Molecular simulation study of the effect of pressure on the vapor-liquid interface of the square-well fluid

We examine a model system to study the effect of pressure on the surface tension of a vapor-liquid interface. The system is a two-component mixture of spheres interacting with the square-well (A-A) and hard-sphere (B-B) potentials and with unlike (A-B) interactions ranging (for different cases) from hard sphere to strongly attractive square well. The bulk-phase and interfacial properties are measured by molecular dynamics simulation for coexisting vapor-liquid phases for various mixture compositions, pressures, and temperatures. The variation of the surface tension with pressure compares well to values given by surface-excess formulas derived from thermodynamic considerations. We find that surface tension increases with pressure only for the case of an inert solute (hard-sphere A-B interactions) and that the presence of A-B attractions strongly promotes a decrease of surface tension with pressure. An examination of density and composition profiles is made to explain these effects in terms of surface-adsorption arguments.     

Some issues on the calculation of interfacial properties by molecular simulation

Some of the pitfalls that may befall molecular simulations of interfaces are discussed. They are all related to the calculation of the pressure tensor profiles, which are needed in order to compute surface tensions. We focus on three controversial points: (1) the calculation of the pressure tensor profiles for polyatomic systems, in particular, when the SHAKE algorithm is employed, (2) the addition of long-range corrections to compensate the truncation of the potential, and (3) the importance of including adequate error intervals with the results. Most of the conclusions are general, but some specifically apply to multiple site molecular-dynamics simulations.     

Extended study of molecular dynamics simulation of homogeneous vapor-liquid nucleation of water

Using the simple point charge/extended water model, we performed molecular dynamics simulations of homogeneous vapor-liquid nucleation at various values of temperature T and supersaturation S, from which the nucleation rate J, critical nucleus size n(*), and the cluster formation free energy DeltaG were derived. As well as providing lots of simulation data, the results were compared with theories on homogeneous nucleation, including the classical, semi-phenomenological, and scaled models, but none of these gave a satisfactory explanation for our results. It was found that two main factors made the theories fail: (1) The average cluster structure including the nonspherical shape and the core structure that is not like the bulk liquid and (2) the forward rate which is larger than assumed by the theories by about one order of magnitude. The quantitative evaluation of these factors is left for future investigations.     

Molecular dynamics simulation study of association in trifluoroethanol/water mixtures

Mixtures of Trifluoroethanol (TFE) and water with different proportions are studied using molecular dynamics simulations. The radial and spatial distribution functions, as well as the size distribution of TFE clusters are obtained from the trajectories. The variation of radial and spatial distribution functions with composition show that the addition of TFE enhances the water structure, but the hydrogen bonds between TFE molecules are broken as TFE is diluted with water. The TFE‐rich solutions have stronger TFE–water hydrogen bonds. The clustering of TFE molecules in low concentration region is attributed to the hydrophobic interactions between CF₃ groups. The distribution of cluster sizes in solution supports these conclusions. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

Molecular simulation study of temperature effect on ionic hydration in carbon nanotubes

Molecular dynamics simulations have been performed to investigate the hydration of Li(+), Na(+), K(+), F(-), and Cl(-) inside the carbon nanotubes at temperatures ranging from 298 to 683 K. The structural characteristics of the coordination shells of ions are studied, including the ion-oxygen radial distribution functions, the coordination numbers, and the orientation distributions of the water molecules. Simulation results show that the first coordination shells of the five ions still exist in the nanoscale confinement. Nevertheless, the first coordination shell structures of cations change more significantly than those of anions because of the preferential orientation of the water molecules induced by the carbon nanotube. The first coordination shells of cations are considerably less ordered in the nanotube than in the bulk solution, whereas the change of the first coordination shell structures of the anions is minor. Furthermore, the confinement induces the anomalous behavior of the coordination shells of the ions with temperature. The first coordination shell of K(+) are found to be more ordered as the temperature increases only in the carbon nanotube with the effective diameter of 1.0 nm, implying the enhancement of the ionic hydration with temperature. This is contrary to that in the bulk solution. The coordination shells of the other four ions do not have such behavior in the carbon nanotube with the effective diameter ranging from 0.73 to 1.00 nm. The easier distortion of the coordination shell of K(+) and the match of the shell size and the nanotube size may play roles in this phenomenon. The exchange of water molecules in the first coordination shells of the ions with the solution and the ion diffusion along the axial direction of the nanotube are also investigated. The mobility of the ions and the stability of the coordination shells are greatly affected by the temperature in the nanotube as in the bulk solutions. These results help to understand the biological and chemical processes at the high temperature.     

Wall-liquid and wall-crystal interfacial free energies via thermodynamic integration: A molecular dynamics simulation study

A method is proposed to compute the interfacial free energy of a Lennard-Jones system in contact with a structured wall by molecular dynamics simulation. Both the bulk liquid and bulk face-centered-cubic crystal phase along the (111) orientation are considered. Our approach is based on a thermodynamic integration scheme where first the bulk Lennard-Jones system is reversibly transformed to a state where it interacts with a structureless flat wall. In a second step, the flat structureless wall is reversibly transformed into an atomistic wall with crystalline structure. The dependence of the interfacial free energy on various parameters such as the wall potential, the density and orientation of the wall is investigated. The conditions are indicated under which a Lennard-Jones crystal partially wets a flat wall.     

Influence of bonded-phase coverage in reversed-phase liquid chromatography via molecular simulation I. Effects on chain conformation and interfacial properties

Particle-based Monte Carlo simulations were employed to examine the effects of bonding density on molecular structure in reversed-phase liquid chromatography. Octadecylsilane stationary phases with five different bonding densities (1.6, 2.3, 2.9, 3.5, and 4.2 mumol/m(2)) in contact with a water/methanol (50/50 mol%) mobile phase were simulated at a temperature of 323 K. The simulations indicate that the alkyl chains become more aligned and form a more uniform alkyl layer as coverage is increased. However, this does not imply that the chains are highly ordered (e.g., all-trans conformation or uniform tilt angle), but rather exhibit a broad distribution of conformations and tilt angles at all bonding densities. At lower densities, significant amounts of the silica surface are exposed leading to an enhanced wetting of the stationary phase. At high densities, the solvent is nearly excluded from the bonded phase and persists only near the residual silanols. An enrichment in the methanol concentration and a disruption in the mobile phase's hydrogen bond network are observed at the interface as bonding density is increased.     

Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study

The import of thiamine pyrophosphate (TPP) through both mitochondrial membranes was studied using a total of 3-µs molecular dynamics simulations. Regarding the translocation through the mitochondrial outer membrane, our simulations support the conjecture that TPP uses the voltage-dependent anion channel, the major pore of this membrane, for its passage to the intermembrane space, as its transport presents significant analogies with that used by other metabolites previously studied, in particular with ATP. As far as passing through the mitochondrial inner membrane is concerned, our simulations show that the specific carrier of TPP has a single binding site that becomes accessible, through an alternating access mechanism. The preference of this transporter for TPP can be rationalized mainly by three residues located in the binding site that differ from those identified in the ATP/ADP carrier, the most studied member of the mitochondrial carrier family. The simulated transport mechanism of TPP highlights the essential role, at the energetic level, of the contributions coming from the formation and breakage of two networks of salt bridges, one on the side of the matrix and the other on the side of the intermembrane space, as well as the interactions, mainly of an ionic nature, formed by TPP upon its binding. The energy contribution provided by the cytosolic network establishes a lower barrier than that of the matrix network, which can be explained by the lower interaction energy of TPP on the matrix side or possibly a uniport activity.

     

Calculation of the crystal-melt interfacial free energy of succinonitrile from molecular simulation

The crystal-metal interfacial free energy for a six-site model of succinonitrile [N triple bond C-(CH(2))(2)-C triple bond N] has been calculated using molecular-dynamics simulation from the power spectrum of capillary fluctuations in interface position. The orientationally averaged magnitude of the interfacial free energy is determined to be (7.0+/-0.4)x10(-3) J m(-2). This value is in agreement (within the error bars) with the experimental value [(7.9+/-0.8)x10(-3) J m(-2)] of Marasli et al. [J. Cryst. Growth 247, 613 (2003)], but is about 20% lower than the earlier experimental value [(8.9+/-0.5)x10(-3) J m(-2)] obtained by Schaefer et al. [Philos. Mag. 32, 725 (1975)]. In agreement with the experiment, the calculated anisotropy of the interfacial free energy of this body-centered-cubic material is small. In addition, the Turnbull coefficient from our simulation is also in agreement with the experiment. This work demonstrates that the capillary fluctuation method of Hoyt et al. [Phys. Rev. Lett. 86, 5530 (2001)] can be successfully applied to determine the crystal-melt interfacial free energy of molecular materials.     

Exploring the effect of aplidin on low molecular weight protein tyrosine phosphatase by molecular docking and molecular dynamic simulation study

The low molecular weight protein tyrosine phosphatase (LMW-PTP) could regulate many signaling pathways, and it had drawn attention as a potential target for cancer. As previous report has indicated that the aplidin could inhibit the LMW-PTP, and thus, the relevant cancer caused by the abnormal regulation of the LMW-PTP could be remission. However, the molecular mechanism of inhibition of the LMW-PTP by the aplidin had not been fully understood. In this study, various computational approaches, namely molecular docking, MDs and post-dynamic analyses were utilized to explore the effect of the aplidin on the LMW-PTP. The results suggested that the intramolecular interactions of the residues in the two sides of the active site (Ser43-Ala55 and Pro121-Asn134) and the P-loop region (Leu13-Ser19) in the LMW-PTP was disturbed owing to the aplidin, meanwhile, the π-π interaction between Tyr131 and Tyr132 might be broken. The Asn15 might be the key residue to break the residues interactions. In a word, this study may provide more information for understanding the effect of inhibition of the aplidin on the LMW-PTP.     

Density-functional study of interfacial properties of colloid-polymer mixtures

Interfacial properties of colloid-polymer mixtures are examined within an effective one-component representation, where the polymer degrees of freedom are traced out, leaving a fluid of colloidal particles interacting via polymer-induced depletion forces. Restriction is made to zero-, one-, and two-body effective potentials, and a free energy functional is used that treats colloid excluded volume correlations within Rosenfeld's fundamental measure theory, and depletion-induced attraction within first-order perturbation theory. This functional allows a consistent treatment of both ideal and interacting polymers. The theory is applied to surface properties near a hard wall, to the depletion interaction between two walls, and to the fluid-fluid interface of demixed colloid-polymer mixtures. The results of the present theory compare well with predictions of a fully two-component representation of mixtures of colloids and ideal polymers (the Asakura-Oosawa model) and allow a systematic investigation of the effects of polymer-polymer interactions on interfacial properties. In particular, the wall surface tension is found to be significantly larger for interacting than for ideal polymers, whereas the opposite trend is predicted for the fluid-fluid interfacial tension.     

Molecular simulation of the shear viscosity and the self-diffusion coefficient of mercury along the vapor-liquid coexistence curve

In earlier work [G. Raabe and R. J. Sadus, J. Chem. Phys. 119, 6691 (2003)] we reported that the combination of an accurate two-body ab initio potential with an empirically determined multibody contribution enables the prediction of the phase coexistence properties, the heats of vaporization, and the pair distribution functions of mercury with reasonable accuracy. In this work we present molecular dynamics simulation results for the shear viscosity and self-diffusion coefficient of mercury along the vapor-liquid coexistence curve using our empirical effective potential. The comparison with experiment and calculations based on a modified Enskog theory shows that our multibody contribution yields reliable predictions of the self-diffusion coefficient at all densities. Good results are also obtained for the shear viscosity of mercury at low to moderate densities. Increasing deviations between the simulation and experimental viscosity data at high densities suggest that not only a temperature-dependent but also a density-dependent multibody contribution is necessary to account for the effect of intermolecular interactions in liquid metals. An analysis of our simulation data near the critical point yields a critical exponent of beta = 0.39, which is identical to the value obtained from the analysis of the experimental saturation densities.     

Model of an asymmetric DPPC/DPPS membrane: effect of asymmetry on the lipid properties. A molecular dynamics simulation study

The study of asymmetric lipid bilayers is of a crucial importance due to the great number of biological process in which they are involved such as exocytosis, intracellular fusion processes, phospholipid-protein interactions, and signal transduction pathway. In addition, the loss of this asymmetry is a hallmark of the early stages of apoptosis. In this regard, a model of an asymmetric lipid bilayer composed of DPPC and DPPS was simulated by molecular dynamics simulation. Thus, the asymmetric membrane was modeled by 264 lipids, of which 48 corresponded to DPPS- randomly distributed in the same leaflet with 96 DPPC. In the other leaflet, 120 DPPC were placed without DPPS-. Due to the presence of a net charge of -1 for the DPPS- in physiological conditions, 48 Na+ were introduced into the system to balance the charge. To ascertain whether the presence of the DPPS- in only one of the two leaflets perturbs the properties of the DPPC in the other leaflet composed only of DPPC, different properties were studied, such as the atomic density of the different components across the membrane, the electrostatic potential across the membrane, the translational diffusion of DPPC and DPPS, the deuterium order parameters, lipid hydration, and lipid-lipid charge bridges. Thus, we obtained that certain properties such as the surface area lipid molecule, lipid head orientation, order parameter, translational diffusion coefficient, or lipid hydration of DPPC in the leaflet without DPPS remain unperturbed by the presence of DPPS in the other leaflet, compared with a DPPC bilayer. On the other hand, in the leaflet containing DPPS, some of the DPPC properties were strongly affected by the presence of DPPS such as the order parameter or electrostatic potential.     

Molecular simulation study of some thermophysical and transport properties of triazolium-based ionic liquids

Results of a molecular dynamics study of several triazolium-based ionic liquids are reported. Triazolium cations include 1,2,4-triazolium, 1,2,3-triazolium, 4-amino-1,2,4-triazolium, and 1-methyl-4-amino-1,2,4-triazolium. Each cation was paired with a nitrate or perchlorate anion. These materials are part of a class of ionic compounds that have been synthesized recently but for which little physical property data are available. Properties of the more common ionic liquid, 1-n-butyl-3-methylimidazolium nitrate, are also computed and compared with the properties of the triazolium-based compounds. A molecular mechanics force field was developed for these materials using a mix of ab initio calculations and parameter fitting using the molecular compound 1H-1,2,4-triazole as a basis for the triazolium cations. Liquid-phase properties that were computed include heat capacities, cohesive energy densities, gravimetric densities/molar volumes as a function of temperature and pressure, self-diffusivities, rotational time constants, and various pair correlation functions. In the solid phase, heat capacities and lattice parameters were computed. Of all of these properties, only lattice parameters have been measured experimentally (and only for four of the triazolium compounds). The agreement with the experimental crystal structures was good. When compared with that of the imidazolium-based ionic liquid, the triazolium-based materials have much smaller molar volumes, higher cohesive energy densities, and larger specific heat capacities. They also tend to be less compressible, have a higher gravimetric density, and have faster rotational dynamics but similar translational dynamics.     

Polymer-nanoparticle interfacial behavior revisited: a molecular dynamics study

By tuning the polymer-filler interaction, filler size and filler loading, we use a coarse-grained model-based molecular dynamics simulation to study the polymer-filler interfacial structural (the orientations at the bond, segment and chain length scales, chain size and conformation), dynamic and stress-strain properties. Simulated results indicate that the interfacial region is composed of partial segments of different polymer chains, which is consistent with the experimental results presented by Chen et al. (Macromolecules, 2010, 43, 1076). Moreover, it is found that the interfacial region is within one single chain size (R(g)) range, irrespective of the polymer-filler interaction and the filler size, beyond which the bulk behavior appears. In the interfacial region, the orientation and dynamic behaviors are induced by the interfacial enthalpy, while the size and conformation of polymer chains near the filler are controlled by the configurational entropy. In the case of strong polymer-filler interaction (equivalent to the hydrogen bond), the innerest adsorbed polymer segments still undergo adsorption-desorption process, the transport of chain mass center in the interfacial region exhibits away from the glassy behavior, and no plastic-like yielding point appears in the stress-strain curve, which indicates that although the mobility of interfacial polymer chains is restricted, there exist no "polymer glassy layers" surrounding the filler. In addition, it is evidenced that the filler particle prefers selectively adsorbing the long polymer chains for attractive polymer-filler interaction, validating the experimental explanation of the change of the bound rubber (BR). In short, this work provides important information for further experimental and simulation studies of polymer-nanoparticle interfacial behavior.     

Comparative study of the effect of tail corrections on surface tension determined by molecular simulation

We report results from a comparative study of the influence of tail corrections on the surface tension of the Lennard-Jones fluid. We find that cutoff-independent surface tensions can be obtained by applying a set of tail corrections recently introduced by Janecek at each step of an interfacial Monte Carlo (MC) or molecular dynamics (MD) simulation. The effect of tail corrections on an alternative methodology for calculating surface tension, the combination of finite-size scaling and grand-canonical transition-matrix Monte Carlo (FSS/GC-TMMC), was also investigated. Using this indirect method, surface tensions were calculated with standard (bulk-fluid) tail corrections and lattice sums, the latter usually considered more accurate but computationally more intensive than the former. With standard tail corrections, we find that the surface tension decreases with increasing cutoff distance, reaching a limiting value corresponding to the maximum cutoff possible, namely half the simulation box length. In contrast, surface tension values obtained with the lattice summation were cutoff-independent. More importantly, these values were equivalent to those surface tension values obtained using standard tail corrections and a cutoff distance of half the box length. We also find that the surface tension values obtained here are in agreement with those found in the literature. Last, we find that surface tension values obtained by MD and FSS/GC-TMMC are in decent agreement so long as the appropriate tail correction schemes are used, and that the relative uncertainties in the surface tensions calculated by MD are generally an order of magnitude greater than those calculated by FSS/GC-TMMC. However, the time required by MD on a single central processing unit is less than that required by FSS/GC-TMMC.     

A molecular dynamics study to determine the solid-liquid interfacial tension using test area simulation method (TASM)

Molecular dynamics (MD) studies on heat transfer from a heated nanoparticle into the surrounding fluid have indicated that the fluid next to a spherical nanoparticle can get heated well above its boiling point without observing a phase change, while a contradicting behavior was observed for a flat surface-fluid interface. Another interesting observation is that the critical heat flux was found to increase with increase in the wetting characteristics of solid. Thus, the interfacial tension or free energy of solid-liquid interface could play a pivotal role in the mechanism of heat transfer. A recent study by Gloor et al. [J. Chem. Phys. 123, 134703 (2005)] has proposed test area simulation method (TASM) for the determination of interfacial tension. The present study involves the determination and the comparison of solid-liquid interfacial tension for planar and spherical interfaces using MD based on TASM and analyze the results. A higher interfacial tension value is observed for spherical nanoparticle fluid interface compared to flat surface fluid interface. The results also indicate that the solid-liquid interfacial tension is a size and temperature dependent property. The results from this study are also expected to give better insights into the possible reasons for the observed differences in the thermal transport for spherical nanoparticle-liquid interface compared to planar-liquid interface.     

Origin of repulsive force and structure/dynamics of interfacial water in OEG-protein interactions: a molecular simulation study

Molecular simulations were performed to investigate the origin of the strong repulsive force acting on a protein as the protein approaches an oligo (ethylene glycol) self-assembled monolayer (OEG-SAM) surface. Since the repulsive force is mainly generated from water molecules, the force from the water molecules near the surface was calculated layer by layer to further identify the molecular origin of the repulsive force. Results show that the strong repulsive force acting on the protein near the OEG-SAM surface is dominantly generated by the interfacial water molecules located between the OEG-SAM surface and lysozyme. A hydroxyl-terminated SAM (OH-SAM) surface was used for comparison. No significant repulsive force was observed from the water molecules between the protein and OH-SAM surface. Further studies show that the dipole distribution of the interfacial water molecules is significantly affected by the OEG-SAM surface, as opposed to the negligible impact from the OH-SAM surface. The interfacial water molecules above the OEG-SAM surface stay longer and reorient more slowly than those above the OH-SAM surface. These results from this work support the hypothesis that the OEG-SAM surface interacts strongly with interfacial water molecules and creates a stable hydration layer that prevents proteins from adsorbing to the surface.