Solving a crystal's structure when you've only got powder
A new mathematical technique enormously expands the power of x-ray crystallography

Date:
January 19, 2022
Source:
University of Connecticut
Summary:
Crystals reveal the hidden geometry of molecules to the naked eye.

Scientists use crystals to figure out the atomic structure of new
materials, but many materials can't be grown large enough. Now,
a team of researchers report a new technique that can lead to the
discovery of the crystalline structure of any substance.



FULL STORY ========================================================================== Crystals reveal the hidden geometry of molecules to the naked
eye. Scientists use crystals to figure out the atomic structure of
new materials, but many can't be grown large enough. Now, a team of
researchers report a new technique in the January 19 issue of Nature
that can discover the crystalline structure of any material.


==========================================================================
To truly understand a chemical, a scientist needs to know how its atoms
are arranged. Sometimes that's easy: for example, both diamond and
gold are made of a single kind of atom (carbon or gold, respectively)
arranged in a cubic grid.

But often it's harder to figure out more complicated ones.

"Every single one of these is a special snowflake -- growing them is
really difficult," says UConn chemical physicist Nate Hohman. Hohman
studies metal organic chacogenolates. They're made of a metal combined
with an organic polymer and an element from column 16 of the periodic
table (sulfur, selenium, tellurium or polonium.) Some are brightly
colored pigments; others become more electrically conductive when light
is shined on them; others make good solid lubricants that don't burn up
in the high temperatures of oil refineries or mines.

It's a large, useful family of chemicals. But the ones Hohman studies --
hybrid chalcogenolates -- are really difficult to crystallize. Hohman's
lab couldn't solve the atomic structures, because they couldn't grow
large perfect crystals.

Even the tiny powdered crystals they could get were imperfect and messy.

X-ray crystallography is the standard way to figure out the atomic
arrangements of more complicated materials. A famous, early example was
how Rosalind Franklin used it to figure out the structure of DNA. She
isolated large, perfect pieces of DNA in crystalline form, and then
illuminated them with x- rays. X-rays are so small they diffract through
the spaces between atoms, the same way visible light diffracts through
slots in metal. By doing the math on the diffraction pattern, you can
figure out the spacing of the slots -- or atoms -- that made it.

Once you know the atomic structure of a material, a whole new world
opens up.

Materials scientists use that information to design specific materials to
do special things. For example, maybe you have a material that bends light
in cool ways, so that it becomes invisible under ultraviolet light. If
you understand the atomic structure, you might be able to tweak it -- substitute a similar element of a different size in a specific spot,
say -- and make it do the same thing in visible light. Voila, an
invisibility cloak!


========================================================================== Hybrid chalcogenolates, the compounds Hohman studies, won't make you
invisible.

But they might make excellent new chemical catalysts and semiconductors.

Currently he's working with ones based on silver. His favorite, mithrene,
is made of silver and selenium and glows a brilliant blue in UV light or "whenever grad students are around," Hohman says.

Elyse Schreiber, a chemistry graduate student in Hohman's lab, convinced
Hohman they should try illuminating some of the small, messy hybrid chalcogenolates in a high powered x-ray beam anyway. If they could figure
out the math, it would solve all their problems.

While working at the Linac Coherent Light Source at the SLAC linear
accelerator in Menlo Park, California, Schreiber met Aaron Brewster,
a researcher at Berkeley. Brewster mentioned he'd solved the math
required to solve the crystal structure of difficult materials using
X-ray crystallography. But he needed something to test it on. Hohman
and Schreiber had the material. They provided plenty of tiny, imperfect chalcogenolate crystals, which they mixed into water emulsified with
Dawn dish soap (another indispensable item in Hohman's lab that glows
blue) and shot jets of them into the accelerator beam. Each X-ray pulse illuminated the crystals incredibly brightly, allowing Brewster to capture
a snapshot of the atomic structures of hundreds of tiny crystals. With
enough snapshots, Brewster was able to run the calculations and figure
out how the atoms were arranged.

Not only did they solve the crystal structures -- they also figured out
that the previous best guesses of what those structures were had been
wrong. In theory, the technique, called small-molecule serial femtosecond crystallography, or smSFX, can be used for any chemical or material.

Computer scientists Nicolas Sauter and Daniel Paley at Lawrence Berkeley National Laboratory also helped develop smSFX. When you have a true
powder, Paley explains, it's like having a million crystals that are
all jumbled together, full of imperfections, and scrambled in every
possible orientation.

Rather than diffracting the whole jumble together and getting a
muddied readout of electron densities, like existing powder diffraction techniques, smSFX is so precise that it can diffract individual grains,
one at a time. "This gives it a special sharpening effect," he said. "So
that is actually the kind of secret sauce of this whole method. Normally
you shoot all million at once, but now you shoot 10,000 all in sequence,"
Paley says.

"There is a huge array of fascinating physical and even chemical
dynamics that occur at ultrafast timescales and this technique could
help us to understand how these dynamic events affect the structure
of microcrystalline materials. In a way, connecting the dots between a material's structure and its function," Schreiber elaborates. Hohman is
equally excited about their success.

"Now that we can solve these hard to crystallize structures, we can
design the best" structures for our purposes, Hohman says. Often,
a material will come close to having a certain desirable property,
but its crystalline structure won't be quite right. Hohman hopes that
with the data they can get from X-ray crystallography using Brewster's technique, they can design better materials from the ground up.

Now, Hohman and Brewster are collaborating with Tess Smidt, a machine
learning specialist at MIT, to try to teach a computer to design materials
with specific properties. The Department of Energy recently awarded the
team a $15 million grant to pursue this and two other projects.

This work involved the use of the SACLA free-electron laser in Japan, the
Linac Coherent Light Source at SLAC National Accelerator Laboratory, and
the Molecular Foundry and National Energy Research Scientific Computing Centers, U.S. Department of Energy Office of Science user facilities
located at Berkeley Lab.

========================================================================== Story Source: Materials provided by University_of_Connecticut. Original
written by Kim Krieger. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Elyse A. Schriber, Daniel W. Paley, Robert Bolotovsky, Daniel J.

Rosenberg, Raymond G. Sierra, Andrew Aquila, Derek Mendez,
Fre'de'ric Poitevin, Johannes P. Blaschke, Asmit Bhowmick,
Ryan P. Kelly, Mark Hunter, Brandon Hayes, Derek C. Popple,
Matthew Yeung, Carina Pareja- Rivera, Stella Lisova, Kensuke Tono,
Michihiro Sugahara, Shigeki Owada, Tevye Kuykendall, Kaiyuan Yao,
P. James Schuck, Diego Solis-Ibarra, Nicholas K. Sauter, Aaron
S. Brewster, J. Nathan Hohman. Chemical crystallography by serial
femtosecond X-ray diffraction. Nature, 2022; 601 (7893): 360 DOI:
10.1038/s41586-021-04218-3 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/01/220119121445.htm

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