Browsing by Author "Collier, W. B."

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A Vibrational Spectroscopy Study on Anserine and Its Aqueous Solutions
(Pergamon-Elsevier Science Ltd, The Boulevard, Langford Lane, Kidlington, Oxford Ox5 1Gb, England, 2015-10-05) Akkaya, Yasemin; Balcı, Kubilay; Gören, Yeliz; Stricker, Moogega C.; Ritzhaupt, G.; Stover, D. D.; Collier, W. B.; AKYÜZ, SEVİM; 175409; 54889; 10127
In this study based on vibrational spectroscopic measurements and Density Functional Theory (OFF), we aimed for a reliable interpretation of the IR and Raman spectra recorded for anserine in the solid phase and water (H2O) and heavy water (D2O) solutions. Initial DFT calculations at the B3LYP/6-31G(d) searched possible conformers of the anserine zwitterion using a systematic conformational search. The corresponding equilibrium geometrical parameters and vibrational spectral data were determined for each of the stable conformers (in water) by the geometry optimization and hessian calculations performed at the same level of theory using the polarized continuum model (PCM). The same calculations were repeated to determine the most energetically preferred dimer structure for the molecule and the associated geometry, force field and vibrational spectral data. The harmonic force constants obtained from these calculations were scaled by the Scaled Quantum Mechanical Force Field (SQM) method and then used in the calculation of the refined wavenumbers, potential energy distributions, IR and Raman intensities. These refined theoretical data, which confirm the zwitterion structure for anserine in the solid phase or aqueous solvents, revealed the remarkable effects of intermolecular hydrogen bonding on the structural properties and observed IR and Raman spectra of this molecule. (C) 2015 Elsevier B.V. All rights reserved.
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An Investigation on the Structure and Group Vibrations of Balenine Molecule by Matrix Isolation IR Spectroscopy, DFT and MP2 Based Calculations
(Pergamon-Elsevier Science Ltd., 2022) Balcı, K.; Akkaya, Y.; Arman, C.; Gören, Y.; AKYÜZ, SEVİM; Hacker, AL; Van Vleet, HJ; Ritzhaupt, G.; Collier, W. B.
Stable conformers of neutral balenine were scanned through molecular dynamics simulations and energy minimizations using Allinger's MM2 force field. For each of the found minimum-energy conformers, geometry optimization and thermochemistry calculations were performed by using B3LYP, MP2, G3MP2B3 methods, 6-31G(d), 6-311++G(d,p) and aug-cc-pvTZ basis sets. The calculation results have indicated that balenine has about twenty stable conformers whose relative energies are in the range of 0-9.5 kcal/mol. Three of these are thought to provide the major contribution to matrix isolation IR spectra of the molecule. Our solvent calculations using the polarized continuum model revealed the stable zwitterion structures which are predicted to dominate IR spectra of balenine in water and heavy water (D2O) solvents. Pulay's SQM-FF method was used in scaling of the harmonic force constants and vibrational spectral data calculated for the neutral and zwitterion structures. These refined calculation data together with those obtained from anharmonic frequency calculations enabled us to correctly interpret the matrix isolation IR spectrum of balenine and the tautomerism-based changes observed in its KBr IR and solution (D2O) IR spectra. The results revealed the crucial role of conformation and zwitterionic tautomerism on the structure and vibrational spectral data of the molecule.
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The effects of conformation and zwitterionic tautomerism on the structural and vibrational spectral data of anserine
(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2016-09) Balcı, Kubilay; Akkaya, Yasemin; Collier, W. B.; Stricker, Moogega C.; Stover, D. D.; Ritzhaupt, G.; Koch, Andreas; Kleinpeter, Erich; AKYÜZ, SEVİM; 54889; 175409; 10127
In this study, the stable conformers of neutral anserine were searched by molecular dynamics simulations and energy minimization calculations using the MM2 force field. Thermochemical calculations at B3LYP/6-31G(d) level of theory followed these preliminary calculations. The results confirmed that neutral anserine has quite a flexible structure and many stable gauche and trans conformers at room temperature. Nevertheless, two are considerably more favourable in energy than the others and expected to dominate the gas-phase and matrix IR spectra of the molecule. The corresponding structural and vibrational spectral data for these two conformers of neutral anserine, whose relative stabilities were also examined by high-accuracy energy calculations carried out using G3MP2B3 method, and for the most stable conformer of anserine in zwitterion form were calculated at B3LYP/6-311++G(d,p) level of theory. The calculated harmonic force constants were refined using the Scaled Quantum Mechanical Force Field (SQM-FF) method and then used to produce the refined wavenumbers, potential energy distributions (PEDs) and IR and Raman intensities. These refined data together with the scaled harmonic wavenumbers obtained using another method, Dual Scale factors (DS), enabled us to correctly analyse the observed IR and Raman spectra of anserine and revealed the effects of conformation and zwitterionic tautomerism on its structural and vibrational spectral data. (C) 2016 Elsevier B.V. All rights reserved.