Preface to the First Edition |
Preface to the Second Edition |
Acknowledgments |
What are Theory, Computation, and Modeling? / 1: |
Definition of Terms / 1.1: |
Quantum Mechanics / 1.2: |
Computable Quantities / 1.3: |
Structure / 1.3.1: |
Potential Energy Surfaces / 1.3.2: |
Chemical Properties / 1.3.3: |
Cost and Efficiency / 1.4: |
Intrinsic Value / 1.4.1: |
Hardware and Software / 1.4.2: |
Algorithms / 1.4.3: |
Note on Units / 1.5: |
Bibliography and Suggested Additional Reading |
References |
Molecular Mechanics / 2: |
History and Fundamental Assumptions / 2.1: |
Potential Energy Functional Forms / 2.2: |
Bond Stretching / 2.2.1: |
Valence Angle Bending / 2.2.2: |
Torsions / 2.2.3: |
Van der Waals Interactions / 2.2.4: |
Electrostatic Interactions / 2.2.5: |
Cross Terms and Additional Non-bonded Terms / 2.2.6: |
Parameterization Strategies / 2.2.7: |
Force-field Energies and Thermodynamics / 2.3: |
Geometry Optimization / 2.4: |
Optimization Algorithms / 2.4.1: |
Optimization Aspects Specific to Force Fields / 2.4.2: |
Menagerie of Modern Force Fields / 2.5: |
Available Force Fields / 2.5.1: |
Validation / 2.5.2: |
Force Fields and Docking / 2.6: |
Case Study: (2R*,4S*)-1-Hydroxy-2,4-dimethylhex-5-ene / 2.7: |
Simulations of Molecular Ensembles / 3: |
Relationship Between MM Optima and Real Systems / 3.1: |
Phase Space and Trajectories / 3.2: |
Properties as Ensemble Averages / 3.2.1: |
Properties as Time Averages of Trajectories / 3.2.2: |
Molecular Dynamics / 3.3: |
Harmonic Oscillator Trajectories / 3.3.1: |
Non-analytical Systems / 3.3.2: |
Practical Issues in Propagation / 3.3.3: |
Stochastic Dynamics / 3.3.4: |
Monte Carlo / 3.4: |
Manipulation of Phase-space Integrals / 3.4.1: |
Metropolis Sampling / 3.4.2: |
Ensemble and Dynamical Property Examples / 3.5: |
Key Details in Formalism / 3.6: |
Cutoffs and Boundary Conditions / 3.6.1: |
Polarization / 3.6.2: |
Control of System Variables / 3.6.3: |
Simulation Convergence / 3.6.4: |
The Multiple Minima Problem / 3.6.5: |
Force Field Performance in Simulations / 3.7: |
Case Study: Silica Sodalite / 3.8: |
Foundations of Molecular Orbital Theory / 4: |
Quantum Mechanics and the Wave Function / 4.1: |
The Hamiltonian Operator / 4.2: |
General Features / 4.2.1: |
The Variational Principle / 4.2.2: |
The Born-Oppenheimer Approximation / 4.2.3: |
Construction of Trial Wave Functions / 4.3: |
The LCAO Basis Set Approach / 4.3.1: |
The Secular Equation / 4.3.2: |
H?uckel Theory / 4.4: |
Fundamental Principles / 4.4.1: |
Application to the Allyl System / 4.4.2: |
Many-electron Wave Functions / 4.5: |
Hartree-product Wave Functions / 4.5.1: |
The Hartree Hamiltonian / 4.5.2: |
Electron Spin and Antisymmetry / 4.5.3: |
Slater Determinants / 4.5.4: |
The Hartree-Fock Self-consistent Field Method / 4.5.5: |
Semiempirical Implementations of Molecular Orbital Theory / 5: |
Semiempirical Philosophy / 5.1: |
Chemically Virtuous Approximations / 5.1.1: |
Analytic Derivatives / 5.1.2: |
Extended Huckel Theory / 5.2: |
CNDO Formalism / 5.3: |
INDO Formalism / 5.4: |
INDO and INDO/S / 5.4.1: |
MINDO/3 and SINDO1 / 5.4.2: |
Basic NDDO Formalism / 5.5: |
MNDO / 5.5.1: |
AM1 / 5.5.2: |
PM3 / 5.5.3: |
General Performance Overview of Basic NDDO Models / 5.6: |
Energetics / 5.6.1: |
Geometries / 5.6.2: |
Charge Distributions / 5.6.3: |
Preface to the First Edition |
Preface to the Second Edition |
Acknowledgments |