Molecular Modelling for Beginners

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ISBN: 9780470513132 | 0470513136
Cover: Hardcover
Copyright: 11/17/2008

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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.

Preface to the Second Edition
Preface to the First Edition
Electric charges and their properties
Point Charges
Coulomb's Law
Pair wise additivity
The Electric Field
Work
Charge distributions
The mutual potential energy U
Relationship between force and mutual potential energy
Electric Multipoles
The electrostatic potential
Polarization and Polarizability
Dipole polarizability
Many-body forces
Problem Set
The Forces between Molecules
The Pair Potential
The multipole expansion
The Charge-Dipole interaction
The dipole-dipole interaction
Taking account of the temperature
The Induction energy
Dispersion energy
Repulsive contributions
Combination rules
Comparison with Experiment
Improved pair potentials
A Numerical potential
Site-site potentials
Problem Set
Balls on Springs
Vibrational Motion
The Force Law
A simple diatomic
Three Problems
The Morse Potential
More Advanced Potentials
Molecular Mechanics
More about balls on springs
Larger systems of balls on springs
Force fields
Molecular Mechanics (MM)
Modelling the solvent
Time-and-Money-saving tricks
Modern Force Fields
Some commercial force fields
The Molecular Potential Energy Surface
Multiple Minima
Saddle Points
Characterization
Finding Minima
Multivariate grid search
Derivative methods
First Order Methods
Second Order methods
Choice of Method
The Z matrix
The end of the Z matrix
Redundant Internal Coordinates
Molecular Mechanics Examples
Geometry Optimization
Conformation Searches
Aminoacids
QSAR
Problem Set
Sharing out the energy
Games of Chance
Enumeration
The Boltzmann Probability
Safety in Numbers
The Partition Function
A two-level quantum system
Lindemann's Theory of Melting
Problem Set
Introduction to Statistical Thermodynamics
The Ensemble
The Internal Energy Uth
The Helmholtz energy A
The entropy S
Equation of state and pressure
Phase space
The Configurational Integral
The Virial of Clausius
Monte Carlo Simulations
Introduction
An Early Paper
The First "Chemical" Monte Carlo Simulation
Importance Sampling
The Periodic Box
Cutoffs
MC Simulation of Rigid Molecules
Flexible Molecules
Molecular Dynamics
The Radial Distribution function
Pair correlation functions
Molecular Dynamics Methodology
Algorithms for time dependence
Molten Salts
Liquid Water
Different Types of Molecular Dynamics
Uses in Conformational Studies
Introduction to quantum modeling
The Schr_dinger equation
The time-independent Schr_dinger equation
Particles in potential wells
The Correspondence Principle
The two-dimensional infinite well
The three-dimensional infinite well
Two non-interacting particles
The Fi
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Molecular Modelling for Beginners

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