Atomic-Resolution Kinked Structure of an Alkylporphyrin on Highly Ordered Pyrolytic Graphite

The atomic structures of the chains of an alkyl porphyrin (5, 10, 15, 20- tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for prophyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and of the many possible atomic structure modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.