A plastic phase of water from computer simulation

We report a member of ices called plastic or rotator phase, in which individual water molecules make facile rotations as in liquid state but are held tightly in an ordered structure. Molecular dynamics simulations of three classical models of water show that a plastic ice phase appears at a temperature when ice VII is heated or liquid water is cooled at high pressures above several gigapascals. A large amount of latent heat is absorbed when ice VII is transformed to the rotator phase at 590 K and 10 GPa, which is a typical characteristic of the plastic transitions for nearly spherical molecules. In addition to the spontaneous formation of plastic phase in the simulations, its existence is supported by robustness of plastic phase for hypothetical water with varying degrees of Coulombic interactions.     

Stability of Ca-montmorillonite hydrates: a computer simulation study

Classic simulations are used to study interlayer structure, swelling curves, and stability of Ca-montmorillonite hydrates. For this purpose, NP(zz)T and muP(zz)T ensembles are sampled for ground level and given burial conditions. For ground level conditions, a double layer hydrate having 15.0 A of basal spacing is the predominant state for relative vapor pressures (p/p0) ranging 0.6-1.0. A triple hydrate counting on 17.9 A of interlaminar distance was also found stable for p/p0 = 1.0. For low vapor pressures, the system may produce a less hydrated but still double layer state with 13.5 A or even a single layer hydrate with 12.2 A of interlaminar distance. This depends on the established initial conditions. On the other hand, the effect of burial conditions is two sided. It was found that it enhances dehydration for all vapor pressures except for saturation, where swelling is promoted.     

Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

Sodium chloride ion pair interaction in water: computer simulation

The thermodynamics and structure of a sodium chloride ion pair in liquid water are studied as a function of the ion pair separation. Distinct minima in the free energy of the system are found for contact and solvent separated ion geometries.     

The structure of the hydration shell of the ionized HCl molecule in water vapor

The H₃O⁺(H₂O) _n Cl^? clusters were simulated by the Monte Carlo method in a grand canonical ensemble in thermal and material contact with water vapor under the conditions close to the natural conditions in the stratosphere. A detailed model including nonpair polarization and covalent interactions was used. The correlation functions, density distributions, and free energy and entropy as functions of the interionic distance were calculated. The mechanism of ionized HCl state stabilization was determined by the formation of a special structure of the hydrate cluster component with low Gibbs energy and entropy.     

Decoupling effects in computer simulation of liquid-state molecular dynamics

Decoupling effects in liquid-state molecular dynamics are unambiguously proven by computer simulations. These can be discribed as the weakening of the dissipative interaction between the system if interest (e.g. molecular angular valocity) and its thermal bath caused by an intense external field of force. The new phenomenon may be used to confirm or challenge the validity of simple models of the liquids state of molecular matter and provide information on the microscopic time scale.     

Collective effects in diffusional motion of water molecules: computer simulation

Structural Chemistry - Molecular dynamics simulation of the system containing 3,456 water molecules in the cubic periodic box was performed. Virtual temperatures were 261 and 297&;nbsp;K....     

Induced contributions in the rayleigh spectra of water: A molecular dynamics simulation

A molecular dynamics simulation of TIP4P water at T=280 K has been performed to calculate the depolarized and isotropic Raman spectra in the translational and librational region. Comparison of the isotropic spectra with experiment confirms the assignment of the low-frequency scattered light to collision-induced phenomena and allows identification of the spectral contributions arising from polarizability modulation due to short-range interactions.     

The phenomenon of water penetration into sodium octanoate micelles studied by molecular dynamics computer simulation

 In this publication we have studied the penetration process of water molecules into the hydrophobic core of a sodium octanoate micelle. The analysis of this phenomenon was based on a molecular dynamics computer simulation. We calculated the probability to find water molecules within a specific sphere which was adjusted in the center of the micelle. It turned out that the position of the micellar mass and geometry center was not too different, so that this reference point was well characterized. Water penetration was observed within the whole aggregate but if the radius is smaller than 300 pm, polar solvent molecules are very rarely observed. The results of our computer simulations suggest that significant water diffusion into the micelle occurs at larger distances from the micellar center with a lower threshold value of about 400 pm. In addition to these calculations, we used the Connolly algorithm in order to determine the solvent accessible surfaces of different micellar equilibrium structures. We observed large dynamical fluctuations with the formation of pores and channels. These structures are occasionally filled with water molecules. Received: 29 April 1998 Accepted: 27 May 1998     

Molecular orientation of monododecyl pentaethylene glycol at water/air and water/oil interfaces. A molecular dynamics computer simulation study

With a molecular dynamics computer simulation we investigated the dynamic properties of a monododecyl pentaethylene glycol (C₁₂E₅) molecule adsorbed at air/water and oil/water interfaces. In these simulations we investigated the molecular orientation of the surfactant molecules in detail. At the air/water interface the maximum of the C₁₂ chain tilt angle distribution measured with respect to the water surface is about 50°. This result is in fairly good agreement with neutron reflection experiments of monododecyl glycol ethers at the air/water interface. At the oil/water interface no significant changes were detected in the molecular orientation. We found that at equilibrium oil molecules penetrate into the hydrophobic monododecyl layer, this was also found by neutron reflection studies of the interactions between C₁₂E₅ and dodecane. The observed oil penetration results in an increase in the surface area per surfactant molecule. Received: 16 July 1999/Accepted in revised form: 28 August 1999     

Structure and diffusion in amorphous aluminum silicate: a molecular dynamics computer simulation

The amorphous aluminum silicate (Al2O3)2(SiO2) [AS2] is investigated by means of large scale molecular dynamics computer simulations. We consider fully equilibrated melts in the temperature range 6100 K> or =T> or =2300 K as well as glass configurations that were obtained from cooling runs from T=2300 to 300 K with a cooling rate of about 10(12) K/s. Already at temperatures as high as 4000 K, most of the Al and Si atoms are fourfold coordinated by oxygen atoms. Thus, the structure of AS2 is that of a disordered tetrahedral network. The packing of AlO4 tetrahedra is very different from that of SiO4 tetrahedra in that Al is involved with a relatively high probability in small-membered rings and in triclusters in which an O atom is surrounded by four cations. We find as typical configurations two-membered rings with two Al atoms in which the shared O atoms form a tricluster. On larger length scales, the system shows a microphase separation in which the Al-rich network structure percolates through the SiO2 network. The latter structure gives rise to a prepeak in the static structure factor at a wave number q=0.5 A(-1). A comparison of experimental x-ray data with the results from the simulation shows good agreement for the structure function. The diffusion dynamics in AS2 is found to be much faster than in SiO2. We show that the self-diffusion constants for O and Al are very similar and that they are by a factor of 2-3 larger than the one for Si.     

A GRID-derived water network stabilizes molecular dynamics computer simulations of a protease

Structural water molecules are crucial for the stability and function of proteins. Recently, we presented a molecular dynamics (MD) study on blood coagulation factor Xa (fXa) to investigate the effect of water molecules on the flexibility of the protein structure. We showed that neglecting important water positions at the outset of the simulation leads to severe structural distortions during the MD simulations: A stable trajectory was obtained with a water set that was derived from all 73 X-ray structures of the protein. However, for many proteins of interest, only limited structural data is available, which precludes the merging of information from many X-ray structures. Here, we show that an in silico assembled water network, derived from molecular interaction fields generated with the GRID program, is a viable alternative to X-ray data. MD simulations with the GRID water set show a significantly improved stability over alternative setups without water or the X-ray resolved water molecules in the starting structure. The performance is comparable to a water setup derived from a recently presented clustering approach.     

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.     

A Stability Indicating LC Method for Vardenafil HCl

A simple, sensitive gradient RP-LC assay method has been developed for the quantitative determination of vardenafil HCl in bulk drug and in pharmaceutical dosage forms, used to treat erectile dysfunction. The developed method is also applicable for the related substances determination. Efficient chromatographic separation was achieved on a C18 stationary phase with simple mobile phase combination delivered in a gradient mode and quantification was carried out using ultraviolet detection at a flow rate of 1.0 mL min^?1. In the developed LC method the resolution between vardenafil and its four potential impurities was found to be greater than 3.0. Regression analysis shows an r ² value (correlation coefficient) greater than 0.99 for vardenafil and its four impurities. This method was capable of detecting all four impurities of vardenafil at a level of 0.009% with respect to test concentration of 1.0 mg mL^?1 for a 10 μL injection volume. The method has shown good and consistent recoveries for vardenafil (98.4–100.6%) and its four impurities (93.5–106.2%). The test solution was found to be stable in the diluent for 48 h. Mass balance was found close to 99.4%.     

Effects of water vapor on the radiolysis of methane over molecular sieve 5A

Effects of the addition of H₂O on the radiation-induced chemical reaction of methane over molecular sieve 5A at 460°C have been studied by product analysis. Hydrogen, carbon monoxide, carbon dioxide and hydrocarbons consisting mainly of C₂ and C₃ alkanes and alkenes were produced from CH₄ + H₂O mixtures at high conversion levels. The yields of hydrocarbons from 3:1 and 3:2 CH₄ + H₂O mixtures decreased slightly with time but those from 3:4 mixture showed no decrease with time. When the molecular sieve 5A that had been irradiated in flowing methane was reirradiated in the presence of H₂O, carbonaceous solid produced from methane on molecular sieve 5A was readily decomposed to carbon dioxide, carbon monoxide, hydrogen and hydrocarbons, mainly alkanes. Therefore, it is concluded that the suppression of decrease of product yields with time by the addition of H₂O is mainly ascribed to decomposition of the carbonaceous solid by H₂O under electron beam irradiation. The role of added H₂O is also discussed in connection with the conventional methane-steam reforming reaction.     

A computer simulation study of water drying at the interface of protein chains

This study investigated the water drying (cavitation) in the interfacial region of two chains of a dimeric protein by nanosecond molecular dynamics simulations using explicit water representation. Separation-induced cavity of water was directly observed in the region. We evaluated the separation length scale of two chains on which the drying transition occurs, and the average number of water molecules that are expelled from the interfacial region during the transition. The obtained values can be rationalized by Kelvin equation for finite lateral size of confinement [K. Lum and A. Luzar, Phys. Rev. E 56, R6283 (1997)]. Also, we found that the drying transition is accompanied by an exponential reduction in the average hydrogen-bond number per interfacial water molecule. The results of this study may deepen the understanding of how hydrophobic interaction drives the assembly of protein chains.     

Ortho-selectivity in aluminophosphate molecular sieves: A molecular simulation study

Monte Carlo adsorption simulations of xylenes have been performed in aluminophosphate molecular sieve structures. A new force field fitted for o-xylene in AlPO₄-5 was used. It is shown that force fields have good transferability among the aluminophosphate sieves series and the new force field adequately describes the experimentally observed adsorption isotherms for xylene/AlPO₄-5. A previous investigation of adsorption isotherms and structural analysis has been extended to AlPO₄-8 and VPI-5 sieves. In AlPO₄-8, like in AlPO₄-5, the variations in the channels diameters and the corresponding interaction energy of the molecule-crystal lattice drive all molecular positioning. In VPI-5, the modulation between wide and narrow regions becomes negligible due to the larger pore diameter, so no ortho-selectivity was observed. The simulations confirm the ortho-selectivity mechanism proposed to aluminophosphates.     

On the dielectric theory and computer simulation of water

The static dielectric properties of ST2 water are carefully examined by means of a computer-adapted Kirkwood theory. “Experimental” data are provided by various molecular dynamics simulations involving 216. 500 and 1000 water molecules and corresponding to a variety of boundary conditions. It is shown that the integral of the respective modified T tensor plays the central role in matching different boundary conditions. Thus a unique dielectric constant σ = 82 ± 15 is obtained for a density p = 1 g/cm³ and a temperature T = 120°C. Furthermore, it is found that the constitutive relation P = [(σ - 1)/4 – is already fulfilled in a sample of a few hundred molecules. Finally, R-dependent Kirkwood g factors are discussed, which give a vivid picture, how different boundary conditions influence orientational correlations between water dipoles.     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

Free energies of molecular crystal surfaces by computer simulation: application to tetrathiophene

We describe a general simulation protocol for the evaluation of the surface free energies of molecular crystals, which are of broad interest for phenomena such as polymorphism and crystal growth. The method has been applied to selected surfaces of two polymorphs of tetrathiophene. The simulations highlight an important temperature-dependent entropic contribution to the surface free energies, which is not included in widely used static simulations of surface structure and energetics.