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Salt-extraction molecule discovered with help from IU supercomputer Big Red II

High performance systems Jun 21, 2019

Yun Liu with 3D printed model of the chloride-capture molecule (photo by Fred Zwicky, University of Illinois at Urbana-Champaign)

By now you’ve likely read about the discovery of a salt extraction molecule by researchers in the Indiana University (IU) Department of Chemistry’s Flood Lab. Yun Liu, lead author of the recent article on the molecule’s design in Science, led the study as a Ph.D. student in the lab of Amar Flood, James F. Jackson Professor of Chemistry and Luther Dana Waterman Professor. But did you know that Big Red, IU’s main system for high-throughput parallel computing, played an important role in its creation?

IU Chemistry Professor Amar Flood

The Flood Lab works primarily on developing molecules with “empty pockets” inside them (i.e., a cage), which are designed to a precise shape and size to capture anions, making it possible to use these designer molecules to capture anions in order to detect, remove, or mitigate their negative impacts on water and soil. As Liu reports, “the cage molecule we [the team has] developed is ‘ridiculously’ good at its job,” and achieves binding strength of a type generally only seen in nature.

To minimize the expense of creating the molecule in the lab, the team began with a series of computations on Big Red II. According to Liu, it’s important for scientists to understand how new molecules they design might be different from the ones they draw on paper. He explains, “to capture the real-world structure of the molecule as accurately as possible, we usually run extensive calculations taking into account the environment in which the molecule will be used, like the solution the molecule will dissolve in.”

The computations created a feedback loop for Liu and his colleagues, letting them know quickly if the molecule they designed worked as they hoped it would, and adjust the design accordingly. Ultimately, the team learned through the computations that the secret of creating a strong hydrogen bond using carbon-hydrogen bonds was the molecule’s rigidity. It had to be rigid enough to maintain its shape, so a vacuum-like cavity can be present without the salt molecule.  

Such extensive computations would have taken at least two months on a laptop, but took only three days on Big Red II. According to Liu, “The speed-up is not only [due to] the better CPU (~20 times faster than my work station); the large memory and ability to use multiple processors (I often call out 32) at the same time changed the game. You can run 16 jobs…which means I can examine multiple designs at the same time.” He also credits the availability of software and the responsive support team with helping ready the project for the expensive, time-consuming process of creating the molecule in the lab.

The molecule’s many possible applications include, most immediately, improving the accuracy of analyses of residual salt content in drinking water. Another possible use involves protecting metal from the corrosive effects of sea water. Most importantly, perhaps, in the long term, the molecule could help increase the availability of potable drinking water.

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