Episode 5: Small molecule structure uncovered via femtosecond-crystallography & algorithm

In this podcast episode, MRS Bulletin’s Laura Leay interviews Nate Hohman from The University of Connecticut about the structure of two chalcogenolates his group uncovered. By combining serial femtosecond crystallography —usually used to characterize large molecules—and a clique algorithm, Hohman’s group was able to analyze the structure of small molecules. With serial femtosecond crystallography, large molecules like proteins produce thousands of spots on the detector; in contrast, small molecule crystals only a produce a few spots. The algorithm uses the pattern that the spots make on the detector to determine the orientation of as many crystals in the liquid jet as possible. The data from each crystal can then be merged together to find the structure. 

Transcript

LAURA LEAY: Welcome to MRS Bulletin’s Materials News Podcast, providing breakthrough news & interviews with researchers on the hot topics in materials research. My name is Laura Leay. When you get down to the level of atoms, some structures are hard to characterize. It can be difficult to make crystals large enough to analyze using the most common techniques.

NATE HOHMAN: The kind of materials that were working with, it’s almost a sort of crystallographic dark matter. 

LL: That was Nate Hohman from The University of Connecticut. Nate is really interested in chalcogenolates, which form layers of metal atoms between organic sheets. The exact structures were unknown as the crystals tend to be small.  This crystallographic dark matter has some really useful properties, similar to graphene but without the need for very careful placement of the individual atomic layers. Chalcogenolates self-assemble from a liquid and so can be much easier to make than graphene.

NH: We have a very simple method where we just take the two reagents, no solvent usually, heat it up in a vial and filter it. What’s unique about it is that there is no nanoscale size effect; it has the property of an isolated 2D material in every layer and we don’t have to worry about how we make it, or how thick it is.

LL: To really understand how these materials work Nate has to know their crystal structure. Since common x-ray characterization techniques don’t work for these small molecules, one of Nate’s graduate students, Elyse Schriber, came to him with a potential solution.

NH: Elyse popped into my office one afternoon and she said, “Nate there’s this machine, it’s going to go down for a year, we only have one shot to apply for it, and it’s going to solve all of our problems.”

LL: Elyse had heard about something known as serial femtosecond crystallography, where a liquid jet containing billions of small crystal is fired into the path of x-rays which are generated by a free-electron laser. This method produces high flux pulses and their short duration means you can make a measurement before the structure is damaged. This equipment isn’t easy to access though; there are only 5 or 6 facilities in the world and they’re usually used to characterize large molecules, not the small crystals that Nate and his team are interested in. The x-rays diffract through the spaces between atoms, creating bright spots on a detector. Large molecules like proteins produce thousands of spots; in contrast, small molecule crystals only a produce a few spots. This isn’t enough to be able to determine the structure. Nate teamed up with researchers at Brookhaven National Laboratory to devise a method that would help. In doing so, they hope to make their new technique easily available to anyone with a small molecule. Aaron Brewster was instrumental in figuring out an algorithm to analyze the data.

NH: He tried to really strip out all the possible knowns and unknowns and he created what he calls a clique algorithm.

LL: The algorithm uses the pattern that the spots make on the detector to determine the orientation of as many crystals in the liquid jet as possible. The data from each crystal can then be merged together to find the structure. Nate’s team has uncovered the structure of two chalcogenolates for the very first time. In doing so, they have discovered why one particular structure, thiroene, which has sulphur and silver in it, glows blue under UV light and it’s all to do with the bonds between the silver.

NH: They’re still arrayed in a 2D layer, but the interactions between the silver atoms are broken in 1D.

LL: These molecules could be used to make novel semiconductors or photovoltaic cells for solar panels, or they could be used for photocatalysis or quantum computing and so could lead to many technological advances. This all starts with knowing the structure of the material at an atomic level. This work was published in a recent issue of Nature (doi: 10.1038/s41586-021-04218-3). 

My name is Laura Leay from the Materials Research Society. For more news, log onto the MRS Bulletin website at mrsbulletin.org and follow us on twitter, @MRSBulletin. Don’t miss the next episode of MRS Bulletin Materials News – subscribe now. Thank you for listening.