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© 2016 American Chemical Society. We demonstrate that systematic errors can be reduced and physical insight gained through investigation of the dependence of free energies for meso-tetraalkylporphyrin self-assembled monolayers (SAMs) polymorphism on the alkyl chain length m. These SAMs form on highly ordered pyrolytic graphite (HOPG) from organic solution, displaying manifold densities and atomic structures. SAMs with m = 11-19 are investigated experimentally while those with m = 6-28 are simulated using density-functional theory (DFT). It is shown that, for m = 15 or more, the alkyl chains crystallize to dominate SAM structure. Meso-tetraalkylporphyrin SAMs of length less than 11 have never been observed, a presumed effect of inadequate surface attraction. Instead, we show that free energies of SAM formation actually enhance as the chain length decreases. The inability to image regular SAMs stems from the appearance of many polymorphic forms of similar free energy, preventing SAM ordering. We also demonstrate a significant odd/even effect in SAM structure arising from packing anomalies. Comparison of the chain-length dependence of formation free energies allows the critical dispersion interactions between molecules, solvent, and substrate to be directly examined. Interpretation of the STM data combined with measured enthalpies indicates that Grimme's D3 explicit-dispersion correction and the implicit solvent correction of Floris, Tomasi and Pascual Ahuir are both quantitatively accurate and very well balanced to each other.

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

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. © 2010 American Chemical Society.

Self-assembled supramolecular structures such as optical wires, films and 2D slabs offer a new generation of electronic and optical devices. In particular, self-assembled porphyrin devices, including those integrated onto silica and silicon platforms, open new opportunities in photonic applications spanning molecular biosensing, photovoltaics and telecommunications. All reports to date, however, largely highlight the potential but have not established a clear pathway to the actual implementation of more complex device prototypes. In this paper, we propose and demonstrate the use of a focused ion beam (FIB) to process and fabricate devices in porphyrin-based supramolecular structures. These self-assembled structures have an initial root mean squared (rms) values for surface roughness of0.5 nm as measured by atomic force microscopy. Under appropriate FIB processing and cutting conditions, the rms value for surface roughness falls to0.4 nm, comparable with some of the best optical flatnesses obtained within, for example, structured optical fibres and integrated optical waveguides. The milling rate of the porphyrin structures was estimated to be approximately 70% of that of silica. The versatility of a FIB as a tool for rapid processing and fabricating 1D and 2D photonic waveguide structures within supramolecular self-assembled platforms is demonstrated by fabricating a 2D coupler, setting the groundwork for true optical device engineering and integration using these new organic systems.

Long porphyrin molecular wires presenting optical transparency and light diffraction are fabricated and characterized using optical and atomic force microscopy. The development of dual photonic/electronic self-assembled devices is discussed.

Self-assembled microrods {based on 5-nitro-10,15,20-trialkylporphyrins [(CnH2n+1)3-NO2P]} and microplates {based on 5,10,15,20-tetraheptylporphyrin [(C7H15)4-P]} are fabricated and characterised using optical microscopy, atomic force microscopy (AFM), and scanning electron microscopy (SEM). The length of the alkyl chains and the deposition surface are found to influence the optical properties and microrod self-assembly. When the deposition surface is silica (α-quartz), 5-nitro-trialkylporphyrins, (C5H11)3-NO2P, (C7H15)3-NO2P and (C11H23)3-NO2P all form microrods of 0.7–0.8 micron diameter; the average length of the microrods varies from 170 microns for (C5H11)3-NO2P to about 11 microns for (C7H15)3-NO2P and (C11H23)3-NO2P, whereas (C19H39)3-NO2P with much longer alkyl chains only gives powders. Controlling the precipitation is crucial in preventing the disordered aggregation of assembled layers observed in the bulk. Very interestingly, the microrods formed from (C7H15)3-NO2P show marked iridescent character. When (C7H15)3-NO2P is deposited on silicon, however, longer curved microrods which do not show iridescence are produced. Single crystal X-ray crystallography of (C7H15)3-NO2P reveals the packing of the bulk material which explains the packing topology of the layers observed by AFM but not the iridescence. The observed structural colour of the (C7H15)3-NO2P microrods is explained by staggering of the layers to produce a corrugated surface with a period of 125 nm, as measured by AFM.