Dimer Atoms Research Articles

A Desorption Mechanism of Hydrogen Atoms Adsorbed on A Graphite Layer: Ab initio Molecular-Dynamics Simulations

We have carried out ab initio molecular-dynamics simulations for the model system of hydrogen-adsorbed graphite to investigate the temperature-induced desorption of hydrogen atoms from the graphite and found for the first time by the ab initio electronic structure calculations the desorption of hydrogen atoms as a hydrogen dimer, which moves almost freely between graphite layers. We have also investigated the microscopic mechanism of the desorption and the dimerization of the hydrogen atoms based on the electron density distribution as well as the overlap population analysis, and clarified that the dimerization occurs through the intermediate `bridge' state such as –C–H–H–C–. Considering the increase in the temperature due to the recrystallization occurred in the nanostructured graphite, our results are consistent with the experimental results, in the sense that the recrystallization of the nanostructured graphite is necessary for the desorption of hydrogen atoms observed experimentally at higher temperature.

Atomic and electronic structures of N interstitials in GaAs

We have carried out electronic structure calculations on N interstitials in GaAs alloys using the first-principles plane-wave pseudopotential (PWPP) and projector augmented-wave (PAW) electronic structure methods in the framework of the density functional theory (DFT). Both the ultrasoft pseudopotential (USPP) method in connection with the generalized gradient approximation (GGA) and the PAW method in connection with the local density approximation (LDA) have been employed. Effects of the single nitrogen atom and nitrogen dimer related interstitial defects on the atomic and electronic structures of GaAs have been studied. Total energies, electronic band structures, and local densities of states have been evaluated. In general, energies of the defects with the NN dimer at the center of the Ga or As tetrahedron are more than 2 eV lower per nitrogen atom than those with a single N impurity at the same sites. We have also found that there are metastable defect candidates with a single N impurity in the middle of a particular edge of the Ga or As tetrahedra. Considering the modifications of the atomic structure of GaAs, our calculations show that the relaxations of the nearest neighbor atoms around the NN dimer at the center of the Ga or As tetrahedron, are essentially smaller than those around the single N impurity at the center of an edge of the Ga tetrahedron. Finally, these defect states induce drastic modifications into the electronic structure of GaAs. Interestingly, the NN dimer related defects cause noticeable changes only to the conduction bands near the conduction band edge, while the single N impurity related defects mainly modify the valence band edge and also induce localized and delocalized states into the band gap. Notably, the NN dimer and N impurity related defects lead to redshift and blueshift behavior of the band gap, respectively. The blueshift behavior is tentatively supported by the recent photoluminescence experiments.

Atomic scale engineering of nanostructures at silicon carbide surfaces

The atomic scale ordering and properties of cubic silicon carbide surfaces are investigated by room and high-temperature scanning tunneling microscopy. In this review, we will focus on the Si-terminated β-SiC(100) surfaces only. Self-formation of Si atomic lines and dimer vacancy chains on the β-SiC(100) surface is taking place at the phase transition between the 3×2 (Si-rich) and c(4×2) surface reconstructions. Using a rigorous protocol in surface preparation, it is possible to build very long, very straight and defect free Si atomic lines, forming a very large superlattice of massively parallel lines. These self-organized atomic lines are driven by stress. They have unprecedented characteristics with the highest thermal stability ever achieved for nanostructures on a surface (900°C) and the longest atomic lines ever built on a surface (micrometer scale long). Investigating their dynamics, we learn that their dismantling at high-temperature results from collective and individual mechanisms including one-by-one dimer removal. Overall, this is a model system especially suitable for nanophysics and nanotechnologies.

Conformation-selective adsorption of 2,3-butanediol on Si(0 0 1)

The adsorption of 2,3-butanediol on the Si(0 0 1) surface is studied by means of first-principles pseudopotential calculations. Molecular adsorption on top of the Si dimers resulting in a 6-membered ring of the O–C–C–O segment with the dimer atoms is energetically favored, in agreement with the interpretation of recent experiments. The adsorption energy difference for butanediol adsorbed in either gauche or anti conformation is nearly one order of magnitude larger than the energy difference between the respective conformers in gas phase, pointing to a conformation-selective adsorption.

A high resolution photoemission study of phenol adsorption on Si(1 0 0)2 × 1

The adsorption of a bi-functional organic molecule like phenol on Si(1 0 0)2 × 1 has been investigated by synchrotron radiation-induced photoemission in the valence band, Si 2p, C 1s and O 1s core-level regions. Experiments have been carried out as a function of phenol exposure at room temperature. Phenol adsorbs on Si(1 0 0)2 × 1 through a dissociative mechanism at room temperature, interacting with the surface by its alcoholic functionality. The line-shape analysis of Si 2p spectra indicates the formation of Si–O and Si–H bonds, as a consequence of the cleavage of the C 6H 5O–H bond and the binding of the fragments (C 6H 5O– group and H atom) to the Si(1 0 0)2 × 1 surface dimers. The progressive quenching of the silicon surface dimer atoms and the corresponding intensity increase of the Si–OC 6H 5 and Si–H components have been observed as a function of phenol exposure. The presence of the phenoxide (C 6H 5O–) group on the silicon surface has been evidenced also by the C 1s spectrum, consisting of two components in a 1:5 intensity ratio, energy splitted by 1.5 eV, which can be assigned to carbon atom linked to oxygen (C–O group) and carbon atoms of the aromatic ring, respectively.

Half-sandwich metal atom complexes with benzene: a model for adsorption onto graphite

A density functional theory study of the preferred binding position in metal–benzene complexes, where the metal atoms include Cu, Ag, Au, Ni, V, Co and Cr, is described. There exists an interesting and useful correlation between the preferred metal atom attachment site in the benzene complex and the preferred binding position of the atom on a graphite surface. Furthermore, the binding of metal atom dimers to benzene appears to reflect much of the electronic interaction of such species on the graphite surface. The binding orientation of silver and nickel dimers on graphite is also reflected in the simpler benzene complex.

Dynamical Singlets and Correlation-Assisted Peierls Transition inVO2

A theory of the metal-insulator transition in vanadium dioxide from the high- temperature rutile to the low- temperature monoclinic phase is proposed on the basis of cluster dynamical mean-field theory, in conjunction with the density functional scheme. The interplay of strong electronic Coulomb interactions and structural distortions, in particular, the dimerization of vanadium atoms in the low-temperature phase, plays a crucial role. We find that VO2 is not a conventional Mott insulator, but that the formation of dynamical V-V singlet pairs due to strong Coulomb correlations is necessary to trigger the opening of a Peierls gap.

Methanol adsorption on silicon (0 0 1)

Using a first-principles pseudopotential technique, we have investigated the adsorption of CH 3OH on the Si(0 0 1) surface. We have found that, in agreement with the overall experimental picture, the most probable chemisorption path for methanol adsorption on silicon (0 0 1) is as follows: the gas phase CH 3OH adsorbs molecularly to the electrophilic surface Si atom via the oxygen atom and then dissociates into Si–OCH 3 and H, bonded to the electrophilic and nucleophilic surface silicon dimer atoms, respectively. Other possible adsorption models and dissociation paths are also discussed. Our calculations also suggest that the most probable methanol coverage is 0.5 ML, i.e., one molecule per Si–Si dimer, in agreement with experimental evidences. The surface atomic and electronic structures are discussed and compared to available theoretical and experimental data. In addition, we propose that a comparison of our theoretical STM images and calculated vibrational modes for the adsorbed systems with detailed experimental investigations could possibly confirm the presented adsorption picture.

Structure and Properties of Fe4 with Different Coverage by C and CO

The electronic and geometrical structure of neutral and singly charged Fe4C2, Fe4C(CO), Fe4(CO)2, Fe4C2CO, Fe4C(CO)2, Fe4C3, and Fe4(CO)3 are studied using density functional theory with a generalized gradient approximation. It is found that the Fe4C2 and Fe4C2(CO) species possess two isomers with separated and dimerized carbon atoms. The latter isomers are lower in total energy by ∼0.3 eV. The Fe4C3 species possess three isomers corresponding to: a C2 dimer and one separated carbon atom (the lowest energies), a C3 trimer (intermediate energies), and three separated carbon atoms (the highest energies). The lowest energy dissociation channel corresponds to the loss of CO, except for Fe4(CO)2 and Fe4C(CO)2+, where the loss of carbon dioxide is the lowest. The computed total energies are used to estimate the energetics of the Boudouard-like disproportionation reactions, Fe4Cn(CO)m + CO → Fe4Cn+1(CO)m-1 + CO2. It is found that the most exothermic reaction in the series is Fe4C(CO)+ + CO → Fe4C2+ + CO2 (by ∼0.3 eV).

Progressive changes in atomic structure and gap states on Si(0 0 1) by Bi adsorption

From ab initio studies employing the pseudopotential method and the density functional scheme, we report on progressive changes in geometry, electronic states, and atomic orbitals on Si(0 0 1) by adsorption of different amounts of Bi coverage. For the 1/4 ML coverage, uncovered Si dimers retain the characteristic asymmetric (tilted) geometry of the clean Si(0 0 1) surface and the Si dimers underneath the Bi dimer have become symmetric (untilted) and elongated. For this geometry, occupied as well as unoccupied surface states are found to lie in the silicon band gap, both sets originating mainly from the uncovered and tilted silicon dimers. For the 1/2 ML coverage, there are still both occupied and unoccupied surface states in the band gap. The highest occupied state originates from an elaborate mixture of the p z orbital at the Si and Bi dimer atoms, and the lowest unoccupied state has a pp σ* antibonding character derived from the Bi dimer atoms. For 1 ML coverage, there are no surface states in the fundamental bulk band gap. The highest occupied and the lowest unoccupied states, lying close to band edges, show a linear combination of the p z orbitals and pp σ* antibonding orbital characters, respectively, derived from the Bi dimer atoms.

Helium dimers and trimers within carbon nanotubes

Helium dimers and trimers in infinite carbon nanotubes are described by wave function constructed as a product of Jastrow–Feenberg (JF) pair correlation and one-particle functions. One-particle functions are the ground state eigenfunctions of one helium atom in the tube; their analytic form is derived by fitting the corresponding numerical solution. Using this function in the Monte Carlo (MC) calculations in two successive stages, VMC (simple variational MC) and DMC (diffusion MC), it is found that binding strongly depends on the tube radius. Among armchair nanotubes binding is the strongest for the (7,7) nanotube. In that case the average distance between helium atoms in dimers and trimers is between 5 and 10 A ̊ . For larger radii the energies of 3 He dimers and trimers are the same within the errorbars, indicating the possible dimerized structure. In the (5,5) nanotube, the binding energies of boson 4 He 3 and fictitious fermion trimer, which has the same mass as 4 He 3 and spin 1 2 , are within the errorbars.

Adaptive quantum design of atomic clusters

Adaptive quantum design identifies the best broken-symmetry configurations of atoms and molecules that enable a desired target function response. In this work, numerical optimization is used to design atomic clusters with specified quasiparticle densities of states. The dominant self-assembled building blocks of these engineered quantum systems are found to depend on the symmetry of the target function. For example, particle-hole symmetric spectra can be constructed from a dilute configuration of atomic dimers, whereas more complex structures such as trimers and quadrumers are required for asymmetric target functions. The convergence of the optimization algorithms depends on the shape of the target function, the density of atoms, and constraints due to substrates and boundary conditions. Hybrids of steepest descent methods, simulated annealing, and genetic algorithms are found to be most efficient.

Adsorption of 2,3-butanediol on Si(1 0 0)

The adsorption of 2,3-butanediol on a Si(100) surface has been investigated by photoelectron spectroscopy. The valence band spectra show features assigned to molecular orbitals of 2,3-butanediol by comparison with calculations, and the surface states of clean Si are removed. The Si 2p reveals core-level shifts with two new components at 0.24 and 0.97 eV from the bulk, which are assigned to Si–H and Si–O bonds, respectively. The C 1s core-level spectrum consists of two major peaks separated by 1.3 eV, which are attributed to carbon atoms in –CHOH and –CH3 groups, in the molecule respectively. From the analysis of the valence band, the Si 2p, C 1s, and O 1s core-level spectra, we conclude that the 2,3-butanediol molecule undergoes a cleavage of the O–H bonds, and is bonded to the surface by the oxygen atoms. The molecule shows no further fragmentation and probably forms a six-membered ring of the O–C–C–O segment with the Si dimer atoms.

An ordered layer of molecular iodine on Ge(1 0 0) 2 × 1

Adsorption of iodine on the Ge(1 0 0) (2 × 1) surface has been investigated by core level and valence band photoelectron spectroscopy and scanning tunnelling microscopy. Iodine binds to dimer atom dangling bonds without disrupting the dimers at all coverages. At saturation a c(2 × 2) ordered layer of molecular iodine develops on top of a (2 × 2) ordered structure of atomic iodine binding to asymmetric Ge-dimers. Annealing destroys the molecular character and etches the surface by Ge dimer bond breaking and attachment of additional iodine to these Ge atoms to form GeI 2, which desorbs from the surface.

Highly Selective Surface Lewis Acid−Base Reaction: Trimethylamine on Si(100)c(4×2)

Adsorption of trimethylamine (TMA) on Si(100)c(4×2) has been studied using scanning tunneling microscopy (STM), valence photoelectron spectroscopy (PES), and high-resolution electron energy spectroscopy (HREELS) between 80 and 300 K. The TMA molecule is adsorbed nondissociatively only on the down dimer atom and appears as a triangle shaped bright protrusion in the occupied state STM image. The saturation coverage of TMA on Si(100) is estimated to be ∼0.25 ML (ML = one molecule per surface Si atom). The PES and HREELS results suggest that TMA is adsorbed through the N lone pair by forming an Si−N dative bond. The HREELS spectra indicate that the symmetry of adsorbed TMA is Cs and the molecular C3 axis is tilted from the surface normal. The stretching mode of the SiN dative bond is observed at 525 cm-1. Thus the combined STM, PES, and HREELS results indicate that the chemisorption of TMA on Si(100)c(4×2) occurs selectively on the down dimer atom via dative bonding. Hence, the TMA adsorption on Si(100)c(4×2) is purely site-specific on the down dimer atom and can be categorized in Lewis acid−base reaction. The acidity of the down dimer atom is also discussed according to the analysis of vibrational spectra.

Selective functionalization of the Si(1 0 0) surface by switching the adsorption linkage of a bifunctional organic molecule

Selective functionalization by switching the adsorption linkage of a bi-functional organic molecule, 1-dimethylamino-2-propyne (DMAP), on Si(1 0 0) has been studied using high-resolution electron energy loss spectroscopy (HREELS) and scanning tunneling microscopy (STM). The HREELS and STM results clearly indicate that DMAP adsorbs at the down dimer atom of Si(1 0 0)c(4 × 2) through an N → Si dative bond leaving the –CCH unit of DMAP free at low temperature (65–90 K). The adsorption linkage is switching from the N → Si dative bond to the Si–C di-σ bonds by annealing the adsorbed surface to 300 K, and thus the tertiary amino group becomes free.

Split-off dimer defects on theSi(001)2×1surface

Dimer vacancy (DV) defect complexes in the Si(001)2x1 surface were investigated using high-resolution scanning tunneling microscopy and first principles calculations. We find that under low bias filled-state tunneling conditions, isolated 'split-off' dimers in these defect complexes are imaged as pairs of protrusions while the surrounding Si surface dimers appear as the usual 'bean-shaped' protrusions. We attribute this to the formation of pi-bonds between the two atoms of the split-off dimer and second layer atoms, and present charge density plots to support this assignment. We observe a local brightness enhancement due to strain for different DV complexes and provide the first experimental confirmation of an earlier prediction that the 1+2-DV induces less surface strain than other DV complexes. Finally, we present a previously unreported triangular shaped split-off dimer defect complex that exists at SB-type step edges, and propose a structure for this defect involving a bound Si monomer.

Indirect adsorbate-adsorbate interactions mediated through the surface electronic structure of the Si(100) surface.

Indirect adsorbate-adsorbate interactions between adsorbed ammonia (NH3) molecules on the Si(100) surface are investigated using density functional theory. Two different nonlocal effects mediated through the surface electronic structure are observed: "poisoning" and hydrogen bonding. We find that adsorbed NH3 "poisons" adsorption of NH3 on neighboring Si dimers on the same side of the dimer row whereas neighboring NH2(a) groups favor this configuration. Adsorption of NH3 involves charge transfer to the surface that localizes on neighboring Si dimer atoms, preventing adsorption of NH3 at these sites. These indirect interactions are similar to Friedel-type interactions observed on metal surfaces with an estimated range of less than 7.8 A on the Si(100) surface. These interactions may be manipulated to construct local ordering of the adsorbates on the surface.

Site determination and thermally assisted tunneling in homogenous nucleation.

A combined low-temperature scanning tunneling microscopy and density functional theory study on the binding and diffusion of copper monomers, dimers, and trimers adsorbed on Cu(111) is presented. Whereas atoms in trimers are found in fcc sites only, monomers as well as atoms in dimers can occupy the fcc as well as the metastable hcp site. In fact the dimer fcc-hcp configuration is only 1.3 meV less favorable with respect to the fcc-fcc configuration. This enables a confined intracell dimer motion, which at temperatures below 5 K is dominated by thermally assisted tunneling.

Mechanism of initial adsorption of NO on the Si(100) surface

High-resolution photoemission study of the adsorption of NO molecules on the $\mathrm{Si}(100)2\ifmmode\times\else\texttimes\fi{}1$ surface at 150 K is performed using undulator synchrotron radiation. N $1s,$ O $1s,$ as well as Si $2p$ core-level spectra are measured for the series of NO exposures from the very initial adsorption to the full monolayer coverage. The metastable adsorption species are observed with N $1s$ binding energies of 396.4 and 395.8 eV, along with the stable major adsorption species of $\mathrm{N}\ensuremath{\equiv}{\mathrm{Si}}_{3}$ at 397.4 eV. Both of the metastable species are ascribed to the intermediate reaction species of $\mathrm{N}={\mathrm{Si}}_{2}$ with a dangling bond. In the O $1s$ spectra, the major O species at 532.4 eV is found to shift toward high binding energies with increasing NO exposures or increasing substrate temperature. This shift is explained by the changes in bonding configurations induced by the active oxygen agglomeration. From these results, it is concluded that NO adsorption above 150 K is completely dissociative without any metastable molecular adsorption species. Instead, it is deduced that the dissociated N atoms metastably form twofold coordinated $\mathrm{N}={\mathrm{Si}}_{2}$ species through multiple dissociation paths involving one or two Si dimer atoms.