A theoretical study of hydrogen bonding involving biomolecules.
Date
2001
Authors
Rankin, Kathryn Nadine.
Journal Title
Journal ISSN
Volume Title
Publisher
Dalhousie University
Abstract
Description
Theoretical calculations play a fundamental role in advancing our understanding of the properties of hydrogen-bonded systems. The plethora of experimental data on systems containing hydrogen bonds, obtained from spectroscopic experiments, is complemented by electronic structure theory calculations. Contemporary density functional theory (DFT) has become a powerful and economic method in electronic structure theory as it enables the effects of electron correlation to be accounted for in the calculation and is extensively utilized in this thesis for the study of hydrogen bonding in a variety of chemical and biochemical systems.
The first study in this thesis, Chapter Three, involves the use of DFT to investigate the hydrogen halide dimers, (HF)2, (HCl)2 and (HBr)2. Emphasis is focused upon an assessment of the performance of the hybrid DFT methods in predicting the geometry, binding energy and vibrational properties of these dimers. Overall, the hybrid density functional methods adequately predict the properties of the halide dimers and the BHandHLYP and B1LYP density functional methods offer a competitive alternative to the popular B3LYP method. In Chapter Four, the ability of hydrogen bonds to act as catalysts is examined. In the study of the aminolysis of 6-chloropyrimidine, derivatives of uracil stabilize the transition structures by the formation of multiple hydrogen bonds, thus catalyzing the aminolysis reaction. This study highlights the catalytic potential of hydrogen bonding and the importance of a well-chosen hydrogen bond acceptor. In the following chapter, Chapter Five, the direct aldol reaction as catalyzed by proline is investigated to assess the feasibility of the proposed reaction mechanism and the potential role of the solvent. This study is a simple example illustrating the potential of small molecules, such as proline, to act as catalysts in biochemical reactions. Chapter Six examines the structural and energetic effect the introduction of electron-withdrawing substitutents on Cgamma has on the cis-trans isomerization in N-acetylproline methylamide. This study illustrates the important role the intramolecular N-H &cdots; N hydrogen bond plays in the cis-trans isomerization and the catalytic potential of hydrogen bonds.
Thesis (Ph.D.)--Dalhousie University (Canada), 2001.
The first study in this thesis, Chapter Three, involves the use of DFT to investigate the hydrogen halide dimers, (HF)2, (HCl)2 and (HBr)2. Emphasis is focused upon an assessment of the performance of the hybrid DFT methods in predicting the geometry, binding energy and vibrational properties of these dimers. Overall, the hybrid density functional methods adequately predict the properties of the halide dimers and the BHandHLYP and B1LYP density functional methods offer a competitive alternative to the popular B3LYP method. In Chapter Four, the ability of hydrogen bonds to act as catalysts is examined. In the study of the aminolysis of 6-chloropyrimidine, derivatives of uracil stabilize the transition structures by the formation of multiple hydrogen bonds, thus catalyzing the aminolysis reaction. This study highlights the catalytic potential of hydrogen bonding and the importance of a well-chosen hydrogen bond acceptor. In the following chapter, Chapter Five, the direct aldol reaction as catalyzed by proline is investigated to assess the feasibility of the proposed reaction mechanism and the potential role of the solvent. This study is a simple example illustrating the potential of small molecules, such as proline, to act as catalysts in biochemical reactions. Chapter Six examines the structural and energetic effect the introduction of electron-withdrawing substitutents on Cgamma has on the cis-trans isomerization in N-acetylproline methylamide. This study illustrates the important role the intramolecular N-H &cdots; N hydrogen bond plays in the cis-trans isomerization and the catalytic potential of hydrogen bonds.
Thesis (Ph.D.)--Dalhousie University (Canada), 2001.
Keywords
Chemistry, Biochemistry., Chemistry, Physical., Biophysics, General.