Growth of Unidirectional Molecular Rows of Cysteine on Au(110)-(1×2) Driven by Adsorbate-Induced Surface Rearrangements (original) (raw)
Related papers
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).
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.
DFT Study of Cysteine Adsorption on Au(111)
The Journal of Physical Chemistry B, 2003
The adsorption of the cysteine amino acid (H-SC H 2-C R H-NH 2-COOH) on the (111) surface of gold is studied by means of periodic density functional calculations. Results for different adsorption sites and molecular configurations show that chemisorption involving S(thiolate)-Au bonds on Au(111) is favored by starting with either cysteine or cystine gas-phase molecular precursors. In the most stable adsorption configuration, the sulfur headgroup sits at the bridge site between two surface Au atoms, and the S-C bond is tilted by 57°w ith respect to the surface normal, whereas the in-plane orientation of the molecular backbone plays a secondary role. The analysis of the electronic properties shows that the hybridization of the p-like S states with the d-like Au states produces both bonding and antibonding occupied orbitals, and the process is well described by a model for the interaction of localized orbitals with narrow-band dispersive electron states. The bonding orbitals well below the Fermi level contribute to the strong chemisorption of cysteine on gold. The calculated sulfur-projected density of states allows us to locate the cysteine molecular orbitals with respect to the system Fermi level, which gives a measure of the injection barrier at the molecule/electrode junction.
DFT study on cysteine adsorption mechanism on Au(111) and Au(110)
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.
Submolecular Electronic Mapping of Single Cysteine Molecules by in Situ Scanning Tunneling Imaging
Langmuir, 2009
We have used L-cysteine (Cys) as a model system to study the surface electronic structures of single molecules at the submolecular leVel in aqueous buffer solution by a combination of electrochemical scanning tunneling microscopy (in situ STM), electrochemistry including voltammetry and chronocoulometry, and density functional theory (DFT) computations. Cys molecules were assembled on single-crystal Au(110) surfaces to form a highly ordered monolayer with a periodic lattice structure of c(2 × 2) in which each unit contains two molecules; this conclusion is confirmed by the results of calculations based on a slab model for the metal surface. The ordered monolayer offers a platform for submolecular scale electronic mapping that is an issue of fundamental interest but remains a challenge in STM imaging science and surface chemistry. Single Cys molecules were mapped as three electronic subunits contributed mainly from three chemical moieties: thiol (-SH), carboxylic (-COOH), and amine (-NH 2 ) groups. The contrasts of the three subunits depend on the environment (e.g., pH), which affects the electronic structure of adsorbed species. From the DFT computations focused on single molecules, rational analysis of the electronic structures is achieved to delineate the main factors that determine electronic contrasts in the STM images. These factors include the molecular orientation, the chemical nature of the elements or groups in the molecule, and the interaction of the elements with the substrate and tip. The computational images recast as constant-current-height profiles show that the most favorable molecular orientation is the adsorption of cysteine as a radical in zwitterionic form located on the bridge between the Au(110) atomic rows and with the amine and carboxyl group toward the solution bulk. The correlation between physical location and electronic contrast of the adsorbed molecules was also revealed by the computational data. The present study shows that cysteine packing in the adlayer on Au(110) from the liquid environment is in contrast to that from the ultrahigh-vacuum environment, suggesting solvent plays a role during molecular assembly.
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.
Using EC-STM to obtain an understanding of amino acid adsorption on Au(111)
AIP Advances
With increasing interest into the origin of life as well as the advancement of medical research using nanostructured architectures, investigations into amino acid assemblies have increased heavily in the field of surface science. Amino acid self/assisted-assembly on metallic surfaces is typically investigated with Scanning Tunneling Microscopy at low temperatures and under ultra-high vacuum in order to maintain a pristine surface and to provide researchers the tools to atomically interrogate the surface. However, in doing so, results often tend to be uncertain when moving to more realistic conditions. The investigation presented focuses on the electrochemical STM study of five simple amino acids as well as two modifications of a single amino acid and the means by which they interact with Au(111). Using EC-STM under in situ conditions, the amino acids were shown to have a considerable interaction with the underlying surface. In all cases, the amino acids trapped diffusing adatoms to form islands. These findings have also been observed under UHV conditions, but this is the first demonstration of the correlation in situ. Results indicate that an increase in the molecular footprint of the amino acid had a subsequent increase in the area of the islands formed. Furthermore, by shifting from a nonpolar to polar side chain, island area also increased. By analyzing the results gathered via EC-STM, fundamental insight can be gained into not only the behavior of amino acids with the underlying surface, but also into the direct comparison of LT-UHV-STM data with imaging performed under ambient conditions.
1992
Monolayer films of alkanethiolates CH3(CH2)nSH at Au(111) films on mica were examined by scanning tunneling microscopy (STM) (n equals 1,9,17) and AFM (n equals 1 - 17). The resulting atomically resolved images reveal the packing arrangement of the overlayer. Observed images correspond to a hexagonally packed array of adsorbates with respective nearest- and next-nearest-neighbor spacings of 0.50 +/- 0.02 nm and 0.87 +/- 0.04 nm with STM and 0.52 +/- 0.03 nm and 0.90 +/- 0.04 nm with the AFM. This packing agrees with the expected ((root)3 X (root)3)R30 degree(s) adlayer structure of the adsorbate. We believe the STM images reflect the arrangement near the gold-bound sulfur interface, whereas the AFM images reveal the arrangement of the alkyl chains.
The Journal of Chemical Physics, 2007
The adsorption of semifluorinated alkanethiols on Au/mica was studied by scanning tunneling microscopy ͑STM͒. The adlayer structure produced is based on a p͑2 ϫ 2͒ structure though lines of molecules displayed extensive kinks and bends. In addition, a considerable variation in the contrast of molecular features is found. Molecular modeling calculations confirm that, for the fluorinated thiols, inequivalently adsorbed molecules within a p͑2 ϫ 2͒ registry are present, an aspect that endows the local structure of the adlayer with a higher flexibility in comparison to nonfluorinated thiols, where one adsorption site is strongly favored in a ͑ͱ3 ϫ ͱ 3͒R30°structure. Simulated STM imaging on the optimized systems successfully recovered the effects on the molecular feature contrast induced by the flexibility of the fluorinated thiol adlayer.
Langmuir
In situ scanning tunneling microscopy (STM) was employed to study the structure of adlayers of crystal violet (CV) and water-soluble porphyrin formed on a sulfur-modified Au(111) electrode in perchloric acid solution. It was confirmed that a well-defined sulfur adlayer with ( 3 × 3)R30°structure can be prepared on Au(111) under potential control. Highly ordered adlayers of the molecules were found to form on the sulfur-modified Au(111) surface. In situ STM revealed the characteristic shape, packing arrangement, and even internal structure of each molecule. It is demonstrated that the sulfur-modified Au(111) electrode can be used as a substrate suitable for the investigation of the adsorption of organic molecules in solution.