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