It is very important for students in organic and biochemistry to understand why molecules adopt their particular geometry. Both length, bond angle, dihedral deformations, and a variety of non-bonded interactions are responsible for specific conformations.

In molecular mechanics all of these contributions to the total strain energy are molded by mathematical equations which are minimized to find the lowest energy configuration. This module allows students to feel the individual forces acting on an atom as they simultaneously view the corresponding graphs. For example, as a carbon atom in an ethane molecule is moved away from the other carbon atom, the restoring force will be felt by the student.

The virtual environment allows students to first choose a particular mathematical equation. Then students are able to pull the atom in the molecule, either stretching or compressing the bond, and simultaneously observe the mathematical graph being generated. There is an audio explanation of the mathematical equations and how they model the chemical processes. One version of the virtual environment (on a PC) uses a force-feedback device (the Phantom) so that users can actually feel the increase in forces acting on the atom. The Web version of this module is an Active-X plugin. Principal programmer: Milan Pradhan. Principal designer: Elizabeth Kaechele.

molecule and mathematical equations

molecule with corresponding graph

Principal Participants:

  Mark Zimmer: Professor of Chemistry

  Elizabeth Kaechele: Studio Art

  Milan Pradhan: Computer Science

Courses where Module will be Used:

  Inorganic Chemistry (CHM202)

  Advanced Topics in Biological Chemistry (CHM417)