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

Abstract

The atomic structure 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 porphyrin 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 structures 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.

Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

“…[87] Briefly, the QM/MM calculations are performed by GAUSSIAN [120] using the EXTERNAL command to supply a specialized molecule-HOPG interaction potential [113] fitted to experimental enthalpy data. [121] This is then combined with the standard AMBER force field [122] describing intermolecular interactions and the B3LYP/6-31G* [8,123] method describing the porphyrin.…”

“…All STM images are processed using our internal calibration and statistical methods to provide accurate lattice dimensions and image shapes. [113] Results…”

“…Four computational approaches are utilized to do this: [87,88,113] (1) A mixed quantum-mechanical/molecular (QM/MM) mechanical method utilizing the classic B3LYP hybrid density functional in conjunction with force fields for treating the intermolecular dispersion interactions. An advantage of this approach is that each individual aspect of the method has been independently verified for accuracy.…”

“…[87,88,113,115,116,117,118,119] This poses a serious technical challenge as electronic-structure computational methods treat surfaces using periodic boundary conditions, therefore demanding that the two lattices (or multiples thereof) be commensurate. The QM/MM calculations overcome this problem as the MM force field only is used for the intermolecular interactions and these are so efficient that a large real-space sum can be performed, including interactions up to very large distances.…”

“…The QM/MM calculations overcome this problem as the MM force field only is used for the intermolecular interactions and these are so efficient that a large real-space sum can be performed, including interactions up to very large distances. [113] However, this approach cannot be used for the DFT calculations and so we introduced a technique whereby all structures are optimized at 10-15 nearby commensurate lattices and the result of lowest free-energy taken. The effects of this approximation, in particular, need to be well understood.…”