Computational Chemistry A Practical Guide for Applying Techniques to Real World Problems

ISBN-10: 0471333689
ISBN-13: 9780471333685
Edition: 2001
Authors: David C. Young
List price: $173.00 Buy it from $30.49
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Description: A practical, easily accessible guide for bench-top chemists, this book focuses on accurately applying computational chemistry techniques to everyday chemistry problems. Provides nonmathematical explanations of advanced topics in computational  More...

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Book details

List price: $173.00
Copyright year: 2001
Publisher: John Wiley & Sons, Incorporated
Publication date: 3/5/2001
Binding: Hardcover
Pages: 408
Size: 6.25" wide x 9.25" long x 1.00" tall
Weight: 1.540
Language: English

A practical, easily accessible guide for bench-top chemists, this book focuses on accurately applying computational chemistry techniques to everyday chemistry problems. Provides nonmathematical explanations of advanced topics in computational chemistry. Focuses on when and how to apply different computational techniques. Addresses computational chemistry connections to biochemical systems and polymers. Provides a prioritized list of methods for attacking difficult computational chemistry problems, and compares advantages and disadvantages of various approximation techniques. Describes how the choice of methods of software affects requirements for computer memory and processing time.

#60;p#62;David C. Young, PhD, is HPC Computational Specialist for Computer Sciences Corp., under contract to the Alabama Supercomputer Authority, where he heads user and application support for research and educational activities. Dr. Young has extensive experience in designing drugs and writing drug design software. He is the author of Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems, also published by Wiley.#60;/p#62;

Preface
Acknowledgments
Symbols Used in This Book
Introduction
Models, Approximations, and Reality
How Computational Chemistry Is Used
Bibliography
Basic Topics
Fundamental Principles
Energy
Electrostatics
Atomic Units
Thermodynamics
Quantum Mechanics
Statistical Mechanics
Bibliography
Ab initio Methods
Hartree-Fock Approximation
Correlation
Moller-Plesset Perturbation Theory
Configuration Interaction
Multi-configurational Self-consistent Field
Multi-reference Configuration Interaction
Coupled Cluster
Quantum Monte Carlo Methods
Natural Orbitals
Conclusions
Bibliography
Semiempirical Methods
Huckel
Extended Huckel
PPP
CNDO
MINDO
MNDO
INDO
ZINDO
SINDO1
PRDDO
AM1
PM3
PM3/TM
Fenske-Hall Method
TNDO
SAM1
Gaussian Theory
Recommendations
Bibliography
Density Functional Theory
Basic Theory
Linear Scaling Techniques
Practical Considerations
Recommendations
Bibliography
Molecular Mechanics
Basic Theory
Existing Force Fields
Practical Considerations
Recommendations
Bibliography
Molecular Dynamics and Monte Carlo Simulations
Molecular Dynamics
Monte Carlo Simulations
Simulation of Molecules
Simulation of Liquids
Practical Considerations
Bibliography
Predicting Molecular Geometry
Specifying Molecular Geometry
Building the Geometry
Coordinate Space for Optimization
Optimization Algorithm
Level of Theory
Recommendations
Bibliography
Constructing a Z-Matrix
Z-Matrix for a Diatomic Molecule
Z-Matrix for a Polyatomic Molecule
Linear Molecules
Ring Systems
Bibliography
Using Existing Basis Sets
Contraction Schemes
Notation
Treating Core Electrons
Common Basis Sets
Studies Comparing Results
Bibliography
Molecular Vibrations
Harmonic Oscillator Approximation
Anharmonic Frequencies
Peak Intensities
Zero-point Energies and Thermodynamic Corrections
Recommendations
Bibliography
Population Analysis
Mulliken Population Analysis
Lowdin Population Analysis
Natural Bond-Order Analysis
Atoms in Molecules
Electrostatic Charges
Charges from Structure Only
Recommendations
Bibliography
Other Chemical Properties
Methods for Computing Properties
Multipole Moments
Fermi Contact Density
Electronic Spatial Extent and Molecular Volume
Electron Affinity and Ionization Potential
Hyperfine Coupling
Dielectric Constant
Optical Activity
Biological Activity
Boiling Point and Melting Point
Surface Tension
Vapor Pressure
Solubility
Diffusivity
Visualization
Conclusions
Bibliography
The Importance of Symmetry
Wave Function Symmetry
Transition Structures
Bibliography
Efficient Use of Computer Resources
Time Complexity
Labor Cost
Parallel Computers
Bibliography
How to Conduct a Computational Research Project
What Do You Want to Know? How Accurately? Why?
How Accurate Do You Predict the Answer Will Be?
How Long Do You Predict the Research Will Take?
What Approximations Are Being Made? Which Are Significant?
Bibliography
Advanced Topics
Finding Transition Structures
Introduction
Molecular Mechanics Prediction
Level of Theory
Use of Symmetry
Optimization Algorithms
From Starting and Ending Structures
Reaction Coordinate Techniques
Relaxation Methods
Potential Surface Scans
Solvent Effects
Verifying That the Correct Geometry Was Obtained
Checklist of Methods for Finding Transition Structures
Bibliography
Reaction Coordinates
Minimum Energy Path
Level of Theory
Least Motion Path
Relaxation Methods
Reaction Dynamics
Which Algorithm to Use
Bibliography
Reaction Rates
Arrhenius Equation
Relative Rates
Hard-sphere Collision Theory
Transition State Theory
Variational Transition State Theory
Trajectory Calculations
Statistical Calculations
Electronic-state Crossings
Recommendations
Bibliography
Potential Energy Surfaces
Properties of Potential Energy Surfaces
Computing Potential Energy Surfaces
Fitting PES Results to Analytic Equations
Fitting PES Results to Semiempirical Models
Bibliography
Conformation Searching
Grid Searches
Monte Carlo Searches
Simulated Annealing
Genetic Algorithms
Distance-geometry Algorithms
The Fragment Approach
Chain-Growth
Rule-based Systems
Using Homology Modeling
Handling Ring Systems
Level of Theory
Recommended Search Algorithms
Bibliography
Fixing Self-Consistent Field Convergence Problems
Possible Results of an SCF Procedure
How to Safely Change the SCF Procedure
What to Try First
Bibliography
QM/MM
Nonautomated Procedures
Partitioning of Energy
Energy Subtraction
Self Consistent Method
Truncation of the QM Region
Region Partitioning
Optimization
Incorporating QM Terms in Force Fields
Recommendations
Bibliography
Solvation
Physical Basis for Solvation Effects
Explicit Solvent Simulations
Analytic Equations
Group Additivity Methods
Continuum Methods
Recommendations
Bibliography
Electronic Excited States
Spin States
CIS
Initial Guess
Block Diagonal Hamiltonians
Higher Roots of a CI
Neglecting a Basis Function
Imposing Orthogonality: DFT Techniques
Imposing Orthogonality: QMC Techniques
Path Integral Methods
Time-dependent Methods
Semiempirical Methods
State Averaging
Electronic Spectral Intensities
Recommendations
Bibliography
Size Consistency
Correction Methods
Recommendations
Bibliography
Spin Contamination
How Does Spin Contamination Affect Results?
Restricted Open-shell Calculations
Spin Projection Methods
Half-electron Approximation
Recommendations
Bibliography
Basis Set Customization
What Basis Functions Do
Creating Basis Sets from Scratch
Combining Existing Basis Sets
Customizing a Basis Set
Basis Set Superposition Error
Bibliography
Force Field Customization
Potential Pitfalls
Original Parameterization
Adding New Parameters
Bibliography
Structure-Property Relationships
QSPR
QSAR
3D QSAR
Comparative QSAR
Recommendations
Bibliography
Computing NMR Chemical Shifts
Ab initio Methods
Semiempirical Methods
Empirical Methods
Recommendations
Bibliography
Nonlinear Optical Properties
Nonlinear Optical Properties
Computational Algorithms
Level of Theory
Recommendations
Bibliography
Relativistic Effects
Relativistic Terms in Quantum Mechanics
Extension of Nonrelativistic Computational Techniques
Core Potentials
Explicit Relativistic Calculations
Effects on Chemistry
Recommendations
Bibliography
Band Structures
Mathematical Description of Energy Bands
Computing Band Gaps
Computing Band Structures
Describing the Electronic Structure of Crystals
Computing Crystal Properties
Defect Calculations
Bibliography
Mesoscale Methods
Brownian Dynamics
Dissipative Particle Dynamics
Dynamic Mean-field Density Functional Method
Nondynamic Methods
Validation of Results
Recommendations
Bibliography
Synthesis Route Prediction
Synthesis Design Systems
Applications of Traditional Modeling Techniques
Recommendations
Bibliography
Applications
The Computational Chemist's View of the Periodic Table
Organic Molecules
Main Group Inorganics, Noble Gases, and Alkali Metals
Transition Metals
Lanthanides and Actinides
Bibliography
Biomolecules
Methods for Modeling Biomolecules
Site-specific Interactions
General Interactions
Recommendations
Bibliography
Simulating Liquids
Level of Theory
Periodic Boundary Condition Simulations
Recommendations
Bibliography
Polymers
Level of Theory
Simulation Construction
Properties
Recommendations
Bibliography
Solids and Surfaces
Continuum Models
Clusters
Band Structures
Defect Calculations
Molecular Dynamics and Monte Carlo Methods
Amorphous Materials
Recommendations
Bibliography
Software Packages
Integrated Packages
Ab initio and DFT Software
Semiempirical Software
Molecular Mechanics/Molecular Dynamics/Monte Carlo Software
Graphics Packages
Special-purpose Programs
Bibliography
Glossary
Bibliography
Index

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