Atomic Images May Aid Structure Elucidation

Chemists may soon be able to routinely use atomic-resolution scanning probe microscopy (SPM) to help identify unknown organic molecules. The technique could assist structural characterization methods such as X-ray crystallography and NMR spectroscopy in identifying molecules with planar substructures, according to Leo Gross of IBM Research, in Zurich, and colleagues (Nat. Chem., DOI: 10.1038/nchem.765). Gross and coworkers first demonstrated SPM’s structure-elucidating potential last year on the planar molecule pentacene (C&EN, Aug. 31, 2009, page 6). They have now tested the ability of the technique to highlight the structural features of a natural product, cephalandole A, an alkaloid whose initially assigned structure was found to be wrong and then later corrected. The researchers note that interpretation of NMR and mass spectrometry data can lead to three different possible structures for the compound. But with SPM—which provides an outline of the planar parts of the structure—coupled with density functional theory calculations, the images produced led straight to the correct structure.