ERA

Download the full-sized PDF of Conformations of Some Amino Acids in Aqueous Solutions by Vibrational Circular Dichroism SpectroscopyDownload the full-sized PDF

Analytics

Share

Permanent link (DOI): https://doi.org/10.7939/R3HT49

Download

Export to: EndNote  |  Zotero  |  Mendeley

Communities

This file is in the following communities:

Graduate Studies and Research, Faculty of

Collections

This file is in the following collections:

Theses and Dissertations

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

Descriptions

Other title
Subject/Keyword
vibrational circular dichroism spectroscopy
amino acid
Type of item
Thesis
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
Department of Chemistry
Specialization

Date accepted
2012-08-28T09:08:47Z
Graduation date
2012-11
Degree
Master of Science
Degree level
Master's
Abstract
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.
Language
English
DOI
doi:10.7939/R3HT49
Rights
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
P. Zhu, G. Yang, M. R. Poopari, Z. Bie, and Y. Xu, Chem. Phys. Chem., 2012, 12, 1272-1281.

File Details

Date Uploaded
Date Modified
2014-05-02T17:39:43.877+00:00
Audit Status
Audits have not yet been run on this file.
Characterization
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 3435171
Last modified: 2015:10:12 16:37:49-06:00
Filename: PeiYan_Zhu_Fall 2012.pdf
Original checksum: 8ebd2fc7eedbd66b337dc18926ce4569
Well formed: false
Valid: false
Status message: Unexpected error in findFonts java.lang.ClassCastException: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject cannot be cast to edu.harvard.hul.ois.jhove.module.pdf.PdfDictionary offset=3398287
Status message: Invalid Annotation list offset=3398287
File title: Abstract
Activity of users you follow
User Activity Date