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

  • Author / Creator
    Zhu, PeiYan
  • 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.

  • Subjects / Keywords
  • Graduation date
    2012-11
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/R3HT49
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Master's
  • Department
    • Department of Chemistry
  • Supervisor / co-supervisor and their department(s)
    • Xu, Yunjie (Chemistry)
  • Examining committee members and their departments
    • Luo, Jingli (Chemical and Material Engineering)
    • Klassen, John (Chemistry)