Molecular Modeling Basics

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.

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.

The Potential Energy SurfaceThe fundamental modelReactants, products, and transition states: Stationary pointsReal and imaginary frequencies: Characterizing stationary points in many dimensionsThe frequencies of planar ammoniaEnergy minimization: Finding and connecting stationary pointsEight practical comments regarding geometry optimizationsThe local minima problem, conformational search, and molecular dynamicsThe multiple minima problem: Energy and free energyVibrational frequenciesCalculating the EnergyMolecular mechanics force fieldsAnd now for something completely different: Quantum mechanicsThe hydrogen atom and the Born–Oppenheimer approximationThe H2 + moleculeThe 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 PhaseThe 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 geometryIntermolecular interactionsMolecular geometry and motionMolecular 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 kineticsIndex