Adenine adsorption on Au(111) and Au(100) electrodes: Characterisation, surface reconstruction effects and thermodynamic study

First-principles calculations of hybrid inorganic-organic interfaces: from state-of-the-art to best practice

The computational characterization of inorganic-organic hybrid interfaces is arguably one of the technically most challenging applications of density functional theory. Due to the fundamentally different electronic properties of the inorganic and the organic components of a hybrid interface, the proper choice of the electronic structure method, of the algorithms to solve these methods, and of the parameters that enter these algorithms is highly non-trivial. In fact, computational choices that work well for one of the components often perform poorly for the other. As a consequence, default settings for one materials class are typically inadequate for the hybrid system, which makes calculations employing such settings inefficient and sometimes even prone to erroneous results. To address this issue, we discuss how to choose appropriate atomistic representations for the system under investigation, we highlight the role of the exchange-correlation functional and the van der Waals correction employed in the calculation and we provide tips and tricks how to efficiently converge the self-consistent field cycle and to obtain accurate geometries. We particularly focus on potentially unexpected pitfalls and the errors they incur. As a summary, we provide a list of best practice rules for interface simulations that should especially serve as a useful starting point for less experienced users and newcomers to the field.

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.

Quantitative Subtractively Normalized Interfacial Fourier Transform Infrared Reflection Spectroscopy Study of the Adsorption of Adenine on Au(111) Electrodes

Quantitative subtractively normalized interfacial Fourier transform infrared reflection spectroscopy (SNIFTIRS) was used to determine the molecular orientation and identify the metal-molecular interactions responsible for the adsorption of adenine from the bulk electrolyte solution onto the surface of the Au(111) electrode. The recorded p-polarized IR spectra of the adsorbed species were subtracted from the collected s-polarized IR spectra to remove the IR contributions of the vibrational bands of the desorbed molecules that are located within the thin layer cavity of the spectroelectrochemical cell. The intense IR band around 1640 cm(-1), which is assigned to the pyrimidine ring stretching vibrations of the C5-C6 and C6-N10 bonds, and the IR band at 1380 cm(-1), which results from a combination of the ring stretching vibration of the C5-C7 bond and the in-plane CH bending vibration, were selected for the quantitative analysis measurements. The transition dipoles of these bands were evaluated by DFT calculations. Their orientations differed by 85 ± 5°. The tilt angles of adsorbed adenine molecules were calculated from the intensity of these two vibrations at different potentials. The results indicate that the molecular plane is tilted at an angle of 40° with respect to the surface normal of the electrode and rotates by 16° around its normal axis with increasing electrode potential. This orientation results from the chemical interaction between the N10 and gold atoms coupled with the π-π parallel stacking interactions between the adjacent adsorbed molecules. Furthermore, the changes in the molecular plane rotation with the electric field suggests that the N1 atom of adenine must also participate in the interaction between the molecule and metal.

Quaternary ammonium bromide surfactant adsorption on low-index surfaces of gold. 2. Au(100) and the role of crystallographic-dependent adsorption in the formation of anisotropic nanoparticles

A qualitative and quantitative description of the coadsorption of a quaternary ammonium bromide surfactant on Au(100) has been determined using electrochemical techniques. Cyclic voltammetry reveals that both the cationic surfactant ion and its halide counterion are adsorbed on the surface of unreconstructed Au(100) over a wide range of electrode potentials or charge densities. The relative Gibbs excesses of the cationic and anionic components of octyltrimethylammonium (OTA(+)) bromide have been determined using the thermodynamics of ideally polarized electrodes. Coadsorbed OTA(+) does not strongly affect the behavior of bromide layers on Au(100) with low-coverage films being replaced by commensurate overlayers at positive electrode charge densities. The presence of surface bromide allows for the stabilization of adsorbed OTA(+) at positive polarizations. Furthermore, charge-induced phase changes in the bromide layer lead to subtle but appreciable changes in the surface excesses of OTA(+) ions which is consistent with a hierarchical model of surfactant adsorbed upon a halide-modified Au(100) surface. A comparison of the OTA(+) adsorption isotherms on Au(100) and Au(111) reveals that the presence of coadsorbed bromide does not lead to preferential accumulation of cationic surfactant ions on a particular crystal facet. These results are inconsistent with explanations of anisotropic nanoparticle formation that invoke a thermodynamic argument of preferred surfactant adsorption on different crystal facets of an embryonic nanoparticle seed crystal.

Electrochemical solid-state phase transformations of silver nanoparticles

Adenosine triphosphate (ATP)-capped silver nanoparticles (ATP-Ag NPs) were synthesized by reduction of AgNO(3) with borohydride in water with ATP as a capping ligand. The NPs obtained were characterized using transmission electron microscopy (TEM), UV-vis absorption spectroscopy, X-ray diffraction, and energy-dispersive X-ray analysis. A typical preparation produced ATP-Ag NPs with diameters of 4.5 ± 1.1 nm containing ~2800 Ag atoms and capped with 250 ATP capping ligands. The negatively charged ATP caps allow NP incorporation into layer-by-layer (LbL) films with poly(diallyldimethylammonium) chloride at thiol-modified Au electrode surfaces. Cyclic voltammetry in a single-layer LbL film of NPs showed a chemically reversible oxidation of Ag NPs to silver halide NPs in aqueous halide solutions and to Ag(2)O NPs in aqueous hydroxide solutions. TEM confirmed that this takes place via a redox-driven solid-state phase transformation. The charge for these nontopotactic phase transformations corresponded to a one-electron redox process per Ag atom in the NP, indicating complete oxidation and reduction of all Ag atoms in each NP during the electrochemical phase transformation.

Application of electrochemical impedance spectroscopy to the study of surface processes

The application of Electrochemical Impedance Spectroscopy to the study of surface electrode processes is reviewed. The impedance expressions and the physical meaning of the parameters included in them are shown for three surface processes: adsorption kinetics, diffusion towards partially blocked electrodes and surface confined redox reactions. The models are applied to selected examples, showing the capability of Electrochemical Impedance Spectroscopy to obtain fundamental kinetic information of these processes. A review with 83 references.

The adsorption of quinizarin on boron-doped diamond

The voltammetric response of the quinone species 'quinizarin' (QZ) and its electrocatalytic reduction of oxygen are studied at a boron doped diamond electrode (BDD). It is demonstrated that, contrary to the widespread belief that adsorption of organic molecules on BDD is minimal, not only does QZ readily adsorb to the electrodes surface but this adsorption is also influenced at low surface coverages by the pre-exposure of the electrode to organic solvents. Furthermore, the nature of this adsorbed QZ species is investigated and a potential dependent phase transition is observed. This is to the authors knowledge the first system to exhibit a phase transition of an adsorbed species on a boron doped diamond surface. At low scan rates the system is found to oscillate; these oscillations are ascribed to the presence of a 'negative differential resistance'.