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| Preface to the First Edition | |
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| Preface to the Second Edition | |
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| Acknowledgments | |
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| What are Theory, Computation, and Modeling? | |
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| Definition of Terms | |
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| Quantum Mechanics | |
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| Computable Quantities | |
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| Structure | |
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| Potential Energy Surfaces | |
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| Chemical Properties | |
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| Cost and Efficiency | |
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| Intrinsic Value | |
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| Hardware and Software | |
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| Algorithms | |
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| Note on Units | |
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| Bibliography and Suggested Additional Reading | |
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| References | |
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| Molecular Mechanics | |
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| History and Fundamental Assumptions | |
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| Potential Energy Functional Forms | |
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| Bond Stretching | |
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| Valence Angle Bending | |
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| Torsions | |
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| Van der Waals Interactions | |
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| Electrostatic Interactions | |
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| Cross Terms and Additional Non-bonded Terms | |
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| Parameterization Strategies | |
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| Force-field Energies and Thermodynamics | |
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| Geometry Optimization | |
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| Optimization Algorithms | |
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| Optimization Aspects Specific to Force Fields | |
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| Menagerie of Modern Force Fields | |
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| Available Force Fields | |
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| Validation | |
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| Force Fields and Docking | |
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| Case Study: (2R*,4S*)-1-Hydroxy-2,4-dimethylhex-5-ene | |
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| Bibliography and Suggested Additional Reading | |
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| References | |
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| Simulations of Molecular Ensembles | |
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| Relationship Between MM Optima and Real Systems | |
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| Phase Space and Trajectories | |
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| Properties as Ensemble Averages | |
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| Properties as Time Averages of Trajectories | |
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| Molecular Dynamics | |
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| Harmonic Oscillator Trajectories | |
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| Non-analytical Systems | |
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| Practical Issues in Propagation | |
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| Stochastic Dynamics | |
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| Monte Carlo | |
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| Manipulation of Phase-space Integrals | |
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| Metropolis Sampling | |
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| Ensemble and Dynamical Property Examples | |
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| Key Details in Formalism | |
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| Cutoffs and Boundary Conditions | |
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| Polarization | |
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| Control of System Variables | |
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| Simulation Convergence | |
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| The Multiple Minima Problem | |
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| Force Field Performance in Simulations | |
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| Case Study: Silica Sodalite | |
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| Bibliography and Suggested Additional Reading | |
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| References | |
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| Foundations of Molecular Orbital Theory | |
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| Quantum Mechanics and the Wave Function | |
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| The Hamiltonian Operator | |
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| General Features | |
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| The Variational Principle | |
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| The Born-Oppenheimer Approximation | |
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| Construction of Trial Wave Functions | |
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| The LCAO Basis Set Approach | |
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| The Secular Equation | |
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| H?uckel Theory | |
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| Fundamental Principles | |
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| Application to the Allyl System | |
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| Many-electron Wave Functions | |
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| Hartree-product Wave Functions | |
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| The Hartree Hamiltonian | |
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| Electron Spin and Antisymmetry | |
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| Slater Determinants | |
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| The Hartree-Fock Self-consistent Field Method | |
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| Bibliography and Suggested Additional Reading | |
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| References | |
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| Semiempirical Implementations of Molecular Orbital Theory | |
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| Semiempirical Philosophy | |
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| Chemically Virtuous Approximations | |
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| Analytic Derivatives | |
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| Extended Huckel Theory | |
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| CNDO Formalism | |
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| INDO Formalism | |
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| INDO and INDO/S | |
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| MINDO/3 and SINDO1 | |
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| Basic NDDO Formalism | |
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| MNDO | |
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| AM1 | |
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| PM3 | |
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| General Performance Overview of Basic NDDO Models | |
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| Energetics | |
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| Geometries | |
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| Charge Distributions | |
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