Electron Catwalks

In a protein, for instance, an electron must travel through the molecule's complex chain of atoms, work its way to the surface and onto an adjacent protein. Imagine walking from one end of a street to the other going through all the rooms of each house. A catwalk spanning and connecting the roofs would simplify the stroll. But no such electron catwalk exists in biological systems. Or so scientists thought.

MIT physicist John D. Joannopoulos and research scientist Kyeongjae Cho along with graduate student Ickjin Park have identified an electron pathway, an alternative to the long and winding route of bond-to-bond electron transport, that may be likened to this catwalk. Using Pittsburgh Supercomputing Center's CRAY C90, they simulated what happens when an extra electron slips into a cluster of six water molecules, creating a molecular interaction called a wet electron. What they have learned from this curious entity has implications for electron transport in biological processes in general.

"How different biological molecules interact, store and transfer energy and react with each other," says Joannopoulos, "to a large degree involves electron transport."

Dangling Hydrogens & an Uninvited Guest

Red lines indicate hydrogen bonds to oxygen in neighboring water molecules of a six molecule cluster.

Water molecules link to each other in clusters through hydrogen bonds, the interactions between the hydrogen atom of one water molecule and the oxygen of another. These are the same bonds that bind DNA and are ubiquitous in the chemistry of living organisms. In a pure solution of water, each atom will try to satisfy its respective attractions, forming as many bonds as possible in a collective molecular effort to reach a state of lowest possible energy. Like wedding guests searching for dance partners, however, invariably some hydrogen atoms are left dangling.

The researchers simulated what happens when an uninvited guest -- an extra electron -- shows up at this microscopic reception. Each of the dangling hydrogen atoms -- those without dance partners -- vies for the companionship of the negatively charged electron, causing the water molecules to form a cage around it, hence the moniker "wet." Although wet electrons have been known to exist since the early 1990s, their atomic interactions have been little understood.

Results: Inside and Outside the Cluster

The computations simulated a process of randomly distorting a wet electron system of six water molecules and allowing it to resettle into its most stable, low energy arrangement. Results showed two possible scenarios. "We found that the system likes to arrange itself in two different ways, both of which bind the electron," says Joannopoulos. "One keeps the electron stuck inside the cluster, and one keeps the electron stuck outside. The typical electron pathway involves moving between atoms, through bonds, but this suggests that the electron could hop through space from one atom to the next. In other words, it doesn't need a bond to relocate."

The Wet Electron: Two Possible Structures
Two possible structures occur when an electron is slipped into a cluster of six water molecules. In both structures, hydrogen atoms (small black balls) vie for the attention of the extra electron. The orange cloud represents the potential location of the extra electron. Smaller red clouds depict orbitals between hydrogen and oxygen atoms. In one structure (left), all six water molecules -- three on top, three on the bottom -- have dangling hydrogens, non-bonded to oxygen atoms of neighboring water molecules. In the other, all the hydrogen atoms of the three top water molecules are bonded. The three lower water molecules, however, have three dangling hydrogens (pointing downward) that draw the extra electron into their vicinity.

"If there were a lot of these dangling hydrogens in a line," adds Joannopoulos, "then this extra electron has a means of transport, and that's a completely new idea." With proteins for instance, strategically arranged dangling hydrogens could create a path for an electron to move through space, the equivalent of a hiker crossing a creek by walking over a bridge, as opposed to trudging through the water over slippery rocks. This dangling hydrogen mode of electron transport could be useful in genetic engineering of proteins and in drug design. "It's a possible new pathway and because of that, maybe someday we can engineer it to drive electrons in certain directions along proteins."

To further map this potential new pathway, Joannopoulos plans to expand his wet electron simulations to model what occurs when an extra electron meets up with hundreds of water molecules. This work will require the increased computing capability of a scalable parallel system such as the CRAY T3D. "We'll be studying the dynamics of the system," says Joannopoulos, "and watching how it evolves over time at different temperatures, so the calculations will be much more time and memory intensive. With its huge memory capacity and high speed, the T3D makes these big projects manageable."

Researchers: John Joannopoulos, Massachusetts Institute of Technology.
Hardware: CRAY C90
Software: User-developed code.
Keywords: electrons, electron transport, electron pathway, wet electron, water molecule, hydrogen bonds, dangling hydrogen atom.

Related Material on the Web:
RLE - John D. Joannopoulos
RLE - Kyeongjae Cho
Ickjin Park's Home Page
Projects in Scientific Computing, PSC's annual research report.

References, Acknowledgements & Credits