Molecular models meet electron microscopy

What does a molecule look like? That’s not really a fair question—molecules are so tiny that only our very best electron microscopes can give us fuzzy, grainy images. Instead, we use a number of different symbols and models to represent them.

A team of Japanese researchers have found a way to combine these two things with a molecular modeling system based on electron microscopy. While it’s similar to the ball-and-stick model you might have used in high school, their model conveys a lot more information – through the size of the atoms.

They say their system, called the ZC model, represents molecules in a way that helps chemists’ intuition when it comes to pictures of very small things. They hope it will also become a useful teaching tool.

The ZC model and how they figured it out is described in an article in PNAS.

Electron micrographs of molecules (far left), followed by the ZC model of atoms, the more conventional CPK model, and drawings of molecules (far right). Photo credit: © 2021 Nakamura, Harano et al.

Molecular models predate actual images of molecules by more than a century. Three-dimensional molecular models are critical to the work of chemists—be it a hand-held ball and stick model or a computer-generated balloon-like space-filling diagram, or something in between.

Transmission electron microscopy (TEM) has made it possible to actually see individual atoms and molecules. But regardless of what you may have seen in movies, they don’t appear like smooth, easy-to-understand balls on screen. In fact, it is difficult to see any similarities between a TEM image and a model of a molecule at all.

Read more: Touching Atoms

“The ball and stick model is far too simple to describe exactly what is really going on in our images,” says Professor Koji Harano from the Department of Chemistry at the University of Tokyo, Japan.

“And the CPK model, which technically shows the propagation of the electron cloud around an atomic nucleus, is too dense to see some detail. The reason is that none of these models show the true size of atoms imaged by AR-TEM [atomic resolution transmission electron microscopy] Show.”

Harano and colleagues addressed this by studying very closely how TEM images correlated with the atoms and molecules they knew were there.

They found that the size of an atom in a TEM image was closely related to its atomic number. (The atomic number, or mass number, is the number of protons in an element and is the large number assigned to each atom on the periodic table. For example, the atomic number of hydrogen is 1 and that of carbon is 6.)

They used this information to propose a new way of representing molecules, in which each atom has a different size according to its atomic number.

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The periodic table of the elements – by size. The CPK model, above, shows the distribution of electrons around an atom. This differs from the mass of the nucleus shown in the ZC model below. Photo credit: © 2021 Nakamura, Harano et al.

The atomic number is also represented by a Z, so the researchers named their system the Z-correlated or ZC system.

“Creating this model has greatly accelerated our research,” says Professor Eiichi Nakamura, also from the University of Tokyo. “Previous molecular models could not explain the molecular images in the TEM well.”

He says their model could eventually help chemists figure out things like molecular structure from TEM images. For now, TEM, while useful for other purposes, isn’t nearly as effective as traditional analytical techniques for finding out the shape of molecules.

“TEM specialists have never thought about our approach,” says Nakamura. “They just accepted that it’s incomprehensible because it’s very complex.”

This new model, which can be used in any molecular imaging software that lets you optimize the size of atoms, unravels some of that complexity.

“With the ZC model, it is now possible to predict the molecular structure from the actual TEM image with fairly high accuracy,” says Nakamura.

“This has opened up the possibility of using TEM in elementary and secondary schools, as well as the development of TEM as a means of studying the dynamic properties of molecules.”

But as the age of “cinematic chemistry,” or photographing real molecules, is rapidly approaching, Nakamura still believes chemists will continue to use old-school models for the foreseeable future.

“No matter how good the AR-TEM gets, it will never be able to capture the three-dimensional structure,” he says.

“Molecular models, which represent molecules three-dimensionally by using different colors of spheres for different types of atoms, are essential for the intuitive understanding of molecules and will continue to help both chemists and the general public understand molecules.”

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