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 (1.03Tc). The crossing of the Frenkel line at about 1.17 GPa is characterized by a crossover in the rotational and translational entropy ratio Srot/Strans, indicating a change in the coupling between translational and rotational motions which is also reflected in the shape of the rotational density of states. The observed isosbestic points in the translational and rotational density of states are also blue-shifted at density and pressure conditions higher than the ones corresponding to the Frenkel line. The first-order phase transition from a rigid liquid to a face-centered cubic plastic crystal phase at about 8.5 GPa is reflected in the discontinuous changes in the translational and rotational entropy, particularly in the significant increase of the ratio Srot/Strans. A noticeable discontinuous increase of the dielectric constant has also been revealed when crossing this melting line, which is attributed to the different arrangement of the water molecules in the plastic crystal phase. The reorientational dynamics in the plastic crystal phase is faster in comparison with the "rigid" liquid-like phase, but it remains unchanged upon a further pressure increase in the range of 8.5-11 GPa.

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 T = 1.03Tc 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 3.4ρc and 1.17 GPa, introducing an alternative approach to locate the crossing of the Frenkel line. Around 8.5 GPa another transition to a face-centered-cubic plastic crystal polymorph with density 5.178ρc is also observed, further confirmed by Gibbs free energy calculations using the two-phase thermodynamic model. The isobaric heat capacity maximum, closely related to the crossing of the Widom line, has also been observed around 0.8ρc, where the local density augmentation is also maximized. Another structural transition has been observed at 0.2ρc, related to the transformation of the fluid to a dilute gas at lower densities. These findings indicate that a near-critical isotherm can be divided into different domains where supercritical water exhibits distinct behavior, ranging from a gaslike one to a plastic crystal one.

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. However, these plastic phases still remain elusive in experiments. Here, we present a complete characterization of the structure, dynamics, and thermodynamics of the computational plastic crystal phases of water using molecular dynamics and the two-phase thermodynamic method and uncover the interplay between them. The relaxation times of different reorientational correlation functions are obtained for the hypothetical body-centered-cubic and face-centered-cubic plastic crystal phases of water at T = 440 K and P = 8 GPa. Results are compared to a high pressure liquid and ice VII phases to improve the understanding of the plastic crystal phases. Entropy results indicate that the fcc crystal is more stable compared to the bcc structure under the studied conditions.

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. Our results show the critical role of the water model in the description of protein-protein interactions and binding.

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. The two nearest water neighbors form hydrogen bonds with the ammonium hydrogen atoms of the cation, whereas the third neighbor interacts with the methyl hydrogen atoms as well. The distribution of the trigonal order parameter exhibits a bimodal behavior, signifying the existence of local orientational heterogeneities in the solvation shell of the dimethylammonium cation. The calculated continuous and intermittent residence and hydrogen bond lifetimes for the cation-water pairs have also been found to be longer in comparison with the water-water ones. The very similar self-diffusion coefficients of the dimethylammonium cation and the water molecules in the bulk dilute solution indicate that the translational motions of the cation are mainly controlled by the translational mobility of the surrounding 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. Chem. Chem. Phys., 2014, 16, 22382-22390]. Here, we investigate two ratios of water and lysine (5.4 water molecules per lysine (saturated) and 11 water molecules per lysine) by means of the complementary use of computer simulations and neutron diffraction. By performing a detailed structural analysis we have been able to explain the anti-freeze properties of lysine by the strong hydrogen bond interactions of interstitial water molecules with lysine that prevent them from forming crystalline seeds. Additional water molecules beyond the 1 : 5.4 proportion are no longer tightly bonded to lysine and therefore are free to form crystals.

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. The calculated hydrogen bond statistics and dynamics provide further indications of the existence of a strongly heterogeneous and rapidly interconverting local orientational structural network in both polymorphs. We have observed a hindered molecular rotation, much more pronounced in the body-centered-cubic phase, which is reflected by the decay of the fourth-order Legendre reorientational correlation functions and angular Van Hove functions. Molecular rotation, however, is additionally hindered in the high-pressure liquid compared to the plastic crystal phase. The results obtained also reveal significant differences in the dielectric properties of the polymorphs due to the different dipolar orientational correlation characterizing each 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 presence of methanol hydrogen bonds with π electrons of the benzene ring of indole can explain the increase in solubility of indole in methanol relative to water. In addition, the excess entropy calculations performed here suggest that this solvation is enthalpically rather than entropically driven.

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. This was done by splitting the excess entropy into two parts: one connected to the relative position of two molecules and the other one related to their relative orientation. A transition between two previously unknown regimes in liquid water is identified at a distance of about ∼6 Å: from a predominantly orientational order at shorter distances to a regime at larger distances of up to ∼9 Å where the order is predominantly positional and molecules are distributed with the same tetrahedral symmetry as the very first molecules.

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. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

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. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r(-6) term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.

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. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ~ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain.

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. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules.

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. In addition, we also examined the behavior of solutions trapped within hydrophilic cavities, in which a set of unsaturated O-sites at the wall were transformed in polar silanol Si-OH groups. In all cases, the overall concentrations of the trapped electrolytes exhibited important reductions that, in the case of the narrowest pores, attained 50% of the bulk value. Local concentrations within the pores also showed important fluctuations. In hydrophobic cavities, the close vicinity of the pore wall was coated exclusively by the solvent, whereas in hydrophilic pores, selective adsorption of Na(+) ions was also observed. Mass and charge transport were also investigated. Individual diffusion coefficients did not present large modifications from what is perceived in the bulk; contrasting, the electrical conductivity exhibited important reductions. The qualitative differences are rationalized in terms of simple geometrical considerations.

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. We also show how to reduce the computational overhead for evaluating the dipoles, introducing to the state-of-the-art methods: the extended Lagrangian method and the always stable predictor corrector method. Finally we discuss the importance of screening the electrostatic interactions at short range, defending this technique against simpler approximations usually made. We compare results of density functional theory and classical force field-based Molecular Dynamics simulations of chloride in water.

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. Furthermore, the residence dynamics in the solvation shells of ethanol and CO(2) have been calculated, revealing much larger residence times for ethanol molecules in the ethanol solvation shell. These results support strongly the ethanol aggregation effects and the slow local environment reorganization inside the ethanol solvation shell, reported in a previous publication of the authors [Skarmoutsos et al., J. Chem. Phys. 126, 224503 (2007)]. The formation of electron donor-acceptor dimers between the ethanol and CO(2) molecules has been also investigated and the calculated lifetimes of these complexes have been found to be similar to those corresponding to ethanol-CO(2) hydrogen bonds, exhibiting a slightly higher intermittent lifetime. However, the average number of these dimers is larger than the number of ethanol-CO(2) hydrogen bonds in the system. Finally, the effect of the hydrogen bonds formed between the individual ethanol molecules on their reorientational and translational dynamics has been carefully explored showing that the characteristic hydrogen bonding microstructure obtained exhibits sufficiently strong influence upon the behavior of them.

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. A clear nonlinear dependence of the librational mode frequencies of the water molecules on the augmented local density around them has also been revealed. This result could be regarded as an additional support of experimental observations suggesting the use of a nonlinear relation when analyzing the density dependence of spectroscopic peak frequencies in order to extract information about local density augmentation in supercritical fluids. The HB dynamics have been also investigated, revealing a plateau in the calculated HB lifetimes at intermediate and higher liquidlike densities and a small increase at low, gaslike densities.

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. The results obtained reveal that the density dependence of HB dynamics has some similarities with local density and residence dynamics, corresponding to very short length scales. Moreover, the effect of mutual reorientation on HB dynamics seems to be more important than that of mutual diffusion. Finally, the reorientational dynamics of several intramolecular vectors of ethanol have been systematically studied. From the results obtained, we may observe that the dynamics of several reorientational modes in the molecule exhibit significant differences between them. Furthermore, the effect of the HB state of each molecule on these dynamics has also been studied, revealing significant differences, especially in the case of the dynamics of HB free molecules.

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. At length scales higher than this cutoff, the local density inhomogeneities affect more significantly the reorganization of the local environment and this becomes even more apparent at length scales corresponding to the second solvation shell radius. Additionally, the residence dynamics for the region extending up to the first solvation shell of ethanol was investigated, and the results obtained reveal that the density dependence of local density dynamics exhibit differences in correspondence to local density dynamics, something which becomes also apparent at length scales higher than the position of the first peak of the radial pair distribution function.

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. The analysis hints that existing classical polarizable force fields lack a description of short-range interactions which causes an overestimation of polarization effects.