Does the S-H Bond Always Break after Adsorption of an Alkylthiol on Au(111)?

The reaction mechanism for the formation of alkyl thiol self-assembled monolayers (SAM) on Au(111) is still not clearly understood. Especially, the role of defects on the chemisorption process is an important goal to be addressed. In this work, different minimum energy reaction paths for R-SH dissociation of thiols (with long and short chains and dithiol species) adsorbed on gold adatom are calculated by using periodic density functional theory (DFT). Our results show a lower energy barrier for the RS-H bond dissociation when two thiols are adsorbed per adatom. In addition, in contrast with the formation of an adatom at the Au(111) which has been shown to depend on the alkyl chain length, the activation energy of the RS-H bond dissociation of thiols adsorbed on an adatom was shown to be independent of the alkyl chain length. The presented results and derived hypothesis support the model that thiols with long alkyl chain thiols mainly adsorb molecularly on Au(111), while for short alkyl chain thiols the S-H bond breaks. This result is explained by the fact that short-chain thiols have lower interchain interaction energies and are thus more mobile compared to the long alkyl chain thiols on the Au(111) surface. This feature enables the short chains to reach adequate geometries, driven by entropy, which could deform the Au(111) more drastically and probably pull Au atoms out from surface to form adatoms. With these results a new mechanism is proposed for the formation of alkyl chain thiols on Au(111).

Mapping the affinity of aluminum(III) for biophosphates: interaction mode and binding affinity in 1 : 1 complexes.

The interaction of aluminum with biomolecular building blocks is a topic of interest as a first step to understand the potential toxic effects of aluminum in biosystems. Among the different molecules that aluminum can bind in a biological environment, phosphates are the most likely ones, due to their negatively charged nature. In the present paper, we combined DFT quantum mechanical calculations with the implicit solvent effect in order to characterize the interaction of Al(III) with these molecules. An extended set composed of a total of 59 structures was investigated, which includes various types of phosphates (monoester, diester, triester-phosphates) and various phosphate units (mono-, di- and tri-phosphate), considering various charge and protonation states, and different binding modes. The goal is to unveil the preferential interaction mode of Al(III) with phosphates in 1 : 1 complexes. Our results reveal that Al(III) prefers to form dicoordinated complexes with two phosphates, in which the interaction with each of the phosphates is of monodentate character. Our results also suggest a high affinity for binding basic phosphate groups, pointing to ATP, phosphorylated peptides, and basic diphosphates (such as 2,3-DPG) as strong aluminum chelators.

Characterization of two-dimensional chiral self-assemblies L- and D-methionine on Au(111).

A combination of XPS, in situ RAIRS, LEED, and STM experiments together with ab initio DFT calculations were used to elucidate the self-assembly properties at the atomic level, and enabled the interpretation of the expression of surface chirality upon adsorption of both enantiomers of methionine on a clean Au(111) surface under UHV conditions. The combination of experimental results, in particular, LEED and STM data with quantum chemical calculations is shown to be a successful setup strategy for addressing this challenge. It was found that the methionine molecular self-assembly consists of the first molecule lying parallel to the gold surface and the second interacting with the first methionine through a 2D H-bond network. The interaction with the gold surface is weak. The stability of the assembly is mainly due to the presence of intermolecular H bonds, resulting in the formation of ziplike dimer rows on the Au(111) surface. The methionine molecules interact with each other via their amino acid functional groups. The assembly shows an asymmetric pattern due to a slightly different orientation of the methionine molecules with respect to the surface. Simulations of the STM image of methionine assemblies were consistent with the experimental STM image. The present study shows another example of Au(111) stabilizing a self-assembled biological layer, which is not chemically perturbed by the surface.

Chlorine-enhanced surface mobility of Au(100).

Motivated by experimental studies of two-dimensional Ostwald ripening on Au(100) electrodes in chlorine-containing electrolytes, we have studied diffusion processes using density functional theory. We find that chlorine has a propensity to temporary form AuCl complexes, which diffuse significantly faster than gold adatoms. With and without chlorine, the lowest activation energy is found for the exchange mechanism. Chlorine furthermore reduces the activation energy for the detachment from kink sites. Kinetic Monte Carlo simulations were performed on the basis of extensive density functional theory calculations. The island-decay rate obtained from these Monte Carlo simulations, as well as the decay rate obtained from the theoretical activation energies and frequency factors when inserted into analytical solutions for Ostwald ripening, are in agreement with experimental island-decay rates in chlorine-containing electrolytes.

Effect of coverage and defects on the adsorption of propanethiol on Au(111) surface: a theoretical study.

Periodic density functional calculations have been carried out to investigate both the thiol adsorption on Au(111) surface and the reaction mechanism for the formation of the self-assembled monolayers, taking propanethiol as a representative example. The effect of coverage and surface defects (adatoms and vacancies) has been analyzed. It is found that the most stable physisorption (undissociated) site is an adatom site, whereas the chemisorption site for the thiol is a vacancy site or protrusion consisting of a pair of adatoms, followed by one adatom site. The results point out that the thiolate self-assembled monolayer adsorption process occurs preferentially on step edges.