Exploring adsorption behavior of sulfur and nitrogen compounds on transition metal-doped Cu(100) surfaces: insights from DFT and MD simulations

We conducted an extensive investigation using density functional theory (DFT) calculations and ReaxFF molecular dynamics (MD) simulations to elucidate the mechanisms of desulfurization and denitrogenation on Cu(100) surfaces. This study encompassed both pristine surfaces and those modified with Pt or Rh transition metals. Our primary objective was to gain a deep understanding of the adsorption behavior of thiophene (C4H4S) and pyridine (C5H5N) molecules on stepped Cu(100) surfaces, which serve as models for sulfur and nitrogen compounds. We systematically explored the interplay among water, adsorption efficiency, and surface regeneration capabilities. Using DFT, we thoroughly examined various aspects, including interaction energies, charge transfers, changes in electron density, and alterations in work function upon molecule adsorption. Notably, we observed a decrease in the interaction energy of thiophene, whereas that of pyridine increased when adsorbed on Pt/Rh-doped surfaces compared to pristine ones. Thiophene adsorption reduced the work function, potentially enhancing detectability, without causing inhibitory effects on any surface. Stepped Cu(100) surfaces demonstrated a strong affinity for thiophene, exhibiting an energy difference of approximately 86 kJ mol-1. However, this trend reversed on doped surfaces, where pyridine displayed stronger adsorption than thiophene, resulting in energy differences of around 123 kJ mol-1 and 62 kJ mol-1 on Pt-Cu and Rh-Cu surfaces, respectively. Moreover, our investigation highlighted the regeneration capacity of these surfaces, indicating that all surfaces can be considered promising candidates for desulfurization, while only Cu and Pt-Cu surfaces were found to be suitable for denitrogenation. Furthermore, results from MD simulations in combination with potential of mean force (PMF) simulations at 300 K, aligned with DFT calculations, confirmed the adsorption configurations of pyridine and thiophene. This analysis demonstrated the competitive advantage of thiophene over pyridine in adsorption and highlighted the inhibitory effect of water on pyridine adsorption on the Cu(100) surface.

Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling

Cysteine (Cys) is an essential amino acid with a carboxylic acid, an amine and a thiol group. We have studied the surface structure and adsorption dynamics of l-cysteine adlayers on Au(100) from aqueous solution using electrochemistry, high-resolution electrochemical scanning tunnelling microscopy (in situ STM), and molecular modelling. Cys adsorption on this low-index Au-surface has been much less studied than Cys adsorption on Au(111)- and Au(110)-electrode surfaces. Chronopotentiometry was employed to monitor the adsorption dynamics at sub-second resolution and showed that adsorption is completed in 30 minutes at Cys concentrations above 100 μM. Two consecutive steps could be fitted to these data. Two separate reductive desorption peaks of Cys adlayers on Au(100) with a total coverage of 2.52 (±0.15) × 10-10 mol cm-2 were observed. In situ STM showed that the adsorbed Cys is organized in stripes with "fork-like" features which co-exist in (11 × 2)-2Cys and (7 × 2)-2Cys lattices, quite differently from Cys adsorption on Au(111)-electrode surfaces. Stripe structures with bright STM contrast in the center suggest that a second Cys adlayer on top of a first adlayer is formed, supporting the dual-peak reductive desorption of Cys adlayers. In addition, monolayers of both pure l-Cys and pure d-Cys and a 1 : 1 racemic mixture of l- and d-Cys on Au(100) were studied. Virtually identical macroscopic electrochemical features were found, but in situ STM discloses many more defects for the racemic mixture than for the pure enantiomers due to structural mismatch of l- and d-Cys. Density functional theory (DFT) calculations combined with a cluster model for the Au(100) surface were carried out to investigate the adsorption energy and geometry of the adsorbed monomer and dimer Cys species in different orientations, with detailed attention to the chirality effects. Optimized DFT geometries were used to construct model STM images, and kinetic Monte Carlo simulations undertaken to illuminate the growth of adsorbate rows and the mechanism of the adlayer formation as well as the Cys adsorption patterns specific to the Au(100)-electrode surface.

Counterintuitive issues in the charge transport through molecular junctions

Whether at phenomenological or microscopic levels, most theoretical approaches to charge transport through molecular junctions postulate or attempt to justify microscopically the existence of a dominant molecular orbital (MO). Within such single level descriptions, experimental current-voltage I-V curves are sometimes/often analyzed by using analytical formulas expressing the current as a cubic expansion in terms of the applied voltage V, and the possible V-driven shifts of the level energy offset relative to the metallic Fermi energy ε0 are related to the asymmetry of molecule-electrode couplings or an asymmetric location of the "center of gravity" of the MO with respect to electrodes. In this paper, we present results demonstrating the failure of these intuitive expectations. For example, we show how typical data processing based on cubic expansions yields a value of ε0 underestimated by a typical factor of about two. When compared to theoretical results of DFT approaches, which typically underestimate the HOMO-LUMO gap by a similar factor, this may create the false impression of "agreement" with experiments in situations where this is actually not the case. Furthermore, such cubic expansions yield model parameter values dependent on the bias range width employed for fitting, which is unacceptable physically. Finally, we present an example demonstrating that, counter-intuitively, the bias-induced change in the energy of an MO located much closer to an electrode can occur in a direction that is opposite to the change in the Fermi energy of that electrode. This is contrary to what one expects based on a "lever rule" argument, according to which the MO "feels" the local value of the electric potential, which is assumed to vary linearly across the junction and is closer to the potential of the closer electrode. This example emphasizes the fact that screening effects in molecular junctions can have a subtle character, contradicting common intuition.