Essentials of Computational Chemistry Theories and Models

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ISBN: 9780470091821 | 0470091827
Cover: Paperback
Copyright: 11/5/2004

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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.

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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Essentials of Computational Chemistry Theories and Models

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