Simulations in the Classroom—Computational Chemistry Makes a Lasting Impression

Undergraduate organic chemistry students work with WebMO, a computational chemistry program
Beth Hartig, a senior, and John Harter, a sophomore, work with WebMO during an organic chemistry lab. Undergraduates at all levels of chemistry classes learn and apply computational chemistry.

“Today, the computer is just as important a tool for chemists as a test tube,” the Royal Swedish Academy said in recognizing computational chemists Martin Karplus, Michael Levitt, and Arieh Warshel as the 2013 Nobel Laureates in chemistry. Their collective contributions generated groundbreaking computational techniques that help scientists predict and explain chemical processes.

Without a doubt, computational chemistry has emerged as a fundamental pillar of chemical research. It is also making an impact in the classroom, and at the University of Wisconsin-Madison, the Department of Chemistry is making a concerted effort to integrate computation into every level of the undergraduate curriculum.

“This should be the standard,” Professor J.R. Schmidt says. “We should have students consistently exposed to computational chemistry, not just in one class, but in small amounts from the beginning [and] all the way through.”

Computational chemistry is first taught in general chemistry labs and continued in higher-level courses. Dr. Chad Wilkinson, general chemistry laboratory director, has worked with Dr. Desiree Bates, computational chemistry leader, and Dr. Cheri Barta, undergraduate research coordinator, to design and implement new general chemistry labs that include computational chemistry components. At this level, students use computer simulations to visualize molecules in 3-D. They also learn to connect these models to key concepts of chemical structure and reactivity.

At the organic chemistry level, Dr. Nick Hill, organic laboratory director, and Dr. Brian Esselman, assistant organic laboratory director, challenge students to predict and analyze the results of their experiments using computational tools. Students perform calculations for two-thirds of the experiments carried out during the course. “They are experiencing how an actual researcher would use computational chemistry,” Esselman says. This effort was supported in part by the Madison Initiative for Undergraduates, which provided funding for Esselman and Hill to revamp the organic lab curriculum.

When students reach inorganic and physical chemistry classes, they begin to learn about the concepts behind computations and the equations used to generate chemical models. Dr. Mark Wendt, physical chemistry laboratory director, and Professors John Berry, Judith Burstyn, and Clark Landis use computational chemistry to help students explore abstract concepts such as molecular orbital theory. The approach allows students to gain a more sophisticated and accurate understanding of molecular structures and bonding.

As they worked to apply the new curriculum changes, the faculty and staff involved identified a need for user-friendly software and enough computing power to accommodate the many undergraduate students taking chemistry classes each semester.

The user-friendly software was made possible by Schmidt, who created the WebMO graphical interface while an undergraduate at Hope College, where he worked with Professor Will Polik. Their goal was to help students learn and apply computational chemistry at the undergraduate level. The web-based interface is easy to use and provides access to the powerful calculations available through cutting-edge computational software such as Gaussian and MolPro.

Administrators of the Chemistry Computing Cluster
Research computation cluster administrators (from left) Paul McGuire, Professor J.R. Schmidt, and Dr. Desiree Bates

Students can access WebMO from any computer, and they can submit multiple computing jobs at once. Learning to use computational tools and to evaluate simulated models, however, can present a significant learning curve. Many students find WebMO challenging at first but later recognize its value.

“It really started horribly,” says Mike Soukup, a junior who conducts research in the Garand group. “However, after wrestling with WebMO for a while, it eventually became second nature. The amount of information you could derive from the calculations really helped my understanding of the molecules.”

The calculations are processed by the departmental research computing cluster, which is partially funded by the National Science Foundation. Bates and Paul McGuire, cluster system administrator, manage the cluster and have created a computation queue dedicated to running calculations for undergraduate classes.

For students who plan to pursue careers in chemistry, exposure to computations is especially beneficial as preparation for both industry work and graduate school. New guidelines from the American Chemical Society (ACS) require graduating seniors to be familiar with computational chemistry in order to receive an ACS-certified bachelor’s degree.

Primed with the necessary resources and innovative educators, UW-Madison is making computations an integral part of chemical education for undergraduates. In the future, Schmidt envisions expanding the curriculum to include molecular simulations, which would edge closer to the types of computations that garnered this year’s Nobel Prize.

Story by Grace Pham, communications project assistant