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We use molecular dynamics simulations to study liquid droplets and bridges inside crystalline pores having triangular, square, hexagonal, and circular cross-sections of varying dimensions. The role of wettability is also investigated by varying solid-fluid interaction strengths. We analyze the stability of liquid droplet or bridge, the density distribution within a droplet or bridge, and the propensity of liquid to occupy corners of polygonal cross-sections of pores. The solid-fluid interfacial free energies calculated from Monte Carlo simulations and a thermodynamic model are used to estimate the free energy change of liquid occupying the corners of a pore. Liquid droplets and liquid bridges are observed for weakly and strongly attractive nanopores, respectively. Both droplets and bridges are unstable inside nanopores having the largest cross-sectional dimension smaller than 10 molecular diameters. Both the liquid configurations are more unstable inside nanopores having hexagonal cross-sections. The propensity of liquid to occupy the corners of a polygonal cross-section of a nanopore decreases with decrease in the number of sides of the polygon. [ABSTRACT FROM AUTHOR]

Abstract Single-layer molybdenum disulfide (MoS 2) is a novel two-dimensional material that has attracted considerable attention because of its excellent properties. In this work, molecular dynamics simulations were performed to investigate the effect of different kinds of alkali metal ions (Li+, Na+, and K+) on the flow resistance of ionic aqueous solutions confined in MoS 2 nanoslits under shearing. Three slit widths (i.e. 1.2, 1.6, and 2.0 nm) were investigated. Simulation results showed that the friction coefficient followed the order of K+ < Na+ < Li+. The friction coefficient decreased with the increasing of slit width. Unique confined spatial distributions of different types of ionic aqueous solutions led to different confined ionic hydrations for different cations. These differences lead to different orientations of surrounding water molecules and then form different hydrogen bond (HB) networks. The friction coefficient was greatly dependent on the number of HBs per water; i.e. , the larger the number of HBs formed, the lower was the flow resistance. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]

Abstract The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of RDFs over volume but can also be obtained from density fluctuations in the grand-canonical ensemble. Various methods have been proposed to estimate KB integrals from molecular simulation. In this work, we review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention is paid to finite-size effects. We also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]

The phase equilibria knowledge of fatty acid and water mixtures play a crucial role in the design and operation of processes such as bio-diesel synthesis, sea water desalination and novel solvent design. Experimental data on the mutual solubility of fatty acid and water are scattered and limited. Atomistic molecular simulation approach can be a viable substitute for these predictions. In this work, a molecular simulation method is proposed that does not require molecular transfer between dense phases as in the Gibbs ensemble method and is based on determining phase equilibria by computing and equating the fugacity of water in the two phases. Assuming that the fugacity of water-rich phase is identical to that of pure water, an expression for the solubility of fatty acid in water is derived. In the current formalism, fugacity is determined by computing the residual chemical potential of water and fatty acids via thermodynamic integration. Mutual solubility between water and three different fatty acids are calculated over a range of temperatures and shown to yield good agreement with experimental data. Microscopic structural properties elucidating the role of the hydrogen bonding interactions between water and fatty acid and the aggregation of water molecules which gives rise to the observed macroscopic properties are also studied. [ABSTRACT FROM AUTHOR]

Molecular dynamics and Monte Carlo simulation studies were carried out to investigate adsorption behavior of carbon dioxide and methane mixtures on illitic clay surfaces under dry conditions. Various compositions of the mixtures and distributions of isomorphic substitutions in clay layers were chosen to explore competitive adsorption depending on component concentration and charge localization. The simulations show that carbon dioxide is preferentially sorbed on the illitic surface and is capable to promote methane desorption. Density distributions of the molecular species in pore space reveal formation of multilayers on the clay surfaces at elevated pressures. Mixed adsorption isotherms were compared with adsorption isotherms of pure compounds and thermodynamic quantities were reported to characterize the interaction of the carbon dioxide and methane with the clay surface. [ABSTRACT FROM AUTHOR]

We report molecular simulation studies of liquid-liquid equilibria (LLE) in mixtures that include polar (water/methanol) and nonpolar/weakly polar (cyclic) components. While vapor-liquid equilibria (VLE) has been widely studied using molecular simulations, there have been relatively few such studies for LLE despite their industrial importance. Often equation of state parameters that work for VLE do not work well for LLE, our studies show, however, that molecular potentials for VLE were successful in predicting reliable results for LLE. Our methodology is an extension of our previous studies for VLE (solubility of gases in liquids). In these studies, we used the generalized AMBER force field (GAFF) with no further adjustments. Our results showed good agreement with recent experimental results for LLE of these systems and showed some interesting trends. We found that the behavior of mixtures of hydrocarbons with both methanol and water present became significantly different when no water was present. After validating our method and models in our LLE studies, we also used these simulations to explore other dynamic and equilibrium properties of these mixtures. Our results showed significant changes in the structural and dynamic behavior of these mixtures as the concentration of water changed. [ABSTRACT FROM AUTHOR]

Heparin is a sulfated glycan widely used as anticoagulant in medicine. Mallard Blue (MalB), a small cationic dye developed in our laboratories, is able to detect heparin in serum and plasma in a dose-response manner, with performance superior to its direct competitors. However, many aspects of MalB/heparin binding still remain to be explored which, once solved, may foster the clinical use of MalB. Among these, the characterization of the energetics that drives the MalB/heparin binding process, the competition for MalB binding by other polyanions (e.g., negatively-charged surfactant micelles), and the interaction of MalB with serum proteins are of particular interest. This work fills this gap by means of a combination of experimental investigations (UV-visible spectroscopy and isothermal titration calorimetry), and computational approaches based on molecular dynamics (MD) simulation techniques. In combination, the results obtained show that MalB efficiently binds to both heparin and SDS, with the binding being enthalpic in nature; yet, SDS is able to extract MalB from its complex with heparin when the surfactant is in its self-assembled form, the driving force underlying SDS-induced MalB/heparin de-complexation being entropic in nature as the two enthalpies of binding effectively cancel each other out. Once bound to SDS, the dye remains electrostatically bound to the micellar surface and does not penetrate the micelle palisade layer, as verified by steered molecular dynamics/umbrella sampling simulations. Finally, the affinity of MalB for human serum albumin (HSA), the most abundant plasma protein, is found to be lower than that for heparin, confirming the ability of the dye to work in complex physiological environments. [ABSTRACT FROM AUTHOR]

The metastable region of binary mixtures is examined with the PC-SAFT equation of state (EOS) and compared to molecular simulations. The studied mixtures are Methane + Ethane, Methanol + Ethanol, Carbon Dioxide + Toluene, Carbon Dioxide + Hydrogen Chloride and Hydrogen Chloride + Toluene. In order to calculate the spinodal, the second partial derivatives with respect to the components molarities are analytically determined for the PC-SAFT EOS. Thermal properties as well as the spinodal points determined using PC-SAFT and molecular simulation are compared. For the studied metastable gas phases the results obtained with PC-SAFT and the molecular simulations agree well. For liquid phases the metastable region calculated with the PC-SAFT EOS is typically broader than that obtained from the molecular simulations. No unphysical results were obtained with PC-SAFT for metastable states. Hence, PC-SAFT EOS is found to be principally suitable for predicting metastable states and spinodals of mixtures. [ABSTRACT FROM AUTHOR]

The confinement of titanium dioxide (TiO 2 ) significantly affects the nanoconfined water molecules behaviors, manifested structurally as fluid layering and dynamically as slowing down of fluid mobility near the confining surface. In this work, we carried out molecular dynamics simulations to investigate temperature-dependent structural characteristics of water molecules confined in rutile (110) nanoslits. Specifically, we studied the microstructure of two layers of water molecules near TiO 2 surface under temperatures ranging from 27 to 800 °C. The simulation results showed that the mean residence time of the first layer of water molecules decreased with temperature. A dramatic decreasing rate occurred when the temperature went beyond 300 °C. Detailed microstructural investigation of confined water molecules showed that with the increase of temperature, the orientation of some water molecules changed. The possible reason is that water molecules obtained more kinetic energy due to the higher interfacial temperature, so as to increase the probability of forming hydrogen bonds between water molecules in layer I. Moreover, dimers of water molecules, which exhibit higher mobility than water monomers near TiO 2 surfaces, began to form at about 300 °C. The formation of hydrogen bonds within the first layer of water molecules is largely responsible for the reduction of mean residence time. The results of this work provide perceptive guidelines for the application of TiO 2 at high temperatures, such as TiO 2 -supported catalysts. [ABSTRACT FROM AUTHOR]

Low-generation viologen-phosphorous dendrimers (VPDs) can be exploited as novel therapeutic agents, since they efficiently inhibit aggregation of amyloid-β into fibrils and are active against several strains of microorganisms. Human serum albumin (HSA), the most abundant plasma protein, is playing an increasing role as drug carrier in the clinical setting. Therefore, with the aim of exploiting HSA as a potential carrier for VPDs, in this work we performed a preliminary investigation of the interaction of six different VPDs 1 – 6 with HSA using a combined computational/experimental approach. First, different modeling techniques were employed to i) determine the dendrimer binding site on the HSA surface; ii) derive the free energy change ΔG b involved in each dendrimer/HSA complex formation; iii) analyze in details all molecular determinants contributing to ΔG b , and iv) evaluate the eventual HSA structural variations induced by dendrimer binding. All modeling predictions were next validated using a series of experimental techniques, including isothermal titration calorimetry (ITC), circular dichroism (CD), and fluorescence quenching and decay. In aggregate, the results from this study allowed us to rank the affinity of the different viologen-phosphorous dendrimers 1 – 6 towards HSA and to formulate a molecular-based rationale for the differential binding thermodynamics of the resulting dendrimer/HSA complexes. According to our data, HSA can successfully and selectively bind VPDs 1 – 6 , dendrimer 4 being the best cargo for this endogenous protein nanocarrier. [ABSTRACT FROM AUTHOR]

The properties of aqueous ionic solutions are determined by strong electrostatic interactions, which are influenced by polarizability and charge transfer interactions. Potential models which include polarizability and charge transfer have been developed for water and single ion properties. Here, the ion–ion interactions are optimized so that the osmotic pressure as a function of concentration is reproduced. Using the optimized potentials, the amount of ion pairing and larger cluster formation is calculated. For NaCl, NaI, and KCl, there is a small amount of pairing, with larger clusters present as well. For KI, there is much more pairing and much larger clusters are observed. The amount of pairing is consistent with the law of matching affinities, with the pairs that show the least pairing also being the most mis-matched in terms of size or solvation free energy. The charge transfered from the anions to water is more than from is transferred from the water to cations, so the water molecules acquire a negative charge, which increases with ion concentration. [ABSTRACT FROM AUTHOR]

A new group contribution method (GCM) approach, based upon the combination of a thermodynamic model and molecular simulation (MS) is introduced. While other conventional GCMs require fitting with experimental data to determine group parameter values, proposed model calculates them directly using the pairwise interaction energy of functional groups (FG), obtained from MS. The solvent activities of a large variety of polymer solutions were estimated using the Helmholtz energy of mixing, based on the modified double lattice (MDL) model. For each polymer/solvent system, the interaction energy term within the Helmholtz energy expression is determined using the aforementioned group parameter derived from MS combined GCM (MS–GCM). From a number of polymer and solvent molecules, eleven FGs are defined. As considering FG connectivity, dummy atoms are introduced at the first adjacent positions in order to prevent impossible configurations during interaction energy calculation. The molecule disassembling method and dummy atom selection for each FG are carefully investigated. Newly proposed approach of MS–GCM could reduce the number of parameter much less than conventional GCMs but successfully predicted solvent activity. Its total deviation average of solvent activity estimation is 3.9%. Although it is little bit higher than previous work of Hu et al. but still remains in acceptable level. [ABSTRACT FROM AUTHOR]

Entropy scaling has proved to be an appealing framework to connect transport properties to microscopic structure for many pure fluids. Its extension to mixtures is not fully straightforward in particular because it requires the definition of an effective molecular mass equivalent to that of the mixture from the transport properties point of view. However, the exact definition of such an effective molecular mass, thanks to a mixing rule, is unknown theoretically apart from the zero-density regime. Thus, in this work, various mixing rules that express the effective molecular mass as a function of molar fractions and molecular masses of the components of the mixture, have been investigated by performing molecular simulations on mixtures of Lennard-Jones fluids at various thermodynamic conditions ranging from low- to high-density states. It has been found that the best results are obtained by decomposing the viscosity into zero-density and residual contributions, the latter being described by a correlation based on the entropy scaling. More precisely, good estimates of the viscosity of mixtures of Lennard-Jones fluids are achieved by using a combination of a van der Waals one fluid-Chapman-Enskog approximation for the zero-density viscosity with a mixing rule derived from the Grunberg-Nissan equation for the residual viscosity. It is even possible to improve these results at high density, using an empirical modification to the Grunberg-Nissan derived mixing rule. • Entropy scaling of viscosity is extended to Lennard-Jones mixtures. • Different mass mixing rules on zero-density and residual contributions to viscosity is required. • van der Waals one fluid approximation is a good option for the zero-density viscosity. • Grunberg-Nissan derived mass mixing rules is a reasonable option for the residual viscosity. [ABSTRACT FROM AUTHOR]

Abstract: Heterogeneous mixtures are said to be in molar isopycnic phase equilibrium when – at least – two of the constituent phases exhibit the same molar volume v or, equivalently, the same molar density ρ. Consequently, the molar densities of the constituent phases experiment inversion (or molar barotropy), thus yielding an interesting singularity that may be observed in both super- and sub-critical equilibrium conditions. This contribution aims to theoretically characterize the molar isopycnic behavior observed in binary mixtures. Accordingly, theoretical predictions and strategically guided molecular simulations of the Lennard–Jones fluid are performed to describe the phase behavior and the interfacial properties of mixtures characterized by molar density inversions. Necessary and sufficient conditions are then deduced to detect molar isopycnicity in binary mixtures and, finally, these limiting conditions are related to the various classes of global phase behavior. Our results indicate that molar isopycnicity is present in mixtures exhibiting Types II, III, IV and V behavior. It follows then that molar density inversions seem to be more common than previously believed and that liquid phase immiscibility provides a natural condition for its existence. It is also observed that the phenomenon is controlled by differences in molecular size and critical properties. Particularly, molar isopycnicity becomes observable in ranges where stable fluid phases can be observed as the constituents’ molecular size ratio increases. Differences in critical properties, in turn, promote wider temperature ranges of molar density inversions. The main classes and mechanisms that constraint molar isopycnic equilibria are illustrated and exemplified by considering binary van der Waals mixtures. [Copyright &y& Elsevier]

Abstract: To understand the effect of protein shape and size on fast dynamics of proteins adsorption onto hydrophobic surfaces we employ dissipative particle dynamics (DPD), a mesoscale particle-based modeling technique, and study the adsorption behavior of model proteins on hydrophobic surfaces. The model proteins are modeled as semi-flexible rod-like objects consisting of a bundle of linear chains formed by coarse-grained beads that represent lumps of proteins. Three water molecules were combined into a coarse-grained bead and hydrophobic surfaces were represented by dense layers of beads formed in a similar fashion that correspond to small sections of hydrophobic surfaces. We compare systems of large elongated proteins and small elongated proteins that approximately represent proteins over 1000 total residues and peptides of about 200 total residues, respectively, in the presence of a hydrophobic surface. We find distinct differences in the adsorption (and desorption) kinetics of the two types of model proteins. In systems containing small proteins, we observe rapid diffusion and adsorption kinetics as well as frequent desorption events. In systems containing large proteins, protein diffusion is rather slow and once these large proteins adsorb on the hydrophobic surfaces desorption events become rather rare. [Copyright &y& Elsevier]

Abstract: Using the method of molecular dynamics (MD), we have estimated the solubility of hydrogen in heavy hydrocarbons for a range of temperatures and pressures. Heavy hydrocarbon systems are known to be challenging not only for experimental measurements but also for reliable estimations using traditional equations of state (EOS). The simulation system used was designed with semi-permeable membranes to mimic actual experimental studies of gas solubility. Binary interaction parameters between the solute gas and the solvent (heavy hydrocarbons) components were adjusted when necessary to improve agreement with experimental results and then used in subsequent multi-component studies. Temperature and pressure ranges studied included higher temperatures and pressures which are especially difficult to investigate experimentally. Simulation results were finally used to adjust the binary interaction parameters (BIP) in simulation packages (e.g. Aspen) to enable quick and reliable predictions. [ABSTRACT FROM AUTHOR]

Abstract: An improved fully flexible fixed-point charges model for water has been developed to predict the vapor–liquid coexistence properties using the NVT-Gibbs ensemble Monte Carlo technique (GEMC) and the pressure in supercritical region. The average deviation between our simulation and experimental data for saturated liquid densities is 2.75% over temperature range of 314–609K. Comparing with experimental data for T c, P c and ρ c (P c =220.064bar, T c =647.096K and ρ c =0.322g/cm3 for the experimental data), our calculated results (P c =213bar, T c =644.3K and ρ c =0.325g/cm3 for our simulations) are acceptable and are better than those by the SPC-E and TIP4P models. The saturated pressure is calculated by evaluating the pressure of vapor from NPT-MD simulation at the coexistence vapor densities at the nominal temperature. The agreement of our simulated pressures of supercritical water at any density and temperature with the experimental values is excellent. The second virial coefficient and radial distribution function in ambient and supercritical conditions are also estimated. The radial distributions consist with experimental data very well. [Copyright &y& Elsevier]

Abstract: This work summarizes some results obtained through equilibrium molecular dynamic simulations regarding the structure and transport properties of several ionic liquids (ILs). The Green–Kubo relationships were employed to evaluate the cation/anion diffusion coefficients, electrical conductivity and shear viscosity at 400K. The ILs investigated were 1-ethyl-3-methylimidazolium salts of Cl−, NO3 − and PF6 − using two different force fields for the cation: a rigid ion model of 1-ethyl-3-methylimidazolium, studied in a previous work [C. Rey-Castro, L.F. Vega, J. Phys. Chem. B 110 (2006) 14426–14435] and the flexible model of Urahata and Ribeiro [S.M. Urahata, M.C.C. Ribeiro, J. Chem. Phys. 120 (2004) 1855–1863]. Regarding the anions, the most evident difference between the local structures in the three ILs is the position of the first peak of the radial distribution function, reflecting the differences in anion sizes and shapes. The velocity autocorrelation functions are particularly sensitive to the relative weights of anion and cation, although the integrated self-diffusion coefficients do not show significant differences between the Cl−, NO3 − and PF6 − salts. The electric conductivity predicted by the rigid ion model of [emim]Cl is lower than the experimental value, whereas the model overestimates the viscosities. In contrast, the flexible model leads to diffusion rates and conductivities that are one order of magnitude higher at the same temperature. The shear viscosities obtained from simulations of the flexible model are in very good agreement with experimental data. The calculated conductivities are compared with values obtained from the diffusion coefficients through the Nernst–Einstein relation in order to determine the importance of cross-correlation among ions. The stress tensor and the distinct van Hove correlation functions indicate that the dynamics of the local structure of the fluid relaxes faster in the flexible model. [Copyright &y& Elsevier]

Choline chloride/urea (1:2) is the most widely used deep eutectic solvent, which has attracted much attention due to its excellent advantages of low cost, environment friendly and easy synthesis. In this work, nanofriction-based molecular dynamics simulations were performed to investigate the effect of interfacial hydrophilicity on the flow resistance of Choline chloride/urea (1:2) confined in ionic model nanoslits. Simulation results showed that the flow resistance of the choline chloride/urea system increases with the increasing interfacial hydrophilicity. Urea molecules form a preferential adsorption layer on the wall. As the interfacial hydrophilicity increases, the number of urea molecules in the interfacial adsorption layer increased, whereas the stability decreased. Unique confined spatial distributions of urea molecules greatly contribute to ionic association between choline cations and chloride anions. Furthermore, with the increase of interfacial hydrophilicity, orientation distributions of urea molecules in the adsorption layer are more orderly, then causing a decrease in the average hydrogen bond number (N HB) of urea molecules. Moreover, the more the N HB of urea molecules, the better is the stability in the interfacial adsorption layer, which in turn results in less flow resistance. [ABSTRACT FROM AUTHOR]

The binary interaction parameters of the nonrandom two liquid (NRTL) thermodynamic model are predicted for several organic mixtures using molecular simulations. Based on the theoretical framework of the two-fluid theory, the binary interaction parameters are expressed in terms of the interaction energies, size of the molecules, and size of the local molecular domains; these quantities are calculated from molecular simulations. We show that our technique is robust in terms of its predictions involving organic mixtures with compatible chemical characteristics while we propose possible modifications in the case of mixtures involving incompatible chemical components or significant size disparity, where there is a notable difference between the interaction parameters calculated from simulations and those obtained from experimental data regression. We further demonstrate that the binary interaction parameters calculated from data regression are not unique and that molecular simulations can guide the parameter selection process by identifying physically relevant binary interaction parameters. Requiring only the local molecular structure information from molecular simulations, the method offers fast and reliable prediction of phase equilibrium properties, especially in cases where limited experimental data are available. [ABSTRACT FROM AUTHOR]

With the emergence of membrane separation and heterogeneous catalysis applications that are associated with confined ethanol/water binary mixture in the pores of two-dimensional (2D) nanomaterials, understanding their confined microstructures is the first step for further relevant applications. In this work, molecular dynamics was performed to investigate the microstructure of ethanol/water binary mixture of 5% mole fraction confined within the four typical 2-nm width 2D-nanoslits (i.e. hBN, GO-0.2, GO-0.4 and Ti 3 C 2 (OH) 2). Results demonstrated that different chemical properties of solid surfaces can induce distinctive microstructures of mixed fluid within the interfacial contact (adsorbed) layer and thus can result in different mobility of water molecules within the subcontact layer. The residence times of water molecules in the subcontact layer were found in the sequence of Ti 3 C 2 (OH) 2 > hBN > GO-0.4 > GO-0.2, whereas their sequence of diffusion coefficient within the x-z plane was Ti 3 C 2 (OH) 2 > hBN > GO-0.2 > GO-0.4. Detailed hydrogen bond (HB) microstructure analysis showed that a high average number of HBs (between fluid molecules of the interfacial contact layer and water molecules of the subcontact layer) induced by solid surfaces could facilitate water molecules to reside in the subcontact layer. Moreover, the small average number of HBs between the water molecules themselves in the subcontact layer could lead to high in-plane diffusion coefficients. [ABSTRACT FROM AUTHOR]

Prediction of derivative properties, such as the isochoric heat capacity, remains a real challenge for equations of state. Molecular-based equations of state are derived through a set of approximations, e. g. , perturbation theory. The subtleness of these approximations, inaccessible to such a macroscopic description, might be tested with molecular simulations via top-down approaches, where the model parameters used in the molecular simulations are taken from a molecular-based equation of state. In this study, we have calculated the isochoric heat capacity of carbon dioxide comparing three different equations of state based on perturbation theory and two different force fields derived from two of the equations of state. The effects of different potentials (discrete and continuous potentials) and the approximations taken in the derivation of the equations of state were thoroughly analyzed. No model was able to accurately predict heat capacity, but the ones using continuous potentials provided the best results. [ABSTRACT FROM AUTHOR]

A combination of Monte Carlo and molecular dynamics simulations was carried out to estimate mixed CO 2 /CH 4 adsorption isotherms on illite surfaces in the presence of water. Three bulk phase mixture compositions are explored to study the effect of concentrations on competitive sorption in illite bearing two positions for the isomorphic substitutions. The computed isotherms are compared with those predicted for dry systems to deduce the effect of water on CO 2 and CH 4 interactions with the clay surfaces. The hydration of the counter-balancing ions in pore space is studied to evaluate sorption-desorption processes at the basal clay surfaces. Sensitivity parameters reflecting preferential CO 2 /CH 4 sorption, density profiles, and surface occupancy times are reported and analyzed. [ABSTRACT FROM AUTHOR]