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.     

Elucidation of the deposition processes and spatial structures of alkanethiol and arylthiol molecules adsorbed on Pt111 electrodes with in situ scanning tunneling microscopy

In situ scanning tunneling microscopy (STM) was used to examine the spatial structures of n-alkane thiols (1-hexanethiol, 1-nonanethiol, and 1-octahexanethiol) and arylthiols (benzenethiol and 4-hydroxybenzenethiol) adsorbed on well-ordered Pt111 electrodes in 0.1 M HClO4. The electrochemical potential and molecular flux were found to be the dominant factors in determining the growth mechanisms, final coverages, and spatial structures of these organic adlayers. Depending on the concentrations of the thiols, deposition of self-assembled monolayers (SAMs) followed either the nucleation-and-growth mechanism or the random fill-in mechanism. Low and high thiol concentrations respectively produced two ordered structures, (2 x 2) and (square root of 3 x square root of 3)R30 degrees , between 0.05 and 0.3 V. On average, an ordered domain spanned 500 A when the SAMs were made at 0.15 V, but this dimension shrank substantially once the potential was raised above 0.3 V. This potential-induced order-to-disorder phase transition resulted from a continuous deposition of thiols, preferentially at domain boundaries of (square root of 3 x square root of 3 x )R30 degrees arrays. All molecular adlayers were completely disordered by 0.6 V, and this restructuring event was irreversible with potential modulation. Since all thiols were arranged in a manner similar to that adopted by sulfur adatoms (Sung et al. J. Am. Chem. Soc. 1997, 119, 194), it is likely that they were adsorbed mainly through their sulfur headgroups in a tilted configuration, irrespective of the coverage. Both the sulfur and phenyl groups of benzenethiol admolecules gave rise to features with different corrugation heights in the molecular-resolution STM images. All thiols were adsorbed strongly enough that they remained intact at a potential as negative as -1.0 V in 0.1 M KOH.     

The structure and crystallization of thin water films on Pt(111)

When water is adsorbed on Pt(111) above 135 K several different ice structures crystallize, depending on the thickness of the ice layer. At low coverage water forms extended islands of ice with a (square root(37) x square root(37))R25(o) unit cell, which compresses as the monolayer saturates to form a (square root(39) x square root(39))R16(o) structure. The square root(39) low-energy electron diffraction (LEED) pattern becomes more intense as the second layer grows, remaining bright for films up of 10-15 layers and then fading and disappearing for films more than ca. 40 layers thick. The ice multilayer consists of an ordered square root(39) wetting layer, on which ice grows as a crystalline film which progressively loses its registry to the wetting layer. Ice films more than ca. 50 layers thick develop a hexagonal LEED pattern, the entire film and wetting layer reorienting to form an incommensurate bulk ice. These changes are reflected in the vibrational spectra which show changes in line shape and intensity associated with the different ice structures. Thin amorphous solid water films crystallize to form the same phases observed during growth, implying that these structures are thermodynamically stable and not kinetic phases formed during growth. The change from a square root(39) registry to incommensurate bulk ice at ca. 50 layers is associated with a change in crystallization kinetics from nucleation at the Pt(111) interface in thin films to nucleation of incommensurate bulk ice in amorphous solid water films more than 50 layers thick.     

Atomic arrangements inside Ru and Os nanoislands spontaneously deposited on Pt(111)

The atomic arrangements inside Ru and Os nanoislands spontaneously deposited on Pt(111) electrode surface were observed with electrochemical scanning tunneling microscopy. The surperlattice of the pristine Ru nanodeposits is (square root of 3 x square root of 3)R30 degrees -RuO+. Upon reduction, the Ru nanodeposits are compressed to a uniaxially incommensurate (square root of 3 x square root of 2)R30 degrees -Ru structure, which does not change during the following reoxidation. The atomic arrangement inside the pristine Os nanodeposits is an incommensurate (square root of 2 x square root of 2)-OsO+ structure, which does not transform during the subsequent reduction-oxidation cycles. The structures of the Ru and Os nanodeposits are discussed in terms of removal and insertion of oxygen ions depending on electrode potential.     

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).     

Atomic rearrangements during the electrochemical treatments of Au(111) covered with irreversibly adsorbed Sb

A morphological variation of Au(111) covered with irreversibly adsorbed Sb was investigated with cyclic voltammetry and EC-STM. At open circuit potential (approximately 0.0 V vs a Ag/AgCl reference electrode), the oxygenated Sb layers were formed as an island on the wide terraces and a terrace at the step edges of Au(111). The ultimate morphology at the open circuit potential was a network adlayer with a (radical3 x radical3)R30 degrees atomic arrangement. When the oxygenated layer was reduced, the adsorption features, such as the island, shrunk or disappeared depending on their sizes. This modification was interpreted in terms of an alloy formation of Sb and Au. All of the Sb atoms, however, were not involved in the alloy formation, although the alloyed and unalloyed domains showed (radical3 x radical3)R30 degrees atomic structures with different brightness in EC-STM images. During oxidation of the reduced Sb layers, the alloyed and unalloyed domains of Sb behaved in a different way: the alloyed Sb was stripped to a soluble species to leave pits, while the unalloyed Sb became an oxygenated adspecies, which desorbed very slowly. A long oxidation led to a Au(111) covered with pits and islands of (1 x 1) without any adsorbed Sb.     

Sb在Pt(100),Pt(110),Pt(111)及Pt(320)上不可逆吸附的电化学特性

研究了Sb在Pt(1 0 0 ) ,Pt(1 1 0 ) ,Pt(1 1 1 )和Pt(32 0 )单晶面上不可逆吸附的电化学特性 .发现当扫描电位的上限Eu≤ 0 .45V时 ,Sbad可以稳定地吸附在Pt(1 0 0 ) ,Pt(1 1 0 )和Pt(1 1 1 )表面 ,而Sbad在Pt(32 0 )表面稳定的电位较低 ,为Eu≤ 0 .40V .从饱和吸附Sb的铂单晶电极出发 ,通过改变电位扫描上限Eu 和电位扫描圈数可以获得不同Sb覆盖度 (θSb)的电极 .根据Sb和H在铂单晶电极表面共吸附的定量数据 ,对Sb在不同铂单晶面上饱和吸附的模型进行了初步探讨 .     

Electrodeposition of Au monolayer on Pt(111) mediated by self-assembled monolayers

In-situ scanning tunneling microscopy (STM), cyclic voltammetry (CV), and infrared reflection-adsorption spectroscopy (IRRAS) have been used to examine the electrodeposition of gold onto Pt(111) electrodes modified with benzenethiol (BT) and benzene-1,2-dithiol (BDT) in 0.1 M HClO4 containing 10 microM HAuCl4. Both BT and BDT were attached to Pt(111) via one sulfur headgroup. STM and IRRAS results indicated that the other SH group of BDT was pendant in the electrolyte. Both BT and BDT formed (2 x 2) structures at the coverage of 0.25, and they were transformed into (square root(3) x square root(3))R30 degrees as the coverage was raised to 0.33. These two organic surface modifiers resulted in 3D and 2D gold islands at BT- and BDT-coated Pt(111) electrodes, respectively. The pendant SH group of BDT could interact specifically with gold adspecies to immobilize gold adatoms on the Pt(111) substrate, which yields a 2D growth of gold deposition. Molecular resolution STM revealed an ordered array of (6 x 2 square root(13)) after a full monolayer of gold was plated on the BDT/Pt(111) electrode. Since BDT was strongly adsorbed on Pt(111), gold adatoms only occupied free sites between BDT admolecules on Pt(111). This is supported by a stripping voltammetric analysis, which reveals no reductive desorption of BDT admolecules at a gold-deposited BDT/Pt(111) electrode. It seems that the BDT adlayer acted as the template for gold deposit on Pt(111). In contrast, a BT adlayer yielded 3D gold deposit on Pt(111). This study demonstrates unambiguously that organic surface modifiers could contribute greatly to the electrodeposition of metal adatoms.     

Self-assembled monolayers on Pt(111): molecular packing structure and strain effects observed by scanning tunneling microscopy

Self-assembled monolayers (SAMs) of octanethiol and benzeneethanethiol were deposited on clean Pt(111) surfaces in ultrahigh vacuum (UHV). Highly resolved images of these SAMs produced by an in situ scanning tunneling microscope (STM) showed that both systems organize into a super-structure mosaic of domains of locally ordered, closely packed molecules. Analysis of the STM images indicated a (square root 3 x square root 3)R30 degrees unit cell for the octanethiol SAMs and a 4(square root 3 x square root 3)R30 degrees periodicity based on 2 x 2 basic molecular packing for the benzeneethanethiol SAMs under the coverage conditions investigated. SAMs on Pt(111) exhibited differences in molecular packing and a lower density of disordered regions than SAMs on Au(111). Electron transport measurements were performed using scanning tunneling spectroscopy. Benzeneethanethiol/Pt(111) junctions exhibited a higher conductance than octanethiol/Pt(111) junctions.     

Electrochemical STM observation of new structures of CO adsorbed on a Pt(111) electrode surface

Presented are two newly observed adstructures of adsorbed CO onto Pt(111), (2 x 2)-3CO-beta and (2 x 2)-4CO, observed during the structural evolution from the well-known (2 x 2)-3CO-alpha structure to the (square root 19 x square root 19)-13CO structure.     

Tellurium adatoms as an in-situ surface probe of (111) two-dimensional domains at platinum surfaces

Irreversibly adsorbed tellurium has been studied as a probe to quantify ordered domains in platinum electrodes. The surface redox process of adsorbed tellurium on the Pt(111) electrode and Pt(111) stepped surfaces takes place around 0.85 V in a well-defined peak. The behavior of this redox process on the Pt(111) vicinal surfaces indicates that the tellurium atoms involved in the redox process are only those deposited on the (111) terrace sites. Moreover, the corresponding charge density is proportional to the number of sites on (111) ordered domains (terraces) that are, at least, three atoms wide. Hence, this charge density can be used to measure the number of (111) terrace sites on any given platinum sample. Structural information about tellurium adsorption is obtained from atomic-resolution STM images for the Pt(111) and Pt(10, 10, 9) electrodes. A rectangular structure (2 x radical 3) and a compact hexagonal structure (11 x 8) were identified. However, the redox peak for adsorbed tellurium on (100) domains at 1.03 V overlaps with peaks arising from steps and (110) sites. Therefore, it cannot be used without problems for the determination of (100) sites on a platinum sample. On the (100) terraces, the surface structure of the adsorbed tellurium is c(2 x 2), as revealed by STM. Finally, tellurium irreversible adsorption has been used to estimate the number of (111) ordered domains terrace sites on different polycrystalline platinum samples, and the results are compared to those obtained with bismuth irreversible adsorption.     

Structural evolution of irreversibly adsorbed Bi on Pt(111) under potential excursion

This work presents a structural evolution of irreversibly adsorbed Bi on Pt(111) studied by electrochemical scanning tunneling microscopy and electrochemistry. The irreversibly adsorbed Bi showed a stable redox couple at 0.33 V whose maximum charge corresponded to the coverage of 0.33. The pristine layer of irreversibly adsorbed Bi grew from islands to large domains of the first monolayer, eventually to large domains of the monolayer with scattered protrusions of the second layer. During an electrochemical treatment from open circuit potential (～0.25 V) to 0.1 V, the domains of the pristine Bi layer shrunk and the Bi in the second layer moved to the first layer to form a compressed layer of elemental Bi. When the elemental Bi was re-oxidized at 0.35 V, there was no structural change to denote that the structures of the pristine and re-oxidized layers of oxygenated Bi differ from each other. The structural evolution during the electrochemical treatments is discussed in terms of removal and reinsertion of oxygen species.     

Platinum nanofilm formation by EC-ALE via redox replacement of UPD copper: studies using in-situ scanning tunneling microscopy

The growth of Pt nanofilms on well-defined Au(111) electrode surfaces, using electrochemical atomic layer epitaxy (EC-ALE), is described here. EC-ALE is a deposition method based on surface-limited reactions. This report describes the first use of surface-limited redox replacement reactions (SLR(3)) in an EC-ALE cycle to form atomically ordered metal nanofilms. The SLR(3) consisted of the underpotential deposition (UPD) of a copper atomic layer, subsequently replaced by Pt at open circuit, in a Pt cation solution. This SLR(3) was then used a cycle, repeated to grow thicker Pt films. Deposits were studied using a combination of electrochemistry (EC), in-situ scanning tunneling microscopy (STM) using an electrochemical flow cell, and ultrahigh vacuum (UHV) surface studies combined with electrochemistry (UHV-EC). A single redox replacement of upd Cu from a PtCl(4)(2-) solution yielded an incomplete monolayer, though no preferential deposition was observed at step edges. Use of an iodine adlayer, as a surfactant, facilitated the growth of uniformed films. In-situ STM images revealed ordered Au(111)-(square root 3 x square root 3)R30 degrees-iodine structure, with areas partially distorted by Pt nanoislands. After the second application, an ordered Moiré pattern was observed with a spacing consistent with the lattice mismatch between a Pt monolayer and the Au(111) substrate. After application of three or more cycles, a new adlattice, a (3 x 3)-iodine structure, was observed, previously observed for I atoms adsorbed on Pt(111). In addition, five atom adsorbed Pt-I complexes randomly decorated the surface and showed some mobility. These pinwheels, planar PtI(4) complexes, and the ordered (3 x 3)-iodine layer all appeared stable during rinsing with blank solution, free of I(-) and the Pt complex (PtCl(4)(2-)).     

Acetaldehyde on Pt(111) and Pt/Sn(111): a DFT study of the adsorption structures and of the vibrational spectra

The relative stability of the eta1mu1 (atop) and eta2mu2 (di-sigma) geometries of acetaldehyde are compared on Pt(111) and on two PtSn alloys ((2 x 2) and (square root(3) x square root(3))R30 degrees) by means of density functional theory (DFT) calculations. At low coverage on Pt (1/9 ML), the two forms are equivalent in energy, with eta1mu1 being slightly more stable. At high coverage (1/4 and 1/3 ML), eta2mu2 is less competitive and acetaldehyde is adsorbed through the aldehydic hydrogen. The evolution of the adsorption energy with the coverage and the apparition of the structure adsorbed through the aldehydic hydrogen are explained by the existence of attractive dipole-dipole interactions. On PtSn, only the eta1mu1 geometry is stable with an adsorption energy equal to that on Pt, in agreement with temperature-programmed desorption (TPD) experiments. The calculated vibrational spectra allow us to conclude that the experimental spectrum corresponds to a mixture of eta1mu1 (majority) and eta2mu2 (minority) structures on Pt and to only eta1mu1 on PtSn. The various interactions and the relative stability of the species on Pt and PtSn are explained by the density of states (DOS) curves.     

Self-assembled monolayers of 4-mercaptopyridine on Au(111): a potential-induced phase transition in sulfuric acid solutions

In situ scanning tunneling microscopy images of self-assembled monolayers (SAMs) of 4-mercaptopyridine (4-MPy) on Au(111) recorded in neat 0.1 M H2SO4 solutions provided evidence for a potential-induced phase transition over the range 0.40-0.15 V versus saturated calomel electrode. Analysis of the data was consistent with the presence of a (5 x square root(3)) and (10 x square root(3)) superstructure (phase A) at the positive end, that is, 0.40 V, for which the local coverage, theta(loc), is about 0.2 (two 4-MPy molecules per unit cell), which compresses at the negative end, that is, 0.15 V, to yield a much denser superstructure (phase B, theta(loc) ca. 0.5). This behavior is unlike that reported for the 4-MPy-Au(111) SAM prepared by identical means, in 0.1 M HClO4 (or in sulfate solutions of a much higher pH) for which only the (5 x square root(3)) superstructure was observed over the same potential range. The compression associated with the phase A to phase B transition is attributed to the formation of a hydrogen-bonded network of bisulfate coordinated in turn to the 4-MPy layer via the acidic hydrogens of the pyridinium moieties. Such conditions promote better packing of adsorbed 4-MPy species, which are aided by intermolecular pi-pi ring interactions, resulting in higher local coverages.     

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.     

Ultrathin TiO(x) films on Pt(111): a LEED, XPS, and STM investigation

Ultrathin ordered titanium oxide films on Pt(111) surface are prepared by reactive evaporation of Ti in oxygen. By varying the Ti dose and the annealing conditions (i.e., temperature and oxygen pressure), six different long-range ordered phases are obtained. They are characterized by means of low-energy electron diffraction (LEED), X-ray photoemission spectroscopy (XPS), and scanning tunneling microscopy (STM). By careful optimization of the preparative parameters, we find conditions where predominantly single phases of TiO(x), revealing distinct LEED pattern and STM images, are produced. XPS binding energy and photoelectron diffraction (XPD) data indicate that all the phases, except one (the stoichiometric rect-TiO2), are one monolayer thick and composed of a Ti-O bilayer with interfacial Ti. Atomically resolved STM images confirm that these TiO(x) phases wet the Pt surface, in contrast to rect-TiO2. This indicates their interface stabilization. At a low Ti dose (0.4 monolayer equivalents, MLE), an incommensurate kagomé-like low-density phase (k-TiO(x) phase) is observed where hexagons are sharing their vertexes. At a higher Ti dose (0.8 MLE), two denser phases are found, both characterized by a zigzag motif (z- and z'-TiO(x) phases), but with distinct rectangular unit cells. Among them, z'-TiO(x), which is obtained by annealing in ultrahigh vacuum (UHV), shows a larger unit cell. When the postannealing of the 0.8 MLE deposit is carried out at high temperatures and high oxygen partial pressures, the incommensurate nonwetting, fully oxidized rect-TiO2 is found The symmetry and lattice dimensions are almost identical with rect-VO2, observed in the system VO(x)/Pd(111). At a higher coverage (1.2 MLE), two commensurate hexagonal phases are formed, namely the w- [(square root(43) x square root(43)) R 7.6 degrees] and w'-TiO(x) phase [(7 x 7) R 21.8 degrees]. They show wagon-wheel-like structures and have slightly different lattice dimensions. Larger Ti deposits produce TiO2 nanoclusters on top of the different monolayer films, as supported both by XPS and STM data. Besides the formation of TiO(x) surfaces phases, wormlike features are found on the bare parts of the substrate by STM. We suggest that these structures, probably multilayer disordered TiO2, represent growth precursors of the ordered phases. Our results on the different nanostructures are compared with literature data on similar systems, e.g., VO(x)/Pd(111), VO(x)/Rh(111), TiO(x)/Pd(111), TiO(x)/Pt(111), and TiO(x)/Ru(0001). Similar and distinct features are observed in the TiO(x)/Pt(111) case, which may be related to the different chemical natures of the overlayer and of the substrate.     

Scanning tunneling microscopy of sulfur and benzenethiol chemisorbed on Ru(0001) in 0.1 M HClO4

In situ scanning tunneling microscopy (STM) combined with linear sweep voltammetry was used to examine spatial structures of sulfur adatoms (SA) and benzenethiol (BT) molecules adsorbed on an ordered Ru(0001) electrode in 0.1 M HClO4. The Ru(0001) surface, prepared by mechanical polishing and electrochemical reduction at -1.5 V (vs RHE) in 0.1 M HClO4, contained atomically flat terraces with an average width of 20 nm. Cyclic voltammograms obtained with an as-prepared Ru(0001) electrode in 0.1 M HClO4 showed characteristics nearly identical to those of Ru(0001) treated in high vacuum. High-quality STM images were obtained for SA and BT to determine their spatial structures as a function of potential. The structure of the SA adlayer changed from (2 x mean square root of 3)rect to domain walls to (mean square root of 7 x mean square root of 7)R19.1 degrees and then to disordered as the potential was scanned from 0.3 to 0.6 V. In contrast, molecules of BT were arranged in (2 x mean square root of 3)rect between 0.1 and 0.4 V, while they were disordered at all other potentials. Adsorption of BT molecules was predominantly through the sulfur headgroup. Sulfur adatoms and adsorbed BT molecules were stable against anodic polarization up to 1.0 V (vs RHE). These two species were adsorbed so strongly that their desorption did not occur even at the onset potential for the reduction of water in 0.1 M KOH.     

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.     

Density functional theory investigation of benzenethiol adsorption on Au(111)

We have studied the adsorption of benzenethiol molecules on the Au(111) surface by using first principles total energy calculations. A single thiolate molecule is adsorbed at the bridge site slightly shifted toward the fcc-hollow site, and is tilted by 61 degrees from the surface normal. As for the self-assembled monolayer (SAM) structures, the (2 square root of 3 x square root of 3)R30 degrees herringbone structure is stabilized against the (square root 3 x square root 3)R30 degrees structure by large steric relaxation. In the most stable (2 square root 3 x square root 3)R30 degrees SAM structure, the molecule is adsorbed at the bridge site with the tilting angle of 21 degrees, which is much smaller compared with the single molecule adsorption. The van der Waals interaction plays an important role in forming the SAM structure. The adsorption of benzenethiolates induces the repulsive interaction between surface Au atoms, which facilitates the formation of surface Au vacancy.