Ab-Initio Simulation Laboratory

A comprehensive atomic model for the reconstructed surface of Si3N4 thin layer grown on Si(lll) is presented. Kikuchi electron holography images clearly show the existence of adatoms on the Si3N4(0001)/Si(111)-(8 x 8) surface. Compared with the nb initio calculations, more than 30 symmetry-inequivalent atomic pairs in the outmost layers are successfully identified. Scanning tunneling microscopy (STM) images show diamond-shaped unit cells and nine adatoms in each cell. High-resolution STM images reveal extra features and are in good agreement with the partial charge density distribution obtained from total-energy calculations.

We find that electron diffraction patterns can be directly inverted to provide three-dimensional atomic structures for the system studied. Depending on the scattering process, either holography or a Patterson inversion scheme is used. For diffraction patterns which were generated from a localized emitter source or predominantly by an inelastic-scattering feature like low-energy Kikuchi electrons, holography inversion is needed. The information obtained from Kikuchi electron holography includes the building blocks on the surface and their relative position to the atoms below the surface layer. On the other hand, for diffraction patterns generated predominantly by an inelastic-scattering feature like low-energy electron diffraction (LEED), a Patterson inversion is needed. The information obtained from the Patterson transform of the LEED I(E) curves is the relative positions of surface atoms to the atoms in underlying layers; no intra-layer information can be extracted with this method. High-fidelity and artifact-free three-dimensional atomic structures obtained by inversion of low-energy Kikuchi electron patterns and low-energy electron diffraction curves are presented. The results from the two inversion methods are complementary and can be used to construct or to discriminate the surface atomic structural models. The future of these direct methods by inverting diffraction patterns is discussed.

We propose all the diffraction patterns can be directly transformed to provide three-dimensional atomic structures for the system studied. Depending on the scattering process, either the holography or Patterson transform scheme is used. For diffraction patterns which are generated from a localized emitter source or dominated by an inelastic-scattering feature like core-level photoelectron or low-energy Kikuchi electron, holography transform is needed. On the other hand, for diffraction patterns which were dominated by elastic-scattering, like grazing-incidence X-ray diffraction, electron correlated thermal diffuse scattering or low-energy electron diffraction curves, Patterson transform is needed. To prove our point, high-fidelity and artifact-free three-dimensional atomic structures obtained by transform of low-energy Kikuchi electron patterns and low-energy electron diffraction curves are presented. The future of these direct methods by transforming diffraction patterns will be discussed. (C) 2001 Elsevier Science Ltd. All rights reserved.

The work function of atomically uniform Ag films grown on Fe(100) is measured as a function of film thickness. It shows layer-resolved variations as a result of quantum confinement of the valence electrons. A first-principles calculation reproduces the observed variations except for very thin films (one and two monolayers), and the differences can be attributed, in part, to strain effects caused by the lattice mismatch between Ag and Fe. These results illustrate the close interaction between interface effects and surface properties.

We have carried out first-principles calculations of Pb (111) films up to 25 monolayers to study the oscillatory quantum size effects exhibited in the surface energy and work function. These oscillations are correlated with the thickness dependence of the energies of confined electrons, which can be properly modeled by an energy-dependent phase shift of the electronic wave function upon reflection at the interface. It is found that a quantitative description of these quantum size effects requires a full consideration of the crystal band structure.

Three-dimensional atomic images of a Pt(111) surface are obtained by direct inversion of multiple low-energy Kikuchi electron-diffraction patterns. The images are in the backscattering direction. and the positions of the images are consistent with those expected from the atomic structure near the Pt(111) surface. The strong electron scattering of the Pt atoms causes no observable problems in the Kikuchi electron holography.

Real-time in situ x-ray studies of continuous Pb deposition on Si(111)-(7x7) at 180 K reveal an unusual growth behavior. A wetting layer forms first to cover the entire surface. Then islands of a fairly uniform height of about five monolayers form on top of the wetting layer and grow to fill the surface. The growth then switches to a layer-by-layer mode upon further deposition. This behavior of alternating layer and island growth can be attributed to spontaneous quantum phase separation based on a first-principles calculation of the system energy.

We present first-principles calculations that provide a detailed diffusion picture of an adsorbed Si atom on the Si(111)-(7x7) surface. Several diffusion paths for the adsorbed Si atom are established by mapping out the total energy as a function of its positions on the surface. For diffusion between the faulted and unfaulted halves, the energy barriers range from 0.96 to 1.21 eV, while remarkable low-energy barriers from 0.3 to 0.7 eV are discovered within the faulted and unfaulted regions.

We have studied the properties of quantum well states in supported Ag(100) films on the Fe substrate by first-principles density-functional calculations. The energies of these quantum well states as a function of thickness N are examined in terms of the characteristic phase shift of the electronic wave function at the interface. These energy-dependent phase shifts are determined numerically for both the film-substrate and film-vacuum interfaces. It is also found that the substrate has a major effect on film stability, enhancing the stability of the N=5 film and reversing that of the N=2 film.

The structure of a type of surface magic cluster is determined by a combination of scanning tunneling microscopy, density-functional calculations, and dynamical low energy electron diffraction. The diffraction method is applicable because these clusters created through hierarchical self-organization of Ga deposited onto a Si(111)-7x7 surface have identical size and structure and form an ordered array with exact translational symmetry. The unprecedented detailed structure information provided by the diffraction measurement is consistent with direct microscopic imaging and theoretical calculations.

Atomically uniform Pb films are successfully prepared on Si(111), despite a large lattice mismatch. Angle-resolved photoemission measurements of the electronic structure show layer-resolved quantum well states which can be correlated with dramatic variations in thermal stability. The odd film thicknesses N=5, 7, and 9 monolayers show sharp quantum well states. The even film thicknesses N=6 and 8 do not, but are much more stable than the odd film thicknesses. This correlation is discussed in terms of a total energy calculation and Friedel-like oscillations in properties.

We investigate the structural, electronic, and optical properties of hydrogen-passivated silicon nanowires along [110] and [111] directions with diameter d up to 4.2 nm from first principles. The size and orientation dependence of the band gap is investigated and the local-density gap is corrected with the GW approximation. Quantum confinement becomes significant for d<2.2 nm, where the dielectric function exhibits strong anisotropy and new low-energy absorption peaks start to appear in the imaginary part of the dielectric function for polarization along the wire axis.

Previous energetic considerations have led to the belief that carbon nanotubes (CNTs) of 4 Angstrom in diameter are the smallest stable CNTs. Using high-resolution transmission electron microscopy, we find that a stable 3 Angstrom CNT can be grown inside a multiwalled carbon nanotube. Density functional calculations indicate that the 3 Angstrom CNT is the armchair CNT(2,2) with a radial breathing mode at 787 cm(-1). Each end can be capped by half of a C(12) cage (hexagonal prism) containing tetragons.

Hydrogenation-induced metal-semiconductor transitions usually occur in simple systems based on rare earths and/or magnesium, accompanied by major reconstructions of the metal host (atom shifts >2 Angstrom). We report on the first such transition in a quaternary system based on a transition element. Metallic LaMg2Ni absorbs hydrogen near ambient conditions, forming the nonmetallic hydride LaMg2NiH7 which has a nearly unchanged metal host structure (atom shifts <0.7 Angstrom). The transition is induced by a charge transfer of conduction electrons into tetrahedral [NiH4](4-) complexes having closed-shell electron configurations.

Using ab initio density-functional theory, the self-diffusion of adatom and dimer on fcc(100) metal surfaces are studied. For adatom diffusion, we find that the exchange mechanism is favored for Al, Ir, Ni, Pd, Pt and Au, while the hopping mechanism is favored for Rh, Cu, and Ag. Except for Ir/Ir(100), the exchange diffusion energy has a surprising large size-effect and decreases as the surface unit cell increases. This is due to the long-ranged strain-field created at the exchange transition state, which needs a larger cell to relax. The hopping diffusion energy, on the other hand, has a very small size-effect and keeps approximately the same value for various surface unit cells. For self-diffusion on lr(100), the formation of covalent bonds are found at the exchange transition state, and thus the exchange diffusion energy has a little size-effect. Our results also indicate that the exchange mechanism is energetically more favorable for dimer diffusion on fcc(100) surface whenever it is favored for adatom diffusion on fcc(100) surface.

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We have used ab initio methods to study the possible transition between icosahedral (ico) and cuboctahedral (fcc) structures in lead nanoclusters of sizes up to 309 atoms. Spontaneous fcc-to-ico transition in Pb-13 was observed in the ab initio molecular dynamics (MD) simulations at various temperatures. The transition path can be described predominantly by an angular variable s, which can, generally be applied to the similar transitions in clusters of larger sizes and was observed to follow the Mackay model. We have calculated the two-dimensional energy surface that describes the transition in Pb-13 and found a barrierless fcc-to-ico transition path, which is consistent with the observed spontaneous transition in the ab initio MD simulations. The atomic displacements in the transition were identified as one of the vibrational eigenmodes of these two Pb-13 clusters. For clusters of larger sizes (Pb-n, where n = 55, 147, and 309), the possible transitions following similar paths were determined not to be barrierless and the sizes of the barriers were determined by the ab initio elastic band method.

Surface-supported planar clusters can sprout active research and create numerous applications in the realm of nanotechnology. Exploitation of these clusters will be more extended if their properties on a supported substrate are thoroughly apprehended, and if they can be fabricated in a controllable way. Here we report finding the magic numbers in two-dimensional Ag clusters grown on Pb quantum islands. We demonstrate, with the images and energy spectra of atomic precision, the transition from electronic origin to a geometric one within the same system. Applying the magic nature, we can also produce a large array of planar clusters with well-defined sizes and shapes.

Using scanning-tunneling microscopy and first-principles total-energy calculations, we have considered the structural properties of the so-called doped clusters formed by depositing additional 0.05 monolayer of In onto the 4x3-periodicity magic-cluster array in the In/Si(100) system. Low-temperature STM observations have revealed that most of the doped clusters have an asymmetric shape. According to the total-energy calculations, these clusters have plausibly Si6In8 composition. In such a cluster, one of the In atoms is mobile and can hop between four equivalent sites within a cluster. The hopping between sites, located in the different 2ax3a halves of the cluster, is characterized by the barrier of about 0.7 eV, and this hopping becomes frozen at 55 K. In contrast, the hopping between the neighboring sites within the same cluster half persists up to very low temperatures, as the barrier height here is an order of magnitude lower. Due to the above structural properties, the doped asymmetric Si6In8 cluster can be treated as a promising switch, logic gate, or memory cell of the atomic-scale size.

We report first-principles calculations of Pb (100) films up to 22 monolayers to study variations in the surface energy and work function as a function of film thickness. An even-odd oscillation is found in these two quantities, while a jelliumlike model for this s-p metal predicts a periodicity of about three monolayers. This unexpected result is explained by considering a coherent superposition of contributions from quantum-well states centered at both the Gamma and M points in the two-dimensional Brillouin zone, demonstrating the importance of crystal band structure in studying the quantum size effect in metal thin films.

Electrical conduction mechanism in ultrathin Pb (111) films formed on the Si(111)root 3x root 3-Pb surface has been investigated by means of in situ conductivity measurements, angle-resolved photoemission spectroscopy, and first-principles calculations. To investigate the origin of the bilayer oscillation observed in the present conductivity measurement, we perform some simulations based on the calculated band structure. They reveal that the density of states near the Fermi level cannot explain the bilayer oscillation, therefore, exclusively assigning it to the relaxation time. Surface roughness during the bilayer film growth seems to play a crucial role in the bilayer oscillation of the relaxation time.

Using density functional calculations, we demonstrate a catalytic reaction path with activation barriers of less than 0.5 eV for CO oxidation on the neutral and unsupported icosahedral nanoclusters of Au(55), Ag(55), and Au(25)Ag(30). Both CO and O(2) adsorb more strongly on these clusters than on the corresponding bulk surfaces. The reaction path consists of an intermediate involving OOCO complex through which the coadsorption energy of CO and O(2) on these clusters is expected to play an important role in the reaction. Based on the studies for the Au and Ag nanoclusters, a model alloy nanocluster of Au(25)Ag(30) was designed to provide a larger coadsorption energy for CO and O2 and was anticipated to be a better catalyst for CO oxidation from energetic analysis. (C) 2008 American Institute of Physics.

The adsorption and desorption of stilbene on Ag/Ge(111)-(root 3 x root 3)R30 degrees (Ag/Ge(111)-root 3) were investigated using low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), temperature-programmed desorption (TPD), and density functional theory (I)FT). Both trans- and cis-stilbenes form a (2 x 1) overlayer structure on Ag/Ge(111)-root 3 at a coverage of similar to 1 ML. The STM images show parallel strips with three equivalent directions, indicating a self-ordered molecular structure. At a coverage of less than I ML, the TPD of cis-stilbene shows only one peak, attributed to submonolayer desorption. The TPD peaks are indistinguishable for desorption of trans-stilbene from the surface submonolayer and multilayer. This is due to the simultaneous desorption and/or thinning of adsorbed multilayers during the TPD process, as determined from the STM analysis of adsorbed trans-stilbene structures before and after annealing. The TPD traces fit the half-order kinetics for molecular desorption of stilbene from Ag/Ge(111)-root 3 with desorption energies of 20.1 (cis-) and 21.3 kcal/mol (trans-), which are comparable with the calculated values using the DFT method. A plausible explanation for the stilbene desorption process on Ag/Ge(111)-root 3 is proposed and discussed.

Experimentally, self-organized Ag planar clusters have been observed on the periodic template found on the Pb quantum islands, which are grown on the Si(111) surface. These planar clusters register a remarkable abundance variation at some specific atomic numbers and possess enhanced stability. They are thus denoted as two-dimensional magic Ag nanoclusters (or nanopucks). In this work, detailed calculations based on ab initio density functional theory are made to illuminate how the size and shape effects related to electronic confinement influence the sequence of these two-dimensional Ag nanostructures. The simulation results demonstrate that the evolution of a sequence of planar magic Ag clusters is strongly correlated with their electronic structures. Meanwhile, the role of substrate in the formation of magic Ag clusters is also examined. The symmetry and size of the periodic pattern on the substrate have helped to build up the distinguishable geometric structures in experiment. Further analysis of the related electronic and geometrical properties of these clusters not only explains the occurrence and sequence of the magic numbers but also helps to elucidate the mechanism of their formation.

Whether photoemission probes surface or bulk properties has long been a topic of interest and debate. This work employs angle-resolved photoemission to map the electronic structure of Ag films of varying thicknesses prepared on Si(111). As expected, the discrete quantum-well states or subbands observed at small thicknesses merge into a continuum as the film thickness approaches the bulk limit. However, a number of discrete states remain isolated within gaps or pockets in the bulk continuum. While these Ag surface states have been predicted previously by calculations, most are experimentally identified herein only for the first time. Copyright (C) EPLA, 2009

The clean-off reaction of AgO added rows by CO on Ag(110) and Au/Ag(110) bimetallic surfaces was studied by scanning tunneling microscopy (STM) and compared with density functional theory (DFT). This combined study of a model system illustrated the complexity of catalytic enhancement in bimetallic systems. By analyzing in situ time-lapsed STM image series, we found that CO oxidation on a Au-enriched Ag(110) surface leads to an exponential depletion of oxygen with time and a reaction rate that is synergistically enhanced by the presence of Au. First principles calculations indicate that the local atomic configuration around the active reaction sites at the chain ends and the preference of An atom substitution into the subsurface second Ag layer are of critical importance. By calculating CO adsorption energies and reaction barriers for plausible reaction pathways, a detailed description of the CO oxidation reaction emerges, For the optimal reaction pathway, a large (similar to 0.09 eV) barrier reduction and a small barrier of similar to 0.01 eV were found for the Eley-Rideal (ER) mechanism. In contrast, a small (similar to 0.03 eV) barrier reduction and a moderate barrier of similar to 0.23 eV were obtained for the Langmuir-Hinshelwood (LH) mechanism. The ER transitional state was also found to be lower in energy. We conclude that, irrespective of whether the ER mechanism is actually rate dominating, it is definitively enhanced.

To assess the accuracy of exchange-correlation approximations within density functional theory (DFT), diffusion quantum Monte Carlo (DMC) and DFT methods are used to calculate the energies of isomers of three covalently bonded carbon and boron clusters (C(20), B(18), and B(20)), and three metallic aluminum and copper clusters (Al(13), Al(55), and Cu(13)). We find that local and semilocal DFT methods predict the same energy ordering as DMC for the metallic clusters but not for the covalent clusters, implying that the DFT functionals are inadequate in such systems. In addition, we find that DFT fails to describe energy reductions arising from Jahn-Teller distortions..

In this study, the 13-atom cluster structures of alkaline metals, alkaline-earth metals, boron group metals, carbon group metals, and 3d, 4d, and 5d transition metals in the periodic table are investigated by density functional theory with three kinds of exchange-correlation (XC) functionals: (i) local-density approximation (LDA); (ii) generalized gradient approximation (GGA) with Perdew-Wang 91; and (iii) generalized gradient approximation with Perdew-Burke-Ernzerhof. The dependence on pseudopotentials (PPs) with and without semicore electrons is also examined. The relative energies of five selected high-symmetry three-dimensional and four low-symmetry layer-type isomers for each element of interest are calculated and studied. Among the 44 metallic 13-atom clusters, our results show that the two GGA XC functionals have a great consistency; LDA and GGA results also reveal a great consistency, apart from the Cr, Mn, Fe, Co, Ni, and Rh 13-atom clusters, for which the results show a significant difference. Meanwhile, for most of the elements, the calculations with and without semicore PPs also produce consistent results, except for Cr, Mo, and V, which require a careful treatment of semicore states in the PPs.

Basing on the results of the scanning tunneling microscopy (STM) observations and density functional theory (DFT) calculations, the structural model for the Cu magic clusters formed on Si(1 1 1)7 x 7 surface has been proposed. Using STM, composition of the Cu magic clusters has been evaluated from the quantitative analysis of the Cu and Si mass transport occurring during magic cluster converting into the Si(1 1 1)’5.5 x 5.5’-Cu reconstruction upon annealing. Evaluation yields that Cu magic cluster accommodates similar to 20 Cu atoms with similar to 20 Si atoms being expelled from the corresponding 7 x 7 half unit cell (HUC). In order to fit these values, it has been suggested that the Cu magic clusters resemble fragments of the Cu2Si-silicide monolayer incorporated into the rest-atom layer of the Si(1 1 1)7 x 7 HUCs. Using DFT calculations, stability of the nineteen models has been tested of which five models appeared to have formation energies lower than that of the original Si(1 1 1)7 x 7 surface. The three of five models having the lowest formation energies have been concluded to be the most plausible ones. They resemble well the evaluated composition and their counterparts are found in the experimental STM images. (C) 2009 Elsevier B.V. All rights reserved.

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Depositing particles randomly on a 1D lattice is expected to result in an equal number of particle pairs separated by even or odd lattice units. Unexpectedly, the even-odd symmetry is broken in the self-selection of distances between indium magic-number clusters on a Si(100)-2 x 1 reconstructed surface. Cluster pairs separated by even units are less abundant because they are linked by silicon atomic chains carrying topological solitons, which induce local strain and create localized electronic states with higher energy. Our findings reveal a unique particle-particle interaction mediated by the presence or absence of topological solitons on alternate lattices.

Adsorption of C-60 onto Si(111)root 3 x root 3-In surface presents a fascinating example of interplay between molecular adsorbate and surface structural defects. It has been found that adsorbing C-60 molecules are trapped by the substitutional Si-defects. In turn, the group of a few adsorbed C-60 can act as a trap for the mobile vacancies of the root 3 x root 3-In reconstruction. Namely, adsorbed C-60 induces a strain in the indium layer, and when a mobile vacancy happens to get into the surface area surrounded by fullerenes, the In atoms between the C-60 and the vacancy shift from the T-4 to the H-3 sites, fixing a vacancy in a given location. (C) 2011 Elsevier B.V. All rights reserved.

The formation process of Al magic clusters on the Si(111)-7 x 7 surface was investigated by means of a variable-temperature scanning tunneling microscope (STM) in situ and was interpreted using density-functional theory (DFT) calculations. At a growth temperature of 450 degrees C, Al atoms hopped among the corner, center, and T4 sites and also across the dimer rows on the Si(111)-7 x 7 surface. At low coverage below 0.08 ML, a single Al atom was adsorbed on the corner or center site. When the coverage was increased to 0.08 ML, Al dimers and trimers appeared, and Al magic clusters were also observed. However, no Al tetramers or pentamers were experimentally confirmed. Careful analysis of STM images suggests that Al trimers could be key precursors for the formation of Al magic clusters, and DFT calculations verified this interpretation. Total-energy calculation results using DFT reveal that this is due to the small energy gain from Al trimer to Al tetramer. These results are important for understanding the atomic structure and the formation mechanism of the magic clusters on the Si(111)-7 x 7 surface.

We have performed calculations of adsorption energetics on the graphene surface using the state-of-the-art diffusion quantum Monte Carlo method. Two types of configurations are considered in this work: the adsorption of a single O, F, or H atom on the graphene surface and the H-saturated graphene system (graphane). The adsorption energies are compared with those obtained from density functional theory with various exchange-correlation functionals. The results indicate that the approximate exchange-correlation functionals significantly overestimate the binding of O and F atoms on graphene, although the preferred adsorption sites are consistent. The energy errors are much less for atomic hydrogen adsorbed on the surface. We also find that a single O or H atom on graphene has a higher energy than in the molecular state, while the adsorption of a single F atom is preferred over the gas phase. In addition, the energetics of graphane is reported. The calculated equilibrium lattice constant turns out to be larger than that of graphene, at variance with a recent experimental suggestion.

The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd13 and Au13, we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au13, which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons.

Scanning tunneling microscopy (STM) observations of the close-packed C60 fullerene arrays on Si(111)
R3xR3-Ag surface have revealed the presence of dim C60 molecules which constitute 9–12% of all fullerenes. The dim C60 fullerenes reside  1.6 A lower than the bright (“normal”) C60.While the brightC60 are in continuous rotation, the dim C60 are fixed in one of the single orientations, indicating a more tight bonding to the surface. At room temperature (RT), the dynamic switching from bright to dim C60 and vice versa has been detected. Switching slows down with decreasing temperature and becomes completely frozen at 110 K, which implies that the switching is a thermally driven process. RT deposition of  0.1 monolayer of Ag onto C60 array eliminates completely the dim C60 molecules. Experimental results can be understood if one assumes that formation of the dim C60 is associated with disintegration of Ag trimer on Si(111)R3xR3- Ag surface under a given C60 fullerene.