Molecular modeling is becoming an increasingly important part of chemical research and education as computers become faster and programs become easier to use. The results, however, have not become easier to understand. Addressing the need for a "workshop-oriented" book, Molecular Modeling Basics provides the fundamental theory needed to understand not only what molecular modeling programs do, but also the gist of research papers that describe molecular modeling results.

Written in a succinct manner using informal language, the book presents concise coverage of key concepts suitable for novices to the field. It begins by examining the potential energy surface (PES), which provides the connection between experimental data and molecular modeling. It explores ways to calculate energy by molecular and quantum mechanics. It describes molecular properties and the condensed phase, and shows how to extract and interpret information from a program output. The author uses hands-on exercises to illustrate concepts and he supplements the text with a blog containing animated tutorials and interactive figures.

Drawn from the author’s own lecture notes from a class he taught for many years at the University of Iowa, this volume introduces topics in such a way that beginners can clearly comprehend molecular modeling results. A perfect supplement to a molecular modeling textbook, the book offers students the "hands-on" practice they need to grasp sophisticated concepts.

In addition to his blog, the author maintains a website describing his research and one detailing his seminars.

Reviews

… very much a primer for those who want to discover the equation behind the picture. In a mere 166 pages, a dizzying number of the mathematical concepts behind modelling are covered, and the equations are good value for money, with 252 set out and annotated with 125 figures

— Henry Rzepa writing in Chemistry World, September 2010

Contents

The Potential Energy Surface
undamental 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 Schrödinger equation: RHF, ROHF, and UHF

Basis set

The self-consistent field procedure

Guessing at the orbitals

Four practical comments regarding RHF c...