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Students Use Laptops to Discover the Secrets of Molecular Structure

Albert Fry
E.B. Nye Professor of Chemistry

by Jolee West
December 2000

Ever wonder what gives water that slippery quality or why the drug Prozac works so well with the human brain's system of neurotransmitters? It's all due to the structure of the molecule, a topic studied in chemistry professor Albert Fry's course in molecular mechanics. Using laptop computers equipped with modeling software, Fry's students simulate molecular systems to determine the optimal configuration of atoms in a molecule. They study how the arrangement of atoms affects a molecule's properties, including its ability to react with other molecules. When students finish the problems Fry poses in class, they share their computerized models for discussion.

With the earliest personal computers," Fry says, "huge amounts of processing time were required, even if a researcher needed to simulate small molecules. Molecular modeling calculations of this type required a mainframe computer, which meant long turnaround time and great difficulty in inputting structures and getting useful output.

In previous years, students completed the computer problem sets outside of class and then discussed their results during the next class meeting. But Fry found this unsatisfactory. "The class didn't move along very quickly," he says, "mostly because I wasn't available when the students were doing the actual assignments on the computer."

Using the AppleCart, a portable cabinet containing 12 Macintosh iBooks, and one G4 desktop computer, all connected to the campus network, Fry created an interactive classroom environment that allowed him to explore the course material in depth and ensure students were receiving the help they needed when they needed it. Now students work together on problem sets during class, get immediate attention from their professor and can discuss the intricacies of their work with their fellow students.

That undergraduate students are now able to investigate molecular structure at all is due to massive changes in computing technology. Fry points out that before the advent of desktop computing, the field of computational chemistry was a very different place altogether. "With the earliest personal computers," Fry says, "huge amounts of processing time were required, even if a researcher needed to simulate small molecules. Molecular modeling calculations of this type required a mainframe computer, which meant long turnaround time and great difficulty in inputting structures and getting useful output." A small molecule, such as ethane, with just two carbon atoms and six hydrogen atoms, might require thousands of individual calculations. As a result, most chemistry students did not even approach molecular mechanics until graduate school.

But desktop computing has changed all that. With specialized modeling software, even a novice chemistry student can explore the world of molecular mechanics in depth. Fry's students use PCMODEL, a molecular mechanics program for the Macintosh that allows the user to draw a molecule on the screen. Based on pre-programmed assumptions about the forces operating on each atom in the molecule, the program calculates the molecule's best geometry by optimizing the various forces, such as strengths of the bonds, attractions and repulsions among atoms, and preferred bond angles. The result is a much better representation of the optimized molecule than any experienced chemist could produce by hand using the traditional three-dimensional models constructed of straws or beads and wire.

The AppleCart was introduced during the Fall 1999 semester, and was used by Fry's Chemistry class, as well as Professor Johan Varekamp's Earth & Environmental Sciences CO2 course, featured at the url http://www.wesleyan.edu/its/acs/profiles/jvarekamp.html. To read more about the AppleCart, see the Apple "Macs in Action" site at http://www.apple.com/education/hed/macsinaction/wesleyan/.