Adsorption of octyl cyanide at the free water surface as studied by Monte Carlo simulation

Monte Carlo simulations of the adsorption layer of octyl cyanide have been performed on the canonical (N, V, T) ensemble at 300 K. The systems simulated cover the range of octyl cyanide surface densities from 0.27 to 7.83 mumol/m2. The surface density value at which the saturation of the adsorption layer occurs is estimated to be 1.7 mumol/m2. At low surface densities, the main driving force of the adsorption is found to be the formation of hydrogen bonds between the water and octyl cyanide molecules, whereas at higher surface concentrations, the dipole-dipole attraction between the neighboring adsorbed octyl cyanide molecules becomes more important. At low surface concentrations, the water-octyl cyanide hydrogen bonds prefer tilted alignments relative to the interface; however, in the case of the saturated adsorption layer, the number of such hydrogen bonds is maximized, leading to the preference of these bonds for the orientation perpendicular to the interface. Contrary to nonionic surfactants of multiple hydrogen bonding abilities (e.g., 1-octanol, C8E3), the increasing surface concentration of octyl cyanide was not found to lead to considerable competition of the molecules for positions of optimal arrangement. As a consequence, the energy and geometry of the water-octyl cyanide hydrogen bonds are found to be insensitive to the octyl cyanide surface concentration.     

Monte Carlo bicanonical ensemble simulation for sodium cation hydration free energy in liquid water

A series of bicanonical ensemble Monte Carlo (BC MC) simulations has been performed to calculate Na⁺ hydration Gibbs energy in aqueous solution. The hydration Gibbs energy of Na⁺ ion in aqueous solution is the difference between formation free energies of Na⁺ (H₂O)_n and (H₂O)_n clusters at n → α. The convergence of the hydration free energy to bulk water value is fast, and the results at n = 60 turned out to be in good agreement with experimental ones and those calculated using free energy perturbation method [1]. The ion–water interaction has been described by Aqvist's pair potential [1] and SPC model [2] has been used for water–water interactions. The behaviour of the absolute Gibbs energy, the entropy, the internal energy of the clusters and the development of hydration shells’ structure with the increase of the number of water molecules are discussed.     

Rheology of polymer brush under oscillatory shear flow studied by nonequilibrium Monte Carlo simulation

The rheological behaviors of polymer brush under oscillatory shear flow were investigated by nonequilibrium Monte Carlo simulation. The grafted chain under oscillatory shear flow exhibited a waggling behavior like a flower, and the segments were found to have different oscillatory phases along the chain contour. Stress tensor was further obtained based on the statistics of sampled configuration distribution functions. The simulation reproduced the abrupt increase of the first normal stress difference N(1) with the flow velocity over a critical value, as observed in the experiment of Klein et al. [Nature (London) 352, 143 (1991)]. However, our simulation did not reproduce the brush thickening with shear velocity increased, which was suggested to be responsible for the abrupt increase of N(1) in the above-mentioned paper. This simulation demonstrates that the increase of normal stress might be an inherent behavior of polymer brush due to chain deformation under flow.     

Structure of the nonionic surfactant triethoxy monooctylether C8E3 adsorbed at the free water surface, as seen from surface tension measurements and Monte Carlo simulations

The adsorption layer of the nonionic surfactant triethoxy monooctylether C8E3 has been investigated at the free water surface by means of both experimental and computer simulation methods. The surface tension of the aqueous solution of C8E3 has been measured by pendant drop shape analysis in the entire concentration range in which C8E3 is soluble in water. The data obtained from these measurements are used to derive the adsorption isotherm. The critical micellar concentration and the surface excess concentration of the saturated adsorption layer are found to be 7.48 mM and 4.03 micromol/m2, respectively, the latter value corresponding to the average area per molecule of 41 A2. In order to analyze the molecular level structure of the unsaturated adsorption layer, Monte Carlo simulations have been performed at four different surface concentration values, i.e., 0.68, 1.36, 2.04, and 2.72 micromol/m2, respectively. It has been found that the water surface is already almost fully covered at the lowest surface density value investigated, and the adsorbed molecules show a strong preference for lying parallel with the interface in elongated conformations. No sign of the penetration of the hydrophilic triethoxy headgroups into the aqueous phase to any extent has been observed. With increasing surface densities the preferential orientation of the apolar octyl tails gradually turns from lying parallel with the interface to pointing toward the vapor phase by their CH3 end, whereas the conformation of the adsorbed molecules becomes gradually less elongated. Both of these changes lead to the increase of the number of C8E3 molecules being in a direct contact (i.e., forming hydrogen bonds) with water. However, the increasing number of the C8E3 molecules hydrogen bonded to water is found to be accompanied by the weakening of this binding, i.e., the decrease of both the number of hydrogen bonds a bound C8E3 molecule forms with water and the magnitude of the average binding energy of the adsorbed C8E3 molecules.     

The theta-temperature depression caused by topological effect in ring polymers studied by Monte Carlo simulation

We studied equilibrium conformations of linear and ring polymers in dilute solutions over the wide range of segment number N of up to 2048 with Monte Carlo simulation, and evaluated N dependence of the radii of gyration, R(g), of chains. The polymer molecules treated in this study are assumed to be composed of beads and bonds, and they are put in a three-dimensional face-centered cubic (FCC) lattice. The values of Flory's critical exponent, ν, for linear and ring polymers were estimated from the N dependence of R(g), and the temperatures at which ν reach 1/2 were obtained. Here we define those as Θ-temperatures in this report. The simulation result shows that the Θ-temperature for ring polymers is evidently lower than that of the linear polymers, and the origin of the Θ-temperature depression is discussed. Since R(g) of a ring polymer is smaller than that for a linear polymer at the same N and temperature, the segment density for a ring polymer is increased by the topological effect and the repulsive force between segments of a ring polymer at the Θ-temperature for a linear polymer is stronger. Thus, the origin of the Θ-temperature depression for ring polymers is the repulsive force emphasized by the topological effect of rings.     

Oxygen island formation on Pt(111) studied by dynamic Monte Carlo simulation

The formation of oxygen islands on the Pt(111) surface has been studied as a function of temperature by low energy electron diffraction (LEED) experiments and dynamic Monte Carlo (DMC) simulations. By raising the temperature, the (2 x 2) LEED spot intensity increases gradually and decays after a peak at around 255 K (T(p)) with full width of half maximum of 160 K. This behavior is interpreted by DMC simulations with the kinematical LEED analysis. In the DMC simulation, an oxygen atom hops to the neighboring site via the activation barrier of the saddle point. The potential energies at initial, saddle, and final points are changed at each hopping event depending on the surrounding oxygen atoms. By comparing the observed T(p) with the simulated one, the interaction energy E of oxygen atoms on Pt(111) was determined to be 25+/-3 meV at 2a(0). The DMC simulations visualize how the oxygen islands are formed and collapse on Pt(111) with increase of the temperature and well reproduce the surface configurations observed by scanning tunneling microscopy.     

Structure and dynamics of a free aquaporin (AQP1) by a coarse-grained Monte Carlo simulation

Structure and dynamics of a free aquaporin (AQP1) are studied by a coarse-grained Monte Carlo simulation as a function of temperature using a phenomenological potential with the input of a knowledge-based residue–residue interaction. Response of the radius of gyration (R _g) of the protein to the temperature (T) is found to be nonlinear: Decay of R _g at T ≤ T _c is followed by a continuous increase at T ≥ T _c before reaching its saturation. In thermo-responsive regime, the protein exhibits segmental globularization with the persistence of three regions along its sequence involving residues ¹M–²⁵V and ²⁵⁰V–²⁶⁹K toward the beginning and end segments with a narrow intermediate region around ¹⁵⁵A–¹⁶³D. A detail analysis of the structure factor S(q) shows a global random coil conformation at high temperatures with an effective dimension D _e ~ 1.74 and a globular structure (D _e ~ 3) at low temperatures. In thermo-responsive regime, the variation of S(q) with the wave vector q reveals a systematic redistribution of self-organizing residues (in globular and fibrous sections) that depends on the length scale and the temperature.     

Biomolecule-directed assembly of nanoscale building blocks studied via lattice Monte Carlo simulation

We perform lattice Monte Carlo simulations to study the self-assembly of functionalized inorganic nanoscale building blocks using recognitive biomolecule linkers. We develop a minimal coarse-grained lattice model for the nanoscale building block (NBB) and the recognitive linkers. Using this model, we explore the influence of the size ratio of linker length to NBB diameter on the assembly process and the structural properties of the resulting aggregates, including the spatial distribution of NBBs and aggregate topology. We find the constant-kernel Smoluchowski theory of diffusion-limited cluster-cluster aggregation describes the aggregation kinetics for certain size ratios.     

Monte Carlo liquid water simulation with four-body interactions included

A four-body interaction potential for water molecules is derived. The new terms are combined with previously developed two- and three-body potential terms and applied in a Metropolis—Monte Carlo simulation at 298 K for an (N, V, T) ensemble with 512 water molecules. Improvements, relative to the results using only two-body, or two- and three-body interactions, are reported for the correlation function g(OO), for the X-ray and neutron-beam scattering intensities, and for the enthalpy.     

Monte Carlo simulation of electron-ion recombination at high pressure

The Monte Carlo method is applied to the study of electron-ion recombination in CO₂, CH₄ and NH₃ over a wide range of pressures. Dissociative recombination is enhanced by energy transfer to the ambient gas molecules and the recombination rates peak at 11, 2 and 9 × 10⁵ CM³ s^?1, respectively. At very high pressures, the rate approaches the Langevin limit.     

Monte Carlo simulation of equilibrium reactions at vapor-liquid interfaces

Chemical reactions are known to behave differently, depending upon their local environment. While the interactions with neighboring molecules may alter both the kinetics of chemical reactions and the overall equilibrium conversion, we have performed simulations of the latter. The particular environment that we address is the vapor-liquid interface, since only a few, limited studies have explored the influence of an interface on equilibrium reaction behavior. Simple dimerization reactions are modeled, as well as more complex multicomponent reactions, using the reactive Monte Carlo (RxMC) simulation technique. We find that the conversion of a reaction can be markedly different at an interface as compared to the bulk vapor and liquid phases, and these trends are analyzed with respect to specific intermolecular interactions. In conjunction, we calculate the surface tension of the reacting fluids at the interface, which is found to have unusual scaling behavior, with respect to the system temperature.     

Adsorption of HCl on the water ice surface studied by X-ray absorption spectroscopy

The adsorption state of HCl at 20 and 90 K on crystalline water ice films deposited under ultrahigh vacuum at 150 K has been studied by X-ray absorption spectroscopy at the O1s K-edge and Cl2p L-edge. We show that HCl dissociates at temperatures as low as 20 K, in agreement with the prediction of a spontaneous ionization of HCl on ice. Comparison between the rate of saturation of the "dangling" hydrogen bonds and the chlorine uptake indicates that hydrogen bonding of HCl with the surface native water "dangling" groups only accounts for a small part of the ionization events (20% at 90 K). A further mechanism drives the rest of the dissociation/solvation process. We suggest that the weakening of the ice surface hydrogen-bond network after the initial HCl adsorption phase facilitates the generation of new dissociation/solvation sites, which increases the uptake capacity of ice. These results also emphasize the necessity to take into account not only a single dissociation event but its catalyzing effect on the subsequent events when modeling the uptake of hydrogen-bonding molecules on the ice surface.     

Acetylcholine in water: Ab-initio potential and Monte Carlo simulation

Ab initio SCF-LCAO-MO computations using a minimal basis set have been carried out on the acetylcholine ion in different conformations. The rotational barrier around the C9-C8-O1-C2 dihedral angle (τ₁) has been also calculated: the curve presents a broad minimum. SCF calculations have been carried out on the system Ach-water at 468 different separations and/or orientations; the interaction energies were then fitted to a pair potential function used in Monte Carlo (MC) simulations of Ach water solution. The rdfs indicate a global first hydration shell with about 38 waters. Details about the hydration shell are presented. The overall MC results indicate that for the Ach ion in water solution at room temperature relative free rotation is possible around τ₁, and that Ach is well represented as a large positively charged hydrated globe with a small mobile tail free of strong interactions with the surrounding water molecules.     

Monte Carlo simulation of bremsstrahlung emission by electrons

The basic components of Monte Carlo simulation of bremsstrahlung emission by electrons are presented. Various theoretical cross-sections that have been used in Monte Carlo codes are described and the emphasis is on the more accurate partial-wave cross-sections for which numerical databases are available. Sampling algorithms for a combination of numerical scaled energy-loss cross-sections and various analytical approximations to the intrinsic angular distribution are presented. Analogue simulation of the energy spectra and angular distribution of X rays from targets irradiated by electron beams is very inefficient and a simple variance-reduction technique, which is easy to implement and has proven to be particularly effective in speeding up these simulations, is described. Results from simulations of X-ray spectra with the general-purpose Monte Carlo code penelope are compared with experimental data for different materials and incident electrons with energies in the 20 keV to 1 GeV energy range.     

Conformational stability and flexibility of the ala dipeptide in free space and water: Monte Carlo computer simulation studies

Monte Carlo determinations of the intramolecular thermodynamics of the Ala dipeptide in the C₇, C₅, α_R, and P_II conformations are reported. The calculations are carried out in the quasiharmonic approximation, with intramolecular entropies determined from the covariance matrix of the atomic displacements. The free energy of transition from C₇ to C₅, α_R, and P_II are found to be endergonic and dominated by the intrinsic energy of disrupting the intramolecular hydrogen bond in the C₇ conformation. These results are combined with previous estimates of the free energy of hydration of the Ala dipeptide in water computed from liquid state Monte Carlo simulations using the probability ratio method. The net free energy of C₇, α_R, and P_II are found to be similar, and it is thus reasonable to expect that all three forms are thermally populated at ambient temperature. The intermolecular carbonyl-water hydrogen bond in C₅, α_R, and P_II competes successfully with the intramolecular N? H…?O? C interaction in C₇.     

Monte Carlo simulation of equilibrium reactions at modified vapor-liquid interfaces

The equilibrium conversion of a chemical reaction is known to be affected by its local environment. Various factors may alter reaction equilibria, including shifts in pressure or temperature, solvation, adsorption within porous materials, or the presence of an interface. Previously, reactive Monte Carlo simulations have been used to predict the equilibrium behavior of chemical reactions at vapor-liquid interfaces. Here, a route is tested for tuning the interfacial conversion of a Lennard-Jones dimerization reaction by adding surfactants to the vapor-liquid interface. Several temperatures are explored as well as several different surfactant models. Even with the addition of a small concentration of surfactants, the simulations predict significant shifts in the conversion at the interface. In general, the shifts in the conversion tend to be related to the values of the interfacial tension.     

Adsorption of monovalent and divalent cations on planar water-silica interfaces studied by optical reflectivity and Monte Carlo simulations

Adsorption on planar silica substrates of various monovalent and divalent cations from aqueous solution is studied by optical reflectivity. The adsorbed amount is extracted by means of a thin slab model. The experimental data are compared with grand canonical Monte Carlo titration simulations at the primitive model level. The surface excess of charge due to adsorbed cations is found to increase with pH and salt concentration as a result of the progressive dissociation of silanol groups. The simulations predict, in agreement with experiments, that the surface excess of charge from divalent ions is much larger than from monovalent ions. Ion-ion correlations explain quantitatively the enhancement of surface ionization by multivalent cations. On the other hand, the combination of experimental and simulation results strongly suggests the existence of a second ionizable site in the acidic region. Variation of the distance of closest approach between the ions and surface sites captures ion specificity of water-silica interfaces in an approximate fashion.     

Monte Carlo simulation of electrodeposition of copper: a multistep free energy calculation

Electrodeposition of copper (Cu) involves length scales of a micrometer or even less. Several theoretical techniques such as continuum Monte Carlo, kinetic Monte Carlo (KMC), and molecular dynamics have been used for simulating this problem. However the multiphenomena characteristics of the problem pose a challenge for an efficient simulation algorithm. Traditional KMC methods are slow, especially when modeling surface diffusion with large number of particles and frequent particle jumps. Parameter estimation involving thousands of KMC runs is very time-consuming. Thus a less time-consuming and novel multistep continuum Monte Carlo simulation is carried out to evaluate the step wise free energy change in the process of electrochemical copper deposition. The procedure involves separate Monte Carlo codes employing different random number criterion (using hydrated radii, bare radii, hydration number of the species, redox potentials, etc.) to obtain the number of species (CuCl(2) or CuSO(4) or Cu as the case may be) and in turn the free energy. The effect of concentration of electrolyte, influence of electric field and presence of chloride ions on the free energy change for the processes is studied. The rate determining step for the process of electrodeposition of copper from CuCl(2) and CuSO(4) is also determined.     

Monte Carlo molecular simulation of the hydration of Na-montmorillonite at reservoir conditions

The hydration of Na-saturated Wyoming-type montmorillonite is investigated by Monte Carlo simulations at constant stress in the NP(zz)T ensemble and at constant chemical potential in the microVT ensemble, at the sedimentary basin temperature of 353 K and pressure of 625 bar, equivalent to 2-4 km depth. The simulations use procedures established in Chavez-Paez et al. [J. Chem. Phys. 114, 1405 (2001)]. At these conditions, simulations predict a single stable form of 1,2-water layer Na-montmorillonite, containing 164.38 mg/g or 53.37 molecules/layer of adsorbed water and having a spacing of 12.72 A. The corresponding density is 0.32 g/ml. Sodium ions are coordinated with six molecules of water separated 2.30-2.33 A. Water molecules are closer to the central interlayer plane and the spacing is larger than that at 300 K and 1 bar. The interlayer configuration consists of two symmetrical layers of oriented water molecules 1.038 A from the central plane, with the hydrogen atoms in two outermost layers, 3.826 A apart, and the sodium ions on the central plane located between the water layers. The interlayer configuration can be considered to be a stable two-layer intermediate between the one- and two-layer hydrates. Our simulations do not predict formation of other hydrates of Na-montmorillonite at 353 K and 615 bar.