Structure of the acetone liquid-vapor interface as seen from Monte Carlo simulations

The orientational order of the molecules at the liquid-vapor interface of acetone has been investigated by computer simulation. To fully describe the orientational preferences of the acetone molecules, the bivariate joint distribution of two independent orientational parameters has been determined at different layers of the interface. The strength of the orientational ordering of the interfacial molecules has been found to be liquid-like rather than crystal-like. The obtained results have revealed that the interfacial acetone molecules have dual orientational preferences. The main symmetry axis of the molecules declines by about 50-70 degrees from the interface normal axis, pointing toward the liquid phase in both of the preferred orientations. However, the plane of the molecules in the orientation preferred on the liquid side of the interface is perpendicular to the interfacial plane, whereas the other preferred orientation, which is present on the vapor side of the interface, corresponds to the alignment obtained from this orientation by an almost 90 degrees rotation around the main symmetry axis. Because the population of the liquid side is higher than that of the vapor side of the interface, the first of the two preferred orientations is the dominant alignment over the entire interface, in good agreement with recent experimental findings (Chen, H.; Gan, W.; Wu, B. H.; Wu, D.; Zhang, Z.; Wang, H. F. Chem. Phys. Lett. 2005, 408, 284).     

Structure of the liquid-vapor interface of water-methanol mixtures as seen from Monte Carlo simulations

Monte Carlo simulation of the vapor-liquid interface of water-methanol mixtures of different compositions, ranging from pure water to pure methanol, have been performed on the canonical (N, V, T) ensemble at 298 K. The analysis of the systems simulated has revealed that the interface is characterized by a double layer structure: methanol is strongly adsorbed at the vapor side of the interface, whereas this adsorption layer is followed at its liquid side by a depletion layer of methanol of lower concentration than in the bulk liquid phase of the system. The dominant feature of the interface has been found to be the adsorption layer in systems of methanol mole fractions below 0.2, and the depletion layer in systems of methanol mole fractions between 0.25 and 0.5. The orientation of the molecules located at the depletion layer is found to be already uncorrelated with the interface, whereas the methanol molecules of the adsorption layer prefer to align perpendicular to the interface, pointing straight toward the vapor phase by their methyl group. Although both the preference of the molecular plane for a perpendicular alignment with the interface and the preference of the methyl group for pointing straight to the vapor phase are found to be rather weak, the preference of the methyl group for pointing as straight toward the vapor phase as possible within the constraint imposed by the orientation of the molecular plane is found to be fairly strong. One of the two preferred orientations of the interfacial water molecules present in the neat system is found to disappear in the presence of methanol, because methanol molecules aligned in their preferred orientation can replace these water molecules in the hydrogen-bonding pattern of the interface.     

Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations

An efficient Monte Carlo (MC) algorithm including concerted rotations is directly compared to molecular dynamics (MD) in all-atom statistical mechanics folding simulations of small polypeptides. The previously reported algorithm "concerted rotations with flexible bond angles" (CRA) has been shown to successfully locate the native state of small polypeptides. In this study, the folding of three small polypeptides (trpzip2/H1/Trp-cage) is investigated using MC and MD, for a combined sampling time of approximately 10(11) MC configurations and 8 micros, respectively. Both methods successfully locate the experimentally determined native states of the three systems, but they do so at different speed, with 2-2.5 times faster folding of the MC runs. The comparison reveals that thermodynamic and dynamic properties can reliably be obtained by both and that results from folding simulations do not depend on the algorithm used. Similar to previous comparisons of MC and MD, it is found that one MD integration step of 2 fs corresponds to one MC scan, revealing the good sampling of MC. The simplicity and efficiency of the MC method will enable its future use in folding studies involving larger systems and the combination with replica exchange algorithms.     

Monte Carlo simulations of heterogeneous electron transfer: New challenges

We report results of MC simulations of electron transfer across a metal electrode/electrolyte solution interface. The model presumes the Landau–Zener theory and a random walk on a two-dimensional lattice formed by crossing parabolic reaction free energy surfaces along the solvent coordinate. Emphasis is put on investigating the activationless discharge regime; the bridge-assisted electron transfer is also partially addressed. We have calculated effective electronic transmission coefficient as a function of the electrode overpotential and temperature in a wide range of orbital overlap. The dependence of the transmission coefficient on the electronic density of states is analyzed as well.     

Monte Carlo simulations of polymer dynamics: Recent advances

A brief review is given of applications of Monte Carlo simulations to study the dynamical properties of coarse-grained models of polymer melts, emphasizing the crossover from the Rouse model toward reptation, and the glass transition. The extent to which Monte Carlo algorithms can mimic the actual chain dynamics is critically examined, and the need for the use of coarse-grained rather than fully atomistic models for such simulations is explained. It is shown that various lattice and continuum models yield qualitatively similar results, and the behavior agrees with the findings of corresponding molecular dynamics simulations and experiments, where available. It is argued that these simulations significantly enhance our understanding of the theoretical concepts on the dynamics of dense macromolecular systems. © 1997 John Wiley & Sons, Inc.     

Equilibrium states of self-assembly systems: Monte Carlo simulations

We investigated the equilibrium states of the self-assembly of amphiphilic molecules in water. The amphiphiles are represented by chains of the type H1T4, where H is the hydrophilic part of the molecule and T is its hydrophobic portion formed by four monomers. We have performed Monte Carlo simulations on a two-dimensional lattice, in which each water molecule occupies a single site, and the amphiphiles occupy five sites of the lattice. We have determined the aggregate distribution curves for the system at low concentration and fixed temperature. We have shown that the criterion to determine the equilibrium states of the system, based on the stabilization of energy curves as a function of the simulation time, is not reliable. The best way to ensure that the equilibrium state was reached was to follow the route to equilibrium of all aggregate sizes of the system.     

Multiple "time step" Monte Carlo simulations: application to charged systems with Ewald summation

Recently, we have proposed an efficient scheme for Monte Carlo simulations, the multiple "time step" Monte Carlo (MTS-MC) [J. Chem. Phys. 117, 8203 (2002)] based on the separation of the potential interactions into two additive parts. In this paper, the structural and thermodynamic properties of the simple point charge water model combined with the Ewald sum are compared for the MTS-MC real-/reciprocal-space split of the Ewald summation and the common Metropolis Monte Carlo method. We report a number of observables as a function of CPU time calculated using MC and MTS-MC. The correlation functions indicate that speedups on the order of 4.5-7.5 can be obtained for systems of 108-500 waters for n=10 splitting parameter.     

A scalable parallel Monte Carlo method for free energy simulations of molecular systems

We present a method of parallelizing flat histogram Monte Carlo simulations, which give the free energy of a molecular system as an output. In the serial version, a constant probability distribution, as a function of any system parameter, is calculated by updating an external potential that is added to the system Hamiltonian. This external potential is related to the free energy. In the parallel implementation, the simulation is distributed on to different processors. With regular intervals the modifying potential is summed over all processors and distributed back to every processor, thus spreading the information of which parts of parameter space have been explored. This implementation is shown to decrease the execution time linearly with added number of processors.     

Molecular simulations of confined liquids: an alternative to the grand canonical Monte Carlo simulations

Commonly, the confinement effects are studied from the grand canonical Monte Carlo (GCMC) simulations from the computation of the density of liquid in the confined phase. The GCMC modeling and chemical potential (μ) calculations are based on the insertion/deletion of the real and ghost particle, respectively. At high density, i.e., at high pressure or low temperature, the insertions fail from the Widom insertions while the performing methods as expanded method or perturbation approach are not efficient to treat the large and complex molecules. To overcome this problem we use a simple and efficient method to compute the liquid's density in the confined medium. This method does not require the precalculation of μ and is an alternative to the GCMC simulations. From the isothermal-isosurface-isobaric statistical ensemble we consider the explicit framework/liquid external interface to model an explicit liquid's reservoir. In this procedure only the liquid molecules undergo the volume changes while the volume of the framework is kept constant. Therefore, this method is described in the Np(n)AV(f)T statistical ensemble, where N is the number of particles, p(n) is the normal pressure, V(f) is the volume of framework, A is the surface of the solid/fluid interface, and T is the temperature. This approach is applied and validated from the computation of the density of the methanol and water confined in the mesoporous cylindrical silica nanopores and the MIL-53(Cr) metal organic framework type, respectively.     

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

The binding of a ligand to a receptor is often associated with the displacement of a number of bound water molecules. When the binding site is exposed to the bulk region, this process may be sampled adequately by standard unbiased molecular dynamics trajectories. However, when the binding site is deeply buried and the exchange of water molecules with the bulk region may be difficult to sample, the convergence and accuracy in free energy perturbation (FEP) calculations can be severely compromised. These problems are further compounded when a reduced system including only the region surrounding the binding site is simulated. To address these issues, we couple molecular dynamics (MD) with grand canonical Monte Carlo (GCMC) simulations to allow the number of water to fluctuate during an alchemical FEP calculation. The atoms in a spherical inner region around the binding pocket are treated explicitly while the influence of the outer region is approximated using the generalized solvent boundary potential (GSBP). At each step during thermodynamic integration, the number of water in the inner region is equilibrated with GCMC and energy data generated with MD is collected. Free energy calculations on camphor binding to a deeply buried pocket in cytochrome P450cam, which causes about seven water molecules to be expelled, are used to test the method. It concluded that solvation free energy calculations with the GCMC/MD method can greatly improve the accuracy of the computed binding free energy compared to simulations with fixed number of water.     

Ion binding to polyelectrolytes: Monte Carlo simulations versus classical mean field theories

The influence of ion size and surface charge model in titrations of ionizable polyelectrolytes is studied by means of the Semi Grand Canonical Monte Carlo simulation method in the context of the primitive model. Three models describing a discrete distribution of charged functional groups on the polyelectrolyte and different values for the radius of the background electrolyte spanning from ionic to hydrated radii values were analyzed. The polyelectrolyte titrations were simulated by calculating the degree of ionization versus pH curves at two ionic strengths. The results allow us to quantify the impact of the sizes of the background salt ions and surface functional groups of the polyelectrolyte on the dissociation degree. This influence is explained in terms of the effectiveness of the screening of the charged surface sites. Finally, by comparison with the Non-Linear Poisson–Boltzmann model, the influence of ionic correlations and finite size of the solution ions is assessed.     

Hydrogen bonded structure and dynamics of liquid-vapor interface of water-ammonia mixture: an ab initio molecular dynamics study

We have carried out ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and ammonia molecules. We have made a detailed analysis of the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and ammonia molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions of bulk and interfacial molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-ammonia hydrogen bonds at the interface with ammonia as the acceptor. The structure of the system is also investigated in terms of inter-atomic voids present in the system. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations.     

Thermal Gaussian molecular dynamics for quantum dynamics simulations of many-body systems: application to liquid para-hydrogen

A new method, here called thermal Gaussian molecular dynamics (TGMD), for simulating the dynamics of quantum many-body systems has recently been introduced [I. Georgescu and V. A. Mandelshtam, Phys. Rev. B 82, 094305 (2010)]. As in the centroid molecular dynamics (CMD), in TGMD the N-body quantum system is mapped to an N-body classical system. The associated both effective Hamiltonian and effective force are computed within the variational Gaussian wave-packet approximation. The TGMD is exact for the high-temperature limit, accurate for short times, and preserves the quantum canonical distribution. For a harmonic potential and any form of operator A?, it provides exact time correlation functions C(AB)(t) at least for the case of B, a linear combination of the position, x, and momentum, p, operators. While conceptually similar to CMD and other quantum molecular dynamics approaches, the great advantage of TGMD is its computational efficiency. We introduce the many-body implementation and demonstrate it on the benchmark problem of calculating the velocity time auto-correlation function for liquid para-hydrogen, using a system of up to N = 2592 particles.     

Gas sorption and barrier properties of polymeric membranes from molecular dynamics and Monte Carlo simulations

It is important for many industrial processes to design new materials with improved selective permeability properties. Besides diffusion, the molecule's solubility contributes largely to the overall permeation process. This study presents a method to calculate solubility coefficients of gases such as O2, H2O (vapor), N2, and CO2 in polymeric matrices from simulation methods (Molecular Dynamics and Monte Carlo) using first principle predictions. The generation and equilibration (annealing) of five polymer models (polypropylene, polyvinyl alcohol, polyvinyl dichloride, polyvinyl chloride-trifluoroethylene, and polyethylene terephtalate) are extensively described. For each polymer, the average density and Hansen solubilities over a set of ten samples compare well with experimental data. For polyethylene terephtalate, the average properties between a small (n = 10) and a large (n = 100) set are compared. Boltzmann averages and probability density distributions of binding and strain energies indicate that the smaller set is biased in sampling configurations with higher energies. However, the sample with the lowest cohesive energy density from the smaller set is representative of the average of the larger set. Density-wise, low molecular weight polymers tend to have on average lower densities. Infinite molecular weight samples do however provide a very good representation of the experimental density. Solubility constants calculated with two ensembles (grand canonical and Henry's constant) are equivalent within 20%. For each polymer sample, the solubility constant is then calculated using the faster (10x) Henry's constant ensemble (HCE) from 150 ps of NPT dynamics of the polymer matrix. The influence of various factors (bad contact fraction, number of iterations) on the accuracy of Henry's constant is discussed. To validate the calculations against experimental results, the solubilities of nitrogen and carbon dioxide in polypropylene are examined over a range of temperatures between 250 and 650 K. The magnitudes of the calculated solubilities agree well with experimental results, and the trends with temperature are predicted correctly. The HCE method is used to predict the solubility constants at 298 K of water vapor and oxygen. The water vapor solubilities follow more closely the experimental trend of permeabilities, both ranging over 4 orders of magnitude. For oxygen, the calculated values do not follow entirely the experimental trend of permeabilities, most probably because at this temperature some of the polymers are in the glassy regime and thus are diffusion dominated. Our study also concludes large confidence limits are associated with the calculated Henry's constants. By investigating several factors (terminal ends of the polymer chains, void distribution, etc.), we conclude that the large confidence limits are intimately related to the polymer's conformational changes caused by thermal fluctuations and have to be regarded--at least at microscale--as a characteristic of each polymer and the nature of its interaction with the solute. Reducing the mobility of the polymer matrix as well as controlling the distribution of the free (occupiable) volume would act as mechanisms toward lowering both the gas solubility and the diffusion coefficients.     

Comparison of kinetic Monte Carlo and molecular dynamics simulations of diffusion in a model glass former

We present results from kinetic Monte Carlo (KMC) simulations of diffusion in a model glass former. We find that the diffusion constants obtained from KMC simulations have Arrhenius temperature dependence, while the correct behavior, obtained from molecular dynamics simulations, can be super-Arrhenius. We conclude that the discrepancy is due to undersampling of higher-lying local minima in the KMC runs. We suggest that the relevant connectivity of minima on the potential energy surface is proportional to the energy density of the local minima, which determines the "inherent structure entropy." The changing connectivity with potential energy may produce a correlation between dynamics and thermodynamics.     

Efficient multiparticle sampling in Monte Carlo simulations on fluids: application to polarizable models

A novel Monte Carlo simulation scheme based on biased simultaneous displacements of all particles of the system has been developed. The method is particularly suited for systems with nonadditive interactions and its efficiency is demonstrated by its implementation for the polarizable Stockmayer fluid. Performance of the method is compared with both the standard one-particle move method and an unbiased multiparticle scheme by computing the mean squared displacements, rotation relaxation, and the speed of equilibration (translational order parameter). It is shown that the proposed biased method is about a factor of 10 faster, for the system considered, when compared with the other schemes.     

Experimental,Monte Carlo and molecular dynamics simulations to investigate corrosion inhibition of mild steel in hydrochloric acid solutions

The efficiency of three furan derivatives, namely 2-(p-toluidinylmethyl)-5-methyl furan (Inh. A), 2-(p-toluidinylmethyl)-5-nitro furan (Inh. B) and 2-(p-toluidinylmethyl)-5-bromo furan (Inh. C), as possible corrosion inhibitors for mild steel in 1.0 M HCl, has been determined by weight loss and electrochemical measurements. These compounds inhibit corrosion even at very low concentrations, and 2-(p-toluidinylmethyl)-5-methyl furan (Inh. A) is the best inhibitor. Polarization curves indicate that all compounds are mixed-type inhibitors, affecting both cathodic and anodic corrosion currents. Adsorption of furan derivatives on the mild steel surface follows the Langmuir adsorption isotherm, and the calculated Gibbs free energy values confirm the chemical nature of the adsorption. Monte Carlo simulations technique incorporating molecular mechanics and molecular dynamics can be used to simulate the adsorption of furan derivatives on mild steel surface in 1.0 M HCl.     

Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.