Molecular Modeling Basics  book cover
1st Edition

Molecular Modeling Basics

ISBN 9781420075267
Published April 26, 2010 by CRC Press
190 Pages 124 B/W Illustrations

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Book Description

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.

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

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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.


… 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