Download the full-sized PDF of Study of solute-solvent interactions with vibrational CD spectroscopy and DFT calculationsDownload the full-sized PDF



Permanent link (DOI):


Export to: EndNote  |  Zotero  |  Mendeley


This file is in the following communities:

Graduate Studies and Research, Faculty of


This file is in the following collections:

Theses and Dissertations

Study of solute-solvent interactions with vibrational CD spectroscopy and DFT calculations Open Access


Other title
solute-solvent interactions
Vibrational Circular Dichroism
Implicit and explicit solvent models
Density Functional Theory
Type of item
Degree grantor
University of Alberta
Author or creator
Supervisor and department
Xu, Yunjie ( Department of Chemistry, University of Alberta)
Examining committee member and department
Polavarapu, Prasad ( Department of Chemistry, Vanderbilt University )
Brown, Alex ( Department of Chemistry, University of Alberta)
Lowary, Todd ( Department of Chemistry, University of Alberta)
Hanna, Gabriel ( Department of Chemistry, University of Alberta)
Department of Chemistry
Physical Chemistry, Spectroscopy, and Theoretical Modelling
Date accepted
Graduation date
Doctor of Philosophy
Degree level
My PhD thesis work is centered on developing a suitable approach to account for solvent effects in solution spectroscopic measurements and on providing significant insights into the intermolecular interactions between chiral solute and solvent, in particular water, molecules. Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectroscopic techniques have been used as the main experimental tools to study conformational distributions and most importantly solute-solvent interactions of a number of prototype chiral molecules in several common solvents. The spectral window from 800 cm-1 to 1800 cm-1 was used for data acquisition. Aqueous solutions, both normal and deuterated water, and organic solvents such as methanol, dimethyl sulfoxide, and chloroform were used. Complementary optical rotatory dispersion measurements have also been carried out. Density functional theory has been employed to perform all calculations for conformational searches, geometry optimizations, VA, VCD, UV, and ECD intensities, and spectral simulations. To account for effects of water solvent, a clusters-in-a-liquid approach has been proposed. Molecular dynamics simulations and radial distribution function calculations have also been carried out to identify the representative hydration clusters, i.e. chiral solute-(water)N. Initial conformational analyses have been done using small basis set like 6-31G(d), which is a compromise between accuracy and computational cost. For final calculations, several larger basis set like 6-31++G(d,p), 6- 311++G(d,p), cc-pVTZ, and aug-cc-pVTZ, have been used and the specific choices depend on the size and complexity of systems under the investigation. Geometries of the molecular systems of interest have been evaluated in the gas phase and in bulk solvent using the implicit solvation polarization continuum model, while the related geometries of the explicit hydration clusters of the targeted chiral molecules have been similarly evaluated. My thesis work shows that inclusion of both explicit and implicit solvent effects simultaneously is essential to interpret the experimental VA and VCD spectra whenever strong hydrogen-bonding interactions are expected between chiral solute and solvent molecules. When no strong solvent–solute hydrogen-bonding interactions are expected, it was found that the gas phase monomer model is adequate but not optimal for spectral interpretations and the inclusion of the implicit bulk water environment is highly recommended.
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
M. R. Poopari, Z. Dezhahang, Y. Xu, “A comparative VCD study of methyl mandelate in methanol, dimethyl sulfoxide, and chloroform: explicit and implicit solvation models”, Phys. Chem. Chem. Phys., 15, 2013, 1655-1665.M. R. Poopari, Z. Dezhahang, Y. Xu, “Identifying dominant conformations of N-acetyl- L-cysteine methyl ester and N-acetyl-L-cysteine in water: VCD signatures of the amide I and the C=O stretching bands”, Spectrochimica Acta - Part A Molecular and Biomolecular Spectroscopy, 2013, DOI: 10.1016/ j.saa.2013.08.118.M. R. Poopari, Z. Dezhahang, G. Yang, Y. Xu, “Conformational distributions of N-acetyl-L-cysteine in aqueous solutions: a combined implicit and explicit solvation treatment of VA and VCD spectra”, ChemPhysChem, 13, 2012, 2310-2321.M. R. Poopari, P. Zhu, Z. Dezhahang, Y. Xu, “Vibrational absorption and vibrational circular dichroism spectra of leucine in water under different pH conditions: hydrogen-bonding interactions with water”, J. Chem. Phys., 137, 2012, 194308.

File Details

Date Uploaded
Date Modified
Audit Status
Audits have not yet been run on this file.
File format: pdf (Portable Document Format)
Mime type: application/pdf
File size: 17911217
Last modified: 2015:10:12 16:59:25-06:00
Filename: Poopari_Mohammad Reza_Spring2014.pdf
Original checksum: f3ac274c4bd6622ab7eced2cebbbae8a
Well formed: true
Valid: true
Status message: Too many fonts to report; some fonts omitted. Total fonts = 1087
Page count: 262
Activity of users you follow
User Activity Date