CiQUS and IBM Scientists Trigger and Observe Reactions in an Individual Molecule

In a new paper published today in the peer-review journal Nature Chemistry (link is external), scientists from IBM Research (link is external), in collaboration with CiQUS, have observed a fascinating molecular rearrangement reaction known as a Bergman cyclization for the first time on the atomic scale. The reaction was first described in 1972 and is named for the American chemist Robert George Bergman.

Prof. Diego Peña, a chemist at the University of Santiago de Compostela and co-author of the paper, explains the significance, “At first the rearrangement was simply considered a curiosity, but in the late 1980's it was discovered in the mechanism of action for some anticancer drugs, which are based on this reaction. This naturally attracted a lot of attention from the scientific community and now it's a very popular reaction in organic chemistry”.

The secret to imaging the Bergman reaction is a technique known as atomic force microscopy (AFM), which makes use of a very sharp tip to measure tiny forces between the tip and the sample.

The AFM was first demonstrated in 1986 by IBM scientists Gerd Binnig, Christoph Gerber and Calvin Quate from Stanford University. Binnig who is solely listed on the first patent was quoted in IEEE Magazine in 2004 saying that the idea for the AFM came to him subconsciously while he was lying on the couch. Not long afterwards Binnig and his colleague the late Heinrich Rohrer received the Nobel Prize for the AFMs predecessor the scanning tunneling microscope (STM).

More recently, IBM scientists in Zurich have modified the tip of their AFM with a single carbon monoxide molecule. This diatomic molecule, which is less than a nanometer long, produces images so clear that scientists are able to study the sample’s chemical nature based on the minute differences between individual bonds.

The IBM team, led by Gerhard Meyer and Leo Gross, first published their technique in 2009 in the journal Science by producing a stunning image of the flat molecule pentacene. During the next several years they worked on refining the technique and pushing its limits beyond what they expected.

Gross comments, “One main differentiator of our technique with respect to other established techniques is that we measure single molecules. Another advantage is that we can use the tip to initiate chemical reactions of individual molecules and we can follow the reactions and study their products at the atomic scale.”

A few years later in 2012 the team produced a string of breakthrough science including measuring the electric field produced by a single molecule, a demonstration of bond-order discrimination and in 2013 the exact measurement of adsorption geometries.

During this period of successful publications the team began receiving requests from scientists around the world including a professor at Aberdeen University, who proposed to use their technique to identify a previously unknown molecule. The molecule was found in a sea organism collected from the deepest place on Earth, which the team successfully imaged to be cephalandole A, a molecule previously isolated from a Taiwanese orchid.

With their latest work, appearing today, the team has found another application for their technique, the ability to induce chemical reactions as in the Bergman cyclization.

“Working at low temperatures and on special, inert surfaces, like the two atom thick layers of salt that we used in our paper, we are able stabilize reactive intermediates that under normal conditions are too short-lived to be studied in detail. Not only can we form highly reactive intermediates using the tip to create and cleave bonds within the molecule, we can even switch between different reaction intermediates. Remarkably, we change almost all important properties of these molecules by switching them, affecting their reactivity, structure and their optic, electronic and magnetic behavior,” said Gross.

Prof Peña comments, “This work suggests the great potential of this technique to discover new unexpected reactions. In conventional solution chemistry, after so many decades of rigorous research, the chances to find new important reactions are quite limited. Compared to this, single molecule chemistry by tip manipulation is in its infancy and I expect extremely exciting discoveries in the near future.”

The next steps for the team will be to synthesize large custom designed molecules and molecular networks with the tip that cannot be made by any other means. The team is also interested in exploring new applications for molecules, such as molecular logic devices based on single electron transfer.

Bruno Schuler, an IBM postdoc and first author of the paper adds, “The molecules we have investigated here are promising building blocks for molecular logic devices. We can envision forming networks with covalent bonds established between these radicals. Moreover, the switching of the molecules, effecting its transport and magnetic properties, might be useful functions for such devices in the future.”