Conformation-selective adsorption of 2,3-butanediol on Si(0 0 1)

The adsorption of 2,3-butanediol on the Si(0 0 1) surface is studied by means of first-principles pseudopotential calculations. Molecular adsorption on top of the Si dimers resulting in a 6-membered ring of the O-C-C-O segment with the dimer atoms is energetically favored, in agreement with the interpretation of recent experiments. The adsorption energy difference for butanediol adsorbed in either gauche or anti conformation is nearly one order of magnitude larger than the energy difference between the respective conformers in gas phase, pointing to a conformation-selective adsorption.     

Reaction of chlorinated benzenes with Si(1 0 0)2 × 1: a theoretical study

Theoretical (HF + DFT) investigations of the adsorption of chlorobenzene (ClPh), 1,2- and 1,4-dichlorobenzene (1,2-diClPh and 1,4-diClPh) on a silicon (1 0 0) surface are reported for the first time, and are compared with one another and with benzene. Binding energies for various structures with the molecules attached on-top and in-between the surface dimer rows are correlated with the STM experimental data. Novel structures with the molecules linking two dimer rows, stabilised by detachment of Cl (or H)-atoms forming Cl-Si (or H-Si) bonds, are described. For 1,4 and 1,2 binding, these linking structures are predicted to attach the phenyl ring parallel or perpendicular to the Si surface, respectively, while preserving its aromaticity. The potential-energy barriers between several different structures are evaluated, and compared with available experimental evidence. For 1,4-diClPh it is shown that the potential-energy barrier for the second Cl transfer is significantly lower than for the first one in contrast to the gas-phase, and comparable to the barrier for lifting the Bz-ring into a vertical position and forming a singly bonded ‘displaced’ structure. The predicted barrier-heights are consistent with the experimentally observed relative occurrence of the on-top, linking, and displaced structures.     

SiO adsorption on a p(2 × 2) reconstructed Si(1 0 0) surface

We have investigated the adsorption mechanism of SiO molecule incident on a clean Si(1 0 0) p(2 × 2) reconstructed surface using density functional theory based methods. Stable adsorption geometries of SiO on Si surface, as well as their corresponding activation and adsorption energies are identified. We found that the SiO molecule is adsorbed on the Si(1 0 0) surface with almost no activation energy. An adsorption configuration where the SiO binds on the channel separating the dimer rows, forming a Si-O-Si bridge on the surface, is the energetically most favourable geometry found. A substantial red-shift in the calculated vibrational frequencies of the adsorbed SiO molecule in the bridging configurations is observed. Comparison of adsorption energies shows that SiO adsorption on a Si(1 0 0) surface is energetically less favourable than the comparable O₂ adsorption. However, the role of SiO in the growth of silicon sub-oxides during reactive magnetron plasma deposition is expected to be significant due to the relatively large amount of SiO molecules incident on the deposition surface and its considerable sticking probability. The stable adsorption geometries found here exhibit structural properties similar to the Si/SiO₂ interface and may be used for studying SiO_x growth.     

The chemisorption of pentacene on Si(0 0 1)-2 × 1

Adsorption structures of the pentacene (C₂₂H₁₄) molecule on the clean Si(0 0 1)-2 × 1 surface were investigated by scanning tunneling microscopy (STM) in conjunction with density functional theory calculations and STM image simulations. The pentacene molecules were found to adsorb on four major sites and four minor sites. The adsorption structures of the pentacene molecules at the four major sites were determined by comparison between the experimental and the simulated STM images. Three out of the four theoretically identified adsorption structures are different from the previously proposed adsorption structures. They involve six to eight Si-C covalent chemical bonds. The adsorption energies of the major four structures are calculated to be in the range 67-128 kcal/mol. It was also found that the pentacene molecule hardly hopped on the surface when applying pulse bias voltages on the molecule, but was mostly decomposed.     

Vacancy charging on Si(1 1 1)-(7 × 7) investigated by density functional theory

The structure and energetics of charged vacancies on Si(1 1 1)-(7 × 7) are investigated using density functional theory calculations supplemented by estimates of ionization entropy. The calculations predict multiple possible charge states for the unfaulted edge vacancy in the adatom layer, although the −2 state is most stable on real Si(1 1 1) surfaces for which the Fermi level lies near the middle of the band gap.     

Function of subsurface boron on Si(0 0 1)-2 × 1: water adsorption

Using density functional theory calculations we investigate the function of subsurface boron in determining surface properties of Si(0 0 1). To demonstrate its effect on surface reactivity we compare the behaviors of water adsorption on the clean and B-modified surfaces. We find that subsurface boron brings about a significant change in surface chemical properties by altering charge polarization of Si(0 0 1) locally. As a consequence, water adsorption on the B-modified surface shows a distinctively different feature from that on the clean surface.     

Diffusion of Pb adatom and ad-dimer on Si(1 0 0) from ab initio studies

The diffusion pathways of Pb adatoms and ad-dimers on Si(1 0 0) are investigated by first-principles calculations. Pb adatoms are found to diffuse on top of the Si(1 0 0) dimer row with an energy barrier of 0.31 eV. However, Pb dimers are energetically more stable. Pb dimers on top of the dimer row have a high energy barrier (0.95 eV) to rotate from the lowest energy configuration to the orientation parallel to the underlying Si(1 0 0) dimer row. Once the ad-dimer is oriented parallel to Si(1 0 0) dimer row, they can diffuse along the dimer row with an energy barrier of only 0.32 eV.     

Diffusion of oxygen atom in the topmost layer of the Si(1 0 0) surface: Structures and oxidation kinetics

The incorporations and migrations of the atomic oxygen in the topmost layer Si(1 0 0)-p(2 × 2) silicon surface, are investigated theoretically using density functional theory. We show that the diffusion is dependent on the starting and the final surrounding environment and does not simply consist in hops from one silicon-silicon bond to another. The activation energies range from 0.11 eV to 2.59 eV.     

Ab initio density functional study of O on the Ag(0 0 1) surface

The adsorption of oxygen on the Ag(1 0 0) is investigated by means of density functional techniques. Starting from a characterization of the clean silver surfaces oxygen adsorption in several modifications (molecularly, on-surface, sub-surface, Ag₂O) for varying coverage was studied. Besides structural parameters and adsorption energies also work-function changes, vibrational frequencies and core level energies were calculated for a better characterization of the adsorption structures and an easier comparison to the rich experimental data.     

Bistability in a H-terminated Si(1 0 0)2 × 1 surface obtained by ab initio transport calculations

We have analyzed electron tunneling due to the electric field from a hydrogen-terminated Si(1 0 0)2 × 1 ultrathin film on a metal substrate by density functional transport calculations. We have obtained a hysteresis loop in the tunneling current, which comes from the existence of two electronic structures. Furthermore, we have clarified that, as a condition of bistable electron transport, a double-barrier potential structure is not necessarily required for zero field, because it can be induced by the electric field.     

Atomic and molecular adsorption on Pt(1 1 1)

The adsorption of several atomic (H, O, N, S, and C) and molecular (N₂, HCN, CO, NO, and NH₃) species and molecular fragments (CN, CNH₂, NH_2, NH, CH₃, CH₂, CH, HNO, NOH, and OH) on the (1 1 1) facet of platinum, an important industrial and fuel cell catalyst, was studied using self-consistent periodic density functional theory (DFT-GGA) calculations at a coverage of 1/4 ML. The best binding site, energy, and position, as well as an estimated diffusion barrier, of each species were determined. The binding strength for all the species can be ordered as follows: N₂ < NH₃ < HCN < NO < CO < CH₃ < OH < NH₂ < H < CN < NH < O < HNO < CH₂ < NOH < CNH₂ < N < S < CH < C. Although the atomic species generally preferred fcc sites, there was no clear trend in site preference by the molecular species or molecular fragments. The vibrational frequencies of all the stable adsorbates in their best and second best adsorption sites were calculated and found to be in good agreement with experimental values reported in the literature. Finally, the decomposition thermochemistry of NOH, HNO, NO, NH₃, N₂, CO, and CH₃ was analyzed.     

Quantum states of hydrogen (H, D, T) atoms on Cu(1 0 0) and (1 1 0) surfaces

We investigate the quantum mechanical behavior of adsorbed hydrogen (H, D, T) on Cu(1 0 0) and (1 1 0) surfaces. We construct potential energy surfaces (PESs) for the motion of the hydrogen H atom on Cu(1 0 0) and (1 1 0) surfaces within the framework of density functional theory. The potential energy takes a minimum value on the hollow site of Cu(1 0 0) and on the short bridge site of Cu(1 1 0). Moreover, we calculate the quantum states of hydrogen atom motion on these calculated PESs. The ground state wave function of the hydrogen atom motion is strongly localized around the hollow site on the Cu(1 0 0) surface. On the other hand, the ground state wave function of the hydrogen atom motion on Cu(1 1 0) is distributed from the short bridge site to two neighboring pseudo-threefold sites. We finally show isotope effects on the quantum states of the motion of hydrogen on both surfaces.     

First-principles study of adsorption and diffusion on Ge/Si(0 0 1)-(2 × 8) and Ge/Si(1 0 5)-(1 × 2) surfaces

Using first-principles total-energy calculations, we have investigated the adsorption and diffusion of Si and Ge adatoms on Ge/Si(0 0 1)-(2 × 8) and Ge/Si(1 0 5)-(1 × 2) surfaces. The dimer vacancy lines on Ge/Si(0 0 1)-(2 × 8) and the alternate S_A and rebonded S_B steps on Ge/Si(1 0 5)-(1 × 2) are found to strongly influence the adatom kinetics. On Ge/Si(0 0 1)-(2 × 8) surface, the fast diffusion path is found to be along the dimer vacancy line (DVL), reversing the diffusion anisotropy on Si(0 0 1). Also, there exists a repulsion between the adatom and the DVL, which is expected to increase the adatom density and hence island nucleation rate in between the DVLs. On Ge/Si(1 0 5)-(1 × 2) surface, the overall diffusion barrier of Si(Ge) along direction is relative fast with a barrier of ∼0.83(0.61) eV, despite of the large surface undulation. This indicates that the adatoms can rapidly diffuse up and down the (1 0 5)-faceted Ge hut island. The diffusion is also almost isotropic along [0 1 0] and directions.     

Comparative DFT study of the adsorption of 1,3-butadiene, 1-butene and 2-cis/trans-butenes on the Pt(1 1 1) and Pd(1 1 1) surfaces

The interaction of 1,3-butadiene, 1-butene and 2-cis/trans-butenes on the Pt(1 1 1) and Pd(1 1 1) surfaces has been studied with density functional theory methods (DFT). The same most stable adsorption modes have been found on both metal surfaces with similar adsorption energies. For 1,3-butadiene the 1,2,3,4-tetra-σ adsorption structure is shown to be the most stable one, in competition with a 1,4-metallacycle-type mode, which is only less stable by 10-12 kJ mol⁻¹. On Pt(1 1 1) these total energy calculations were combined with simulations of the vibrational spectra. This confirms that the 1,2,3,4-tetra-σ adsorption is the most probable adsorption structure, but cannot exclude the 1,4-metallacycle as a minority species. Although similar in type and energy, the adsorption on the Pd(1 1 1) surface shows a markedly different geometry, with a smaller molecular distortion upon adsorption. The most stable adsorption structure for the butene isomers is the di-σ-mode. Similarly to the case of the 1,3-butadiene, the adsorption geometry is closer to the gas phase one on Pd than on Pt, hence explaining the different spectroscopic results, without the previously assumed requirement of a different binding mode. Moreover the present study has shown that the different selectivity observed on Pt(1 1 1) and Pd(1 1 1) for the hydrogenation reaction of butadiene cannot be satisfactory explained by the single comparison of the relative stabilities of 1,3-butadiene and 1-butene on these metals.     

NO dissociation pathways on Rh(1 0 0), (1 1 0), and (1 1 1) surfaces: A comparative density functional theory study

The chemisorption and dissociation pathways of NO on the Rh(1 0 0), (1 1 0), and (1 1 1) surfaces are studied by the plane-wave density functional theory (DFT) with CASTEP program. In addition, the electronic and geometrical effects that affect the NO dissociation reactions have been investigated in detail. The calculation results are presented as following: The effective activation energies of the best NO dissociation pathways on the Rh(1 0 0), the Rh(1 1 0), and the Rh(1 1 1) are 0.63, 0.66 and 1.77 eV, respectively. The activity of the Rh planes for NO dissociation is in the order of Rh(1 0 0) ≈ Rh(1 1 0) > Rh(1 1 1). The low dissociation barrier for Rh(1 0 0) and Rh(1 1 0) is associated with the existence of a lying-down NO structure which acts as a precursor for dissociation. By Mulliken population analysis and structure analysis, both electronic and geometrical effects are found to affect the NO dissociation reactions, but the geometrical effect exceed the electronic. The energy decomposition scheme has been used to provide further insight into the NO dissociation reactions. Based on the calculations, the interaction energy between N and O in the transition state on the Rh(1 1 1) is found much larger than that on the Rh(1 0 0) and the Rh(1 1 0). The major differences of should originate from the variation of the bonding competition effect.     

Adsorption of N@C60 on Si(1 0 0)

The interactions between endohedrally doped N@C₆₀ molecules and the Si(1 0 0) surface have been explored via ab initio total energy calculations. Configurations which have the cage located upon the dimer row bonded to two dimers (r2) and within the dimer trench bonded to four dimers (t4) have been investigated, as these have previously been found to be the most stable for the C₆₀ molecule. We have investigated the differences between the adsorption of the C₆₀ and N@C₆₀ molecules upon the Si(1 0 0) surface and found that there are only minimal differences. Two interesting cases are the r2g and t4d configurations, as they both exhibit differences that are not present in the other configurations. These subtle differences have been explored in-depth. It is shown that the effects on the endohedral nitrogen atom, due to its placement within the fullerene cage, are small. Bader analysis has been used to explore differences between the C₆₀ and N@C₆₀ molecules.     

First-principles studies of the oxygen adsorption on unreconstructed and reconstructed Ni(1 1 0) surfaces

First-principles calculations have been performed to investigate the adsorption of oxygen on unreconstructed and reconstructed Ni(1 1 0) surfaces. The energetics, structural, electronic and magnetic properties are given in detail. For oxygen adsorption on unreconstructed surface, (n×1)(n=2,3) substrate with oxygen atom on short-bridge site is found to be the most stable adsorption configuration. Whereas energetically most favorable adsorption phase of reconstructed surface is p(n×1) substrate with oxygen atom located at long-bridge site. Our calculations suggest that the surface reconstruction is induced by the oxygen adsorption. We also find there are redistributions of electronic structure and electron transfer from the substrate to adsorbate. Our calculations also indicate surface magnetic moment is enhanced on clean surfaces and oxygen atoms are magnetized weakly after oxygen adsorption. Interestingly, adsorption on unreconstructed surface does not change surface magnetic moment. However, adsorbate leads to reduction of surface magnetic moment in reconstructed system remarkably.     

Initial incorporation of sulfur into the Pd(1 1 1) surface: A theoretical study

Density functional theory is used to investigate the initial inclusion of sulfur into the subsurface interstitial sites of Pd(1 1 1) surface. Pure subsurface adsorption is found to be less energetically favorable than on-surface adsorption. The incorporation of sulfur into the metal becomes more favorable than continuous adsorption on the surface after a critical on-surface sulfur coverage. We find subsurface sulfur occupation to be energetically favorable after adsorption of more than half a monolayer on the surface. Occupation of subsurface sites induces a pronounced structural distortion of the Pd(1 1 1) surface. We find significant expansion of interplanar spacing between the uppermost surface metal layers and rearrangement of the S overlayer. The interplay between the energy cost due to structural distortion of Pd(1 1 1) and the energy gain due to bond formation for different structures is discussed.     

Density functional theory investigation of CN on Cu(1 1 1), Ni(1 1 1) and Ni(1 0 0)

The adsorption of CN on Cu(1 1 1), Ni(1 1 1) and Ni(1 0 0) has been investigated using density functional theory (DFT). While experimental studies of CN on Cu(1 1 1) show the molecular axis to be essentially parallel to the surface, the normally-preferred DFT approach using the generalised gradient approximation (GGA) yields a lowest energy configuration with the C-N axis perpendicular to the surface, although calculations using the local density approximation (LDA) do indicate that the experimental geometry is energetically favoured. The same conclusions are found for CN on Ni(1 1 1); on both surfaces bonding through the N atom is always unfavourable, in contrast to some earlier published results of ab initio calculations for Ni(1 1 1)/CN and Ni(1 0 0)/CN. The different predictions of the GGA and LDA approaches may lie in subtly different relative energies of the CN 5σ and 1π orbitals, a situation somewhat similar to that for CO adsorbed on Pt(1 1 1) which has proved challenging for DFT calculations. On Ni(1 0 0) GGA calculations favour a lying-down species in a hollow site in a geometry rather similar to that found experimentally and in GGA calculations for CN on Ni(1 1 0).     

Formation and stabilization of Fe-induced magic clusters on Si(1 1 1)-(7 × 7) template

We demonstrate the growth of Fe-induced magic clusters on Si(1 1 1)-(7 × 7) template by in situ scanning tunneling microscopy (STM). These clusters form near a dimer row at one side of the half-unit cell (HUC); and with three different equivalent orientations. A cluster model comprising three top layer Si atoms bonded to six Fe atoms at the next layer in the 7 × 7 faulted-half template is proposed. The optimized cluster structure determined by first-principles total-energy calculation shows an inward-shifting of the three center Fe atoms. The clusters and the nearby center-adatoms of the next HUCs appear with a significantly reduced height below bias voltages 0.4 V in high resolution empty-state STM images, suggesting an energy gap opening near the Fermi level at these localized cluster and adatom sites. We explain the stabilization of the clusters on the 7 × 7 template using the gain in electronic energy as the driving force for cluster formation.