@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{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{smith_gemperline_2002, title={Bootstrap methods for assessing the performance of near-infrared pattern classification techniques}, volume={16}, ISSN={["0886-9383"]}, DOI={10.1002/cem.715}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF CHEMOMETRICS}, author={Smith, BM and Gemperline, PJ}, year={2002}, month={May}, pages={241–246} }
 @article{smith_franzen_2002, title={Single-pass attenuated total reflection Fourier transform infrared spectroscopy for the analysis of proteins in H2O solution}, volume={74}, ISSN={["0003-2700"]}, DOI={10.1021/ac020103v}, abstractNote={The application of single-pass attenuated total reflection Fourier transform infrared (ATR-FT-IR) microscopy was investigated for secondary structure analysis of 15 representative proteins in H2O solution. This is the first reported application of single-pass ATR-FT-IR for protein analysis; thus, the method was validated using transmission FT-IR and multipass ATR-FT-IR as referee methods. The single-pass ATR-FT-IR technique was advantageous since the single-pass geometry permits rapid secondary structure analysis on small volumes of protein in H2O solution without the use of demountable thin path length sample cells. Moreover, the fact that H2O backgrounds were small allowed the simultaneous observation of the amide I-III, A, and B regions without having to perform H2O subtraction. A comparison of replicate protein spectra indicated that the single-pass ATR-FT-IR method yields more reproducible data than those acquired by transmission FT-IR. The observed trends for the amide I-III and A bands obtained by single-pass ATR-FT-IR agreed with those in the literature for conventional transmission FT-IR.}, number={16}, journal={ANALYTICAL CHEMISTRY}, author={Smith, BM and Franzen, S}, year={2002}, month={Aug}, pages={4076–4080} }
 @article{smith_oswald_franzen_2002, title={Single-pass attenuated total reflection Fourier transform infrared spectroscopy for the prediction of protein secondary structure}, volume={74}, ISSN={["0003-2700"]}, DOI={10.1021/ac020104n}, abstractNote={Principal component regression (PCR) was applied to a spectral library of proteins in H2O solution acquired by single-pass attenuated total reflectance (ATR) Fourier transform infrared (FT-IR) spectroscopy. PCR was used to predict the secondary structure content, principally alpha-helical and the beta-sheet content, of proteins within a spectral library. Quantitation of protein secondary structure content was performed as a proof of principle that use of single-pass ATR-FT-IR is an appropriate method for protein secondary structure analysis. The ATR-FT-IR method permits acquisition of the entire spectral range from 700 to 3900 cm(-1) without significant interference from water bands. An "inside model space" bootstrap and a genetic algorithm (GA) were used to improve prediction results. Specifically, the bootstrap was utilized to increase the number of replicates for adequate training and validation of the PCR model. The GA was used to optimize PCR parameters, particularly wavenumber selection. The use of the bootstrap allowed for adequate representation of variability in the amide A, amide B, and C-H stretching regions due to differing levels of sample hydration. Implementation of the bootstrap improved the robustness of the PCR models significantly; however, the use of a GA only slightly improved prediction results. Two spectral libraries are presented where one was better suited for beta-sheet content prediction and the other for alpha-helix content prediction. The GA-optimized PCR method for alpha-helix content prediction utilized 120 wavenumbers within the amide I, II, A, B, and IV and the C-H stretching regions and 18 factors. For beta-sheet content predictions, 580 wavenumbers within the amide I, II, A, and B and the C-H stretching regions and 18 factors were used. The validation results using these two methods yielded an average absolute error of 1.7% for alpha-helix content prediction and an average absolute error of 2.3% for beta-sheet content prediction. After the PCR models were developed and validated, they were used to predict the alpha-helix and beta-sheet content of two unknowns, casein and immunoglobulin G.}, number={14}, journal={ANALYTICAL CHEMISTRY}, author={Smith, BM and Oswald, L and Franzen, S}, year={2002}, month={Jul}, pages={3386–3391} }