Dimer Rows Research Articles

Boron ions B + interaction with Si(100) and Ge(100) surfaces

The goal of this work is simulation of possible structures, formed by boron ions (B +) during adsorption on Si(100) and Ge(100) surfaces. Calculations were carried out using a semi-empirical method, known as the Modified Neglect of Differential Overlap method (MNDO). The surface was simulated using of Si 49(Ge 49) and Si 63(Ge 63) clusters. Results of quantum-chemical calculations the boron ion (B +) interaction with Si(100) − 2 × 1 and Ge(100) − 2 × 1 surfaces are presented and show adsorption barriers for boron ions and migration barriers of adsorbed boron ion (during migration along surface dimer row and along surface dimer).

Possibility of direct exchange diffusion of hydrogen on theCl/Si(100)−2×1surface

The diffusion behavior of hydrogen substitutional sites on the chlorine-terminated Si(100) surface was investigated at elevated temperatures using time-lapse scanning tunneling microscopy (STM). STM movies show that each hydrogen atom undergoes Brownian motion within a monochloride dimer row. The position of a hydrogen substitutional site is exchanged directly with that of an immediate neighboring chlorine atom in either the same dimer (intradimer diffusion) or in one of the two adjacent dimers in the same row (intrarow diffusion). Accordingly, conceptual direct exchange diffusion (DED) in a two-dimensional lattice was experimentally observed. Analysis of STM movies at various temperatures yielded rather low attempt frequencies and energy barriers, leading to the suggestion that the diffusion mechanism involves an intermediate low-energy molecular state. Density-functional theory (DFT) calculations were also performed and provided partial support for the proposed diffusion mechanism.

Structural and electronic properties of Ge-Si, Sn-Si, and Pb-Si dimers on Si(001) from density-functional calculations

Using first-principles methods we studied structural and electronic properties of asymmetric heterogeneous $X\text{-Si}$ ($X=\text{Ge}$, Sn, and Pb) dimers on the Si(001) surface and their scatterings for the quasi-one-dimensional ${\ensuremath{\pi}}^{\ensuremath{\ast}}$ electrons. The $X\text{-Si}$ dimer with impurity atom $X$ at the lower position scatters more strongly the ${\ensuremath{\pi}}^{\ensuremath{\ast}}$ electrons than that with $X$ at the upper position. Calculated scattering potentials can be qualitatively explained by the difference in $p$-orbital energy between Si and the lower atom of the $X\text{-Si}$ dimer. We predict that the amplitude of electronic standing waves changes significantly between the two oppositely buckled $X\text{-Si}$ dimers in differential conductance images of scanning tunneling microscopy. This suggests the possibility of fabricating atomic switches to control the conduction of ${\ensuremath{\pi}}^{\ensuremath{\ast}}$ electrons along the dimer row. Our proposed atomic switches could be achieved by flipping the impurity dimers on the Si(001) surface using the method developed in recent experiments [K. Sagisaka et al., Phys. Rev. Lett. 91, 146103 (2003)]. Finally, we proposed the model for dimer-flipping mechanism, which can explain previous experiment [K. Sagisaka and D. Fujita, Phys. Rev. B 71, 245319 (2005)].

Electric-field effects on the diffusion of Si and Ge adatoms on Si(001) studied by density functional simulations

We present results of density functional theory (DFT) calculations of the electric-field effects on the clean Si(001) surface and the diffusion of Si or Ge adatoms on Si(001) surface. Our results indicate that the electric field only slightly affected the dimer bond lengths and buckling angles of the clean Si(001), implying that the electric field of scanning tunneling microscopy tip should not be responsible for the observation of symmetric dimers and the flip-flop motion of the buckling dimers. Also, the electric field mainly influences the diffusion along the dimer row, and the diffusion barrier could be reduced greatly under a positive electric field. It can be expected that the positive field should make the diffusion of Si or Ge adatoms on the Si(001) surface become more anisotropic.

The preserved aromaticity of aniline molecules adsorbed on a Si(5 5 12)−2×1 surface

We present a scanning tunneling microscopy and first-principles calculations study of the adsorption structures of aniline on a Si(5 5 12)-2x1 surface. Dissociation from the aniline molecules of one or two H atom(s) bonded to N is favored, and then adsorption onto adatom, tetramer, and dimer rows of Si(5 5 12)-2x1 occurs in several distinct configurations. On the adatom row, aniline binds to an adatom in a tilted configuration, which is formed via a sigma bond between the adatom and N, with one dissociated H atom adsorbed on a nearby adatom. No further hydrogen dissociation occurs. On the tetramer and dimer rows, the structures with two dissociated hydrogens and upright configurations are the most stable. Aniline does not adsorb onto the honeycomb chains; this adsorption configuration has a low adsorption energy. In all the adsorption configurations of aniline on this surface, the molecule's aromaticity is preserved. Thus Si-N bonding of aromatic amine molecules provides a strategy for the homogeneous aromatic functionalization of high index Si surfaces.

Intrarow Adsorption Structure of Glycine on Ge(100)

The adsorption structure of glycine on Ge(100) was investigated using scanning tunneling microscopy (STM), density functional theory (DFT) calculations, and high-resolution core-level photoemission spectroscopy (HRCLPES). We found a major adsorption feature of glycine on Ge(100) in the STM images. This feature appeared as a bright protrusion between two dimer rows with a dark adjacent dimer. The position of the bright protrusion located in the middle of the two dimer rows indicates a multibonding adsorption structure. The results of the theoretical calculations confirm that the adsorption structure of glycine on Ge(100) (between two possible multibonding adsorption structures) is an "intrarow O-H dissociated and N dative bonded structure". In the HRCLPES experiments, we found an N 1s peak (at 399.5 eV) and two O 1s peaks (at 531.1 and 532.0 eV), which represent strong evidence that the adsorption configuration of glycine on Ge(100) is composed of both O-H dissociation and N dative bonding. All our STM, DFT, and HRCLPES results suggest that the adsorption structure of glycine molecules on Ge(100) is an "intrarow O-H dissociated and N dative bonded structure".

Irreversible structural transformation of Si(1 1 4)-2 × 1 induced by subsurface carbon

Using scanning tunneling microscopy (STM), it has been found that the reconstruction of Si(1 1 4) is transformed irreversibly from a 2 × 1 structure composed of dimer (D), rebonded atom (R), and tetramer (T) rows (phase A) to a different kind of 2 × 1 structure composed of D, T, and T rows (phase B) by C incorporation. It has been confirmed by high-resolution synchrotron core-level photoemission spectroscopy (PES) that such an irreversible structural transformation is due to stable subsurface C atoms. They induce anisotropic compressive stress on the surface, which results in insertion of Si dimers to an R row to form a T row.

High-Resolution STM Studies of Terephthalic Acid Molecules on Rutile TiO2(110)-(1 × 1) Surfaces

The structure of terephthalic acid (TPA) molecules adsorbed on rutile TiO2(110)-(1 × 1) has been investigated by scanning tunneling microscopy (STM). Molecularly resolved STM images show formation of monolayer with the tendency of TPA molecules to form dimer rows along the [001] substrate direction. The ability to image functional groups by the STM tip, and single molecule diffusion are demonstrated. The quality and stability of the monolayer are tested, including the resistance against air exposure. On the basis of results obtained, the model of TPA adsorption on the rutile TiO2(110)-(1 × 1) is proposed.

Growth Mechanism of a 1D Molecular Line across the Dimer Rows on H-Terminated Si(001)

Based on first-principles density-functional calculations, we propose a novel growth mechanism of the 1D molecular lines on the H-terminated Si(001) surface where the line is directed across the Si dimer rows. The proposed structural model of the allyl mercaptan (ALM) line shows that the molecules adsorb across two Si dimers in the adjacent dimer rows with the Si-C and Si-S bonds, thereby yielding a higher thermodynamic stability compared to other alkene lines (containing a single Si-C bond per molecule) grown along the dimer rows. This accounts for a successful growth of ALM lines which were observed to be stable even at a high temperature of 650 K.

Hydrogen adsorption configurations on Ge(001) probed with STM

The adsorption of hydrogen on Ge(001) has been studied with scanning tunneling microscopy at 77 K. For low doses (100 L) a variety of adsorption structures has been found. We have found two different atomic configurations for the Ge-Ge-H hemihydride and a third configuration that is most likely induced by the dissociative adsorption of molecular hydrogen. The Ge-Ge-H hemihydride is either buckled antiparallel or parallel to the neighboring Ge-Ge dimers. The latter configuration has recently been predicted by M. W. Radny et al. [J. Chem. Phys. 128, 244707 (2008)], but not observed experimentally yet. Due to the presence of phasons some dimer rows appear highly dynamic.

Formation of extended straight molecular chains by pairing of thymine molecules on the Ag–Si(111) surface

Here, we report on the assembly of thymine molecules into extended straight chains of single and multiple dimer rows on a Si(111)/Ag \(\sqrt{3}\times \sqrt{3}\) R30° surface. Using variable temperature scanning tunneling microscopy, we follow the nucleation process and formation of self-assembled structures. Submonolayer coverages at 120 K are disordered and exhibit a high density of thymine dimers. Upon annealing the dimers assemble into extended dimer chains along three equivalent high-symmetry surface directions. At low coverages single dimer rows are favored. At increased coverage chains with multiple dimer rows are observed, with a preference to an even multiplicity. We show that a complex cross-talk between H-bond thymine–thymine interactions and commensurization of dimer chains to the Ag/Si surface leads to this specific layout.

Theoretical Study of Dispersion Binding of Hydrocarbon Molecules to Hydrogen-Terminated Silicon(100)-2×1

Noncovalent interactions between organic molecules and hydrogen-terminated silicon(100)-2×1 influence surface chemistry and diffusion. To develop our understanding of these interactions, we studied the dispersion binding of two model hydrocarbons, methane and benzene, on hydrogen-terminated silicon(100)-2×1 using a density-functional theory (DFT) technique incorporating dispersion corrections. The corrections were implemented using previously developed carbon-centered potentials (DiLabio, G. A. Chem. Phys. Lett. 2008, 455, 348−353.) and newly developed silicon-centered potentials, designed to correct the well-known erroneous long-range behavior of DFT methods. Our calculations predict that the preferred position for methane binding to the surface occurs over the area between two dimer rows (the “gulley”) and between two sets of dimers (binding energy (BE) = 2.2 kcal/mol). When the methane is positioned over a dimer row, BE = 1.9 kcal/mol. Diffusion of methane along the dimer row direction was calculated to be only marginally more facile than diffusion across rows. In the case of benzene, the preferred binding position is over the dimer row with the benzene roughly parallel to the surface and centered over one surface hydrogen (BE = 5.6 kcal/mol). The complex in which the benzene is over the gulley is less strongly bound (BE = 5.3 kcal/mol). Additional higher energy structures were also found. A detailed potential energy surface map reveals that diffusion of benzene in the row direction is more facile than diffusion across dimer rows. The calculated, room-temperature rate constant associated with diffusion along the row is calculated to be 1.7 times larger than that for diffusion in the perpendicular-to-row direction. Our findings show that surface anisotropy and molecule shape contribute to a directional preference for diffusion.

Indium Nanowire Growth on Si (001) Surface Using Density Functional Theory

Density functional theory was utilized to investigate the growth of an indium nanowire on a Si (001) buckled surface. A site between the edge of two Si dimers is most favorable when the first In atom is adsorbed on the surface at an adsorption energy level of 2.26 eV. The energy barriers for migration from other sites to the most favorable site are low. When the second In atom is adsorbed next to the first In atom to form an In dimer perpendicular to the Si dimer row, the adsorption energy is the highest among all adsorption sites. The third In atom prefers either of the sites next to the In dimer along the In dimer direction. The fourth In atom exhibited the same tendency showed by the second atom. The second and fourth In adsorption energy levels are higher than the first and third levels as the In atoms consume the third valence electron by forming In dimers. Therefore, the In nanowire grows perpendicular to the Si dimer row on the Si (001) surface, as it satisfies the bonding of the three valence electrons of the In atoms.

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 O 2 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/SiO 2 interface and may be used for studying SiO x growth.

Discrimination of Chiral Adsorption Configurations: Styrene on Germanium(100)

We investigated the adsorption geometries and desorption temperatures of styrene on a Ge surface using scanning tunneling microscopy (STM), temperature programmed desorption (TPD), and ab initio density functional theory (DFT) calculations. Our STM results show that styrene molecules attach via the vinyl group in two adsorption configurations: (i) on the top of single Ge dimers by forming di-σ bonds (OT) and (ii) in a paired end-bridge between two adjacent Ge dimers within the same dimer row (PEB). Moreover, the PEB configurations are divided into two types of adsorption configurations depending on the arrangement of the phenyl rings of the two styrene molecules: either the axis running through the two phenyl rings is diagonal to the dimer row direction (trans-PEB) or perpendicular to the dimer row direction (cis-PEB). STM images can discriminate the OT configurations with (S) and (R) chiralities, as well as the PEB configurations with diastereomeric (R,S) and enantiomeric (R,R) and (S,S) chiralities at t...

Simulations of CVD Diamond Film Growth Using a Simplified Monte Carlo Model

AbstractA simple 1-dimensional Monte Carlo (KMC) model has been developed to simulate the chemical vapour deposition (CVD) of a diamond (100) surface. The model considers adsorption, etching/desorption, lattice incorporation, and surface migration along and across the dimer rows. The reaction probabilities for these processes are re-evaluated in detail and their effects upon the predicted growth rates and morphology are described. We find that for standard CVD diamond conditions, etching of carbon species from the growing surface is negligible. Surface migration occurs rapidly, but is mostly limited to CH2 species oscillating rapidly back and forth between two adjacent radical sites. Despite the average number of migration hops being in the thousands, the average diffusion length for a surface species is <2 sites.

The Formation of Self-Assembled Nanowire Arrays on Ge(001): a DFT Study of Pt Induced Nanowire Arrays

AbstractNanowire (NW) arrays form spontaneously after high temperature annealing of a sub monolayer deposition of Pt on a Ge(001) surface. These NWs are a single atom wide, with a length limited only by the underlying beta-terrace to which they are uniquely connected. Using ab-initio density functional theory (DFT) calculations we study possible geometries of the NWs and substrate. Direct comparison to experiment is made via calculated scanning tunneling microscope (STM) images. Based on these images, geometries for the beta-terrace and the NWs are identified, and a formation path for the nanowires as function of increasing local Pt density is presented. We show the beta-terrace to be a dimer row surface reconstruction with a checkerboard pattern of Ge-Ge and Pt-Ge dimers. Most remarkably, comparison of calculated to experimental STM images shows the NWs to consist of germanium atoms embedded in the Pt-lined troughs of the underlying surface, contrary to what was assumed previously in experiments.

Behavior of Emitted Si Atoms for the Initial Stage of Oxidation on Si(100)-(2*1) Surface Observed by Scanning Tunneling Microscope

Changes of surface structure for the initial stage of oxidation in the Langmuir type adsorption range on Si(100)-(2×1) surfaces were observed using a scanning tunneling microscope (STM). On the Si(100)-(2×1) surfaces exposed to oxygen (O2) at room temperature, bright spots located on the center of a dimer row and dark sites appeared, and increased in number with increasing of O2 exposure. It is considered that the bright spots correspond to the isolated Si dimer emitted by the oxidation-induced strain at SiO2/Si interface. At 380oC, O2 exposure induced the formation of one-dimensional Si islands and an SB step flow growth due to the surface diffusion of the emitted Si atoms. These STM observation results clarify that the SB step flow growth causes the decrease of 1×2/2×1 domain ratio and the behavior of emitted Si atoms support the unified Si oxidation reaction model proposed by Takakuwa.

Adsorption and organisation of para-hexaphenyl molecules on Si(100)

Para-hexaphenyl molecules (p-6P: C36H26) can be grown as nanofibres on various surfaces having optical properties of technological relevance. We report here the first observations of the initial stages of adsorption of individual p-6P molecules on Si(100)-(2×1) using room temperature Scanning Tunnelling Microscopy (STM). Depending on the substrate temperature, the hexaphenyl molecules adsorb in two configurations; indicating both weak and strong chemisorption. All six phenyl rings are clearly visible and the molecules are found to adsorb with characteristic angles between the long axis of the molecule and the silicon dimer rows. A statistical analysis of the spatial distribution of the molecules suggests that the clustering required for crystallographic nanofibre growth does not occur at the atomic scale under the experimental conditions used here.

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

The interactions between endohedrally doped N@C60 molecules and the Si(100) 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(100) 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.