DFT Study of Cysteine Adsorption on Au(111)

2013

Periodic density functional theory calculations were used to investigate relevant aspects of adsorption mechanisms of cysteine dimers in protonated form on Au(111) and Au surfaces. The projected densities of states are explicitly discussed for all main chemical groups of cysteine, i.e. the amino group (NH2), the thiol group (SH) and the carboxylic group (COOH) to identify differences in adsorption mechanism. Special emphasis is put on the analysis of changes in the electronic structure of molecules adsorbed on Au(111) and Au(110) surfaces as well as the accompanying charge transfer mechanisms at molecule-substrate interaction.

Langmuir, 2006

The amino acid L-cysteine (Cys) adsorbs in highly ordered (3 3 × 6) R30°lattices on Au(111) electrodes from 50 mM ammonium acetate, pH 4.6. We provide new high-resolution in situ scanning tunneling microscopy (STM) data for the L-Cys adlayer. The data substantiate previous data with higher resolution, now at the submolecular level, where each L-Cys molecule shows a bilobed feature. The high image resolution has warranted a quantum chemical computational effort. The present work offers a density functional study of the geometry optimized adsorption of four L-Cys formssthe molecule, the anion, the neutral radical, and its zwitterion adsorbed a-topsat the bridge and at the threefold hollow site of a planar Au(111) Au 12 cluster. This model is crude but enables the inclusion of other effects, particularly the tungsten tip represented as a single or small cluster of W-atoms, and the solvation of the L-Cys surface cluster. The computational data are recast as constant current-height profiles as the most common in situ STM mode. The computations show that the approximately neutral radical, with the carboxyl group pointing toward and the amino group pointing away from the surface, gives the most stable adsorption, with little difference between the a-top and threefold sites. Attractive dipolar interactions screened by a dielectric medium stabilize around a cluster size of six L-Cys entities, as observed experimentally. The computed STM images are different for the different L-Cys forms. Both lateral and vertical dimensions of the radical accord with the observed dimensions, while those of the molecule and anion are significantly more extended. A-top L-Cys radical adsorption further gives a bilobed height profile resembling the observed images, with comparable contributions from sulfur and the amino group. L-Cys radical a-top adsorption therefore emerges as the best representation of L-Cys adsorption on Au(111).

Nanoscale

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...

Colloids and Surfaces A: Physicochemical and Engineering Aspects, 2000

L-Cysteine has been deposited on Au(111) surfaces from the solution phase. Chemical and structural information on the L-cysteine/Au(111) interface have been obtained by X-ray photoelectron spectroscopy (XPS) and scanning tunnelling microscopy (STM). XPS measurements provided a chemical characterisation of the interface. The deconvolution of the Au4f and S2p core level regions reveals a peak splitting, which can be explained by the formation of a chemical bond between the cysteine thiol group and the gold surface. The analysis of the N1s spectrum indicates that L-cysteine is present in the zwitterionic state. The STM structural characterisation performed in air at room temperature reveals that the molecular chemisorption results in the lifting of the (22× 3) gold reconstruction accompanied by the formation of depressions, a few nm in size, one gold layer in depth, as in alkanethiol/Au(111) systems. Molecular resolution images show that the L-cysteine overlayer forms a hexagonal lattice, which, in a few regions, presents a striped modulation. : S 0 9 2 7 -7 7 5 7 ( 0 0 ) 0 0 5 2 1 -5

Physical Review Letters, 2004

Using scanning tunneling microscopy we have studied the nucleation and growth of unidirectional molecular rows upon adsorption of the amino acid cysteine onto the anisotropic Au(110)-(1×2) surface under ultrahigh vacuum conditions. By modeling a large variety of possible molecular adsorption geometries using density-functional theory calculations, we find that in the optimum, lowest energy configuration, no significant intermolecular interactions exist along the growth direction. Instead the driving force for formation of the unidirectional molecular rows is an adsorbate-induced surface rearrangement, providing favorable adsorption sites for the molecules.

Journal of Raman Spectroscopy, 2019

Understanding the physical mechanisms of thiolated molecules adsorption on metal surfaces has required copious research, particularly on Au-cysteine systems due to the affinity of sulfur molecules to gold surfaces, as well as the interesting structural modifications that this strong interaction induces and the peculiar optical, chiroptical, and electronic properties of Au(SR) systems. Here, we present vibrational experimental data on the adsorption of Land D-cysteine on small gold nanoparticles (<2 nm) by means of Raman spectroscopy. Land D-cysteine molecules adopt the same strained conformation upon adsorption on colloidal gold nanoparticles, regaining structure due to the stabilization that the gold nanoparticle induces on the cysteine, reflected in the recuperation of vibrational bands from their polymorphically distinctive crystalline forms. Through the analysis of Raman vibrational modifications after adsorption, we found experimental evidence that confirms a stabilized cysteine conformation locating the carboxyl group in the antiposition (P C isomeric rotamer) for both molecules. This result is supported by extensive density functional theory (DFT) calculations and simulated Raman spectra, considering zwitterionic cysteine adsorbed on a Au 34 cluster, emulating experimental nanoparticle sizes. Our Raman spectroscopy experimental and DFT results determine one of the oxygen atoms of the carboxyl group as a second adsorption site after the sulfur atom, confirming that independent of its polymorphism and enantiomerism, zwitterionic cysteine interacts with gold nanoparticles through the thiol group and the carboxyl group as adsorption sites.

The Journal of Chemical Physics, 2003

The adsorption of the thiophene-2-thiolate and thiophen-2-yl-methanethiolate radicals has been investigated on the Au͑111͒ surface using density functional theory under the framework of the generalized gradient approximation for the exchange-correlation functionals. In order to underscore the quantum size effects on the adsorption geometry, the Au͑111͒ surface was modeled using a finite-sized cluster (Au 3 and Au 24 ) truncated from the surface as well as a periodic slab consisting of 100 atoms. The results reveal that the preferential adsorption site differs for the cluster models and slab approaches. The directional nature of the Au-S bond and the influence of the back bond of the terminal sulfur atom are found to play key roles in the adsorption geometry. The adsorption energies suggest that the binding energies for the cluster models are stronger than the slab. Inclusion of an alkyl group in between the thiophene ring and the thiol group enhances the interaction energies of the gold-sulfur bonds.

The Journal of Physical Chemistry B, 2005

The adsorption of N-acetyl-L-cysteine from ethanol solution on gold has been studied by in situ attenuated total reflection infrared (ATR-IR) spectroscopy, polarization modulation infrared reflection absorption spectroscopy, and a quartz crystal microbalance. After an initial fast adsorption, in situ ATR-IR revealed two considerably slower processes, besides further adsorption. The appearance of carboxylate bands and the partial disappearance of the carboxylic acid bands demonstrated that part of the molecules on the surface underwent deprotonation. In addition, the CdO stretching vibration of the carboxylic acid group shifted to lower and the amide II band to higher wavenumbers, indicating hydrogen-bonding interactions within the adsorbate layer. Based on the initial ATR-IR spectrum, which did not reveal deprotonation, the orientation of the molecule within the adsorbate layer was determined. For this, density functional theory was used to calculate the transition dipole moment vectors of the vibrational modes of N-acetyl-L-cysteine. The projections of the latter onto the z-axis of the fixed surface coordinate system were used to determine relative band intensities for different orientations of the molecule. The analysis revealed that the amide group is tilted with respect to and points away from the surface, whereas the carboxylic acid is in proximity to the surface, which is also supported by a shift of the CO -H bending mode. This position of the acid group favors its deprotonation assisted by the gold surface and easily enables intermolecular interactions. Periodic acid stimuli revealed reversible protonation/deprotonation of part of the adsorbed molecules. However, only nonhydrogen-bonded carboxylic acid groups showed a response toward the acid stimuli.

Langmuir, 2010

We have studied the first stages leading to the formation of self-assembled monolayers of S-cysteine molecules adsorbed on a Au(111) surface. Density functional theory (DFT) calculations for the adsorption of individual cysteine molecules on Au(111) at room temperature show low-energy barriers all over the 2D Au(111) unit cell. As a consequence, cysteine molecules diffuse freely on the Au(111) surface and they can be regarded as a 2D molecular gas. The balance between molecule-molecule and molecule-substrate interactions induces molecular condensation and evaporation from the morphological surface structures (steps, reconstruction edges, etc.) as revealed by scanning tunnelling microscopy (STM) images. These processes lead progressively to the formation of a number of stable arrangements, not previously reported, such as single-molecular rows, trimers, and 2D islands. The condensation of these structures is driven by the aggregation of new molecules, stabilized by the formation of electrostatic interactions between adjacent NH 3 þ and COOgroups, together with adsorption at a slightly more favorable quasi-top site of the herringbone Au reconstruction.

Langmuir, 2010

We have studied the first stages leading to the formation of self-assembled monolayers of S-cysteine molecules adsorbed on a Au(111) surface. Density functional theory (DFT) calculations for the adsorption of individual cysteine molecules on Au(111) at room temperature show low-energy barriers all over the 2D Au(111) unit cell. As a consequence, cysteine molecules diffuse freely on the Au(111) surface and they can be regarded as a 2D molecular gas. The balance between molecule-molecule and molecule-substrate interactions induces molecular condensation and evaporation from the morphological surface structures (steps, reconstruction edges, etc.) as revealed by scanning tunnelling microscopy (STM) images. These processes lead progressively to the formation of a number of stable arrangements, not previously reported, such as single-molecular rows, trimers, and 2D islands. The condensation of these structures is driven by the aggregation of new molecules, stabilized by the formation of electrostatic interactions between adjacent NH 3 þ and COO - groups, together with adsorption at a slightly more favorable quasi-top site of the herringbone Au reconstruction.