A Bit About Modeling

Chemistry is three dimensional. Molecular modeling has advanced rapidly during the past decade because of amazing advances in software and hardware. This technology has many applications in chemical education.

There are two basic kinds of programs. Visualizers read in prepared structures (usually from a file of Cartesian coordinates in a specific format) and present a 3 dimensional color model that you can rotate on the screen or visualize in different ways (ball& stick, space-filling etc.) The images - from water to DNA - are absolutely spectacular. Several excellent visualization programs are available as shareware and some even work directly with www browsers. The number of structures available on the www is growing quickly!

Beyond simple visualization is an much complex type of program that allows you to build structures with a graphical user interface (GUI), perform various levels of computational modeling and visualize the results. Notwithstanding their sophistication, the best of these programs still are remarkably easy to use.

Three basic "models" exist. In order of increasing sophistication (and demands for computer resources), these models are:

Force Field or "Molecular Mechanics": Molecules are treated primarily by classical mechanics as balls held together by springs. Stretching, bending, twisting and coulombic interactions are all described by Hooke's law potentials and force constants that are often derived from experiment. Calculations are fast even for large molecules.

Semiempirical Methods: An approximate quantum mechanical method. Valence atomic orbitals (s, p, d) are combined to give delocalized molecular orbitals. The total energy comes from iterative solution of the Hartree-Fock (HF) equation, an approximation to the famous Schrödinger equation. This includes kinetic energy of the electrons, electron-nuclear attraction, electron-electron repulsion and other components. This method works reasonably well for most problems and can still be applied to large molecules. It is easy to visualize molecular orbitals.

Ab Initio ("from basic principles") methods: A more accurate (hopefully) and sophisticated Hartree-Fock quantum mechanical method that includes all the electrons and makes minimal approximations. Results improve with increasingly complex "basis sets" which are the specific mathematical functions that are used to describe the atomic orbitals and with inclusion of electron correlation. Calculation on large molecules can take hours or days of computer time! Many levels of theory exist. Another formulation is known as "density functional theory".

The 1998 Nobel Prize in chemistry was awarded to two of the pioneers in this field: Walter Kohn, University of California at Santa Barbara, developed density functional theory. John A. Pople, Northwestern University, Evanston, Illinois, USA developed much of the methodology used in modern quantum chemistry programs.

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