Crystallographic study of interaction between adspecies on metal surfaces

The interaction among adsorbed atoms and molecules (adspecies) on metal surfaces plays a decisive role in catalytic reactions. Such interaction may cause structural changes of the local adsorption geometry which, together with spectroscopic and energetic data, may afford useful physical and chemical insights into the basic mechanisms of surface processes. When the adsorption geometry of a single adspecies is considered as a function of coverage, a deeper understanding of the nature of the adsorbate-substrate bonding can be obtained. Depending on the adsorbate coverage, the magnitude of adsorbate-induced relaxations and reconstructions vary widely. Occasionally, chemisorption systems transform gradually into adsorbate-substrate compounds, such as oxides, nitrides, hydrides, and sulfides. For the case of adsorption of different adspecies, coadsorption, structural data can make a vital contribution to our understanding of reaction intermediates, the promotion effect in heterogeneously catalyzed reactions, and the formation of ultra-thin compound films.     

Wetting properties of passivated metal nanocrystals at liquid-vapor interfaces: a computer simulation study

Molecular dynamics simulations have been employed to determine the contact angles of alkylthiol passivated gold nanocrystals adsorbed at the air-water interface. Simulations were performed using butane-, dodecane-, and octadecanethiol passivated nanoparticles. We demonstrate how the length of the surfactant chain can profoundly influence the wetting behavior of these nanoparticles. All particles were found to be stable at the air-water interface, possessing large, well-defined contact angles. We find that the shape of the dodecane- and octadecanethiol particles is strongly perturbed by the interface. We also present an analysis of the orientational ordering of water molecules at the dodecane-water interface and around butane- and dodecanethiol passivated nanoparticles. The orientational ordering translates into an electrostatic field around the nanoparticles, the magnitude of which corresponds with that of the water liquid-vapor interface.     

The influence of gaseous impurities on the gold welding of metal surfaces

The analysis of the properties of cold welded metallic junctions as monitored by contact resistance measurements is extended to include the effects of impurities. Brittle fracture of both iron and copper similar metal, cold welded junctions was observed. This is in marked contrast to the bulk properties of these materials. It is believed the fracture properties of these materials were influenced by impurities embrittling the junctions. If impurities caused this behavior, the surface energy would consequently be lowered by these impurities and evidence of this is noted.     

Embedded cluster model studies of impurities at metal surfaces

A knowledge of the electronic properties of impurities at metal surfaces is of great value in the understanding of such important phenomena as chemisorption and surface segregation in alloys. We have adopted here a unified approach based on an Embedded Cluster model to study the properties of surface impurities. We have mainly concentrated on hydrogen impurities either adsorbed above the surface or incorporated into the bulk of metals. We have also considered the case of substitutional metal impurities at the surface of host metals.For hydrogen chemisorption we have considered such substrates as free-electron, transition and noble metals as well as bimetallic substrates composed of a single metal impurity in a host matrix or a metallic overlayer on a metal support. The electronic structure of the chemisorbed system is compared to photoemission data when available, from which interpretation of the details of the experimental spectra may be made. It is found that hydrogen adsorption on transition and noble metals results in the formation of a pair of bonding/antibonding resonances on either side of the metal d-band, while for hydrogen on free-electron metals a single hydrogen induced resonance is observed. One-electron energy differences between the H on jellium and H on metal systems are estimated and trends in such energies across the 3d and 4d transition series are compared to the trends in experimental chemisorption energies for H on these metals. The change in hydrogen chemisorption capacity of an inert substrate due to the introduction of chemically active impurities is investigated. The different properties of Pd overlayers with respect to Pd surfaces are also investigated. Interaction energies between adatoms on surfaces are estimated in order to predict the geometry of ordered structures on surfaces.One-electron heats of segregation for binary alloys are calculated. These show a strong solute surface segregation for noble metal impurities in group VIII metals, which is due to the higher d-band occupancy of the noble metal.     

Stability of Ca-montmorillonite hydrates: a computer simulation study

Classic simulations are used to study interlayer structure, swelling curves, and stability of Ca-montmorillonite hydrates. For this purpose, NP(zz)T and muP(zz)T ensembles are sampled for ground level and given burial conditions. For ground level conditions, a double layer hydrate having 15.0 A of basal spacing is the predominant state for relative vapor pressures (p/p0) ranging 0.6-1.0. A triple hydrate counting on 17.9 A of interlaminar distance was also found stable for p/p0 = 1.0. For low vapor pressures, the system may produce a less hydrated but still double layer state with 13.5 A or even a single layer hydrate with 12.2 A of interlaminar distance. This depends on the established initial conditions. On the other hand, the effect of burial conditions is two sided. It was found that it enhances dehydration for all vapor pressures except for saturation, where swelling is promoted.     

Molecular dynamics simulation study of interaction between model rough hydrophobic surfaces

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work, we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes: it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions, we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in the case of the charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo as the two plates are brought together.     

Water as a lubricant for graphite: a computer simulation study

The phase state and shear behavior of water confined between parallel graphite sheets are studied using the grand canonical Monte Carlo technique and TIP4P model for water. In describing the water-graphite interaction, two orientation-dependent potentials are tried. Both potentials are fitted to many-body polarizable model predictions for the binding energy and the equilibrium conformation of the water-graphite complex [K. Karapetian and K. D. Jordan in Water in Confining Geometries, edited by V. Buch and J. P. Devlin (Springer, Berlin, 2003), pp. 139-150]. Based on the simulation results, the property of water to serve as a lubricant between the rubbing surfaces of graphitic particles is associated, first, with the capillary condensation of water occurring in graphitic pores of monolayer width and, second, with the fact that the water monolayer compressed between graphite particles retains a liquidlike structure and offers only slight resistance to shear.     

Sodium chloride ion pair interaction in water: computer simulation

The thermodynamics and structure of a sodium chloride ion pair in liquid water are studied as a function of the ion pair separation. Distinct minima in the free energy of the system are found for contact and solvent separated ion geometries.     

Hydrogen bonding in liquid alcohols: a computer simulation study

A series of molecular dynamics simulations has been performed to investigate hydrogen bonding in liquid alcohols. The systems considered have been methanol, ethanol, ethylene glycol and glycerol at 298 K. The hydrogen bonding statistics as well as the mean lifetime of the hydrogen bonds are analyzed. The results are compared with those corresponding to liquid water.     

Molecular dynamics simulation study of the water-mediated interaction between zwitterionic and charged surfaces

We calculated the potential of mean force (PMF) for the interaction between a model zwitterionic bilayer and a model charged bilayer. To understand the role of water, we separated the PMF into two components: one due to direct interaction and the other due to water-mediated interaction. In our calculations, we observed that water-mediated interaction is attractive at larger distances and repulsive at shorter. The calculation of the entropic and enthalpic contributions to the solvent-mediated components of the PMF showed that attraction is entropically dominant, while repulsion is dominated by the enthalpy.     

Arrest of fluid demixing by nanoparticles: a computer simulation study

We use lattice Boltzmann simulations to investigate the formation of arrested structures upon demixing of a binary solvent containing neutrally wetting colloidal particles. Previous simulations for symmetric fluid quenches pointed to the formation of "bijels": bicontinuous interfacially jammed emulsion gels. These should be created when a glassy monolayer of particles forms at the fluid-fluid interface, arresting further demixing and rigidifying the structure. Experimental work has broadly confirmed this scenario, but it shows that bijels can also be formed in volumetrically asymmetric quenches. Here, we present new simulation results for such quenches, compare these to the symmetric case, and find a crossover to an arrested droplet phase at strong asymmetry. We then make extensive new analyses of the postarrest dynamics in our simulated bijel and droplet structures, on time scales comparable to the Brownian time for colloid motion. Our results suggest that, on these intermediate time scales, the effective activation barrier to ejection of particles from the fluid-fluid interface is smaller by at least 2 orders of magnitude than the corresponding barrier for an isolated particle on a flat interface.     

Anesthetic molecules embedded in a lipid membrane: a computer simulation study

The effect of four general anesthetic molecules, i.e., chloroform, halothane, diethyl ether and enflurane, on the properties of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) membrane is studied in detail by long molecular dynamics simulations. Furthermore, to address the problem of pressure reversal, the effect of pressure on the anesthetic containing membranes is also investigated. In order to ensure sufficient equilibration and adequate sampling, the simulations performed have been at least an order of magnitude longer than the studies reported previously in the literature on general anesthetics. The results obtained can help in resolving several long-standing contradictions concerning the effect of anesthetics, some of which were the consequence of too short simulation time used in several previous studies. More importantly, a number of seeming contradictions are found to originate from the fact that different anesthetic molecules affect the membrane structure differently in several respects. In particular, halothane, being able to weakly hydrogen bound to the ester group of the lipid tails, is found to behave in a markedly different way than the other three molecules considered. Besides, we also found that two changes, namely lateral expansion of the membrane and increasing local disorder in the lipid tails next to the anesthetic molecules, are clearly induced by all four anesthetic molecules tested here in the same way, and both of these effects are reverted by the increase in pressure.     

Adhesive transitions in Newton black films: a computer simulation study

We report molecular dynamics simulations of Newton black films (NBFs), ultra thin films of aqueous solutions stabilized with two monolayers of ionic surfactants, sodium dodecyl sulfate. We show that at low water content conditions and areas per surfactant corresponding to experimental estimates in NBFs, homogeneous films undergo an adhesion "transition," which results in a very thin adhesive film coexisting with a thicker film. We identify the adhesive film with the equilibrium structure of the Newton black film. We provide here a direct microscopic view of the formation of these important structures, which have been observed in experimental studies of emulsions and foams. We also report a detailed investigation of the structural properties and interfacial fluctuation spectrum of the adhesive film. Our analysis relies on the definition of an "intrinsic surface," which is used to remove the averaging effect that the capillary waves have on the film properties.     

Free volume properties of a linear soft polymer: a computer simulation study

Molecular dynamics simulation of a linear soft polymer has been performed and the free volume properties of the system have been analyzed in detail in terms of the Voronoi polyhedra of the monomers. It is found that there are only small density fluctuations present in the system. The local environment of the monomers is found to be rather spherical, even in comparison with liquids of atoms or small molecules. The monomers are found to be, on average, eight coordinated by their nearest geometric neighbors, including intra-chain and inter-chain ones. The packing of the monomers is found to be rather compact, in a configuration of 1900 monomers there are, on average, only three voids large enough to incorporate a spherical particle as large as a monomer, indicating that the density of the large vacancies in the system is considerably, i.e., by a few orders of magnitude lower than in molecular liquids corresponding to roughly the same reduced densities.     

The behavior of fluids near solutes: a density functional theory and computer simulation study

The density distribution of solvent near a solute particle is studied using density functional theory and Monte Carlo simulation. The fluid atoms interact with each other via a hard sphere plus Yukawa potential, and interact with the solute via a hard sphere potential. For small solute sizes, the solvent displays liquidlike ordering near the particle. When the solute become larger, a drying transition is observed at state points near the coexistence conditions of the solvent. These predictions are similar to those of a recent theory for the hydrophobic effect by Lum, Chandler, and Weeks [J. Phys. Chem. 103, 4570 (1999)], although a comparison with simulations shows that the theory of this work is quantitatively more accurate. The connection between density functional methods and the LCW approach is also established.     

Attractive interaction between transition-metal atom impurities and vacancies in graphene: a first-principles study

We present a density functional theory study of transition metal adatoms on a graphene sheet with vacancy-type defects. We calculate the strain fields near the defects and demonstrate that the strain fields around these defects reach far into the unperturbed hexagonal network and that metal atoms have a high affinity to the non-perfect and strained regions of graphene. Metal atoms are therefore attracted by the reconstructed defects. The increased reactivity of the strained graphene makes it possible to attach metal atoms much more firmly than to pristine graphene and supplies a tool for tailoring the electronic structure of graphene. Finally, we analyze the electronic band structure of graphene with defects and show that some defects open a semiconductor gap in graphene, which may be important for carbon-based nanoelectronics.     

Free energies of molecular crystal surfaces by computer simulation: application to tetrathiophene

We describe a general simulation protocol for the evaluation of the surface free energies of molecular crystals, which are of broad interest for phenomena such as polymorphism and crystal growth. The method has been applied to selected surfaces of two polymorphs of tetrathiophene. The simulations highlight an important temperature-dependent entropic contribution to the surface free energies, which is not included in widely used static simulations of surface structure and energetics.     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

On the Debye-Waller factor of hexagonal ice: a computer simulation study

We investigate by molecular dynamics (MD) simulations the temperature dependence of the Debye-Waller (DW) factor of hexagonal ice with 25 different proton-disordered configurations. Each initial configuration is composed of 288 water molecules with no net dipole moment. The intermolecular interaction of water is described by TIP4P potential. Each production run of the simulation is 15 ns or longer. We observe a change in slope of the DW factor around 200 K, which cannot be explained within the framework of either classical or quantum harmonic approximation. Configurations generated by MD simulations are subjected to the steepest descent energy minimization. Analysis of the local energy minimum structures reveals that water molecules above 200 K jump to other lattice sites via some local energy minimum structures which contain some water molecules sitting on the locations other than the lattice sites. As time evolves, these defect molecules move back and forth to the lattice sites yielding defect-free structures. Those motions are responsible for the unusual increase in the DW factor at high temperatures. In making a transition from an energy-minimum structure to another one, a small number of water molecules are involved in a highly cooperative fashion. The larger DW factor at higher temperature arises from jump-like motions of water molecules among these locally stable configurations which may or may not be a family of the proton-disordered ice forms satisfying the "ice rule".     

Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study

The phase behaviour of achiral banana-shaped molecules was studied by computer simulation. The banana-shaped molecules were described by model intermolecular interactions based on the Gay-Berne potential. The characteristic molecular structure was considered by joining two calamitic Gay-Berne particles through a bond to form a biaxial molecule of point symmetry group C 2v with a suitable bending angle. The dependence on temperature of systems of N =1024 rigid banana-shaped molecules with bending angle ϕ=140° has been studied by means of Monte Carlo simulations in the isobaric-isothermal ensemble ( NpT ). On cooling an isotropic system, two phase transitions characterized by phase transition enthalpy, entropy and relative volume change have been observed. For the first time by computer simulation of a many-particle system of banana-shaped molecules, at low temperature an untilted smectic phase showing a global phase biaxiality and a spontaneous local polarization in the layers, i.e. a local polar arrangement of the steric dipoles, with an antiferroelectric-like superstructure could be proven, a phase structure which recently has been discovered experimentally. Additionally, at intermediate temperature a nematic-like phase has been proved, whereas close to the transition to the smectic phase hints of a spontaneous achiral symmetry breaking have been determined. Here, in the absence of a layered structure a helical superstructure has been formed. All phases have been characterized by visual representations of selected configurations, scalar and pseudoscalar correlation functions, and order parameters.