Substrate-induced supramolecular ordering of functional molecules: theoretical modelling and STM investigation of the PEBA/Ag(1 1 1) system Original Research Article

We model the geometry, binding site and absolute orientation of the self-assembled monolayer of 4-[pyrid-4-yl-ethynyl] benzoic acid (PEBA) adsorbed on the (1 1 1) surface of silver by means of molecular dynamics and first principles calculations, and compare these results with those we obtain from scanning tunneling microscopy experiments. Our results indicate that the adsorbate–substrate interaction controls the overall orientation of the self-assembled molecular superstructures. We investigate the nature of this interaction, which is found to induce some degree of readjustment of the molecular structure and substantial stretching of the inter-molecular hydrogen bonds. This is consistent with the nodal structure of the interaction-induced ab initio differential charge density, which can be interpreted in terms of a simple extended Hückel model.