@article{lampert_papanikolas_lappi_reynolds_2017, title={Intrinsic gain and gain degradation modulated by excitation pulse width in a semiconducting conjugated polymer}, volume={94}, ISSN={["1879-2545"]}, DOI={10.1016/j.optlastec.2017.03.019}, abstractNote={We have previously reported that substantially higher optical gain values can be achieved in the conjugated polymer poly[2-methoxy-5-(2′-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) through use of transient excitation conditions. In the present paper, we report on a systematic investigation of this behavior to elucidate the physical mechanisms involved, which enables us to distinguish between the fundamental intrinsic gain and an excitation induced degraded gain. Using pump laser pulses having temporal widths longer and shorter than the photoluminescence (PL) decay time of MEH-PPV, both quasi-steady-state (QSS) and transient excitation regimes are explored in our encapsulated waveguide heterostructures [Si(1 0 0)/SiO2/MEH-PPV/poly(methyl methacrylate)]. Under transient excitation (25 ps pump pulses), extremely large optical gain is observed, reaching a value of 700 cm−1 at a maximum pump energy density of 85 µJ/cm2. However, under QSS conditions (8 ns pulses), considerably lower gain coefficients are achieved with a maximum of ∼130 cm−1 at an energy density of 2,000 µJ/cm2; this factor of 5 decrease in optical gain performance is observed at the same excitation density as that for transient excitation using ps pulses. We have also employed unencapsulated waveguide structures [Si(1 0 0)/SiO2/MEH-PPV/air], which allows us to achieve additional insight on gain degradation under QSS conditions. It is clear that the gain measured under transient conditions is more representative of the intrinsic gain whereas that determined in the QSS regime is degraded by defect-mediated dissociation of emissive states due to localized thermal and oxidative damage to the films. It is in the QSS regime in which most optical gain measurements to date have been performed. These results suggest that further optimization of MEH-PPV – and most likely other conjugated polymers – as a robust optical gain medium can be achieved by consideration of the excitation pulse width.}, journal={OPTICS AND LASER TECHNOLOGY}, author={Lampert, Zach E. and Papanikolas, John M. and Lappi, Simon E. and Reynolds, C. Lewis, Jr.}, year={2017}, month={Sep}, pages={77–85} }
 @article{iasmin_dean_lappi_ducoste_2014, title={Factors that influence properties of FOG deposits and their formation in sewer collection systems}, volume={49}, ISSN={["0043-1354"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84889588357&partnerID=MN8TOARS}, DOI={10.1016/j.watres.2013.11.012}, abstractNote={Understanding the formation of Fat, Oil, and Grease (FOG) deposits in sewer systems is critical to the sustainability of sewer collection systems since they have been implicated in causing sewerage blockages that leads to sanitary sewer overflows (SSOs). Recently, FOG deposits in sewer systems displayed strong similarities with calcium-based fatty acid salts as a result of a saponification reaction. The objective of this study was to quantify the factors that may affect the formation of FOG deposits and their chemical and rheological properties. These factors included the types of fats used in FSEs, environmental conditions (i.e. pH and temperature), and the source of calcium in sewer systems. The results of this study showed that calcium content in the calcium based salts seemed to depend on the solubility limit of the calcium source and influenced by pH and temperature conditions. The fatty acid profile of the calcium-based fatty acid salts produced under alkali driven hydrolysis were identical to the profile of the fat source and did not match the profile of field FOG deposits, which displayed a high fraction of palmitic, a long chain saturated fatty acid. It is hypothesized that selective microbial metabolism of fats and/or biologically induced hydrogenation may contribute to the FOG deposit makeup in sewer system. Therefore, selective removal of palmitic in pretreatment processes may be necessary prior to the discharge of FSE wastes into the sewer collection system.}, journal={WATER RESEARCH}, author={Iasmin, Mahbuba and Dean, Lisa O. and Lappi, Simon E. and Ducoste, Joel J.}, year={2014}, month={Feb}, pages={92–102} }
 @article{lampert_lappi_papanikolas_reynolds_2013, title={Intrinsic optical gain in thin films of a conjugated polymer under picosecond excitation}, volume={103}, number={3}, journal={Applied Physics Letters}, author={Lampert, Z. E. and Lappi, S. E. and Papanikolas, J. M. and Reynolds, C. L.}, year={2013} }
 @article{he_reyes_leming_dean_lappi_ducoste_2013, title={Mechanisms of Fat, Oil and Grease (FOG) deposit formation in sewer lines}, volume={47}, ISSN={["0043-1354"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84879016648&partnerID=MN8TOARS}, DOI={10.1016/j.watres.2013.05.002}, abstractNote={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.}, number={13}, journal={WATER RESEARCH}, publisher={Elsevier BV}, author={He, Xia and Reyes, Francis L., III and Leming, Michael L. and Dean, Lisa O. and Lappi, Simon E. and Ducoste, Joel J.}, year={2013}, month={Sep}, pages={4451–4459} }
 @article{lampert_lappi_papanikolas_reynolds_aboelfotoh_2013, title={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]}, volume={113}, number={23}, journal={Journal of Applied Physics}, author={Lampert, Z. E. and Lappi, S. E. and Papanikolas, J. M. and Reynolds, C. L. and Aboelfotoh, M. O.}, year={2013} }
 @article{he_iasmin_dean_lappi_ducoste_reyes_2011, title={Evidence for Fat, Oil, and Grease (FOG) Deposit Formation Mechanisms in Sewer Lines}, volume={45}, ISSN={["1520-5851"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79956022597&partnerID=MN8TOARS}, DOI={10.1021/es2001997}, abstractNote={The presence of hardened and insoluble fats, oil, and grease (FOG) deposits in sewer lines is a major cause of line blockages leading to sanitary sewer overflows (SSOs). Despite the central role that FOG deposits play in SSOs, little is known about the mechanisms of FOG deposit formation in sanitary sewers. In this study, FOG deposits were formed under laboratory conditions from the reaction between free fatty acids and calcium chloride. The calcium and fatty acid profile analysis showed that the laboratory-produced FOG deposit displayed similar characteristics to FOG deposits collected from sanitary sewer lines. Results of FTIR analysis showed that the FOG deposits are metallic salts of fatty acid as revealed by comparisons with FOG deposits collected from sewer lines and pure calcium soaps. Based on the data, we propose that the formation of FOG deposits occurs from the aggregation of excess calcium compressing the double layer of free fatty acid micelles and a saponification reaction between aggregated calcium and free fatty acids.}, number={10}, journal={ENVIRONMENTAL SCIENCE & TECHNOLOGY}, author={He, Xia and Iasmin, Mahbuba and Dean, Lisa O. and Lappi, Simon E. and Ducoste, Joel J. and Reyes, Francis L., III}, year={2011}, month={May}, pages={4385–4391} }
 @article{grenko_reynolds_barlage_johnson_lappi_ebert_preble_paskova_evans_2010, title={Physical Properties of AlGaN/GaN Heterostructures Grown on Vicinal Substrates}, volume={39}, ISSN={0361-5235 1543-186X}, url={http://dx.doi.org/10.1007/S11664-010-1153-0}, DOI={10.1007/s11664-010-1153-0}, number={5}, journal={Journal of Electronic Materials}, publisher={Springer Science and Business Media LLC}, author={Grenko, J. A. and Reynolds, C. L., Jr. and Barlage, D. W. and Johnson, M. A. L. and Lappi, S. E. and Ebert, C. W. and Preble, E. A. and Paskova, T. and Evans, K. R.}, year={2010}, month={Mar}, pages={504–516} }
 @article{rhodes_lappi_fischer_sambasivan_genzer_franzen_2008, title={Characterization of monolayer formation on aluminum-doped zinc oxide thin films}, volume={24}, ISSN={["0743-7463"]}, DOI={10.1021/la701741m}, abstractNote={The optical and electronic properties of aluminum-doped zinc oxide (AZO) thin films on a glass substrate are investigated experimentally and theoretically. Optical studies with coupling in the Kretschmann configuration reveal an angle-dependent plasma frequency in the mid-IR for p-polarized radiation, suggestive of the detection of a Drude plasma frequency. These studies are complemented by oxygen depletion density functional theory studies for the calculation of the charge carrier concentration and plasma frequency for bulk AZO. In addition, we report on the optical and physical properties of thin film adlayers of n-hexadecanethiol (HDT) and n-octadecanethiol (ODT) self-assembled monolayers (SAMs) on AZO surfaces using reflectance FTIR spectroscopy, X-ray photoelectron spectroscopy (XPS), contact angle, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Our characterization of the SAM deposition onto the AZO thin film reveals a range of possible applications for this conducting metal oxide.}, number={2}, journal={LANGMUIR}, author={Rhodes, Crissy L. and Lappi, Simon and Fischer, Daniel and Sambasivan, Sharadha and Genzer, Jan and Franzen, Stefan}, year={2008}, month={Jan}, pages={433–440} }
 @misc{franzen_lappi_2007, title={Single pass attenuated total reflection fourier transform infrared microscopy apparatus and method for identifying protein secondary structure, surface charge and binding affinity}, volume={7,255,835}, number={2007 Aug. 14}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Franzen, S. and Lappi, S. E.}, year={2007} }
 @article{smith_efimenko_fischer_lappi_kilpatrick_genzer_2007, title={Study of the packing density and molecular orientation of bimolecular self-assembled monolayers of aromatic and aliphatic organosilanes on silica}, volume={23}, ISSN={["0743-7463"]}, DOI={10.1021/la062475v}, abstractNote={Bimolecular self-assembled monolayers (SAMs) of aromatic and aliphatic chlorosilanes were self-assembled onto silica, and their characteristics were established by contact angle measurement, near-edge X-ray absorption fine structure spectroscopy, and Fourier transform infrared spectroscopy. Three aromatic constituents (phenyltrichlorosilane, benzyltrichlorosilane, and phenethyltrichlorosilane) were studied in combination with four aliphatic coadsorbates (butyltrichlorosilane, butyldimethylchlorosilane, octadecyltrichlorosilane, and octadecyldimethylchlorosilane). Our results demonstrate that whereas SAMs made of trichlorinated organosilanes are densely packed, SAMs prepared from monochlorinated species are less dense and poorly ordered. In mixed systems, trichlorinated aromatics and trichlorinated aliphatics formed SAMs with highly tunable compositions; their surfaces were compositionally homogeneous with no large-scale domain separation. The homogeneous nature of the resulting SAM was a consequence of the formation of in-plane siloxane linkages among neighboring molecules. In contrast, when mixing monochlorinated aliphatics with trichlorinated aromatics, molecular segregation occurred. Although the two shortest aromatic species did not display significant changes in orientation upon mixing with aliphatics, the aromatic species with the longest polymethylene spacer, phenethyltrichlorosilane, displayed markedly different orientation behavior in mixtures of short- and long-chain aliphatics.}, number={2}, journal={LANGMUIR}, author={Smith, Matthew B. and Efimenko, Kirill and Fischer, Daniel A. and Lappi, Simon E. and Kilpatrick, Peter K. and Genzer, Jan}, year={2007}, month={Jan}, pages={673–683} }
 @article{belyea_belyea_lappi_franzen_2006, title={Resonance Raman study of ferric heme adducts of dehaloperoxidase from Amphitrite ornata}, volume={45}, ISSN={["0006-2960"]}, DOI={10.1021/bi0609218}, abstractNote={The study of axial ligation by anionic ligands to ferric heme iron by resonance Raman spectroscopy provides a basis for comparison of the intrinsic electron donor ability of the proximal histidine in horse heart myoglobin (HHMb), dehaloperoxidase (DHP), and horseradish peroxidase (HRP). DHP is a dimeric hemoglobin (Hb) originally isolated from the terebellid polychaete Amphitrite ornata. The monomers are structurally related to Mb and yet DHP has a peroxidase function. The core size marker modes, v2 and v3, were observed using Soret excitation, and DHP-X was compared to HHMb-X for the ligand series X = F, Cl, Br, SCN, OH, N3, and CN. Special attention was paid to the hydroxide adduct, which is also formed during the catalytic cycle of peroxidases. The Fe-OH stretching frequency was observed and confirmed by deuteration and is higher in DHP than in HHMb. The population of high-spin states of the heme iron in DHP was determined to be intermediate between HHMb and HRP. The data provide the first direct measurement of the effect of axial ligation on the heme iron in DHP. The Raman data support a modified charge relay in DHP, in which a strongly hydrogen-bonded backbone carbonyl (>C=O) polarizes the proximal histidine. The charge relay mechanism by backbone carbonyl >C=O-His-Fe is the analogue of the Asp-His-Fe of peroxidases and Glu-His-Fe of flavohemoglobins.}, number={48}, journal={BIOCHEMISTRY}, author={Belyea, Jennifer and Belyea, Curtis M. and Lappi, Simon and Franzen, Stefan}, year={2006}, month={Dec}, pages={14275–14284} }
 @article{bin-salamon_brewer_depperman_franzen_kampf_kirk_kumar_lappi_peariso_preuss_et al._2006, title={Testing Bridge-Mediated Differences in Dinuclear Valence Tautomeric Behavior}, volume={45}, ISSN={0020-1669 1520-510X}, url={http://dx.doi.org/10.1021/ic060170y}, DOI={10.1021/ic060170y}, abstractNote={Two structurally characterized dinuclear valence tautomers are described. Cobalt ions are bridged by p- and m-phenylene units connected to 2,2‘-bipyridines. X-ray crystal structures show that the molecules are in the [(CoIII)(CoIII)] forms at ca. 125 K, while spectroscopic studies show that both molecules can achieve the [(CoII)(CoII)] form above 400 K and confirm the [(CoIII)(CoIII)] form below 10 K. Magnetic susceptibility studies are also included. Our results highlight the necessity of studying both crystalline and amorphous samples to distinguish the effects of intrinsic electronic structure and intermolecular forces on valence tautomeric behavior.}, number={11}, journal={Inorganic Chemistry}, publisher={American Chemical Society (ACS)}, author={Bin-Salamon, Sofi and Brewer, Scott H. and Depperman, Ezra C. and Franzen, Stefan and Kampf, Jeff W. and Kirk, Martin L. and Kumar, R. Krishna and Lappi, Simon and Peariso, Katrina and Preuss, Kathryn E. and et al.}, year={2006}, month={May}, pages={4461–4467} }
 @article{bin-salamon_brewer_franzen_feldheim_lappi_shultz_2005, title={Supramolecular control of valence-tautomeric equilibrium on nanometer-scale gold clusters}, volume={127}, ISSN={["0002-7863"]}, DOI={10.1021/ja042520q}, abstractNote={This communication describes the preparation and characterization of a valence tautomer complex covalently attached to gold nanoparticles. Variable-temperature IR spectroscopy is used to determine the equilibrium thermodynamic parameters for the valence tautomerization. These results are compared with a nonsurface combined valence tautomer complex. The results show that surface confinement attenuates both ΔH° and ΔS°. We attribute these changes to a reduced accessible molecular surface area.}, number={15}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Bin-Salamon, S and Brewer, S and Franzen, S and Feldheim, DL and Lappi, S and Shultz, DA}, year={2005}, month={Apr}, pages={5328–5329} }
 @article{moses_brewer_lowe_lappi_gilvey_sauthier_tenent_feldheim_franzen_2004, title={Characterization of single- and double-stranded DNA on gold surfaces}, volume={20}, ISSN={["0743-7463"]}, DOI={10.1021/la0492815}, abstractNote={Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5‘-C6H12SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation−infrared reflection absorption spectroscopy (PM−IRRAS). The formation of dsDNA on the surface was identified by PM−IRRAS by a dsDNA IR signature at ∼1678 cm-1 that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 °C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au−S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.}, number={25}, journal={LANGMUIR}, author={Moses, S and Brewer, SH and Lowe, LB and Lappi, SE and Gilvey, LBG and Sauthier, M and Tenent, RC and Feldheim, DL and Franzen, S}, year={2004}, month={Dec}, pages={11134–11140} }
 @article{smith_lappi_brewer_dembowy_belyea_franzen_2004, title={Covalent attachment of a nickel nitrilotriacetic acid group to a germanium attenuated total reflectance element}, volume={20}, ISSN={["0743-7463"]}, DOI={10.1021/la034194i}, abstractNote={The surface of a germanium internal reflectance element (IRE) was modified to bind 6X-histidine (his)-tagged biomolecules. The step-by-step surface modification was monitored via single-pass attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR). Initially an adlayer of 7-octenyltrimethoxysilane (7-OTMS) was formed on the Ge crystal through the surface hydroxyl groups, which were produced via ozonolysis of the Ge surface. The vinyl moiety of 7-OTMS was oxidized to a carboxylic acid, which was activated by 1,1‘-carbonydiimidazole (CDI) to produce a labile imidazole. The labile imidazole that resulted from the CDI coupling was then displaced by the primary amine of nitrilotriacetic acid (NTA). Nickel sulfate was added to the system, and it coordinated with the three carbonyl groups and the nitrogen on NTA, thus leaving the ability of Ni to coordinate with two adjacent histidine residues. Binding of his-tagged biotin to nickel nitrilotriacetic acid (Ni-NTA) was observed by ATR-FT-IR spectroscopy. The surface modification method presented in this paper had minimal nonspecific binding, the Ni-NTA surface was reusable if stored properly, and complete removal of the organic surface was achievable.}, number={4}, journal={LANGMUIR}, author={Smith, BM and Lappi, SE and Brewer, SH and Dembowy, S and Belyea, J and Franzen, S}, year={2004}, month={Feb}, pages={1184–1188} }
 @article{shapkina_lappi_franzen_wollenzien_2004, title={Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome}, volume={32}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkh320}, abstractNote={Escherichia coli ribosomes were irradiated with a KrF excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10-40 mJ for a 1 cm2 area, corresponding to fluences of 4.5 to 18 x 10(9) W m(-2), to determine strand breakage yields and the frequency and pattern of RNA-RNA cross- linking in the 16S rRNA. Samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. The yield of strand breaks per photon was intensity dependent, with values of 0.7 to 1.3 x 10(-3) over the incident intensity range studied. The yield for RNA-RNA cross-linking was 3 x 10(-4) cross-links/photon at the intensity of 4.5 x 10(9) W m(-2), an approximately 4-fold higher yield per photon than obtained with a transilluminator. The cross-link yield/photon decreased at higher light intensities, probably due to intensity-dependent photoreversal. The pattern of cross-linking was similar to that observed with low intensity irradiation but with four additional long-range cross-links not previously seen in E.coli ribosomes. Cross- linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than are frequencies obtained with transilluminator irradiation.}, number={4}, journal={NUCLEIC ACIDS RESEARCH}, author={Shapkina, T and Lappi, S and Franzen, S and Wollenzien, P}, year={2004}, month={Feb}, pages={1518–1526} }
 @article{lappi_franzen_2004, title={Eigenvector mapping: a method for discerning solvent effects on vibrational spectra}, volume={60}, DOI={10.1016/S1386-1425(03)00248-8}, abstractNote={This paper reports a density functional theory (DFT) analysis of the adenine spectra in a hydrogen-bonding environment. We compare the theoretical vibrational spectra of 26 model systems in which water has been hydrogen bonded to adenine with the experimental frequencies of the solid state infrared spectra (150-1700 cm(-1)) of polycrystalline adenine and the experimental frequencies observed in matrix isolation spectra of adenine [J. Phys. Chem. 100 (1996) 3527]. The vibrational eigenvectors of adenine are compared by taking the dot product to determine how the normal modes of the 15-adenine atoms are affected by different hydrogen bonding geometries. Using the isolated adenine molecule as a reference permits a comparison of different calculated spectra in terms of the projections of various normal modes and the determination of the potential energy redistribution among normal modes. This method creates a map of the normal modes using the isolated adenine molecule as a reference. Improvement in agreement between the polycrystalline data and a model of adenine with four waters is most striking. The improvement in the fit between matrix isolation data and a model of adenine with a single water was not as dramatic as the fit seen for the polycrystalline data, but the fact that a single hydrogen-bonded water shifted the spectra of the model to a closer fit than that of isolated adenine is important. We call this method eigenvector mapping. The eigenvector mapping method can be used to extract the normal modes of a parent molecule from a solvent model system. The application of this method is important because it aids in the interpretation of complex molecular interactions in terms of the spectrum of an isolated molecule. The eigenvector mapping procedure will be shown to greatly improve the correspondence between the model and the experimental data.}, number={02-Jan}, journal={Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy.}, author={Lappi, S. E. and Franzen, Stefan}, year={2004}, pages={357–370} }
 @article{brewer_allen_lappi_chasse_briggman_gorman_franzen_2004, title={Infrared detection of a phenylboronic acid terminated alkane thiol monolayer on gold surfaces}, volume={20}, ISSN={["0743-7463"]}, DOI={10.1021/la035037m}, abstractNote={Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid moiety to form a phenylboronate ester. Vibrationally resonant sum frequency generation (VR-SFG) spectroscopy confirmed the ordering of the substituted phenyl groups of the PBA adlayer on the gold surface. Solution FTIR spectra and density functional theory were used to confirm the identity of the observed vibrational modes on the gold surface of PBA with and without bound sugar. The detection of the binding of glucose on the gold surface was confirmed in part by the presence of a C-O stretching mode of glucose and the observed O-H stretching mode of glucose that is shifted in position relative to the O-H stretching mode of boronic acid. An IR marker mode was also observed at 1734 cm(-1) upon the binding of glucose. Additionally, changes in the peak profile of the B-O stretching band were observed upon binding, confirming formation of a phenylboronate ester on the gold surface. The binding of mannose and lactose were also detected primarily through the IR marker mode at approximately 1736 to 1742 cm(-1) depending on the identity of the bound sugar.}, number={13}, journal={LANGMUIR}, author={Brewer, SH and Allen, AM and Lappi, SE and Chasse, TL and Briggman, KA and Gorman, CB and Franzen, S}, year={2004}, month={Jun}, pages={5512–5520} }
 @article{lappi_smith_franzen_2004, title={Infrared spectra of (H2O)-O-16, (H2O)-O-18 and D2O in the liquid phase by single-pass attenuated total internal reflection spectroscopy}, volume={60}, ISSN={["1386-1425"]}, DOI={10.1016/j.saa.2003.12.042}, abstractNote={Mid-infrared attenuated total internal reflection (ATR) spectra of H216O, H218O and D216O in the liquid state were obtained and normal coordinate analysis was performed based on the potential energy surface obtained from density functional theory (DFT) calculations. Fits of the spectra to multiple Gaussians showed a consistent fit of three bands for the bending region and five bands for the stretching region for three isotopomers, H216O, H218O and D216O. The results are consistent with previous work and build on earlier studies by the inclusion of three isotopomers and mixtures using the advantage of single-pass ATR to obtain high quality spectra of the water stretching bands. DFT calculation of the vibrational spectrum of liquid water was conducted on seven model systems, two systems with periodic boundary conditions (PBC) consisting of four and nine H216O molecules, and five water clusters consisting of 4, 9, 19, 27 and 32 H216O molecules. The PBC and cluster models were used to obtain a representation of bulk water for comparison with experiment. The nine-water PBC model was found to give a good fit to the experimental line shapes. A difference is observed in the broadening of the water bending and stretching vibrations indicative of a difference in the rate of pure dephasing. The nine-water PBC calculation was also used to calculate the wavenumber shifts observed in the water isotopomers.}, number={11}, journal={SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY}, author={Lappi, SE and Smith, B and Franzen, S}, year={2004}, month={Sep}, pages={2611–2619} }
 @article{marinkovic_huang_bromberg_sullivan_toomey_miller_sperber_moshe_jones_chouparova_et al._2002, title={Center for Synchrotron Biosciences' U2B beamline: an international resource for biological infrared spectroscopy}, volume={9}, ISSN={["1600-5775"]}, DOI={10.1107/S0909049502008543}, abstractNote={A synchrotron infrared (IR) beamline, U2B, dedicated to the biomedical and biological sciences has been constructed and is in operation at the National Synchrotron Light Source (NSLS) of Brookhaven National Laboratory. The facility is operated by the Center for Synchrotron Biosciences of the Albert Einstein College of Medicine in cooperation with the NSLS. Owing to the broadband nature of the synchrotron beam with brightness 1000 times that of conventional sources, Fourier transform IR spectroscopy experiments are feasible on diffraction-limited sample areas at high signal-to-noise ratios and with relatively short data-acquisition times. A number of synchrotron IR microscopy experiments that have been performed in the mid-IR spectral range (500-5000 cm(-1)) are summarized, including time-resolved protein-folding studies in the microsecond time regime, IR imaging of neurons, bone and other biological tissues, as well as imaging of samples of interest in the chemical and environmental sciences. Owing to the high flux output of this beamline in the far-IR region (50-500 cm(-1)), investigations of hydrogen bonding and dynamic molecular motions of biomolecules have been carried out from 10 to 300 K using a custom-made cryostat and an evacuated box. This facility is intended as an international resource for biological IR spectroscopy fully available to outside users based on competitive proposal.}, number={2002 Jul}, journal={JOURNAL OF SYNCHROTRON RADIATION}, author={Marinkovic, NS and Huang, R and Bromberg, P and Sullivan, M and Toomey, J and Miller, LM and Sperber, E and Moshe, S and Jones, KW and Chouparova, E and et al.}, year={2002}, month={Jul}, pages={189–197} }
 @article{lappi_collier_franzen_2002, title={Density functional analysis of anharmonic contributions to adenine matrix isolation spectra}, volume={106}, ISSN={["1089-5639"]}, DOI={10.1021/jp026017g}, abstractNote={This paper reports the analysis of adenine spectra using both harmonic and anharmonic approximations to the vibrational frequencies reported in matrix isolation studies. The harmonic approximation procedure consists of the application of a scaled ab initio calculated harmonic force field to predict the frequencies, and infrared intensities, of adenine. Theoretical calculations were made using Hartree−Fock density functional theory (DFT) B3-LYP/6-31G* and GGA/DNP computational methods. The equilibrium calculated force constants were scaled according to the method of Pulay (Pulay, P.; Fogarasi, G.; Pang, F.; Boggs, J. E. J. Am. Chem. Soc. 1979, 101, 2550−2560) and compared with the experimentally determined frequencies, and intensities, to assess the accuracy and fit of the theoretical calculation. Good agreement is found except for the in-plane X−H bending or stretching and the out-of-plane X−H bending or wagging modes (X = C and N) which exhibit cubic and quartic anharmonicity, respectively. The NH2 pucke...}, number={47}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, author={Lappi, SE and Collier, W and Franzen, S}, year={2002}, month={Nov}, pages={11446–11455} }
 @article{brewer_anthireya_lappi_drapcho_franzen_2002, title={Detection of DNA hybridization on gold surfaces by polarization modulation infrared reflection absorption spectroscopy}, volume={18}, ISSN={["0743-7463"]}, DOI={10.1021/la025613z}, abstractNote={Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) was used to detect DNA hybridization on gold surfaces. Mixed monolayers of 6-mercapto-1-hexanol (MCH) and single-stranded DNA (ssDNA) with a C6−SH 5‘ modifier were first formed on the gold surface by co-deposition. Then hybridization with the complementary ssDNA strand was performed to obtain double-stranded DNA (dsDNA). The PM-IRRAS spectra obtained contained absorptive features indicative of DNA arising from the phosphodiester backbone and the purine and pyrimidine rings. An infrared signature of dsDNA was observed at 1655 cm-1 that was absent in the ssDNA spectra. This band permitted the distinction between ssDNA and dsDNA to be made thus allowing for the detection of DNA hybridization on gold surfaces by PM-IRRAS.}, number={11}, journal={LANGMUIR}, author={Brewer, SH and Anthireya, SJ and Lappi, SE and Drapcho, DL and Franzen, S}, year={2002}, month={May}, pages={4460–4464} }