1st Edition

Molecular Modeling Basics

By Jan H. Jensen Copyright 2010
    190 Pages 124 B/W Illustrations
    by CRC Press

    by CRC Press

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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.

    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


    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