Visualizing the invisible
A new model to aid interpretation of atomic resolution molecular images


Date:
March 29, 2022
Source:
University of Tokyo
Summary:
With the advent of cutting-edge apparatus that can image samples
at the atomic scale, scientists found that traditional molecular
models did not fit the images they saw. Researchers have devised
a better way to visualize molecules building on these traditional
methods. Their models fit the imaging data they acquire well,
and they hope the models can therefore help chemists with their
intuition for interpreting molecular images.



FULL STORY ========================================================================== There are multiple ways to create two- and three-dimensional models of
atoms and molecules. With the advent of cutting-edge apparatus that can
image samples at the atomic scale, scientists found that traditional
molecular models did not fit the images they saw. Researchers have
devised a better way to visualize molecules building on these traditional methods. Their models fit the imaging data they acquire well, and they
hope the models can therefore help chemists with their intuition for interpreting molecular images.


========================================================================== Anyone reading this is likely familiar with traditional ball-and-stick
models of atoms and molecules, where balls of different size and color represent the various atomic nuclei, and the sticks represent properties
of the bonds between atoms. Although these are useful educational tools,
they are far simpler than the reality they reflect. Chemists tend to use
models such as the Corey- Pauling-Koltun (CPK) model, which is similar
to the ball-and-stick model but with the balls inflated so that they
overlap. The CPK model tells chemists more about the way components of
a molecule interact far better than the ball-and- stick model.

In recent years, it has finally become possible not only to capture the structures of molecules but even to record their motion and interactions
in videos thanks to technologies like atomic resolution transmission
electron microscopy (AR-TEM). This is sometimes called "cinematic
molecular science." However, it is with this leap in our capacity to
visualize the invisible that the ball-and-stick or CPK models become a hindrance rather than a help. When researchers from the Department of
Chemistry at the University of Tokyo tried to fit these models with the
images they were seeing, they ran into some problems.

"The ball-and-stick model is far too simple to accurately describe what
is really going on in our images," said Professor Koji Harano. "And the
CPK model, which technically shows the spread of the electron cloud
around an atomic nucleus, is too dense to discern some details. The
reason is that neither of those models demonstrate the true sizes of
atoms that images from AR-TEM show." In AR-TEM images, the size of
each atom directly correlates with that atom's atomic weight, known
simply as Z. So Professor Eiichi Nakamura and his team opted to modify
a ball-and-stick model to fit their images, where each nucleus in the
model was sized according to the Z number of the nucleus it represents,
and named it Z-correlated (ZC) molecular model. They kept the same color
system used in the CPK model, originally introduced by American chemists
Robert Corey and Linus Pauling in 1952.

"A picture is worth a thousand words, and you can compare AR-TEM images
to the first-ever photograph of a black hole," said Nakamura. "They
both show reality as never seen before, and both are far less clear
than how people probably imagine those things should look. This is
why models are so important, to bridge the gap between imagination and
reality. We hope the Z-correlated molecular model will help chemists
analyze electron microscope images based on intuition without even
the need for any theoretical calculations, and open up a new world of 'cinematic molecular science.'" This research is supported by the
Japan Society for the Promotion of Science (JSPS) KAKENHI (JP19H05459, JP20K15123, and JP21H01758) and the Japan Science and Technology Agency
(CREST JPMJCR20B2).


========================================================================== Story Source: Materials provided by University_of_Tokyo. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. Junfei Xing, Keishi Takeuchi, Ko Kamei, Takayuki Nakamuro,
Koji Harano,
Eiichi Nakamura. Atomic-number (Z)-correlated atomic sizes for
deciphering electron microscopic molecular images. Proceedings
of the National Academy of Sciences, 2022; 119 (14) DOI:
10.1073/pnas.2114432119 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/03/220328150610.htm

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