Double dative bond configuration: pyrimidine on Ge(100)

The adsorption of pyrimidine onto Ge(100) surfaces has been investigated using real-time scanning tunneling microscopy (STM), temperature-programmed desorption (TPD), and density-functional theory (DFT) calculations. Our results show that the adsorbed pyrimidine molecules are tilted about 40 degrees with respect to the Ge surface, and through a Lewis acid-base reaction form bridges between the down-Ge atoms of neighboring Ge dimer rows by double Ge-N dative bonding without loss of aromaticity. For coverages of pyrimidine up to 0.25 ML, a well-ordered c(4x2) structure results from states that appear in STM micrographs as oval-shaped protrusions, which correspond to pyrimidine molecules datively adsorbed on every other dimer. However, above 0.25 ML, the oval-shaped protrusions gradually change into brighter zigzag lines. At 0.50 ML, a p(2x2) structure results from the states that appear in STM as zigzag lines. The zigzag lines are formed by the attachment of pyrimidine molecules to the down-Ge atoms of every Ge dimer. However, the unstable p(2x2) structure eventually reconstructs into a c(4x2) structure due to steric hindrance between the adsorbed pyrimidine molecules after stopping the exposure of pyrimidine to the surface.     

乙炔在Ge(001)表面吸附的反应路径

采用第一性原理方法研究了乙炔分子在Ge(001)表面的吸附反应.通过系统考察0.5和1.0ML覆盖度时形成di-σ和end-bridge构型的反应路径,研究在表面形成di-σ和paired-end-bridge构型的反应几率.除了表面反应以外,本文还涉及了亚表层Ge原子参与的吸附反应,乙炔在亚表层原子上吸附形成的亚稳态结构sub-di-σ,是形成end-bridge结构的第二条途径,此反应机理对于表面吸附结构的形成起重要的作用.与乙炔分子不同的是,表面以下原子参与时乙烯分子的吸附反应为吸热反应.综合热力学和动力学的分析表明,paired-end-bridge构型是乙炔分子吸附的主要构型,此结论解释了乙炔分子在Ge(001)表面吸附构型的实验结果.对于乙烯和乙炔两分子在Ge(001)表面吸附的分析比较揭示了导致两者之间差异的原因.     

锌电极上2-巯基吡啶自组装单层的原位表面增强拉曼光谱电化学观察

利用原位表面增强拉曼散射(SERS)技术, 观察了2-巯基吡啶在锌电极上单层吸附和脱附行为. SERS实验结果表明, 2-巯基吡啶分子主要通过巯基上的硫原子垂直吸附于锌表面. 原位SERS光谱电化学发现, 当外加电位达到－1.4 V vs. SCE时, 分子开始从表面脱附, 并伴随吸附构型变化, 在－1.6 V时发生完全脱附.     

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.     

STM observation of a ruthenium dye adsorbed on a TiO2(110) surface

Individual Ru(4,4'-dicarboxy-2,2'-bipyridine)2(NCS)2 molecules, commonly known as N3, adsorbed on a TiO2 surface were visualized with a scanning tunneling microscope (STM) operated in ultrahigh vacuum. A TiO2(110)-(1 x 1) crystal was taken out from the vacuum vessel and immersed into an acetonitrile solution of N3. A monolayer of pivalate ((CH3)3CCOO-) ions was used to protect the (1 x 1) surface from contamination during the wetting process of the N3 adsorption. The N3 molecules adsorbed on the flat terraces protruded by 0.65 nm from the pivalate monolayer. The image height difference of the admolecules could be understood with the assumption that the N3 molecules anchor to the TiO2 surface via two carboxyl groups. The number density of the N3 molecules on the steps was higher than that on the terraces. The poorly coordinated Ti atoms exposed at the step edges form preferential sites where the carboxyl groups can approach, due to a lower steric obstacle or because the structure of the adsorbed N3 molecules suffers less distortion.     

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.     

Gd5-xYxTt4 (Tt = Si or Ge): effect of metal substitution on structure, bonding, and magnetism

A crystallographic study and theoretical assessment of the Gd/Y site preferences in the Gd 5- x Y x Tt 4 ( Tt = Si, Ge) series prepared by high-temperature methods is presented. All structures for the Gd 5- x Y x Si 4 system belong to the orthorhombic, Gd 5Si 4-type (space group Pnma). For the Gd 5- x Y x Ge 4 system, phases with x < 3.6 and x >or= 4.4 adopt the orthorhombic, Sm 5Ge 4-type structure. For the composition range of 3.6 相似文献   

Studies of CO adsorption on Pt(100), Pt(410), and Pt(110) surfaces using density functional theory

Adsorption of CO on Pt(100), Pt(410), and Pt(110) surfaces has been investigated by density functional theory (DFT) method (periodic DMol(3)) with full geometry optimization and without symmetry restriction. Adsorption energies, structures, and vibrational frequencies of CO on these surfaces are studied by considering multiple possible adsorption sites and comparing them with the experimental data. The same site preference as inferred experiments is obtained for all the surfaces. For Pt(100), CO adsorbs at the bridge site at low coverage, but the atop site becomes most favorable for the c(2 x 2) structure at 1/2 monolayer. For Pt(410) (stepped surface with (100) terrace and (110) step), CO adsorbs preferentially at the atop site on the step edge at 1/4 monolayer, but CO populates also at other atop and bridge sites on the (100) terrace at 1/2 monolayer. The multiple possible adsorption sites probably correspond to the multiple states in the temperature-programmed desorption spectra for CO desorption. For Pt(110), CO adsorbs preferentially at the atop site on the edge for both the reconstructed (1 x 2) and the un-reconstructed (1 x 1) surfaces. When adjacent sites along the edge row begin to be occupied, the CO molecules tilt alternately by ca. 20 degrees from the surface normal in opposite directions for both the (1 x 2) and (1 x 1) surfaces.     

Ge(001) as a template for long-range assembly of π-stacked coronene rows

The adsorption of coronene molecules (C(24)H(12)) on the Ge(001) surface has been studied by means of scanning tunnelling microscopy (STM). Upon room temperature deposition, the coronene molecules adsorb in an upright geometry forming compact layers patterned in rows for coverages of one monolayer and less, being the only example investigated so far in which a pure aromatic hydrocarbon forms a well-ordered monolayer on a non-passivated semiconductor surface. At half monolayer, the molecular rows consist of long chains of π-stacked molecules and the distance between molecular planes is 8 ?. This configuration is maintained upon cooling the system below the transition temperature of Ge(001) (~220 K), but the molecular layer experiences also a transition from rows perpendicular to rows parallel to the Ge dimer rows. We interpret our observations in terms of a weak bonging between molecules and substrate, which facilitates the formation of large ordered domains of molecules, revealing Ge(001) as an ideal template for the growth of this and other aromatic hydrocarbons.     

Ab initio study of surface acid-base reactions. The case of molecular and dissociative adsorption of ammonia on the (011) surface of rutile TiO2

The interaction of ammonia molecules with Lewis acid centers (Ti4+ metal ions) of the (011) surface of rutile TiO2 is investigated by density functional theory in order to understand, from first principle, the nature of acid-base reactions on solid surfaces. Unlike the rutile (110) surface that contains alternating rows of 5-fold and 6-fold Ti atoms, all Ti atoms of the (011) surface are 5-fold coordinated. This surface has shown considerable activity for numerous chemical reactions and is thus an ideal prototype. At 1/2 monolayer coverage, with respect to surface Ti atoms, the adsorption energy is found to be equal to 100 kJ mol-1, and drops to 58 kJ mol-1 at one monolayer coverage. Analysis of the electronic density of states (DOS) revealed information regarding the mode of adsorption. In particular, the nitrogen 3a1 and 2a1 orbitals appear to undergo significant changes upon adsorption, in agreement with photoelectron spectroscopy studies. Dissociative adsorption was also investigated on the same surface. Both NH2(Tis) + H(Os) and NH(Tis) + 2H(Os) modes of dissociative adsorption, where s stands for surface, are found to be less stable than the molecular (non dissociated) adsorption.     

1,2-Dibromoethane on Cu(100): bonding structure and transformation to C2H4

Temperature-programmed reaction/desorption, mass spectrometry, reflection-absorption infrared spectroscopy, x-ray photoelectron spectroscopy, and density functional theory calculations have been employed to explore the reaction and bonding structure of 1,2-C(2)H(4)Br(2) on Cu(100). Both the trans and gauche conformers are found to dissociate by breaking the C-Br bonds on clean Cu(100) at 115 K, forming C(2)H(4) and Br atoms. Theoretical investigations for the possible paths of 1,2-C(2)H(4)Br(2) → C(2)H(4) + 2Br on Cu(100) suggest that the barriers of the trans and gauche molecules are in the ranges of 0-4.2 and 0-6.5 kcal/mol, respectively. The C-Br scission temperature of C(2)H(4)Br(2) is much lower than that (~170 K) of C(2)H(5)Br on Cu(100). Adsorbed Br atoms can decrease the dissociation rate of the 1,2-C(2)H(4)Br(2) molecules impinging the surface. The 1,2-C(2)H(4)Br(2) molecules adsorbed in the first monolayer are structurally distorted. Both the trans and gauche molecules exist in the second monolayer, but with no preferential adsorption orientation. However, the trans molecule is the predominant species in the third or higher layer formed at 115 K. The layer structure is not thermally stable. Upon heating the surface to 150 K, the orientation of the trans 1,2-C(2)H(4)Br(2) molecules in the layer changes, leading to the rotation of the BrCCBr skeletal plane toward the surface normal on average and the considerable growth of the CH(2) scissoring peak. On oxygen-precovered Cu(100), decomposition of 1,2-C(2)H(4)Br(2) to form C(2)H(4) is hampered and no oxygenated hydrocarbons are formed. The presence of the oxygen atoms also increases the adsorption energy of the second-layer molecules.     

Initial oxidation of the Rh(110) surface: ordered adsorption and surface oxide structures

The initial oxidation of the Rh(110) surface was studied by scanning tunneling microscopy, core level spectroscopy, and density functional theory. The experiments were carried out exposing the Rh(110) surface to molecular or atomic oxygen at temperatures in the 500-700 K range. In molecular oxygen ambient, the oxidation terminates at oxygen coverage close to a monolayer with the formation of alternating islands of the (10x2) one-dimensional surface oxide and (2x1)p2mg adsorption phases. The use of atomic oxygen facilitates further oxidation until a structure with a c(2x4) periodicity develops. The experimental and theoretical results reveal that the c(2x4) structure is a "surface oxide" very similar to the hexagonal O-Rh-O trilayer structures formed on the Rh(111) and Rh(100) substrates. Some of the experimentally found adsorption phases appear unstable in the phase diagram predicted by thermodynamics, which might reflect kinetic hindrance. The structural details, core level spectra, and stability of the surface oxides formed on the three basal planes are compared with those of the bulk RhO2 and Rh2O3.     

Atomic structures of benzene and pyridine on Si(5 5 12)-2 x 1

The adsorption structures of benzene and pyridine on Si(5 5 12)-2 x 1 were studied at 80 K by using a low-temperature scanning tunneling microscope and density functional theory calculations. These structures are different from those observed on low-index Si surfaces: benzene molecules exclusively bind to two adatoms, that is, with di-sigma bonds between carbon atoms and silicon adatoms, leading to the loss of benzene aromaticity; in contrast, pyridine molecules interact with adatom(s) through either Si-N dative bonding or di-sigma bonds. Dative bonding configurations with pyridine aromaticity are the dominant adsorption features and are more stable than di-sigma bonding configurations. Thus the dative bonding of nitrogen-containing heteroaromatic molecules provides a strategy for the controlled attachment of aromatic molecules to high-index surfaces.     

First-principles study of the adsorption of cesium on Si(001)(2 x 1) surface

First-principles calculations based on density functional theory-generalized gradient approximation method have been performed on cesium adsorption on Si(001)(2 x 1) surface. The optimized geometries and adsorption energies have been obtained and the preferred binding sites have been determined for the coverage (Theta) of one monolayer and half a monolayer. At Theta = 0.5 ML the most stable adsorption site is shown to be T3 site. At Theta = 1 ML two Cs atoms are adsorbed at HH and T3 sites, respectively. It was found that the saturation coverage of Cs for the Si(001)(2 x 1)-Cs surface is one monolayer instead of half a monolayer. This finding supports the majority of experimental observations but does not support recent coaxial impact collision ion scattering spectroscopy investigations [Surf. Sci. 531, L340 (2003)] and He(+) Rutherford backscattering spectroscopy studies [Phys. Rev. B 62, 4545 (2000)]. Mulliken charge and overlap population analysis showed that the Cs-Si bond is indeed ionic rather than polarized covalent as generally assumed for alkali metal (AM) on Si(001)(2 x 1) surface. Geometrical structure analysis seems to have limitations in determining the nature of AM-substrate bond. We also found that the silicon surface is metallic and semiconducting for the coverages of 0.5 and 1 ML, respectively.     

The nature of alkanethiol self-assembled monolayer adsorption on sputtered gold substrates

A detailed study of the self-assembly and coverage by 1-nonanethiol of sputtered Au surfaces using molecular resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) is presented. The monolayer self-assembles on a smooth Au surface composed predominantly of [111] oriented grains. The domains of the alkanethiol monolayer are observed with sizes typically of 5-25 nm, and multiple molecular domains can exist within one Au grain. STM imaging shows that the (4 x 2) superlattice structure is observed as a (3 x 2) structure when imaged under noncontact AFM conditions. The 1-nonanethiol molecules reside in the threefold hollow sites of the Au[111] lattice and aligned along its [112] lattice vectors. The self-assembled monolayer (SAM) contains many nonuniformities such as pinholes, domain boundaries, and monatomic depressions which are present in the Au surface prior to SAM adsorption. The detailed observations demonstrate limitations to the application of 1-nonanethiol as a resist in atomic nanolithography experiments to feature sizes of approximately 20 nm.     

Binding characteristics of pyridine on Ag(110)

A combination of low-temperature scanning tunneling microscopy and density functional theory calculations was used to determine the binding characteristics of single pyridine molecules at a low coverage on a silver surface. The results indicated that pyridine binds to silver through the nitrogen atom in either a perpendicular or a parallel configuration with the latter structure being more prevalent. Both configurations are produced predominantly through electrostatic interaction between nitrogen and silver atoms. This is induced by charge redistribution in the pyridine molecule and nearby silver atoms upon pyridine adsorption.     

New insights in the c(4 x 2) reconstruction of hexadecanethiol on Au(111) revealed by grazing incidence X-ray diffraction

The c(4 x 2) structure of C16H33SH alkanethiol monolayers self-assembled on Au(111) has been studied by grazing incidence X-ray diffraction. This structure coexists on the surface with the (radical3x radical3)R30 degrees phase. The structural refinement of the c(4 x 2) phase has been accomplished by omitting the fractional order reflections common to both structures. The surface unit cell consists of four symmetry-independent molecules with atomic displacements related by couples, such that only two nonequivalent chains are present in the surface cell. The stability between neighbor chains is due to van der Waals interactions. The substrate plays an important and non-negligible role in the c(4 x 2) reconstruction. The lateral and normal substrate relaxations to the surface plane are small, and gold atom displacements are lower than 0.25 angstroms but contribute very strongly to the fractional order intensities. The molecular chains form a close packed structure tilted by 37 degrees from the surface normal with no indications of dimer formation between closest S atoms.     

An equilibrium ab initio atomistic thermodynamics study of chlorine adsorption on the Cu(001) surface

The effect of chlorine (Cl) chemisorption on the energetics and atomic structure of the Cu(001) surface over a wide range of chlorine pressures and temperatures has been studied using equilibrium ab initio atomistic thermodynamics to elucidate the formation of cuprous chloride (CuCl) as part of the Deacon reaction on copper metal. The calculated surface free energies show that the 1/2 monolayer (ML) c(2 × 2)-Cl phase with chlorine atoms adsorbed at the hollow sites is the most stable structure for a wide range of Cl chemical potential, in agreement with experimental observations. It is also found that at very low pressure and exposure, but elevated temperature, the 1/9 ML and 1/4 ML phases become the most stable. By contrast, a high coverage of Cl does not lead to thermodynamically stable geometries. The subsurface adsorption of Cl atoms, however, dramatically increases the stability of the 1 ML and 2 ML adsorption configurations providing a possible pathway for the formation of the bulk-chloride surface phases in the kinetic regime.     

Extreme differences in oxidation states: synthesis and structural analysis of the germanide oxometallates A10[Ge9]2[WO4] as well as A(10+x)[Ge9]2[W(1–x)Nb(x)O4] with A = K and Rb containing [Ge9]4- polyanions

Semitransparent dark-red or ruby-red moisture- and air-sensitive single crystals of A(10+x)[Ge(9)](2)[W(1-x)Nb(x)O(4)] (A = K, Rb; x = 0, 0.35) were obtained by high-temperature solid-state reactions. The crystal structure of the compounds was determined by single-crystal X-ray diffraction experiments. They crystallize in a new structure type (P2(1)/c, Z = 4) with a = 13.908(1) ?, b = 15.909(1) ?, c = 17.383(1) ?, and β = 90.050(6)° for K(10.35(1))[Ge(9)](2)[W(0.65(1))Nb(0.35(1))O(4)]; a = 14.361(3) ?, b = 16.356(3) ?, c = 17.839(4) ?, and β = 90.01(3)° for Rb(10.35(1))[Ge(9)](2)[W(0.65(1))Nb(0.35(1))O(4)]; a = 13.8979(2) ?, b = 15.5390(3) ?, c = 17.4007(3) ?, and β = 90.188(1)° for K(10)[Ge(9)](2)WO(4); and a = 14.3230(7) ?, b = 15.9060(9) ?, c = 17.8634(9) ?, and β = 90.078(4)° for Rb(10)[Ge(9)](2)WO(4). The compounds contain discrete Ge(9)(4-) Wade's nido clusters and WO(4)(2-) (or NbO(4)(3-)) anions, which are packed according to a hierarchical atom-to-cluster replacement of the Al(2)Cu prototype and are separated by K and Rb cations, respectively. The alkali metal atoms occupy the corresponding tetrahedral sites of the Al(2)Cu prototype. The amount of the alkali metal atoms on these diamagnetic compounds corresponds directly to the amount of W substituted by Nb. Thus, the transition metals W and Nb appear with oxidation numbers +6 and +5, respectively, in the vicinity of a [Ge(9)](4-) polyanion. The crystals of the mixed salts were further characterized by Raman spectroscopy. The Raman data are in good agreement with the results from the X-ray structural analyses.     

Surface dependence of CO2 adsorption on Zn2GeO4

An understanding of the interaction between Zn(2)GeO(4) and the CO(2) molecule is vital for developing its role in the photocatalytic reduction of CO(2). In this study, we present the structure and energetics of CO(2) adsorbed onto the stoichiometric perfectly and the oxygen vacancy defect of Zn(2)GeO(4) (010) and (001) surfaces using density functional theory slab calculations. The major finding is that the surface structure of the Zn(2)GeO(4) is important for CO(2) adsorption and activation, i.e., the interaction of CO(2) with Zn(2)GeO(4) surfaces is structure-dependent. The ability of CO(2) adsorption on (001) is higher than that of CO(2) adsorption on (010). For the (010) surface, the active sites O(2c)···Ge(3c) and Ge(3c)-O(3c) interact with the CO(2) molecule leading to a bidentate carbonate species. The presence of Ge(3c)-O(2c)···Ge(3c) bonds on the (001) surface strengthens the interaction of CO(2) with the (001) surface, and results in a bridged carbonate-like species. Furthermore, a comparison of the calculated adsorption energies of CO(2) adsorption on perfect and defective Zn(2)GeO(4) (010) and (001) surfaces shows that CO(2) has the strongest adsorption near a surface oxygen vacancy site, with an adsorption energy -1.05 to -2.17 eV, stronger than adsorption of CO(2) on perfect Zn(2)GeO(4) surfaces (E(ads) = -0.91 to -1.12 eV) or adsorption of CO(2) on a surface oxygen defect site (E(ads) = -0.24 to -0.95 eV). Additionally, for the defective Zn(2)GeO(4) surfaces, the oxygen vacancies are the active sites. CO(2) that adsorbs directly at the Vo site can be dissociated into CO and O and the Vo defect can be healed by the oxygen atom released during the dissociation process. On further analysis of the dissociative adsorption mechanism of CO(2) on the surface oxygen defect site, we concluded that dissociative adsorption of CO(2) favors the stepwise dissociation mechanism and the dissociation process can be described as CO(2) + Vo → CO(2)(δ-)/Vo → CO(adsorbed) + O(surface). This result has an important implication for understanding the photoreduction of CO(2) by using Zn(2)GeO(4) nanoribbons.