Now you see me!

There once was a time, long ago, when I was told that “atoms are the smallest things in the world, and we will never be able to see them.” Who knew then that science would advance to such an extent that not only can we distinguish atoms, but can detect intermolecular interactions and observe chemical reactions as they happen!

These discoveries have all been made possible by the advancement of a technology called atomic force microscopy (AFM). This is a technique where a cantilever taps a surface as it sweeps over it, feeding back information about how far the lever has to dip in order to touch the said surface, enabling the user to create a 3D map of the sample. For a more detailed explanation of how AFM works, have a look at the first few slides of this animated slide show:

For a number of years, AFM has been used to capture images of things like strands of DNA on a surface, as shown above. This year, however, there have been significant advancements in the field that have allowed us to see much, much more. Not only is it now possible to see bonds between individual atoms in molecules, but an actual chemical reaction has been observed!

atomic force microscope images
Images taken using a microscope (top) and AFM (middle), compared to their molecular structure diagrams (bottom)

The picture above shows snapshots of a chemical before and after it has been chemically transformed. There are some red/yellow blurs taken using a microscope and it’s fair to say that you can’t really tell what they are. In the middle images taken using AFM, however, it is much easier to distinguish the structures of the molecules – they even resemble the drawn representations that scientists typically use to draw molecules! As a scientist and a chemist, this is hugely exciting. Who knows what the future of AFM could be? Maybe we might one day be able to observe reactions in real-time, and conventional methods of characterisation like NMR (which is presently the instrument that can tell you the most about what your molecule looks like) might one day become obsolete?

That research was published in May of this year, and yesterday even more astonishing research was published. The image below shows four molecules interacting with each other using hydrogen bonds. Hydrogen bonds are one of, if not the most important intermolecular interaction. They water its unusual properties, they hold together our double stranded DNA helices, they reinforce fibres such as nylon, as well as many other things; but they have never been witnessed until now (because they are much less strong than actual chemical bonds).

An AFM image (left) of four molecules(8-hydroxyquinoline) hydrogen bonding with each other, compared to another representation used by chemists to draw molecules. Grey = carbon, white = hydrogen, blue = nitrogen, red = oxygen, dotted line = hydrogen bond.

This is, again, a massive breakthrough for science. Being able to see the ways in which molecules interact with each other could not only give us information about how some chemical reactions proceed, but why they proceed in that way.

All in all, this research leaves me very excited about where science can go, the amount of power a chemist may one day have to analyse molecules, and in eager anticipation of the day I get to use an AFM machine and see an atom or molecule for myself.

For more of my blogs go to

Science340 (2013), 1434-1437 (DOI: 10.1126/science.1238187)
Science (DOI: 10.1126/science.1242603)

Dan Jenkinson

Final year chemistry student at the University of Sheffield, wanting to share my love for science with the world.

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