Contact Information

  • James E. Hutchison
  • Professor
  • Chemistry
  • Univ. of Oregon
  • Eugene, OR 97403
(541) 346 - 4228

Molecular Mechanics Modeling

Laboratory Procedures (PDF)

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Computational methods are useful in predicting the most stable structure of a compound prior to its synthesis. Such methods are of importance, for example, in screening a series of compounds for potential biological activity. For large molecules, quantum mechanics cannot be readily employed due to the long computational times required. However, methods such as molecular mechanics and molecular dynamics that are based on classical or Newtonian mechanics are applicable to both small and large molecular systems. In this experiment, an initial structure of the compounds cis- and trans-stilbene, 4-methylcyclohexane, 1,4-bis(1-hydroxycyclohexyl)-1,3-butadiyne, and 5,10,20-tetraphenylporphyrin dianion are generated from molecular fragments, their energy computed using molecular mechanics in the program SPARTAN, and the structure corresponding to the global minimum in energy identified. The concepts of local vs. global minima are introduced. The link to the laboratory procedure includes pre- and post-lab questions.

Summary prepared July 2005 by Jerry C. Smith, Department of Chemistry at Georgia State University.


Doxsee, K. M.; Hutchison, J. E. Green Organic Chemistry - Strategies, Tools, and Laboratory Experiments, Print 2004; pp 174-181.

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Chemistry Concepts
  • Computational Chemistry
  • Molecular Mechanics/Dynamics
  • Molecular Modeling
Green Chemistry Principles
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  • Prevent Waste
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  • Organic Chemistry
  • Physical Chemistry
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