Aggregation of FeCl2 clusters in supercritical water investigated by molecular dynamics simulations

We have carried out molecular dynamics (MD) simulations of the aggregation of FeCl 2 clusters in supercritical water. The particle formation in systems of 2048 water molecules (rigid SPC/E-model) and 120 Fe (2+) ions and 240 Cl (-) ions has been investigated for 250 ps at five different state points at temperatures from 798 to 873 K and system densities from 0.18 g/cm (3) to 0.13 g/cm (3). We describe the particle growth by means of properties of the largest cluster in a system as well as cluster size averaged and time averaged observables. From preexisting or immediately formed units of Fe (2+)-Cl (-), Fe (2+)-Cl (-) 2, Fe (2+)-Cl (-) 3 etc., the further growth of clusters is dominated by aggregation of such small building blocks. Clusters up to 10 ions in size with large charge imbalances are found during the growth process while a balanced positive to negative charge ratio is found on the average with time and cluster size development. Water molecules are found within the FeCl 2 clusters during the whole time interval covered by the simulations, which is in agreement with the existence of crystal water in FeCl 2 crystals grown from aqueous solutions. The radial distribution functions obtained from the simulation data are in good agreement with experimental results of slightly distorted FeCl 2.4H 2O crystals.     

Kinetics of NaCl nucleation in supercritical water investigated by molecular dynamics simulations

At system pressures between 17 MPa and 25 MPa the nucleation and growth of NaCl nanoparticles in water at supercritical conditions was investigated by molecular dynamics simulations at different system temperatures and system densities. Our results show that particle formation takes place within a few hundred picoseconds after the jump from ambient to supercritical conditions. After nucleation a phase of growth by adding monomers is followed by growth via cluster-cluster collisions. We present results on the time development of distributions of cluster sizes, cluster compositions, and cluster temperatures as well as radial distribution functions and nucleation rates.     

Nucleation of NaCl nanoparticles in supercritical water: molecular dynamics simulations

Formation of NaCl nanoparticles in supercritical water is studied using molecular dynamics simulation method. We have simulated particle nucleation and growth in NaCl-H2O fluids, with salt concentration of 5.1 wt %, in the temperature and density range of 673-1073 K and 0.17-0.34 g/cm(3), respectively. The cluster size distributions, the size of critical nuclei and cluster lifetimes are reported. The size distribution of emerging clusters shows a very strong dependence on the system's density, with larger clusters forming at lower densities. Clusters consisting of approximately 14-24 ions appear critical for the thermodynamic states examined. The local structures of critical clusters are found to be amorphous. The lifetime values for clusters containing more than 20 ions are in the range of 10-50 ps. We have calculated the NaCl nucleation rates, which appear to be on the order of 10(28) cm(-3) s(-1).     

The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations

The i‐motif tetrameric structure is built up from two parallel duplexes intercalated in a head‐to‐tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i‐motif structure, one with outermost 3′ extremities and the other with outermost 5′ extremities, called the 3′E and 5′E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3′E and 5′E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3′E topology of the [d(C2)]4 is much more stable than the 5′E topology, and that the former is the only species observed in solution. In order to understand the reason for this atypical behavior, the NMR structure of the [Xd(C2)]4 was determined and analyzed by molecular dynamics simulations. In the NMR structure, the width of the narrow groove is slightly smaller than in previously determined i‐motif structures, which supports the importance of phosphodiester backbone interactions in the structure stability. The simulations show that the stacking of cytosines, essential for the i‐motif stability, is produced by a similar and non‐negative twisting of the phosphodiester backbones. The twisting is induced by an interaction between the backbones; the [Xd(C2)]4 in 5′E topology, exhibiting very limited interaction between the phosphodiester backbones, is thus unstable. Copyright © 2002 John Wiley & Sons, Ltd.     

MPSA effects on copper electrodeposition investigated by molecular dynamics simulations

In superconformal filling of copper-chip interconnects, organic additives are used to fill high-aspect-ratio trenches or vias from the bottom up. In this study we report on the development of intermolecular potentials and use molecular dynamics simulations to provide insight into the molecular function of an organic additive (3-mercaptopropanesulfonic acid or MPSA) important in superconformal electrodeposition. We also investigate how the presence of sodium chloride affects the surface adsorption and surface action of MPSA as well as the charge distribution in the system. We find that NaCl addition decreases the adsorption strength of MPSA at a simulated copper surface and attenuates the copper-ion association with MPSA. The model also was used to simulate induced-charge effects and adsorption on a nonplanar electrode surface.     

Homogeneous nucleation and growth in supersaturated zinc vapor investigated by molecular dynamics simulation

Homogeneous nucleation and growth of zinc from supersaturated vapor are investigated by nonequilibrium molecular dynamics simulations in the temperature range from 400 to 800 K and for a supersaturation ranging from log S=2 to 11. Argon is added to the vapor phase as carrier gas to remove the latent heat from the forming zinc clusters. A new parametrization of the embedded atom method for zinc is employed for the interaction potential model. The simulation data are analyzed with respect to the nucleation rates and the critical cluster sizes by two different methods, namely, the threshold method of Yasuoka and Matsumoto [J. Chem. Phys. 109, 8451 (1998)] and the mean first passage time method for nucleation by Wedekind et al. [J. Chem. Phys. 126, 134103 (2007)]. The nucleation rates obtained by these methods differ approximately by one order of magnitude. Classical nucleation theory fails to describe the simulation data as well as the experimental data. The size of the critical cluster obtained by the mean first passage time method is significantly larger than that obtained from the nucleation theorem.     

Structure of liquid formic acid investigated by first principle and classical molecular dynamics simulations

The structure of liquid formic acid has been investigated by Car-Parrinello and classical molecular dynamics simulations, focusing on the characterization of the H-bond network and on the mutual arrangement of pairs of bonded molecules. In agreement with previous computational studies, two levels of H-bonded structures have been found. Small clusters, characterized by O-H...O bonds, are held together by weak C-H...O bonds to form large branched structures. From the ab initio simulation we infer the importance of cyclic H-bond dimer configurations, typical of the gas phase. Most of these dimer structures are however found to be embedded into H-bonded chains. When only O-H...O bonds are taken into account, linear H-bond chains are detected as basic structures of the liquid. More branched structures occur when C-H...O bonds are also considered. Regarding the arrangement of molecular pairs, we observed that O-H...O bonds favor the occurrence of configurations with parallel molecular planes, whereas no preferential orientation is observed for molecules forming C-H...O bonds.     

Stochastic boundary conditions for molecular dynamics simulations of ST2 water

The deformable stochastic boundary method developed previously for treating simple liquids without periodic boundary conditions, is extended to the ST2 model of water. The method is illustrated by a molecular dynamics simulation of a sphere containing 98 water molecules. Comparison with the results of the periodic boundary simulation by Stillinger and Rahman shows very good agreement for structural and dynamic properties.     

Monte Carlo simulations of critical cluster sizes and nucleation rates of water

We have calculated the critical cluster sizes and homogeneous nucleation rates of water at temperatures and vapor densities corresponding to experiments by Wolk and Strey [J. Phys. Chem B 105, 11683 (2001)]. The calculations have been done with an expanded version of a Monte Carlo method originally developed by Vehkamaki and Ford [J. Chem. Phys. 112, 4193 (2000)]. Their method calculates the statistical growth and decay probabilities of molecular clusters. We have derived a connection between these probabilities and kinetic condensation and evaporation rates, and introduce a new way for the calculation of the work of formation of clusters. Three different interaction potential models of water have been used in the simulations. These include the unpolarizable SPC/E [J. Phys. Chem. 91, 6269 (1987)] and TIP4P [J. Chem. Phys. 79, 926 (1983)] models and a polarizable model by Guillot and Guissani [J. Chem. Phys. 114, 6720 (2001)]. We show that TIP4P produces critical cluster sizes and a temperature and vapor density dependence for the nucleation rate that agree well with the experimental data, although the magnitude of nucleation rate is constantly overestimated by a factor of 2 x 10(4). Guissani and Guillot's model is somewhat less successful, but both the TIP4P and Guillot and Guissani models are able to reproduce a much better experimental temperature dependency of the nucleation rate than the classical nucleation theory. Using SPC/E results in dramatically too small critical clusters and high nucleation rates. The water models give different average binding energies for clusters. We show that stronger binding between cluster molecules suppresses the decay probability of a cluster, while the growth probability is not affected. This explains the differences in results from different water models.     

Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.     

Molecular dynamics simulations of ice nucleation by electric fields

Molecular dynamics simulations are used to investigate heterogeneous ice nucleation in model systems where an electric field acts on water molecules within 10-20 ? of a surface. Two different water models (the six-site and TIP4P/Ice models) are considered, and in both cases, it is shown that a surface field can serve as a very effective ice nucleation catalyst in supercooled water. Ice with a ferroelectric cubic structure nucleates near the surface, and dipole disordered cubic ice grows outward from the surface layer. We examine the influences of temperature and two important field parameters, the field strength and distance from the surface over which it acts, on the ice nucleation process. For the six-site model, the highest temperature where we observe field-induced ice nucleation is 280 K, and for TIP4P/Ice 270 K (note that the estimated normal freezing points of the six-site and TIP4P/Ice models are ～289 and ～270 K, respectively). The minimum electric field strength required to nucleate ice depends a little on how far the field extends from the surface. If it extends 20 ?, then a field strength of 1.5 × 10(9) V/m is effective for both models. If the field extent is 10 ?, then stronger fields are required (2.5 × 10(9) V/m for TIP4P/Ice and 3.5 × 10(9) V/m for the six-site model). Our results demonstrate that fields of realistic strength, that act only over a narrow surface region, can effectively nucleate ice at temperatures not far below the freezing point. This further supports the possibility that local electric fields can be a significant factor influencing heterogeneous ice nucleation in physical situations. We would expect this to be especially relevant for ice nuclei with very rough surfaces where one would expect local fields of varying strength and direction.     

What does zeolitic water look like?: Modelization by molecular dynamics simulations

In this paper, we present Monte Carlo and molecular dynamics simulations of water molecules inside a ferrierite-type framework. Detailed analyses of the energetic, structural, and dynamical properties are carried out and compared with liquid water results in order to study the influence of the framework on the physisorbed water molecules.     

Atomistic insights on the LCST behavior of PMEO2MA in water by molecular dynamics simulations

Fully atomistic molecular dynamics simulations of poly(2‐[2‐methoxyethoxy]ethyl methacrylate) (PMEO₂MA) in water at temperatures below and above its lower critical solution temperature (LCST) were performed to improve the understanding of its LCST behavior. Atomic trajectories were used to calculate various structural and dynamic properties. Simulation results show that PMEO₂MA undergo a distinct coil‐to‐globule transition above LCST. Detailed analyses of the number of first hydration shell water molecules around various atomic regions are revealed that the water solubility of PMEO₂MA below LCST is mainly provided by the hydrophobic hydration around the side chain carbon atoms. This is achieved by the cage‐like water network formations which are disrupted when the temperature is increased above LCST, accompanied by significant amount of water molecule release and local water‐ordering reduction, which leads to the LCST phase transition. Furthermore, other analyses such as the number of hydrogen bonds and hydrogen bond lifetimes suggest that intermolecular hydrogen bondings between polymer and water molecules have little effect on the phase transition. Our results will contribute to a better understanding on the LCST phase transition of oligo(ethylene glycol) methyl ether methacrylate (OEGMA)‐based homopolymers at atomistic level that will be useful when designing homo‐ and co‐polymers of OEGMAs with desired properties. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 429–441     

Void-induced dissolution in molecular dynamics simulations of NaCl and water

To gain a better understanding of the interaction of water and NaCl at the surface during dissolution, we have used molecular dynamics to simulate the interface with two equal-sized slabs of solid NaCl and liquid water in contact. The introduction of voids in the bulk of the salt, as well as steps or pits on the surface of the NaCl slab results in a qualitative change of system structure, as defined by radial distribution functions (RDFs). As an example, the characteristic Na-Na RDF for the system changes from regularly spaced narrow peaks (corresponding to an ordered crystalline structure), to a broad primary and smaller secondary peak (corresponding to a disordered structure). The change is observed at computationally short time scales of 100 ps, in contrast with a much longer time scale of 1 mus expected for complete mixing in the absence of defects. The void fraction (which combines both bulk and surface defects) required to trigger dissolution varies between 15%-20% at 300 K and 1 atm, and has distinct characteristics for the physical breakdown of the crystal lattice. The void fraction required decreases with temperature. Sensitivity studies show a strong dependence of the critical void fraction on the quantity and distribution of voids on the surface, with systems containing a balanced number of surface defects and a rough surface showing a maximum tendency to dissolve. There is a moderate dependence on temperature, with a 5% decrease in required void fraction with a 100 K increase in temperature, and a weak dependence on water potential model used, with the SPC, SPC/E, TIP4P, and RPOL models giving qualitatively identical results. The results were insensitive to the total quantity of water available for dissolution and the duration of the simulation.     

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

Molecular dynamics simulations have been used to investigate the binding of Mg(2+) ions to the deep groove of the eubacterial 5S rRNA loop E. The simulations suggest that long-lived and specific water-mediated interactions established between the hydrated ions and the RNA atoms lining up the binding sites contribute to the stabilization of this motif. The Mg(2+) binding specificity is modulated by two factors: (i) a required electrostatic complementarity and (ii) a structural correspondence between the hydrated ion and its binding pocket that can be estimated by its degree of dehydration and the resulting number and lifetime of the intervening water-mediated contacts. Two distinct binding modes for pentahydrated Mg(2+) ions that result in a significant freezing of the tumbling motions of the ions are described, and mechanistic details related to the stabilization of nucleic acids by divalent ions are provided.     

On combining molecular dynamics and stochastic dynamics simulations to compute reaction rates in liquids

An approach that combines molecular dynamics and stochastic dynamics calculations for obtaining reaction rates in liquids is investigated by studying the cis-->trans isomerization of HONO in liquid krypton. The isomerization rates are computed for several liquid densities by employing full-dimensional molecular-dynamics simulations. The rates are also computed by employing the stochastic dynamics method for a wide range of collision frequencies. Comparisons of the two sets of the computed rates show that for a wide range of liquid densities there is a simple linear relation between the liquid density rho and the collision frequency alpha, that is, alpha=crho. This suggests that once the constant c is determined from a molecular-dynamics calculation at a single density, the reaction rates can be obtained from stochastic dynamics calculations for the entire range of liquid densities where alpha=crho holds. The applicability of the combined molecular dynamics and stochastic dynamics approach provides a practical means for obtaining rate constants at considerable savings of computer time compared to that required by using full-dimensional molecular-dynamics simulations alone.     

Thermodynamic properties of methane/water interface predicted by molecular dynamics simulations

Molecular dynamics simulations have been performed to examine the thermodynamic properties of methane/water interface using two different water models, the TIP4P/2005 and SPC/E, and two sets of combining rules. The density profiles, interfacial tensions, surface excesses, surface pressures, and coexisting densities are calculated over a wide range of pressure conditions. The TIP4P/2005 water model was used, with an optimized combining rule between water and methane fit to the solubility, to provide good predictions of interfacial properties. The use of the infinite dilution approximation to calculate the surface excesses from the interfacial tensions is examined comparing the surface pressures obtained by different approaches. It is shown that both the change of methane solubilities in pressure and position of maximum methane density profile at the interface are independent of pressure up to about 2 MPa. We have also calculated the adsorption enthalpies and entropies to describe the temperature dependency of the adsorption.     

Supramolecular self-assembly of water-soluble cavitands: investigated by molecular dynamics simulation

In this study, we have examined supramolecular self-assembly process of a hydrophobic guest with a water-soluble host known by the trivial name octa acid (OA). Two octa acids form a capsular assembly only in presence of a nonpolar guest(s). Size and shape of the guest control the stoichiometry of the capsular complex. Here, all atom molecular dynamics simulation has been utilized to investigate complex formation mechanisms of a nonpolar guest (nonylbenzene) with two OA cavitands. Nonylbenzene was encapsulated into the nonpolar cavity of OA capsule owing to solvophobic interactions. Upon encapsulation it was twisted and bent due to lack of free space within the capsule. These unusual forms obtained from the simulation study were in accord with experimental findings. The post-complexation attributes of the guest were regulated by the available free space within the OA and favorable non-covalent interactions between the guest and the walls of the OA capsule. In the identical simulation condition two OA cavitands did not form a capsule without a guest, thus indicating requirement of a guest during the self-assembly of OA cavitands.     

Stability and disintegration of ultrathin heptane films in water: molecular dynamics simulations

Molecular dynamics simulations of ultrathin heptane films (less than 5 nm in thickness) in water were conducted to study their stability and disintegration behavior. The density distributions of heptane and water molecules across the film were determined for different equilibrium film thicknesses ranging from 1.5 to 4 nm. The potential energy of the system was computed as a function of the heptane number fraction, and the results were employed to determine the excess energy of mixing of heptane in water. The diffusion coefficients of heptane and water obtained from the MD simulations were also compared with experimental data. A good agreement was found between the heptane self-diffusivity obtained from the MD simulations and its literature reported value. Following an analysis of the equilibrium properties of the heptane films and associated structures, we performed simulations where the shapes of the heptane films were initially perturbed. Different perturbations of these ultrathin films led to formation of various associated structures, including cylindrical rodlike heptane droplets, films with holes, and intact films. The different shapes are formed in systems with the same heptane/water composition. An analysis of this behavior is presented showing the possibility of multiple associated structures with similar total energy in these highly confined systems.