A novel approach for designing simple point charge models for liquid water with three interaction sites

A simultaneous improvement of the diffusion and dielectric properties of the simple point charge (SPC) model for liquid water appears to be very difficult with conventional reparametrization of the commonly used Lennard-Jones and Coulomb interaction functions and without including a self-energy correction in the effective pair-potential as is done in the SPC/E model. Here, a different approach to circumvent this problem is presented. A short-range interaction term, which corrects the oxygen-oxygen energy at small distances by small amounts of energy, was introduced in the nonbonded interaction function. This additional force-field term allows to derive new parameter sets for SPC-like water models that yield better agreement with experimental data on liquid water. Based on previous investigations of the force-field parameter dependence of the water properties of SPC-like models, the necessary parameter changes to obtain a lower diffusion coefficient and a larger dielectric permittivity were specified and accordingly six new models were developed. They all represent an improvement over SPC in terms of structural and diffusional properties, four of them show better dielectric properties also. One model, SPC/S, has been characterized in more detail, and represents most properties of liquid water better than SPC while avoiding the larger discrepancies with experimental values regarding density, thermal compressibility, energy, and free energy of the SPC/E model. We conclude that the use of a simple, short-ranged additional oxygen-oxygen interaction term makes a simultaneous improvement of the diffusion coefficient and the dielectric properties of water feasible.     

Molecular dynamics simulation study of interaction between model rough hydrophobic surfaces

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work, we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes: it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions, we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in the case of the charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo as the two plates are brought together.     

Solution of three-dimensional reference interaction site model and hypernetted chain equations for simple point charge water by modified method of direct inversion in iterative subspace

We proposed a modified procedure of the direct inversion in the iterative subspace (DIIS) method to accelerate convergence in the integral equation theory of liquids. We update the DIIS basis vectors at each iterative step by using the approximate residual obtained in the DIIS extrapolation. The procedure is tested by solving the 3-dimensional (3-D) generalization of the reference interaction site model equation together with the hypernetted chain closure, as well as their 1-D version. We calculated the 3-D site distribution of water, represented by the simple point charge model, around one water molecule considered as a central particle. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 928–936, 1999     

Solubility of ethane int-butanol + water mixtures and a hydrophobic interaction study

The solubilities of ethane int-butanol (TBA) and water mixtures have been determined at 10, 15, and 20°C and pressures up to 3.1 MPa. Thermodynamic properties have also been calculated based on the measured solubility data and the hydrophobic interaction for the methane-methane pair interaction in the mixed solvent is discussed.     

Comparison of rigid and flexible simple point charge water models at supercritical conditions

This study investigates the differences between the predictions of various properties of rigid and flexible simple point charge water models at supercritical conditions. Molecular dynamics simulations were conducted for supercritical water in a temperature range of 773–1073 K and densities in the range 115–659 kg/m³. We present thermodynamic data, pair correlation functions, self-diffusivity, power spectra, dielectric constants, and variaous measures of hydrogen bonding at different state conditions. The flexible water model performs better in predicting the pressures along the supercritical isotherms simulated. Agreement between experimental and calculated dielectric constants is superior for the flexible water model, particularly at high densities. The flexible model exhibits a greater degree of hydrogen bonding and more persistent hydrogen bonds than does the rigid model. The structural features of supercritical water at high densities are identical for the two water models. At low densities, however, the flexible potential exhibits pair correlation functions with enhanced peaks. Inclusion of flexibility in the potential model does not result in a significant shift in the position of the rotational/librational peak in the power spectrum. The self-diffusivities obtained from the simulations are within the accuracy of the experimental values for both the rigid and flexible models. On balance the inclusion of flexibility improves agreement with the properties of real supercritical water while incurring little or no additional computational burden. © 1996 by John Wiley & Sons, Inc.     

Water's hydrogen bonds in the hydrophobic effect: a simple model

We propose a simple analytical model to account for water's hydrogen bonds in the hydrophobic effect. It is based on computing a mean-field partition function for a water molecule in the first solvation shell around a solute molecule. The model treats the orientational restrictions from hydrogen bonding, and utilizes quantities that can be obtained from bulk water simulations. We illustrate the principles in a 2-dimensional Mercedes-Benz-like model. Our model gives good predictions for the heat capacity of hydrophobic solvation, reproduces the solvation energies and entropies at different temperatures with only one fitting parameter, and accounts for the solute size dependence of the hydrophobic effect. Our model supports the view that water's hydrogen bonding propensity determines the temperature dependence of the hydrophobic effect. It explains the puzzling experimental observation that dissolving a nonpolar solute in hot water has positive entropy.     

Theoretical study of the gas-phase interaction between a chloride ion and a solvent molecule

Ten different ion clusters, ⁻(RH), are investigated by means of SCF and Cl computations in a double-zeta plus polarization basis set. For RH = H₂O, CH₃OH and other compounds with a hydroxy group, Cl⁻ is located along the line somewhat deviated from the extension of the OH bond. This bridge-type structure comes from the electrostatic bonding force plus the minor covalent nature of the OH. Cl⁻ bond. The standard OH...Cl− distance is obtained to be 2.2–2.4 A. The calculated stabilization energies are found to be in reasonable agreement with the available gas-phase experimental values of ΔH⁰ except for Cl⁻(HCOOH).     

Computer simulation study of water using a fluctuating charge model

Hydrogen bonding in small water clusters is studied through computer simulation methods using a sophisticated, empirical model of interaction developed by Ricket al (S W Rick, S J Stuart and B J Berne 1994J. Chem. Phys. 101 6141) and others. The model allows for the charges on the interacting sites to fluctuate as a function of time, depending on their local environment. The charge flow is driven by the difference in the electronegativity of the atoms within the water molecule, thus effectively mimicking the effects of polarization of the charge density. The potential model is thus transferable across all phases of water. Using this model, we have obtained the minimum energy structures of water clusters up to a size often. The cluster structures agree well with experimental data. In addition, we are able to distinctly identify the hydrogens that form hydrogen bonds based on their charges alone, a feature that is not possible in simulations using fixed charge models. We have also studied the structure of liquid water at ambient conditions using this fluctuating charge model.     

Mode coupling behavior of a Lennard-Jones binary mixture: a comparison between bulk and confined phases

We present a quantitative comparison at equivalent thermodynamical conditions of bulk and confined dynamical properties of a Lennard-Jones binary mixture upon supercooling. Both systems had been previously found to display a behavior in agreement with the mode coupling theory of the evolution of glassy dynamics. Differences and analogies of behavior are discussed focusing, in particular, on the role of hopping in reducing spatially correlated dynamics in the confined system with respect to the bulk.     

Nanobubbles at the interface between water and a hydrophobic solid

A very thin layer (5-80 nm) of gas phase, consisting of discrete bubbles with only about 40 000 molecules, is quite stable at the interface between a hydrophobic solid and water. We prepare this gas phase from either ambient air or from CO(2)(g) through a solvent exchange method reported previously. In this work, we examine the interface using attenuated total internal reflection infrared spectroscopy. The presence of rotational fine structure in the spectrum of CO(2) and D(2)O proves that molecules are present in the gas phase at the interface. The air bubbles are stable for more than 4 days, whereas the CO(2) bubbles are only stable for 1-2 h. We determine the average gas pressure inside the CO(2) bubbles from the IR spectrum in two ways: from the width of the rotational fine structure (P(gas) < 2 atm) and from the intensity in the IR spectrum (P(gas) = 1.1 +/- 0.4 atm). The small difference in gas pressure between the bubbles and the ambient (1 atm) is consistent with the long lifetime. The dimensions and curvature of a set of individual bubbles was determined by atomic force microscopy. The pressures of individual bubbles calculated from the measured curvature using the Laplace equation fall into the range P(gas) = 1.0-1.7 atm, which is concordant with the average pressure measured from the IR spectrum. We believe that the difference in stability of the CO(2) bubbles and the air bubbles is due to a combination of the much lower pressure of CO(2) in the atmosphere and the greater solubility of CO(2) in water, compared to N(2) and O(2). As expected, smaller bubbles have a shorter average lifetime than larger bubbles, and the average pressure and the curvature of individual bubbles decreases with time. Surface plasmon resonance measurements provide supporting evidence that the film is in the gas state: the thin film has a lower refractive index than water, and there are few common contaminants that satisfy this condition. Interfacial gas bubbles are not ubiquitous on hydrophobic solids: bubble-free and bubble-decorated hydrophobic interfaces can be routinely prepared.     

The orientation and charge of water at the hydrophobic oil droplet-water interface

We established the charge and structure of the oil/water interface by combining ζ-potential measurements, sum frequency scattering (SFS) and molecular dynamics simulations. The SFS experiments show that the orientation of water molecules can be followed on the oil droplet/water interface. The average water orientation on a neat oil droplet/water interface is the same as the water orientation on a negatively charged interface. pH dependent experiments show, however, that there is no sign of selective adsorption of hydroxide ions. Molecular dynamics simulations, both with and without intermolecular charge transfer, show that the balance of accepting and donating hydrogen bonds is broken in the interfacial layer, leading to surface charging. This can account for the negative surface charge that is found in experiments.     

高岭石与水分子相互作用的理论研究

为从微观角度深入探讨单个水分子与高岭石最易解理晶面不同暴露末端的作用特点,本工作通过密度泛函理论的计算方法对不同吸附形态的水分子与不同暴露末端的稳定作用构型进行几何结构与电子结构分析.吸附能的计算结果表明水分子在铝氧八面体羟基作为暴露末端的表面上最稳定的吸附方式为水分子的氧原子和氢原子分别与相邻两个羟基的氢原子和氧原子...     

Free energy simulations: Applications to the study of liquid water,hydrophobic interactions and solvent effects on conformational stability

Free energy simulations using the Metropolis Monte Carlo method and the coupling parameter approach with umbrella sampling are described for several problems of interest in structural biochemistry: the liquid water, the hydrophobic interaction of alkyl and phenyl groups in water, and solvent effects on the conformational stability of the alanine dipeptide and the dimethyl phosphate anion in water. Proximity analysis of the results is employed to identify stabilizing factors. Implications of the result with respect to the structural chemistry of proteins and nucleic acids is considered.     

Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects

A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces.     

Beyond the Lennard-Jones model: a simple and accurate potential function probed by high resolution scattering data useful for molecular dynamics simulations

Scattering data, measured for rare gas-rare gas systems under high angular and energy resolution conditions, have been used to probe the reliability of a recently proposed interaction potential function, which involves only one additional parameter with respect to the venerable Lennard-Jones (LJ) model and is hence called Improved Lennard-Jones (ILJ). The ILJ potential eliminates most of the inadequacies at short- and long-range of the LJ model. Further reliability tests have been performed by comparing calculated vibrational spacings with experimental values and calculated interaction energies at short-range with those obtained from the inversion of gaseous transport properties. The analysis, extended also to systems involving ions, suggests that the ILJ potential model can be used to estimate the behavior of unknown systems and can help to assess the different role of the leading interaction components. Moreover, due to its simple formulation, the physically reliable ILJ model appears to be particularly useful for molecular dynamics simulations of both neutral and ionic systems.     

Conformation of a flexible chain in explicit solvent: exact solvation potentials for short Lennard-Jones chains

The average conformation of a flexible chain molecule in solution is coupled to the local solvent structure. In a dense solvent, local chain structure often mirrors the pure solvent structure, whereas, in a dilute solvent, the chain can strongly perturb the solvent structure which, in turn, can lead to either chain expansion or compression. Here we use Monte Carlo (MC) simulation to study such solvent effects for a short Lennard-Lones (LJ) chain in monomeric LJ solvent. For an n-site chain molecule in solution these many-body solvent effects can be formally mapped to an n-body solvation potential. We have previously shown that for hard-sphere and square-well chain-in-solvent systems this n-body potential can be decomposed into a set of two-body potentials. Here, we show that this decomposition is also valid for the LJ system. Starting from high precision MC results for the n = 5 LJ chain-in-solvent system, we use a Boltzmann inversion technique to compute numerically exact sets of two-body solvation potentials which map the many-body chain-in-solvent problem to a few-body single-chain problem. We have carried out this mapping across the full solvent phase diagram including the dilute vapor, dense liquid, and supercritical regions and find that these sets of solvation potentials are able to encode the complete range of solvent effects found in the LJ chain-in-solvent system. We also show that these two-site solvation potentials can be used to obtain accurate multi-site intramolecular distribution functions and we discuss the application of these exact short chain potentials to the study of longer chains in solvent.