AFM rules: Supports spectroscopic insights

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  • Published: May 15, 2016
  • Author: David Bradley
  • Channels: Atomic
thumbnail image: AFM rules: Supports spectroscopic insights

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An atomic force microscope was able to take a snapshot of the atoms before and after the reaction, but also found two supposedly short-lived intermediates (center) in this reaction of two enediyne molecules. Credit: UC Berkeley

Non-contact atomic force microscopy has been used to investigate simple chemical reactions at atomic resolution confirming what chemists knew from spectroscopy. The research offers new rules for predicting the properties of catalytic reactions and for designing novel catalysts.

The bond making and breaking in common chemical reactions happen on a timescale far too short to capture the intermediate stages using conventional analytical techniques without recourse to some way of freezing the action. Of course, these changes, occurring in picoseconds can sometimes be snapped if the flashgun of one's "camera" is a femtosecond burst of laser light. The burst of light virtually freezing the action as dancers under a strobe light in a nightclub.

However, chemists and physicists at the University of California, Berkeley, and Lawrence Berkeley National Laboratory point out that some intermediate structures on the surface of a catalyst are less photogenic. "Intuitively, we did not expect to see these transient intermediates, because they are so short lived," explains Berkeley's Felix Fischer. "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."

Force for good

Three years ago, Fischer and Berkeley physicist Michael Crommie teamed up to apply the atom-scale precision of atomic force microscopy to take snapshots of molecules before and after a reaction, trying to confirm what chemists have always inferred. Fischer and his colleagues are now putting together the 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. These tools could also impact fields such as materials science, nanotechnology, biology and medicine.

"The way chemists think about heterogeneous catalysis appears to be an incomplete picture of what is actually happening on the surface," Fischer explains. "If we can understand how to take this tool box and use it in the design of new structures or the synthesis of new materials, that opens a whole new field of chemistry that so far has been dark to us, because we did not know how to actually visualize what is going on."

Writing in the journal Nature Chemistry, the team explains how nc-AFM, hovers above a surface and detects individual atoms via a microscopic vibrating probe with a carbon monoxide molecule at its tip. Molecules placed on a gold or silver surface and heated can be snapped with the AFM tip as the reaction takes place. The details that are becoming apparent provide new insights into catalytic reactions of which chemists previously had only a vague notion.

Chemistry to a different tune

In their preliminary work, imaging a reaction between two molecules revealed not only the starting chemicals and the final product, but also two unexpected intermediate chemical structures. The intermediates of complicated rearrangements are slower because of their higher energy barrier and would be expected, but the team was observing intermediates that should have disappeared the fastest based on current theories.

Insights from chemical engineering rather than organic chemistry were invoked to explain this unexpected observation. In chemical engineering terms, some intermediate states are bound more closely to the catalytic surface and lose energy to it, slowing the reaction. So, rather than rolling downhill towards the final product, it is as if the reaction slams into a rock on the way down.

Fischer's colleague, Angel Rubio of the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg and the University of the Basque Country in Spain, carried out extensive supercomputer calculations on the surface binding and could not predict the intermediates the team observed. It was not until they added in the entropy that each step of the observed reaction began to mesh with the calculations. It was as if some transitions that seem energetically favourable were inhibited because they shift from a flexible loosely bound structure - a high entropy state - to a more rigid, tightly bound and thus lower-entropy position.

"Taking entropy into account could help you understand the distribution of products you get from a heterogeneous catalysis reaction," Rubio explains. "It could help you predict which intermediates have a long lifetime on the surface, which ones could move around, adsorb or desorb from the surface, leading to a product distribution that might not be what you want. Then you could tune the reaction towards the product that you desire."

"Our goal is to use the unique surface reactivity to make molecules/reactions possible that have been inaccessible using traditional techniques," Fischer told SpectroscopyNOW. "One example is the synthesis of peripentacene. It was first proposed by Clar more than 60 years ago but nobody had been able to make it. We demonstrated that the tools we learned from studying surface reactions can be used to make these molecules for the first time. This is very exciting as they have very exotic physical properties that emerge from the structure (an antiferromagnetic ground state) and could have very interesting applications for optical or magnetic devices."

Related Links

Nature Chem 2016, online: "Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy"

Article by David Bradley

The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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