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Conformations of Some Amino Acids in Aqueous Solutions by Vibrational Circular Dichroism Spectroscopy Open Access


Other title
vibrational circular dichroism spectroscopy
amino acid
Type of item
Degree grantor
University of Alberta
Author or creator
Zhu, PeiYan
Supervisor and department
Xu, Yunjie (Chemistry)
Examining committee member and department
Luo, Jingli (Chemical and Material Engineering)
Klassen, John (Chemistry)
Department of Chemistry

Date accepted
Graduation date
Master of Science
Degree level
Vibrational circular dichroism (VCD) spectroscopy has been utilized to reveal the detailed conformational distributions of the dominant serine species and leucine species in aqueous solutions under three representative pH conditions, together with vibrational absorption (VA) spectroscopy, density functional theory (DFT), and molecular dynamics simulation. For both serine and leucine, the experimental VA and VCD spectra in H2O and D2O in the finger-print region at three pHs have been obtained. DFT calculations at the B3LYP/6-311++G(d,p) level have been carried out for the protonated, zwitterionic, and deprotonated species. In the leucine case, preliminary results based on the comparison of the experimental VA spectra of leucine in H2O and D2O in the finger-print region to the simulated spectra of different leucine species in the gas phase and with the polarizable continuum model (PCM) are presented. In the serine case, the comparison between the gas phase simulations and the experimental VA and VCD spectra suggests that one or two of the most stable conformers of each species contribute predominantly to the observed data, although some discrepancies have been noted. To account for the solvent effects, both the polarizable continuum model and the explicit solvation model have been considered. The hydrogen-bonded protonated, zwitterionic, and deprotonated serine-(water)6 clusters have been constructed based on the radial distribution function analyses and molecular dynamics snap shots. Geometry optimization and VA and VCD simulations have been performed for these clusters at the B3LYP/6-311++G(d,p) level. The detailed conformational distributions of the dominant serine and leucine species at three pHs have been investigated using VA and VCD spectroscopy together with ab initio calculations. Inclusion of the explicit water molecules has been found to improve the agreement between theory and experiment noticeably in all three cases, thus enabling conclusive conformational distribution analyses of serine in aqueous solutions directly.
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Citation for previous publication
P. Zhu, G. Yang, M. R. Poopari, Z. Bie, and Y. Xu, Chem. Phys. Chem., 2012, 12, 1272-1281.

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