Dynamical reaction pathways in Eley-Rideal recombination of nitrogen from W(100)

The scattering of atomic nitrogen over a N-pre-adsorbed W(100) surface is theoretically described in the case of normal incidence off a single adsorbate. Dynamical reaction mechanisms, in particular Eley-Rideal (ER) abstraction, are scrutinized in the 0.1-3.0?eV collision energy range and the influence of temperature on reactivity is considered between 300 and 1500 K. Dynamics simulations suggest that, though non-activated reaction pathways exist, the abstraction process exhibits a significant collision energy threshold (0.5 eV). Such a feature, which has not been reported so far in the literature, is the consequence of a repulsive interaction between the impinging and the pre-adsorbed nitrogens along with a strong attraction towards the tungsten atoms. Above threshold, the cross section for ER reaction is found one order of magnitude lower than the one for hot-atoms formation. The abstraction process involves the collision of the impinging atom with the surface prior to reaction but temperature effects, when modeled via a generalized Langevin oscillator model, do not affect significantly reactivity.     

Atomic hydrogen interaction with Ru(1010)

The interaction of atomic hydrogen with clean and deuterium precovered Ru(1010) was studied by means of temperature-programmed desorption (TPD) spectroscopy. Compared to molecular hydrogen experiments, after exposure of the clean surface to gas-phase atomic hydrogen at 90 K, two additional peaks grow in the desorption spectra at 115 and 150 K. The surface saturation coverage, determined by equilibrium between abstraction and adsorption reactions, is 2.5 monolayers. Preadsorbed deuterium abstraction experiments with gas-phase atomic hydrogen show that a pure Eley-Rideal mechanism is not involved in the process, while a hot atom (HA) kinetics describes well the reaction. By least-squares fitting of the experimental data, a simplified HA kinetic model yields an abstraction cross section value of 0.5 +/- 0.2 angstroms2. The atomic hydrogen interaction with an oxygen precovered surface was also studied by means of both TPD and x-ray photoelectron spectroscopy: oxygen hydrogenation and water production take place already at very low temperature (90 K).     

Configurational probabilities for symmetric dimers on a lattice: an analytical approximation with exact limits at low and high densities

A new approach is developed for lattice density functional theory of interacting symmetric dimers at high temperatures. Equations of equilibrium for two-dimensional square and three-dimensional cubic lattices are derived for the complete set of configurations in the first three shells around the central dimer, and rules of truncation for higher shells are based on exact results from the mathematical theory of domino tilings. This provides exact limits for both low and high densities. The new model predicts contributions of particular configurations which are in agreement with Monte Carlo simulations over the whole range of densities, including agreement with pocket Monte Carlo simulations at high densities.     

Monte Carlo studies of isomers, structures, and properties in benzene-cyclohexane clusters: computation strategy and application to the dimer and trimer, (C6H6)(C6H12)n, n = 1-2

Low-temperature isomeric energies, structures, and properties of benzene-cyclohexane clusters are investigated via Monte Carlo simulations. The Monte Carlo strategy is first documented and then applied to (C(6)H(6))(C(6)H(12)) and (C(6)H(6))(C(6)H(12))(2) using four different potential energy surfaces. Results identify a single parallel-displaced dimer isomer. MP2 optimizations and frequency calculations support the Monte Carlo dimer structure and identify the van der Waals mode observed in vibronic spectra. Caloric simulations identify two temperatures where structural transitions occur and imply an experimental temperature below 10 K for dimers in cold supersonic expansions. The (C(6)H(6))(C(6)H(12))(2) studies identify eight independent trimer isomers: three form parallel-stacked (sandwich) arrangements with the two cyclohexane moieties related through a D(6)(h) transformation. The remaining five trimer isomers are trigonal, with no overall symmetry. Caloric studies indicate that the sandwich and trigonal isomeric classes coexist independently below 60 K, consistent with trimer vibronic spectra that contain two independent van der Waals progressions.     

Quantum Monte Carlo simulations of selected ammonia clusters (n = 2-5): isotope effects on the ground state of typical hydrogen bonded systems

Variational Monte Carlo, diffusion Monte Carlo, and stereographic projection path integral simulations are performed on eight selected species from the (NH(3))(n), (ND(3))(n), (NH(2)D)(n), and (NH(3))(n-1)(ND(3)) clusters. Each monomer is treated as a rigid body with the rotation spaces mapped by the stereographic projection coordinates. We compare the energy obtained from path integral simulations at several low temperatures with those obtained by diffusion Monte Carlo, for two dimers, and we find that at 4 K, the fully deuterated dimer energy is in excellent agreement with the ground state energy of the same. The ground state wavefunction for the (NH(3))(2-5) clusters is predominantly localized in the global minimum of the potential energy. In all simulations of mixed isotopic substitutions, we find that the heavier isotope is almost exclusively the participant in the hydrogen bond.     

Stochastic simulation of catalytic surface reactions in the fast diffusion limit

The master equation of a lattice gas reaction tracks the probability of visiting all spatial configurations. The large number of unique spatial configurations on a lattice renders master equation simulations infeasible for even small lattices. In this work, a reduced master equation is derived for the probability distribution of the coverages in the infinite diffusion limit. This derivation justifies the widely used assumption that the adlayer is in equilibrium for the current coverages and temperature when all reactants are highly mobile. Given the reduced master equation, two novel and efficient simulation methods of lattice gas reactions in the infinite diffusion limit are derived. The first method involves solving the reduced master equation directly for small lattices, which is intractable in configuration space. The second method involves reducing the master equation further in the large lattice limit to a set of differential equations that tracks only the species coverages. Solution of the reduced master equation and differential equations requires information that can be obtained through short, diffusion-only kinetic Monte Carlo simulation runs at each coverage. These simulations need to be run only once because the data can be stored and used for simulations with any set of kinetic parameters, gas-phase concentrations, and initial conditions. An idealized CO oxidation reaction mechanism with strong lateral interactions is used as an example system for demonstrating the reduced master equation and deterministic simulation techniques.     

Energetics driving the short-range order in CuxPd1-x/Ru(0001) monolayer surface alloys

The energetics determining the distinct short-range order in two-dimensional (2D) monolayer Cu(x)Pd(1-x) surface alloys on a Ru(0001) substrate were investigated by Monte Carlo simulations and density functional theory calculations. Using a 2D lattice gas Hamiltonian based on effective pair interaction (EPI) parameters, the EPIs were derived for different Cu concentrations with Monte Carlo (MC) simulations by comparing with the atomic distributions obtained from atomic resolution STM images and the related Warren-Cowley short-range order parameters (Hoster et al., Phys. Rev. B, 2006, 73 165413). The ground state structures and mixing energies at 0 K derived from these EPIs agree well with mixing energies determined from DFT calculations of different ordered surface alloys. Additional MC simulations yield rather low transition temperatures which explain the absence of ordered 2D phases in the experiments. The consequences of our findings for the use of alloy surfaces and surface alloys as model systems for adsorption and catalytic reaction studies are discussed.     

Database of atomistic reaction mechanisms with application to kinetic Monte Carlo

Kinetic Monte Carlo is a method used to model the state-to-state kinetics of atomic systems when all reaction mechanisms and rates are known a priori. Adaptive versions of this algorithm use saddle searches from each visited state so that unexpected and complex reaction mechanisms can also be included. Here, we describe how calculated reaction mechanisms can be stored concisely in a kinetic database and subsequently reused to reduce the computational cost of such simulations. As all accessible reaction mechanisms available in a system are contained in the database, the cost of the adaptive algorithm is reduced towards that of standard kinetic Monte Carlo.     

Adsorption of phenylacetylene on Si(100)-2 x 1: kinetics and structure of the adlayer

Direct adsorption of phenylacetylene on clean silicon surface Si(100)-2 x 1 is studied in ultrahigh vacuum (UHV). The combination of scanning tunnel microscopy (STM) and surface differential reflectance spectroscopy (SDRS) with Monte Carlo calculations are put together to draw a realistic kinetic model of the evolution of the surface coverage as a function of the molecular exposure. STM images of weakly covered surfaces provide evidence of two very distinct adsorption geometries for phenylacetylene, with slightly different initial sticking probabilities. One configuration is detected with STM as a bright spot that occupies two dangling bonds of a single dimer, whereas the other configuration occupies three dangling bonds of adjacent dimers. These data are used to implement a Monte Carlo model which further serves to design an accurate kinetic model. The resulting evolution toward saturation is compared to the optical data from surface differential reflectance spectroscopy (SDRS). SDRS is an in situ technique that monitors the exact proportion of affected adsorption sites and therefore gives access to the surface coverage which is evaluated at 0.65. We investigate the effect of surface temperature on this adsorption mechanism and show that it has no major effect either on kinetics or on structure, unless it passes the threshold of dissociation measured at ca. 200 degrees C. This offers a comprehensive image of the whole adsorption process of phenylacetylene from initial up to complete saturation.     

Interaction of water with DNA single and double helix in the B conformation

The interaction energy between water and B-DNA in the single and double helix is computed at a number of planar cross sections perpendicular to the helix long axis and for a few cylindrical surfaces enclosing the helix. In addition, Monte Carlo simulations are presented for a small cluster of water around regions of energy minima. On the base of these simulations the structure of water for B-DNA in solution, the quaternary structure of B-DNA, is proposed and discussed. The intermolecular interaction used in the Monte Carlo computation has been derived from ab initio computations of complexes between water and the DNA bases, diethylphosphate, a ribose derivative, and other model compounds.     

Mechanism of the CO oxidation reaction on O-precovered Pt(111) surfaces studied with near-edge x-ray absorption fine structure spectroscopy

The mechanism of CO oxidation reaction on oxygen-precovered Pt(111) surfaces has been studied by using time-resolved near-edge x-ray absorption fine structure spectroscopy. The whole reaction process is composed of two distinct paths: (1) a reaction of isolated oxygen atoms with adsorbed CO, and (2) a reaction of island-periphery oxygen atoms after the CO saturation. CO coadsorption plays a role to induce the dynamic change in spatial distribution of O atoms, which switches over the two reaction paths. These mechanisms were confirmed by kinetic Monte Carlo simulations. The effect of coadsorbed water in the reaction mechanism was also examined.     

Computational studies on thermodynamic properties, effective diameters, and free volume of argon using an ab initio potential

A quantum mechanical derived ab initio interaction potential for the argon dimer was tested in molecular simulations to reproduce the thermophysical properties of the vapor-liquid phase equilibria using the Gibbs ensemble Monte Carlo simulations as well as the liquid and supercritical equation of state using the NVT Monte Carlo simulations. The ab initio interaction potential was taken from the literature. A recently developed theory [R. Laghaei et al., J. Chem. Phys. 124, 154502 (2006)] was used to compute the effective diameters of argon in fluid phases and the results were subsequently applied in the generic van der Waals theory to compute the free volume of argon. The calculated densities of the coexisting phases, the vapor pressure, and the equation of state show excellent agreement with experimental values. The effective diameters and free volumes of argon are given over a wide range of densities and temperatures. An empirical formula was used to fit the effective diameters as a function of density and temperature. The computed free volume will be used in future investigations to calculate the transport properties of argon.     

Reactive Monte Carlo and grand-canonical Monte Carlo simulations of the propene metathesis reaction system

The influence of silicalite-1 pores on the reaction equilibria and the selectivity of the propene metathesis reaction system in the temperature range between 300 and 600 K and the pressure range from 0.5 to 7 bars has been investigated with molecular simulations. The reactive Monte Carlo (RxMC) technique was applied for bulk-phase simulations in the isobaric-isothermal ensemble and for two phase systems in the Gibbs ensemble. Additionally, Monte Carlo simulations in the grand-canonical ensemble (GCMC) have been carried out with and without using the RxMC technique. The various simulation procedures were combined with the configurational-bias Monte Carlo approach. It was found that the GCMC simulations are superior to the Gibbs ensemble simulations for reactions where the bulk-phase equilibrium can be calculated in advance and does not have to be simulated simultaneously with the molecules inside the pore. The confined environment can increase the conversion significantly. A large change in selectivity between the bulk phase and the pore phase is observed. Pressure and temperature have strong influences on both conversion and selectivity. At low pressure and temperature both conversion and selectivity have the highest values. The effect of confinement decreases as the temperature increases.     

Thermally activated mechanisms of hydrogen abstraction by growth precursors during plasma deposition of silicon thin films

Hydrogen abstraction by growth precursors is the dominant process responsible for reducing the hydrogen content of amorphous silicon thin films grown from SiH(4) discharges at low temperatures. Besides direct (Eley-Rideal) abstraction, gas-phase radicals may first adsorb on the growth surface and abstract hydrogen in a subsequent process, giving rise to thermally activated precursor-mediated (PM) and Langmuir-Hinshelwood (LH) abstraction mechanisms. Using results of first-principles density functional theory (DFT) calculations on the interaction of SiH(3) radicals with the hydrogen-terminated Si(001)-(2x1) surface, we show that precursor-mediated abstraction mechanisms can be described by a chemisorbed SiH(3) radical hopping between overcoordinated surface Si atoms while being weakly bonded to the surface before encountering a favorable site for hydrogen abstraction. The calculated energy barrier of 0.39 eV for the PM abstraction reaction is commensurate with the calculated barrier of 0.43-0.47 eV for diffusion of SiH(3) on the hydrogen-terminated Si(001)-(2x1) surface, which allows the radical to sample the entire surface for hydrogen atoms to abstract. In addition, using the same type of DFT analysis we have found that LH reaction pathways involve bond breaking between the silicon atoms of the chemisorbed SiH(3) radical and the film prior to hydrogen abstraction. The LH reaction pathways exhibit energy barriers of 0.76 eV or higher, confining the abstraction only to nearest-neighbor hydrogens. Furthermore, we have found that LH processes compete with radical desorption from the hydrogen-terminated Si(001)-(2x1) surface and may be suppressed by the dissociation of chemisorbed SiH(3) radicals into lower surface hydrides. Analysis of molecular-dynamics simulations of the growth process of plasma deposited silicon films have revealed that qualitatively similar pathways for thermally activated hydrogen abstraction also occur commonly on the amorphous silicon growth surface.     

Torsional anharmonicity in transition state theory calculations

We present a new application for the Torsional Path Integral Monte Carlo (TPIMC) method in which the TPI partition functions are introduced into the calculation of Transition State Theory (TST) rate constants. In this way, an explicit treatment of torsional anharmonicity is included in the TST calculations and the magnitude of these effects can be assessed. The new method is tested on the C(2)H(6) + H hydrogen abstraction reaction and concerted hydrogen transfer in the carbonic acid dimer, for which we have developed torsional potential energy surfaces. For the C(2)H(6) + H reaction the rate constants are halved at room temperature on including a treatment of torsional anharmonicity, while the effects are found to be much smaller for the hydrogen transfer reaction in the carbonic acid dimer.     

Multiscale simulation of irreversible deposition in presence of double layer interactions

Sequential lattice Monte Carlo simulations, in which the transition probabilities are derived from the discrete form of the continuum-level mass conservation law, are used to predict the morphology of colloidal deposits. The simulations account for particle-surface (P-S) and particle-particle (P-P) electrostatic and van der Waals interactions. Simulation results for maximum coverage for monolayer deposition are in quantitative agreement with the hard-sphere RSA jamming limit. Moreover, as reported in earlier studies, monolayer simulations in the absence of P-S interactions qualitatively predict the monotonic increases in fractional coverage with increasing ionic strength, characterized by the Debye screening length (kappa a). Monolayer simulations with P-S interactions show that the dependence of fractional coverage on kappa a is strongly influenced by the ratio of particle to surface potentials (Psi(p)/Psi(s)). P-S and P-P forces achieve their respective maximum at different values of kappa a leading to a nonmonotonic trend in surface coverage as a function of kappa a. These results indicate that the incorporation of P-S interactions into colloidal deposition studies allows more accurate interpretation of the experimental data. In multilayer deposition simulations, balance between long-ranged weak interactions and short-ranged strong interactions between P-P and P-S, coupled with physical screening effects, resulted in widely varying coverages with height of the deposit, ionic strength, and Psi(p)/Psi(s). Moreover, fractal dimension of the deposit ranged from approximately 1 (kappa a < 1) to 1.7 (kappa a > 1). Qualitative kinetic analysis showed widely varying deposition rates in different layers depending on Psi(p)/Psi(s) and ionic strength. The multilayer system approached the monolayer system in the limit kappa a--> infinity and Psi(p)/Psi(s)--> infinity.     

Water desorption from an oxygen covered Pt(111) surface: multichannel desorption

Mixed OH/H2O structures, formed by the reaction of O and water on Pt(111), decompose near 200 K as water desorbs. With an apparent activation barrier that varies between 0.42 and 0.86 eV depending on the composition, coverage, and heating rate of the film, water desorption does not follow a simple kinetic form. The adsorbate is stabilized by the formation of a complete hydrogen bonding network between equivalent amounts of OH and H2O, island edges, and defects in the structure enhancing the decomposition rate. Monte Carlo simulations of water desorption were made using a model potential fitted to first-principles calculations. We find that desorption occurs via several distinct pathways, including direct or proton-transfer mediated desorption and OH recombination. Hence, no single rate determining step has been found. Desorption occurs preferentially from low coordination defect or edge sites, leading to complex kinetics which are sensitive to both the temperature, composition, and history of the sample.     

Irreversible adsorption of particles at random-site surfaces

Irreversible adsorption of negatively charged polystyrene latex particles (averaged diameter 0.9 microm) at heterogeneous surfaces was studied experimentally. The substrate bearing a controlled number of adsorption sites was produced by precovering mica sheets by positively charged polystyrene latex (averaged diameter of 0.45 microm). Positive latex (site) deposition was carried out under diffusion-controlled transport conditions and its coverage was determined by direct particle counting using the optical microscopy. Deposition kinetics of larger latex particles (averaged diameter 0.9 microm) at heterogeneous surfaces produced in this way was studied by direct optical microscope observations in the diffusion cell (under no-convection transport conditions). It was demonstrated that the structure of larger particle monolayers, characterized in terms of the pair correlation function, showed much more short-range ordering than it was predicted for homogeneous surface monolayers at the same coverage. This was found in agreement with theoretical predictions derived from the Monte Carlo simulations. On the other hand, particle adsorption kinetics was quantitatively interpreted in terms of numerical solutions of the governing diffusion equation with the nonlinear boundary condition derived from Monte Carlo simulations. From these kinetic measurements maximum (jamming) coverage of particles was determined in an accurate way by extrapolation. It was concluded that both the monolayer structure and jamming coverage were strongly influenced by the site multiplicity (coordination) effect.     

Argon and nitrogen adsorption in disordered nanoporous carbons: simulation and experiment

We report experimental measurements of the isosteric heats of adsorption for argon and nitrogen in two microporous saccharose-based carbons, using a Tian-Calvet microcalorimeter. These data are used to test recently developed molecular models of these carbons, obtained by a constrained reverse Monte Carlo method. Grand canonical Monte Carlo simulation is used to calculate the adsorption isotherms and isosteric heats for these systems, and the results for the latter are compared to the experimental data. For argon, excellent quantitative agreement is obtained over the entire range of pore filling. In the case of nitrogen, very good agreement is obtained over the range of coverage 0.25 < or = gamma/gamma 0 < or = 0.85, but discrepancies are observed at lower and higher coverages. The discrepancy at low coverage may be due to the presence of oxygenated groups on the pore surfaces, which are not taken into account in the model. The differences at high coverage are believed to arise from the presence of a few mesopores, which again are not included in the model. Pair correlation functions (argon-carbon and argon-argon) are determined from the simulations and are discussed as a function of pore filling. Snapshots of the simulations are presented and provide a picture of the pore filling process.