Products of chemical reactions involving organic compounds are typically characterized by analysing bulk samples with techniques such as NMR spectroscopy, mass spectrometry and — if you are lucky enough to get good-quality crystals — X-ray crystallography. Advances in scanning probe microscopies have, however, reached a point where it is possible to image single molecules resting on a surface and, in some cases, can reveal the precise bonding arrangement of the constituent atoms. Although it would be impractical to determine the structure of every single product molecule from a given reaction in this way, direct imaging can potentially provide structural information that may be difficult to glean from other techniques.
Now, a team of researchers from the USA and Spain led by Michael Crommie and Felix Fischer have taken 'before' and 'after' pictures of individual oligo(phenylethynylene) molecules that undergo various thermally activated isomerization reactions on a silver surface. Images of the starting material and products were captured with a scanning tunnelling microscope, and the different blob-like features present on the surface following the reaction suggested that a range of products are formed. Higher-resolution images obtained using non-contact atomic force microscopy — in which the tip of the microscope is functionalized with a single CO molecule — revealed the different covalent-bond frameworks (pictured) of the molecules formed in a series of cyclization reactions.
For the two most abundant products, Crommie, Fischer and co-workers investigated possible reaction pathways with density functional theory calculations. The starting material can be considered to be made up of overlapping enediyne systems that can undergo a range of different reactions, including Bergman cyclizations and radical shifts. For each reaction, it was found that the initial cyclization process presents the highest energy barrier and so is the rate-determining step. The different products arise from the possibility of cyclization reactions giving 4-, 5- or 6-membered rings, with 5-membered rings seemingly more favoured under the experimental conditions used in this study than is usually the case.
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Cantrill, S. Structural snapshots. Nature Chem 5, 640 (2013). https://doi.org/10.1038/nchem.1723