A new method is presented to identify the truly interfacial molecules at fluid/fluid interfaces seen molecular resolution, a situation that regularly occurs in computer simulations. In method, surface scanned by moving probe sphere of given radius along large set test lines are perpendicular plane interface. The hit spheres regarded as ones, and position when they contact with give an estimate surface. dependence on various parameters, particular, size discussed detail. Based list identified...

Pytim is a versatile python framework for the analysis of interfacial properties in molecular simulations. The code implements several algorithms identification instantaneous interfaces arbitrary shape, and tools written specifically study properties, such as intrinsic profiles. language, makes use n umpy s cipy packages to deliver high computational performances. relies on MDAnalysis library analyze trajectory file formats popular simulation gromacs , charmm namd lammps or Amber, can be...

The structure of water has been analyzed at eight different thermodynamic states from ambient to supercritical conditions both by molecular dynamics (MD) and Reverse Monte Carlo (RMC) simulation. MD simulations have carried out with two potential models, a polarizable one the most successful nonpolarizable i.e., well known Simple Point Charge in its revised version labeled E (SPC/E). It found that, although model can reproduce experimental partial pair correlation functions high temperature...

The aggregation behavior of two bile acid salts (i.e., sodium cholate and deoxycholate) has been studied in their aqueous solutions three different concentrations 30, 90,and 300 mM) by means molecular dynamics computer simulations. To let the systems reach thermodynamic equilibrium, rather long simulations have performed: equilibration period, lasting for 20-50 ns, followed a 20 ns production phase, during which average size aggregates (regarded to be slowest varying observable) already...

Substantial progress in our understanding of interfacial structure and dynamics has stemmed from the recent development algorithms that allow for an intrinsic analysis fluid interfaces. These work by identifying instantaneous location interface, at atomic level, each molecular configuration then computing properties relative to this location. Such a procedure eliminates broadening interface caused capillary waves reveals underlying features system. However, precise definition which molecules...

We present a generalized version of the ITIM algorithm for identification interfacial molecules, which is able to treat arbitrarily shaped interfaces. The exploits similarities between concept probe sphere used in ITIMand circumsphere criterion α-shapes approach, and can be regarded either as reference-frame independent former, or an extended latter that includes atomic excluded volume. new applied compute intrinsic orientational order parameters water around dodecylphosphocholine cholic...

The preferential orientation of the water molecules near water/1,2-dichloroethane interface is analyzed in detail at different distances from on basis a grand canonical ensemble Monte Carlo simulation. individual described by angular polar coordinates normal vector local coordinate frame fixed to particular molecule, and bivariate joint distribution two angles calculated. It found that have distinct orientational preferences, these preferences exist simultaneously among penetrating farthest...

The orientational statistics of water molecules at the vicinity water/CCl4 liquid–liquid interface is analyzed different levels on basis a Monte Carlo computer simulation. Profiles describing average orientation various molecule-fixed vectors relative to along normal axis, monovariate distributions parameters these orientations, as well bivariate joint probability distribution two independent in layers are determined. It demonstrated that complete description preferences entire molecule can...

The relative arrangement of the neighboring bile ions and shape hydrophobic hydrogen-bonded primary micelles as well large secondary formed by these are analyzed in detail on basis molecular dynamics computer simulations 30 300 mM sodium cholate deoxycholate solutions. In lower concentration considered, systems only contain micelles, whereas both also present. performed were long enough that reached thermodynamic equilibrium. It is found prefer alignments which their quasi-planar tetracyclic...

Molecular dynamics simulations of the vapor-liquid interface water-methanol mixtures five different compositions were performed on canonical (N,V,T) ensemble at 298 K. In addition, two neat systems was simulated, as well. The obtained configurations analyzed by means novel identification truly interfacial molecules method, which provides a full list that are right surface (i.e., boundary phases). molecular level roughness surface, adsorption methanol layer, orientation molecules, residence...

Substantial improvements in the molecular level understanding of fluid interfaces have recently been achieved by recognizing importance detecting intrinsic surface coexisting condensed phases computer simulations (i.e., after removal corrugations caused capillary waves) and developing several methods for identifying molecules that are indeed located at boundary two phases. In our previous paper [J. Phys. Chem. C 2010, 114, 11169], we critically compared those terms reliability, robustness,...

Interfaces are ubiquitous objects, whose thermodynamic behavior we only recently started to understand at the microscopic detail. Here, borrow concepts from techniques of surface identification and intrinsic analysis, provide a complementary point view on density, stress, energy, free energy distribution across liquid ("soft") interfaces by analyzing respective contributions coming successive layers.

The excess free energy profile of H2O, O2, CO, CO2, NO, and CHCl3 has been computed across a fully hydrated dimyristoylphosphatidylcholine (DMPC) bilayer by cavity insertion variant the Widom test particle method. This Cavity Insertion (CIW) method modifies original procedure in such way that, analogously to biased insertions used grand canonical Gibbs ensemble Monte Carlo simulations, it inserts into cavities suitable radius only. Results on aqueous systems show that this modification can...

Structural, thermodynamic, and dielectric properties of three polarizable two nonpolarizable water models are compared with experimental data at four different thermodynamic states from ambient to supercritical conditions. Pair-correlation functions obtained Monte Carlo simulations, performed both on the (N,V,T) (N,p,T) ensembles. The constants determined molecular Ornstein–Zernike theory. It is found that can reproduce structure considerably better than ones high-temperature states. In...

A generalized version of the Voronoi−Delaunay method is used to study relatively large intermolecular voids in a model hydrated DMPC bilayer, obtained from all-atom Monte Carlo simulation. Application original for molecular systems has been hampered by fact that these geometrically represent ensembles partially overlapping spheres different radii. The based on using additively weighed Voronoi diagram, representing locus spatial points being equally far surface rather than center...

The adsorption isotherm of methanol on ice at 200 K has been determined both experimentally and by using the Grand Canonical Monte Carlo computer simulation method. experimental simulated isotherms agree well with each other; their deviations can be explained a small (about 5 K) temperature shift in data and, possibly, non-ideality surface situation. analysis results revealed that saturated layer is monomolecular. At low coverage, driven methanol-ice interaction; however, full...

The adsorption of water vapor at the surface magnetite nanoparticles has been investigated both by experimental and computer simulation methods. adsorption/desorption isotherm measured on freshly prepared nanocrystals size below 10 nm. change isosteric heat with coverage determined from temperature dependence this using method. also performing a set grand canonical Monte Carlo simulations 300 K. X-ray photoelectron spectroscopy results as well clearly indicates that dissociative...

Molecular dynamics simulations of the interface water with four different apolar phases, namely vapour, liquid carbon tetrachloride, dichloromethane (DCM) and dichloroethane (DCE) are performed on canonical ensemble at 298 K. The resulting configurations analysed using novel method identification truly interfacial molecules (ITIM). Properties first three molecular layers phases (e.g. width, spacing, roughness, extent in-layer hydrogen bonding network) as well constituting these (e.g.,...

The adsorption layer of five different surfactants, namely, pentanol, octanol, dodecanol, dodecyl trimethyl ammonium chloride, and sodium sulfate, has been analyzed on the basis molecular dynamics simulation results at two surface densities, 1 4 μmol/m(2). analyses have primarily focused question how deeply, in terms atomistic layers, surfactant molecules are immersed into aqueous phase. orientation conformation also analyzed. obtained reveal a clear difference between immersion behavior...

The adsorption of four aromatic hydrocarbon compounds, benzene, naphthalene, anthracene, and phenanthrene, at the surface Ih ice is investigated by grand canonical Monte Carlo (GCMC) computer simulation under tropospheric conditions 200 K. By systematic variation value adsorbate chemical potential in simulations, isotherms are determined. It found that follows Langmuir mechanism only up to a rather low relative pressure every case. In this range specific sites, called α which molecules can...

The tangential pressure profile has been calculated across the liquid–vapor interface of five molecular liquids, i.e., CCl4, acetone, acetonitrile, methanol, and water, in dynamics simulations using a recently developed method. Because value surface tension is directly related to integral this profile, obtained results can be interpreted terms distribution along normal, both as function distance, either from Gibbs dividing or capillary wave corrugated real, intrinsic liquid surface, also...

Amphiphilic surfactants are changing the surface tension of solutions by adsorbing at their surfaces. In general, however, little is known about actual distribution across interface, as well extent contribution different moieties to tension. Here, we consider liquid–vapor interface five amphiphilic molecules, representative anionic, cationic and nonionic (alcoholic) surfactants. We investigate, means molecular dynamics simulations, various chemical species in these aqueous coverages. find...

The effect of cholesterol on the properties lipid membranes has been investigated by computer simulations. For this purpose, crossmembrane free energy profiles eight penetrants, i.e., H2O, O2, CO, CO2, NO, NH3, CHCl3, and formamide, have calculated cavity insertion Widom (CIW) method in four simulated dimyristoylphosphatidylcholine (DMPC)/cholesterol mixed different compositions, containing 0%, 4%, 8%, 40% cholesterol. compositions two component selected from both sides DMPC/cholesterol...

All-atom Monte Carlo simulations of four different fully hydrated dimyristoylphosphatidylcholine (DMPC)/cholesterol mixed bilayers have been performed at physiological conditions (i.e., 37 °C and 1 atm). The composition the samples has chosen from both sides DMPC/cholesterol miscibility gap; mole fraction cholesterol was 0, 0.04, 0.08, 0.40 in systems simulated. configurations obtained are analyzed detail, order to shed some light on role played by presence molecules structure such...