even more important to the formation of active intermediates than in conventional peroxidases. Therefore, one can infer that the precise conformation H55 may greatly affect the enzymatic activity. Using site-direct mutagenesis at position T56, immediately adjacent to H55, we have confirmed that subtle changes in the conformation of H55 affect the catalytic efficiency of DHP. Mutating T56 to a smaller amino acid appears to permit H55 to rotate with relatively low barriers between conformations in the distal pocket, which may lead to an increase in catalytic activity. On the other hand, larger amino acids in the neighboring site appear to restrict the rotation of H55 due to the steric hindrance. In the case of T56V, which is an isosteric mutation, H55 appears less mobile, but forced to be closer to the heme iron than in wild type. Both proximity to the heme iron and flexibility of motion in some of the mutants can result in an increased catalytic rate, but can also lead to protein inactivation due to ligation of H55 to the heme iron, which is known as hemichrome formation. A balance of enzymatic rate and protein stability with respect to hemichrome formation appears to be optimum in wild type DHP (WT-DHP). DA - 2013/10// PY - 2013/10// DO - 10.1016/j.bbapap.2013.06.005 VL - 1834 IS - 10 SP - 2020-2029 SN - 1878-1454 KW - Enzyme kinetics KW - Catalytic efficiency KW - Hemichrome KW - Resonance Raman KW - Molecular dynamics ER - TY - JOUR TI - Quantum Critical Transition Amplifies Magnetoelastic Coupling in Mn[N(CN)(2)](2) AU - Brinzari, T. V. AU - Chen, P. AU - Sun, Q. -C. AU - Liu, J. AU - Tung, L. -C. AU - Wang, Y. AU - Schlueter, J. A. AU - Singleton, J. AU - Manson, J. L. AU - Whangbo, M. -H. AU - Litvinchuk, A. P. AU - Musfeldt, J. L. T2 - PHYSICAL REVIEW LETTERS AB - We report the discovery of a magnetic quantum critical transition in $\mathrm{Mn}[\mathrm{N}(\mathrm{CN}{)}_{2}{]}_{2}$ that drives the system from a canted antiferromagnetic state to the fully polarized state with amplified magnetoelastic coupling as an intrinsic part of the process. The local lattice distortions, revealed through systematic phonon frequency shifts, suggest a combined ${\mathrm{MnN}}_{6}$ octahedra $\mathrm{\text{distortion}}+\mathrm{\text{counterrotation}}$ mechanism that reduces antiferromagnetic interactions and acts to accommodate the field-induced state. These findings deepen our understanding of magnetoelastic coupling near a magnetic quantum critical point and away from the static limit. DA - 2013/6/5/ PY - 2013/6/5/ DO - 10.1103/physrevlett.110.237202 VL - 110 IS - 23 SP - SN - 1079-7114 ER - TY - JOUR TI - Quantitation of Hydrogen Peroxide Fluctuations and Their Modulation of Dopamine Dynamics in the Rat Dorsal Striatum Using Fast-Scan Cyclic Voltammetry AU - Spanos, Marina AU - Gras-Najjar, Julie AU - Letchworth, Jeremy M. AU - Sanford, Audrey L. AU - Toups, J. Vincent AU - Sombers, Leslie A. T2 - ACS CHEMICAL NEUROSCIENCE AB - The dopaminergic neurons of the nigrostriatal dopamine (DA) projection from the substantia nigra to the dorsal striatum become dysfunctional and slowly degenerate in Parkinson's disease, a neurodegenerative disorder that afflicts more than one million Americans.There is no specific known cause for idiopathic Parkinson's disease; however, multiple lines of evidence implicate oxidative stress as an underlying factor in both the initiation and progression of the disease.This involves the enhanced generation of reactive oxygen species, including hydrogen peroxide (H 2 O 2 ), whose role in complex biological processes is not well understood.Using fast-scan cyclic voltammetry at bare carbon-fiber microelectrodes, we have simultaneously monitored and quantified H 2 O 2 and DA fluctuations in intact striatal tissue under basal conditions and in response to the initiation of oxidative stress.Furthermore, we have assessed the effect of acute increases in local H 2 O 2 concentration on both electrically evoked DA release and basal DA levels.Increases in endogenous H 2 O 2 in the dorsal striatum attenuated electrically evoked DA release, and also decreased basal DA levels in this brain region.These novel results will help to disambiguate the chemical mechanisms underlying the progression of neurodegenerative disease states, such as Parkinson's disease, that involve oxidative stress. DA - 2013/5// PY - 2013/5// DO - 10.1021/cn4000499 VL - 4 IS - 5 SP - 782-789 SN - 1948-7193 KW - oxidative stress KW - reactive oxygen species KW - H2O2 KW - FSCV KW - Parkinson's disease KW - basal dopamine concentrations ER - TY - JOUR TI - Programmable DNA-binding small molecules AU - Blackledge, Meghan S. AU - Melander, Christian T2 - BIOORGANIC & MEDICINAL CHEMISTRY AB - Aberrant gene expression is responsible for a myriad of human diseases from infectious diseases to cancer. Precise regulation of these genes via specific interactions with the DNA double helix could pave the way for novel therapeutics. Pyrrole-imidazole polyamides are small molecules capable of binding to pre-determined DNA sequences up to 16 base pairs with affinity and specificity comparable to natural transcription factors. In the three decades since their development, great strides have been made relating to synthetic accessibility and improved sequence specificity and binding affinity. This perspective presents a brief history of early seminal developments in the field and highlights recent reports of the utility of polyamides as both genetic modulators and molecular probes. DA - 2013/10/15/ PY - 2013/10/15/ DO - 10.1016/j.bmc.2013.04.023 VL - 21 IS - 20 SP - 6101-6114 SN - 0968-0896 KW - Polyamide KW - Transcription KW - Minor groove KW - DNA binding ER - TY - JOUR TI - Overcoming Resistance to beta-Lactam Antibiotics AU - Worthington, Roberta J. AU - Melander, Christian T2 - JOURNAL OF ORGANIC CHEMISTRY AB - β-Lactam antibiotics are one of the most important antibiotic classes but are plagued by problems of resistance, and the development of new β-lactam antibiotics through side-chain modification of existing β-lactam classes is not keeping pace with resistance development. In this JOCSynopsis, we summarize small molecule strategies to overcome resistance to β-lactam antibiotics. These approaches include the development of β-lactamase inhibitors and compounds that interfere with the ability of the bacteria to sense an antibiotic threat and activate their resistance mechanisms. DA - 2013/5/3/ PY - 2013/5/3/ DO - 10.1021/jo400236f VL - 78 IS - 9 SP - 4207-4213 SN - 1520-6904 ER - TY - JOUR TI - N-Alkyl-N-methylpyrrolidinium difluoro(oxalato)borate ionic liquids: Physical/electrochemical properties and Al corrosion AU - Allen, J. L. AU - McOwen, D. W. AU - Delp, S. A. AU - Fox, E. T. AU - Dickmann, J. S. AU - Han, S. D. AU - Zhou, Z. B. AU - Jow, T. R. AU - Henderson, W. A. T2 - Journal of Power Sources DA - 2013/// PY - 2013/// VL - 237 SP - 104-111 ER - TY - JOUR TI - Morphology and chain aggregation dependence of optical gain in thermally annealed films of the conjugated polymer poly[2-methoxy-5-(2 '-ethylhexyloxy)-p-phenylene vinylene] AU - Lampert, Z. E. AU - Lappi, S. E. AU - Papanikolas, J. M. AU - Reynolds, C. L. AU - Aboelfotoh, M. O. T2 - Journal of Applied Physics DA - 2013/// PY - 2013/// VL - 113 IS - 23 ER - TY - JOUR TI - Isoprenoid Biosynthesis: Ferraoxetane or Allyl Anion Mechanism for IspH Catalysis? AU - Li, Jikun AU - Wang, Ke AU - Smirnova, Tatyana I. AU - Khade, Rahul L. AU - Zhang, Yong AU - Oldfield, Eric T2 - ANGEWANDTE CHEMIE-INTERNATIONAL EDITION AB - The catalytic mechanism of the enzyme IspH, involved in formation of isopentenyl diphosphate and dimethylallyl diphosphate, was investigated by using HYSCORE spectroscopy combined with DFT. The results indicate the formation of an allyl anion bound to a HiPIP-like oxidized 4Fe–4S cluster, rather than formation of a cyclic, ferraoxetane intermediate, as has been proposed elsewhere. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. DA - 2013/// PY - 2013/// DO - 10.1002/anie.201302343 VL - 52 IS - 25 SP - 6522-6525 SN - 1433-7851 KW - biosynthesis KW - enzyme catalysis KW - iron-sulfur cluster KW - metalloproteins KW - terpenes ER - TY - JOUR TI - Integration of multiple chromophores with native photosynthetic antennas to enhance solar energy capture and delivery AU - Harris, Michelle A. AU - Parkes-Loach, Pamela S. AU - Springer, Joseph W. AU - Jiang, Jianbing AU - Martin, Elizabeth C. AU - Qian, Pu AU - Jiao, Jieying AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Olsen, John D. AU - Bocian, David F. AU - Holten, Dewey AU - Hunter, C. Neil AU - Lindsey, Jonathan S. AU - Loach, Paul A. T2 - Chemical Science AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/C3SC51518D VL - 4 IS - 10 SP - 3924 J2 - Chem. Sci. LA - en OP - SN - 2041-6520 2041-6539 UR - http://dx.doi.org/10.1039/C3SC51518D DB - Crossref ER - TY - JOUR TI - Influence of dopants on the thermal conductance of GaN-sapphire interface AU - Zheng, H. AU - Jagannadham, K. T2 - IEEE Transactions on Electron Devices DA - 2013/// PY - 2013/// VL - 60 IS - 6 SP - 1911-1915 ER - TY - JOUR TI - Indole-triazole conjugates are selective inhibitors and inducers of bacterial biofilms AU - Minvielle, Marine J. AU - Bunders, Cynthia A. AU - Melander, Christian T2 - MEDCHEMCOMM AB - Herein is described a method of accessing indole/triazole and benzothiophene/triazole analogues that selectively promote or inhibit biofilm formation by Gram-positive and Gram-negative bacteria. Structure/function studies revealed that the addition of a bromine atom at the 2-position of the indole/triazole scaffold altered activity against both Gram-negative and Gram-positive bacteria and could transform a biofilm inhibitor into a biofilm inducer. Isosteric replacement of the indole core by a benzothiophene significantly impaired anti-biofilm activity. A competition assay exposing Escherichia coli to the most potent biofilm inducer and an inhibitor of E. coli biofilm formation was performed. The inducer exhibited the ability to mute the effect of the anti-biofilm compound for this targeted bacterial population. DA - 2013/6// PY - 2013/6// DO - 10.1039/c3md00064h VL - 4 IS - 6 SP - 916-919 SN - 2040-2511 ER - TY - JOUR TI - Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT): A Novel Glycan-Relative Quantification Strategy AU - Walker, S. Hunter AU - Taylor, Amber D. AU - Muddiman, David C. T2 - JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY AB - The Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT) strategy for the sample preparation, data analysis, and relative quantification of N-linked glycans is presented. Glycans are derivatized with either natural (L) or stable-isotope labeled (H) hydrazide reagents and analyzed using reversed phase liquid chromatography coupled online to a Q Exactive mass spectrometer. A simple glycan ladder, maltodextrin, is first used to demonstrate the relative quantification strategy in samples with negligible analytical and biological variability. It is shown that after a molecular weight correction attributable to isotopic overlap and a post-acquisition normalization of the data to account for any systematic bias, a plot of the experimental H:L ratio versus the calculated H:L ratio exhibits a correlation of unity for maltodextrin samples mixed in different ratios. We also demonstrate that the INLIGHT approach can quantify species over four orders of magnitude in ion abundance. The INLIGHT strategy is further demonstrated in pooled human plasma, where it is shown that the post-acquisition normalization is more effective than using a single spiked-in internal standard. Finally, changes in glycosylation are able to be detected in complex biological matrices, when spiked with a glycoprotein. The ability to spike in a glycoprotein and detect change at the glycan level validates both the sample preparation and data analysis strategy, making INLIGHT an invaluable relative quantification strategy for the field of glycomics. DA - 2013/9// PY - 2013/9// DO - 10.1007/s13361-013-0681-2 VL - 24 IS - 9 SP - 1376-1384 SN - 1879-1123 KW - Glycomics KW - Hydrazide Reagents KW - Stable Isotope Labeling KW - Normalization KW - Hydrazone KW - Formation KW - Relative Quantification KW - N-Linked Glycans ER - TY - JOUR TI - Flux Growth of Single-Crystal Na2Ta4O11 Particles and their Photocatalytic Hydrogen Production AU - McLamb, Nathan AU - Sahoo, Prangya Parimita AU - Fuoco, Lindsay AU - Maggard, Paul A. T2 - CRYSTAL GROWTH & DESIGN AB - Single-crystal particles of the layered natrotantite, i.e., Na2Ta4O11, were prepared within a K2SO4/Na2SO4 flux for flux-to-reactant molar ratios from 12:1 to 1:1 at a reaction temperature of 1000 °C for 2 h. Depending on the conditions, the flux reactions yielded crystals of Na2Ta4O11 that ranged in size from ∼100 nm to ∼1000 nm. The highest and lowest flux amounts yielded more isolated single crystals with sharper facets and surfaces, whereas intermediate flux amounts yielded more aggregates of particles with smooth and rounded surface features. All products were characterized by UV–vis diffuse reflectance techniques and were found to exhibit an indirect bandgap size of ∼4.1–4.3 eV and a larger direct bandgap transition of ∼4.5 eV. When the crystals are suspended in aqueous solutions and irradiated by ultraviolet light, they exhibit stable photocatalytic rates for hydrogen production of ∼13.4 μmol of H2·g–1·h–1 to ∼34.1 μmol of H2·g–1·h–1. The higher photocatalytic rates are found for the single crystals with the highly faceted and nanoterraced surfaces. Electronic structure calculations based on density functional theory confirm the lowest-energy bandgap transition is indirect and between the Γ and M k-points in the valence and conduction band states, respectively. The bandgap excitation is found to result in delocalization of the excited electrons over a layer of condensed TaO7 pentagonal bipyramids, which is a relatively unexplored structural feature for photocatalytic metal oxides. DA - 2013/6// PY - 2013/6// DO - 10.1021/cg301859d VL - 13 IS - 6 SP - 2322-2326 SN - 1528-7483 ER - TY - JOUR TI - Factorial Experimental Designs Elucidate Significant Variables Affecting Data Acquisition on a Quadrupole Orbitrap Mass Spectrometer AU - Randall, Shan M. AU - Cardasis, Helene L. AU - Muddiman, David C. T2 - JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY AB - Instrument parameter values for a quadrupole Orbitrap mass spectrometer were optimized for performing global proteomic analyses. Fourteen factors were evaluated for their influence on data-dependent acquisition with an emphasis on both the rate of sequencing and spectral quality by maximizing two individually tested response variables (unique peptides and protein groups). Of the 14 factors, 12 factors were assigned significant contrast values (P < 0.05) for both response variables. Fundamentally, when optimizing parameters, a balance between spectral quality and duty cycle needs to be reached in order to maximize proteome coverage. This is especially true when using a data-dependent approach for sequencing complex proteomes. For example, maximum ion injection time, automatic gain control settings, and minimum threshold settings for triggering MS/MS isolation and activation all heavily influence ion signal, the number of spectra collected, and spectral quality. To better assess the effect these parameters have on data acquisition, all MS/MS data were parsed according to ion abundance by calculating the percent of the AGC target reached for each MS/MS event and then compared with successful peptide-spectrum matches. This proved to be an effective approach for understanding the effect of ion abundance on successful peptide-spectrum matches and establishing minimum ion abundance thresholds for triggering MS/MS isolation and activation. DA - 2013/10// PY - 2013/10// DO - 10.1007/s13361-013-0693-y VL - 24 IS - 10 SP - 1501-1512 SN - 1044-0305 KW - Design of experiments KW - Data dependent acquisition KW - Proteome coverage KW - Q Exactive KW - FTMS ER - TY - JOUR TI - Expanded use of sense codons is regulated by modified cytidines in tRNA AU - Cantara, William A. AU - Murphy, Frank V. AU - Demirci, Hasan AU - Agris, Paul F. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Codon use among the three domains of life is not confined to the universal genetic code. With only 22 tRNA genes in mammalian mitochondria, exceptions from the universal code are necessary for proper translation. A particularly interesting deviation is the decoding of the isoleucine AUA codon as methionine by the one mitochondrial-encoded tRNA Met . This tRNA decodes AUA and AUG in both the A- and P-sites of the metazoan mitochondrial ribosome. Enrichment of posttranscriptional modifications is a commonly appropriated mechanism for modulating decoding rules, enabling some tRNA functions while restraining others. In this case, a modification of cytidine, 5-formylcytidine (f 5 C), at the wobble position-34 of human mitochondrial ( ) enables expanded decoding of AUA, resulting in a deviation in the genetic code. Visualization of the codon•anticodon interaction by X-ray crystallography revealed that recognition of both A and G at the third position of the codon occurs in the canonical Watson–Crick geometry. A modification-dependent shift in the tautomeric equilibrium toward the rare imino-oxo tautomer of cytidine stabilizes the f 5 C 34 •A base pair geometry with two hydrogen bonds. DA - 2013/7/2/ PY - 2013/7/2/ DO - 10.1073/pnas.1222641110 VL - 110 IS - 27 SP - 10964-10969 SN - 0027-8424 KW - modified nucleosides KW - ribosome crystallography KW - tautomerism ER - TY - JOUR TI - Comparison of the Reactivity of 2-Li-C6H4CH2NMe2 with MCl4 ( M = Th, U): Isolation of a Thorium Aryl Complex or a Uranium Benzyne Complex AU - Seaman, Lani A. AU - Pedrick, Elizabeth A. AU - Tsuchiya, Takashi AU - Wu, Guang AU - Jakubikova, Elena AU - Hayton, Trevor W. T2 - ANGEWANDTE CHEMIE-INTERNATIONAL EDITION AB - Why do U react like that? Reaction of 2-Li-C6H4CH2NMe2 with [MCl4(DME)n] (M=Th, n=2; M=U, n=0) results in the formation of a thorium aryl complex, [Th(2-C6H4CH2NMe2)4] or a uranium benzyne complex, [Li][U(2,3-C6H3CH2NMe2)(2-C6H4CH2NMe2)3]. A DFT analysis suggests that the formation of a benzyne complex with U but not with Th is a kinetic and not thermodynamic effect. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. DA - 2013/9/27/ PY - 2013/9/27/ DO - 10.1002/anie.201303992 VL - 52 IS - 40 SP - 10589-10592 SN - 1521-3773 KW - aryl KW - benzyne KW - bonding analysis KW - thorium KW - uranium ER - TY - JOUR TI - Sulfoxides as Response Elements for Fluorescent Chemosensors AU - Kathayat, Rahul S. AU - Finney, Nathaniel S. T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - Sulfoxides are shown to be viable reporting groups for fluorescent chemosensor development. Metal coordination of sulfoxide-appended fluorophores suppresses excited-state pyramidal inversion of the sulfoxide, leading to enhanced fluorescence emission. This new structural motif allows the construction of fluorescent chemosensors that do not require nitrogen coordination as part of the signaling process, that have a range of selectivities and affinities for oxophilic metal ions, and that can function in water. DA - 2013/8/28/ PY - 2013/8/28/ DO - 10.1021/ja407099a VL - 135 IS - 34 SP - 12612-12614 SN - 0002-7863 ER - TY - JOUR TI - Mechanisms of Fat, Oil and Grease (FOG) deposit formation in sewer lines AU - He, Xia AU - Reyes, Francis L., III AU - Leming, Michael L. AU - Dean, Lisa O. AU - Lappi, Simon E. AU - Ducoste, Joel J. T2 - WATER RESEARCH AB - FOG deposits in sewer systems have recently been shown to be metallic salts of fatty acids. However, the fate and transport of FOG deposit reactant constituents and the complex interactions during the FOG deposit formation process are still largely unknown. In this study, batch tests were performed to elucidate the mechanisms of FOG deposit formation that lead to sanitary sewer overflows (SSOs). We report the first formation of FOG deposits on a concrete surface under laboratory conditions that mimic the formation of deposits in sewer systems. Results showed that calcium, the dominant metal in FOG deposits, can be released from concrete surfaces under low pH conditions and contribute to the formation process. Small amounts of additional oil to grease interceptor effluent substantially facilitated the air/water or pipe surface/water interfacial reaction between free fatty acids and calcium to produce surface FOG deposits. Tests of different fatty acids revealed that more viscous FOG deposit solids were formed on concrete surfaces, and concrete corrosion was accelerated, in the presence of unsaturated FFAs versus saturated FFAs. Based on all the data, a comprehensive model was proposed for the mechanisms of FOG deposit formation in sewer systems. DA - 2013/9/1/ PY - 2013/9/1/ DO - 10.1016/j.watres.2013.05.002 VL - 47 IS - 13 SP - 4451-4459 SN - 0043-1354 KW - Sanitary sewer overflows (SSOs) KW - Fat, Oil and Grease (FOG) deposits KW - Free fatty acids (FFAs) KW - Calcium KW - FOG deposit formation KW - Sewer lines ER - TY - JOUR TI - Kinetic Study of the Inhibition Mechanism of Dehaloperoxidase-Hemoglobin A by 4-Bromophenol AU - Zhao, Jing AU - Franzen, Stefan T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - The mechanism of dehaloperoxidase-hemoglobin (DHP) inhibition by 4-bromophenol (4-BP) was investigated using Michealis-Menten and transient-state kinetic analyses. Transient-state kinetics using the stopped-flow technique to mix DHP and H2O2 in the presence of inhibitor concentrations less than 10-fold greater than the enzyme concentration show that 4-BP does not fully impede H2O2 entering the distal pocket to activate DHP. It is not clear whether an oxoferryl intermediate is formed under these conditions and there may be alternative pathways for H2O2 reaction in the 4-BP bound form of DHP. Two new species have been identified during the reaction of 4-BP bound form of DHP in the transient-state kinetic experiment by using Singular Value Decomposition (SVD) and global-fitting analysis. Rather than forming Compound ES in the unbound form, an inhibitor bound intermediate that possesses blue-shifted Soret band and a double peaked Q-band is observed. This intermediate is subsequently converted to the end-point species that is distinguished from Compound RH formed in the uninhibited enzyme. Bench-top mixing kinetics of DHP were conducted in order to determine the inhibitor binding constant and to understand the enzyme inhibition mechanism from a thermodynamic perspective. It was found that the inhibition constant, Ki, decreased from 2.56 mM to 0.15 mM over the temperature range from 283 to 298 K, which permits determination of the enthalpy and entropy for inhibitor binding as −135.5 ± 20.9 kJ/mol and 526.1 ± 71.9 J/(mol·K), respectively, leading to the conclusion that inhibitor binding is entropically driven . DA - 2013/7/18/ PY - 2013/7/18/ DO - 10.1021/jp3116353 VL - 117 IS - 28 SP - 8301-8309 SN - 1520-6106 ER - TY - JOUR TI - Free energies of (Co, Fe, Ni, Zn)Fe2O4 spinels and oxides in water at high temperatures and pressure from density functional theory: results for stoichiometric NiO and NiFe2O4 surfaces AU - O'Brien, C. J. AU - Rak, Z. AU - Brenner, D. W. T2 - Journal of Physics. Condensed Matter DA - 2013/// PY - 2013/// VL - 25 IS - 44 ER - TY - JOUR TI - Elucidating Band-Selective Sensitization in Iron(II) Polypyridine-TiO2 Assemblies AU - Bowman, David N. AU - Blew, James H. AU - Tsuchiya, Takashi AU - Jakubikova, Elena T2 - INORGANIC CHEMISTRY AB - Iron(II) polypyridines represent a cheaper and nontoxic alternative to analogous Ru(II) polypyridine dyes successfully used as photosensitizers in dye-sensitized solar cells (DSSCs). We employ density functional theory (DFT) and time-dependent DFT (TD-DFT) to study ground and excited state properties of [Fe(bpy)(CN)4](2-), [Fe(bpy-dca)(CN)4](2-), and [Fe(bpy-dca)2(CN)2] complexes, where bpy = 2,2'-bipyridine and dca = 4,4'-dicarboxylic acid. Quantum dynamics simulations are further used to investigate the interfacial electron transfer (IET) between the excited Fe(II) dyes and a TiO2 nanoparticle. All three dyes investigated display two bands in the visible region of the absorption spectrum, with the major transitions corresponding to the metal-to-ligand charge transfer states. The calculated IET rates from the particle states created by the excitation of the lower-energy absorption band are comparable to or slower than the rate of the excited state decay into the nonemissive, metal-centered states of the Fe(II) dyes (∼100 fs), indicating that the IET upon the excitation of this band is unlikely. Several particle states in the higher-energy absorption band display IET rates at or below 100 fs, suggesting the possibility of the IET between the Fe(II)-sensitizer and TiO2 nanoparticle upon excitation with visible light. Our results are consistent with the previous experimental work on Fe(II) sensitizers (Ferrere, S. Chem. Mater. 2000, 12, 1083) and elucidate the band-selective nature of the IET in these compounds. DA - 2013/8/5/ PY - 2013/8/5/ DO - 10.1021/ic4007839 VL - 52 IS - 15 SP - 8621-8628 SN - 1520-510X ER - TY - JOUR TI - Electrochemical characterization of dehaloperoxidase adsorbates on COOH/OH mixed self-assembled monolayers AU - Chen, Thomas K. AU - Bowden, Edmond F. T2 - JOURNAL OF ELECTROANALYTICAL CHEMISTRY AB - Electrochemical characterization of Amphitrite ornata dehaloperoxidase, a monomeric hemoglobin, adsorbed on COOH/OH-terminated alkanethiolate mixed self-assembled monolayers (SAMs) is reported. Adsorption was achieved by simple electrode exposure to low ionic strength protein solution at pH 6.0, and cyclic voltammetry (CV) was employed to measure surface concentration, electron transfer rate, and formal potential under anaerobic conditions. Surface concentration values determined by CV were found to be inversely proportional to scan rate, a behavior that is different than that observed for electron transfer proteins such as cytochrome c. We attribute this behavior to a dynamic heterogeneous adsorbate layer that permits some fraction of the molecules to undergo reorientation during a CV scan. A model was proposed that classifies adsorbates among three populations with respect to their most stable orientations, namely, electroactive adsorbates, latent electroinactive adsorbates capable of undergoing reorientation to electroactive states, and electroinactive adsorbates. Electrochemical results and the proposed model are discussed in terms of the tertiary structure and surface properties of dehaloperoxidase and are compared to the docking and electron transfer reactions of the myoglobin/cytochrome b5 system. Examination of the effects of ionic strength and mixed SAM composition provide support for the proposed model. DA - 2013/8/15/ PY - 2013/8/15/ DO - 10.1016/j.jelechem.2013.05.023 VL - 703 SP - 23-28 SN - 1873-2569 KW - Dehaloperoxidase KW - Protein adsorption KW - Globin electrochemistry KW - Diffusionless voltammetry KW - Self-assembled monolayers ER - TY - JOUR TI - Distinct Photophysical and Electronic Characteristics of Strongly Coupled Dyads Containing a Perylene Accessory Pigment and a Porphyrin, Chlorin, or Bacteriochlorin AU - Wang, Jieqi AU - Yang, Eunkrung AU - Diers, James R. AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Bocian, David F. AU - Lindsey, Jonathan S. AU - Holten, Dewey T2 - JOURNAL OF PHYSICAL CHEMISTRY B AB - 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. DA - 2013/8/8/ PY - 2013/8/8/ DO - 10.1021/jp405004d VL - 117 IS - 31 SP - 9288-9304 SN - 1520-5207 ER - TY - JOUR TI - Amphiphilic chlorins and bacteriochlorins in micellar environments. Molecular design, de novo synthesis, and photophysical properties AU - Aravindu, Kunche AU - Mass, Olga AU - Vairaprakash, Pothiappan AU - Springer, Joseph W. AU - Yang, Eunkyung AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - Chemical Science AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/C3SC51335A VL - 4 IS - 9 SP - 3459 J2 - Chem. Sci. LA - en OP - SN - 2041-6520 2041-6539 UR - http://dx.doi.org/10.1039/C3SC51335A DB - Crossref ER - TY - JOUR TI - meso-Pyridyl BODIPYs with tunable chemical, optical and electrochemical properties AU - Bartelmess, J. AU - Weare, W. W. AU - Latortue, N. AU - Duong, C. AU - Jones, D. S. T2 - New Journal of Chemistry DA - 2013/// PY - 2013/// VL - 37 IS - 9 SP - 2663-2668 ER - TY - JOUR TI - The Electronic Nature of Terminal Oxo Ligands in Transition-Metal Complexes: Ambiphilic Reactivity of Oxorhenium Species AU - Smeltz, Jessica L. AU - Lilly, Cassandra P. AU - Boyle, Paul D. AU - Ison, Elon A. T2 - JOURNAL OF THE AMERICAN CHEMICAL SOCIETY AB - The synthesis of the Lewis acid–base adducts of B(C6F5)3 and BF3 with [DAAmRe(O)(X)] DAAm = N,N-bis(2-arylaminoethyl)methylamine; aryl = C6F5 (X = Me, 1, COCH3, 2, Cl, 3) as well as their diamidopyridine (DAP) (DAP=(2,6-bis((mesitylamino)methyl)pyridine) analogues, [DAPRe(O)(X)] (X = Me, 4, Cl, 5, I, 6, and COCH3,7), are described. In these complexes the terminal oxo ligands act as nucleophiles. In addition we also show that stoichiometric reactions between 3 and triarylphosphine (PAr3) result in the formation of triarylphosphine oxide (OPAr3). The electronic dependence of this reaction was studied by comparing the rates of oxygen atom transfer for various para-substituted triaryl phosphines in the presence of CO. From these experiments a reaction constant ρ = −0.29 was obtained from the Hammett plot. This suggests that the oxygen atom transfer reaction is consistent with nucleophilic attack of phosphorus on an electrophilic metal oxo. To the best of our knowledge, these are the first examples of mono-oxo d2 metal complexes in which the oxo ligand exhibits ambiphilic reactivity. DA - 2013/6/26/ PY - 2013/6/26/ DO - 10.1021/ja401390v VL - 135 IS - 25 SP - 9433-9441 SN - 1520-5126 ER - TY - JOUR TI - Review of Cellulose Non-Derivatizing Solvent Interactions with Emphasis on Activity in Inorganic Molten Salt Hydrates AU - Sen, Sanghamitra AU - Martin, James D. AU - Argyropoulos, Dimitris S. T2 - ACS Sustainable Chemistry & Engineering AB - During cellulose dissolution in non-derivatizing solvents, the inter- and intramolecular hydrogen bonds of the polymer are deconstructed. This occurs either by hydrogen bond formation between one or more components of the solvent systems and the hydroxyl groups of the cellulose or by coordination bond formation between the metal ion present in the medium and the hydroxyl group of cellulose molecules. None of the polymer molecules are actually chemically modified during dissolution. In the first part of this review, we examine the literature pertaining to the different interaction mechanisms between cellulose and non-derivatizing solvent systems with emphasis on the inorganic molten salt hydrates. In the second part of this effort, we further review inorganic molten salt hydrates from the point of view of the changes they impart to the physical properties of the cellulose and the various chemical reactions that can be performed in it. DA - 2013/6/4/ PY - 2013/6/4/ DO - 10.1021/sc400085a VL - 1 IS - 8 SP - 858-870 J2 - ACS Sustainable Chem. Eng. LA - en OP - SN - 2168-0485 2168-0485 UR - http://dx.doi.org/10.1021/sc400085a DB - Crossref KW - Cellulose KW - Non-derivatizing solvents of cellulose KW - Inorganic molten salt hydrates KW - Crystallinity KW - Cellulose hydrolysis KW - Degradation of cellulose ER - TY - JOUR TI - Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa AU - Shi, R. AU - Shuford, C. M. AU - Wang, Jack P. AU - Sun, Y. H. AU - Yang, Z. C. AU - Chen, H. C. AU - Tunlaya-Anukit, S. AU - Li, Q. Z. AU - Liu, J. AU - Muddiman, David AU - Sederoff, R. R. AU - Chiang, V. L. T2 - Planta DA - 2013/// PY - 2013/// DO - 10.1007/s00425-013-1905-1 VL - 238 IS - 3 SP - 487–497 ER - TY - JOUR TI - Phonon Bottleneck in Graphene-Based Josephson Junctions at Millikelvin Temperatures AU - Borzenets, I. V. AU - Coskun, U. C. AU - Mebrahtu, H. T. AU - Bomze, Yu. V. AU - Smirnov, A. I. AU - Finkelstein, G. T2 - PHYSICAL REVIEW LETTERS AB - We examine the nature of the transitions between the normal and superconducting branches in superconductor-graphene-superconductor Josephson junctions. We attribute the hysteresis between the switching (superconducting to normal) and retrapping (normal to superconducting) transitions to electron overheating. In particular, we demonstrate that the retrapping current corresponds to the critical current at an elevated temperature, where the heating is caused by the retrapping current itself. The superconducting gap in the leads suppresses the hot electron outflow, allowing us to further study electron thermalization by phonons at low temperatures (T≲1 K). The relationship between the applied power and the electron temperature was found to be P∝T3, which we argue is consistent with cooling due to electron-phonon interactions. DA - 2013/7/9/ PY - 2013/7/9/ DO - 10.1103/physrevlett.111.027001 VL - 111 IS - 2 SP - SN - 1079-7114 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84880100049&partnerID=MN8TOARS ER - TY - JOUR TI - Orbital Analysis and Excited-State Calculations in an Energy-Based Fragmentation Method AU - Tsuchiya, Takashi AU - Shrestha, Kushal AU - Jakubikova, Elena T2 - JOURNAL OF CHEMICAL THEORY AND COMPUTATION AB - Covalently bound molecular arrays composed of porphyrins or related pigments have gained a lot of interest as components of artificial light-harvesting systems and molecular photonic devices. The large size of these arrays, however, makes their theoretical investigation employing the ab initio or density functional methodologies difficult. Energy-based fragmentation methods (EBF) represent a set of conceptually simple approaches to theoretical investigation of large systems and were therefore chosen as a tool to study these systems. Here a new approach to EBF, EBF-MO, is introduced that enables one to obtain orbitals and orbital energies and to perform population analysis and excited-state calculations of large systems composed of hundreds of atoms. This approach was implemented into a parallel program, JETT, and the benchmark calculations have shown its accuracy and applicability to the ground- and excited-state calculations of systems containing transition metals and extended π-conjugation. EBF-MO was then applied to the density functional theory (DFT) and the time-dependent density functional theory (TDDFT) calculations of ground- and excited-state properties of a porphyrin-based molecular photonic wire composed of 472 atoms and 4265 basis functions at the B3LYP/LANL08,6-31G* level. The TDDFT calculations have revealed the character of the excited states, and the unidirectionality of the excitation energy transfer across the array relevant to its signal transfer function. The computational approaches introduced here have widened the applicability of the ab initio and density functional methodologies to calculations of extended systems such as natural and artificial light-harvesting systems and molecular photonic devices. DA - 2013/8// PY - 2013/8// DO - 10.1021/ct400025a VL - 9 IS - 8 SP - 3350-3363 SN - 1549-9626 ER - TY - JOUR TI - On the nature of the photochemical reaction of polypyridyl Ru(II) complexes leading to sunlight-to-chemical energy conversion: density functional analysis AU - Kasapbasi, E. E. AU - Whangbo, M. H. T2 - RSC Advances DA - 2013/// PY - 2013/// VL - 3 IS - 24 SP - 9414-9418 ER - TY - JOUR TI - Multi-peptide nLC-PC-IDMS-SRM-based Assay for the quantification of biomarkers in the chicken ovarian cancer model AU - Kingon, Genna L. Andrews AU - Petitte, James N. AU - Muddiman, David C. AU - Hawkridge, Adam M. T2 - METHODS AB - A novel form of ovomacroglobulin/ovostatin (OVOS2) predicted from EST data was previously identified in the chicken ovarian cancer model using a mass spectrometry-based shotgun label-free proteomics strategy. The quantitative label-free data from plasma showed a significant increase over time with the spontaneous onset and progression of ovarian cancer making it a potential protein biomarker for further study. Two other proteins of interest identified from this initial study included vitellogenin-1 (Vit-1), a lipid-transport protein tied to egg production, and transthyretin (TTR), a retinol binding transport protein currently used in the clinical management of ovarian cancer. A multiplexed protein cleavage isotope dilution mass spectrometry (PC-IDMS) assay was developed to quantify OVOS2, Vit-1, and TTR by selected reaction monitoring (SRM). A total of 6 stable isotope labeled (SIL) peptide standards were used in the assay with three tryptic peptides from OVOS2, one for Vit-1, and two for TTR. The assay was developed for use with un-depleted raw plasma combined with the filter assisted sample preparation (FASP) method and its use was also demonstrated for matched ovary tissue samples. The PC-IDMS data for the two TTR peptides did not correlate with each other with more than a 10-fold difference in concentration for all 5 time points measured. The PC-IDMS data from the longitudinal plasma samples correlated well for OVOS2 and Vit-1 whereas TTR was inconclusive. Interestingly, the absolute amount for one of the OVOS2 SIL peptides was 2-fold less compared with the other two SIL peptides. These data illustrate the successes and challenges of qualifying quantitative levels of proteins from an in-gel digestion sample preparation followed by LC-MS/MS (GeLC) label-free discovery-based approach to a targeted SRM-based quantitative assay in plasma and tissues. DA - 2013/6/15/ PY - 2013/6/15/ DO - 10.1016/j.ymeth.2013.04.004 VL - 61 IS - 3 SP - 323-330 SN - 1095-9130 KW - Proteomics KW - Quantification KW - Ovarian cancer KW - Chicken KW - Biomarkers ER - TY - JOUR TI - Magnetic Properties of the RbMnPO4 Zeolite-ABW-Type Material: A Frustrated Zigzag Spin Chain AU - Nenert, Gwilherm AU - Bettis, Jerry, Jr. AU - Kremer, Reinhard AU - Ben Yahia, Hamdi AU - Ritter, Clemens AU - Gaudin, Etienne AU - Isnard, Olivier AU - Whangbo, Myung-Hwan T2 - INORGANIC CHEMISTRY AB - The crystal structure and magnetic properties of the RbMnPO4 zeolite-ABW type material have been studied by temperature-dependent neutron powder diffraction, low temperature magnetometry and heat capacity measurements. RbMnPO4 represents a rare example of a weak ferromagnetic polar material, containing Mn2+ ions with TN = 4.7 K. The neutron powder diffraction pattern recorded at T = 10 K shows that the compound crystallizes in the chiral and polar monoclinic space group P21 (No. 4) with the unit-cell parameters: a = 8.94635(9) {\AA}, b = 5.43415(5) {\AA}, c = 9.10250(8) {\AA} and beta = 90.4209(6){\deg}. A close inspection of the crystal structure of RbMnPO4 shows that this material presents two different types of zigzag chains running along the b axis. This is a unique feature among the zeolite-ABW type materials exhibiting the P21 symmetry. At low temperature, RbMnPO4 exhibits a canted antiferromagnetic structure characterized by the propagation vector k1 = 0 resulting in the magnetic symmetry P21. The magnetic moments lie mostly along the b axis with the ferromagnetic component being in the ac plane. Due to the geometrical frustration present in this system, an intermediate phase appears within the temperature range 4.7 - 5.1 K characterized by the propagation vector k2 = (kx, 0, kz) with kx/kz = 2. This ratio is reminiscent of the multiferroic phase of the orthorhombic RMnO3 phases (R = rare earth). This suggests that RbMnPO4 could present some multiferroic properties at low temperature. Our density functional calculations confirm the presence of magnetic frustration, which explains this intermediate incommensurate phase. Taking into account the strongest magnetic interactions, we are able to reproduce the magnetic structure observed experimentally at low temperature. DA - 2013/8/19/ PY - 2013/8/19/ DO - 10.1021/ic401408f VL - 52 IS - 16 SP - 9627-9635 SN - 1520-510X ER - TY - JOUR TI - Excitonic states in a ( Ti6O12)(3) nanotube AU - Papas, B. N. AU - Whitten, J. L. T2 - Journal of Chemical Physics DA - 2013/// PY - 2013/// VL - 138 IS - 5 ER - TY - JOUR TI - Engineering polyketide synthases and nonribosomal peptide synthetases AU - Williams, Gavin J T2 - Current Opinion in Structural Biology AB - Naturally occurring polyketides and nonribosomal peptides with broad and potent biological activities continue to inspire the discovery of new and improved analogs. The biosynthetic apparatus responsible for the construction of these natural products has been the target of intensive protein engineering efforts. Traditionally, engineering has focused on substituting individual enzymatic domains or entire modules with those of different building block specificity, or by deleting various enzymatic functions, in an attempt to generate analogs. This review highlights strategies based on site-directed mutagenesis of substrate binding pockets, semi-rational mutagenesis, and whole-gene random mutagenesis to engineer the substrate specificity, activity, and protein interactions of polyketide and nonribosomal peptide biosynthetic machinery. DA - 2013/8// PY - 2013/8// DO - 10.1016/j.sbi.2013.06.012 VL - 23 IS - 4 SP - 603-612 J2 - Current Opinion in Structural Biology LA - en OP - SN - 0959-440X UR - http://dx.doi.org/10.1016/j.sbi.2013.06.012 DB - Crossref ER - TY - JOUR TI - Comparison of the growth and degradation of Poly(glycolic acid) and Poly(epsilon-caprolactone) brushes AU - Hu, X. F. AU - Hu, G. F. AU - Crawford, K. AU - Gorman, C. B. T2 - Journal of Polymer Science. Part A, Polymer Chemistry DA - 2013/// PY - 2013/// VL - 51 IS - 21 SP - 4643-4649 ER - TY - JOUR TI - Catalytic diversification upon metal scavenging in a prebiotic model for formation of tetrapyrrole macrocycles AU - Soares, Ana R. M. AU - Anderson, Dana R. AU - Chandrashaker, Vanampally AU - Lindsey, Jonathan S. T2 - NEW JOURNAL OF CHEMISTRY AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/c3nj00498h VL - 37 IS - 9 SP - 2716-2732 SN - 1369-9261 ER - TY - JOUR TI - Voltammetry of dehaloperoxidase on self-assembled monolayers: Reversible adsorptive immobilization of a globin AU - D'Antonio, Edward L. AU - Chen, Thomas K. AU - Turner, Abigail H. AU - Santiago-Capeles, Lisandra AU - Bowden, Edmond F. T2 - Electrochemistry Communications AB - Abstract Dehaloperoxidase (DHP), a monomeric hemoglobin, was adsorptively immobilized under low ionic strength conditions on binary self-assembled monolayers composed of OH- and COOH-terminated alkylthiols. Voltammetry of its Fe(III)/Fe(II) reactions revealed adsorbed DHP to be electroactive and native under both anaerobic and aerobic conditions. The chemically reversible nature of the adsorptive immobilization was established from voltammetric desorption/re-adsorption experiments. Cyclic voltammetric determination of electroactive surface concentration uncovered an unusual inverse scan rate dependence that was rationalized by means of Hoffman's dynamic docking electron transfer model [Z.-X. Liang et al., J. Am. Chem. Soc. 126 (2004) 2785]. This result represents the first evidence for dynamic docking control of protein electron transfer in an electrochemical setting. DA - 2013/1// PY - 2013/1// DO - 10.1016/j.elecom.2012.10.011 VL - 26 SP - 67-70 J2 - Electrochemistry Communications LA - en OP - SN - 1388-2481 UR - http://dx.doi.org/10.1016/j.elecom.2012.10.011 DB - Crossref KW - Dehaloperoxidase KW - Adsorptive immobilization KW - Protein monolayer KW - Diffusionless voltammetry KW - Dynamic docking ER - TY - JOUR TI - Tuning donut profile for spatial resolution in stimulated emission depletion microscopy AU - Neupane, Bhanu AU - Chen, Fang AU - Sun, Wei AU - Chiu, Daniel T. AU - Wang, Gufeng T2 - Review of Scientific Instruments AB - In stimulated emission depletion (STED)-based or up-conversion depletion-based super-resolution optical microscopy, the donut-shaped depletion beam profile is of critical importance to its resolution. In this study, we investigate the transformation of the donut-shaped depletion beam focused by a high numerical aperture (NA) microscope objective, and model STED point spread function (PSF) as a function of donut beam profile. We show experimentally that the intensity profile of the dark kernel of the donut can be approximated as a parabolic function, whose slope is determined by the donut beam size before the objective back aperture, or the effective NA. Based on this, we derive the mathematical expression for continuous wave (CW) STED PSF as a function of focal plane donut and excitation beam profiles, as well as dye properties. We find that the effective NA and the residual intensity at the center are critical factors for STED imaging quality and the resolution. The effective NA is critical for STED resolution in that it not only determines the donut shape but also the area the depletion laser power is dispersed. An improperly expanded depletion beam will have negligible improvement in resolution. The polarization of the depletion beam also plays an important role as it affects the residual intensity in the center of the donut. Finally, we construct a CW STED microscope operating at 488 nm excitation and 592 nm depletion with a resolution of 70 nm. Our study provides detailed insight to the property of donut beam, and parameters that are important for the optimal performance of STED microscopes. This paper will provide a useful guide for the construction and future development of STED microscopes. DA - 2013/4// PY - 2013/4// DO - 10.1063/1.4799665 VL - 84 IS - 4 SP - 043701 J2 - Review of Scientific Instruments LA - en OP - SN - 0034-6748 1089-7623 UR - http://dx.doi.org/10.1063/1.4799665 DB - Crossref ER - TY - JOUR TI - Transient thermoreflectance from graphene composites with matrix of indium and copper AU - Zheng, H. AU - Jagannadham, K. T2 - AIP Advances DA - 2013/// PY - 2013/// VL - 3 IS - 3 ER - TY - JOUR TI - Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata AU - Zhao, Jing AU - Serrano, Vesna AU - Zhao, Junjie AU - Le, Peter AU - Franzen, Stefan T2 - BIOCHEMISTRY AB - X-ray crystal structures of dehaloperoxidase-hemoglobin A (DHP A) from Amphitrite ornata soaked with substrate, 2,4,6-tribromophenol (2,4,6-TBP), in buffer solvent with added methanol (MeOH), 2-propanol (2-PrOH), and dimethyl sulfoxide (DMSO) reveal an internal substrate binding site deep in the distal pocket above the α-edge of the heme that is distinct from the previously determined internal inhibitor binding site. The peroxidase function of DHP A has most often been studied using 2,4,6-trichlorophenol (2,4,6-TCP) as a substrate analogue because of the low solubility of 2,4,6-TBP in an aqueous buffer solution. Previous studies at low substrate concentrations pointed to the binding of substrate 2,4,6-TCP at an external site near the exterior heme β- or δ-edge as observed in the class of heme peroxidases. Here we report that the turnover frequencies of both substrates 2,4,6-TCP and 2,4,6-TBP deviate from Michaelis–Menten kinetics at high concentrations. The turnover frequency reaches a maximum in the range of 1400–1700 μM, with a decrease in rate at higher concentrations that is both substrate- and solvent-dependent. The X-ray crystal structure is consistent with the presence of an internal active site above the heme α-edge, in which the substrate would be oxidized in two consecutive steps inside the enzyme, followed by attack by H2O via a water channel in the protein. The physiological role of the internal site may involve interactions with any of a number of aromatic toxins found in benthic ecosystems where A. ornata resides. DA - 2013/4/9/ PY - 2013/4/9/ DO - 10.1021/bi301307f VL - 52 IS - 14 SP - 2427-2439 SN - 0006-2960 ER - TY - JOUR TI - Simultaneous Single-Particle Superlocalization and Rotational Tracking AU - Gu, Yan AU - Wang, Gufeng AU - Fang, Ning T2 - ACS NANO AB - Superlocalization of single molecules and nanoparticles has become an essential procedure to bring new insights into nanoscale structures and dynamics of biological systems. In the present study, superlocalization is combined with the newly introduced differential interference contrast (DIC) microscopy-based single-particle orientation and rotational tracking. The new technique overcomes the difficulty in localization of the antisymmetric DIC point spread function by using a dual-modality microscope configuration for simultaneous rotational tracking and localization of single gold nanorods with nanometer-scale precision. The new imaging setup has been applied to study the steric hindrance induced by relatively large cargos in the microtubule gliding assay and to track nanocargos in the crowded cellular environment. This technique has great potential in the study of biological processes where both localization and rotational information are required. DA - 2013/2// PY - 2013/2// DO - 10.1021/nn305640y VL - 7 IS - 2 SP - 1658-1665 SN - 1936-086X KW - imaging KW - microscopy KW - superlocalization KW - gold nanorods KW - rotational tracking KW - kinesin ER - TY - JOUR TI - Role of Polarity of the Distal Pocket in the Control of Inhibitor Binding in Dehaloperoxidase-Hemoglobin AU - Plummer, Ashlee AU - Thompson, Matthew K. AU - Franzen, Stefan T2 - BIOCHEMISTRY AB - Dehaloperoxidase (DHP A), a unique multifunctional enzyme, from the marine annelid Amphitrite ornata dehalogenates 2,4,6-tribromophenol to form 2,6-dibromo-1,4-benzoquinone. The catalytic cycle of DHP is similar to that of horseradish peroxidase (HRP), involving a high-valent ferryl heme and two single-electron transfers from the aromatic substrate to the enzyme. Like HRP, DHP has been investigated as a potential bioremediation enzyme. However, DHP fails as a bioremediation enzyme because, unlike HRP, it has an internal binding cavity on the distal side of the heme capable of accommodating p-bromophenols, which act as an inhibitor of peroxidase function. Blocking internal binding in DHP may be the key to allowing the enzyme to function effectively as a peroxidase on the full range of halogenated phenols. The distal cavity of DHP is surrounded by several hydrophobic amino acids that stabilize internal binding of the monohalogenated phenols, including a leucine residue near the back edge of the heme (L100). We have expressed the L100F, L100Q, L100T, and L100V mutants of DHP in an effort to prevent internal binding and thereby convert the inhibitors into substrates. Kinetic assays and resonance Raman indicate that the peroxidase activity of the L100T and L100F mutants is increased compared to that of native DHP in the presence of 4-bromophenol (4-BP), suggesting a reduction in the inhibitor binding constant. In addition, the X-ray crystal structure of L100F clearly indicates a reduced occupancy of the 4-BP inhibitor in the distal cavity of DHP. However, at the same time, the L100F structure reveals that steric interference alone is insufficient to exclude the inhibitor. Instead, the comparison of L100T and isosteric L100V reveals that an increase in polarity plays a decisive role in excluding the inhibitor from the distal binding pocket. DA - 2013/4/2/ PY - 2013/4/2/ DO - 10.1021/bi301509r VL - 52 IS - 13 SP - 2218-2227 SN - 0006-2960 ER - TY - JOUR TI - Preparation and characterization of multi-cationic BODIPYs and their synthetically versatile precursors AU - Bartelmess, Juergen AU - Weare, Walter W. T2 - DYES AND PIGMENTS AB - We report the synthesis and characterization of a family of mono-, di- and tri-cationic boron dipyrromethene (BODIPY) dyes and their versatile precursors using convenient and high yielding synthetic procedures. The distyryl substituted precursors for the cationic target molecules presented in this study allow for further functionalization in a variety of ways, and are promising starting materials for further synthetic development of BODIPY dyes. The fluorescent, red-absorbing di- and tri-cationic dyes are well soluble in water and polar organic solvents and offer possibilities for fluorescence marking in biochemistry, photodynamic therapy, chemical sensing and other aqueous applications. The introduction of a pyridine substituent in the meso position of the BODIPY allows for control over fluorescence properties and offers the future possibility for the development of novel coordination complexes. This combination of properties allows these BODIPY derivatives to be possible building blocks for multi-purpose functional materials. DA - 2013/4// PY - 2013/4// DO - 10.1016/j.dyepig.2012.11.017 VL - 97 IS - 1 SP - 1-8 SN - 1873-3743 KW - Cationic boron dipyrromethene KW - Cationic BODIPY KW - Water-soluble dye KW - Fluorescence dye KW - Fluorescence spectroscopy KW - Modular organic synthesis ER - TY - JOUR TI - Perfluorinated Alcohols and Acids Induce Coacervation in Aqueous Solutions of Amphiphiles AU - Khaledi, Morteza G. AU - Jenkins, Samuel I. AU - Liang, Shuang T2 - LANGMUIR AB - We have discovered that water-miscible perfluorinated alcohols and acids (FA) can induce simple and complex coacervation in aqueous solutions of a wide range of amphiphilic molecules such as synthetic surfactants, phospholipids, and bile salts as well as polyelectrolytes. This unique phenomenon seems to be nearly ubiquitous, especially for complex coacervate systems composed of mixed catanionic amphiphiles. In addition, coacervation and aqueous phase separation were observed over a wide range of surfactants concentrations and for different mole fractions of the oppositely charged amphiphile. DA - 2013/2/26/ PY - 2013/2/26/ DO - 10.1021/la303035h VL - 29 IS - 8 SP - 2458-2464 SN - 0743-7463 ER - TY - JOUR TI - Palette of lipophilic bioconjugatable bacteriochlorins for construction of biohybrid light-harvesting architectures AU - Reddy, Kanumuri Ramesh AU - Jiang, Jianbing AU - Krayer, Michael AU - Harris, Michelle A. AU - Springer, Joseph W. AU - Yang, Eunkyung AU - Jiao, Jieying AU - Niedzwiedzki, Dariusz M. AU - Pandithavidana, Dinesh AU - Parkes-Loach, Pamela S. AU - Kirmaier, Christine AU - Loach, Paul A. AU - Bocian, David F. AU - Holten, Dewey AU - Lindsey, Jonathan S. T2 - Chemical Science AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/C3SC22317E VL - 4 IS - 5 SP - 2036 J2 - Chem. Sci. LA - en OP - SN - 2041-6520 2041-6539 UR - http://dx.doi.org/10.1039/C3SC22317E DB - Crossref ER - TY - JOUR TI - EPR assessment of protein sites for incorporation of Gd(III) MRI contrast labels AU - Lagerstedt, Jens O. AU - Petrlova, Jitka AU - Hilt, Silvia AU - Marek, Antonin AU - Chung, Youngran AU - Sriram, Renuka AU - Budamagunta, Madhu S. AU - Desreux, Jean F. AU - Thonon, David AU - Jue, Thomas AU - Smirnov, Alex I. AU - Voss, John C. T2 - CONTRAST MEDIA & MOLECULAR IMAGING AB - We have engineered apolipoprotein A‐I (apoA‐I), a major protein constituent of high‐density lipoprotein (HDL), to contain DOTA‐chelated Gd(III) as an MRI contrast agent for the purpose of imaging reconstituted HDL (rHDL) biodistribution, metabolism and regulation in vivo . This protein contrast agent was obtained by attaching the thiol‐reactive Gd[MTS‐ADO3A] label at Cys residues replaced at four distinct positions (52, 55, 76 and 80) in apoA‐I. MRI of infused mice previously showed that the Gd‐labeled apoA‐I migrates to both the liver and the kidney, the organs responsible for HDL catabolism; however, the contrast properties of apoA‐I are superior when the ADO3A moiety is located at position 55, compared with the protein labeled at positions 52, 76 or 80. It is shown here that continuous wave X‐band (9 GHz) electron paramagnetic resonance (EPR) spectroscopy is capable of detecting differences in the Gd(III) signal when comparing the labeled protein in the lipid‐free with the rHDL state. Furthermore, the values of NMR relaxivity obtained for labeled variants in both the lipid‐free and rHDL states correlate to the product of the X‐band Gd(III) spectral width and the collision frequency between a nitroxide spin label and a polar relaxation agent. Consistent with its superior relaxivity measured by NMR, the rHDL‐associated apoA‐I containing the Gd[MTS‐ADO3A] probe attached to position 55 displays favorable dynamic and water accessibility properties as determined by X‐band EPR. While room temperature EPR requires >1 m m Gd(III)‐labeled and only >10 µ m nitroxide‐labeled protein to resolve the spectrum, the volume requirement is exceptionally low (~5 µl). Thus, X‐band EPR provides a practical assessment for the suitability of imaging candidates containing the site‐directed ADO3A contrast probe. Copyright © 2013 John Wiley & Sons, Ltd. DA - 2013/// PY - 2013/// DO - 10.1002/cmmi.1518 VL - 8 IS - 3 SP - 252-264 SN - 1555-4309 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84876786430&partnerID=MN8TOARS KW - apolipoprotein A-I KW - magnetic resonance imaging (MRI) KW - electron paramagnetic resonance (EPR) spectroscopy KW - protein contrast agent KW - high-density lipoprotein (HDL) KW - site-directed MRI label ER - TY - JOUR TI - Cu2(OH)PO4, a Near-Infrared-Activated Photocatalyst AU - Wang, Gang AU - Huang, Baibiao AU - Ma, Xiangchao AU - Wang, Zeyan AU - Qin, Xiaoyan AU - Zhang, Xiaoyang AU - Dai, Ying AU - Whangbo, Myung-Hwan T2 - ANGEWANDTE CHEMIE-INTERNATIONAL EDITION AB - Crystal power! Libethenite, Cu2(OH)PO4 (see 4–5 μm×1.5 μm image), absorbs strongly in the near-infrared (NIR) region and is an effective photocatalyst for the decomposition of 2,4-dichlorophenol in aqueous solution under NIR irradiation. This NIR activation of the photocatalyst is due to a facile transfer of photogenerated electrons from the trigonal bipyramidal CuII sites to the adjacent octahedral CuII sites. DA - 2013/// PY - 2013/// DO - 10.1002/anie.201301306 VL - 52 IS - 18 SP - 4810-4813 SN - 1521-3773 KW - copper KW - nanocrystals KW - near-infrared light KW - photocatalysts KW - photochemistry ER - TY - JOUR TI - Comparative Proteomic Analysis and IgE Binding Properties of Peanut Seed and Testa (Skin) AU - White, Brittany L. AU - Goekce, Emine AU - Nepomuceno, Angelito I. AU - Muddiman, David C. AU - Sanders, Timothy H. AU - Davis, Jack P. T2 - JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY AB - To investigate the protein composition and potential allergenicity of peanut testae or skins, proteome analysis was conducted using nanoLC-MS/MS sequencing. Initial amino acid analysis suggested differences in protein compositions between the blanched seed (skins removed) and skin. Phenolic compounds hindered analysis of proteins in skins when the conventional extraction method was used; therefore, phenol extraction of proteins was necessary. A total of 123 proteins were identified in blanched seed and skins, and 83 of the proteins were common between the two structures. The skins contained all of the known peanut allergens in addition to 38 proteins not identified in the seed. Multiple defense proteins with antifungal activity were identified in the skins. Western blotting using sera from peanut-allergic patients revealed that proteins extracted from both the blanched seed and skin bound significant levels of IgE. However, when phenolic compounds were present in the skin protein extract, no IgE binding was observed. These findings indicate that peanut skins contain potentially allergenic proteins; however, the presence of phenolic compounds may attenuate this effect. DA - 2013/4/24/ PY - 2013/4/24/ DO - 10.1021/jf400184y VL - 61 IS - 16 SP - 3957-3968 SN - 1520-5118 KW - IgE binding KW - LC-MS/MS KW - peanut KW - proteomics KW - skins KW - testae ER - TY - JOUR TI - Combination approaches to combat multidrug-resistant bacteria AU - Worthington, Roberta J. AU - Melander, Christian T2 - TRENDS IN BIOTECHNOLOGY AB - The increasing prevalence of infections caused by multidrug-resistant bacteria is a global health problem that has been exacerbated by the dearth of novel classes of antibiotics entering the clinic over the past 40 years. Herein, we describe recent developments toward combination therapies for the treatment of multidrug-resistant bacterial infections. These efforts include antibiotic-antibiotic combinations, and the development of adjuvants that either directly target resistance mechanisms such as the inhibition of β-lactamase enzymes, or indirectly target resistance by interfering with bacterial signaling pathways such as two-component systems (TCSs). We also discuss screening of libraries of previously approved drugs to identify nonobvious antimicrobial adjuvants. DA - 2013/3// PY - 2013/3// DO - 10.1016/j.tibtech.2012.12.006 VL - 31 IS - 3 SP - 177-184 SN - 1879-3096 KW - antibiotic resistance KW - antibiotic adjuvant ER - TY - JOUR TI - Avidity-mediated virus separation using a hyperthermophilic affinity ligand AU - Hussain, Mahmud AU - Lockney, Dustin AU - Wang, Ruqi AU - Gera, Nimish AU - Rao, Balaji M. T2 - BIOTECHNOLOGY PROGRESS AB - Abstract Immunoaffinity separation of large multivalent species such as viruses is limited by the stringent elution conditions necessary to overcome their strong and highly avid interaction with immobilized affinity ligands on the capture surface. Here we present an alternate strategy that harnesses the avidity effect to overcome this limitation. Red clover necrotic mosaic virus (RCNMV), a plant virus relevant to drug delivery applications, was chosen as a model target for this study. An RCNMV binding protein (RBP) with modest binding affinity ( K D ∼100 nM) was generated through mutagenesis of the Sso7d protein from Sulfolobus solfataricus and used as the affinity ligand. In our separation scheme, RCNMV is captured by a highly avid interaction with RBP immobilized on a nickel surface through a hexahistidine (6xHis) tag. Subsequently, disruption of the multivalent interaction and release of RCNMV is achieved by elution of RBP from the nickel surface. Finally, RCNMV is separated from RBP by exploiting the large difference in their molecular weights (∼8 MDa vs. ∼10 kDa). Our strategy not only eliminates the need for harsh elution conditions, but also bypasses chemical conjugation of the affinity ligand to the capture surface. Stable non‐antibody affinity ligands to a wide spectrum of targets can be generated through mutagenesis of Sso7d and other hyperthermophilic proteins. Therefore, our approach may be broadly relevant to cases where capture of large multivalent species from complex mixtures and subsequent release without the use of harsh elution conditions is necessary. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2013 DA - 2013/// PY - 2013/// DO - 10.1002/btpr.1655 VL - 29 IS - 1 SP - 237-246 SN - 8756-7938 KW - avidity KW - affinity ligand KW - hyperthermophilic KW - multivalent ER - TY - JOUR TI - Synthesis and evaluation of cationic bacteriochlorin amphiphiles with effective in vitro photodynamic activity against cancer cells at low nanomolar concentration AU - Sharma, Sulbha K. AU - Krayer, Michael AU - Sperandio, Felipe F. AU - Huang, Liyi AU - Huang, Ying-Ying AU - Holten, Dewey AU - Lindsey, Jonathan S. AU - Hamblin, Michael R. T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - 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. DA - 2013/// PY - 2013/// DO - 10.1142/s108842461250126x VL - 17 IS - 1-2 SP - 73-85 SN - 1099-1409 KW - photodynamic therapy KW - HeLa cancer cells KW - bacteriochlorins KW - confocal microscopy KW - subcellular localization KW - apoptosis ER - TY - JOUR TI - Surface Electrostatics of Lipid Bilayers by EPR of a pH-Sensitive Spin-Labeled Lipid AU - Voinov, Maxim A. AU - Rivera-Rivera, Izarys AU - Smirnov, Alex I. T2 - Biophysical Journal AB - Many biophysical processes such as insertion of proteins into membranes and membrane fusion are governed by bilayer electrostatic potential. At the time of this writing, the arsenal of biophysical methods for such measurements is limited to a few techniques. Here we describe a, to our knowledge, new spin-probe electron paramagnetic resonance (EPR) approach for assessing the electrostatic surface potential of lipid bilayers that is based on a recently synthesized EPR probe (IMTSL-PTE) containing a reversibly ionizable nitroxide tag attached to the lipids' polar headgroup. EPR spectra of the probe directly report on its ionization state and, therefore, on electrostatic potential through changes in nitroxide magnetic parameters and the degree of rotational averaging. Further, the lipid nature of the probe provides its full integration into lipid bilayers. Tethering the nitroxide moiety directly to the lipid polar headgroup defines the location of the measured potential with respect to the lipid bilayer interface. Electrostatic surface potentials measured by EPR of IMTSL-PTE show a remarkable (within ±2%) agreement with the Gouy-Chapman theory for anionic DMPG bilayers in fluid (48°C) phase at low electrolyte concentration (50 mM) and in gel (17°C) phase at 150-mM electrolyte concentration. This agreement begins to diminish for DMPG vesicles in gel phase (17°C) upon varying electrolyte concentration and fluid phase bilayers formed from DMPG/DMPC and POPG/POPC mixtures. Possible reasons for such deviations, as well as the proper choice of an electrostatically neutral reference interface, have been discussed. Described EPR method is expected to be fully applicable to more-complex models of cellular membranes. DA - 2013/1// PY - 2013/1// DO - 10.1016/j.bpj.2012.11.3806 VL - 104 IS - 1 SP - 106-116 J2 - Biophysical Journal LA - en OP - SN - 0006-3495 UR - http://dx.doi.org/10.1016/j.bpj.2012.11.3806 DB - Crossref ER - TY - JOUR TI - Solvate Structures and Computational/Spectroscopic Characterization of Lithium Difluoro(oxalato)borate (LiDFOB) Electrolytes AU - Han, Sang-Don AU - Allen, Joshua L. AU - Jonsson, Erlendur AU - Johansson, Patrik AU - McOwen, Dennis W. AU - Boyle, Paul D. AU - Henderson, Wesley A. T2 - JOURNAL OF PHYSICAL CHEMISTRY C AB - Lithium difluoro(oxalato)borate (LiDFOB) is a relatively new salt designed for battery electrolyte usage. Limited information is currently available, however, regarding the ionic interactions of this salt (i.e., solvate formation) when it is dissolved in aprotic solvents. Vibrational spectroscopy is a particularly useful tool for identifying these interactions, but only if the vibrational bands can be correctly linked to specific forms of anion coordination. Single crystal structures of LiDFOB solvates have therefore been used to both explore the DFOB–...Li+ cation coordination interactions and serve as unambiguous models for the assignment of the Raman vibrational bands. The solvate crystal structures determined include (monoglyme)2:LiDFOB, (1,2-diethoxyethane)3/2:LiDFOB, (acetonitrile)3:LiDFOB, (acetonitrile)1:LiDFOB, (dimethyl carbonate)3/2:LiDFOB, (succinonitrile)1:LiDFOB, (adiponitrile)1:LiDFOB, (PMDETA)1:LiDFOB, (CRYPT-222)2/3:LiDFOB, and (propylene carbonate)1:LiDFOB. DFT calculations have been incorporated to provide additional insight into the origin (i.e., vibrational modes) of the Raman vibrational bands to aid in the interpretation of the experimental analysis. DA - 2013/3/21/ PY - 2013/3/21/ DO - 10.1021/jp309102c VL - 117 IS - 11 SP - 5521-5531 SN - 1932-7447 ER - TY - JOUR TI - Poly Specific trans-Acyltransferase Machinery Revealed via Engineered Acyl-CoA Synthetases AU - Koryakina, Irina AU - McArthur, John AU - Randall, Shan AU - Draelos, Matthew M. AU - Musiol, Ewa M. AU - Muddiman, David C. AU - Weber, Tilmann AU - Williams, Gavin J. T2 - ACS CHEMICAL BIOLOGY AB - Polyketide synthases construct polyketides with diverse structures and biological activities via the condensation of extender units and acyl thioesters. Although a growing body of evidence suggests that polyketide synthases might be tolerant to non-natural extender units, in vitro and in vivo studies aimed at probing and utilizing polyketide synthase specificity are severely limited to only a small number of extender units, owing to the lack of synthetic routes to a broad variety of acyl-CoA extender units. Here, we report the construction of promiscuous malonyl-CoA synthetase variants that can be used to synthesize a broad range of malonyl-CoA extender units substituted at the C2-position, several of which contain handles for chemoselective ligation and are not found in natural biosynthetic systems. We highlighted utility of these enzymes by probing the acyl-CoA specificity of several trans-acyltransferases, leading to the unprecedented discovery of poly specificity toward non-natural extender units, several of which are not found in naturally occurring biosynthetic pathways. These results reveal that polyketide biosynthetic machinery might be more tolerant to non-natural substrates than previously established, and that mutant synthetases are valuable tools for probing the specificity of biosynthetic machinery. Our data suggest new synthetic biology strategies for harnessing this promiscuity and enabling the regioselective modification of polyketides. DA - 2013/1// PY - 2013/1// DO - 10.1021/cb3003489 VL - 8 IS - 1 SP - 200-208 SN - 1554-8937 ER - TY - JOUR TI - Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes AU - Chen, Hsi-Chuan AU - Song, Jina AU - Williams, Cranos M. AU - Shuford, Christopher M. AU - Liu, Jie AU - Wang, Jack P. AU - Li, Quanzi AU - Shi, Rui AU - Gokce, Emine AU - Ducoste, Joel AU - Muddiman, David C. AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PLANT PHYSIOLOGY AB - 4-Coumaric acid:coenzyme A ligase (4CL) is involved in monolignol biosynthesis for lignification in plant cell walls. It ligates coenzyme A (CoA) with hydroxycinnamic acids, such as 4-coumaric and caffeic acids, into hydroxycinnamoyl-CoA thioesters. The ligation ensures the activated state of the acid for reduction into monolignols. In Populus spp., it has long been thought that one monolignol-specific 4CL is involved. Here, we present evidence of two monolignol 4CLs, Ptr4CL3 and Ptr4CL5, in Populus trichocarpa. Ptr4CL3 is the ortholog of the monolignol 4CL reported for many other species. Ptr4CL5 is novel. The two Ptr4CLs exhibited distinct Michaelis-Menten kinetic properties. Inhibition kinetics demonstrated that hydroxycinnamic acid substrates are also inhibitors of 4CL and suggested that Ptr4CL5 is an allosteric enzyme. Experimentally validated flux simulation, incorporating reaction/inhibition kinetics, suggested two CoA ligation paths in vivo: one through 4-coumaric acid and the other through caffeic acid. We previously showed that a membrane protein complex mediated the 3-hydroxylation of 4-coumaric acid to caffeic acid. The demonstration here of two ligation paths requiring these acids supports this 3-hydroxylation function. Ptr4CL3 regulates both CoA ligation paths with similar efficiencies, whereas Ptr4CL5 regulates primarily the caffeic acid path. Both paths can be inhibited by caffeic acid. The Ptr4CL5-catalyzed caffeic acid metabolism, therefore, may also act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux. A high level of caffeic acid was detected in stem-differentiating xylem of P. trichocarpa. Our results suggest that Ptr4CL5 and caffeic acid coordinately modulate the CoA ligation flux for monolignol biosynthesis. DA - 2013/3// PY - 2013/3// DO - 10.1104/pp.112.210971 VL - 161 IS - 3 SP - 1501-1516 SN - 0032-0889 ER - TY - JOUR TI - Mid-infrared surface plasmon resonance in zinc oxide semiconductor thin films AU - Sachet, Edward AU - Losego, Mark D. AU - Guske, Joshua AU - Franzen, Stefan AU - Maria, Jon-Paul T2 - Applied Physics Letters AB - Surface plasmon resonance (SPR) in semiconducting materials at mid-infrared (mid-IR) energies offers the potential for new plasmonic functionalities and integration schemes. Mainstream semiconductors are transparent to mid-IR energies, thus a tightly integrated monolithic package for SPR sensing becomes feasible. We report mid-IR surface plasmon resonance in zinc oxide as a model material for semiconductors with 4 × 1019 to 8 × 1019 cm−3 carriers. The surface plasmon modes were characterized using spectroscopic IR-ellipsometry and compared to a reflectivity simulation. The data confirm the feasibility of mid-IR SPR, show a generic ability for plasmon tuning, and demonstrate the predictive power of the reflectivity model. DA - 2013/2/4/ PY - 2013/2/4/ DO - 10.1063/1.4791700 VL - 102 IS - 5 SP - 051111 J2 - Appl. Phys. Lett. LA - en OP - SN - 0003-6951 1077-3118 UR - http://dx.doi.org/10.1063/1.4791700 DB - Crossref ER - TY - JOUR TI - Microfabricated microelectrode sensor for measuring background and slowly changing dopamine concentrations AU - Dengler, Adam K. AU - McCarty, Gregory S. T2 - JOURNAL OF ELECTROANALYTICAL CHEMISTRY AB - The electrochemical detection of neurotransmitters in vivo has centered on fast scan cyclic voltammetry (FSCV) due to its temporal resolution, sensitivity and chemical selectivity. FSCV is a differential technique that records phasic (second-to-second) changes in the concentration of electroactive neurotransmitters such as dopamine (DA). To isolate the currents due to fluctuations in analyte concentration, in other words to make these phasic measurements, requires the subtraction of a large background current. The subtraction of this background and its volatility renders FSCV unable to determine background or slowly varying concentrations of electroactive analytes. However, there is still a need to readily determine the background and slowly changing concentrations of electroactive analytes in tissue. For example, the background concentrations of DA vary throughout the brain and can affect the dynamics of dopaminergic systems. So, this report presents a microfabricated electrochemical sensor for measuring background and slowly changing concentrations of DA in vitro with the selectivity and sensitivity of FSCV. The sensor is comprised of two microfabricated microelectrodes which are spaced 8 μm apart. Varying the applied potential of the outer electrode manipulates the local concentration of electroactive species including concentration at the inner electrode. These changes are measured at the inner electrode using FSCV. The resulting signal with calibration can determine the background and slowly changing concentration of DA with the selectivity and sensitivity of FSCV. In this study the background of DA is determined in vitro using this sensor. The DA signal is shown to be the result of adsorption/desorption at the outer electrode. Interference from ascorbate on the DA signal is shown to be minimal for this approach. DA - 2013/3/15/ PY - 2013/3/15/ DO - 10.1016/j.jelechem.2013.01.022 VL - 693 SP - 28-33 SN - 1572-6657 KW - Dopamine KW - Tonic level KW - Electrochemical measurement KW - Basal level KW - Biochemical sensor KW - Microfabricated sensor ER - TY - JOUR TI - Magnetic and Electrical Transport Properties of LaBaCo2O5.5+delta Thin Films on Vicinal (001) SrTiO3 Surfaces AU - Ma, Chunrui AU - Liu, Ming AU - Collins, Gregory AU - Wang, Haibin AU - Bao, Shanyong AU - Xu, Xing AU - Enriquez, Erik AU - Chen, Chonglin AU - Lin, Yuan AU - Whangbo, Myung-Hwan T2 - ACS APPLIED MATERIALS & INTERFACES AB - Highly epitaxial LaBaCo2O5.5+δ thin films were grown on the vicinal (001) SrTiO3 substrates with miscut angles of 0.5°, 3.0°, and 5.0° to systemically study strain effect on its physical properties. The electronic transport properties and magnetic behaviors of these films are strongly dependent on the miscut angles. With increasing the miscut angle, the transport property of the film changes from semiconducting to semimetallic, which results most probably from the locally strained domains induced by the surface step terraces. In addition, a very large magnetoresistance (34% at 60 K) was achieved for the 0.5°-miscut film, which is ∼30% larger than that for the film grown on the regular (001) SrTiO3 substrates. DA - 2013/1/23/ PY - 2013/1/23/ DO - 10.1021/am302553y VL - 5 IS - 2 SP - 451-455 SN - 1944-8252 KW - epitaxial thin film KW - LaBaCo2O5.5+delta KW - magnetoresistance KW - surface and interface KW - vicinal surface KW - electronic transport ER - TY - JOUR TI - Direct Analysis of Textile Fabrics and Dyes Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometry AU - Cochran, Kristin H. AU - Barry, Jeremy A. AU - Muddiman, David C. AU - Hinks, David T2 - ANALYTICAL CHEMISTRY AB - The forensic analysis of textile fibers uses a variety of techniques from microscopy to spectroscopy. One such technique that is often used to identify the dye(s) within the fiber is mass spectrometry (MS). In the traditional MS method, the dye must be extracted from the fabric and the dye components are separated by chromatography prior to mass spectrometric analysis. Direct analysis of the dye from the fabric allows the omission of the lengthy sample preparation involved in extraction, thereby significantly reducing the overall analysis time. Herein, a direct analysis of dyed textile fabric was performed using the infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source for MS. In MALDESI, an IR laser with wavelength tuned to 2.94 μm is used to desorb the dye from the fabric sample with the aid of water as the matrix. The desorbed dye molecules are then postionized by electrospray ionization (ESI). A variety of dye classes were analyzed from various fabrics with little to no sample preparation allowing for the identification of the dye mass and in some cases the fiber polymer. Those dyes that were not detected using MALDESI were also not observed by direct infusion ESI of the dye standard. DA - 2013/1/15/ PY - 2013/1/15/ DO - 10.1021/ac302519n VL - 85 IS - 2 SP - 831-836 SN - 0003-2700 ER - TY - JOUR TI - Catalytic efficiency of dehaloperoxidase A is controlled by electrostatics - application of the vibrational Stark effect to understand enzyme kinetics AU - Schkolnik, Gal AU - Utesch, Tillmann AU - Zhao, Junjie AU - Jiang, Shu AU - Thompson, Matthew K. AU - Mroginski, Maria-Andrea AU - Hildebrandt, Peter AU - Franzen, Stefan T2 - BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS AB - The vibrational Stark effect is gaining popularity as a method for probing electric fields in proteins. In this work, we employ it to explain the effect of single charge mutations in dehaloperoxidase-hemoglobin A (DHP A) on the kinetics of the enzyme. In a previous communication published in this journal (BBRC 2012, 420, 733-737) it has been shown that an increase in the overall negative charge of DHP A through mutation causes a decrease in its catalytic efficiency. Here, by labeling the protein with 4-mercaptobenzonitrile (MBN), a Stark probe molecule, we provide further evidence that the diffusion control of the catalytic process arises from the electrostatic repulsion between the enzyme and the negatively charged substrate. The linear correlation observed between the nitrile stretching frequency of the protein-bound MBN and the catalytic efficiency of the single-site mutants of the enzyme indicates that electrostatic interactions play a dominant role in determining the catalytic efficiency of DHP A. DA - 2013/1/18/ PY - 2013/1/18/ DO - 10.1016/j.bbrc.2012.12.047 VL - 430 IS - 3 SP - 1011-1015 SN - 1090-2104 KW - Vibrational Stark effect KW - Hemoglobin KW - 4-mercaptobenzonitrile KW - Enzyme kinetics KW - Electric field ER - TY - JOUR TI - Volume fraction of graphene platelets in copper-graphene composites AU - Jagannadham, K. T2 - Metallurgical and Materials Transactions. A, Physical Metallurgy and Materials Science DA - 2013/// PY - 2013/// VL - 44A IS - 1 SP - 552-559 ER - TY - JOUR TI - Tunable topological surface and realization of insulating massive Dirac fermion state in Bi2Te2Se with co-substitution AU - Niu, Chengwang AU - Dai, Ying AU - Guo, Meng AU - Ma, Yandong AU - Huang, Baibiao AU - Whangbo, Myung-Hwan T2 - JOURNAL OF MATERIALS CHEMISTRY C AB - The ternary topological insulator Bi2Te2Se is exceptional as it has a larger bulk resistivity than previously studied topological insulators. Here we explored the possibility of modifying the topological surface states and achieving the insulating massive Dirac fermion state in Bi2Te2Se on the basis of density functional calculations. Substitution of O for the outmost-layer Te leads to tunable surface states with an ideal Dirac cone. The co-substitution of Cr and O, as well as that of Mn and F, for the surface Bi and Te places the Dirac point inside the bulk band gap and opens a band gap at the Dirac point, hence creating the insulating massive Dirac fermion state. The co-substitution of magnetic and non-magnetic elements is a promising way of tuning the properties of topological insulators. DA - 2013/// PY - 2013/// DO - 10.1039/c2tc00017b VL - 1 IS - 1 SP - 114-120 SN - 2050-7534 ER - TY - JOUR TI - Thioureas as Reporting Elements for Metal-Responsive Fluorescent Chemosensors AU - Vonlanthen, Mireille AU - Finney, Nathaniel S. T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Proof that sulfur is a viable reporting element for the development of fluorescent chemosensors for metal ions is presented. To date, the majority of metal-responsive fluorescent chemosensors have relied on metal–nitrogen coordination to provide a fluorescence response, most commonly by suppressing photoinduced electron transfer (PET) quenching. While chemosensors with direct application to biology, medicine, and analytical chemistry have been so developed, reliance on the coordination chemistry of nitrogen remains a practical and conceptual limitation. Building on the fact that thioureas can quench fluorescence emission by PET, it is shown that the quenched emission of thiourea-appended naphthalimides can be restored by metal binding and that metal affinity and selectivity can be controlled through structural modification of the thiourea substituents. Further, such chemosensors can function in aqueous media and, unlike nitrogen-based chemosensors, are unresponsive to increases in [H+]. Given that the coordination properties of sulfur are distinct from those of nitrogen, this work lays the foundation for the development of a new class of interesting and useful metal-responsive fluorescent probes. DA - 2013/4/19/ PY - 2013/4/19/ DO - 10.1021/jo4003129 VL - 78 IS - 8 SP - 3980-3988 SN - 1520-6904 ER - TY - JOUR TI - The use of a xylosylated plant glycoprotein as an internal standard accounting for N-linked glycan cleavage and sample preparation variability AU - Walker, S. H. AU - Taylor, A. D. AU - Muddiman, David T2 - Rapid Communications in Mass Spectrometry AB - RATIONALE Traditionally, free oligosaccharide internal standards are used to account for variability in glycan relative quantification experiments by mass spectrometry. However, a more suitable internal standard would be a glycoprotein, which could also control for enzymatic cleavage efficiency, allowing for more accurate quantitative experiments. METHODS Hydrophobic, hydrazide N ‐linked glycan reagents (both native and stable‐isotope labeled) are used to derivatize and differentially label N ‐linked glycan samples for relative quantification, and the samples are analyzed by a reversed‐phase liquid chromatography chip system coupled online to a Q‐Exactive mass spectrometer. The inclusion of two internal standards, maltoheptaose (previously used) and horseradish peroxidase (HRP) (novel), is studied to demonstrate the effectiveness of using a glycoprotein as an internal standard in glycan relative quantification experiments. RESULTS HRP is a glycoprotein containing a xylosylated N ‐linked glycan, which is unique from mammalian N ‐linked glycans. Thus, the internal standard xylosylated glycan could be detected without interference to the sample. Additionally, it was shown that differences in cleavage efficiency can be detected by monitoring the HRP glycan. In a sample where cleavage efficiency variation is minimal, the HRP glycan performs as well as maltoheptaose. CONCLUSIONS Because the HRP glycan performs as well as maltoheptaose but is also capable of correcting and accounting for cleavage variability, it is a more versatile internal standard and will be used in all subsequent biological studies. Because of the possible lot‐to‐lot variation of an enzyme, differences in biological matrix, and variable enzyme activity over time, it is a necessity to account for glycan cleavage variability in glycan relative quantification experiments. Copyright © 2013 John Wiley & Sons, Ltd. DA - 2013/// PY - 2013/// DO - 10.1002/rcm.6579 VL - 27 IS - 12 SP - 1354–1358 ER - TY - JOUR TI - Single Cell Optical Imaging and Spectroscopy AU - Stender, Anthony S. AU - Marchuk, Kyle AU - Liu, Chang AU - Sander, Suzanne AU - Meyer, Matthew W. AU - Smith, Emily A. AU - Neupane, Bhanu AU - Wang, Gufeng AU - Li, Junjie AU - Cheng, Ji-Xin AU - Huang, Bo AU - Fang, Ning T2 - CHEMICAL REVIEWS AB - ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTSingle Cell Optical Imaging and SpectroscopyAnthony S. Stender†, Kyle Marchuk†, Chang Liu†, Suzanne Sander†, Matthew W. Meyer†, Emily A. Smith†, Bhanu Neupane‡, Gufeng Wang‡, Junjie Li§, Ji-Xin Cheng§, Bo Huang∥, and Ning Fang*†View Author Information† Department of Chemistry, Iowa State University, and Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States‡ Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States§ Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States∥ Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States*E-mail: [email protected]Cite this: Chem. Rev. 2013, 113, 4, 2469–2527Publication Date (Web):February 14, 2013Publication History Received15 August 2012Published online14 February 2013Published inissue 10 April 2013https://doi.org/10.1021/cr300336eCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views12877Altmetric-Citations232LEARN 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 InReddit Read OnlinePDF (35 MB) Get e-AlertscloseSUBJECTS:Fluorescence,Fluorescence resonance energy transfer,Microscopy,Nanoparticles,Raman spectroscopy Get e-Alerts DA - 2013/4// PY - 2013/4// DO - 10.1021/cr300336e VL - 113 IS - 4 SP - 2469-2527 SN - 1520-6890 ER - TY - JOUR TI - Photophysical Properties and Electronic Structure of Bacteriochlorin-Chalcones with Extended Near-Infrared Absorption AU - Yang, Eunkyung AU - Ruzie, Christian AU - Krayer, Michael AU - Diers, James R. AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY AB - Abstract Synthetic 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 ( τ s , Φ f , Φ ic , Φ isc , τ T , k f , k ic , k isc ) of the bacteriochlorins have been characterized. The bacteriochlorins absorb strongly in the 780–800 nm region and have fluorescence quantum yields ( Φ f ) 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. DA - 2013/// PY - 2013/// DO - 10.1111/php.12053 VL - 89 IS - 3 SP - 586-604 SN - 1751-1097 ER - TY - JOUR TI - Molecular Electronic Tuning of Photosensitizers to Enhance Photodynamic Therapy: Synthetic Dicyanobacteriochlorins as a Case Study AU - Yang, Eunkyung AU - Diers, James R. AU - Huang, Ying-Ying AU - Hamblin, Michael R. AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY AB - Abstract Photophysical, 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) 2 BC and corresponding zinc (NC) 2 BC‐Zn and palladium chelate (NC) 2 BC‐Pd. The order of PDT activity against HeLa human cancer cells in vitro is (NC) 2 BC‐Pd > (NC) 2 BC > (NC) 2 BC‐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) 2 BC‐Pd. Phosphorescence from (NC) 2 BC‐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) 2 BC‐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. DA - 2013/// PY - 2013/// DO - 10.1111/php.12021 VL - 89 IS - 3 SP - 605-618 SN - 1751-1097 ER - TY - JOUR TI - Midblock-sulfonated triblock ionomers derived from a long-chain poly[styrene-b-butadiene-b-styrene] triblock copolymer AU - Vargantwar, Pruthesh H. AU - Brannock, Molly C. AU - Tauer, Klaus AU - Spontak, Richard J. T2 - JOURNAL OF MATERIALS CHEMISTRY A AB - Selective sulfonation of a poly[styrene-b-butadiene-b-styrene] (SBS) triblock copolymer has been performed with a sulfur trioxide–dioxane (SO3–dioxane) complex to generate midblock-sulfonated triblock ionomers possessing varying degrees of sulfonation (DOS). Products of the sulfonation reaction have been characterized by proton nuclear magnetic resonance and Fourier-transform infrared spectroscopies to ensure sulfonation only involves the B midblocks. Due to this targeted sulfonation, the lower glass transition temperature (Tg) disappears completely in all the ionomers examined, indicating that the formation of ionic aggregates restricts the mobility of the B midblocks. Such aggregates hinder microphase separation and promote a diffuse interface, as established by progressive broadening of the upper Tg with increasing DOS. Additional evidence of diffuse interfaces and matrix densification is provided by small-angle X-ray scattering, which reveals a concurrent size reduction in microdomain spacing with increasing DOS. A sulfonation-induced order–order morphological transition from cylinders to lamellae is likewise observed. Due to the retention of microphase-separated glassy microdomains that serve as physical crosslinks, these triblock ionomers are capable of absorbing remarkably high solvent levels and forming highly swollen gel networks in polar media, thereby making them suitable for use in hygiene and healthcare applications, as well as in devices requiring ion transport. DA - 2013/// PY - 2013/// DO - 10.1039/c2ta00022a VL - 1 IS - 10 SP - 3430-3439 SN - 2050-7496 ER - TY - JOUR TI - Infrared Matrix-Assisted Laser Desorption Electrospray Ionization (IR-MALDESI) Imaging Source Coupled to a FT-ICR Mass Spectrometer AU - Robichaud, Guillaume AU - Barry, Jeremy A. AU - Garrard, Kenneth P. AU - Muddiman, David C. T2 - JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY AB - Mass spectrometry imaging (MSI) allows for the direct monitoring of the abundance and spatial distribution of chemical compounds over the surface of a tissue sample. This technology has opened the field of mass spectrometry to numerous innovative applications over the past 15 years. First used with SIMS and MALDI MS that operate under vacuum, interest has grown for mass spectrometry ionization sources that allow for effective imaging but where the analysis can be performed at ambient pressure with minimal or no sample preparation. We introduce here a versatile source for MALDESI imaging analysis coupled to a hybrid LTQ-FT-ICR mass spectrometer. The imaging source offers single shot or multi-shot capability per pixel with full control over the laser repetition rate and mass spectrometer scanning cycle. Scanning rates can be as fast as 1 pixel/second and a spatial resolution of 45 μm was achieved with oversampling. DA - 2013/1// PY - 2013/1// DO - 10.1007/s13361-012-0505-9 VL - 24 IS - 1 SP - 92-100 SN - 1044-0305 KW - FTMS KW - Mass spectrometry imaging KW - Infrared laser KW - MALDESI KW - Atmospheric pressure ER - TY - JOUR TI - Expanded combinatorial formation of porphyrin macrocycles in aqueous solution containing vesicles. A prebiotic model AU - Soares, Ana R. M. AU - Taniguchi, Masahiko AU - Chandrashaker, Vanampally AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/c3nj41041b VL - 37 IS - 4 SP - 1073 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/c3nj41041b DB - Crossref ER - TY - JOUR TI - Crystal Chemistry, Band Engineering, and Photocatalytic Activity of the LiNb3O8-CuNb3O8 Solid Solution AU - Sahoo, Prangya Parimita AU - Maggard, Paul A. T2 - INORGANIC CHEMISTRY AB - A new solid solution has been prepared in the system LiNb3O8–CuNb3O8, and the impacts of chemical composition and crystal structure have been investigated for the resulting band gap sizes and photocatalytic activities for water reduction to hydrogen under visible light. All members of the solid solution were synthesized by solid-state methods within evacuated fused-silica vessels, and their phase purities were confirmed via powder X-ray diffraction techniques (space group P21/a, a = 15.264(5)–15.367(1) Å, b = 5.031(3)–5.070(1) Å, c = 7.456(1)–7.536(8) Å, and β = 107.35(1)–107.14(8)°, for 0 ≤ x ≤ 1). Rietveld refinements were carried out for the x = 0.09, 0.50, and 0.70 members of the solid solution, which reveal the prevailing isostructurality of the continuous solid solution. The structure consists of chains of (Li/Cu)O6 and NbO6 octahedra. The optical band gap size across the solid solution exhibits a significant red-shift from ∼3.89 eV (direct) to ∼1.45 eV and ∼1.27 eV (direct and indirect) with increasing Cu(I) content, consistent with the change in sample color from white to dark brown to black. Electronic structure calculations based on density-functional theory methods reveal the rapid formation of a new Cu 3d10-based valence band that emerges higher in energy than the O 2p band. While the pure LiNb3O8 is a highly active UV-photocatalyst for water reduction, the Li1–xCuxNb3O8 solid is shown to be photocatalytically active under visible-light irradiation for water reduction to hydrogen. DA - 2013/4/15/ PY - 2013/4/15/ DO - 10.1021/ic302649s VL - 52 IS - 8 SP - 4443-4450 SN - 1520-510X ER - TY - JOUR TI - Aqueous–membrane partitioning of β-substituted porphyrins encompassing diverse polarity AU - Soares, Ana R. M. AU - Thanaiah, Yugaananthy AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. T2 - New Journal of Chemistry AB - 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. DA - 2013/// PY - 2013/// DO - 10.1039/c3nj41042k VL - 37 IS - 4 SP - 1087 J2 - New J. Chem. LA - en OP - SN - 1144-0546 1369-9261 UR - http://dx.doi.org/10.1039/c3nj41042k DB - Crossref ER - TY - JOUR TI - A flexible approach to 1,4-di-substituted 2-aminoimidazoles that inhibit and disperse biofilms and potentiate the effects of beta-lactams against multi-drug resistant bacteria AU - Furlani, Robert E. AU - Yeagley, Andrew A. AU - Melander, Christian T2 - EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY AB - The pyrrole-imidazole alkaloids are a 2-aminoimidazoles containing family of natural products that possess anti-biofilm activity. A library of 1,4-di-substituted 2-aminoimidazole/triazoles (2-AITs) was synthesized, and its anti-biofilm activity as well as oxacillin resensitization efficacy toward methicillin resistant Staphylococcus aureus (MRSA) was investigated. These 2-AITs were found to inhibit biofilm formation by MRSA with low micromolar IC50 values. Additionally, the most active compound acted synergistically with oxacillin against MRSA lowering the minimum inhibitory concentration (MIC) 4-fold. DA - 2013/4// PY - 2013/4// DO - 10.1016/j.ejmech.2012.12.005 VL - 62 SP - 59-70 SN - 1768-3254 KW - Biofilms KW - MRSA KW - Suppression of antibiotic resistance KW - 2-Aminoimidazoles ER - TY - JOUR TI - Synthesis and characterization of lipophilic, near-IR absorbing metallobacteriochlorins AU - Sun, E. J. AU - Chen, C. Y. AU - Lindsey, J. S. T2 - Chemical Journal of Chinese Universities DA - 2013/// PY - 2013/// VL - 34 IS - 4 SP - 776-781 ER - TY - JOUR TI - Metastable Cu(I)-Niobate Semiconductor with a Low-Temperature, Nanoparticle-Mediated Synthesis AU - Choi, Jonglak AU - King, Nacole AU - Maggard, Paul A. T2 - ACS NANO AB - A nanoparticle synthetic strategy for the preparation of a new metastable Cu(I)-niobate is described, and that involves multipored Li3NbO4 nanoparticles as a precursor. A hydrothermal reaction of HNbO3 and LiOH·H2O in PEG200 and water at ∼180 °C yields ∼15–40 nm Li3NbO4 particles. These particles are subsequently used in a solvothermal copper(I)-exchange reaction with excess CuCl at 150 °C. Heating these products within the used CuCl flux (mp = 430 °C) to 450 °C for 30 min yields ∼4–12 nm Cu2Nb8O21 crystalline nanoparticles, and for a heating time of 24 h yields μm-sized, rod-shaped crystals. The new structure was characterized by single-crystal X-ray diffraction to have a condensed network consisting of NbO7 polyhedra and chains of elongated CuO4 tetrahedra. The compound thermally decomposes starting at ∼250 °C and higher temperatures, depending on the particle sizes, owing to the loss of the weakly coordinated Cu(I) cations from the structure and a concurrent disproportionation reaction at its surfaces. Thus, conventional solid-state reactions involving higher temperatures and bulk reagents have proven unsatisfactory for its synthesis. The measured bandgap size is ∼1.43–1.65 eV (indirect) and shows a dependence on the particle sizes. Electronic structure calculations based on density functional theory show that the bandgap transition results from the excitation of electrons at the band edges between filled Cu(I) 3d10-orbitals and empty Nb(V) 4d0-orbitals, respectively. The p-type nature of the Cu2Nb8O21 particles was confirmed in photoelectrochemical measurements on polycrystalline films that show a strong photocathodic current under visible-light irradiation in aqueous solutions. These results demonstrate the general utility of reactive nanoscale precursors in the synthetic discovery of new Cu(I)-based semiconducting oxides and which also show promise for use in solar energy conversion applications. DA - 2013/2// PY - 2013/2// DO - 10.1021/nn305707f VL - 7 IS - 2 SP - 1699-1708 SN - 1936-086X KW - nanoscale synthesis KW - solar energy KW - metastability KW - copper niobate KW - lithium niobate ER - TY - JOUR TI - Magnetic Order Through Super-Superexchanges in the Polar Magnetoelectric Organic-Inorganic Hybrid Cr[(D3N-(CH2)(2)-PO3)(Cl)(D2O)] AU - Nenert, Gwilherm AU - Koo, Hyun-Joo AU - Colin, Claire V. AU - Bauer, Elvira M. AU - Bellitto, Carlo AU - Ritter, Clemens AU - Righini, Guido AU - Whangbo, Myung-Hwan T2 - INORGANIC CHEMISTRY AB - The crystal and magnetic structures of the organic-inorganic hybrid compound Cr(II) ammoniumethylphosphonate chloride monohydrate, Cr[D(3)N-(CH(2))(2)-PO(3))(Cl)(D(2)O)] (1), have been studied by temperature-dependent neutron powder diffraction and superconducting quantum interference device (SQUID) magnetometry. The compound represents a rare example of a magnetoelectric polar organic-inorganic hybrid solid, containing high spin Cr(2+) ions (S = 2) and is a canted antiferromagnet (weak ferromagnet) below T(N) = 5.5 K. The neutron powder diffraction pattern recorded at T = 10 K, shows that the partially deuterated compound crystallizes in the same non centrosymmetric monoclinic space group P2(1) (No. 4) with the following unit-cell parameters: a = 5.24041(4) Å, b =13.93113(8) Å, c = 5.26081(4) Å, and β = 105.4347(5)°. Powder neutron diffraction of a partially deuterated sample has enabled us, for the first time, to locate the water molecule. At low temperature, the compound presents a canted antiferromagnetic state characterized by k = 0 resulting in the magnetic symmetry P2(1)'. This symmetry is in agreement with the previously reported large magnetodielectric effect. The crystal structure of (1) can be described as being built up of triangular lattice planes made up of [Cr(II)O(4)Cl] square pyramids which are separated by ammonium ethyl groups along the b axis. The transition from paramagnetic to weakly ferromagnetic state results from super-superexchanges only. Surprisingly, while the overall magnetic behavior is antiferromagnetic, the Cr(II)O(4)Cl planes are ferromagnetic, and the strongest antiferromagnetic coupling is via the ammonium ethyl groups. Our density functional calculations confirm these aspects of the spin exchange interactions of (1) and that the spin exchange interactions between Cr(II) ions are considerably weak compared with the single-ion anisotropy of Cr(II). DA - 2013/1/21/ PY - 2013/1/21/ DO - 10.1021/ic301874v VL - 52 IS - 2 SP - 753-760 SN - 1520-510X ER - TY - JOUR TI - MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform AU - Robichaud, Guillaume AU - Garrard, Kenneth P. AU - Barry, Jeremy A. AU - Muddiman, David C. T2 - JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY AB - During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs. DA - 2013/5// PY - 2013/5// DO - 10.1007/s13361-013-0607-z VL - 24 IS - 5 SP - 718-721 SN - 1879-1123 KW - Mass spectrometry imaging KW - Software KW - High mass resolving power KW - FT-ICR-MS KW - Open-source ER - TY - JOUR TI - Flux Synthesis of Na2Ca2Nb4O13: The Influence of Particle Shapes, Surface Features, and Surface Areas on Photocatalytic Hydrogen Production AU - Arney, David AU - Fuoco, Lindsay AU - Boltersdorf, Jonathan AU - Maggard, Paul A. T2 - JOURNAL OF THE AMERICAN CERAMIC SOCIETY AB - The layered perovskite ( n = 4) Ruddlesden‐Popper phase Na 2 Ca 2 Nb 4 O 13 was prepared within molten NaCl and Na 2 SO 4 fluxes, yielding either rod‐shaped or platelet‐shaped particles, respectively. The flux‐to‐reactant molar ratios of 5:1 or 20:1 were found to significantly influence particle sizes and surface areas, while still maintaining the overall particle shapes. Measured surface areas of flux‐prepared Na 2 Ca 2 Nb 4 O 13 particles ranged from ∼0.36 to 4.6 m 2 /g, with the highest surface areas obtained using a 5:1 ( NaCl ‐to‐ Na 2 Ca 2 Nb 4 O 13 ) molar ratio. All samples exhibited a bandgap size of ∼3.3 eV, as determined by UV –Vis diffuse reflectance measurements. Photocatalytic rates for hydrogen production under ultraviolet light for platinized Na 2 Ca 2 Nb 4 O 13 particles in an aqueous methanol solution ranged from ∼230 to 1355 μmol H 2 g − 1 h − 1 when using the photochemical deposition ( PCD ) method of platinization, and ∼113–1099 μmol H 2 g − 1 h − 1 when using the incipient wetness impregnation ( IWI ) method of platinization. The higher photocatalytic rates were obtained for the rod‐shaped particles with the highest surface areas, with an apparent quantum yield ( AQY ) measured at ∼6.5% at 350 nm. For the platelet‐shaped particles, the higher photocatalytic rates were observed for the sample with the lowest surface area but the largest concentration of stepped edges and grooves observed at the particle surfaces. The latter origin of the photocatalytic activity is confirmed by the significant enhancement of the photocatalytic rates by the PCD method that allows for the preferential deposition of the surface Pt cocatalyst islands at the stepped edges and grooves, while the photocatalytic enhancement is much smaller when using the more general IWI platinization method. DA - 2013/4// PY - 2013/4// DO - 10.1111/jace.12122 VL - 96 IS - 4 SP - 1158-1162 SN - 0002-7820 ER - TY - JOUR TI - Magnetic properties and energy-mapping analysis AU - Xiang, Hongjun AU - Lee, Changhoon AU - Koo, Hyun-Joo AU - Gong, Xingao AU - Whangbo, Myung-Hwan T2 - DALTON TRANSACTIONS AB - The magnetic energy levels of a given magnetic solid are closely packed in energy because the interactions between magnetic ions are weak. Thus, in describing its magnetic properties, one needs to generate its magnetic energy spectrum by employing an appropriate spin Hamiltonian. In this review article we discuss how to determine and specify a necessary spin Hamiltonian in terms of first principles electronic structure calculations on the basis of energy-mapping analysis and briefly survey important concepts and phenomena that one encounters in reading the current literature on magnetic solids. Our discussion is given on a qualitative level from the perspective of magnetic energy levels and electronic structures. The spin Hamiltonian appropriate for a magnetic system should be based on its spin lattice, i.e., the repeat pattern of its strong magnetic bonds (strong spin exchange paths), which requires one to evaluate its Heisenberg spin exchanges on the basis of energy-mapping analysis. Other weaker energy terms such as Dzyaloshinskii-Moriya (DM) spin exchange and magnetocrystalline anisotropy energies, which a spin Hamiltonian must include in certain cases, can also be evaluated by performing energy-mapping analysis. We show that the spin orientation of a transition-metal magnetic ion can be easily explained by considering its split d-block levels as unperturbed states with the spin-orbit coupling (SOC) as perturbation, that the DM exchange between adjacent spin sites can become comparable in strength to the Heisenberg spin exchange when the two spin sites are not chemically equivalent, and that the DM interaction between rare-earth and transition-metal cations is governed largely by the magnetic orbitals of the rare-earth cation. DA - 2013/// PY - 2013/// DO - 10.1039/c2dt31662e VL - 42 IS - 4 SP - 823-853 SN - 1477-9234 ER - TY - JOUR TI - Transition metal complexes of donor-acceptor biradicals AU - Kirk, M. L. AU - Shultz, D. A. T2 - Coordination Chemistry Reviews DA - 2013/// PY - 2013/// VL - 257 IS - 1 SP - 218-233 ER - TY - JOUR TI - Reaction pathways for butanoic acid decarboxylation on the (111) surface of a Pd nanoparticle AU - Lamb, H. Henry AU - Sremaniak, Laura AU - Whitten, Jerry L. T2 - Surface Science AB - Many-electron theory is applied to investigate decarboxylation of butanoic acid on the (111) surface of a Pd42 nanoparticle. Butanoic acid adsorbs weakly as an intact molecule (ΔH = − 28 kJ/mol) with the COOH moiety nearly parallel to the surface. In comparison, dissociative adsorption of butanoic acid to form surface butanoate (PrCOO) species and adsorbed H is exothermic by only 5 kJ/mol. Pathways for propane and CO2 formation are presented starting from adsorbed butanoic acid, PrCOO (ads) and a RCHCOO (R = C2H5) surface intermediate. An intramolecular pathway involves rotating the H of COOH toward the target (alpha) carbon. Following a series of bond distortions, the H is close enough to the target C to form a stretched HC bond. After propane begins to form, CO2 linearizes and CC dissociation is energetically favorable and rapid. Reaction of PrCOO (ads) and H (ads) also results in direct formation of propane and CO2. The energy barriers for H insertion are ~ 100 kJ/mol for both pathways; however, the dissociative pathway involves a high-energy precursor state with H in a 3-fold site under the CC bond undergoing reaction. An alternative decarboxylation pathway starting from RCHCOO leads to gas-phase CO2 and propylidene (in the absence of adsorbed H) or propyl (via insertion of adsorbed H) with energy barriers of 75 and 32 kJ/mol, respectively. The energy of the RCHCOO intermediate relative to gas-phase butanoic acid increases from 43 to 109 kJ/mol in the presence of adsorbed H, compensating for the lower decomposition barrier. DA - 2013/1// PY - 2013/1// DO - 10.1016/j.susc.2012.08.023 VL - 607 SP - 130-137 J2 - Surface Science LA - en OP - SN - 0039-6028 UR - http://dx.doi.org/10.1016/j.susc.2012.08.023 DB - Crossref KW - Configuration interaction theory KW - Palladium KW - Fatty acid KW - Adsorption KW - Decarboxylation KW - Transition state KW - Adsorbed hydrogen ER - TY - JOUR TI - N-Substituted 2-aminoimidazole inhibitors of MRSA biofilm formation accessed through direct 1,3-bis(tert-butoxycarbonyl)guanidine cyclization AU - Yeagley, Andrew A. AU - Su, Zhaoming AU - McCullough, Kara D. AU - Worthington, Roberta J. AU - Melander, Christian T2 - ORGANIC & BIOMOLECULAR CHEMISTRY AB - Antibiotic resistance is a significant problem and is compounded by the ability of many pathogenic bacteria to form biofilms. A library of N-substituted derivatives of a previously reported 2-aminoimidazole/triazole (2-AIT) biofilm modulator was constructed via α-bromoketone cyclization with 1,3-bis(tert-butoxycarbonyl)guanidine, followed by selective substitution. Several compounds exhibited the ability to inhibit biofilm formation by three strong biofilm forming strains of methicillin resistant Staphylococcus aureus (MRSA). Additionally, a number of members of this library exhibited synergistic activity with oxacillin against planktonic MRSA. Compounds with this type of dual activity have the potential to be used as adjuvants with conventional antibiotics. DA - 2013/// PY - 2013/// DO - 10.1039/c2ob26469b VL - 11 IS - 1 SP - 130-137 SN - 1477-0539 ER - TY - JOUR TI - Antiferromagnetic ordering through a hydrogen-bonded network in the molecular solid CuF2(H2O)(2)(3-chloropyridine) AU - Lapidus, Saul H. AU - Manson, Jamie L. AU - Park, Hyunsoo AU - Clement, Alexander J. AU - Ghannadzadeh, Saman AU - Goddard, Paul AU - Lancaster, Tom AU - Moeller, Johannes S. AU - Blundell, Stephen J. AU - Telling, Mark T. F. AU - Kang, Jinhee AU - Whangbo, Myung-Hwan AU - Schlueter, John A. T2 - CHEMICAL COMMUNICATIONS AB - CuF(2)(H(2)O)(2)(3-chloropyridine) possesses a five-coordinate Cu(2+) center with a slightly distorted trigonal bypyramidal coordination geometry. Strong intermolecular F···H-O hydrogen bonds enable the formation of 2D layers and provide the primary magnetic exchange path that leads to the stabilization of long-range antiferromagnetic (AFM) order below T(N) = 2.1 K. DA - 2013/// PY - 2013/// DO - 10.1039/c2cc37444g VL - 49 IS - 5 SP - 499-501 SN - 1359-7345 ER -