A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

Abstract

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 polymorphdependent 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.self-assembled monolayers | density functional theory | dispersion | free energy | polymorphism A priori calculations of the free energies of chemical reactions using density functional theory (DFT) and/or ab initio methods are now well established for gas-phase processes (1, 2), gas surface reactions (3), and, using continuum self-consistent reaction field (SCRF) methods, for condensed phase processes also (4). Over the last few years, a major advance in computational methods has occurred, however, allowing for rapid and accurate evaluation of intermolecular dispersion interactions. This makes feasible similar SCRF calculations for physisorption, macromolecule structuring, and other self-assembly processes in condensed phases. We present the first application of this type, to our knowledge, considering the free energy of formation of various polymorphs of tetraalkylporphyrin self-assembled monolayers (SAMs) at solid/liquid interfaces on highly ordered pyrolytic graphite (HOPG) surfaces. Calculated structures and free energies are used to interpret new and existing high-resolution scanning tunneling microscopy (STM) images, focusing on the critical roles played by the dispersion interaction in driving SAM formation and by entropy and dispersion-based desolvation effects that oppose it.Calculating a priori free energies for SAM formation from solution is a significant challenge. Accurate representations of the substrate−molecule energies, the intermolecular energies, the solvent interaction energies, and the effects of solvent structure are required, a set of tasks that, with a few exceptions (see e.g., refs. 5 and 6), has remained prohibitive a priori. Alternatively, model calculations have been useful for identifying key qualitative features (7-11), whereas some full molecular dynamics si...

Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology

“…[368,369] The molecular structures determined from modelling of large areas of the L and M polymorphs are shown, as is how they seamlessly meld together to form the interface layers. The L polymorph is observed for all odd-length chain molecules studied (lengths m from 11 to 19) [253,363,366,368] but not for the even chain Free-electron gas, exact description n molecule studied, 2H-C 12 P, [364,365] while three M polymorphs [253,364,365,368] of quite different form named M a , M b , and M c are observed for 2H-C 11 P, 2H-C 12 P, and 2H-C 13 P, respectively. The L structures have all four alkyl chains lying flat on the surface while the M polymorphs have two such chains with the other two somehow oriented into the solution.…”

“…Our work has focussed on the self-assembly of tetraalkylporphyrin molecules synthesized by Max Crossley on highly ordered pyrolytic graphite (HOPG) surfaces from solution in 1-phenyloctane, octanoic acid, or n-tetradecane. [253,[363][364][365][366][367][368] This involved measurement of STM images and the simulation [253,363,369] of the Gibbs free-energy of formation for a wide range of possible atomic structures for each image. The molecules considered are shown in Chart 2.…”

“…After optimization, only at most 22 stable SAMs were realised, named Ma to Mv. Structure assignment was made by comparing these structures to experiment, considering: [253,363,366,369] -Agreement of observed and calculated lattice parameters. To do this, new experimental techniques based on internal calibration and repeated measurements were developed to significantly reduce the experimental uncertainties in the lattice parameters, allowing for discrimination between the calculated structures.…”

“…7), and the development of molecules (see later) and methods for measuring the free energy of polymorphism of self-assembled monolayers on hydrophobic surfaces. [253] That we were able to predict and design functional system properties for Crossley's molecules [244,249,250,[254][255][256][257][258] provided an important aspect to their success. These predictions integrated the traditional electron-transfer theories of Hush with the parallel understandings of Craig, as described in the preceding section.…”

Voltammetry and molecular assembly of G-quadruplex DNAzyme on single-crystal Au(111)-electrode surfaces – hemin as an electrochemical intercalator

“…Both hydrophobic and hydrophilic interactions act among the hemin molecules in the monolayer. The hemin molecule at the center is moreover mirror symmetric relative to the molecules at the corners of the rectangle, and the pairs stabilized by both hydrogen bonds and hydrophobic interactions between the hemin side groups [48][49][50][51] . …”