Molecular dynamics simulation of liquid water: hybrid density functionals

The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Molecular dynamics simulations of the surface tension of ionic liquids

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law.     

Molecular dynamics simulation of cellobiose in water

The conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

Molecular dynamics study of the surface tension of a binary immiscible fluid

The planar interface between two liquids having two degrees of affinity to mix has been studied by molecular dynamics simulations. The surface tension is calculated from the normal, PN, and transverse, PT, components of the pressure tensor P for a wide range of temperatures. An unusual increase in surface tension with increasing temperature is attributed to a pressure induced void transfer mechanism that is justified by basic thermodynamic arguments. This effect is diminished on the addition of a modest attractive potential between the two species, and there is a turnover point at higher temperatures beyond which the surface tension decreases with increasing temperature. An order parameter is identified as the gradient of the mole fraction distribution through the interfacial region. An additional effect is the dramatic inversion of the kinetic and potential contributions to the PN profile as the temperature is varied. It is found that a commonly used approximation for P, the Irving-Kirkwood 1 or IK1 method, results in a relatively modest unphysical variability in PN that weakly violates the condition of local mechanical stability. However, this artifact does not prevent the IK1 method from producing an interfacial tension which is nearly identical to that derived from the complete IK formula with no additional approximations.     

Changes in density and surface tension of water in silica pores

 The density and surface tension of water in small pores of silicas have been investigated. These physical properties of water in the pores were calculated from a comparison of pore volumes and pore radii which were estimated from adsorption and desorption isotherms of nitrogen and water. Below a pore radius of about 5 nm both the density and the surface tension of water in the pores were smaller than those of the bulk liquid and decreased with a decrease in pore size. The density of water in the pores decreased with an increase in the concentration of surface hydroxyl groups. Similarly the surface tension of water in the pores is influenced by the surface hydroxyl groups. Anomalous changes in the density and surface tension of the water in the pores are attributed to the interaction of water molecules with surface hydroxyl groups and hydrogen-bond formation among water molecules. Received: 20 April 1999 Accepted in revised form: 17 November 1999     

Molecular dynamics simulation of the free surface of liquid formamide

Molecular dynamics simulations of liquid formamide (HCONH₂) were carried out using the GROMOS software. The formamide molecule is represented by all of its atoms with all internal degrees of freedom. In contrast to other simulations dealing with bulk properties, this study focuses on the interface liquid–vacuum for the first time. We show that the molecular plane is tilted out of the surface, exposing the HCO group to the vacuum. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63 : 1123–1131, 1997     

Molecular dynamics simulation of water in a contact with an iron pyrite FeS2 surface

A strong adsorption of the water molecules to the pyrite surface is shown by a molecular dynamic simulation of the water-iron pyrite FeS2 interface. Water molecules closest to the pyrite surface are bound by an electrostatic interaction to the iron atoms in grooves running parallel to one of the crystal axes. The grooves are about two atoms wide and are directed along 010 for the (001) surface. The position of the water-surface potential minimum and the energy of adsorption were determined by optimization for a single water molecule at the interface. At room temperature and normal density there are altogether three distinguishable layers of water above the surface. One is associated with the groove: one with H bonding to the sulphur atoms comprising the ridges separating the grooves, and the third with the soft wall boundary between the absorbed water layers and bulk region of water. Simulations were also used to explore the effect of a temperature range significant for geophysical studies.     

Molecular dynamics simulation of a water/metal interface

First results of a molecular dynamics study of a water/metal interface, lasting 3.3 ps at an average temperature of 294 K, are reported. The basic periodic box contains 216 water molecules and a crystal slab of 550 platinum atoms with (100) surface planes. A combination of a Lennard-Jones potential between centers of mass and a Coulomb potential arising from dielectric interactions of the water charge distribution with the metal is employed for the water-wall interaction, the ST2 model for the water-water, and a nearest-neighbour harmonic potential for the platinum-platinum interactions. Considerable adsorption at the interface together with a drastic change of the water structure is observed.     

Molecular dynamics simulation of liquid water between two walls

A molecular dynamics simulation, lasting ≈25 ps, has been performed with 150 ST2 water molecules between two quasi-hard repulsive walls, at a temperature of 302 K. A number of static and dynamic properties have been computed as a function of the distance from the walls, showing that water near the walls is in general more “ordered” than in the bulk, and that this bulk water behaves like ordinarv liquid ST2 water.     

Molecular dynamics simulation of the association of nonpolar spheres in water

We apply molecular dynamics (MD) simulations to the study of the association of nonpolar spheres of effective radii between 1.6 and 6.1 A dissolved in water. The constrained MD method is used to calculate the potential of mean force (PMF) of the interaction between spheres. The depth of the potential of mean force increases with increasing radius of the nonpolar sphere. Our results suggest that the PMF is largely governed by size or entropic effects, and that energetic effects associated with the breaking or distortion of hydrogen bonds are of minor importance.     

Structure and dynamics of water at a clay surface from molecular dynamics simulation

We report a molecular dynamics study of the structure and dynamics of water at a clay surface. The negative charge of the surface and the presence of surface oxygen atoms perturbs water over two to three molecular layers, while the nature of the counterions (Na(+)or Cs(+)) has only a small effect. In the first molecular layer, approximately half of the water molecules are H-bonded to the surface. We also analyze the H-bond network between surface water molecules. The diffusion of water molecules along the surface is slowed down compared to the bulk case. As far as the orientational order and dynamics of the water dipole are concerned, only the component normal to the clay surface is perturbed. We investigate the surface H-bond formation and dissociation dynamics and their coupling to the release of molecules from the first molecular layer. We introduce a simple kinetic model in the spirit of Luzar and Chandler [Nature, 1996, 379, 55] to allow for a comparison with bulk water dynamics. This model semi-quantitatively reproduces the molecular simulation results and suggests that H-bond formation is faster with the surface than in the bulk, while H-bond dissociation is slower.     

Molecular dynamics simulation on the interaction between polymer inhibitors and anhydrite surface

Investigation on the microscopic interaction between polymer inhibitors and calcium sulfate will be helpful for understanding its scale inhibition mechanism and can provide a theoretical guidance to developing new scale inhibitors. In this work, molecular dynamics simulations with COMPASS force field have been performed to simulate the interaction between hydrolyzed polymaleic anhydride (HPMA), polyaspartic acid (PASP), polyepoxysuccinic acid (PESA), polyacrylic acid (PAA) and the (001) and (020) surfaces of anhydrite (AD) crystal with and without water. The results show that the sequence of binding energies between four polymer inhibitors and AD (001) and (020) with water is PESA > PASP > HPMA > PAA. The binding energy of the same polymer inhibitor on AD (001) is smaller than that on AD (020). Water molecules weaken the deformations of HPMA and PAA but aggravate those of PASP and PESA. Natural bond orbital (NBO) charges of the repeat units of polymer inhibitors were calculated by B3LYP/6‐31G* method. The Coulomb interaction is formed between the O atoms of polymer inhibitors and the Ca atoms of AD crystal. The system of polymer–AD is mainly contributed from the non‐bonding interaction. Polymer inhibitors do not interact directly with AD crystal, but indirectly through the interactions between inhibitor–H₂O and H₂O–AD, i.e. water molecules participate in scale inhibition of polymer inhibitors to AD crystal. Water molecules cannot be ignored when the interaction models are constructed, i.e. solvent effect cannot be ignored. Copyright © 2015 John Wiley & Sons, Ltd.     

Molecular dynamics simulation of the renin inhibitor H142 in water

Summary H142 is a synthetic decapeptide designed to inhibit renin, an enzyme acting in the regulation of blood pressure. The inhibiting effect of H142 is caused by a reduction of a-Leu-Val-peptide bond (i. e. C(=O)-NHCH₂-NH). The conformational and dynamical properties of H142 and its unreduced counterpart (H142n) was modelled by means of molecular dynamics simulations. Water was either included explicitly in the simulations or as a dielectric continuum. When water molecules surround the peptides, they remain in a more or less extended conformation through the simulation. If water is replaced by a dielectric continuum, the peptides undergo a conformational change from an extended to a folded state. It is not clear whether this difference is a consequence of a too short simulation time for the water simulations, a force-field artifact promoting extended conformations, or if the extended conformation represents the true conformational state of the peptide. A number of dynamic properties were evaluated as well, such as overall rotation, translational diffusion, side-chain dynamics and hydrogen bonding.     

Molecular dynamics simulation of the PEO sulfonic acid anion in water

Atomistic molecular modeling has been used to study the sulfonic acid anion of poly(ethylene oxide) (PEO sulfonic acid anion) in vacuum and a polymer electrolyte system consisting of the PEO sulfonic acid anion in water. The vibrational spectra of the molecules were simulated by the local mode method and found to be in good agreement with the experimental IR and Raman spectra. The structure of PEO sulfonic acid anion was studied in vacuum and water and compared to the structure of an isolated PEO sulfonic acid in vacuum. The simulated value for the root mean square end-to-end distance for the PEO sulfonic acid anion was 22 Å in vacuum and 12 Å in water. The root mean square radius of gyration of the PEO sulfonic acid anion was 8.4 Å in vacuum and 5.6 Å in water. The PEO sulfonic acid anion was randomly coiled in water and in an extended shape in vacuum.     

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.     

Surface tension and density of binary mixtures of monoalcohols,water and acetonitrile: equation of correlation of the surface tension

Measurements of the surface tension (σ) and density (ρ) of binary mixtures of monoalcohols, water and acetonitrile at 298.15 K and at atmospheric pressure, as a function of mole fraction (x) have been made. The experimental values of the deviation of surface tension and the excess of molar volume (Δσ, V ^E) have been correlated by the Redlich–Kister equation. An empirical correlation equation is presented for the study of the surface tension of these mixtures, and comparisons are made of the experimental values of surface tension versus those obtained with the correlation equation and with other models of correlation. Finally, with the purpose of corroborating the validity of the correlation equation, the latter is applied to other reference binary mixtures.