Visualize the invisible | Eurek alert!
There are several ways to create two-dimensional and three-dimensional models of atoms and molecules. With the advent of advanced devices capable of imaging samples at the atomic scale, scientists found that traditional molecular models did not match the images they saw. Researchers have developed a better way to visualize molecules by building on these traditional methods. Their models match well with the imaging data they acquire, and they hope the models can therefore help chemists with their intuition for interpreting molecular images.
Anyone reading this is probably familiar with the traditional ball-and-stick models of atoms and molecules, where balls of different sizes and colors represent the different atomic nuclei, and the sticks represent the properties of the bonds between atoms. Although these are useful educational tools, they are much 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 how the components of a molecule interact much better than the ball and stick model.
In recent years, it has finally become possible not only to capture the structures of molecules but also to record their movement 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 ability to visualize the unseen 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 to the images they were seeing, they ran into a few problems.
“The ball and stick model is far too simple to accurately describe what is actually happening in our images,” said Professor Koji Harano. “And the CPK model, which technically shows the propagation of the electron cloud around an atomic nucleus, is too dense to discern certain details. The reason for this is that none of these models demonstrate the actual size of the atoms that the AR-TEM images show.
In AR-TEM images, the size of each atom is directly correlated to the atomic weight of that atom, known simply as the Z. Professor Eiichi Nakamura and his team therefore chose to modify a ball and stick model to fit their images, where each core of the model was sized according to the Z number of the kernel it represents, and named it Z– correlated molecular model (ZC). They retained 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 very first photograph of a black hole,” Nakamura said. “They both show reality like never before, and both are much less clear than what people probably imagine these things should look like. This is why models are so important, to bridge the gap between imagination and reality. We hope the Z-the correlated molecular model will help chemists to analyze electron microscope images based on intuition without even needing theoretical calculations, and will open a new world of “cinematic molecular science”.
Junfei Xing, Keishi Takeuchi, Ko Kamei, Takayuki Nakamuro, Koji Harano, and Eiichi Nakamura, “Atomic Sizes Correlated to Atomic Number (Z) for Deciphering Molecular Images by Electron Microscope”, Proceedings of the National Academy of Sciences of the United States
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).
Graduate School of Science – https://www.su-tokyo.ac.jp/en/
Department of Chemistry – https://www.chem.su-tokyo.ac.jp/en
Professor Koji Harano – [email protected]
Professor Takayuki Nakamuro – [email protected]
Professor Eiichi Nakamura – [email protected]
Department of Chemistry, University of Tokyo,
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, JAPAN
Mr. Rohan Mehra
Division of Strategic Public Relations, University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, JAPAN
Email: [email protected]jp
About the University of Tokyo
The University of Tokyo is Japan’s leading university and one of the top research universities in the world. The vast research output of some 6,000 scholars is published in the world’s top journals in the arts and sciences. Our vibrant student body of approximately 15,000 undergraduate students and 15,000 graduate students includes over 4,000 international students. For more information, visit www.u-tokyo.ac.jp/en/ or follow us on Twitter at @UTokyo_News_en.
Proceedings of the National Academy of Sciences
The title of the article
Atomic sizes correlated to atomic number (Z) for deciphering molecular images with an electron microscope
Publication date of articles
March 28, 2022
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