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Conformational Analysis and Absolute Configuration Determination of Some Organic and Coordination Chemistry Compounds Using Chiroptical Spectroscopy and DFT calculations Open Access


Other title
Conformational Analysis
DFT calculations
Chiroptical Spectroscopy
Absolute Configuration
Type of item
Degree grantor
University of Alberta
Author or creator
Dezhahang, Zahra
Supervisor and department
Xu, Yunjie (Chemistry)
Examining committee member and department
Brown, Alexander (Chemsitry)
Herrebout, Wouter (Chemistry)
Zeng, Hongbo (Chemical and Material Engineering)
Veinot, Jonathan (Chemsitry)
Bergens, Steven (Chemsitry)
Department of Chemistry

Date accepted
Graduation date
Doctor of Philosophy
Degree level
My PhD thesis projects revolve around three main parts, namely synthesis, conformational analysis, and absolute configuration determination of a number of chiral Schiff base ligands and axial chiral binaphthyl type ligands or molecules and some of their transition metal complexes in solution. To obtain the structural information of these chiral systems in solution, chiroptical spectroscopic techniques, such as electronic and vibrational circular dichroism (ECD and VCD) spectroscopy, as well as the related linear spectroscopy, i.e., IR and UV-Vis spectroscopy, have been used as the main experimental tools. In addition, density functional theory (DFT) has been employed to perform all calculations for the conformational searches, geometry optimizations, and simulations of VA, VCD, UV-Vis, and ECD spectra. Comparison of the theoretical and experimental spectra has been utilized to provide detailed and rigorous spectral interpretations and therefore to extract essential structural properties of the targeted species in solution. To account for the bulk solvent environment, the implicit solvation approach, i.e. the polarizable continuum model (PCM), has been applied where no strong solvent–solute hydrogen-bonding interactions are expected. Initial conformational analyses of the systems studied have been performed using small basis sets, such as 6-31G(d). For the final calculations, several larger basis sets, namely 6-31++G(d,p), 6-311++G(d,p), and cc-pVTZ have been used for the C, H, N, O atoms and the LanL2DZ basis sets for the metal atoms. We found that flexible ligands, such as the multidentate nitrogen donor ligands, BINAP and related ligands, show a number of minima on their potential energy surfaces. Further coordination to one or more metal centers often introduces dramatically the structural rigidity and consequently results in a smaller number of minima. For example, in the case of Pd(BINAP)Cl2 and Pd(TOLBINAP)Cl2, a single conformation has been identified in solution. Especially for the VCD spectra observed, it has been demonstrated that the gas phase models failed to capture the experimental optical responses properly, and the inclusion of solvent whether implicitly or explicitly has been shown to be of high importance. In addition, in the study of a triply axial chiral binaphthyl based molecule, it has been demonstrated that the solute concentration may play a crucial role on its conformational landscape as well as its axial chirality in solution. To probe structural properties including induced chirality at the metal centers, the bis(pyrrol-2-ylmethyleneamine)-cyclohexane (H2L) ligand and its five metal complexes (e.g. Ni (II), Cu (II), Pd (II), Pt (II), and Zn (II)) have been synthesized and their VA, VCD, UV-Vis and ECD spectra have been recorded and analyzed. We found that while M-Ni-(R,R)-L, M-Cu-(R,R)-L, M-Pd-(R,R)-L, and M-Pt-(R,R)-L complexes take on the mono-nuclear geometries, the [M-Zn-(R,R)-L]2 complex in solution exists in the dinuclear geometry. Furthermore, these metal complexes take on M-helicity as dictated by the chirality of the (R,R)-ligand.
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. 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.
Citation for previous publication
Poopari, M.R., Dezhahang, Z., Yang, G., Xu, Y. Conformational distributions of N-acetyl-L-cysteine in aqueous solutions: A combined implicit and explicit solvation treatment of VA and VCD spectra (2012) ChemPhysChem, 13 (9), pp. 2310-2321.Dezhahang, Z., Merten, C., Poopari, M.R., Xu, Y. Vibrational circular dichroism spectroscopy of two chiral binaphthyl diphosphine ligands and their palladium complexes in solution (2012) Dalton Transactions, 41 (35), pp. 10817-10824.Dezhahang, Z., Poopari, M.R., Xu, Y. Conformations of [(R,R)-1,5-diaza-cis-decalin] copper (II) complex and its hydrogen bonding interaction with the crystal water: A combined experimental VA, UV-Vis and ECD spectroscopic and DFT study (2012) Journal of Molecular Structure, 1024, pp. 123-13.Poopari, M.R., Zhu, P., Dezhahang, Z., Xu, Y. Vibrational absorption and vibrational circular dichroism spectra of leucine in water under different pH conditions: Hydrogen-bonding interactions with water (2012) Journal of Chemical Physics, 137 (19), art. no. 194308.Poopari, M.R., Dezhahang, Z., Xu, Y. A comparative VCD study of methyl mandelate in methanol, dimethyl sulfoxide, and chloroform: Explicit and implicit solvation models (2013) Physical Chemistry Chemical Physics, 15 (5), pp. 1655-1665.Dezhahang, Z., Poopari, M.R., Xu, Y. Vibrational circular dichroism spectroscopy of three multidentate nitrogen donor ligands: Conformational flexibility and solvent effects (2013) Chemistry - An Asian Journal, 8 (6), pp. 1205-1212.Dezhahang, Z., Poopari, M.R., Hernández, F.E., Diaz, C., Xu, Y. Diastereomeric preference of a triply axial chiral binaphthyl based molecule: A concentration dependent study by chiroptical spectroscopies (2014) Physical Chemistry Chemical Physics, 16 (25), pp. 12959-12967.Poopari, M.R., Dezhahang, Z., Xu, Y. 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 CO stretching bands (2015) Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy, 136 (PA), pp. 131-140.

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