Molecular Modeling Basics

The Potential Energy Surface The fundamental model Reactants, products, and transition states: Stationary points Real and imaginary frequencies: Characterizing stationary points in many dimensions The frequencies of planar ammonia Energy minimization: Finding and connecting stationary points Eight practical comments regarding geometry optimizations The local minima problem, conformational search, and molecular dynamics The multiple minima problem: Energy and free energy Vibrational frequencies Calculating the Energy Molecular mechanics force fields And now for something completely different: Quantum mechanics The hydrogen atom and the Born-Oppenheimer approximation The H2 + molecule The orbital approximation and the variational principle Electron spin and the Schrodinger equation: RHF, ROHF, and UHF Basis set The self-consistent field procedure Guessing at the orbitals Four practical comments regarding RHF calculations Semiempirical methods The correlation energy Density functional theory (DFT) Energy vs free energy Molecular Properties and the Condensed Phase The electron density The electrostatic potential Charges, dipoles, and higher multipoles Molecules in solution: Explicit solvent models Molecules in solution: Implicit solvent models Excited states Other spectroscopy Illustrating the Concepts Introductory remarks Atoms Bonding Molecular geometry Intermolecular interactions Molecular geometry and motion Molecular motion and energy Chemical kinetics The Details of the Calculations Introductory remarks Atoms Bonding Molecular geometry Intermolecular interactions Molecular geometry and motion Molecular motion and energy Chemical kinetics Index