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Modern Methods for Theoretical Physical Chemistry of Biopolymers (2006)

Modern Methods for Theoretical Physical Chemistry of Biopolymers provides an interesting selection of contributions from an international team of researchers in theoretical chemistry. This book is extremely useful for tackling the complicated scientific problems connected with biopolymers' physics and chemistry. The applications of both the classical molecular-mechanical and molecular-dynamical methods and the quantum chemical methods needed for bridging the gap to structural and dynamical properties dependent on electron dynamics are explained. Also included are ways to deal with complex problems when all three approaches need to be considered at the same time. The book gives a rich spectrum of applications: from theoretical considerations of how ATP is produced and used as ?energy currency? in the living cell, to the effects of subtle solvent influence on properties of biopolymers and how structural changes in DNA during single-molecule manipulation may be interpreted.

Contents

SECTION 1. Quantum Chemistry

Chapter 1. Theoretical development of the fragment molecular orbital (FMO) method

Chapter 2. Developments and applications of ABINIT-MP software based on the Fragment Molecular Orbital

Chapter 3. Combined DFT and electrostatic calculations of pKa's in proteins: Study of cytochrome c oxidase

Chapter 4. Watson-Crick hydrogen bonds: Nature and role in DNA replication

Chapter 5. Quantum chemical modeling of charge transfer in DNA

SECTION 2. Molecular Mechanics

Chapter 6. Solvent effects on biomolecular dynamics simulations: A comparison between TIP3P, SPC and SPC/E water models acting on the glucocorticoid receptor DNA-binding domain

Chapter 7. Computer simulations of DNA stretching

Chapter 8. On the art of computing the IR spectra of molecules in condensed phase

Chapter 9. High Throughput in-silico screening of large ligand databases for rational drug design

Chapter 10. Enzymatic recognition of radiation produced oxidative DNA lesion. Molecular dynamics approach

Chapter 11. Nucleation of polyglutamine amyloid fibres modelling using molecular dynamics

Chapter 12. Drug discovery using grid technology

Chapter 13. Simple models for nonlinear states of double stranded DNA

Chapter 14. Thermodynamics and kinetic analysis of FoF1-ATPase

SECTION 3. Statistical Methods

Chapter 15. Monte Carlo method: Some applications to problems in protein science

Chapter 16. Protein structure generation and elucidation: Applications of automated histogram filtering cluster analysis

Chapter 17. All atom protein folding with stochastic optimization methods

SECTION 4. Model Hamiltonians

Chapter 18. The effects of bridge motion on electron transfer reactions mediated by tunneling

Chapter 19. Modeling molecular conduction in DNA wires: Charge transfer theories and dissipative quantum transport

Chapter 20. Electronic structure of DNA derivatives and mimics by Density Functional Theory

Chapter 21. Electronic structure theory of DNA: from semi-empirical theory

Chapter 22. Electronic transport and localization in short and long DNA

Chapter 23. Polaronic charge transport mechanism in DNA

Chapter 24. Atomistic models of biological charge transfer

Chapter 25. Nonlinear Models in DNA conductivity

SECTION 5. Electric Properties

Chapter 26. Embedding method for conductance studies of large molecules

Chapter 27. Ballistic conductance for all-atom models of native and chemically modified DNA: a review of Kubo-formula-based approach

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