Scanning tunneling microscopy, Fourier transform infrared spectroscopy, and electrochemical characterization of 2-naphthalenethiol self-assembled monolayers on the Au surface: a study of bridge-mediated electron transfer in Ru(NH3)6(2+)/Ru(NH3)6(3+) redox reactions

We have studied the structure, adsorption kinetics, and barrier properties of self-assembled monolayers of 2-naphthalenethiol on Au using electrochemical techniques, grazing-angle Fourier transform infrared (FTIR) spectroscopy, and scanning tunneling microscopy (STM). The results of cyclic voltammetric and impedance measurements using redox probes show that 2-naphthalenethiol on Au forms a stable and reproducible, but moderately blocking, monolayer. Annealing of the self-assembled monolayer (SAM)-modified surface at 72 +/- 2 degrees C remarkably improves the blocking property of the monolayer of 2-naphthalenethiol on Au. From the study of kinetics of SAM formation, we find that the self-assembly follows Langmuir adsorption isotherm. Our STM and FTIR results show that the molecules are adsorbed with the naphthalene ring tilted from the surface normal by forming a square root 3 x 3 R30 degrees overlayer structure. From our studies, we conclude that the electron-transfer reaction of ferro/ferricyanide in the freshly formed monolayer occurs predominantly through the pinholes and defects present in the monolayer. However, in the case of thermally annealed specimen, although the ferro/ferricyanide reaction is almost completely blocked, the electron-transfer reaction of hexaammineruthenium(III) chloride is not significantly inhibited. It is proposed that the electron-transfer reaction in the case of the ruthenium redox couple takes place by a tunneling mechanism through the high-electron-density aromatic naphthalene ring acting as a bridge between the monolayer-modified electrode and the ruthenium complex.     

X-ray emission spectroscopy of (2 square root of 3 x 2 square root of 3)R30 degrees CO/Ru(0001): comparison to c(2x2)CO/Ni(100) and c(2x2)CO/Cu(100)

The atom specific electronic structure of (2 square root of 3 x 2 square root of 3)R30 degrees CO on hcp Ru(0001) has been determined with resonantly excited x-ray emission spectroscopy. We find that the general features of the local adsorbate electronic structure are similar to the situation of CO adsorbed on the fcc metals Ni(100) and Cu(100). The interpretation of the surface chemical bond of (2 square root of 3 x 2 square root of 3)R30 degrees CO/Ru(0001) based on the direct application of the local, allylic model from on-top adsorption on the fcc(100) surfaces Ni(100) and Cu(100) explains many aspects of the surface chemical bond. However, also nonlocal contributions like adsorbate-adsorbate interaction and the deviation from upright on-top adsorption on the Ru(0001) surface influence observables like the heat of adsorption and the Me-CO bond strength.     

Adsorption and in situ scanning tunneling microscopy of cysteine on Au(111): Structure, energy, and tunneling contrasts

The amino acid L-cysteine (Cys) adsorbs in highly ordered (3 square root of 3 x 6) R30 degrees 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 forms-the molecule, the anion, the neutral radical, and its zwitterion adsorbed a-top-at the bridge and at the threefold hollow site of a planar Au(111) Au12 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).     

Scanning tunneling microscopy of template-stripped Au surfaces and highly ordered self-assembled monolayers

Template stripping of Au films in ultrahigh vacuum (UHV) produces atomically flat and pristine surfaces that serve as substrates for highly ordered self-assembled monolayer (SAM) formation. Atomic resolution scanning tunneling microscopy of template-stripped (TS) Au stripped in UHV confirms that the stripping process produces a flat, predominantly 111 textured, atomically clean surface. Octanethiol SAMs vapor deposited in situ onto UHV TS Au show a c(4 x 2) superlattice with (square root 3 x square root 3) R30 degrees basic molecular structure having an ordered domain size up to 100 nm wide. These UHV results validate the TS Au surface as a simple, clean and high-quality surface preparation method for SAMs deposited from both vapor phase and solution phase.     

Chlorine adsorption on Au(111): chlorine overlayer or surface chloride?

We report the first scanning tunneling microscope (STM) investigation, combined with density functional theory calculations, to resolve controversy regarding the bonding and structure of chlorine adsorbed on Au(111). STM experiments are carried out at 120 K to overcome instability caused by mobile species upon chlorine adsorption at room temperature. Chlorine adsorption initially lifts the herringbone reconstruction. At low coverages (<0.33 ML), chlorine binds to the top of Au(111)-(1 x 1) surface and leads to formation of an overlayer with (square root(3) x square root(3))R30 degree structure at 0.33 ML. At higher coverages, packing chlorine into an overlayer structure is no longer favored. Gold atoms incorporate into a complex superlattice of a Au-Cl surface compound.     

Adlayers of C60-C60 and C60-C70 fullerene dimers formed on au(111) in benzene solutions studied by STM and LEED

Scanning tunneling microscopy (STM) and low-energy electron diffraction were used to reveal the structures of ordered adlayers of [2+2]-type C60-C60 fullerene dimer (C120) and C60-C70 cross-dimer (C130) formed on Au(111) by immersingit in abenzene solution containing C120 or C130 molecules. High-resolution STM images clearly showed the packing arrangements and the electronic structures of C120 and C130 on the Au(111) surface in ultrahigh vacuum. The (2 square root3 x 4square root3)R30 degrees, (2square root3 x 5square root3)R30 degrees, and (7 x 7) structures were found for the C120 adlayer on the Au(111) surface, whereas C130 molecules were closely packed on the surface. Each C60 or C70 monomer cage was discerned in the STM image of a C130 molecule.     

Bonding mechanism and atomic geometry of an ordered hydroxyl overlayer on Pt(111)

Exposing water to a (2 x 2)-O precovered Pt(111) surface at 100 K and subsequently annealing at 155 K led to the formation of a well-ordered (square root 3 x square root 3)R30 degrees overlayer. The structure of this overlayer is determined by DFT and full dynamical LEED calculations. There are two O containing groups per (square root 3 x square root 3)R30 degrees unit cell and both occupy near on-top positions with a Pt-O bond length of (2.11 +/- 0.04) A. DFT calculations determined the hydrogen positions of the OH species and clearly indicate hydrogen bonds between the neighboring adsorbed OH groups whose interaction is mainly of electrostatic nature. A theoretical comparison with H(2)O shows the hybridization of OH on Pt(111) to be sp(3).     

Electrocatalytic oxidation of formic acid and methanol on Pt deposits on Au(111)

This work presents characteristics of Pt deposits on Au(111) obtained by the use of spontaneous deposition and investigated by electrochemical scanning tunneling microscopy (EC-STM). On such prepared and STM characterized Au(111)/Pt surfaces, we studied electrocatalytic oxidation of formic acid and methanol. We show that the first monatomic layer of Pt displays a (square root 3 x square root 3)R30 degrees surface structure, while the second layer is (1 x 1). After prolonged deposition, multilayer Pt deposits are formed selectively on Au(111) surface steps and are 1-20 nm wide and one to five layers thick. On the optimized Au(111)/Pt surface, formic acid oxidation rates are enhanced by a factor of 20 compared to those of pure Pt(111). The (square root 3 x square root 3)R30 degrees-Pt yields very low methanol oxidation rates, but the rates increase significantly with further Pt growth.     

Assembly dynamics and detailed structure of 1-propanethiol monolayers on Au(111) surfaces observed real time by in situ STM

1-Propanethiol is chosen as a model alkanethiol to probe detailed mechanisms of the self-assembled monolayer (SAM) formation at aqueous/Au(111) interfaces. The assembly processes, including initial physi- and chemisorption, pit formation, and domain growth, were recorded into movies in real-time with high resolution by in situ scanning tunneling microscopy (STM) under potential control. Two major adsorption steps were disclosed in the propanethiol SAM formation. The first step involves weak interactions accompanied by the lift of the Au(111) surface reconstruction, which depends reversibly on the electrochemical potentials. The second step is chemisorption to form a dense monolayer, accompanied by formation of pits as well as structural changes in the terrace edges. Pits emerged at the stage of the reconstruction lift and increased to a maximum surface coverage of 4.0 +/- 0.4% at the completion of the SAM formation. Well-defined triangular pits in the SAM were found on the large terraces (more than 300 nm wide), whereas few and small pinholes appeared at the terrace edge areas. Smooth edges were converted into saw-like structural features during the SAM formation, primarily along the Au(111) atomic rows. These observations suggest that shrinking and rearrangement of gold atoms are responsible for both formation of the pits and the shape changes of the terrace edges. STM images disclose a (2 square root 3 x 3)R30 degrees periodic lattice within the ordered domains. Along with electrochemical measurements, each lattice unit is assigned to contain four propanethiol molecules exhibiting different electronic contrasts, which might originate in different surface orientations of the adsorbed molecules.     

Two-site adsorption model for the (square root 3 x square root 3)-R30 degrees dodecanethiolate lattice on Au(111) surfaces

The surface structure of dodecanethiolate self-assembled monolayers (SAMs) on Au(111) surfaces, formed from the liquid phase, have been studied by grazing incidence X-ray diffraction (GIXRD), scanning tunneling microscopy (STM), and electrochemical techniques. STM images show that the surface structure consists of (square root 3 x square root 3)-R30 degrees domains with only a few domains of the c(4 x 2) lattice. The best fitting of GIXRD data for the (square root 3 x square root 3)-R30 degrees lattice is obtained with alkanethiolate adsorption at the top sites, although good fittings are also obtained for the fcc and hcp hollow sites. On the basis of this observation, STM data, electrochemical measurements, and previously reported data, we propose a two-site model that implies the formation of incoherent domains of alkanethiolate molecules at top and fcc hollow sites. This model largely improves the fitting of the GIXRD data with respect to those observed for single adsorption sites and, also, for the other possible two-site combinations. The presence of alkanethiolate molecules adsorbed at the less favorable top sites could result from the adsorption pathway that involves an initial physisorption step which, for steric reasons, takes place at on top sites. Once the molecules are chemisorbed, the presence of energy barriers for alkanethiolate surface diffusion, arising mostly from chain-chain interactions, "freezes" some of them at the on top sites, hindering their movement toward fcc hollow sites. By considering the length of the hydrocarbon chain and the adsorption time, the two-site model could be a tool to explain most of the controversial results on this matter reported in the literature.     

Structure and bonding of alkanethiols on Cu(111) and Cu(100)

The local structure of the sulfur atom of methanethiolate and ethanethiolate on the Cu(111) and Cu(100) surfaces was investigated from first principles employing the periodic supercell approach in the framework of density functional theory. On the 111 surface, we investigated the (square root 3 x square root 3)R30 degrees and (2 x 2) structures, whereas on the 100 surface, we investigated the p(2 x 2) and c(2 x 2) structures. The landscape of the potential energy surface on each metal surface presents distinctive features that explain the local adsorption structure of thiolates found experimentally. On the Cu(111) surface, the energy difference between the hollow and bridge sites is only 3 kcal/mol, and consequently, adsorption sites ranging from the hollow to the bridge site were observed for increasing surface coverages. On the Cu(100) surface, there is a large energy difference of 12 kcal/mol between the hollow and bridge sites, and therefore, only the 4-fold coordination was observed. The high stabilization of thiolates on the hollow site of Cu(100) may be the driving force for the pseudosquare reconstruction observed experimentally on Cu(111). Density of states analysis and density difference plots were employed to characterize the bonding on different surface sites. Upon interaction with the metal d bands, the pi* orbital of methanethiolate splits into several peaks. The two most prominent peaks are located on either edge of the metal d band. They correspond to bonding and antibonding S-Cu interactions. In the case of ethanethiolate, all the back-bonds are affected by the surface bonding, leading to alternating regions of depletion and accumulation of charge in the successive bonds.     

An STM study on nonionic fluorosurfactant zonyl FSN self-assembly on Au(111): large domains, few defects, and good stability

Nonionic Fluorosurfactant Zonyl FSN self-assembly on Au(111) is investigated with scanning tunneling microscopy under ambient conditions. STM reveals that the FSN forms SAMs on Au(l11) with very large domain size and almost no defects. A (mean square root of 3 x mean square root of 3)R3 degree arrangement of the FSN SAM on Au(111) is observed. The SAMs show excellent chemical stability and last for at least a month in atmospheric conditions. The structure and stability of the FSN SAMs are compared with those of alkanethiols SAMs. It is expected that FSN may serve as a new kind of molecule to form SAMs for surface modification, which would benefit wider applications for various purposes.     

Comparative investigation of underpotential deposition of Ag from aqueous and ionic electrolytes: An electrochemical and in situ STM study

Underpotential deposition (UPD) of Ag on Au(111) has been studied with two different electrolytes: aqueous 0.1 M H2SO4 solution in comparison with the ionic liquid 1-butyl-3-methylimidazolium chloride BMICl + AlCl3. Of particular interest is the distinct behavior of 2D phase formation at both interfaces, which has been investigated by cyclic and linear sweep voltammetry in combination with in situ electrochemical scanning tunneling microscopy (STM). It is found that one monolayer (ML) of Ag is formed in the UPD region in both electrolytes. In aqueous solution, atomically resolved STM images at 500 mV versus Ag/Ag+ show a (3 x 3) adlayer of Ag, whereas after sweeping the potential just before the commencement of the bulk Ag deposition, a transition from expanded (3 x 3) to pseudomorphic ML of Ag on Au(111) occurs. In BMICl-AlCl3, the first UPD process of Ag exhibits two peaks at 410 and 230 mV indicating that two distinct processes on the surface take place. For the first time, STM images with atomic resolution reveal a transition from an inhomogeneous to an ordered phase with a (square root of 3 x square root of 3)R30 degrees structure and an adsorption of AlCl4- anions having a superlattice of (1.65 x square root of 3)R30 degrees preceding the deposition of Ag.     

In situ scanning tunneling microscopy of 1,6-hexanedithiol, 1,9-nonanedithiol, 1,2-benzenedithiol, and 1,3-benzenedithiol adsorbed on pt(111) electrodes

Cyclic voltammetry (CV) and in situ scanning tunneling microscopy (STM) were used to examine four dithiol molecules, including 1,6-hexanedithiol, 1,9-nonanedithiol, 1,2-benzenedithiol, and 1,3-benzenedithiol, adsorbed on well-ordered Pt(111) electrodes in 0.1 M HClO(4). The open-circuit potential (OCP) of Pt(111) electrodes decreased substantially from 0.95 to 0.3 V (versus reversible hydrogen electrode) upon the adsorption of dithol molecules, which indicates that these adsorbates injected electrons into the Pt electrode. For all dithiol molecules, ordered adlattices of p(2 x 2) and (square root 3 x square root 3)R30 degrees were formed when the dosing concentration was lower than 150 microM and the potential of Pt(111) was more negative than 0.5 V. Raising the potential of Pt(111) from 0.1 to 0.4 V or more positive values could transform p(2 x 2) to (square root 3 x square root 3)R30 degrees before it turned disarray. The insensitivity of the structure of dithiol adlayers with their chemical structures was explained by upright molecular orientation with the formation of one Pt-S bond per dithiol molecule. This molecular orientation was independent of the coverage of dithiol molecules, as nucleation seeds produced at the beginning of adsorption were also constructed with p(2 x 2). The triangular-shaped STM molecular resolution suggested 3-fold binding of sulfur headgroup on Pt(111). All dithiols were adsorbed so strongly on Pt(111) electrodes that switching the potential negatively to the onset of hydrogen evolution in 0.1 M HClO(4) or water reduction in 1 M KOH could not displace dithiol admolecules.     

Adlayers of Sb irreversibly adsorbed on Pt(111): an electrochemical scanning tunneling microscopy study

This work presents an electrochemical scanning tunneling microscopy study of Sb irreversibly adsorbed on Pt(111) at various potentials. At an open circuit potential (0.46 V vs a Ag/AgCl electrode), well-ordered structures of SbO+ were found: four (4 x 3)-3SbO+ structures and one (2 square root(3) x 2 square root(3))R30 degrees-3SbO+ structure. In addition, several unidentifiable transient structures of SbO+ were observed, and their relations to the well-ordered structures of (4 x 3) and (2 square root(3) x 2 square root(3))R30 degrees, regarding structural evolution, were proposed. At a reducing potential (0 V), the Pt(111) surface was covered with irreversibly adsorbed Sb which consisted of three different domains: protruded domain, domain of uniaxially incommensurate (square root(3) x square root(2))-Sb, and domain of bare (1 x 1) Pt(111). During oxidation of elemental Sb at 0.30 V, the Sb domains of the (square root(3) x square root(2)) structure were oxidized, while the protruded domains were not oxidized. After underpotential deposition of additional Sb onto the Pt(111) covered with irreversibly adsorbed Sb, the whole surface was filled with the Sb domains where each Sb atoms were separated by the square root(2a) distance (a = one Pt-Pt distance, 0.277 nm). The observed electrochemical inactivity below 0.3 V was discussed in terms of the protruded domain of a presumable incommensurate (square root(2) x square root(2)) structure.     

Conformation and dynamics of arylthiol self-assembled monolayers on Au(111)

We report a computational investigation of the conformation and the dynamics of self-assembled monolayers (SAMs) of a set of aromatic thiols arranged in the ( radical3 x radical3)-R30 degrees packing ratio on a Au(111) surface using molecular dynamics (MD) simulations. It was found that the molecular conformations were better defined for the arylthiol with two phenyl groups as compared to those with a single phenyl group and that the chemical structure of the head and tail groups had a considerable influence on the system geometry. In line with the density functional theory (DFT) calculations of small thiol molecules, we found for the SAMs that the face-centered cubic (fcc) site on the Au(111) surface was the most preferred, followed by the hexagonal close-packed (hcp) site, while the bridge position showed the characteristics of a local energy maximum. The dynamics of thiol head groups on these three Au sites was found to govern the overall dynamics of SAMs as measured by the mean square displacement. We also report that both the conformation and the dynamics on the studied time scale were driven by the SAM formation energy.     

Highly ordered C60 monolayer self-assembled by using an iodine template on an Au(111) surface in solution

An iodine-modified Au(111) surface, (I/Au(111)), was used as a substrate to prepare a C 60 adlayer by self-organization in a benzene solution. A highly ordered C 60 adlayer was successfully prepared due to the moderate C 60-I/Au(111) interaction. Two lattice structures, (2 square root 3 x 2 square root 3) R30 degrees and p(2 x 2), were imaged for this C 60 adlayer. For the first structure, a featureless ball-like molecular shape was imaged, ascribed to the molecular rotation resulting from a symmetrical location between C 60 and iodine atoms. For the p(2 x 2) structure, the asymmetrical location of C 60 with respect to the iodine atoms freezes the C 60 molecules on the substrate, leading to a clear image of intramolecular structure. The intermediate iodine atoms in the C 60/I/Au(111) adlayer can be desorbed by electrochemically reduction without significantly affecting the ordering of the C 60 adlayer. However, the internal pattern of C 60 disappears in the absence of iodine.     

Self-assembled monolayers of aromatic selenolates on noble metal substrates

Self-assembled monolayers (SAMs) formed from bis(biphenyl-4-yl) diselenide (BBPDSe) on Au(111) and Ag(111) substrates have been characterized by high-resolution X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, infrared reflection absorption spectroscopy, water contact angle measurements, and scanning tunneling microscopy (STM). BBPDSe was found to form contamination-free, densely packed, and well-ordered biphenyl selenolate (BPSe) SAMs on both Au and Ag. Spectroscopic data suggest very similar packing density, orientational order, and molecular inclination in BPSe/Au and BPSe/Ag. STM data give a similar intermolecular spacing of 5.3 +/- 0.4 A on both Au and Ag but exhibit differences in the exact arrangement of the BPSe molecules on these two substrates, with the (2 square root[3] x square root[3])R30 degrees and (square root[3] x square root[3])R30 degrees unit cells on Au and Ag, respectively. There is strong evidence for adsorbate-mediated substrate restructuring in the case of Au, whereas no clear statement on this issue can be made in the case of Ag. The film quality of the BPSe SAMs is superior to their thiol analogues, which is presumably related to a better ability of the selenolates to adjust the surface lattice of the substrate to the most favorable 2D arrangement of the adsorbate molecules. This suggests that aromatic selenolates represent an attractive alternative to the respective thiols.     

Covalent attachment of a transition metal coordination complex to functionalized oligo(phenylene-ethynylene) self-assembled monolayers

We have investigated the reaction of tetrakis(dimethylamido)titanium, Ti[N(CH(3))(2)](4), with N-isopropyl-N-[4-(thien-3-ylethynyl) phenyl] amine and N-isopropyl-N-(4-{[4-(thien-3-ylethynyl) phenyl]ethynyl}phenyl) amine self-assembled monolayers (SAMs), on polycrystalline Au substrates. The structure of the SAMs themselves has also been investigated. Both molecules form SAMs on polycrystalline Au bound by the thiophene group. The longer-molecular-backbone molecule forms a denser SAM, with molecules characterized by a smaller tilt angle. X-ray photoelectron spectroscopy (XPS) and angle-resolved XPS have been employed to examine the kinetics of adsorption, the spatial extent of reaction, and the stoichiometry of reaction. For both the SAMs, adsorption is described well by first-order Langmuirian kinetics, and adsorption is self-limiting from T(s) = -50 to 30 degrees C. The use of angle-resolved XPS clearly demonstrates that the Ti[N(CH(3))(2)](4) reacts exclusively with the isopropylamine end group via ligand exchange, and there is no penetration of the SAM, followed by reaction at the SAM-Au interface. Moreover, the SAM molecules remain bound to the Au surface via their thiopene functionalites. From XPS, we have found that, in both cases, approximately one Ti[N(CH(3))(2)](4) is adsorbed per two SAM molecules.     

Self-assembly of semifluorinated n-alkanethiols on {111}-oriented Au investigated with scanning tunneling microscopy experiment and theory

The adsorption of semifluorinated alkanethiols on Au/mica was studied by scanning tunneling microscopy (STM). The adlayer structure produced is based on a p(2 x 2) 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 p(2 x 2) 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 (radical 3 x radical 3) R30 degrees 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.