Ma Nap Tak. / Thesis submitted in: December 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 109-114). / Abstracts in English and Chinese. / ABSTRACT (ENGLISH) --- p.iii / ABSTRACT (CHINESE) --- p.iv / ACKNOWLEDGMENTS --- p.v / ABBREVIATION --- p.vi / TABLE OF CONTENTS --- p.vii / LIST OF FIGURES --- p.x / LIST OF TABLES AND GRAPHS --- p.xii / Chapter CHAPTER 1 --- Introduction and Background --- p.1 / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- Hydrogen bonds (H-bonds) in DNA --- p.2 / Chapter 1.2.1 --- Experimental Evidences of Hydrogen Bonding --- p.3 / Chapter 1.3 --- Three-centered hydrogen bond (TCHB) --- p.4 / Chapter 1.3.1 --- Definition of Three-centered hydrogen bond (TCHB) --- p.5 / Chapter 1.3.2 --- Significance of Three-centered hydrogen bond (TCHB) --- p.6 / Chapter 1.3.3 --- Characterization of Three-centered hydrogen bond (TCHB) --- p.7 / Chapter 1.3.4 --- Classification of Three-centered hydrogen bond (TCHB) --- p.7 / Chapter 1.4 --- Charge transfer in DNA --- p.9 / Chapter 1.4.1 --- Theory of DNA charge transfer --- p.9 / Chapter 1.4.2 --- Short and long range hole transfer in DNA --- p.10 / Chapter 1.4.3 --- Electron transfer in DNA --- p.12 / Chapter 1.4.4 --- Summary of DNA charge transfer --- p.12 / Chapter 1.5 --- Thesis Scope --- p.13 / Chapter CHAPTER 2 --- Theory and methodology --- p.16 / Chapter 2.1 --- Introduction --- p.16 / Chapter 2.2 --- Theory --- p.17 / Chapter 2.2.1 --- Density Functional Theory (DFT) --- p.17 / Chapter 2.2.2 --- Basis set selection --- p.18 / Chapter 2.2.3 --- Natural Bond Orbital (NBO) --- p.19 / Chapter 2.2.3.1 --- Natural Population Analysis (NPA) --- p.20 / Chapter 2.2.3.2 --- E(2) --- p.20 / Chapter 2.2.3.2 --- bond index --- p.21 / Chapter 2.2.4 --- spin-spin coupling constants --- p.22 / Chapter 2.2.5 --- Molecular Orbital (MO) --- p.23 / Chapter 2.3 --- Methodology --- p.24 / Chapter 2.3.1 --- Test calculation for TCHBs by NBO --- p.24 / Chapter 2.3.2 --- Geometry Optimization --- p.24 / Chapter 2.3.3 --- NBO analysis --- p.25 / Chapter 2.3.4 --- J-coupling constants (lhJnx) and MO calculations --- p.26 / Chapter 2.4 --- Summary --- p.26 / Chapter CHAPTER 3 --- Results and Discussion --- Hydrogen bonding in DNA --- p.27 / Chapter 3.1 --- Introduction --- p.27 / Chapter 3.2 --- Method for extracting DNA dimer models --- p.27 / Chapter 3.3 --- Computed results of Inter H-bonds of the ten dimer models --- p.33 / Chapter 3.3.1 --- Geometric parameters --- p.33 / Chapter 3.3.2 --- Natural Bond Orbital (NBO) Analysis --- p.36 / Chapter 3.3.2.1 --- E(2) and Wiberg Bond index --- p.36 / Chapter 3.3.2.2 --- The relationship of E(2) and bond distance --- p.40 / Chapter 3.3.2.3 --- The relationship of E(2) and bond angle --- p.42 / Chapter 3.3.2.4 --- The relationship of E(2) and bond index --- p.44 / Chapter 3.3.3 --- Spin-Spin Coupling Constants of inter-H bonds --- p.46 / Chapter 3.3.3.1 --- The relationship of spin-spin coupling constant and distance --- p.49 / Chapter 3.3.3.2 --- The relationship of spin-spin coupling constant and bond angle --- p.50 / Chapter 3.3.3.3 --- The relationship of spin-spin coupling constant and E(2) energy --- p.52 / Chapter 3.4 --- Experimental Characterization of Three-centered H-bonds --- p.54 / Chapter 3.5 --- Theoretical Characterization of Three-centered H-bonds --- p.55 / Chapter 3.5.1 --- Geometry properties (360°C Rule) --- p.55 / Chapter 3.5.2 --- NMR properties (Spin-Spin Coupling Constants) --- p.55 / Chapter 3.5.3 --- NBO properties (E(2) and Wiberg bond index) --- p.56 / Chapter 3.6 --- Computed results of Three-centered hydrogen bonds (TCHBs) of the ten dimer models --- p.56 / Chapter 3.6.1 --- Natural Bond Orbital (NBO) Analysis --- p.56 / Chapter 3.6.1.1 --- Determination of TCHBs in the ten dimer models --- p.56 / Chapter 3.6.1.2 --- Analysis of TCHB interactions (E(2) and bond index) --- p.62 / Chapter 3.6.1.3 --- The relationship between E(2) and bond distance of TCHBs --- p.63 / Chapter 3.6.1.4 --- The relationship between E(2) and bond angle of TCHBs --- p.65 / Chapter 3.6.2 --- Spin-Spin Coupling Constants of TCHBs --- p.66 / Chapter 3.6.2.1 --- The relationship between spin-spin coupling constant and bond distance of TCHBs --- p.68 / Chapter 3.6.2.2 --- The relationship between spin-spin coupling constant and E(2) energy of TCHBs --- p.69 / Chapter 3.6.3 --- Geometry of TCHBs --- p.71 / Chapter 3.7 --- Summary --- p.72 / Chapter CHAPTER 4 --- Results and Discussion --- Charge location and charge transfer in DNA --- p.77 / Chapter 4.1 --- Introduction --- p.77 / Chapter 4.2 --- Method --- p.78 / Chapter 4.3 --- Computed results of the charge location of the trimer models --- p.81 / Chapter 4.3.1 --- Location of excess positive charge --- p.81 / Chapter 4.3.2 --- Location of excess negative charge --- p.90 / Chapter 4.4 --- Role of TCHBs in charge transfer --- p.95 / Chapter 4.4.1 --- Introduction --- p.95 / Chapter 4.4.2 --- "Analysis of G1G2C3, C3A4A5 and A8A9C10 trimers" --- p.96 / Chapter 4.4.3 --- Analysis of A7A8A9 and A8A9C10 trimers --- p.103 / Chapter 4.5 --- Summary --- p.105 / Chapter CHAPTER 5 --- Concluding Remarks --- p.107 / REFERENCES / APPENDIX

Chi-Keung Lam. / "August 2002." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 202-210). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

"March 2003." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (p. 116-126). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

The 1,3 dipolar cycloaddition between carbonyl ylids (generated from cyclobutene epoxides flanked by esters) and norbornyl alkenes – the ACE reaction – offers a facile method for the construction of polynorbornyl molecular frameworks. This reaction has, as described in this dissertation, underpinned the construction of molecular frameworks that have peptides and amino acids attached. Such highly rigid peptide-frameworks are of use in the field of peptidomimetics; the template molecule governs the final positioning of any attached groups such that a precise arrangement of amino acids can be achieved without the need to construct entire proteins. In the course of any ACE reaction the ester flanked cyclobutene epoxide is transformed to a 1,3 dipole, the esters serve to stablise this reactive intermediate and are as a consequence incorporated in the reaction product. Modification of these esters provides pseudo-equatorial points for peptide attachment. These methyl esters were replaced with tert-butyl esters to provide pseudo-axial attachment points that could be selectively addressed. The optimal strategy for peptide-framework construction involved direct condensation of carboxyl protected amino acids to bicyclo[2.2.1]hept-5-ene-2-endo-carboxylic acid as well as condensation of amino acids to cyclobutene epoxides derived from this acid. The ACE reaction of (±) bicycloheptene-2-endo-carboxylic acid derivatives with cyclobutene epoxides synthesised from such racemic acid derivatives provided a mixture of enantiomers and meso compounds. In order to control the position of the attachment points – and hence the final location of the attached peptides – the ACE reaction required chiral starting materials. Accordingly, all peptidoframeworks were derived from the chiral (2S)-(-)-bicycloheptene carboxylic acid. The ACE reaction of this (S)-norbornene with the (S)-epoxide provided a peptide framework in which the attached amino acids were positioned pseudo-axially. Deprotection of the amino acid allowed peptide chain building in the pseudo-axial direction. Using this strategy a framework with an alanine residue and a triglycine peptide was synthesised. By combining this strategy with the ter-butyl ester variant a framework with pseudo-axial alanine and pseudo-equatorial glycine residues was manufactured.

Thesis (M.S.)--Rochester Institute of Technology, 2007. / Typescript. Includes bibliographical references (leaf 30).

Thesis (Ph. D.)--University of Texas at Austin, 2002. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (Ph. D.)--Chemistry and Biochemistry, Georgia Institute of Technology, 2009. / Committee Chair: Haskell W. Beckham; Committee Co-Chair: David Bucknall; Committee Member: Andrew Lyon; Committee Member: Jiri Janata; Committee Member: Lawrence Bottomley; Committee Member: Mohan Srinivasarao. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

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