Seeing Molecules: Kekulé's Dream Writ Large

As a chemist in a former life, I can't help but comment on this watershed moment in science, even though it's probably been blogged to death. Nanotechnologists at IBM Zürich have imaged the naturally occurring organic molecule pentacene (essentially, 5 benzene ring-molecules bolted together in a row). Why is this a big deal?


First off, it's just astounding to see an image of an organic molecule that actually looks so much like the molecular models (the balls and sticks below the image) that were (are still?) so commonly used for demonstations in chem lectures. Linus Pauling would be impressed, I imagine. But there's much more to this image than meets the eye.

A word of caution: Roughly speaking, the diameter of a carbon atom is about 1/3rd of a nanometer or 3.3 × 10^-10 m. The bond length between each carbon atom in benzene is known to be 140 pm or 1.4 × 10^-10 m, which is a carbon atom radius. In other words, the stick and ball model is rather misleading with respect to the relative size and spacing of atoms and the overlap between electron orbitals. I don't know enough about the imaging technique to interpret the detailed structure of actual pentacene and thereby account for why the two images are so much alike.

One hundred years ago, Albert Einstein was awarded his Ph.D. from the University of Zürich (not the ETH) for a thesis entitled, A New Determination of Molecular Dimensions. The conventional scientific wisdom of his time was that atoms were a useful concept (since Dalton) but they didn't really exist. Einstein was hell-bent on demonstrating that they did. To accomplish this goal, he used Boltzmann's molecular-kinetic interpretation of thermodynamics. In other words, the myriad of point particles in Boltzmann's equations actually corresponded to real atoms. As a consequence of publishing some papers related to his thesis, Einstein (along with some other researchers) did successfully convince the scientific community that molecules must indeed exist. Otherwise, it was next to impossible to explain such easily observed phenomena as surface tension, capillary action and Brownian motion.

Today, all this seems so obvious to us, we can hardly believe that the scientific community of 100 years ago was so skeptical. But don't feel too smug. Have you ever actually seen a molecule, up close and personal? Even Einstein claimed that we could never hope to see molecules. He was both right and wrong. He meant we couldn't see them by means of light in the visible region of the spectrum (which is correct), but today we have other ways of "seeing," viz., STM and AFM: forms of microscopy that use electron effects rather than visible photons.

Most of the images you've seen of crystalline surfaces, use STM microscopy. But STM doesn't work when it comes to creating the image of pentacene shown above. Like it's smaller constituent benzene—a single hexagonal ring of carbon atoms whose structure was originally guessed (possibly in a dream) by Friedrich Kekulé in 1865—the pentacene molecule is covered by a cloud of electrons that prevents STM from forming a clear image of the combined ring structure. Without getting into Molecular Orbital Theory (parts of which Linus Pauling helped to develop), here's a video animation of how the π-orbital hybridization forms two electron clouds that hover above and below the plane of the benzene ring, keeping it flat. Modern organic chemists depict these clouds symbolically by a circle inside the benzene hexagon (last diagram).

Here's the kicker for me. To penetrate pentacene's π-cloud, not only was the fine copper probe usually associated with AFM required, but it was also necessary to electrostatically pick up a single carbon monoxide molecule and dangle it from the end of that tip! (PDF See p. 8) The CO molecule conditions the probe so that it can see through the π-cloud. BTW, that pentacene molecule should be jumping and vibrating all over the place, according to Boltzmann. It isn't, not because Boltzmann was wrong, but because the image was produced at a temperature of 5 K (−268 °C) with the pentacene adsorbed to a copper substrate, thus removing most of its bulk kinetic energy.

If you consider the "old fashioned" stick and ball model of pentacene that has been used for many decades prior to the production of the above image, it strikes me as a stunning testament to how much science can know without seeing.