Molecular Modelling for Beginners, 2nd Edition

by Alan Hinchliffe (The University of Manchester, UK )

• ISBN13: 9780470721544
• ISBN10: 0470721545
• Format: eBook
• Copyright: 2008-11-01
• Publisher: Wiley

Summary

A concise, basic introduction to modelling and computational chemistry which focuses on the essentials, including MM, MC, and MD, along with a chapter devoted to QSAR and Discovery Chemistry. Includes supporting website featuring background information, full colour illustrations, questions and answers tied into the text,Visual Basic packages and many realistic examples with solutions Takes a hands-on approach, using state of the art software packages G03/W and/or Hyperchem, Gaussian .gjf files and sample outputs. Revised with changes in emphasis and presentation to appeal to the modern student.

Table of Contents

Chapter 1: Electric charges and their properties.1.1 Point Charges.1.2 Coulomb's Law.1.3 Pair wise additivity.1.4 The Electric Field.1.5 Work.1.6 Charge distributions.1.7 The mutual potential energy U.1.8 Relationship between force and mutual potential energy.1.9 Electric Multipoles.1.10 The electrostatic potential.1.11 Polarization and Polarizability.1.12 Dipole polarizability.1.13 Many-body forces.1.14 Problem Set.Chapter 2: The Forces between Molecules.2.1 The Pair Potential.2.2 The multipole expansion.2.3 The Charge-Dipole interaction.2.4 The dipole-dipole interaction.2.5 Taking account of the temperature.2.6 The Induction energy.2.7 Dispersion energy.2.8 Repulsive contributions.2.9 Combination rules.2.10 Comparison with Experiment.2.11 Improved pair potentials.2.12 A Numerical potential.2.13 Site-site potentials.2.14 Problem Set.Chapter 3: Balls on Springs.3.1 Vibrational Motion.3.2 The Force Law.3.3 A simple diatomic.3.4 Three Problems.3.5 The Morse Potential.3.6 More Advanced Potentials.Chapter 4: Molecular Mechanics (MM).4.1 More about balls on springs.4.2 Larger systems of balls on springs.4.3 Force fields.4.4 Molecular Mechanics (MM).4.5 Modelling the solvent.4.6 Time-and-Money-saving tricks.4.7 Modern Force Fields.4.8 Some commercial force fields.Chapter 5: The Molecular Potential Energy Surface (PES).5.1 Multiple Minima.5.2 Saddle Points.5.3 Characterization.5.4 Finding Minima.5.5 Multivariate grid search.5.6 Derivative methods.5.7 First Order Methods.5.8 Second Order methods.5.9 Choice of Method.5.10 The Z matrix.5.11 The end of the Z matrix.5.12 Redundant Internal Coordinates.Chapter 6: Molecular Mechanics Examples.6.1 Geometry Optimization.6.2 Conformation Searches.6.3 Aminoacids.6.4 QSAR.6.5 Problem Set.Chapter 7: Sharing out the energy.7.1 Games of Chance.7.2 Enumeration.7.3 The Boltzmann Probability.7.4 Safety in Numbers.7.5 The Partition Function.7.6 A two-level quantum system.7.7 Lindemann's Theory of Melting.7.8 Problem Set.Chapter 8: Quick guide to Statistical Thermodynamics.8.1 The Ensemble.8.2 The Internal Energy Uth.8.3 The Helmholtz energy A.8.4 The entropy S.8.5 Equation of state and pressure.8.6 Phase space.8.7 The Configurational Integral.8.8 The Virial of Clausius.Chapter 9: Monte Carlo Simulations.9.1 Introduction.9.2 An Early Paper.9.3 The First "Chemical" Monte Carlo Simulation.9.4 Importance Sampling.9.5 The Periodic Box.9.6 Cutoffs.9.7 MC Simulation of Rigid Molecules.9.8 Flexible Molecules.Chapter 10: Molecular Dynamics.10.1 The Radial Distribution function.10.2 Pair correlation functions.10.3