An Introduction to Molecular Modeling

Review The sections of your lecture textbook dealing with 

The energies of alkenes with respect to degree of substitution 

The relative energies of cis- and frans-alkenes New Essay Molecular Modeling and Molecular Mechanics 

To perform this experiment, you must use computer software that has the ability to perform molecular mechanics (MM2 or MM3) calculations with minimization of the strain energy. Either your instructor will provide directions for using the software or you will be given a handout with instructions. 

The acyclic butane molecule has several conformations derived by rotation about the C2-C3 bond. The relative energies of these conformations have been well established experimentally and are listed in the following table. 

---

For new or would-be users of models, I present in Chapter 11 an introduction to molecular modeling, demonstrating how modern graphics programs allow users to display and manipulate models and to perform powerful structure analysis, even on desktop computers. This chapter also provides information on how to use the World Wide Web to obtain graphics programs and learn how to use them. It also provides an introduction to the Protein Data Bank (PDB), a World Wide Web resource from which you can obtain most of the available macromolecular models. 

Kubicki, J.D. and Bleam, W.F., An introduction to molecular modeling, in Molecular Modeling of Clays and Mineral Surfaces, Kubicki, J.D. and Bleam, W.F., Eds., Clay Minerals Society, in press. 

---