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
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_325264 |
| Date | January 2005 |
| Contributors | Ma, Nap Tak., Chinese University of Hong Kong Graduate School. Division of Chemistry. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, bibliography |
| Format | print, xii, 116 leaves : ill. ; 30 cm. |
| Rights | Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
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