Structure of monolayers built during adsorption process is strongly related to the properties of adsorbed particles. The most important factor is their shape. For example, adsorption of elongated molecules on patterned surfaces may produce certain orientational order inside a covering layer. This study, however, focuses on random adsorption of dimers on flat, homogeneous surfaces. It has been observed that despite the lack of global orientational ordering, adsorbed dimers may form local, orientationally ordered structures [1, 2]. Our investigations focus on the dependence between domain size distribution and environmental parameters such as ionic strength, which affects the range of electrostatic interaction between molecules.
We report studies of random sequential adsorption on the pre-patterned Bethe lattice. We consider a partially covered Bethe lattice, on which monomers and dimers deposit competitively. Analytical solutions are obtained and discussed in the context of recent efforts to use pre-patterning as a tool to improve self-assembly in micro- and nano-scale surface structure engineering.
Saturated random packing of particles built of two identical, relatively shifted spheres in two and three dimensional flat and homogeneous space was studied numerically using random sequential adsorption algorithm. The shift between centers of spheres varied from 0.0 to 8.0 sphere diameters. Numerical simulations allowed determine random sequential adsorption kinetics, saturated random coverage ratio as well as available surface function and density autocorrelation function.
Adsorption of dimers is modelled using random sequential adsorption algorithm. The interaction between molecules is given by screened electrostatic potential. The paper focuses on the properties of adsorbed monolayers as well as the dependence of adsorption kinetics on interaction range. We designate random maximal coverage ratios, density autocorrelations and orientational ordering inside layers. Moreover the detailed analysis of adsorption kinetics is presented including a discussion of Feder's law validity and new numerical method for modelling diffusion driven adsorption. Results of numeri…
The first theoretical study of a dimer's adsorption process at homogenous surface is presented. By using the RSA algorithm, we show example monolayers, discuss estimations of random jamming coverage and measure the surface blocking function, which could be used for calculating real systems kinetics. We also found the correlation function for generated coverages and analyzed orientational ordering inside the adsorbed monolayer. Results were compared with theoretical and experimental data. Keywords: adsorption, RSA, monolayer, colloid particles
Atomically precise dopant arrays in Si are being pursued for solid-state quantum computing applications. We propose a guided self-assembly process to produce atomically precise arrays of single dopant atoms in lieu of lithographic patterning. We leverage the self-assembled c(4x2) structure formed on Br- and I-Si(100) and investigate molecular precursor adsorption into the generated array of single-dimer window (SDW) adsorption sites with density functional theory (DFT). The adsorption of several technologically relevant dopant precursors (PH$_3$, BCl$_3$, AlCl$_3$, GaCl$_3$) into SDWs formed w…
Doping of Si using the scanning probe hydrogen depassivation lithography technique has been shown to enable placing and positioning small numbers of P atoms with nanometer accuracy. Several groups have now used this capability to build devices that exhibit desired quantum behavior determined by their atomistic details. What remains elusive, however, is the ability to control the precise number of atoms placed at a chosen site with 100% yield, thereby limiting the complexity and degree of perfection achievable. As an important step towards precise control of dopant number, we explore the adsorp…
In this work we perform a first-principles study of the adsorption properties of an In adatom deposited on 1.75 monolayers (ML) InAs, forming a wetting layer on GaAs$(001)$ with the $α_2 (2\times4)$ or $β_2 (2\times4)$ reconstruction. The structural properties of these reconstructions have been studied: we determine the equilibrium geometry of the surfaces and their stability for various growth conditions. We have then carried out a detailed study of the potential energy surface (PES) for an In adsorbate, finding the minima and the saddle points. The main characteristics of the PES and the bon…
We present an ab initio study of the structural and electronic properties of styrene molecules adsorbed on the dimerized Si(100) surface at different coverages, ranging from the single-molecule to the full monolayer. The adsorption mechanism primarily involves the vinyl group via a [2+2] cycloaddition process that leads to the formation of covalent Si-C bonds and a local surface derelaxation, while it leaves the phenyl group almost unperturbed. The investigation of the functionalized surface as a function of the coverage (e.g. 0.5 -- 1 ML) and of the substrate reconstruction reveals two major …
Using density functional theory, we investigate the possible adsorption sites of CO molecules on the recently discovered Pt induced Ge nanowires on Ge(001). Calculated STM images are compared to experimental STM images to identify the experimentally observed adsorption sites. The CO molecules are found to adsorb preferably onto the Pt atoms between the Ge nanowire dimer segments. This adsorption site places the CO in between two nanowire dimers, pushing them outward, blocking the nearest equivalent adsorption sites. This explains the observed long-range repulsive interaction between CO molecul…
Graphene has various potential applications in electronics and scientists are seeking to introduce magnetic properties on graphene. Here we report our theoretical findings that a local magnetic moment as large as 1 $μ_B$ can be generated from the adsorption of the diamagnetic beryllium dimer on perfect diamagnetic graphene. Unexpectedly the adsorption system is remarkably stable as evidenced by the binding energy of 1.04 eV, indicating that the formation of beryllium dimer is energetically much favorable. Analyses reveal that the magnetic moment and stability is originated from the spontaneous…
Application of Regional Chemical Potential Analysis to Si Adsorption on the Diamond (001) Surface
Institute for Solid State Physics, The University of Tokyo（东京大学固体离子体研究所）；Department of Advanced Materials Science, The University of Tokyo（东京大学先进材料科学系）
First-principles calculations using density functional theory based on norm-conserving pseudopotentials have been performed to investigate the Mg adsorption on the Si(001) surface for 1/4, 1/2 and 1 monolayer coverages. For both 1/4 and 1/2 ML coverages it has been found that the most favorable site for the Mg adsorption is the cave site between two dimer rows consistent with the recent experiments. For the 1 ML coverage we have found that the most preferable configuration is when both Mg atoms on 2x1 reconstruction occupy the two shallow sites. We have found that the minimum energy configurat…
In this study we employ Density Functional Theory (DFT) methods to investigate the surface energy barrier for electron emission (surface barrier) and thermodynamic stability of Ba and Ba-O species adsorption under conditions of high temperature (approximately 1200 K) and low pressure (approximately $10^{-10}$ Torr) on the low index surfaces of bixbyite $Sc_2O_3$. The role of Ba in lowering the cathode surface barrier is investigated via adsorption of atomic Ba and Ba-O dimers, where the highest simulated dimer coverage corresponds to a single monolayer film of rocksalt BaO. The change of the s…
Irreversible adsorption of spheres on flat collectors having dimension $d<2$ is studied. Molecules are adsorbed on Sierpinski's Triangle and Carpet like fractals ($1<d<2$), and on General Cantor Set ($d<1$). Adsorption process is modeled numerically using Random Sequential Adsorption (RSA) algorithm. The paper concentrates on measurement of fundamental properties of coverages, i.e. maximal random coverage ratio and density autocorrelation function, as well as RSA kinetics. Obtained results allow to improve phenomenological relation between maximal random coverage ratio and collector dimension.…
Adsorption of trimers and hexamers built of identical spheres was studied numerically using the Random Sequential Adsorption (RSA) algorithm. Particles were adsorbed on a two dimensional, flat and homogeneous surface. Numerical simulations allow to establish the maximal random coverage ratio, RSA kinetics as well as the Available Surface Function (ASF), which is crucial for determining kinetics of the adsorption process obtained experimentally. Additionally, the density autocorrelation function was measured. All the results were compared with previous results obtained for spheres, dimers and t…
Based on numerically accurate density functional theory (DFT) calculations, we systematically investigate the ground-state structure and the spin and orbital magnetism including the magnetic anisotropy energy (MAE) of 3d- and 4d-transition-metal dimer benzene complexes (TM2Bz, TM = Fe, Co, Ni, Ru, Rh, Pd; Bz = C6H6). These systems are chosen to model TM-dimer adsorption on graphene or on graphite. We find that Fe2, Co2, Ni2, and Ru2 prefer the upright adsorption mode above the center of the benzene molecule, while Rh2 and Pd2 are adsorbed parallel to the benzene plane. The ground state of Co2B…
The adsorption behavior and the magnetic states of cobalt atoms and dimers on single vacancies in a graphene sheet are investigated by means of relativistic density functional calculations. It is found that local magnetic moments are formed in both cases, despite strong chemical binding. Of particular interest are kinetically stable isomers with two cobalt atoms attached to the same side of the graphene sheet. Magnetic bi-stability with an anisotropy barrier of about 50 meV is possible in this geometry. The feasibility of its preparation is discussed.
The ability of metal adsorption to transfer charge to the surface of single molecular carbon sheets is explored in this paper. Though other metals are considered we basically will deal with Lithium We concentrate on fairly small sheets and examined the minimum threshold size of a molecular surface needed to separate metals. From our quantum chemical calculations we deduce that a molecular surface of six benzene rings is needed for Lithium dimers to be separated. We further observe symmetry breaking, when two lithium atoms are adsorbed right opposite to each other on the two sides of the sheet.
Density Functional Theory calculations are used to investigate the role of substrate-induced cooperative effects on the adsorption of water on a partially oxidized transition metal surface, O(2x2)/Ru(0001). Focussing particularly on the dimer configuration, we analyze the different contributions to its binding energy. A significant reinforcement of the intermolecular hydrogen-bond (H-bond), also supported by the observed frequency shifts of the vibration modes, is attributed to the polarization of the donor molecule when bonded to the Ru atoms in the substrate. This result is further confirmed…
We show by first-principles calculations that the electronic properties of zigzag graphene nanoribbons (Z-GNRs) adsorbed on Si(001) substrate strongly depend on ribbon width and adsorption orientation. Only narrow Z-GNRs with even rows of zigzag chains across their width adsorbed perpendicularly to the Si dimer rows possess an energy gap, while wider Z-GNRs are metallic due to width-dependent interface hybridization. The Z-GNRs can be metastably adsorbed parallel to the Si dimer rows, but show uniform metallic nature independent of ribbon width due to adsorption induced dangling-bond states on…
We used DFT to study the energetics of the decomposition of alane, AlH3, on the Si(001) surface, as the acceptor complement to PH3. Alane forms a dative bond with the raised atoms of silicon surface dimers, via the Si atom lone pair. We calculated the energies of various structures along the pathway of successive dehydrogenation events following adsorption: AlH2, AlH and Al, finding a gradual, significant decrease in energy. For each stage, we analyse the structure and bonding, and present simulated STM images of the lowest energy structures. Finally, we find that the energy of Al atoms incorp…
Employing first principles total energy calculations we have studied the behavior of Ga and Al adatoms on the GaAs(001)-beta2 surface. The adsorption site and two relevant diffusion channels are identified. The channels are characterized by different adatom-surface dimer interaction. Both affect in a novel way the adatom migration: in one channel the diffusing adatom jumps across the surface dimers and leaves the dimer bonds intact, in the other one the surface dimer bonds are broken. The two channels are taken into account to derive effective adatom diffusion barriers. From the diffusion barr…
The vibrational and structural properties of a single-domain Si(001)-(2x1) surface upon ethylene adsorption have been studied by density functional cluster calculations and high-resolution electron energy loss spectroscopy. The detailed analysis of the theoretically and the experimentally determined vibrational frequencies reveals two coexisting adsorbate configurations. The majority ethylene species is di-sigma bonded to the two Si atoms of a single Si-Si dimer. The local symmetry of this adsorption complex for ethylene saturation is reduced to C2 as determined by surface selection rules for …
Iron pyrite (FeS$_{2}$) is the most abundant metal sulfide on Earth. Owing to its reactivity and catalytic activity, pyrite has been studied in various research fields such as surface science, geochemistry, and prebiotic chemistry. Importantly, native iron-sulfur clusters are typically coordinated by cysteinyl ligands of iron-sulfur proteins. In the present paper, we study the adsorption of L-cysteine and its oxidized dimer, L-cystine, on the FeS$_{2}$ surface, using electronic structure calculations based density functional theory and Raman spectroscopy measurements. Our calculations suggest …
Ab initio self-consistent total energy calculations using second order Moller-Plesset perturbation theory and Hay-Wadt effective core potentials with associated basis sets (HWECP's) for gallium and arsenic have been used to investigate the chemisorption properties of atomic aluminum on the Ga-rich GaAs(100)-(2x1) and beta(4x2) surfaces. Finite sized hydrogen saturated clusters with the experimental zinc-blende lattice constant of 5.654 ang. and the energy optimized Ga dimer bond length of 2.758 ang. have been used to model the semiconductor surface. To investigate the effects of the core elect…
The interaction of methanethiol molecules CH$_{3}$SH with the Au(111) surface is investigated, and it is found for the first time that the S-H bond remains intact when the methanethiol molecules are adsorbed on the regular Au(111) surface. However, it breaks if defects are present in the Au(111) surface. At low coverage, the fcc region is favored for S atom adsorption, but at saturated coverage the adsorption energies at various sites are almost iso-energetic. The presented calculations show that a methanethiol layer on the regular Au(111) surface does not dimerize.
The energetics of H$_2$ interacting with the Si(100) surface is studied by means of {\em ab initio} total energy calculations within the framework of density functional theory. We find a direct desorption pathway from the mono-hydride phase which is compatible with experimental activation energies and demonstrate the importance of substrate relaxation for this process. Both the transition state configuration and barrier height depend crucially on the degree of buckling of the Si dimers on the Si(100) surface. The adsorption barrier height on the clean surface is governed by the buckling via it…
Employing density functional theory calculations we explore initial stage of competitive alloying of co-deposited silver and indium atoms into a silicon surface. Particularly, we identify respective adsorption positions and activation barriers governing their diffusion on the dimer-reconstructed silicon surface. Further, we develop a growth model that properly describes diffusion mechanisms and silicon morphology with the account of silicon dimerization and the presence of C-type defects. Based on the surface kinetic Monte Carlo simulations we examine dynamics of bimetallic adsorption and elab…
Although perovskite oxides hold promise in applications ranging from solid oxide fuel cells to catalysts, their surface chemistry is poorly understood at the molecular level. Here we follow the formation of the first monolayer of water at the (001) surfaces of Sr$_{n+1}$Ru$_n$O$_{3n+1}$ ($n$ = 1, 2) using low-temperature scanning tunnelling microscopy, X-ray photoelectron spectroscopy, and density functional theory. These layered perovskites cleave between neighbouring SrO planes, yielding almost ideal, rocksalt-like surfaces. An adsorbed monomer dissociates and forms a pair of hydroxide ions.…
The diffusivity of Ga and Al adatoms on the (2x4) reconstructed GaAs(001) surface are evaluated using detailed ab initio total energy calculations of the potential energy surface together with transition state theory. A strong diffusion anisotropy is found, with the direction of fastest diffusion being parallel to the surface As-dimer orientation. In contrast to previous calculations we identify a short--bridge position between the two As atoms of a surface dimer as the adsorption site for Al and Ga adatoms.
Equilibrium structure, local densities of states, and electronic transport in a gold nanowire made of a four-atom chain supported by two gold electrodes, which has been imaged recently by high-resolution electron microscopy, and chemical modification of the wire via the adsorption of a methylthiol molecule, are investigated with ab-initio local density functional simulations. In the bare wire at the imaged geometry the middle two atoms dimerize, and the structure is strongly modified by the adsorption of the molecule with an accompanying increase of the ballistic conductance through the wire.
The adsorption of hydrogen at nonpolar GaN(1-100) surfaces and its impact on the electronic and vibrational properties is investigated using surface electron spectroscopy in combination with density functional theory (DFT) calculations. For the surface mediated dissociation of H2 and the subsequent adsorption of H, an energy barrier of 0.55 eV has to be overcome. The calculated kinetic surface phase diagram indicates that the reaction is kinetically hindered at low pressures and low temperatures. At higher temperatures ab-initio thermodynamics show, that the H-free surface is energetically fav…
We present a density functional study of the structural and electronic properties of small Cu_n (n=1,4) aggregates on defect-free MgO(100). The calculations employ a slab geometry with periodic boundary conditions, supercells with up to 76 atoms, and include full relaxation of the surface layer and of all adsorbed atoms. The preferred adsorption site for a single Cu adatom is on top of an oxygen atom. The adsorption energy and Cu-O distance are E_S-A = 0.99 eV and d_S-A = 2.04 Angstroems using the Perdew-Wang gradient corrected exchange correlation functional. The saddle point for surface diff…
Recent experiments on the silicon terminated $3\times 2$ SiC(100) surface indicated an unexpected metallic character upon hydrogen adsorption. This effect was attributed to the bonding of hydrogen to a row of Si atoms and to the stabilization of a neighboring dangling bond row. Here, on the basis of Density-Functional calculations, we show that multiple-layer adsorption of H at the reconstructed surface is compatible with a different geometry: besides saturating the topmost Si dangling bonds, H atoms are adsorbed at rather unusual sites, \textit{i.e.} stable bridge positions above third-layer …
We report on the structure and adsorption properties of Pd$_n$ ($n=1-4$) clusters supported on the rutile TiO$_2$ (110) surfaces with the possible presence of a surface oxygen vacancy or a subsurface Ti-interstitial atom. As predicted by the density functional theory, small Pd clusters prefer to bind to the stoichiometric titania surface or at sites near subsurface Ti-interstitial atoms. The adsorption of Pd clusters changes the electronic structure of the underlying surface. For the surface with an oxygen vacancy, the charge localization and ferromagnetic spin states are found to be largely a…
We use scanning tunneling microscopy (STM) and Auger electron spectroscopy to study the behavior of adsorbed phosphine (PH$_{3}$) on Si(001), as a function of annealing temperature, paying particular attention to the formation of the Si-P heterodimer. Dosing the Si(001) surface with ${\sim}$0.002 Langmuirs of PH$_{3}$ results in the adsorption of PH$_{x}$ (x=2,3) onto the surface and some etching of Si to form individual Si ad-dimers. Annealing to 350$^{\circ}$C results in the incorporation of P into the surface layer to form Si-P heterodimers and the formation of short 1-dimensional Si dimer …
Ubiquitous graphene is a stricly 2D material representing an ideal adsorbing platform due to its large specific surface area as well as its mechanical strength and resistance to both thermal and chemical stresses. However, graphene as a bulk material has the tendency to form irreversible agglomerates leading to 3D graphitic structures with a significant decrease of the area available for adsorption and no room for gas intercalation. In this paper a novel nanoporous graphite formed by graphtriyne sheets is introduced: its 3D structure is theoretically assessed by means of electronic structure a…
Heteroepitaxial structures based on Bi$_{2}$Te$_{3}$-type topological insulators (TIs) exhibit exotic quantum phenomena. For optimal characterization of these phenomena, it is desirable to control the interface structure during film growth on such TIs. In this process, adatom mobility is a key factor. We demonstrate that Pb mobility on the Bi$_{2}$Te$_{3}$(111) surface can be modified by the engineering local strain, ε, which is induced around the point-like defects intrinsically forming in the Bi$_{2}$Te$_{3}$(111) thin film grown on a Si(111)-7 $\times$ 7 substrate. Scanning tunneling micros…
Oxygen (O2) adsorbed on metal oxides is important in catalytic oxidation reactions, chemical sensing, and photocatalysis. Strong adsorption requires transfer of negative charge from oxygen vacancies (VOs) or dopants, for example. With scanning tunneling microscopy, we observed, transformed, and, in conjunction with theory, identified the nature of O2 molecules on the (101) surface of anatase (titanium oxide, TiO2) doped with niobium. VOs reside exclusively in the bulk, but we pull them to the surface with a strongly negatively charged scanning tunneling microscope tip. O2 adsorbed as superoxo …
Herein, we invesgate the consequence of local voltage pulses on the adsorption state of single indigo molecules on the Cu(111) surface as well as on the atomic structure underneath the molecule. With a scanning tunneling microscope, at 5 K, intact molecules are imaged as two lobes corresponding to the electron density of each indoxyl moiety of the molecule which are connected by a carbon double bond. Then, two short successive voltage pulses with the tip placed above the molecule generate irreversible modifications, as revealed by consecutive scanning tunneling microscopy (STM) imaging. Densit…
