Adatom Sites Research Articles

Ga and In adsorption on Si(112): Adsorption sites and superstructure

The adsorption of the two group-III metals Ga and In on Si(112) has strong influence on the morphology of the intrinsically faceted Si(112) surface. Upon Ga or In adsorption, the Si(112) surface is smoothed, and quasi-1D adsorbate structures along the $[1\overline{1}0]$ direction are observed. These structures consist of ($N\ifmmode\times\else\texttimes\fi{}1$) building blocks of different sizes, the periodicity of which can be controlled by surface coverage and deposition temperature, as revealed by spot profile analysis low-energy electron diffraction. From x-ray standing-wave measurements, building blocks consisting of two parallel rows of adsorbate atoms are identified for both Ga/Si(112) and In/Si(112). One adsorption site is identified as a terrace (substitutional) site and the other one as a step-edge (adatom) site. These experimental results are compared to several relaxed model structural configurations obtained from density functional theory calculations. In the case of Ga/Si(112), a previously reported structural model by Snijders et al. [Phys. Rev. B 72, 125343 (2005)], including two Ga vacancies per unit cell is corroborated, while for In/Si(112), existing models by Gai et al. [Phys. Rev. B 61, 9928 (2000)] and by Bentmann et al. [Phys. Rev. B 80, 085311 (2009)] can be ruled out, and a new structural model including only one In vacancy per unit cell in the step-edge site is concluded on, similar to the Al/Si(112) model introduced by Gupta and Batra [Phys. Rev. B 72, 165352 (2005)].

Molecular and atomic manipulation mediated by electronic excitation of the underlying Si(111)-7x7 surface

We report the local atomic manipulation properties of chemisorbed toluene molecules on the Si(111)-7x7 surface and of the silicon adatoms of the surface. Charge injected directly into the molecule, or into its underlying bonding silicon adatom, can induce the molecule to change bonding site. The voltage dependence of the rates of these processes match closely with scanning tunnelling spectroscopy of the toluene and adatom species. The branching ratio between toluene molecules which are moved to a neighbouring site, or those that travel further is invariant to voltage, suggesting a common final manipulation step for both injection into the molecule and into the bonding adatom site. At low temperatures the rate of silicon adatom manipulation matches that of toluene manipulation, further suggesting that all these manipulation processes are driven by electronic excitation of the underlying silicon surface. Our results therefore suggest that a common non-adiabatic process mediates atomic and molecular manipulation induced by the STM on the Si(111)-7x7 surface and may also mediate similar manipulation induced by the laser irradiation of the Si(111)-7x7 surface.

Zero energy modes in a superconductor with ferromagnetic adatom chains and quantum phase transitions

We study Majorana zero energy modes (MZEM) that occur in an s-wave superconducting surface, at the ends of a ferromagnetic (FM) chain of adatoms, in the presence of Rashba spin–orbit interaction (SOI) considering both non self-consistent and self-consistent superconducting order. We find that in the self-consistent solution, the average superconducting gap function over the adatom sites has a discontinuous drop with increasing exchange interaction at the same critical value where the topological phase transition occurs. We also study the MZEM for both treatments of superconducting order and find that the decay length is a linear function of the exchange coupling strength, chemical potential and superconducting order. For wider FM chains the MZEM occur at smaller exchange couplings and the slope of the decay length as a function of exchange coupling grows with chain width. Thus we suggest experimental detection of different delocalization of MZEM in chains of varying widths. We discuss similarities and differences between the MZEM for the two treatments of the superconducting order.

Reflectance anisotropy spectroscopy of the Si(111)−(5×2)Au surface

Hybrid DFT calculations of atomic structure, electronic band structure, and reflectance anisotropy (RA) are used to correlate atomic and electronic structures and optical transitions of eight structures for the $\mathrm{Si}(111)\text{\ensuremath{-}}(5\ifmmode\times\else\texttimes\fi{}2)\mathrm{Au}$ phase with Au coverage and Si adatom site occupancy. The structure recently proposed by Kwon and Kang (KK) [S. G. Kwon and M. H. Kang, Phys. Rev. Lett. 113, 086101 (2014)] and strongly supported by surface x-ray diffraction [T. Shirasawa et al., Phys. Rev. Lett. 113, 165501 (2014)] is found to be the most stable in the Au coverage range from 0.6 to 0.8 ML. The band structure of the Si adatom covered $(5\ifmmode\times\else\texttimes\fi{}4)$ surface has a surface state whose dispersion and position agree very well with the prominent ${S}_{1}$ surface state observed in angle-resolved photoemission experiment. Reflectance anisotropy spectra in the energy range 0.5 to 5 eV for the eight surface structures show variations with Au and Si adatom coverage which can be explained in terms of filling of this surface state. The best agreement between predicted and measured RA spectra, which are sensitive to both Au atom and Si adatom coverage, is found for coverages from 0.7 to 0.75 ML Au, when the surface has regions where Si adatoms are absent and where there are sufficient adatoms to cause surface-state band filling, in equal parts. Surface formation energy calculations favor a coverage of 0.7-ML Au. The structures of the $(5\ifmmode\times\else\texttimes\fi{}2)$ KK and $(6\ifmmode\times\else\texttimes\fi{}6)\mathrm{Au}$ phases on the Si(111) surface are compared and it is shown that the repeat unit of the KK phase also occurs in the $(6\ifmmode\times\else\texttimes\fi{}6)$ structure.

Temporally and Spatially Resolved Oxidation of Si(111)-(7 × 7) Using Kinetic Energy Controlled Supersonic Beams in Combination with Scanning Tunneling Microscopy

The site-specific locations of molecular oxygen reactivity on Si(111)-(7 × 7) surfaces were examined using kinetic energy selected supersonic molecular beams in conjunction with in situ scanning tunneling microscopy. We herein present a detailed visualization of the surface as it reacts in real-time and real-space when exposed to molecular oxygen with translational energy Ei = 0.37 eV. Atomically resolved images reveal two channels for oxidation leading to the formation of dark and bright reaction sites. The darks sites dominate the reaction throughout the range of exposures sampled and exhibit almost no preference for occurrence at the corner or inner adatom sites of the reconstructed (7 × 7) unit cell. The bright sites show a small preference for corner vs inner site reactivity on the reconstructed (7 × 7) unit cell. The bright site corner preference seen here at elevated kinetic energies and with selected incident kinematics is smaller than that typically observed for more conventional thermal (backgro...

Co on Fe3O4(001): Towards precise control of surface properties.

A novel approach to incorporate cobalt atoms into a magnetite single crystal is demonstrated by a combination of x-ray spectro-microscopy, low-energy electron diffraction, and density-functional theory calculations. Co is deposited at room temperature on the reconstructed magnetite (001) surface filling first the subsurface octahedral vacancies and then occupying adatom sites on the surface. Progressive annealing treatments at temperatures up to 733 K diffuse the Co atoms into deeper crystal positions, mainly into octahedral ones with a marked inversion level. The oxidation state, coordination, and magnetic moments of the cobalt atoms are followed from their adsorption to their final incorporation into the bulk, mostly as octahedral Co(2+). This precise control of the near-surface Co atoms location opens up the way to accurately tune the surface physical and magnetic properties of mixed spinel oxides.

Cooperative Chemisorption-Induced Physisorption of CO2 Molecules by Metal-Organic Chains.

Effective CO2 capture and reduction can be achieved through a molecular scale understanding of interaction of CO2 molecules with chemically active sites and the cooperative effects they induce in functional materials. Self-assembled arrays of parallel chains composed of Au adatoms connected by 1,4-phenylene diisocyanide (PDI) linkers decorating Au surfaces exhibit self-catalyzed CO2 capture leading to large scale surface restructuring at 77 K (ACS Nano 2014, 8, 8644-8652). We explore the cooperative interactions among CO2 molecules, Au-PDI chains and Au substrates that are responsible for the self-catalyzed capture by low temperature scanning tunneling microscopy (LT-STM), X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), temperature-programmed desorption (TPD), and dispersion corrected density functional theory (DFT). Decorating Au surfaces with Au-PDI chains gives the interfacial metal-organic polymer characteristics of both a homogeneous and heterogeneous catalyst. Au-PDI chains activate the normally inert Au surfaces by promoting CO2 chemisorption at the Au adatom sites even at <20 K. The CO2(δ-) species coordinating Au adatoms in-turn seed physisorption of CO2 molecules in highly ordered two-dimensional (2D) clusters, which grow with increasing dose to a full monolayer and, surprisingly, can be imaged with molecular resolution on Au crystal terraces. The dispersion interactions with the substrate force the monolayer to assume a rhombic structure similar to a high-pressure CO2 crystalline solid rather than the cubic dry ice phase. The Au surface supported Au-PDI chains provide a platform for investigating the physical and chemical interactions involved in CO2 capture and reduction.

Dynamic Observation of Confined Molecules in Self-Assembled Molecular Corrals

Molecular corrals self-assembled on a Si(111)-(7 × 7) surface after pyrrole exposure, enclosing silicon adatom sites where trimethylphosphine (TMP) was then datively adsorbed. The phosphine’s dynamic motion was investigated by scanning tunneling microscopy. The TMP was confined by the corral, hopping on adatom sites within it. Density functional theory calculations showed covalent bonding between the pyrroles and surface silicon atoms because of N–H dissociative adsorption. An electropositive potential around the TMP/Si cluster may induce electrostatic repulsion between the adsorbed molecules.

Transition voltages of vacuum-spaced and molecular junctions with Ag and Pt electrodes.

The transition voltage of vacuum-spaced and molecular junctions constructed with Ag and Pt electrodes is investigated by non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that, similarly to the case of Au-vacuum-Au previously studied, the transition voltages of Ag and Pt metal-vacuum-metal junctions with atomic protrusions on the electrode surface are determined by the local density of states of the p-type atomic orbitals of the protrusion. Since the energy position of the Pt 6p atomic orbitals is higher than that of the 5p/6p of Ag and Au, the transition voltage of Pt-vacuum-Pt junctions is larger than that of both Ag-vacuum-Ag and Au-vacuum-Au junctions. When one moves to analyzing asymmetric molecular junctions constructed with biphenyl thiol as central molecule, then the transition voltage is found to depend on the specific bonding site for the sulfur atom in the thiol group. In particular agreement with experiments, where the largest transition voltage is found for Ag and the smallest for Pt, is obtained when one assumes S binding at the hollow-bridge site on the Ag/Au(111) surface and at the adatom site on the Pt(111) one. This demonstrates the critical role played by the linker-electrode binding geometry in determining the transition voltage of devices made of conjugated thiol molecules.

Adsorption and dissociation of oxygen molecules on Si(111)-(7×7) surface

The adsorption and dissociation of O2 molecules on Si(111)-(7×7) surface have been studied by first-principles calculations. Our results show that all the O2 molecular species adsorbed on Si(111)-(7×7) surface are unstable and dissociate into atomic species with a small energy barrier about 0.1 eV. The single O2 molecule adsorption tends to form an ins×2 or a new metastable ins×2* structure on the Si adatom sites and the further coming O2 molecules adsorb on those structures to produce an ad-ins×3 structure. The ad-ins×3 structure is indeed highly stable and kinetically limited for diving into the subsurface layer to form the ins×3-tri structure by a large barrier of 1.3 eV. Unlike the previous views, we find that all the ad-ins, ins×2, and ad-ins×3 structures show bright images, while the ins×2*, ins×3, and ins×3-tri structures show dark images. The proposed oxidation pathways and simulated scanning tunneling microscope images account well for the experimental results and resolve the long-standing confusion and issue about the adsorption and reaction of O2 molecules on Si(111) surface.

Effect of van der Waals interactions on H2 dissociation on clean and defected Ru(0001) surface

Ab initio computational methods are used to study the relevance of van der Waals interactions in the case of a hydrogen molecule adsorption on the Ru(0001) surface. In addition to the clean surface, the effects of ruthenium adatom and vacancy on the process are studied. The adsorption characteristics are analyzed in terms of two dimensional cuts of the potential energy surface (PES). Based on the earlier studies for such systems, we mostly concentrate on the trajectories where the hydrogen molecule approaches the surface in parallel orientation. The results indicate that for a clean Ru(0001) the calculations applying the non-local van der Waals potentials yield higher barriers for the dissociation of the H2 molecule. Of the high symmetry sites on Ru(0001), the top site is found to be the most reactive one. The vacancy and ruthenium adatom sites exhibit high dissociation barriers compared with the clean surface.

MAGNETIC IMPURITY IN THE VICINITY OF A VACANCY IN BILAYER GRAPHENE

We use quantum Monte Carlo method to study a magnetic impurity located next to a vacancy in Bernal stacked bilayer graphene. Due to the broken symmetry between two sublattices in bilayer system, there exist two different types of vacancy induced localized state. We find that the magnetic property of the adatom located on the adjacent site of the vacancy depends on whether the vacancy belongs to A or B sublattice. In general, local moment is more strongly suppressed if the vacancy belongs to the sublattice A near the zero-energy. We switch the values of the chemical potential and study the basic thermodynamic quantities and the correlation functions between the magnetic adatom and carbon sites.

Force mapping on a partially H-covered Si(111)-(7×7) surface: Influence of tip and surface reactivity

We report force mapping experiments on Si(111)-(7$\ifmmode\times\else\texttimes\fi{}$7) surfaces with adsorbed hydrogen, using atomic force microscopy at room temperature supported by density functional theory (DFT) simulations. On the basis of noncontact atomic force microscopy (NC-AFM) images as well as force versus distance curves measured over both hydrogen-passivated and bare Si adatoms, we identified two types of tip termination, which result in different modes of interaction with the surface. The statistics of the tip dependence of the measured forces, which are effectuated using various tip states with different cantilevers, reveal the typical values of the force and their distribution in the two characteristic interaction modes. The experimental results are corroborated by DFT calculations performed for different tip structures. As a reactive tip, the dimer-terminated Si tip yields results in satisfactory agreement with experimental force curves for hydrogen-passivated and nonpassivated Si adatom sites. An oxidized Si dimer tip that bears a hydroxyl group on its apex reproduces well the experimental force curves acquired by nonreactive tips. This tip model could thus be used to interpret the experimentally obtained weak image contrast for the Si(111)-(7$\ifmmode\times\else\texttimes\fi{}$7) surface. The forces are thought to arise as a result of a weak electrostatic interaction involving a permanent dipole at the tip apex enhanced by the charge density redistribution due to the interaction with surface adatoms.

Direct observation of hopping and merging of single Au adatoms to form dimers on Si(111)-(7 × 7)

Au single adatoms and dimers were imaged on Si(111)-(7 × 7) at different temperatures and bias voltages using a variable-temperature scanning tunneling microscope. At room temperature (RT), a single Au adatom induces sharp highlighted triangular features in the half unit cells (HUCs) of Si(111)-(7 × 7). These triangular features become fuzzy at temperatures lower than 225 K, as a result of the reduced moving speed of the single Au adatoms inside the HUCs. The formation of an Au adatom dimer was directly observed at RT when a single Au adatom in a HUC jumped into a neighboring HUC that already contained a single Au adatom. The Au adatom dimer appears either as a noisy feature in the central area of the HUC defined by three Si center adatoms or as a bright protrusion located close to a corner Si adatom site at RT. It was observed that a noisy feature also can change into a bright protrusion, inducing charge redistribution in the nearby Si adatoms in both the occupied and neighboring HUCs.

Bidentate Surface Structures of Glycylglycine on Si(111)7×7 by High-Resolution Scanning Tunneling Microscopy: Site-Specific Adsorption via N–H and O–H or Double N–H Dissociation

The early adsorption stage of glycylglycine on Si(111)7×7 surface has been studied by scanning tunneling microscopy (STM). Filled-state imaging shows that glycylglycine adsorbs dissociatively in a bidentate fashion on two adjacent Si adatoms across a dimer wall or an adatom-restatom pair, with the dissociated H atoms on neighboring restatoms. The present STM result validates our hypothesis that both bidentate configurations involving N-H and O-H dissociation and double N-H dissociation are equally probable. Our STM results further show that the relative surface concentrations of the five bidentate configurations follow a specific ordering. This suggests that N-H dissociation at a center adatom site would likely be followed by N-H dissociation at an adjacent restatom, while N-H dissociation at a corner adatom site would be succeeded by O-H dissociation at an adatom across the dimer wall. Evidently, the strong bidentate interactions also inhibit surface diffusion of the adsorbed glycylglycine fragment, and the adsorption apparently follows random sequential adsorption statistics. The random nature of adsorption is also supported by the similar relative occupancies of the center adatom and corner adatom sites, indicating that the relative reactivities of these adatom sites do not play a significant role. Our DFT computational study shows that all three bidentate (Si-)NHCH(2)CONHCH(2)COO(-Si) adatom-adatom configurations (center-center, corner-corner, center-corner) have similar adsorption energies for a double adatom-adatom pair across the dimer wall, while the (Si-)NHCH(2)CON(-Si)CH(2)COOH bidentate adatom-restatom configuration is energetically favorable. The free -CONH- and -COOH groups remaining on the respective bidentate adstructures could facilitate adsorption of the second adlayer through the formation of hydrogen bonding.

Direct Imaging of Hydrogen Bond Formation in Dissociative Adsorption of Glycine on Si(111)7×7 by Scanning Tunneling Microscopy

Adsorption of glycine on a Si(111)7×7 surface at room temperature has been studied by scanning tunneling microscopy (STM). The observed STM images provide strong evidence for dissociative adsorption of glycine through N–H bond cleavage (and N–Si bond formation) as reported in our recent X-ray photoemission study. In particular, the dissociated H atom is found to anchor on a restatom while the N–H dissociated glycine molecule adsorbs on an adatom in a tilted, unidentate geometry. STM study for higher exposures further reveals that the second adlayer is mediated by vertical hydrogen bonding, in excellent accord with our recent X-ray photoemission results. In addition to this vertical hydrogen bonding between a glycine molecule and the N–H dissociated glycine adsorbate, we also observe horizontal hydrogen bonding, not seen before, between two N–H dissociated glycine adsorbates at two neighboring adatom sites. These hydrogen-bonded adstructures, as implicated in the STM images, have been corroborated with our computational DFT/B3LYP/6-31++(d,p) results by using the two largest model surfaces: a Si16H18 cluster to simulate an adatom–restatom pair and a Si26H24 cluster to model a double adatom–adatom pair across the dimer wall of the 7×7 surface. Furthermore, statistical analysis of the STM images for different exposures shows that the center adatom is more reactive than the corner adatom and that the faulted half is more reactive than the unfaulted half. The horizontal hydrogen bonding appears to be favored at a lower exposure than the vertical hydrogen bonding, which becomes dominant at a higher exposure as formation of the second adlayer proceeds. The present work illustrates the importance of hydrogen bonding in the early growth and site-specific chemistry of glycine on Si(111)7×7 surfaces.

Competing Pathways in N-Allylurea Adsorption on Si(111)-(7 × 7)

Functionalization of silicon surfaces with N-allylurea (CH2═CH–CNH–CO–NH2) represents a valuable strategy to obtain covalently bonded Si–C interfaces with amino and/or carbonyl termination. In this work, we studied N-allylurea adsorption on the Si(111)-(7 × 7) surface by combining X-ray and ultraviolet photoemission spectroscopy (XPS and UPS) with high resolution energy loss spectroscopy (HREELS) measurements. XPS core level analysis provides information on the molecular attachment process. Si–C covalent bonding is evidenced by the presence of a C 1s component at 284.8 eV, while interaction through N–Si bonding is proved by the presence of a N 1s component at 397.8 eV. Three different adsorption mechanisms are envisaged: (I) [2 + 2]-like cycloaddition occurring at the rest atom–adatom dimer through cleavage of the vinyl group, (II) Si–N bonding at adatom sites upon cleavage of NH2 and rearrangement of the ureic group to form an imidol species (−N═C–OH), with release of a H atom, and (III) hydrosilylation ...

Self-Assembled Monolayers on Au(111): Structure, Energetics, and Mechanism of Reconstruction Lifting

Density-functional theory calculations are used to compare competing structural models for SH molecules on Au(111) and to explain the effect of the adsorbed molecules on the energetics of surface reconstruction. Our results indicate that dumbbells, formed by binding two SH molecules to an adatom, are energetically stable structures at low and intermediate coverages, while the recently proposed c(4 × 2) structure with partial occupancies for adatom and vacancy sites [A. Cossaro et al., Science2008, 321, 943] is preferred at full coverage. Lifting of the Au(111) herringbone reconstruction is attributed to reduction of surface stress due to outward in-plane relaxations of surface Au atoms under the adsorbed species. The smallest reduction of surface stress per molecule occurs when SH molecules are adsorbed in the form of dumbbells, while isolated adatoms and SH molecules have similar effects on the surface stress and reconstruction energy. SH molecules are predicted to energetically favor the fcc region of t...

Effect of Coverage and Defects on the Adsorption of Propanethiol on Au(111) Surface: A Theoretical Study

Periodic density functional calculations have been carried out to investigate both the thiol adsorption on Au(111) surface and the reaction mechanism for the formation of the self-assembled monolayers, taking propanethiol as a representative example. The effect of coverage and surface defects (adatoms and vacancies) has been analyzed. It is found that the most stable physisorption (undissociated) site is an adatom site, whereas the chemisorption site for the thiol is a vacancy site or protrusion consisting of a pair of adatoms, followed by one adatom site. The results point out that the thiolate self-assembled monolayer adsorption process occurs preferentially on step edges.

Absolute coverage determination in the K/Si(111):B-23×23R30∘surface

In this paper, we report on the experimental determination of alkali absolute coverage in the K/Si(111):$B$-$2\sqrt{3}\ifmmode\times\else\texttimes\fi{}2\sqrt{3}R30$\ifmmode^\circ\else\textdegree\fi{} surface. To this end, we carried out a comparative study with the closest system, namely, K/Si(111)-$3\ifmmode\times\else\texttimes\fi{}1$, for which potassium coverage has been widely demonstrated to be $1/3$ of a monolayer. We used x-ray photoemission spectroscopy to count and compare the number of potassium atoms in both surfaces, together with a scanning tunneling microscopy in order to check the completion of these ultrathin layers. The analysis leads to a $1/2$ monolayer coverage in the $2\sqrt{3}\ifmmode\times\else\texttimes\fi{}2\sqrt{3}R30$\ifmmode^\circ\else\textdegree\fi{} surface, that is six potassium atoms per unit cell. Assuming this coverage, we can propose a simple model structure with potassium atoms arranged in trimers; we discuss the effect of such a reconstruction in terms of two distinct ``up'' and ``down'' Si adatom sites as well as the resulting surface electronic properties.