Reaction Snapshots

High-resolution atomic force microscopy (AFM) has been extended to a new application—taking before and after pictures of ­individual molecules as they undergo a chemical reaction.

A group led by chemistry professor Felix R. Fischer and physics professor Michael F. Crommie of the University of California, Berkeley, used AFM to image an enediyne compound and its thermally induced cyclization products on a silver surface (Science 2013, DOI: 10.1126/science.1238187).

The researchers chose the enediyne system to study because they thought it would lead to graphenelike structures, Fischer says. He and his colleagues are interested in developing surface-supported reactions that will yield such structures for molecular electronics applications.

Enediynes undergo a variety of competing cyclization processes, producing a multitude of products that are challenging to identify. Structural identification techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy sometimes fail, such as when all of the products have the same mass and NMR spectra of product mixtures have overlapping peaks that are hard to resolve.

AFM made headlines several years ago when IBM researchers released images of atoms and bonds in single molecules of pentacene. That technique has since been used to aid structure determination of natural products, identify bond-order differences between individual bonds in C₆₀ and polycyclic aromatic hydrocarbons, and reveal interconversions between dibenzo[a,h]thianthrene isomers.

In the new work, Fischer, Crommie, and their colleagues deposited 1,2-bis[(2-ethynylphenyl)ethynyl]benzene on a silver surface, imaged the molecules, and then heated the surface to greater than 90 °C to induce cyclization. They then imaged the products. They found that half of the molecules transformed into a polycyclic aromatic structure composed of five six-membered rings and two five-membered rings fused together. Another quarter of the molecules formed into a structure composed of four six-membered rings connected through one four-membered and two five-membered rings. The remaining products were oligomeric structures and minor polycyclic isomers.

Fischer says that the results surprised the team in two ways. One was that the reaction produces a relatively clean set of two major products. The other was the structure of those products. “From intuition and training, we could draw a dozen different products that we would expect to come out of the reaction,” he says. “None of them matches what happened on the surface.” In solution, the pathways to the products observed in the surface experiment have high activation barriers. The interaction of the molecules with surface atoms likely facilitated the unexpected chemistry, Fischer says.

The work “is a great example of what you can do with atomic force microsopy now,” says Leo Gross, a staff researcher at IBM’s Zurich research center. Gross led the team that visualized pentacene and has carried out several AFM molecular imaging studies since. AFM continues to demonstrate its potential for structure determination, especially as the technique is further refined to reveal more atomic detail, Gross says.