The structure, the surface bonding, and the energetics of alkanethiols adsorbed on Cu(111), Ag(111), and Au(111) surfaces were studied under low and high coverages. The potential energy surfaces (PES) for the thiol/metal interaction were investigated in the absence and presence of externally applied electric fields in order to simulate the effect of the electrode potential on the surface bonding. The electric field affects the corrugation of the PES which decreases for negative fields and increases for positive fields. In the structural investigation, we considered the relaxation of the adsorbate and the surface. The highest relaxation in a direction perpendicular to the surface was observed for gold atoms, whereas silver atoms presented the highest relaxation in a plane parallel to the surface. The surface relaxation is more important in the low coverage limit. The surface bonding was investigated by means of the total and projected density of states analysis. The highest ionic character was observed on the copper surface whereas the highest covalent character occurs on gold. This leads to a strong dependence of the PES with the tilt angle of the adsorbate on Au(111) whereas this dependence is less pronounced on the other metals. Thus, the adsorbate-relaxation and the metal-relaxation contributions to the binding energy are more important on gold. The adsorption of thiols on gold was investigated on the 111 surface as well as on a surface with gold adatoms in order to elucidate the effect of thiols on the surface diffusion of gold. The CH(3)CH(2)S radical adsorbs ontop of the gold adatom. The diffusional barrier of the CH(3)CH(2)SAu species is lower than that for a bare gold adatom and is also lower than that for the bare thiol radical. The adsorption of the molecular species CH(3)SH and CH(3)CH(2)SH was also investigated on Au(111). They adsorb via the sulfur atom ontop of a gold atom. On the other hand, the adsorption of the alkanethiol radicals on the perfect 111 surfaces occurs on the face centered cubic (fcc)-bridge site in the low coverage limit for all metals and shifts toward the fcc site at high coverage on copper and silver.

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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.

The structure and stability of mixed self-assembled monolayers (SAMs) of 3-mercaptopropionic acid (MPA) and 11-mercaptoundecanoic acid (MUA) prepared by immersion in ethanolic solutions were studied by cyclic voltammetry, electrochemical impedance spectroscopy, ellipsometry, and STM as a function of the thiol composition of the forming solution. The presence of a single reductive desorption peak in the voltammograms of the mixed SAMs and the lack of phase segregation observed by STM support the formation of homogeneous SAMs despite the large chain length difference between MPA and MUA. To explain the driving force leading to the formation of a homogeneous mixture, intermolecular interactions within the SAM were investigated using density functional theory. The carboxyl groups of adjacent MPA and MUA molecules in a compact monolayer can form a stable head to head cyclic dimer with a hydrogen bond strength of 16.2 kcal/mol. The flexibility of the alkyl chain of MUA allows the carboxyl groups of adjacent MPA and MUA molecules to be located on the same plane. However, the carboxyls of adjacent MPA-MPA and MUA-MUA pairs form much weaker hydrogen bonds because steric constraints avoid the formation of the stable cyclic dimer. Therefore, the prevalence of MPA-MUA interactions over MPA-MPA and MUA-MUA interactions explains the homogeneous mixing of MPA and MUA. The potential chemical switchability properties of mixed monolayers of mercaptoalcanoic acids of different chain lengths as a function of the solution pH are discussed.

We investigated the formation and stability of layers of methylthiolate prepared on the Au(111) surface by the method of immersion in an ethanolic solution of dimethyl disulfide (DMDS). The surface species were characterized by electrochemical reductive desorption and high-resolution photoelectron spectroscopy. Both techniques confirmed the formation of a methylthiolate monolayer at short immersion times (around 1 min). As the immersion time increased, the electrochemical experiments showed the disappearance of the methylthiolate reductive desorption current peak and the appearance of a current peak at ca. -0.9 V which was attributed to sulfur species. At long immersion times, the XPS measurements showed two main components for the S 2p signal: a component at ca. 161 eV which corresponds to atomic sulfur and a component at ca. 162 eV which we attributed to polysulfide species. We propose that the breakage of the S-C bond of methylthiolate is responsible for the appearance of sulfur species on the surface. Density functional theory (DFT) calculations were performed to identify the elementary steps that may lead to the decomposition of methylthiolate. We found that the cleavage of the S-C bond is only activated by the oxidative dehydrogenation of the methyl group of methylthiolate. Thio-oxymethylene, SCH 2 O, is the key intermediate leading to the breakage of the S-C bond because it decomposes into atomic sulfur and formaldehyde with an activation energy barrier of only 1.1 kcal/mol.

We investigated the influence of intermolecular interactions and subsurface oxidation on the structure, surface bonding, and reactivity of compact monolayers of small organic and inorganic molecules bound to the Si(111) surface via Si-C, Si-N, and Si-O bonds. We considered the following modified surfaces: Si-CH 3 , Si-CCH, Si-CN, Si-CH 2 CH 3 , Si-OCH 3 , Si-OH, Si-NH 2 , Si-NHOH, and Si-ONH 2 . The highest hydrogen bond strength (7.5 kcal/mol) was observed for the (1 × 1) Si-NHOH monolayer. The (1 × 1) Si-CH 2 CH 3 monolayer had the highest repulsion at the DFT level, 9.1 kcal/mol. However, inclusion of dispersion interactions yielded a repulsion of only 1.8 kcal/mol. Subsurface oxidation was investigated for -H, -CH 3 , and -CH 2 CH 3 terminated surfaces with surface coverages of 100 and 50%. The oxidation of the third Si-Si backbond is considerably more exothermic than the oxidation of the first and second backbonds. For monolayers with a surface coverage of 50%, the oxidation of alkylated silicon atoms is more stable than the oxidation of hydrogenated silicon atoms. The oxidation of alkylated silicon atoms stabilizes the organic monolayer for two reasons: a decrease of repulsive interactions between adjacent alkyl chains (due to the increase in intermolecular separations) and a strengthening of the Si-C surface bond. The reactivity of the grafted surfaces was investigated in the low coverage limit for the surface hydroxylation reaction with water. The highest activation barriers are obtained for the -CH 3 (40.3 kcal/mol) and -CH 2 CH 3 (40.4 kcal/mol) terminated surfaces. The presence of conjugation in the organic molecule lowers the activation barrier. On the -CCH terminated surface, the activation energy decreases to 29.2 kcal/mol. The nucleophilic attack of silicon by water is facilitated on the -Cl, -OCH 3 , and -NH 2 terminated surfaces due to the increased positive charge of the silicon atom. The -NH 2 and -Cl grafted surfaces are the most reactive with activation energies of 7.9 and 13.4 kcal/mol.

The reactivity of the hydrogenated Si(111) surface toward H2O and O2 was investigated in order to elucidate the mechanism of oxidation of the first silicon bilayer in air. Density functional theory calculations were performed to identify elementary reaction steps and their corresponding activation energy barriers. The perfect surface is unreactive toward H2O and O2 at room temperature as deduced from the high energy barriers found. However, isolated Si dangling bonds, (Si3)Si·, surrounded by SiH groups, readily react with O2 (but not with H2O), producing a silanone intermediate of the form (Si2O)SiO· where one of the silicon back bonds is oxidized. This intermediate is reached after a series of elementary steps with very small activation energy barriers. In the next step, the oxygen atom of the silanone group inserts into a Si–Si back bond, and the surface silicon dangling bond is regenerated as a (SiO2)Si· moiety in which the silyl group has two oxidized back bonds. This initiates a surface chain reaction in which the oxidized silyl group abstracts a hydrogen atom from a neighboring SiH thus producing a new Si dangling bond that is oxidized by O2 in the next step of the chain reaction. This radical propagation mechanism explains the two-dimensional oxide growth in air and the lack of surface SiOH groups. Therefore, the oxidation of the H–Si(111) surface requires the presence of radicals in air that, upon reaction with the hydrogenated surface, produce silicon dangling bonds where the oxidation begins and propagates by hydrogen abstraction from nonoxidized neighboring SiH groups.

The interaction of 1-octanethiol, 1,8-octanedithiol, 1-hexadecanethiol, and 16-mercaptohexadecanoic acid with polycrystalline copper surfaces was investigated comparatively using forming solutions with polar (0.05 M NaOH solution) and apolar (n-hexane) solvents. The thiol layers were formed on the freshly chemically polished copper surface as well as on the anodically oxidized surface. The effects of the alkanethiol chain length and terminal group on the blocking properties of the surface were investigated. We show for the first time that compact monolayers and multilayers can be obtained from an alkaline forming solution. Copper oxides are completely reduced in the alkaline forming solution for all of the thiols investigated after an immersion time of 45 min. On the contrary, the presence of a surface oxide was always detected after the formation of the thiol layer in the n-hexane solution. The mechanism of Cu 2 O reduction by thiols was investigated by means of density functional theory calculations. The surface reactions involve the protonation of the surface oxygen atoms of the oxide which act as Lewis base sites. In the alkaline electrolyte, the proton transfer involves the water molecules of the solvent, whereas in the n-hexane solution the proton transfer involves the -SH group of the alkanethiol. The surface reactions are not the rate limiting step because they have very low activation energy barriers. The higher reduction rate observed in the alkaline thiol solutions is due to the high concentration of the reacting water molecules, whereas the lower reaction rate in the n-hexane solutions correlates with the lower concentration of the reactant alkanethiol molecules.