Influence of the solvent on the stability of bis(terpyridine) structures on graphite

Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics

This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an "on/off"-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system's π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO  is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.

How Equilibrium Gets Mimicked During Kinetic and Thermodynamic Control in Porphyrin and Phthalocyanine Self-Assembled Monolayers

The recent review of Hipps and Mazur is extended to consider the origins and significance of their conclusion that "surface structures vary with relative component concentration in a way that may mimic equilibria but is not". How this situation can arise during self-assembly is discussed, as well as a range of qualitative and quantitative observations and high-level free-energy calculations that document the effect for meso-tetraalkylporphyrins self-assembled monolayer (SAM) polymorphs. This leads to a discussion of modern challenges facing quantification of the effects caused by kinetic control, as well as to the usefulness of equilibrium mimicking in the design and synthesis of SAMs.

Role of solvents in the electronic transport properties of single-molecule junctions

We report on an experimental study of the charge transport through tunnel gaps formed by adjustable gold electrodes immersed into different solvents that are commonly used in the field of molecular electronics (ethanol, toluene, mesitylene, 1,2,4-trichlorobenzene, isopropanol, toluene/tetrahydrofuran mixtures) for the study of single-molecule contacts of functional molecules. We present measurements of the conductance as a function of gap width, conductance histograms as well as current-voltage characteristics of narrow gaps and discuss them in terms of the Simmons model, which is the standard model for describing transport via tunnel barriers, and the resonant single-level model, often applied to single-molecule junctions. One of our conclusions is that stable junctions may form from solvents as well and that both conductance-distance traces and current-voltage characteristics have to be studied to distinguish between contacts of solvent molecules and of molecules under study.

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

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.