Atomic force microscope reveals ghostly molecules

A new technique has helped researchers take snapshots of molecules in chemical reactions and begin to build a toolbox that will help design or improve catalytic reactions.

The team of researchers at University of California, Berkeley, and Lawrence Berkeley National Laboratory has used non-contact atomic force microscope, or nc-AFM, to capture the fleeting molecular structures that reacting chemicals form on their way to a final product.

In a paper put online this week in advance of publication in the journal Nature Chemistry, the researchers reported that they had taken snapshots of two molecules reacting on the surface of a catalyst, and found intermediate structures lasting for the 20 minutes or so it takes to snap a photo.

Chemical reactions often take place within picoseconds, or a trillionth of a second, a process so rapid that chemists expect intermediate steps in the reaction to be too brief to observe. Only lasers firing in femtosecond bursts can capture the fleeting molecular structures that reacting chemicals form on their way to a final product.

"Intuitively, we did not expect to see these transient intermediates, because they are so short lived," said Felix Fischer, an assistant professor of chemistry at UC Berkeley. "Based on our traditional understanding, you would expect to see the starting materials and very shortly after, only the product. But we see these intermediates, so something else is going on."

The explanation for these intermediates, or ghostly molecules, is now fleshing out details of catalytic reactions that chemists have only vaguely understood until now, and providing new rules for chemical reactions that chemists can exploit to make reactions go faster or more efficiently, or build molecules never before seen.

Fischer is beginning to build a toolbox that will help design or improve catalytic reactions, which are the workhorse of the world's chemical industry, responsible for producing everything from fuel to the building blocks of plastics, according to a news release from UC Berkeley on Monday.

The tools could also impact fields such as materials science, nanotechnology, biology and medicine.

In the past, chemists could only infer how chemicals change during the process, as bonds between atoms break and reform, branches rotate or join to form rings, and three-dimensional structures shift.

Three years ago, Fischer and UC Berkeley's Michael Crommie, a professor of physics, teamed up to apply atomic force microscopy to take snapshots of molecules before and after a reaction, trying to confirm what chemists have always inferred.

The nc-AFM hovers above a surface and detects individual atoms via a microscopic vibrating probe with a sensitive carbon monoxide molecule at its tip.

Fischer, Crommie and their colleagues place molecules on a gold or silver surface and heat them to make them react slowly, then use the nc-AFM to take snapshots over the course of the reaction.

During their first attempt to image a reaction between two molecules, they saw not only the starting chemicals and end product, but also two intermediate chemical structures that should not have been there.

Fischer used his growing toolbox last year to make a molecule that was predicted more than half a century ago but unachievable using standard organic chemistry in solution. Instead, he built it on the surface of a catalyst from custom-made molecules that would normally not react in the right way.

"We used this toolbox of surface chemistry and the rules we have learned to make a molecule that no one had been able to make in 60 years," he said.

"This is an example of why it is important to understand what is happening on these surfaces, and how you can use this understanding to access structures and reactivities that are not accessible with the standard tools we have right now." Endit