Honeycomb Chain Research Articles

Role of Electronic Structures and Dispersion Interactions in Adsorption Selectivity of Pyrimidine Molecules with a Si(5 5 12) Surface

We show that the resonance energy and dispersion interactions (DIs) are critical factors in determining the selectivity and configuration in the reaction of pyrimidine molecules with a silicon surface. The atomic structures of the pyrimidine molecules after they reacted with a Si(5 5 12)–2 × 1 surface were studied. Binding configurations of the pyrimidines were distinct from those of other molecules with N lone-pair electrons and aromaticity. The pyrimidine molecules were adsorbed to produce two σ bonds to silicon with N2 and C5 on the adatom row (Adr) and honeycomb chain (Hnc) sites and with C1 and C4 on the dimer row (Dmr) and the tetramer row (Ttr) sites. The reactions occurred via a [4 + 2]-type cycloaddition to produce planar-type configurations with loss of aromaticity. That is, the atoms of the aromatic ring of pyrimidine form chemical bonds with silicon atoms, which is in contrast to the adsorption behaviors reported for other N-containing aromatic molecules. When pyrimidine is adsorbed, its molec...

Multilayer silicene: clear evidence of Ag-terminated bulk silicon

The existence of silicite, a new allotrope of silicon based on a stacking of hexagonal silicene planes, is one of the most discussed topics in the field of two-dimensional materials. Using grazing incidence x-ray diffraction (GIXD), we have followed the in situ growth of Si films on Ag(1 1 1) in the low-temperature growth regime (510–520 K). GIXD experiments demonstrate that Si films have a diamond-like structure, with an average lattice constant slightly different from that of bulk Si. The diffracted intensities associated with Si films are well reproduced by the Ag/Si(1 1 1) honeycomb chain model, whereas models with Ag-free Si surfaces fail to reproduce the experimental data.

One-dimensional diffusion of Sr atoms on Sr/Si(111)-3 × 2 reconstruction surface

The electronic and geometric structures of the Sr/Si(111)-3×2 surface were investigated by scanning tunnelling microscopy and scanning tunnelling spectroscopy. The honeycomb-chain (HCC) model may be used to describe the reconstruction structure of the Sr/Si(111)-3×2 surface.Furthermore, one-dimensional (1D) concerted motion of Sr atom chains on the Sr/Si(111)-3×2 surface was observed at room temperature. Three reasons contribute to this 1D self-diffusion: low metal coverage of the Sr/Si(111)-3×2 reconstruction surface, weak interaction between the Sr and Si substrate, and surface vacancies and thermal fluctuation energy at room temperature.From this study, the origin of the long-existing blurred low energy electron diffraction pattern of alkali-earth metal induced-Si(111)3×2 surface was clarified, and the self-diffusion of metal atoms at room temperature also explains the common phase transition phenomenon on these reconstructed surfaces.

Atomic and electronic structures of Si(1 1 1)--Au and (6 × 6)-Au surfaces

Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the -Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the -Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the -Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the -Au phase. Extra Au atoms bound in interstitial sites of the -Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a -Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the -Au structure. The -Au phase is 2D chiral and this is evident in computed and actual STM images. -Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si–Au top layers of the -Au and -Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given.

Terbium induced nanostructures on Si(111)

Abstract The growth of self-assembled Tb induced nanostructures on the Si(111) surface is investigated using scanning tunneling microscopy. Depending on the growth conditions, three regimes are identified in which different types of nanostructures appear. At very low Tb coverages and moderate growth temperatures, the 7 × 7 periodicity of the Si(111) surface remains intact and magic clusters form within single 7 × 7 half unit cells. In the intermediate regime of Tb coverages below one monolayer, the formation of different superstructures is observed. Here, a chain-like 5 × 2 superstructure, a 2√3 × 2√3 R30° superstructure, and elongated islands showing a 2 × 1 reconstruction on top are found. From a detailed study of the 5 × 2 superstructure it is demonstrated that it consists of alternating Si Seiwatz and Si honeycomb chains with rows of Tb atoms in the channels in between. Moreover, registry shifts between the Tb rows lead to different configurations of this superstructure. At coverages exceeding one monolayer, the growth of islands of two-dimensional TbSi 2 monolayers and three-dimensional Tb 3 Si 5 multilayers dominates.

Identification of the structure model of the Si(111)-(5 × 2)-Au surface.

The atomic structure of the Si(111)-(5 × 2)-Au surface, a periodic gold chain on the silicon surface, has been a long-debated issue in surface science. The recent three candidates, the so-called Erwin-Barke-Himpsel (EBH) model [S. C. Erwin, I. Barke, and F. J. Himpsel, Phys. Rev. B 80, 155409 (2009)], the Abukawa-Nishigaya (AN) model [T. Abukawa and Y. Nishigaya, Phys. Rev. Lett. 110, 036102 (2013)], and the Kwon-Kang (KK) model [S. G. Kwon and M. H. Kang, Phys. Rev. Lett. 113, 086101 (2014)] that has one additional Au atom than the EBH model are tested by surface x-ray diffraction data. A two-dimensional Patterson map constructed from the in-plane diffraction intensities rejects the AN model and prefers the KK model over the EBH model. On the basis of the arrangement of Au obtained from the Patterson map, all the reconstructed Si atoms, such as the so-called honeycomb chain structure, are directly imaged out by utilizing a holographic method. The KK model reproduces out-of-plane diffraction data as well.

Spin disorder in an Ising honeycomb chain cobaltate

We report on a member of the spin-disordered honeycomb lattice antiferromagnet in a quasi-one-dimensional cobaltate Ba_3Co_2O_6(CO_3)_0.7. Resistivity exhibits as semimetallic along the face-sharing CoO6 chains. Magnetic susceptibility shows strongly anisotropic Ising-spin character with the easy axis along the chain due to significant spin-orbit coupling and a trigonal crystal field. Nevertheless, ^135Ba NMR detects no indication of the long-range magnetic order down to 0.48 K. Marginally itinerant electrons possess large entropy and low-lying excitations with a Wilson ratio R_W = 116, which highlight interplays of charge, spin, and orbital in the disordered ground state.

Optical Fingerprints of Si Honeycomb Chains and Atomic Gold Wires on the Si(111)-(5×2)-Au Surface

The intensively studied Si(111)-(5×2)-Au surface is reexamined using reflectance anisotropy spectroscopy and density functional theory simulations. We identify distinctive spectral features relating directly to local structural motifs such as Si honeycomb chains and atomic gold wires that are commonly found on Au-reconstructed vicinal Si(111) surfaces. Optical signatures of chain dimerization, responsible for the observed (×2) periodicity, are identified. The optical response, together with STM simulations and first-principles total-energy calculations, exclude the new structure proposed very recently based on the reflection high-energy electron diffraction technique analysis of Abukawa and Nishigaya [Phys. Rev. Lett. 110, 036102 (2013)] and provide strong support for the Si honeycomb chain with the triple Au chain model of Erwin et al. [Phys. Rev. B 80, 155409 (2009)]. This is a promising approach for screening possible models of complex anisotropic surface structures.

Reflectance anisotropy spectroscopy of Si(111)-(3×1)Li and Ag surfaces

The Si(111)-($3\ifmmode\times\else\texttimes\fi{}1$)Li and Ag surface structures consist of Si honeycomb chains separated by channels occupied by Li or Ag atoms. The dimerization of neighboring Ag atoms results in a larger $c(12\ifmmode\times\else\texttimes\fi{}2)$Ag superstructure. We report calculations of the electronic surface states, dielectric function, and reflectance anisotropy spectrum of these surfaces using hybrid density functional theory (DFT) methods. The positions of surface states and the reflectance anisotropy spectrum calculated using DFT are in very good agreement with experimental results, where they have been reported. The surface states which contribute to the reflectance anisotropy below the band gap are identified for each orientation of the incident electromagnetic field.

Periodic variations in the local surface potential of Si(111)-(5×2)-Au

The image-state-derived field-emission resonances (FERs) on a Si(111)-($7\ifmmode\times\else\texttimes\fi{}7$) surface that is partially covered by the gold-induced Si(111)-($5\ifmmode\times\else\texttimes\fi{}2$)-Au reconstruction, were probed by scanning tunneling spectroscopy measurements. On Si(111)-($5\ifmmode\times\else\texttimes\fi{}2$)-Au, a shift of the FER peak positions is observed compared to the bare $7\ifmmode\times\else\texttimes\fi{}7$ surface. Spatially resolved $dI/dV$ maps reveal a periodic variation of the higher-order FERs in the direction perpendicular to the chains of the quasi-one-dimensional Si(111)-($5\ifmmode\times\else\texttimes\fi{}2$)-Au reconstruction. The effect appears on a length scale of less than one nanometer and can be attributed to the local surface potential. Simple one-dimensional models reproduce the first seven FERs perfectly and allow extraction of the potential landscape. This landscape is confirmed by density-functional theory calculations, revealing an attractive well above the graphitic Si honeycomb chains due to low electron density.

Origin of enhanced Ge interdiffusion at the initial stage of Ge deposition on Si(5 5 12)-2 × 1: Tensile stress induced by substrate chain structures

By combined investigation of STM and synchrotron PES on Ge/Si(5 5 12)-2×1 at 530°C, it has been found that, in addition to the upward-relaxed surface Si atoms, a subsurface Si atom is also readily replaced by an arriving Ge atom at the initial adsorption stage. Such enhanced interdiffusion is due to a unique character of one-dimensional chain structures of the reconstructed substrate, such as π-bonded and honeycomb chains not existing on other low-index Si surfaces such as Si(001)-c(4×2) and Si(111)-7×7, applying a tensile surface stress to the neighbouring subsurface atoms. Interdiffusion of Ge having lower surface energy induces adsorption of the displaced Si atoms on the surface to form sawtooth-like facets composed of (113)/(335) and (113)/(112) with arriving Ge atoms until the surface is filled with those facets. Such displacive adsorption is the origin of high Si concentration of formed facets.

Synchrotron photoemission studies on reconstructed strained surfaces

Recently, based on scanning tunneling microscopy studies of the reconstructed Si(5 5 12)−2×1 surface, it has been suggested that its unit cell simply consists of four kinds of one-dimensional (1D) structures: π-bonded (π) chain, honeycomb (H) chain, tetramer (T) row, and dimer-adatom (D-A) row. In the present study, by angle-resolved ultraviolet photoelectron spectroscopy, it has been found out that the Si(5 5 12)−2×1 surface has two kinds of surface states, one with a negligible dispersion originating from row structures (T/D-A) and the other with a strong dispersion originating from chain structures (π/H). Also, the Si 2p core-level spectrum shows at least two kinds of surface components, one with 0.23 eV higher binding energy originating from upward-relaxed surface atoms and subsurface atoms, and the other with 0.52 eV lower binding energy originating from downward-relaxed surface atoms. It can be realized that these spectroscopic results quantitively match with the structural model of Si(5 5 12)−2×1 having four kinds of 1D structures.

Structure of the quasi-one-dimensional Si(553)-Au surface: Gold dimer row and silicon honeycomb chain

The Si(553)-Au surface consists of a periodic array of single steps and (111) terraces with a quasi-one-dimensional electronic structure. In this paper, the determination of the atomic structure of this surface with x-ray diffraction is reported. The gold coverage of the surface was measured to be 0.5 monolayer using x-ray fluorescence spectroscopy, i.e., two gold atoms per primitive unit cell. A structural model was constructed directly from the x-ray diffraction intensities with a step-by-step approach. First, the relative positions of the gold atoms were obtained from the Patterson map. Using the positions of the gold atoms, the deconvolution of the Patterson map was calculated and the positions of the gold atoms relative to the substrate were determined. Finally, the positions of the silicon atoms at the surface were obtained from a reconstruction of the electron density with an iterative phase and amplitude recovery algorithm. The main features of the structural model obtained in this way are a row of gold dimers on the (111) terraces in the topmost layer of the surface, and a honeycomb chain of silicon atoms near the step edge. Structural refinement of this model with the experimental diffraction data gave reasonable atomic positions and a ${\ensuremath{\chi}}^{2}$ value of 3.35, better than previous models. The model is related to the $\ifmmode\times\else\texttimes\fi{}2\text{ }\text{m}1$ model recently proposed by Krawiec [Phys. Rev. B 81, 115436 (2010)] but without the strong $\ifmmode\times\else\texttimes\fi{}2$ modulation.

Structural model of the Au-induced Si(553) surface: Double Au rows

A structural model of Au induced Si(553) surface is proposed. The model is based on the recently revised value of Au coverage of 0.48 monolayers, which suggests the formation of two gold chains on each Si(553) terrace. The resulting structural model, such as the models of other vicinal Si surfaces, features the honey-comb chain, but no buckling of the step edge is observed, unlike in the case of the Si(335)-Au and Si(557)-Au surfaces. The present model is more stable than the models with single Au chain only, and agrees well with existing experimental data. In particular, calculated band structure, featuring two metallic bands coming from the hybridization of gold in both chains with neighboring Si atoms, matches well the photoemission data. Moreover, theoretical scanning tunneling microscopy topographs remain in good agreement with the experiment.

Theoretical studies of Sm/Si(1 1 1)– n × 1 ( n = 5, 7) and Sm/Si(1 1 1)–(8 × 2) structures

In this study we employ a state-of-the-art pseudopotential method to perform local density of states (LDOS) calculations of n × 1 ( n = 5, 7) and (8 × 2) reconstructions induced by the adsorption of rare-earth samarium (RE) in the submonolayer range. We conducted a full comparison between images from scanning tunneling microscopy (STM) and theoretical LDOS. Images taken of both filled and empty states show the effects induced by honeycomb chains and Seiwatz chains. We conclude that LDOS calculations are consistent with the assignment of features observed experimentally by STM.

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.

Structural Study of the Si(553)-Au Surface

When gold is deposited onto the Si(553) surface, a highly ordered surface with a quasi-one-dimensional electronic structure can be prepared. This Si(553)-Au surface was investigated by surface X-ray diffraction to determine the surface structure. A structure model was constructed from the Patterson function of the experimental diffracted intensities. There is one gold atom in the primitive unit cell. It substitutes for a top-layer silicon atom on the terraces. The silicon atoms near the step edge reconstruct to form a honey-comb chain. [DOI: 10.1380/ejssnt.2009.533]

Stability and structure of atomic chains on Si(111)

We study the stability and structure of self-assembled atomic chains on Si(111) induced by monovalent, divalent, and trivalent adsorbates, using first-principles total-energy calculations and scanning tunneling microscopy. We find that only structures containing exclusively silicon honeycomb or silicon Seiwatz chains are thermodynamically stable, while mixed configurations, with both honeycomb and Seiwatz chains, may be kinetically stable.

Ca-induced intermediate reconstructions on the Si(111) surface

The geometric and electronic properties of the Ca-induced intermediate reconstructions on the Si(111) surface, particularly $\text{Ca}/\text{Si}(111)\text{\ensuremath{-}}(5\ifmmode\times\else\texttimes\fi{}n)$ with $n=1$, 2, and 4, are theoretically investigated using the pseudopotential method and the local-density approximation (LDA) of the density-functional theory. The geometrical models for the three reconstructions are based on deposition of different Ca lines on the top of a combination of a honeycomb chain channel and a Seiwatz chain formed by Si atoms. These structural models are found to produce semiconducting surface band structures with clear LDA energy gaps. We have identified one, three, and four surface states within the bulk band gap for the $(5\ifmmode\times\else\texttimes\fi{}1)$, $(5\ifmmode\times\else\texttimes\fi{}2)$, and $(5\ifmmode\times\else\texttimes\fi{}4)$ reconstructions, respectively. The relative stabilities of these reconstructions are discussed as a function of Ca coverage. Significant charge transfer from the Ca adatoms to neighboring Si atoms has been concluded by analyzing electronic charge density and scanning tunneling microscopy simulations.

Thermal evolution of Co islands on Ag/Si(111)‐√3 × √3 and Ag/Ge(111)‐√3 × √3 surfaces

AbstractThermal evolution of Co islands on Ag/Ge(111)‐√3 × √3 and Ag/Si(111)‐√3 × √3 surfaces was studied by scanning tunneling microscopy (STM) and low‐energy electron diffraction (LEED). Ag‐√3 × √3 buffer layer can avoid alloy formation of Co and Si or Ge below the annealing temperature 500 °C. The growth behavior of Co on Ag/Si(111)‐√3 × √3 surfaces is very different from that on Ag/Ge(111)‐√3 × √3 surfaces, although both the √3 structures can be classified as honeycomb chain trimer (HCT) model. Submonolayer Co on Ag/Si(111)‐√3 × √3 surfaces prefer to form clusters below 500 °C. However, Co clusters nucleate and construct two‐dimensional islands (2D islands) on Ag/Ge(111)‐√3 × √3 surfaces after annealing to 300 °C. The result of different growth behavior comes from two major factors. One is antiphase boundaries (APBs) with extra electron states, which trap Co clusters on Ag/Si(111)‐√3 × √3 surfaces. The other is the strong binding force that exists between Ge and Co atoms to cause the formation of Co period islands on Ag/Ge(111)‐√3 × √3 surfaces. Copyright © 2008 John Wiley & Sons, Ltd.