Study of adsorption and decomposition of H2O on Ge(100)

The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of H2O on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, H2O molecules are bound to the surface via Ge-O dative bonds between the O atom of H2O and the electrophilic down atom of the Ge dimer. In the dissociative adsorption geometry, the H2O molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in an H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the H2O coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the H2O molecule from the molecular adsorption to the dissociative adsorption geometry.     

The chemisorption of coronene on Si(001)-2 x 1

Coronene (C24H12) adsorption on the clean Si(001)-2 x 1 surface was investigated by scanning tunneling microscopy and by density-functional calculations. The coronene adsorbed randomly at 25 degrees C on the surface and did not form two-dimensional islands. The scanning tunneling microscopy measurements revealed three adsorption sites for the coronene molecule on the Si(001) surface at low coverage. The major adsorption configuration involves coronene bonding to four underlying Si atoms spaced two lattice spacings apart in a dimer row. The two minor adsorption configurations involve asymmetrical bonding of a coronene molecule between Si dimer rows and form surface species with a mirror plane symmetry to their chiral neighbor species. The two minor bonding arrangements are stabilized by a type-C defect on the Si(001) surface.     

Chemical reactions and adsorption geometries of pyrrole on Ge(100)

The adsorption structures of pyrrole (C(4)H(5)N) on a Ge(100) surface at various coverages have been investigated with both scanning tunneling microscopy (STM) and ab initio density-functional theory (DFT) calculations. Three distinct features are observed in the STM images at low coverages. The comparison of the STM images with the simulation reveals that the most dominant flowerlike feature with a dark side is that the adsorbed pyrrole molecules with H dissociated form bridges between two down Ge atoms of neighboring Ge dimer rows through N-Ge bonding and beta-carbon-Ge interaction. The flowerlike feature without a dark side is also observed as a minority, which is identified as nearly the same structure as the most dominant one where a dissociated H is out of the feature. The third feature showing bright protrusions may be due to a C- and N-end-on (CN) configuration, where the pyrrole molecule is located on one dimer row. At higher coverages, the number of localized configurations increases.     

Ethylenediamine on Ge(100)-2 x 1: the role of interdimer interactions

We have investigated the reaction of the bifunctional molecule ethylenediamine on Ge(100)-2 x 1 using multiple internal reflection Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and density functional theory calculations. Ethylenediamine exhibits different adsorption behavior than simple methylamines on the Ge(100)-2 x 1 surface. At low coverages, ethylenediamine undergoes dissociative chemisorption via an interdimer dual N-H dissociation reaction. As coverage increases, the N-H dissociation reaction is inhibited and formation of a Ge-N dative-bonded structure dominates.     

Formation of highly ordered organic monolayers by dative bonding: pyridine on ge(100)

The adsorption of pyridine onto the Ge(100) surface has been studied using both real-time scanning tunneling microscopy (STM) and ab initio pseudopotential density functional calculations. The results show that pyridine molecules adsorb on the electron-deficient down-Ge atoms of the Ge=Ge dimers via Ge-N dative bonding, with the pyridine ring tilted to the surface. The electron-rich up-Ge atoms remaining after adsorption of pyridine induce an asymmetric dimer row, which is mainly reconstructed to the c(4 x 2) structure. At pyridine coverage of 0.25 ML, the adsorbed pyridine molecules form a perfectly ordered monolayer. The entire Ge substrate underlying this organic monolayer rearranges into the c(4 x 2) structure.     

Density functional theory study of enantiospecific adsorption at chiral surfaces

Density functional theory calculations are carried out for the adsorption of a chiral molecule, (S)- and (R)-HSCH(2)CHNH(2)CH(2)P(CH(3))(2), on a chiral surface, Au(17 11 9)(S)(). The S-enantiomer is found to bind more strongly than the R-enantiomer by 8.8 kJ/mol, evidencing that the chiral nature of the kink sites at the Au(17 11 9) surface leads to enantiospecific binding. The adsorption of two related chiral molecules, HSCH(2)CHNH(2)COOH ("cysteine") and HSCH(2)CHNH(2)CH(2)NH(2), does not, however, lead to enantiospecific binding. The results of the density functional calculations are broken down into a local binding model in which each of the chiral molecule's three contact points with the surface provides a contribution to the overall adsorption bond strength. The enantiospecific binding is demonstrated to originate from the simultaneous optimization of these three local bonds. In the model, the deformation energy costs of both the molecule and the surface are further included. The model reveals that the molecule may undergo large deformations in the attempt to optimize the three bonds, while the surface deforms to a lesser extent. The most favorable binding configurations of each enantiomer are, however, characterized by small deformation energies only, justifying a local binding picture.     

Initial nitridation of the Ge(100)-2 x 1 surface by ammonia

The reaction of ammonia (NH(3)) on the Ge(100)-2 x 1 surface is investigated using density functional theory (DFT). We find that NH(3) adsorbs molecularly onto Ge(100)-2 x 1 via the formation of a dative bond. The calculations also show that, unlike Si(100)-2 x 1, the activation barrier for subsequent dissociation of NH(3) adsorbed on Ge(100)-2 x 1 is higher than that of reversible desorption, which indicates that NH(3) has a low reactive sticking probability on the Ge(100)-2 x 1 surface. We also predict that nitrogen insertion into the Ge-Ge dimer requires NH(3) overexposure because the activation barrier for NH(2) insertion into the Ge-Ge dimer is significantly above the entrance channel. The nitridation reaction pathway results in the N-H bridge-bonded state, which is found to be 17.4 kcal/mol more stable than the reactants. We find that the reactions of NH(3) on the Ge(100)-2 x 1 surface generally involve higher activation barriers and less stable intermediates than the analogous reactions on the Si(100)-2 x 1 surface.     

Calculation of dye-dye and dye-AgX surface interaction energies

The computation of the interaction energy between an adsorbed dye molecule and the silver halide surface has been accomplished through the use of a new code which is based upon CHEMLAB. The surface interaction energies have been computed for 1,1′-ethylene-2,2′-cyanine, a dye molecule, in both monomeric and aggregated configurations on the (100) surfaces of AgBr and AgCl. The model predicts reasonable configurations for the adsorbed dye monomer and its H- and B-aggregates. At high dye levels, the adsorption of aggregated forms is found to be favored over an adsorbed monolayer of monomeric dye molecules. Using the current interaction potentials, however, it was found that the adsorption of the dye on the AgCl (100) surface was slightly favored over that on the AgBr (100) surface. This finding, although at variance with experimental data, may be attributed to the use of an unrelaxed silver halide surface in these computations.     

Self-induced 1-D molecular chain growth of thiophene on Ge(100)

The adsorption of thiophene on Ge(100) has been studied using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculations. Until now, thiophene is known to react with the Ge(100) dimer through a [4 + 2] cycloaddition reaction at room temperature, similar to the case of thiophene on Si(100). However, we found that thiophene has two adsorption geometries on Ge(100) at room temperature, such as a kinetically favorable Ge-S dative bonding configuration and a thermodynamically stable [4 + 2] cycloaddition adduct. Moreover, our STM results show that under 0.25 ML thiophene molecules preferentially produce one-dimensional molecular chain structures on Ge(100) via the Ge-S dative bonding configuration.     

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.     

Density functional study of XH4 (XSi and Ge) reactivity upon dissociative adsorption onto the Si(100) surface

Total energy calculations based on density functional theory (DFT) with generalized gradient approximation (GGA) and ultrasoft pseudopotential approximation and an analysis tool of atom‐resolved density of states (ADOS) have been used to investigate (1) the energetic profiles for the possible initial dissociative adsorption of XH₄ (X?Si and Ge) onto the Si(100)? (2 × 2) surface to evaluate their reactivity and (2) the effect of surface electronic states of Si(100)? (2 × 2) on gaseous molecular precursors XH₄ (X?Si and Ge) during initial dissociative adsorption to understand the factors governing their reactivity. Our calculated lower‐energy barrier for initial dissociative adsorption of GeH₄ is due to the forming of stronger bond of Si? H between H within GeH₄ and buckled‐down Si atom on the Si(100)? (2 × 2) surface accompanying the larger extent of unbuckling of the buckled Si?Si dimer on the Si(100)? (2 × 2) surface at the transition state. Our evaluated better reactivity for GeH₄ than SiH₄ (a factor of around 14.6) is slightly larger than observed higher reactivity for GeH₄ than SiH₄ (a factor of between 2 and 5 depending on the incident kinetic energy) employed supersonic molecular bean techniques. Finally, our calculated ADOS indicate that the surface electronic states of buckled Si?Si dimer on the Si(100)? (2 × 2) surface energetically favorably participate in the transition state during GeH₄ initial dissociative adsorption to reduce the energy barrier, i.e., enhance its reactivity, in comparison with SiH₄ initial dissociative adsorption onto the Si(100)? (2 × 2) surface under the same reaction conditions. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Self-directed chain reaction by small ketones with the dangling bond site on the Si(100)-(2 x 1)-H surface: acetophenone, a unique example

Using scanning tunneling microscope (STM) at 300 K, we studied the growth of one-dimensional molecular assemblies (molecular lines) on the Si(100)-(2 x 1)-H surface through the chain reaction of small ketone (CH 3COCH 3, PhCOPh, and PhCOCH 3) molecules with dangling bond (DB) sites of the substrate. Acetone and benzophenone show the growth of molecular lines exclusively parallel to the dimer row direction. In contrast, acetophenone molecules show some molecular lines perpendicular, in addition to parallel, to the dimer row direction. Most of the molecular lines perpendicular to the dimer row direction were grown by self-turning the propagation direction of a chain reaction from parallel to perpendicular directions relative to the dimer row. A chiral center created upon adsorption of an acetophenone molecule allows the adsorbed molecules to align with identical as well as alternate enantiomeric forms along the dimer row direction, whereas such variations in molecular arrangement are not observed in the case of acetone and benzophenone molecules. The observed molecular lines growth both parallel and perpendicular to dimer row directions appears to be unique to acetophenone among all the molecules studied to date. Hence, the present study opens new possibility for fabricating one-dimensional molecular assemblies of various compositions in both high-symmetry directions on the Si(100)-(2 x 1)-H 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.     

Adsorption Sequence of Multifunctional Groups: A Study on the Reaction Pathway and the Adsorption Structure of Homocysteine on the Ge(100) Surface

We investigated the adsorption mechanism of homocysteine (HS? CH₂? CH₂? CH(NH₂)? COOH) on the Ge(100) surface along with its electronic structures and adsorption geometries to determine the sequence of adsorption of this amino acid′s functional groups using core‐level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations. We found that the “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” and the “SH‐dissociated OH‐dissociation‐bonded structure” were preferred at a monolayer (ML) coverage of 0.30 (lower coverage) and 0.60 (higher coverage), respectively. The “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” was the most stable structure. Moreover, we systematically confirmed the sequence of adsorption of the functional groups of the homocysteine molecule on the Ge(100) surface, which is thiol group (? SH), carboxyl group (? COOH), and amine group (? NH₂).     

Surface S(N)2 reaction by H2O on chlorinated Si(100)-2 x 1 surface

The potential energy surfaces of one, two, and three water molecule sequential adsorptions on the symmetrically chlorinated Si(100)-2 x 1 surface were theoretically explored with SIMOMM:MP2/6-31G(d). The first water molecule adsorption to the surface dimer requires a higher reaction barrier than the subsequent second water molecule adsorption. The lone pair electrons of the incoming water molecule nucleophilically attack the surface Si atom to which the leaving Cl group is bonded, yielding an S(N)2 type transition state. At the same time, the Cl abstracts the H atom of the incoming water molecule, forming a unique four-membered ring conformation. The second water molecule adsorption to the same surface dimer requires a much lower reaction barrier, which is attributed to the surface cooperative effect by the surface hydroxyl group that can form a hydrogen bond with the incoming second water molecule. The third water molecule adsorption exhibits a higher reaction barrier than the first and the second water molecule adsorption channels but yields a thermodynamically more stable product. In general, it is expected that the surface Si-Cl bonds can be subjected to the substitution reactions by water molecules, yielding surface Si-OH bonds, which can be a good initial template for subsequent surface chemical modifications. However, oversaturations can be a competing side reaction under severe conditions, suggesting that the precise control of surface kinetic environments is necessary to tailor the final surface characteristics.     

Chemisorption of barrelene on Si(100) from first principles calculations

The chemisorption of C8H8 bicyclo[2.2.2]-2,5,7-octatriene (barrelene) on the Si(100) surface is studied from first principles calculations. We find that, in the most stable configuration, barrelene is bonded to Si(100) through four Si-C bonds, with the C-C bonds which are orthogonal to the underlying Si dimers. The chemisorption reaction responsible for this structure is driven by the biradical nature of the Si-Si dimer bond. Two others, slightly less stable configurations, exist which are also characterized by four Si-C bonds but have a different orientation or location with respect to the Si(100) surface. The properties of these and other, less stable configurations have been investigated. For the most stable structures, the effect of different surface coverages has been also studied, showing a tendency to easily form complete monolayers of barrelene on the Si surface. On the basis of energetic and kinetic considerations, we expect that chemisorption of barrelene monolayers on the Si(100) surface will be characterized however by a certain amount of disorder. Finally, several possible reaction pathways, leading from one stable structure to another of lower energy or from a molecule in the gas phase to a chemisorbed configuration, have been investigated in detail and estimates of the relative energy barriers are given.     

Reaction Behaviors of S-, O-, and N-containing Aliphatic Molecules with a Propyl Moiety on Ge(100) Surface

The reaction pathways of 1-propanethiol, 1-propanol, and propylamine molecules, containing a propyl moiety, on a Ge(100) surface were investigated using high-resolution photoemission spectroscopy (HRPES) experiments and density functional theory (DFT) calculations. Upon analysis of the HRPES data, the adsorption of 1-propanethiol and 1-propanol was found to occur through a dissociation reaction, whereas that of propylamine took place via N dative bonding at room temperature. On the basis of our DFT results, adsorption geometries and transition states for each of these molecules on the Ge(100) surface were confirmed. Systematic studies of S-, O-, and N-containing molecules, composed of an identical propyl moiety, on the Ge(100) surface provide insight into the adsorption mechanism of aliphatic molecules containing alkyl chains on the Ge(100) surface.     

Bidentate Surface Structures of Glycylglycine on Si(111)7×7 by High-Resolution Scanning Tunneling Microscopy: Site-Specific Adsorption via N-H and O-H or Double N-H Dissociation

The early adsorption stage of glycylglycine on Si(111)7×7 surface has been studied by scanning tunneling microscopy (STM). Filled-state imaging shows that glycylglycine adsorbs dissociatively in a bidentate fashion on two adjacent Si adatoms across a dimer wall or an adatom-restatom pair, with the dissociated H atoms on neighboring restatoms. The present STM result validates our hypothesis that both bidentate configurations involving N-H and O-H dissociation and double N-H dissociation are equally probable. Our STM results further show that the relative surface concentrations of the five bidentate configurations follow a specific ordering. This suggests that N-H dissociation at a center adatom site would likely be followed by N-H dissociation at an adjacent restatom, while N-H dissociation at a corner adatom site would be succeeded by O-H dissociation at an adatom across the dimer wall. Evidently, the strong bidentate interactions also inhibit surface diffusion of the adsorbed glycylglycine fragment, and the adsorption apparently follows random sequential adsorption statistics. The random nature of adsorption is also supported by the similar relative occupancies of the center adatom and corner adatom sites, indicating that the relative reactivities of these adatom sites do not play a significant role. Our DFT computational study shows that all three bidentate (Si-)NHCH(2)CONHCH(2)COO(-Si) adatom-adatom configurations (center-center, corner-corner, center-corner) have similar adsorption energies for a double adatom-adatom pair across the dimer wall, while the (Si-)NHCH(2)CON(-Si)CH(2)COOH bidentate adatom-restatom configuration is energetically favorable. The free -CONH- and -COOH groups remaining on the respective bidentate adstructures could facilitate adsorption of the second adlayer through the formation of hydrogen bonding.