Science Gazette

Visualizing the Unseen


There are several methods for producing two- and three-dimensional representations of atoms and molecules. Scientists discovered that standard molecular models did not suit the pictures they observed after the development of cutting-edge gear capable of imaging materials at the atomic scale. Researchers have improved on these old approaches to provide a better way to see molecules. Their models suit the imaging data they collect well, and they expect that the models can aid chemists with their intuition for understanding molecular pictures.

Anyone reading this is probably acquainted with conventional ball-and-stick models of atoms and molecules, in which balls of various sizes and colors represent distinct atomic nuclei and sticks indicate features of atomic bonds. Although they are valuable instructional aids, they are significantly less complex than the world they depict. Chemists often use models such as the Corey-Pauling-Koltun (CPK) model, which is similar to the ball-and-stick model but with the balls expanded to overlap. The CPK model teaches scientists significantly more about how molecule components interact than the ball-and-stick model.

Thanks to technology such as atomic resolution transmission electron microscopy, it is now feasible not only to capture the architecture of molecules but also to record their mobility and interactions in movies (AR-TEM). This is referred to as “cinematic molecular science” at times. The ball-and-stick or CPK models, on the other hand, become a barrier rather than an assistance with this jump in our ability to envision the unseen. When researchers from the University of Tokyo’s Department of Chemistry attempted to match these models to the pictures they were seeing, they ran into some difficulties.

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“The ball-and-stick model is just too basic to fully represent what is going on in our photographs,” Professor Koji Harano remarked. “Furthermore, the CPK model, which technically depicts the dispersion of the electron cloud surrounding an atomic nucleus, is too thick to distinguish certain features. The reason for this is because none of those models shows the exact sizes of atoms that AR-TEM pictures display.”

The size of each atom in AR-TEM pictures is precisely proportional to its atomic weight, denoted simply as Z. So Professor Eiichi Nakamura and his colleagues modified a ball-and-stick model to match their photographs, sizing each nucleus in the model according to the Z number of the nucleus it represents, and dubbed it the Z-correlated (ZC) molecular model. They employed the same color scheme as in the CPK model, which was first developed in 1952 by American scientists Robert Corey and Linus Pauling.

“A picture is worth a thousand words,” Nakamura said, comparing AR-TEM photos to the first-ever snapshot of a black hole. “They both depict reality as it has never been seen before, and both are significantly less clear than how most people assume it should be. This is why models are so useful in bridging the gap between imagination and reality. We expect that the Z-correlated molecular model will enable chemists to examine electron microscope pictures intuitively, without the need for any theoretical computations, and thus usher in a new era of ‘cinematic molecular research.'”

The Japan Society for the Promotion of Science (JSPS) KAKENHI (JP19H05459, JP20K15123, and JP21H01758) and the Japan Science and Technology Agency are funding this study (CREST JPMJCR20B2).

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