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A Paradigm Shift in Understanding Chemical Reactions

By Robert Perkins
March 22, 2012

Anna Krylov is professor of chemistry in USC Dornsife and the paper's co-corresponding author. Photo by Phil Channing.

Anna Krylov is professor of chemistry in USC Dornsife and the paper's co-corresponding author. Photo by Phil Channing.

Scientists at USC and Lawrence Berkeley National Lab have discovered a new route by which a proton (a hydrogen atom that lost its electron) can move from one molecule to another — a basic component of countless chemical and biological reactions.

“This is a radically new way by which proton transfer may occur,” said Anna Krylov, professor of chemistry in USC Dornsife. Krylov is a co-corresponding author of a paper on the new process that was published online on March 18 by Nature Chemistry.

Krylov and her colleagues demonstrated that protons are not obligated to travel along hydrogen bonds, as previously believed. The finding suggests that protons may move efficiently in stacked systems of molecules, which are common in plant biomass, membranes, DNA and elsewhere.

Armed with the new knowledge, scientists may be able to better understand chemical reactions involving catalysts, how biomass (plant material) can be used as a renewable fuel source, how melanin (which causes skin pigmentation) protects our bodies from the sun’s rays and damage to DNA.

“By better understanding how these processes operate at a molecular level, scientists will be able to design new catalysts, better fuels and more efficient drugs,” Krylov said.

Hydrogen atoms often are shared between two molecules, forming a so-called hydrogen bond. This bond determines structures and properties of everything from liquid water to the DNA double helix and proteins.

Hydrogen bonds also serve as pathways by which protons may travel from one molecule to another, like a road between two houses. But what happens if there’s no road?

To find out, Krylov and fellow corresponding author Ahmed Musahid of the Lawrence Berkeley National Lab created a system in which two molecules were stacked on top of each other, without hydrogen bonds between them. Then they ionized one of the molecules to coax a proton to move from one place to another.

Ahmed and Krylov discovered that when there’s no straight road between the two houses, the houses (molecules) can rearrange themselves so that their front doors are close together. In that way, the proton can travel from one to the other with no hydrogen bond and with little energy. Then the molecules return to their original positions.

“We’ve come up with the picture of a new process,” Krylov said.

This research was performed under the auspices of the iOpenShell Center and supported by the U.S. Department of Energy, the Defense Threat Reduction Agency and the National Science Foundation.