Dimer Rows Research Articles

Self-assembly of Fe nanocluster arrays on templated surfaces

The growth of Fe nanoclusters on the Ge(001) and MoO2/Mo(110) surfaces has been studied using low-temperature scanning tunneling microscopy (STM) and X-ray magnetic circular dichroism (XMCD). STM results indicate that at low coverage Fe atoms self-assemble on both surfaces into well-separated nanoclusters, which nucleate at equivalent surface sites. Their size, shape, and the observed spatial separation are dictated by the substrate and depend on preparation conditions. Annealing the Fe nanoclusters on Ge(001) at 420 K leads to the formation of linear nanocluster arrays, which follow the Ge dimer rows of the substrate, due to cluster mobility at such temperature. In turn, linear Fe nanocluster arrays are formed on the MoO2/Mo(110) surface at room temperature at a surface coverage greater than 0.5 monolayer. This is due to the more pronounced row pattern of the MoO2/Mo(110) surface compared to Ge(001). These nanocluster arrays follow the direction of the oxide rows of the strained MoO2/Mo(110) surface. The Fe nanoclusters formed on both surfaces show a superparamagnetic behavior as measured by XMCD.

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 Å. 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.

Initial oxidation structure of chlorinated Si(001)

The Cl-saturated Si(001) surface is investigated by employing density functional theory calculations. From the electronic density of states, the low- and the high-bias filled-state images and the empty-state images are found to originate from Cl(3p) states directed in-plane, in parallel with the Si dimer row, and perpendicular to the surface (z), respectively. The bright triplet, which is a characteristic scanning tunneling microscopy (STM) feature of an unchlorinated bare Si dimer, is attributed to an occupied dangling bond state of the bare Si dimer that is hybridized with the neighboring Cl(3pz) orbital. The previously observed split-dimer feature is confirmed to be the dimer-bond oxidized structure. Finally, we suggest that the initial back-bond oxidation does not occur on the chlorinated Si(001) surface because it is energetically not favored compared with dimer-bond oxidation and because its STM simulation does not match experimental images.

Guided Self-Assembly of Mn Wires on the Si(100)(2 × 1) Surface

Doping of group IV semiconductors with Mn is a critical building block in the development of novel spintronics devices, and the fabrication of magnetic nanostructures is the next challenge in this field. The growth of monatomic Mn wires on Si(100)(2 × 1) at room temperature is investigated with scanning tunneling microscopy (STM) and described with a kinetic Monte Carlo (kMC) simulation. Mn forms monatomic wires on the Si(100)(2 × 1) surface, which are always oriented perpendicular to the Si dimer rows, and the Mn wire growth competes with the formation of nanoclusters. The wire quality and wire length distributions are controlled by the vacancy concentration of predominantly C-type defects on the Si surface and the Mn coverage. The phase space covered in this study includes vacancy concentration of 1–18% and coverages of 0.1–0.8 monolayer (ML), at which point the growth of the second layer becomes dominant. A surface phase diagram is established, and the highest wire quality can be achieved for vacancy c...

Selective Reactions and Adsorption Structure of Pyrazine on Si(100): HRPES and NEXAFS Study

We have investigated adsorption of pyrazine molecules on the Si(100)-2×1 surface at 300 K by using high-resolution photoemission spectroscopy (HRPES) and near-edge X-ray absorption fine structure (NEXAFS) in partial electron yield mode. The Si 2p, C 1s, and N 1s core-level spectra reveal that pyrazine is directly bonded to silicon surface dimer rows through two para-nitrogen atoms, forming two new Si–N σ-linkages at 300 K. The π* orbitals of C═C bonds in the carbon K-edge NEXAFS spectra show a good angular dependence providing an average tilt-angle α ∼ 34 ± 5° of the C═C bond for the chemisorbed pyrazine with respect to the surface. The experimentally measured angle of α ∼ 34° agrees reasonably well with the cross-row configuration structure

Si2H6 Dissociative Chemisorption and Dissociation on Si(100)-(2×1) and Ge(100)-(2×1)

Atomically controlled epitaxy of semiconductor-on-semiconductor is important for the construction of nanometer-scale devices such as quantum dots, qubits for quantum computing, nanoelectromechanical systems (NEMS) oscillators, and nanobiomedical devices. For instance, patterned atomic layer epitaxy (ALE) using a scanning tunneling microscopy tip to depassivate an area of a H-terminated Si(001) surface, creating a pattern for subsequent Si growth, should lead to a new generation of atomically precise structures. Vapor phase epitaxy is well-suited to achieve controlled deposition, as the precursors are not reactive with the H-terminated background, unlike Si atoms from solid-source evaporation. Disilane (Si2H6) is arguably the best precursor for Si ALE on Si or Ge surfaces at moderate temperatures; yet, its adsorption configuration and subsequent decomposition pathways are not well understood. Combining experimental data from in situ infrared absorption spectroscopy (IRAS), scanning tunneling microscopy (STM), and X-ray photoelectron spectroscopy (XPS) after saturation by disilane of both Si(100)-(2×1) and Ge(100)-(2×1) surfaces, with first-principles calculations of candidate surface structures, we show that Si2H6 chemisorbs through a β-hydride elimination pathway as Si2H5 and H, instead of the previously proposed SiH3, and subsequently decomposes into an ad-monohydride dimer. The initial chemisorption process takes place on a single dimer and produces a monohydride ad-dimer oriented perpendicular to the substrate dimer rows. The ad-dimer can be located either in between two adjacent, initially clean dimers from the same dimer row, or in a bridging position over the trench between two adjacent dimer rows. These findings provide clear guidance for the formation of atomic size structures defined by local removal of hydrogen on H-terminated Si surfaces.

The adsorption and reconstruction of strong electron acceptor tetracyanoethylene (TCNE) on Si(001)-(2 × 1): A density functional theory investigation

The adsorption and reconstruction of strong electron-acceptor TCNE on the Si(001)-(2×1) surface are investigated by density functional theory (DFT). The results show that TCNE prefers to adsorb on the trench between two adjacent dimer rows and the CC double bond is parallel to dimer rows. Charge density difference calculation and Bader charge analysis indicate that abundant negative charge transfers from dimer Si to TCNE. Strong interaction makes it difficult for TCNE to move on Si(001), which is confirmed by nudged elastic band (NEB) analysis. In addition, the correlations between simulated STM images and molecular orbitals are discussed and two surface reconstructions of (2×1) and (4×2) are predicted at different TCNE coverages.

Self-assembled line growth of allyl alcohol on the H-terminated Si(100)-(2 × 1) surface

Using first-principles density-functional calculations, we investigate the growth mechanism of allyl alcohol (ALA) line on the H-terminated Si(100)-(2×1) surface. Unlike the allyl mercaptan (CH2=CH−CH2−SH) line, which was observed to grow across the Si dimer rows, we find that ALA (CH2=CH−CH2−OH) has the line growth along the Si dimer row. The self-assembled growth of ALA line occurs via the radical chain reaction mechanism, similar to the case of a typical alkene molecule, styrene. Our calculated energy profile along the reaction pathway shows that the different growth direction of ALA line compared with that of allyl mercaptan line is ascribed to the great instability of the oxygen radical intermediate, which prevents the line growth across the dimer rows.

Ag-induced Si(100) reconstruction: Si(100)-(22×22)R45∘-Ag

A type of Ag-induced Si(100) reconstruction described as Si(100)-(2$\sqrt{2}\ifmmode\times\else\texttimes\fi{}2\sqrt{2})R{45}^{\ensuremath{\circ}}$-Ag has been fabricated by breaking Si dimers and forcing Ag atoms to bond directly to these Si atoms. High-resolution scanning tunneling microscopy images and density functional theory calculations reveal that the basic unit of the reconstruction contains two Ag atoms bonded to Si dimers and two Ag atoms located at the grooves between neighboring dimer rows. These four Ag atoms constitute an elongated ring-shaped feature and are distributed on one or two neighboring dimer rows to form two types of reconstruction with the same reconstruction label. Such reconstructions are semiconducting, and the band gaps vary from 0.12 eV for two-row reconstruction to 0.26 eV for one-row reconstruction.

Directed Long-Range Migratory Reaction of Benzene on Si(100)

Electron impact on chemisorbed benzene at Si(100) is shown by scanning tunneling microscopy to cause long-range molecular recoil in the plane of the surface, followed by chemisorptive reattachment at a substantial distance (on average, 48 Å) from the originating event. Several indicators—directionality of migration, persistance of motion over obstacles, and insignificant probability of desorption—all point to a rolling mechanism in which the recoiling molecule cartwheels across the surface in a physisorbed state. In distinction to our previous report of long-range migration of alkenes on the same surface [Nat. Chem. 2011, 3, 400−408], in the present case, the benzene molecules migrate substantially further and favor motion along the dimer rows rather than across them. Ab initio theory provides a qualitive model that satisfactorily explains these experimental observations.

Stress-driven structural transformation of Sb-passivated Si(114)

Combined investigation of STM, high-resolution synchrotron photoemission, and density functional theory calculations allowed us to understand the Sb-induced structural-transformation of Si(114)-2×1. When 2ML of Sb is deposited on Si(114)-2×1 at room temperature and postannealed at 500°C, all of the surface Si atoms with dangling bonds are replaced by Sb atoms. Among one-dimensional (1D) structures consisting of Si(114)-2×1, such as a dimer with a 6-membered ring (D6) row, a rebonded-atom (R) row, and a tetramer (T) row [D6-R-T], the T row is split into a dimer row with a 7-membered ring (D7) and an R row [D6-R-D7-R]. Since the R-D7-R unit, a building block of Sb/Si(113)2×2, is under stress-balance, the Sb/Si(114)-2×1 surface is stressed compressively due to the extra D6 unit. As a result, with additional postannealing at 600°C, two periods of this 2×1 [(D6-R-D7-R)-(D6-R-D7-R)] are gradually converted to 2×2 [(D6-R-D6-R)-(R-D7-R)], where the D6-R (115) unit is stress-balanced. The corresponding photoemission data obtained from both of the phases show that all of the surface components of the clean surface have disappeared, instead the single Sb–Si interfacial component has appeared, which indicates that the charge transfers from interfacial Si to surface Sb atoms. Finally, the density functional theory calculations have also confirmed that there are two distinct phases determined by the chemical potential of passivating Sb atoms.

Adhesion and Diffusion of Zinc-Phthalocyanines on the ZnO (101̅0) Surface

We study the adhesion and the diffusion of single zinc-phthalocyanine (ZnPc) molecules on a ZnO (1010) surface by means of model potential molecular dynamics. We find that the molecule is easily adsorbed on the surface, and we identify the ZnPc adsorption sites. The diffusion at room temperature is studied by metadynamics. We find that the molecule is able to diffuse by hopping between the surface dimer rows along the [010] crystallographic direction with a free energy barrier as small as ∼0.4 eV. At temperatures T > 700 K, a different mechanism is found with large diffusion paths along the surface trench grooves.

Macromolecular organization of ATP synthase and complex I in whole mitochondria

We used electron cryotomography to study the molecular arrangement of large respiratory chain complexes in mitochondria from bovine heart, potato, and three types of fungi. Long rows of ATP synthase dimers were observed in intact mitochondria and cristae membrane fragments of all species that were examined. The dimer rows were found exclusively on tightly curved cristae edges. The distance between dimers along the rows varied, but within the dimer the distance between F(1) heads was constant. The angle between monomers in the dimer was 70° or above. Complex I appeared as L-shaped densities in tomograms of reconstituted proteoliposomes. Similar densities were observed in flat membrane regions of mitochondrial membranes from all species except Saccharomyces cerevisiae and identified as complex I by quantum-dot labeling. The arrangement of respiratory chain proton pumps on flat cristae membranes and ATP synthase dimer rows along cristae edges was conserved in all species investigated. We propose that the supramolecular organization of respiratory chain complexes as proton sources and ATP synthase rows as proton sinks in the mitochondrial cristae ensures optimal conditions for efficient ATP synthesis.

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.

Carbon nanotunnels form from single-walled carbon nanotubes interacting with a diamond (100)–(2 × 1) surface

A quantum chemical study of the interaction of (5,5), (7,7), (9,9) and (8,0) single-walled carbon nanotubes with a clean (100)-(2 × 1) diamond surface is reported. Stable structures with covalent bonds at the interface were found for carbon nanotubes oriented parallel or perpendicular to the dimer rows on the reconstructed (100) surface. The binding energy of the most stable (5,5) nanotube-diamond structure is 1.7 eV/Å, and is attributed to strong covalent bonds formed between the carbon nanotube and the diamond surface. The structure of the nanotube is distorted by adsorption on the surface such that it adopts a tunnel-like geometry. Two other nanotunnel geometries were found for the (5,5) nanotube, with binding energies of 1.39 and 1.09 eV/Å. In the most stable (5,5) nanotube-diamond structure the interaction between the nanotube and the diamond surface produces a 0.6 eV band gap near the Fermi level, but the metallic character of the nanotube is maintained in the two other, less strongly bound nanotunnel structures. No charge transfer occurs between the diamond surface and the nanotunnels in any of the three orientations. Binding energies decrease with increases in tube diameter, to the extent that one of the three nanotunnel structures is not formed by (9,9) carbon nanotubes.

Anisotropic Diffusion Evolution of Vacancies Created by Oxygen Etching on a Si Surface

We report the diffusion behavior of dimer vacancies on a Si(100)-(2×1) surface by using ultrahigh-vacuum scanning tunneling microscopy. The dimer vacancies are created by oxygen etching of Si atoms at elevated temperatures. By annealing the sample at 600–750 °C, the dimer vacancies uniformly distribute on the terrace nucleate to form larger elongated voids of one atomic layer deep. The long axis of these voids is parallel to the Si dimer rows. During annealing, the surface morphology evolves in a way dominantly caused by the anisotropic diffusion of the dimer vacancies. A difference of diffusion barriers of 0.17±0.09eV is obtained between the [110] and [11̄0] directions.

MODELING OF CO-DEPOSITION OF INDIUM AND TIN ON SILICON(100): A KINETIC MONTE CARLO STUDY

A growth model for co-deposition of Sn and In on Si (100) at room-temperature was simulated using Kinetic Monte Carlo methods to shed light on the chemical selectivity and lack of dimer ordering seen in [Jure et al., Appl. Surf. Sci.162, 638 (2000)], a Scanning Tunneling Microscopy (STM) study. In this work, the experimental observation that the number of mixed In – Sn dimers is unaffected even when the relative flux rates are adjusted to favor In over Sn (by 100:1) — a manifestation of some sort of chemical selectivity — was investigated. Our simulations reveal that this phenomenon is ultimately related to the fact that the number of Sn -terminated chains is largely unaffected by the relative flux rate. Finally, we found that the attraction between metal dimers (whether of the same or different species) within a Si dimer row has only negligible effect on the apparent lack of dimer ordering seen in the STM study. Instead, dimer ordering is controlled by the detachment barriers in dimer-terminated islands.

Atomic and electronic structure of styrene on Ge(100)

Coverage-dependent adsorption structures of styrene on a Ge(100) surface were investigated using density functional theory (DFT) calculations. The most favorable configuration at room temperature is that the two styrene molecules are bound to two Ge dimers with paired end-bridged (PEB) configuration via the reaction of the vinyl C C double bond. The phenyl rings of the two styrene molecules are trans relative to the Ge dimer rows. Due to the bulky and electronic nature of the phenyl ring, its spatial orientation relative to the Ge surface affects the thermodynamic stability of each configuration. The buckling properties of surface Ge dimers also affect their interaction with the phenyl ring. Simulated STM images of this PEB configuration for empty states explain well the adsorption features observed in the experiment, as well as for filled states. Detailed electronic structures were also investigated through the PDOS analysis.

Cardiolipin Affects the Supramolecular Organization of ATP Synthase in Mitochondria

F 1F 0 ATP synthase forms dimers that tend to assemble into large supramolecular structures. We show that the presence of cardiolipin is critical for the degree of oligomerization and the degree of order in these ATP synthase assemblies. This conclusion was drawn from the statistical analysis of cryoelectron tomograms of cristae vesicles isolated from Drosophila flight-muscle mitochondria, which are very rich in ATP synthase. Our study included a wild-type control, a cardiolipin synthase mutant with nearly complete loss of cardiolipin, and a tafazzin mutant with reduced cardiolipin levels. In the wild-type, the high-curvature edge of crista vesicles was densely populated with ATP synthase molecules that were typically organized in one or two rows of dimers. In both mutants, the density of ATP synthase was reduced at the high-curvature zone despite unchanged expression levels. Compared to the wild-type, dimer rows were less extended in the mutants and there was more scatter in the orientation of dimers. These data suggest that cardiolipin promotes the ribbonlike assembly of ATP synthase dimers and thus affects lateral organization and morphology of the crista membrane.

Embedded Co islands on Ge(001)

The adsorption of Cobalt (Co) on Germanium (Ge) (001) surfaces has been studied using scanning tunneling microscopy. Upon annealing at temperatures of 500–550 K well-ordered rectangular shaped embedded islands are formed. Based on our scanning tunneling microscopy data we propose that the elementary building block of these embedded islands consist of six Co atoms arranged in a hexagonal pattern. A statistical analysis reveals that the embedded Co islands exhibit an attractive interaction in a direction perpendicular to the substrate dimer rows and a repulsive interaction in a direction along the substrate dimer rows. The embedded Co islands eventually convert to perfectly straight and micrometers long nanowires upon annealing at temperatures that exceed 700–750 K.