分子模拟的原理和应用(第2版)(英文版)

This important new edition is for graduate students studying Molecular Modelling, Computational Chemistry within Chemistry, Medicinal Chemistry and Biochemistry. Postgraduates and researchers in academia and in the chemical and pharmaceutical industries. This new edition introduces background theory and techniques of molecular modelling, also illustrates applications in studying physical, chemical and biological phenomena. It includes simple numerical examples and numerous explanatory figures and a colour plate section.

Preface to the Second Edition
Preface to the First Edition
Symbols and Physical Constants
Acknowledgements
1 Useful Concepts in Molecular Modelling
1.1 Introduction
1.2 Coordinate Systems
1.3 Potential Energy Surfaces
1.4 Molecular Graphics
1.5 Surfaces
1.6 Computer Hardware and Software
1.7 Units of Length and Energy
1.8 The Molecular Modelling Literature
1.9 The Internet
1.10 Mathematical Concepts
Further Reading
References
2 An Introduction to Computational Quantum Mechanics
2.1 Introduction
2.2 One-electron Atoms
2.3 Polyelectronic Atoms and Molecules
2.4 Molecular Orbital Calculations
2.5 The Hartree-Fock Equations
2.6 Basis Sets
2.7 Calculating Molecular Properties Using ab initio Quantum Mechanics
2.8 Approximate Molecular Orbital Theories
2.9 Semi-empirical Methods
2.10 Hiickel Theory
2.11 Performance of Semi-empirical Methods
Appendix 2.1 Some Common Acronyms Used in Computational Quantum Chemistry
Further Reading
References
3 Advanced ab initio Methods, Density Functional Theory and Solid-state Quantum Mechanics
3.1 Introduction
3.2 Open-shell Systems
3.3 Electron Correlation
3.4 Practical Considerations When Performing ab initio Calculations
3.5 Energy Component Analysis
3.6 Valence Bond Theories
3.7 Density Functional Theory
3.8 Quantum Mechanical Methods for Studying the Solid State
3.9 The Future Role of Quantum Mechanics: Theory and Experiment
Working Together
Appendix 3.1 Alternative Expression for a Wavefunction Satisfying Bloch Function
Further Reading
References
4 Empirical Force Field Models: Molecular Mechanics
4.1 Introduction
4.2 Some General Features of Molecular Mechanics Force Fields
4.3 Bond Stretching
4.4 Angle Bending
4.5 Torsional Terms
4.6 Improper Torsions and Out-of-plane Bending Motions
4.7 Cross Terms: Class 1, 2 and 3 Force Fields
4.8 Introduction to Non-bonded Interactions
4.9 Electrostatic Interactions
4.10 Van der Waals Interactions
4.11 Many-body Effects in Empirical Potentials
4.12 Effective Pair Potentials
4.13 Hydrogen Bonding in Molecular Mechanics
4.14 Force Field Models for the Simulation of Liquid Water
4.15 United Atom Force Fields and Reduced Representations
4.16 Derivatives of the Molecular Mechanics Energy Function
4.17 Calculating Thermodynamic Properties Using a Force Field
4.18 Force Field Parametrisation
4.19 Transferability of Force Field Parameters
4.20 The Treatment of Delocalised 7r Systems
4.21 Force Fields for Inorganic Molecules
4.22 Force Fields for Solid-state Systems
4.23 Empirical Potentials for Metals and Semiconductors
Appendix 4.1 The Interaction Between Two Drude Molecules
Further Reading
References
5 Energy Minimisation and Related Methods for Exploring the Energy Surface
6 Computer Simulation Methods
7 Molecular Dynamics Simulation Methods
8 Monte Carlo Simulation Methods
9 Conformational Analysis
10 Protein Structure Prediction,Sequence Analysis and Protein Folding
11 Four Challenges in Molecular Modelling Free Energies,Solvation,Reactions and Solid-state Defects
12 The Use of Molecular Modeling and Chemoinformatics to Discover and Design New Molecules
Index

The impetus for this second edition is a desire to include some of the new techniques that have emerged in recent years and also extend the scope of the book to cover certain areas that were under,represented (even neglected) in the first edition. In this second volume there are three topics that fall into the first category (density functional theory, bioinformatics/protein structure analysis and chemoinformatics) and one main area in the second category (modelling of the solid state). In addition, of course, a new edition provides an oppor..