A better way to see molecules

A new modelling system could make electron microscope pictures easy to understand.

This resource is best suited to Year 8, 9 and 10 Chemistry students who are learning about elements, the periodic table and atomic structure.

Word Count: 685

The ball-and-stick molecular model. Credit: John Lamb / Getty Images

What does a molecule look like? This isn’t 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 range of different symbols and models to represent them.

A team of Japanese researchers have come up with a way to combine these two things, with a molecular modelling system based on electron microscopy. While it looks similar to the ball-and-stick model you might have used in high school, their model conveys much more information – through the sizes of the atoms.

They say that their system, called the ZC model, represents molecules in a way that will help chemists’ intuition when dealing with pictures of very tiny things. They hope it will become a useful educational tool, too.

The ZC model, and the way they figured it out, is described in a paper in PNAS.

Molecular models predate actual images of molecules by over a century. Three-dimensional molecular models are crucial to chemists’ work – whether 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 might have seen in movies, they don’t show up on the screen like smooth, easy-to-comprehend balls. In fact, it’s difficult to spot any similarities between a TEM image and a model of a molecule at all.

“The ball-and-stick model is far too simple to accurately describe 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 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 [atomic resolution transmission electron microscopy] show.”

Harano and colleagues addressed this by looking very closely at how TEM images correlated to the atoms and molecules they knew were present.

They found that the size of an atom in a TEM image was linked closely to its atomic number. (Atomic number, or mass number, is an element’s number of protons, and the big number attached to each atom in the periodic table. Hydrogen’s atomic number is 1, and carbon’s is 6, for instance.)

They used this information to suggest a new way to depict molecules, where every atom is sized differently according to its atomic number.

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

Electron microscope imagery of molecules (far left), followed by the ZC model of the atoms, the CPK model, and drawings of molecules (far right). Credit: © 2021 Nakamura, Harano et al.

“The creation of this model has greatly accelerated our research,” says Nakamura. “Previous molecular models could not explain well the molecular images in the TEM.”

He says that their model could eventually help chemists to figure out things like molecular structure from TEM images. At the moment, while TEM is useful for other things, it’s nowhere near as effective as conventional analytical techniques for figuring out molecules’ shape.

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

“Using the ZC model, it is now possible to predict molecular structure from the actual TEM image with a fairly high degree of accuracy. This has opened up the possibility of using TEM in primary and secondary education as well as the development of TEM as a means to study the dynamic properties of molecules.”

But, while the age of “cinematic chemistry”, or photographing actual molecules, is fast approaching, Nakamura still thinks that chemists will be using the old-school models for the foreseeable future, too.

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

The periodic table of elements – by size. The CPK model, top, depicts the distribution of electrons around an atom. This is different to the size of the atom’s nucleus, which is depicted below in the ZC model. Creedit: © 2021 Nakamura, Harano et al.

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

Learn more about this research on Cosmos.

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Years: 8, 9, 10


Chemical Sciences – Atoms, Particle Models

Additional: Careers, Technology, Engineering.

Concepts (South Australia):

Chemical Sciences – Properties of Matter, Change of Matter