Molecular Modeling Basics: 1st Edition (Paperback) book cover

Molecular Modeling Basics

1st Edition

By Jan H. Jensen

CRC Press

190 pages | 124 B/W Illus.

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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.


… 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

Table of Contents

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 Schrödinger 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



Molecular geometry

Intermolecular interactions

Molecular geometry and motion

Molecular motion and energy

Chemical kinetics

The Details of the Calculations

Introductory remarks



Molecular geometry

Intermolecular interactions

Molecular geometry and motion

Molecular motion and energy

Chemical kinetics


About the Author

Jan H. Jensen, Ph.D., was born in Denmark in 1969 and came to the United States as a foreign exchange student in 1985. He received his B.A. in chemistry from Concordia College in 1989 and his Ph.D. in theoretical chemistry from Iowa State University in 1995, working with Mark Gordon. He continued in the Gordon group as a postdoctoral associate until 1997, when he moved to the University of Iowa where he was first assistant and then associate professor of chemistry until 2006. In 2006 he moved to the University of Copenhagen where he is now professor of bio-computational chemistry in the Department of Chemistry. His research interests are primarily in the area of computational molecular biophysics—at the intersection of molecular physics, quantum chemistry, and structural biology/bioinformatics.

Subject Categories

BISAC Subject Codes/Headings:
SCIENCE / Chemistry / Physical & Theoretical
SCIENCE / Mathematical Physics