When they started, they expected to see a run-of-the-mill chemical reaction.
What they discovered was an atomic-level dance that no one predicted.
After three years of study, researchers at Texas Tech University and the Physics Institute of the University of Freiburg, Germany, have found that one type of a certain chemical reaction fundamental to cellular biochemistry is actually more complex than originally thought.
Knowledge of how these SN2 chemical reactions occur at the atomic level could mean better-engineered drugs or a greater understanding of metabolic chemistry and medicine, said William "Bill" Hase, the Robert A. Welch Professor of Chemistry in the Department of Chemistry and Biochemistry at Texas Tech University.
"Understanding this kind of reaction in terms of cell biology may help us to predict rates of chemical changes in a cell and understand how changes of molecular structure affect cell function," Hase said. "When you take drugs, they are there to alter the chemistry of the cell, or to alter the course of a chemical process. To understand exactly how these types of SN2 reactions occur could lead to changes in how we design drugs."
Their work was published in the December issue of Science. It was funded by grants from the National Science Foundation and the Robert A. Welch Foundation.
Hase, a pioneer of computerized simulations of chemical reactions, said that the SN2 reaction is fundamental to cellular metabolism. Hase, with research colleagues U. Lourderaj and Jiaxu Zhang, used supercomputers to generate exactly what happens in the SN2 reaction when a chloride ion came in contact with methyl iodide (CH3I).
"We discovered a fundamentally new mechanism for this reaction that no one would have discovered without computer simulation," Hase said. "We discovered there was an exciting new way that the atoms move for the reaction to occur. I could never have conceived of how this type of reaction occurs before I’d seen the actual computer simulation."
Instead of a linear-type reaction, where the chloride ion knocks the iodine atom off the compound, Hase found that the chloride ion actually roundhouse kicks the methyl iodide compound in a circle before the iodide ion falls off. Researchers weren’t expecting to see the complex gymnastics involved, he said.
Philip Smith, senior director of Texas Tech’s High Performance Computing Center, said Hase’s research numerically simulates collections of atoms, and is a very computer-intensive endeavor.
Some of his simulations may run for weeks or even months on 32 or more processors, Smith said. Usually, these computers must run hundreds of such simulations to obtain chemically meaningful results.
"These computations lead to insights on how atoms react to form molecules and how catalysts work," Smith said. "It is our job at the High Performance Computing Center to help configure the hardware and software to support such activities. We also "tune" the codes that Bill uses so that they run two to 10 times faster than they would ‘out of the box.’ "
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