Theoretical study of three-centered hydrogen bonds (TCHBs) in DNA dimers and trimers ion radicals: DFT and NBO studies.

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