Simulating reactions in cyberspace earns Nobel Prize in chemistry | Science News


Simulating reactions in cyberspace earns Nobel Prize in chemistry

12:49PM, October 9, 2013

By Meghan Rosen and Beth Mole

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Research that created computer simulations of complex chemical reactions has won the Nobel Prize in chemistry.

Martin Karplus of Harvard University and the University of Strasbourg, Michael Levitt of Stanford University and Arieh Warshel of the University of Southern California will share the prize.

Using computer programs that marry the power of quantum physics with the low computing demands of classical physics, the three scientists made it possible to describe ultrafast chemical reactions. The work helps chemists to predict the outcomes of chemical reactions, such as those that occur in photosynthesis or when a drug docks with a molecule in the body. As a result, chemists can rely less on experimental lab work.

“We save a lot of money, we save a lot of time and we save a lot of effort by doing the theoretical work first,” says Sven Lidin, an inorganic chemist at Lund University in Sweden who chairs the Nobel committee.

Warshel, awake at 3:00 a.m. in California to receive the news by phone, said he was feeling “extremely well.”

Warshel’s path to the prize began in 1968 as a graduate student at the Weizmann Institute of Science in Rehovot, Israel, where he worked with Levitt, then a visiting scholar fresh off his bachelor’s degree in chemistry. Together, the pair created some of the first computer simulations of energy states of molecules. The first models involved only a few atoms.

Later simulations grew in complexity. “They came up with a really simple and really fast way to calculate the energy of a system that contains many, many atoms,” says computational chemist Kenneth Merz of Michigan State University in East Lansing.

In the early 1970s, Warshel worked with Karplus at Harvard, who had already made major strides in quantum descriptions of chemical reactions. Together they devised a method to study the relaxed and excited energy states of molecules whose atoms lie in a flat plane. In the calculations, the team combined classical physics to describe the nuclei and electrons that sit in the plane with quantum physics to describe electrons floating above. “This was the first time anyone ever merged the quantum and classical worlds in chemistry,” says Gunnar Karlström, a theoretical chemist at Lund University in Sweden and a member of the Nobel committee.  

Just a few years later, merging the two types of physics let Warshel and Levitt build computer simulations to study a chemical reaction involving lysozyme, an enzyme in tears and saliva that can chop through bacterial cell walls. The duo used similar programs to describe how a protein folds itself into a three-dimensional structure. Their theoretical prediction nearly matched the protein structure that researchers had observed using experimental methods.

Work in Karplus’s lab went on to simulate how proteins fold and wiggle, creating one of the first bridges between computational chemistry and structural biology.That theoretical work helped scientists realize how dynamic proteins are, Merz says. “We think about proteins now as always moving and doing things, not just bricks that are coursing through our veins or in our cells.”

The Nobelists’ easier way to study reactions has already helped chemists design drugs, predict how ions move through a channel and understand how certain enzymes react with their targets.“I think nearly everybody that works in the area of theoretical and computational chemistry have for sure used the methods and programs developed by the three that won the prize today,” says theoretical chemist David Clary of the University of Oxford.

Further Reading

J. Gorman. Ions on the Move: Theory of hydroxide’s motion overturned. Science News. June 29, 2002.

M. Levitt and A. Warshel. Computer simulation of protein folding. Nature. Vol. 253, February 27, 1975, p. 694. doi: 10.1038/253694a0.

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