Density functional theory study of the adsorption of alkanethiols on Cu(111), Ag(111), and Au(111) in the low and high coverage regimes

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.     

Configurational correlations in the coverage dependent adsorption energies of oxygen atoms on late transition metal fcc(111) surfaces

The coverage dependence of oxygen adsorption energies on the fcc(111) surfaces of seven different transition metals (Rh, Ir, Pd, Pt, Cu, Au, and Ag) is demonstrated through density functional theory calculations on 20 configurations ranging from one to five adsorption sites and coverages up to 1 ML. Atom projected densities of states are used to demonstrate that the d-band mediated adsorption mechanism is responsible for the coverage dependence of the adsorption energies. This common bonding mechanism results in a linear correlation that relates the adsorption energies of each adsorbate configuration across different metal surfaces to each other. The slope of this correlation is shown to be related to the characteristics of the valence d-orbitals and band structure of the surface metal atoms. Additionally, it is shown that geometric similarity of the configurations is essential to observe the configurational correlations.     

L-cysteine adsorption structures on Au(111) investigated by scanning tunneling microscopy under ultrahigh vacuum conditions

Adsorption structures formed upon vapor deposition of the natural amino acid L-cysteine onto the (111) surface of gold have been investigated by scanning tunneling microscopy under ultrahigh vacuum conditions. Following deposition at room temperature and at cysteine coverages well below saturation of the first monolayer, we found coexistence of unordered molecular islands and extended domains of a highly ordered molecular overlayer of quadratic symmetry. As the coverage was increased, a number of other structures with local hexagonal order emerged and became dominant. Neither of the room temperature, as-deposited, ordered structures showed any fixed rotational relationship to the underlying gold substrate, suggesting a comparatively weak and nonspecific molecule-substrate interaction. Annealing of the cysteine-covered substrate to 380 K lead to marked changes in the observed adsorption structures. At low coverages, the unordered islands developed internal order and their presence started to perturb the appearance of the surrounding Au(111) herringbone reconstruction. At coverages beyond saturation of the first monolayer, annealing led to development of a ( radical3 x radical3)R30 degrees superstructure accompanied by the formation of characteristic monatomically deep etch pits, i.e., the behavior typically observed for alkanethiol self-assembled monolayers on Au(111). The data thus show that as-deposited and thermally annealed cysteine adsorption structures are quite different and suggest that thermal activation is required before vacuum deposited cysteine becomes covalently bound to single crystalline Au(111).     

CO adsorption and reaction on clean and oxygen-covered Au(211) surfaces

We have used primarily temperature-programmed desorption (TPD) and infrared reflection-absorption spectroscopy (IRAS) to investigate CO adsorption on a Au(211) stepped single-crystal surface. The Au(211) surface can be described as a step-terrace structure consisting of three-atom-wide terraces of (111) orientation and a monatomic step with a (100) orientation, or 3(111) x (100) in microfacet notation. CO was only weakly adsorbed but was more strongly bound at step sites (12 kcal mol(-1)) than at terrace sites (6.5-9 kcal mol(-1)). The sticking coefficient of CO on the Au(211) surface was also higher ( approximately 5x) during occupation of step sites compared to populating terrace sites at higher coverages. The nu(CO) stretching band energy in IRAS spectra indicated that CO was adsorbed at atop sites at all coverages and conditions. A small red shift of nu(CO) from 2126 to 2112 cm(-1) occurred with increasing CO coverage on the surface. We conclude that the presence of these particular step sites at the Au(211) surface imparts stronger CO bonding and a higher reactivity than on the flat Au(111) surface, but these changes are not remarkable compared to chemistry on other more reactive crystal planes or other stepped Au surfaces. Thus, it is unlikely that the presence or absence of this particular crystal plane alone at the surface of supported Au nanoparticles has much to do with the remarkable properties of highly active Au catalysts.     

氢和硫原子在Pd、Au和Cu及PdAu、PdCu合金(111)表面吸附的密度泛函研究

用密度泛函理论研究了氢和硫原子在金属Pd、Au、Cu以及合金PdM3、Pd2M2 和Pd3M(111)表面的吸附(M=Au, Cu), 得到了覆盖率为0.25时最稳定的吸附位、结合能以及吸附前后表面的驰豫情况. 结果表明, 氢和硫均与Pd形成最稳定的吸附, Cu次之, Au的吸附最弱, 其在三种纯金属(111)表面的最稳定吸附位均为fcc位. 由于PdAu合金具有较大的晶格常数, Pd3Au 合金吸附氢的结合能甚至较纯Pd更大, 除此之外, 氢和硫在PdM合金表面的吸附基本随M组分的增加而减弱, 而最稳定的吸附位随金属种类和组成变化而变化. 根据计算得到的吸附结合能, 发现与PdCu合金相比, PdAu合金在Au含量较低(约25%, 摩尔分数)时, 氢和硫吸附的结合能下降较慢, 而Au含量较高(跃50%)时, 结合能迅速下降, 这表明含金量为25%-50%的PdAu合金有可能在保持相近透氢性能的同时, 比PdCu合金具有更好的抗硫毒性.     

Two-dimensional Molecular Phase Transition of Alkylated-TDPB on Au(111) and Cu(111) Surfaces

The derivatives of aromatic cores bearing alkyl chains with different lengths are of potential interest in on-surface chemistry, and thus have been widely investigated both at liquid-solid interfaces and in vacuum. Here, we report on the structural evaluation of self-assembled 1,3,5-tri(4-dodecylphenyl)benzene(TDPB) molecules with increased molecular coverages on both Au(111) and Cu(111) surfaces. As observed on Au(111), rhombic and herringbone structures emerge successively depending on surface coverage. In the case of Cu(111), the same process of phase conversion is also observed, but with two distinct structures. In comparison, the self-assembled structures on Au(111) surface are packed more densely than that on Cu(111) surface under the same preparation conditions. This may fundamentally result from the higher adsorption energy of TDPB molecules on Cu(111), restricting their adjustment to optimize a thermodynamically favorable molecular packing.     

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.     

Bromine Adsorption and Thermal Stability on Rh(111): A Combined XPS,LEED and DFT Study

This study addresses a fundamental question in surface science: the adsorption of halogens on metal surfaces. Using synchrotron radiation-based high-resolution X-ray photoelectron spectroscopy (XPS), temperature-programmed XPS, low-energy electron diffraction (LEED) and density functional theory (DFT) calculations, we investigated the adsorption and thermal stability of bromine on Rh(111) in detail. The adsorption of elemental bromine on Rh(111) at 170 K was followed in situ by XPS in the Br 3d region, revealing two individual, coverage-dependent species, which we assign to fcc hollow- and bridge-bound atomic bromine. In addition, we find a significant shift in binding energy upon increasing coverage due to adsorbate-adsorbate interactions. Subsequent heating shows a high thermal stability of bromine on Rh(111) up to above 1000 K, indicating strong covalent bonding. To complement the XPS data, LEED was used to study the long-range order of bromine on Rh(111): we observe a (√3×√3)R30° structure for low coverages (≤0.33 ML) and a star-shaped compression structure for higher coverages (0.33–0.43 ML). Combining LEED and DFT calculations, we were able to visualize bromine adsorption on Rh(111) in real space for varying coverages.     

甲酸在Au（997）台阶表面的氧化反应

金催化是纳米催化的代表性体系之一,但对金催化作用的理解还存在争议,特别是金颗粒尺寸对其催化作用的影响.金颗粒尺寸减小导致的表面结构主要变化之一是表面配位不饱和金原子密度的增加,因此研究金原子配位结构对其催化作用的影响对于理解金催化作用尺寸依赖性具有重要意义.具有不同配位结构的金颗粒表面可以利用金台阶单晶表面来模拟.我们研究组以同时具有Au(111)平台和Au(111)台阶的Au(997)台阶表面为模型表面,发现Au(111)台阶原子在CO氧化、NO氧化和NO分解反应中表现出与Au(111)平台原子不同的催化性能.负载型Au颗粒催化甲酸氧化反应是重要的Au催化反应之一.本文利用程序升温脱附/反应谱(TDS/TPRS)和X射线光电子能谱(XPS)研究了甲酸在清洁的和原子氧覆盖的Au(997)表面的吸附和氧化反应,观察到Au(111)台阶原子和Au(111)平台原子不同的催化甲酸根氧化反应行为.与甲酸根强相互作用的Au(111)台阶原子表现出比与甲酸根弱相互作用的Au(111)平台原子更高的催化甲酸根与原子氧发生氧化反应的反应活化能.在清洁Au(997)表面,甲酸分子发生可逆的分子吸附和脱附.甲酸分子在Au(111)台阶原子的吸附强于在Au(111)平台原子的吸附. TDS结果表明,吸附在Au(111)台阶原子的甲酸分子的脱附温度在190 K,吸附在Au(111)平台原子的甲酸分子的
　　脱附温度在170 K. XPS结果表明,分子吸附甲酸的C 1s和O 1s结合能分别位于289.1和532.8 eV.利用多层NO2的分解反应在Au(997)表面控制制备具有不同原子氧吸附位和覆盖度的原子氧覆盖Au(997)表面,包括氧原子吸附在(111)台阶位的0.02 ML-O(a)/Au(997)、氧原子同时吸附在(111)台阶位和(111)平台位的0.12 ML-O(a)/Au(997)、氧原子和氧岛吸附在(111)平台位和氧原子吸附在(111)台阶位的0.26 ML-O(a)/Au(997). TPRS和XPS结果表明,甲酸分子在105 K与Au(997)表面原子氧物种反应生成甲酸根和羟基物种,但甲酸根物种的进一步氧化反应依赖于Au原子配位结构和各种表面物种的相对覆盖度.在0.02 ML-O(a)/Au(997)表面暴露0.5 L甲酸时, Au(111)台阶位氧原子完全反应,甲酸过量.表面物种是Au(111)台阶位吸附的甲酸根、羟基和甲酸分子.在加热过程中,甲酸分子与羟基在181 K反应生成甲酸根和气相水分子(HCOOH(a)+ OH(a)= H2O + HCOO(a)),甲酸根在340 K发生歧化反应生成气相HCOOH和CO2分子(2HCOO(a)= CO2+ HCOOH).在0.12 ML-O(a)/Au(997)和0.26 ML-O(a)/Au(997)表面暴露0.5 L甲酸时,甲酸分子完全反应,原子氧过量.表面物种是Au(111)平台位和Au(111)台阶位吸附的甲酸根、羟基和原子氧.在加热过程中, Au(111)平台位和Au(111)台阶位的甲酸根分别在309和340 K同时发生氧化反应(HCOO(a)+ O(a)= H2O + CO2)和歧化反应(2HCOO(a)= CO2+ HCOOH)生成气相CO2, H2O和HCOOH分子.在0.26 ML-O(a)/Au(997)表面暴露10 L甲酸时,甲酸分子和原子氧均未完全消耗.表面物种是Au(111)平台位和Au(111)台阶位吸附的甲酸根、羟基、甲酸分子和原子氧.在加热过程中,除了上述甲酸根的氧化反应和歧化反应,还发生171 K的甲酸分子与羟基的反应(HCOOH(a)+ OH(a)= H2O + HCOO(a))和216 K的羟基并和反应(OH(a)+ OH(a)= H2O + O(a)).     

Interaction between NO and Na, O, S, Cl on Au and Pd(111) surfaces

NO co-adsorption with X (X = Na, O, S, and Cl) on Au and Pd(111) surfaces is studied using density functional theory (DFT) calculations to get a deeper insight into the extraordinary sulfur enhanced adsorption on the Au surface. It is found that both electronegative and electropositive adatoms can enhance NO adsorption on Au(111). In Na + NO/Au(111), the strong electrostatic attraction between Na and NO dominates and stabilizes NO adsorption, though Na-induced surface negative charging weakens NO adsorption. In (O, S, Cl) + NO/Au, the electronegative atoms would induce a slight surface distortion and enhance NO adsorption accordingly. NO adsorption on Pd(111) is enhanced by Na, but weakened by electronegative species. We suggest that the unique features of noble metals, i.e., the narrow DOS at the Fermi level (E(F)) and the deep buried d-band center, should play an important role in the promotion of NO adsorption on their surface as the CO case.     

Density functional theory (DFT) investigation of the adsorption of the CH3OH/Au(100) system

The adsorption of methanol on flat Au (100) surface with different coverages (θ = 1.0, 0.5 and 0.25 monolayer (ML)) is studied using density functional theory. Among the three sites (top, bridge and hollow) and coverages investigated in the present work, no adsorption is stable for θ = 1.0 ML. The most energetically preferred site of adsorption for CH₃OH is found to be the hollow site for coverages of 0.25 ML and 0.50 ML. We also find that for all adsorption sites, an increase in CH₃OH coverage triggers a decrease in the adsorption energy. The geometric parameters, local density of states and work function changes are analysed in detail. The coadsorption of methoxy and hydrogen has also investigated. In addition, the dissociation of methanol on Au(100) has been studied, and an activation energy was found to be 1.72 eV. This result compare with existing data in the literature for Au(111) surface. Copyright © 2013 John Wiley & Sons, Ltd.     

Au adatoms in self-assembly of benzenethiol on the Au(111) surface

Self-assembly of benzenethiol at low coverage on Au(111) was studied using low-temperature scanning tunneling microscopy. Phenylthiolate species (PhS), formed by thermal dehydrogenation of the parent PhSH molecule, was found to self-assemble into surface-bonded complexes with gold adatoms. Each complex involves two PhS species and one gold adatom. The PhS species form either cis- or trans-geometry relative to each other. At a higher coverage, the complexes coalesce, most likely due to the formation of weak C-H...S hydrogen bonds facilitated by the spatial arrangement of the PhS groups. Our findings thus establish that the self-assembly of arenethiols on the Au(111) surface is driven by gold adatom chemistry, which has recently been found to be the key ingredient in the self-assembly of alkanethiols on gold.     

Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study

We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.     

Formation of gold-methanethiyl self-assembled monolayers

The energetics of formation of thiyl-gold self-assembled monolayers is investigated using density-functional theory simulations. It is found that the chemisorption of dimethyl disulfide on the reconstructed Au(111) (22 x radical3) surface is most favored at the fcc reconstruction stripe, with initial physisorption leading to disulfide dissociation, adatom/vacancy-pair formation, and then, at a coverage of 7.8% sulfur atoms per gold atom, surface reconstruction lifting. At higher coverages, monolayer formation proceeds similarly on the unreconstructed surface, leading to surface pitting. Formation of the analogous adatom/vacancy-pair bound dissociated adsorbate complex on exposure of the clean unreconstructed surface to methanethiol is shown to be endothermic, however.     

Solvent effects on the adsorption and self-organization of Mn12 on Au(111)

A sulfur-containing single molecule magnet, [Mn12O12(O2CC6H4SCH3)16(H2O)4], was assembled from solution on a Au(111) surface affording both submonolayer and monolayer coverages. The adsorbate morphology and the degree of coverage were inspected by scanning tunneling microscopy (STM), while X-ray photoelectron spectroscopy (XPS) allowed the determination of the chemical nature of the adsorbate on a qualitative and quantitative basis. The properties of the adsorbates were found to be strongly dependent on the solvent used to dissolve the magnetic complex. In particular, systems prepared from tetrahydrofuran solutions gave arrays of isolated and partially ordered clusters on the gold substrate, while samples prepared from dichloromethane exhibited a homogeneous monolayer coverage of the whole Au(111) surface. These findings are relevant to the optimization of magnetic addressing of single molecule magnets on surfaces.     

Bond character of thiophene on Ge(100): Effects of coverage and temperature

We have studied the adsorption and decomposition of thiophene (C4H4S) on Ge(100) using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculation. Analysis of S 2p core-level spectra reveals three adsorption geometries, which we assign to a Ge-S dative bonding state, a [4 + 2] cycloaddition bonding state, and a decomposed bonding state (desulfurization reaction product). Furthermore, we found that the number ratio of the three adsorption geometries depended on the molecular coverage and the annealing temperature. At low coverages, the kinetically favorable dative bonding state is initially formed at room temperature. As the molecular coverage increases, thermodynamically stable [4 + 2] cycloaddition reaction products are additionally produced. In addition, we found that as the surface temperature increased, the [4 + 2] cycloaddition reaction product either possibly desorbed as molecular thiophene or decomposed to form a metallocycle-like species (C4H4Ge2) and a sulfide (Ge2S). We systematically elucidate the changes in the bonding states of adsorbed thiophene on Ge(100) according to the thiophene coverage and annealing temperature.     

Coverage-dependent adsorption of atomic sulfur on Fe(110): a DFT study

Adsorption of atomic sulfur at different coverages on the Fe(110) surface is examined using density functional theory (DFT) in order to investigate the effect that adsorbate-adsorbate interactions may have on the surface properties. S is adsorbed in the high-symmetry adsorption sites: 4-fold hollow, bridge, and atop sites in the following surface arrangements: c(2 x 2) and p(1 x 1) which correspond to coverages of 1/2 and 1 monolayer, respectively. The binding energy, work function change, adsorption geometry, charge density distribution, magnetic properties, and density of states are examined and compared to our previous study of S adsorbed at 1/4 monolayer coverage and p(2 x 2) arrangement [Spencer et al. Surf. Sci. 2003, 540, 420]. It was found that S forms polar covalent bonds to the surface. The bonding goes from being S-Fe dominated at the low coverages to being S-S dominated at the higher coverages where the S atoms are located closer together on the surface and interact with each other.     

Transient hydroxyl formation from water on oxygen-covered Au(111)

We present evidence for the formation of transient hydroxyls from the reaction of water with atomic oxygen on Au(111) and investigate the effect of adsorbed oxygen on the hydrogen bonding of water. Water is evolved in peaks at 175 and 195 K in temperature programed reaction experiments following adsorption of water on oxygen-covered Au(111). The peak at 175 K is ascribed to sublimation of multilayers of water, whereas the peak at 195 K is associated with oxygen-stabilized water or a water-hydroxyl surface complex. Infrared reflection absorption spectra are consistent with the presence of molecular water over the entire range of coverages studied, indicating that isolated stable hydroxyls are not formed. Isotopic exchange of adsorbed (16)O with H(2)(18)O following adsorption and subsequent temperature programed reaction, however, indicates that transient OH species are formed. The extent of oxygen exchange was considerable--up to 70%. The degree of oxygen exchange depends on the initial coverage of oxygen, the surface temperature when preparing oxygen adatoms, and the H(2)(18)O coverage. The hydroxyls are short-lived, forming and disproportionating multiple times before water desorption during temperature programed reaction. It was also found that chemisorbed oxygen is critical in the formation of hydroxyls and stabilizing water, whereas gold oxide does not contribute to these effects. These results identify transient hydroxyls as species that could play a critical role in oxidative chemical reactions on gold, especially in ambient water vapor. The crystallinity of adsorbed water also depended on the degree of surface ordering and chemical modification based on scanning tunneling microscopy and infrared spectra. These results demonstrate that oxidation of interfaces has a major impact on their interaction with water.     

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.     

Gold catalyzed reduction of a hexavalent aromatic sulfonyl phthalimide to sulfur

The reduction of N-(p-fluorobenzenesulfonyl)phthalimide on polycrystalline gold and Au(111) was studied. Our key finding is the decomposition of the compound on the surface, leaving only sulfur behind. This was supported by X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV) and scanning tunneling microscopy (STM). The modification leads to observation by STM of well-known as well as new phases for the S modified Au(111) surface.