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.     

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-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.     

First-principles investigation of the adsorption of the 2,5-pyridine di-carboxylic acid onto the Cu(011) surface

First-principles calculations within the density functional theory (DFT) framework have been performed in order to investigate various conformations of the 2,5-pyridine di-carboxylic acid (PDCA) molecule adsorbed onto the Cu(011) surface. By means of DFT calculations the adsorption geometry, the bond formation and the electronic properties of PDCA molecule conformations on the Cu(011) surface have been studied. The most important structural property is the orientation of the COOH H atom which can point either toward the aromatic ring or toward the vacuum. This H atom position determines the possible reactions in which the adsorbed molecule can get involved and also has a significant impact on the value of the Cu-molecule system work function. Thus, we find that simply by changing the H atom orientation (from up to down) the Cu-molecule system work function can be varied with more than 2.5 eV. This is a significant result as a lot of effort is put nowadays in finding efficient ways for the in situ variation of the systems work function. Scanning tunneling microscopy (STM) images, reflexion absorption infrared vibrational spectra (RAIRS) as well as various thermodynamic properties (adsorption entropies, enthalpies) have also been investigated in order to get a better insight into the system studied and to provide support to possible experimental studies (STM or RAIRS experiments).     

The initial growth behavior of perylene on Cu(100)

Using scanning tunneling microscopy (STM) together with density functional theory (DFT) the growth behavior of perylene on the Cu(100) substrate has been investigated. As revealed by STM images, perylene molecules prefer to adopt lying configuration with their molecular plane parallel to the substrate, and two symmetrically equivalent ordered domains were observed. DFT calculations show that perylene molecule prefers to adsorb on the top site of substrate Cu atoms with its long molecular axis aligning along the [011] or [01-1] azimuth of the substrate which is the most stable adsorption geometry according to its highest binding energy. Consequently, two adsorption structures of c(8×4) and c(8×6), each containing two perylene molecules per unit cell, are proposed based on our STM images. The growth mechanism for ordered perylene domains on Cu(100) can be attributed to the balance between weak adsorbate-adsorbate interaction and comparable adsorbate-substrate interaction.     

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.     

Atomic imaging of nucleation of trimethylaluminum on clean and H2O functionalized Ge(100) surfaces

The direct reaction of trimethylaluminum (TMA) on a Ge(100) surface and the effects of monolayer H(2)O pre-dosing were investigated using ultrahigh vacuum techniques, such as scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and x-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). At room temperature (RT), a saturation TMA dose produced 0.8 monolayers (ML) of semi-ordered species on a Ge(100) surface due to the dissociative chemisorption of TMA. STS confirmed the chemisorption of TMA passivated the bandgap states due to dangling bonds. By annealing the TMA-dosed Ge surface, the STM observed coverage of TMA sites decreased to 0.4 ML at 250?°C, and to 0.15 ML at 450?°C. XPS analysis showed that only carbon content was reduced during annealing, while the Al coverage was maintained at 0.15 ML, consistent with the desorption of methyl (-CH(3)) groups from the TMA adsorbates. Conversely, saturation TMA dosing at RT on the monolayer H(2)O pre-dosed Ge(100) surface followed by annealing at 200?°C formed a layer of Ge-O-Al bonds with an Al coverage a factor of two greater than the TMA only dosed Ge(100), consistent with Ge-OH activation of TMA chemisorption and Ge-H blocking of CH(3) chemisorption. The DFT shows that the reaction of TMA has lower activation energy and is more exothermic on Ge-OH than Ge-H sites. It is proposed that the H(2)O pre-dosing enhances the concentration of adsorbed Al and forms thermally stable Ge-O-Al bonds along the Ge dimer row which could serve as a nearly ideal atomic layer deposition nucleation layer on Ge(100) surface.     

Molecular Dissociation on the SiC(0001) 3×3 Surface

In the framework of density functional theory, the adsorption of the halogenated polycyclic aromatic hydrocarbon 2,11‐diiodohexabenzocoronene (HBC‐I₂) on the SiC(0001) 3×3 surface has been investigated. Nondissociative and dissociative molecular adsorption is considered, and simulated scanning tunneling microscopy (STM) images are compared with the corresponding experimental observations. Calculations show that dissociative adsorption is favorable and reveal the crucial importance of the extended flat carbon core on molecule–surface interactions in dissociative adsorption; the iodine atom–surface interaction is of minor importance. Indeed, removing iodine atoms does not significantly affect the STM images of the central part of the molecule. This study shows that the dissociation of large halogenated polycyclic aromatic hydrocarbon molecules can occur on the SiC surface. This opens up interesting perspectives in the chemical reactivity and functionalization of wide band gap semiconductors.     

First-principles Calculations of H2O Adsorption Reaction on the GaN（0001） Surface

The adsorption and decomposition of H2O on GaN（0001） surface have been explored employing density functional theory （DFT）. Two distinct adsorption features of H2O on GaN（0001） corresponding to molecular adsorption and H-OH dissociative adsorption are revealed by our calculations. The activities of the surface reactions of H2O on GaN（0001） surface are investigated. For the stepwise processes of H2O decomposition into H2 in gas phase and adsorbed O atom （H2O（g）→H2O（chem）→OH（chem） ＋ H（chem）→2H（chem） ＋ O（chem）→H2（g） ＋ O（chem））, the first and second steps are facile and can even occur at room temperature; while the last two have high barriers and thus are difficult to proceed, especially the fourth step is endothermic. In short, H2O adsorption and decomposition into H2 in gas phase and adsorbed O atom on GaN（0001） surface are exothermic by -43.98 kcal/mol.     

Properties of ternary insulating systems: the electronic structure of MgSO4.H2O

Structural and electronic properties of (100)-oriented MgSO(4) and MgSO(4).H(2)O surfaces and the adsorption of water on the latter were investigated theoretically with a combination of ab initio and semiempirical methods. Ab initio electronic structure calculations were based on a density functional theory (DFT)-Hartree-Fock (HF) hybrid approach. The semiempirical method MSINDO was used for the determination of the local adsorption geometry of the water molecule. With the hybrid method good agreement was obtained with the experimental band gap of 7.4 eV determined with electron energy loss spectroscopy of polycrystalline MgSO(4).H(2)O samples under ultrahigh vacuum conditions. The valence bands of the (100) surfaces of both MgSO(4) and MgSO(4).H(2)O are formed mainly by the O2p levels, whereas the S2p states contribute to the lower part of the conduction band. The preferred adsorption site of water at MgSO(4).H(2)O (100) is above a surface Mg atom. The water molecule is stabilized by two additional hydrogen bonds with surface atoms. Only small differences between the electronic structure of MgSO(4).H(2)O and MgSO(4) were observed. Also, the molecular adsorption of water on the MgSO(4).H(2)O surface leads to only small shifts of the electronic energy levels.     

Methanol adsorption on the beta-Ga2O3 surface with oxygen vacancies: theoretical and experimental approach

Methanol adsorption on beta-Ga2O3 surface has been studied by Fourier transform infrared spectroscopy (FTIR) and by means of density functional theory (DFT) cluster model calculations. Adsorption sites of tetrahedral and octahedral gallium ions with different numbers of oxygen vacancies have been compared. The electronic properties of the adsorbed molecules have been monitored by computing adsorption energies, optimized geometry parameters, overlap populations, atomic charges, and vibrational frequencies. The gallia-methanol interaction has different behaviors according to the local surface chemical composition. The calculations show that methanol can react in three different ways with the gallia surface giving rise to a nondissociative adsorption, a dissociative adsorption, and an oxidative decomposition. The surface without oxygen vacancies is very reactive and produces the methanol molecule decomposition. The molecule is nondissociatively adsorbed by means of a hydrogen bond between the alcoholic hydrogen atom and a surface oxygen atom and a bond between the alcoholic oxygen atom and a surface gallium atom. Two neighbor oxygen vacancies on tetrahedral gallium sites produce the dissociation of the methanol molecule and the formation of a bridge bond between two surface gallium atoms and the methoxy group.     

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.     

Study of CO adsorption on perfect and defective pyrite(100)surfaces by density functional theory

First-principles calculations based on density functional theory (DFT) and the generalized gradient approximation (GGA) have been used to study the adsorption of CO molecule on the perfect and defective FeS 2 (100) surfaces. The defective Fe 2 S(100) surfaces are caused by sulfur deficiencies. Slab geometry and periodic boundary conditions are employed with partial relaxations of atom positions in calculations. Two molecular orientations, Cand O-down, at various distinct sites have been considered. Total energy calculations indicated that no matter on perfect or deficient surfaces, the Fe position is relatively more favored than the S site with the predicted binding energies of 120.8 kJ/mol and 140.8 kJ/mol, respectively. Moreover, CO was found to be bound to Fe atom in vertical configuration. The analysis of density of states and vibrational frequencies before and after adsorption showed clear changes of the C–O bond.     

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.     

Interaction of dihydrogen with small and light molecules

Second-order M?ller-Plesset (MP2) calculations (using the approximate resolution of the identity, RI-MP2), explicitly correlated MP2 (MP2-R12) calculations, and coupled-cluster calculations including all single and double excitations with a perturbative estimate of triple excitations [CCSD(T)] are performed to study the interaction of molecular hydrogen with the small molecules HF, H2O, NH3, and LiOH. Different adsorption positions are studied. In the cases of H2O and NH3, the most favorable configuration places H2 in an end-on fashion on the O or N atom, respectively. In the cases of HF and LiOH, the H2 molecule takes a side-on position on the H atom of HF or the Li atom. With respect to MP2 calculations in a triple-zeta basis, both the enlargement of the basis set and the extension of the correlation treatment (CCSD(T) vs MP2) increase the interaction energy. The basis set limit CCSD(T) estimates of the interaction energy of H2 with the HF, H2O, NH3, and LiOH molecules amount to 4.40, 2.67, 3.02, and 10.74 kJ mol-1, respectively. The interaction energy for the simultaneous interaction of H2 with two LiOH molecules does not significantly exceed the value obtained for the interaction with a single LiOH molecule. Furthermore, the interaction energies (by MP2) of H2 with glycine, the glycine dimer, and imidazolium chloride amount to 2.78, 5.00, and 6.30 kJ mol-1, respectively.     

Direct and indirect causes of Fermi level pinning at the SiO/GaAs interface

The correlation between atomic bonding sites and the electronic structure of SiO on GaAs(001)-c(2x8)/(2x4) was investigated using scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and density functional theory (DFT). At low coverage, STM images reveal that SiO molecules bond Si end down; this is consistent with Si being undercoordinated and O being fully coordinated in molecular SiO. At approximately 5% ML (monolayer) coverage, multiple bonding geometries were observed. To confirm the site assignments from STM images, DFT calculations were used to estimate the total adsorption energies of the different bonding geometries as a function of SiO coverage. STS measurements indicated that SiO pins the Fermi level midgap at approximately 5% ML coverage. DFT calculations reveal that the direct causes of Fermi level pinning at the SiO GaAs(001)-(2x4) interface are a result of either local charge buildups or the generation of partially filled dangling bonds on Si atoms.     

Adsorption of functionalized benzoic acids on MgSO4.H2O (100).

Using a combination of ab initio and semiempirical methods, adsorption problems on surfaces with large unit cells and low symmetry can still be studied. Here, a hybrid approach of density functional theory (DFT) and Hartree-Fock (HF) was used. As an example, we determined the geometry and the electronic properties of benzoic acid (BA), salicylic acid (SA) and para-salicylic acid (p-SA) adsorbed on MgSO(4).H(2)O (100), which are used as conditioner molecules for the electrostatic separation of minerals. Contrary to general expectations, these molecules are chemisorbed, with binding energies around 1.9 eV, forming bonds through the carboxylic O atom of the COOH groups in a nonplanar geometry, although the surface is a stoichiometric wide-band-gap insulator and the molecules stay intact. In contrast, a planar adsorption geometry turned out to be nonbonding. Bonding takes place by means of surface-molecule resonances due to the overlap of the valence band with molecular orbitals, assisted by a small charge-transfer molecule to the surface of around 0.15e. These combined interactions cause an intramolecular twist between the COOH group and the benzene ring.     

Ni(115)台阶面对氢表面微观动力学行为的影响

用５参数Ｍｏｒｓｅ势模拟氢－镍表面体系相互作用势，考察了氢原子在Ｎｉ（１１５）台面上吸附扩散行为。同时构造了氢分子与Ｎｉ（１００）和Ｎｉ（１１５）台阶面 相互作用推广的ＬＥＰＳ势面面，考察了氢分子解离化学吸附的微观动力学性质。     

Coverage‐Dependent Variation of Adsorption Configurations of Methionine on Ge(100)

The adsorption configurations of methionine molecules on the Ge(100) surface have been studied by using DFT calculations, core‐level photoemission spectroscopy (CLPES), and low‐energy electron diffraction (LEED) to scrutinize the adsorption structure as a function of coverage. At first, we obtained two important and stable structures. One is the most stable structure between these structures described as an “O H dissociated‐N dative‐S dative‐bonded structure” and the other is a less stable adsorption structure of these indicating an “O H dissociated‐S dative‐bonded structure” by using DFT calculations. We also performed CLPES to clarify our DFT calculation results. Through the spectral analysis of the S 2p, C 1s, N 1s, and O 1s core‐level spectra, we acquired the reasonable results that also revealed quite different bonding configurations depending on the methionine coverage. At low coverage (ca. 0.30 ML), a single type of sulfur and charged nitrogen peaks, which indicate an “O H dissociated‐N dative‐S dative‐bonded structure”, were observed. On the other hand, two types of sulfur peaks with thiol formation and two nitrogen peaks with neutralized and charged characteristics were monitored at a higher coverage (0.60 ML and above), which can be described as an “O H dissociated‐S dative‐bonded structure”. Hence, we can clearly demonstrate that our results obtained from CLPES spectra and DFT calculations are matched well with each other. Moreover, we additionally confirmed that the relative population of the two types of thiols and amines being included in methionine in between half monolayer induces a surface reorientation in the ordering from 2×1 to 1×1 employing LEED. This interesting variation of the methionine adsorbed on the Ge(100) surface by coverage dependence will be precisely discussed by using DFT calculations, CLPES, and LEED.     

First-principle study of adsorption of hydrogen on Ti-doped Mg(0001) surface

Ab initio density functional theory (DFT) calculations are performed to study the adsorption of H2 molecules on a Ti-doped Mg(0001) surface. We find that two hydrogen molecules are able to dissociate on top of the Ti atom with very small activation barriers (0.103 and 0.145 eV for the first and second H2 molecules, respectively). Additionally, a molecular adsorption state of H2 above the Ti atom is observed for the first time and is attributed to the polarization of the H2 molecule by the Ti cation. Our results parallel recent findings for H2 adsorption on Ti-doped carbon nanotubes or fullerenes. They provide new insight into the preliminary stages of hydrogen adsorption onto Ti-incorporated Mg surfaces.