A preliminary scanning tunnelling microscopy study of the surface-organised structures of gramicidin S hydrochloride on highly oriented pyrolytic graphite

For an initial study of potentially surface-structural self-organising systems of biological significance by scanning tunnelling microscopy (STM), gramicidin S, a pseudocentrosymmetric cyclodecapeptide with antibiotic properties, was chosen as prototype, recognising its structure as having both intramolecular and intermolecular hydrogen-bond forming propensity. The surface-organised structures, based on gramicidin S hydrochloride deposited on a highly oriented pyrolytic graphite (HOPG) substrate, have been observed by STM in air under ambient conditions. These are characterised in the main by rectangular or rectangle-like structural elements identified with the individual gramicidin S hydrochloride molecules. Two kinds of arrangements of gramicidin S hydrochloride in a two-dimensional array are found, i.e., as a centred rectangular lattice and a primitive rectangular lattice. The STM topographical arrays and the molecular dimensions obtained are in good quantitative agreement with the corresponding X-ray crystallographic data. The differences between the STM results, the theoretical models, and the X-ray crystallographic data are attributed to the intermolecular interactions present in the three-dimensional gramicidin S crystal but absent in the lower dimensional arrays and to the environments in which a gramicidin S hydrochloride molecule finds itself during deposition and drying on the HOPG substrate.