Essentials of Computational Chemistry Theories and Models

by Cramer, Christopher J.

• ISBN13: 9780470091821
• ISBN10: 0470091827
• Edition: 2nd
• Format: Paperback
• Copyright: 2004-10-29
• Publisher: WILEY

Summary

Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject.  Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas.  The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.

Author Biography

Christopher Cramer, Professor of Computational Chemistry Department of Chemistry, University of Minnesota,Minneapolis, USA

Table of Contents

Preface to the First Edition

Preface to the Second Edition

Acknowledgments

What are Theory, Computation, and Modeling?

Definition of Terms

Quantum Mechanics

Computable Quantities

Structure

Potential Energy Surfaces

Chemical Properties

Cost and Efficiency

Intrinsic Value

Hardware and Software

Algorithms

Note on Units

Bibliography and Suggested Additional Reading

References

Molecular Mechanics

History and Fundamental Assumptions

Potential Energy Functional Forms

Bond Stretching

Valence Angle Bending

Torsions

Van der Waals Interactions

Electrostatic Interactions

Cross Terms and Additional Non-bonded Terms

Parameterization Strategies

Force-field Energies and Thermodynamics

Geometry Optimization

Optimization Algorithms

Optimization Aspects Specific to Force Fields

Menagerie of Modern Force Fields

Available Force Fields

Validation

Force Fields and Docking

Case Study: (2R*,4S*)-1-Hydroxy-2,4-dimethylhex-5-ene

Bibliography and Suggested Additional Reading

References

Simulations of Molecular Ensembles

Relationship Between MM Optima and Real Systems

Phase Space and Trajectories

Properties as Ensemble Averages

Properties as Time Averages of Trajectories

Molecular Dynamics

Harmonic Oscillator Trajectories

Non-analytical Systems

Practical Issues in Propagation

Stochastic Dynamics

Monte Carlo

Manipulation of Phase-space Integrals

Metropolis Sampling

Ensemble and Dynamical Property Examples

Key Details in Formalism

Cutoffs and Boundary Conditions

Polarization

Control of System Variables

Simulation Convergence

The Multiple Minima Problem

Force Field Performance in Simulations

Case Study: Silica Sodalite

Bibliography and Suggested Additional Reading

References

Foundations of Molecular Orbital Theory

Quantum Mechanics and the Wave Function

The Hamiltonian Operator

General Features

The Variational Principle

The Born-Oppenheimer Approximation

Construction of Trial Wave Functions

The LCAO Basis Set Approach

The Secular Equation

H?uckel Theory

Fundamental Principles

Application to the Allyl System

Many-electron Wave Functions

Hartree-product Wave Functions

The Hartree Hamiltonian

Electron Spin and Antisymmetry

Slater Determinants

The Hartree-Fock Self-consistent Field Method

Bibliography and Suggested Additional Reading

References

Semiempirical Implementations of Molecular Orbital Theory

Semiempirical Philosophy

Chemically Virtuous Approximations

Analytic Derivatives

Extended Huckel Theory

CNDO Formalism

INDO Formalism

INDO and INDO/S

MINDO/3 and SINDO1

Basic NDDO Formalism

MNDO

AM1

PM3

General Performance Overview of Basic NDDO Models

Energetics

Geometries

Charge Distributions

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