A comprehensive molecular dynamics simulation of plastic and liquid succinonitrile: Structural, dynamic, and dielectric properties.

Molecular dynamics simulations at constant temperature and pressure were carried out to investigate the structural, dynamical, and dielectric properties of succinonitrile in its plastic and liquid phases at several thermodynamic states. A six-site united atom model was employed with a force field incorporating an intramolecular torsional term that accurately describes gauche and trans conformers. Analysis of the radial distribution function showed that succinonitrile adopts a body-centered cubic arrangement below its melting point, transitioning to a less ordered state in the liquid phase.

Fingerprints of the Crossing of the Frenkel and Melting Line on the Properties of High-Pressure Supercritical Water.

Using molecular dynamics simulations in combination with the two-phase thermodynamic model, we reveal novel characteristic fingerprints of the crossing of the Frenkel and melting line on the properties of high-pressure water at a near-critical temperature (1.03). The crossing of the Frenkel line at about 1.

On the Different Faces of the Supercritical Phase of Water at a Near-Critical Temperature: Pressure-Induced Structural Transitions Ranging from a Gaslike Fluid to a Plastic Crystal Polymorph.

The present study reports a systematic analysis of a wide variety of structural, thermodynamic, and dynamic properties of supercritical water along the near-critical isotherm of = 1.03 and up to extreme pressures, using molecular dynamics and Monte Carlo simulations. The methodology employed provides solid evidence about the existence of a structural transition from a liquidlike fluid to a compressed, tightly packed liquid, in the density and pressure region around 3.

Structure and dynamics of water plastic crystals from computer simulations.

Water has a rich phase diagram with several crystals, as confirmed by experiments. High-pressure and high-temperature water is of interest for Earth's mantle and exoplanetary investigations. It is in this region of the phase diagram of water that new plastic crystal phases of water have been revealed via computer simulations by both classical forcefields and ab initio calculations.

Effect of the Water Model in Simulations of Protein-Protein Recognition and Association.

We study self-association of ubiquitin and the disordered protein ACTR using the most commonly used water models. We find that dissociation events are found only with TIP4P-EW and TIP4P/2005, while the widely used TIP3P water model produces straightforward aggregation of the molecules due to the absence of dissociation events. We also find that TIP4P/2005 is the only water model that reproduces the fast association/dissociation dynamics of ubiquitin and best identifies its binding surface.

Solvation structure and dynamics of the dimethylammonium cation diluted in liquid water: A molecular dynamics approach.

Classical molecular dynamics simulation techniques were employed to investigate the local solvation structure and related dynamics of the dimethylammonium cation diluted in liquid water at ambient conditions. The translational and orientational order around the dimethylammonium cation was investigated in terms of the corresponding radial and angular distribution functions. The results obtained revealed that the first solvation shell of the dimethylammonium consists mainly of two and, less frequently, three water molecules.

On the microscopic origin of the cryoprotective effect in lysine solutions.

The amino acid lysine has been shown to prevent water crystallization at low temperatures in saturated aqueous solutions [S. Cerveny and J. Swenson, Phys.

The effect of polymorphism on the structural, dynamic and dielectric properties of plastic crystal water: A molecular dynamics simulation perspective.

We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic crystal phases of water. Our results reveal significant differences in the local orientational structure and rotational dynamics of water molecules for the two polymorphs. The probability distributions of trigonal and tetrahedral order parameters exhibit a multi-modal structure, implying the existence of significant local orientational heterogeneities, particularly in the face-centered-cubic phase.

On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility.

Although they are both highly polar liquids, there are a number of compounds, such as many pharmaceuticals, which show vastly different solubilities in methanol compared with water. From theories of the hydrophobic effect, it might be predicted that this enhanced solubility is due to association between drugs and the less polar -CH3 groups on methanol. In this work, detailed analysis on the atomic structural interactions between water, methanol and the small molecule indole - which is a precursor to many drugs and is sparingly soluble in water yet highly soluble in methanol - reveal that indole preferentially interacts with both water and methanol via electrostatic interactions rather than with direction interactions to the -CH3 groups.

The structure of liquid water beyond the first hydration shell.

To date there is a general consensus on the structure of the first coordination shells of liquid water, namely tetrahedral short range order of molecules. In contrast, little is known about the structure at longer distances and the influence of the tetrahedral molecular arrangement of the first shells on the order at these length scales. An expansion of the distance dependent excess entropy is used in this contribution to find out which molecular arrangements are important at each distance range.

Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy.

Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching.

In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces.

Excess protons in mesoscopic water-acetone nanoclusters.

We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules and n = 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase.

Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field.

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials.

Aqueous electrolytes confined within functionalized silica nanopores.

Molecular dynamics simulations have been carried out to investigate structural and dynamical characteristics of NaCl aqueous solutions confined within silica nanopores in contact with a "bulk-like" reservoir. Two types of pores, with diameters intermediate between 20 Å and 37.5 Å, were investigated: The first one corresponded to hydrophobic cavities, in which the prevailing wall-solution interactions were of the Lennard-Jones type.

The polarizable point dipoles method with electrostatic damping: implementation on a model system.

Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method.

Hydrogen bond, electron donor-acceptor dimer, and residence dynamics in supercritical CO(2)-ethanol mixtures and the effect of hydrogen bonding on single reorientational and translational dynamics: A molecular dynamics simulation study.

The hydrogen bonding and dynamics in a supercritical mixture of carbon dioxide with ethanol as a cosolvent (X(ethanol) approximately 0.1) were investigated using molecular dynamics simulation techniques. The results obtained reveal that the hydrogen bonds formed between ethanol molecules are significantly more in comparison with those between ethanol-CO(2) molecules and also exhibit much larger lifetimes.

Effect of the local hydrogen bonding network on the reorientational and translational dynamics in supercritical water.

Molecular dynamics simulations have been performed in a wide range of densities along a near critical isotherm of supercritical water in order to reveal the interconnection between the local hydrogen bonding (HB) network and several related dynamic properties. The results obtained have revealed a significant slowing down of reorientational dynamics of the water molecules as the value of the number of hydrogen bond per molecule increases and this is reflected on the increase in the reorientational correlation times. The calculated reorientational times exhibit also an increasing trend by increasing the bulk density, and this effect is more pronounced in the case of the first-order Legendre reorientational correlation functions.

On Ion and Molecular Polarization of Halides in Water.

The high polarizability of halide anions affects, in aqueous solutions, many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. In this Letter dipolar interactions of halides in water are investigated through Car-Parrinello Molecular Dynamics simulations. Contrary to previous studies, a different polarization of first and second hydration shell water molecules is found.

Local structural effects and related dynamics in supercritical ethanol. 2. Hydrogen-bonding network and its effect on single reorientational dynamics.

The local hydrogen-bonding (HB) network and its possible interconnection with the single reorientational dynamics in pure supercritical (sc) ethanol have been systematically investigated by employing molecular dynamics simulation techniques. The results obtained reveal a nonlinear density dependence of the calculated average number of hydrogen bonds n(HB), similar to that of the calculated coordination numbers N(c), signifying also the interrelation between the local HB network and the local density augmentation in sc ethanol. Additionally, the HB dynamics were investigated in terms of several appropriate time correlation functions.

Local structural effects and related dynamics in supercritical ethanol. 1. Mechanisms of local density reorganization and residence dynamics.

The length scale effects on the relaxation processes describing the local density reorganization and residence dynamics of pure supercritical ethanol have been systematically investigated by employing molecular dynamics simulation techniques. The calculated static local density augmentation and enhancement values of ethanol have been found to be comparable to those of methanol at similar conditions but significantly lower than those of the strong associating fluid water, indicating thus the effect of hydrogen-bonding interactions on the creation of local density inhomogeneities in supercritical fluids. The bulk density dependence of local density reorganization dynamics has been studied as a function of the shell cutoff radius, revealing a significant change at length scales higher than the position of the first maximum of the radial pair distribution function.

Exploring the picosecond time domain of the solvation dynamics of coumarin 153 within beta-cyclodextrins.

We report molecular dynamics simulation results of equilibrium and dynamical characteristics pertaining to the solvation of the dye coumarin 153 (C153) trapped within hydrophobic cavities of di- and trimethylated beta-cyclodextrins (CD) in aqueous solutions. We found that stable configurations of the encapsulated probe are characterized by a slanted docking, in which the plane of the C153 lies mostly parallel to one of the glucose units of the CD. "In and out" dynamical modes of the encapsulated probe present very small amplitudes.

Protons in non-ionic aqueous reverse micelles.

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules.

Hydrogen bond structure and dynamics in aqueous electrolytes at ambient and supercritical conditions.

Hydrogen bond (HB) connectivity in aqueous electrolyte solutions at ambient and supercritical conditions has been investigated by molecular dynamics techniques. Alkali metal and halides with different sizes have been considered. Modifications in the water HB architecture are more noticeable in the first ionic solvation shells and do not persist beyond the second shells.

Protons in supercritical water: a multistate empirical valence bond study.

Molecular dynamics simulations have been performed to analyze microscopic details related to aqueous solvation of excess protons along the supercritical T = 673 K isotherm, spanning a density interval from a typical liquid down to vapor environments. The simulation methodology relies on a multistate empirical valence bond Hamiltonian model that includes a proton translocation mechanism. Our results predict a gradual stabilization of the solvated Eigen cation [H(3)O.