Imaging Breakthrough: See Atomic Bonds Before and After Molecular Reaction

ORIGINAL: Wired

By Nadia Drake
05.30.13

A ringed, carbon-containing molecule, shown both before and after it has rearranged itself, with the two most common reaction products included. The scale bars measure 3 angstroms, or three ten-billionths of a meter, across. Image and Caption: Lawrence Berkeley National Laboratory and University of California at Berkeley

The reactant molecule, shown on a silver surface, before rearrangement into products. Image: S. Wickenburg, A. Riss, D. J. Mowbray, F. R. Fischer

Product 2 is one of the two most common molecules produced. Image: S. Wickenburg, A. Riss, D. J. Mowbray, F. R. Fischer

Product 3 is one of the two most common molecules produced. Image: S. Wickenburg, A. Riss, D. J. Mowbray, F. R. Fischer

Product 4 is an unexpected reaction molecule. Image: S. Wickenburg, A. Riss, D. J. Mowbray, F. R. Fischer

The team predicted the existence of Product 5, but it accounted for less than 1 percent of the reaction mixture. Image: S. Wickenburg, A. Riss, D. J. Mowbray, F. R. Fischer

For the first time, scientists have visually captured a molecule at single-atom resolution in the act of rearranging its bonds. The images look startlingly similar to the stick diagrams in chemistry textbooks.

Until now, scientists were only able to infer molecular structures. Using atomic force microscopy, the individual atomic bonds — each a few ten-millionths of a millimeter long – that connect the carbon molecule’s 26 carbon and 14 hydrogen atoms are clearly visible. The results are reported online May 30 in Science.

The team initially set out to precisely assemble nanostructures made from graphene, a single-layer material in which carbon atoms are arranged in repeating, hexagonal patterns. Building the carbon honeycombs required rearranging atoms from a linear chain into the six-sided shapes; the reaction can produce several different molecules. UC Berkeley chemist Felix Fischer and his colleagues wanted to visualize the molecules to make sure they’d done it right.

To document the graphene recipe, Fischer needed a powerful imaging device, and he turned to the atomic force microscope housed in physicist Michael Crommie’s UC Berkeley lab. Non-contact atomic force microscopy uses a very fine, sharp point to read the electrical forces produced by molecules; as the tip is moved near a molecule’s surface, it’s deflected by different charges, producing an image of how the atoms and bonds are aligned.

With it, the team managed to visualize not only the carbon atoms but the bonds between them, created by shared electrons. They placed a ringed carbon structure on a silver plate and heated it until the molecule rearranged. Subsequent cooling trapped the reaction products, which as it turned out, contained three unexpected products and one molecule the scientists had predicted.