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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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Possible Results of an SCF Procedure | |

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How to Safely Change the SCF Procedure | |

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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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Creating Basis Sets from Scratch | |

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Combining Existing Basis Sets | |

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Customizing a Basis Set | |

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Basis Set Superposition Error | |

| |

| |

Bibliography | |

| |

| |

| |

Force Field Customization | |

| |

| |

| |

Potential Pitfalls | |

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Original Parameterization | |

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Adding New Parameters | |

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Bibliography | |

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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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Recommendations | |

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Bibliography | |

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| |

Computing NMR Chemical Shifts | |

| |

| |

| |

Ab initio Methods | |

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Semiempirical Methods | |

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Empirical Methods | |

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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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Recommendations | |

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Bibliography | |

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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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Recommendations | |

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Bibliography | |

| |

| |

| |

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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Describing the Electronic Structure of Crystals | |

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Computing Crystal Properties | |

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| |

Defect Calculations | |

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| |

Bibliography | |

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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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Synthesis Design Systems | |

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Applications of Traditional Modeling Techniques | |

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Recommendations | |

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Bibliography | |

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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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Main Group Inorganics, Noble Gases, and Alkali Metals | |

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Transition Metals | |

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Lanthanides and Actinides | |

| |

| |

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 | |

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| |

Simulating Liquids | |

| |

| |

| |

Level of Theory | |

| |

| |

| |

Periodic Boundary Condition Simulations | |

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Recommendations | |

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| |

Bibliography | |

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| |

Polymers | |

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| |

| |

Level of Theory | |

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Simulation Construction | |

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Properties | |

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| |

Recommendations | |

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| |

Bibliography | |

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| |

Solids and Surfaces | |

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| |

Continuum Models | |

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Clusters | |

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Band Structures | |

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| |

Defect Calculations | |

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| |

| |

Molecular Dynamics and Monte Carlo Methods | |

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| |

Amorphous Materials | |

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| |

Recommendations | |

| |

| |

Bibliography | |

| |

| |

| |

Software Packages | |

| |

| |

| |

Integrated Packages | |

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| |

| |

Ab initio and DFT Software | |

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| |

Semiempirical Software | |

| |

| |

| |

Molecular Mechanics/Molecular Dynamics/Monte Carlo Software | |

| |

| |

| |

Graphics Packages | |

| |

| |

| |

Special-purpose Programs | |

| |

| |

Bibliography | |

| |

| |

Glossary | |

| |

| |

Bibliography | |

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Index | |