Taking an image of an individual molecule while it undergoes a chemical reaction has been deemed one of the holy grails of chemistry. Scientists at the University of Berkeley and the University of the Basque Country (UPV-EHU) have managed, for the very first time, to take direct, single-bond-resolved images of individual molecules just before and immediately after a complex organic reaction. The images enable appreciating the processes of the rupture and creation of links between the atoms making up a molecule. The article, entitled Direct Imaging of Covalent Bond Structure in Single-Molecule Chemical Reactions, appears today, the 30 of May, in the online Science Express as an outstanding research work and will be published in the print edition of Science in the middle of June. The authors are the teams of Felix Fischer (Department of Chemistry at Berkeley), Michael Crommie (Department of Physics at the same university) and Ángel Rubio (Professor at the UPV/EHU and researcher at the CSIC-UPV/EHU Centre for the Physics of Materials and at the Donostia International Physics Center). The lead author of the article is Mr. Dimas Oteyza, who has just been reincorporated into the CSIC-UPV/EHU Centre for the Physics of Materials after his postdoctoral term in Berkeley.
Organic chemical reactions are, in general, fundamental processes that underlie all biology, as well as highly important industrial processes, such as the production of liquid fuel. The structural models of molecules that we have traditionally relied on to understand these processes come from indirect measurements averaged over an enormous number of molecules (in the order of 1020) as well as from theoretical calculations. Nobody has ever before taken direct, single-bond-resolved images of individual molecules right before and immediately after a complex organic reaction.
“The importance of our discovery is that we were able to image the detailed microscopic structures that a molecule can transform into on a surface, thus allowing us to directly determine the microscopic atomic motions that underlie these chemical transformations”, explained Ángel Rubio. More specifically, researchers were able to record highly resolved images of an oligo-enediyne (a simple molecule composed of three benzene rings linked by carbon atoms) deposited on a flat gold surface. The technique used is called non-contact Atomic Force Microscopy (nc-AFM), based on an instrument with an extraordinarily sensitive tactile probe. This AFM uses a very fine needle that can sense even the smallest atomic-scale bumps on a surface in much the same way that you would use the tip of your fingers to read/feel a word written in Braille. Given that the oligo-enediyne molecules studied are so small (~10–9 m) the probe tip of this instrument was configured to consist of only a single oxygen atom. This arises from a single carbon monoxide (CO) molecule adsorbed onto the AFM microscope tip and acting as an “atomic finger” in tactile reading.”
By moving this “atomic finger” back and forth along the surface they obtained height profiles corresponding to the precise positions of atoms and chemical bonds of the oligo-enediyne molecules studied. Recent advances in this microscopy technique have made it so precise that we can even distinguish the bond order between carbon atoms (single or double or triple bonds). On heating the surface supporting our molecules, they induced a chemical reaction that is closely related to “cyclisations”. Cyclisations, discovered by Berkeley Professor Bergman in the early 1970s, cause carbon atoms linked in chains (aromatic rings) to “fold up” into closed-ring formations. “The height profiles we recorded after the molecules react clearly show how new chemical bonds are formed and how atoms within the molecules rearrange to form new structures”, explained Dimas Oteyza. The results have been interpreted and analysed microscopically thanks to simulations carried out by Mr Rubio’s team.
Apart from achieving surprising visual confirmation of the microscopic mechanisms underlying theoretically predicted organic chemical reactions, this work has relevance in the manufacture of new, high-precision customised materials and electronic apparatus at a nanometric scale.