Simple Point Charge Model Research Articles

Force Field for Molecular Dynamics Studies of Glycine/Water Mixtures in Crystal/Solution Environments

Defining a force field for the theoretical predictions of the structure and growth of pharmaceutical crystals is very difficult because of the complex intermolecular bonding found in these crystals. Here, we investigate the accuracy of the AMBER ff03 force field for alpha-glycine molecules using molecular dynamics. The validation of the force field is carried out in both solution and crystal/solution environments. The molecule alpha-glycine is chosen because it has a simple molecular structure while displaying complex intermolecular interactions typical of pharmaceutical crystals. We estimate the atomic charge for glycine from density-functional theory and represent water by the extended simple point charge (SPC/E) model. In a pure solution environment, our simulation results agree well with the experimental data available for solution density, radial distribution functions, hydration number, and diffusion coefficient of glycine. In the crystal/solution environment, the lattice energy calculations are in agreement with the available literature results and also the force field is able to identify the hydrophilic nature of the (010) surface of glycine crystal. The good agreement between simulation results and experimental data indicates that the chosen force field can be used to investigate the growth of glycine crystals from aqueous solutions.

Structure and Dynamics of Water Confined in Single-Wall Nanotubes

The structure and dynamics of water confined in model single-wall carbon- and boron-nitride nanotubes (called SWCNT and SWBNNT, respectively) of different diameters have been investigated by molecular dynamics (MD) simulations at room temperature. The simulations were performed on periodically extended nanotubes filled with an amount of water that was determined by soaking a section of the nanotube in a water box in an NpT simulation (1 atm, 298 K). All MD production simulations were performed in the canonical (NVT) ensemble at a temperature of 298 K. Water was described by the extended simple point charge (SPC/E) model. The wall-water interactions were varied, within reasonable limits, to study the effect of a modified hydrophobicity of the pore walls. We report distribution functions for the water in the tubes in spherical and cylindrical coordinates and then look at the single-molecule dynamics, in particular self-diffusion. While this motion is slowed down in narrow tubes, in keeping with previous findings (Liu et al. J. Chem. Phys. 2005, 123, 234701-234707; Liu and Wang. Phys. Rev. 2005, 72, 085420/1-085420/4; Liu et al. Langmuir 2005, 21, 12025-12030) bulk-water like self-diffusion coefficients are found in wider tubes, more or less independently of the wall-water interaction. There may, however, be an anomaly in the self-diffusion for the SWBNNT.

The Wolf method applied to the liquid-vapor interface of water

The Wolf method for the calculation of electrostatic interactions is applied in a liquid phase and at the liquid-vapor interface of water and its results are compared with those from the Ewald sums method. Molecular dynamics simulations are performed to calculate the radial distribution functions at room temperature. The interface simulations are used to obtain the coexisting densities and surface tension along the coexistence curve. The water model is a flexible version of the extended simple point charge model. The Wolf method gives good structural results, fair coexistence densities, and poor surface tensions as compared with those obtained using the Ewald sums method.

X-ray structure refinement using aspherical atomic density functions obtained from quantum-mechanical calculations

An approach is outlined for X-ray structure refinement using atomic density fragments obtained by Hirshfeld partitioning of quantum-mechanical density fragments. Results are presented for crystal structure refinements of urea and benzene using these 'Hirshfeld atoms'. Using this procedure, the quantum-mechanical non-spherical electron density is taken into account in the structural model based on the conformation found in the crystal. Contrary to current consensus in structure refinement, the anisotropic displacement parameters of H atoms can be reproduced from neutron diffraction measurements simply from a least-squares fit using the Hirshfeld atoms derived from the BLYP level of theory and including a simple point-charge model to treat the crystal environment.

A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models

We investigate the properties of geometrically modified water models by performing molecular dynamics simulations of perturbations of the extended simple point charge (SPC/E) model of water over a wide range of temperatures at 1 bar. The geometric modification consists of altering the H-O-H angle in SPC/E. The dipole moment is held constant by altering the O-H bond length, while the electrostatic charges are left unchanged. We find that a H-O-H angle of at least 100 degrees is necessary for the appearance of density anomalies and of solubility extrema with respect to temperature for small apolar solutes. We observe the occurrence of two incompatible types of structural order in these models: Tetrahedral, with waterlike translational order for bent models with H-O-H angles in excess of 100 degrees ; and linear, with Lennard-Jones-like orientationally averaged translational order for smaller H-O-H angles. Increasing the H-O-H angle causes the density to increase, while at the same time shifting waterlike anomalies to progressively higher temperatures. For bent models with H-O-H angle greater than SPC/E's, we observe arrest of translational motion at 300 K (115 degrees) and 330 K (120 degrees).

Inelastic neutron scattering study of crystalline-electric-field interaction in Ce3Ir4Sn13

The Ce3Ir4Sn13 single crystal was grown using Sn-flux method. Inelastic neutron scattering measurements were performed on the Ce3Ir4Sn13 powder sample at T=5.3 and 200K. Two magnetic origin peaks of ΔE1=4.4 and ΔE2=45.9meV in the inelastic neutron scattering spectra were detected as the crystalline-electric-field excitations for Ce3Ir4Sn13. The results of our neutron data are roughly consistent with the calculation by fitting the magnetic susceptibility curve using a simple point-charge model.

Connection of translational and rotational dynamical heterogeneities with the breakdown of the Stokes-Einstein and Stokes-Einstein-Debye relations in water

We study the Stokes-Einstein (SE) and the Stokes-Einstein-Debye (SED) relations, Dt=kBT/6pietaR and Dr=kBT/8pietaR3, where Dt and Dr are the translational and rotational diffusivity, respectively, T is the temperature, eta the viscosity, kB the Boltzmann constant, and R the "molecular" radius. Our results are based on molecular dynamics simulations of the extended simple point charge model of water. We find that both the SE and SED relations break down at low temperature. To explore the relationship between these breakdowns and dynamical heterogeneities (DHs), we also calculate the SE and SED relations for subsets of the 7% "fastest" and 7% "slowest" molecules. We find that the SE and SED relations break down in both subsets, and that the breakdowns occur on all scales of mobility. Thus these breakdowns appear to be generalized phenomena, in contrast with a view where only the most mobile molecules are the origin of the breakdown of the SE and SED relations, embedded in an inactive background where these relations hold. At low temperature, the SE and SED relations in both subsets of molecules are replaced with "fractional" SE and SED relations, Dt approximately (tau/T)-xit and Dr approximately (tau/T)-xir, where xit approximately 0.84(<1) and xir approximately 0.75(<1). We also find that there is a decoupling between rotational and translational motion, and that this decoupling occurs in both the fastest and slowest subsets of molecules. Further, we find that, the decoupling increases upon cooling, but that the probability of a molecule being classified as both translationally and rotationally fastest also increases. To study the effect of time scale for SE and SED breakdown and decoupling, we introduce a time-dependent version of the SE and SED relations, and a time-dependent function that measures the extent of decoupling. Our results suggest that both the decoupling and SE and SED breakdowns originate at a time scale corresponding to the end of the cage regime, when diffusion starts. This is also the time scale when the DHs are more relevant. Our work also demonstrates that selecting DHs on the basis of translational or rotational motion more strongly biases the calculation of diffusion constants than other dynamical properties such as relaxation times.

Integral equation study of hydrophobic interaction: A comparison between the simple point charge model for water and a Lennard-Jones model for solvent

The hydrophobic interaction that is characterized by a potential of mean force (PMF) between spherical apolar solutes immersed in the simple point charge (SPCE) model for water was studied using an interaction site model integral equation based on a density-functional theory for molecular fluids. For comparison with the PMFs for various size solutes in the SPCE model, the PMFs in a Lennard-Jones (LJ) model for a solvent whose diameter is same as the SPCE model were also studied using a hypernetted chain integral equation. It is noted in the LJ model that the hydrogen bond and its network structure are completely ignored, but the translational entropy is taken into account. Both PMFs obtained from the SPCE model and from the LJ model have a large first minimum at a contact distance of solutes. In the case that the solute size is about three times larger than water, these PMFs also have a large maximum at a longer distance than the contact position. The strong attraction is attributed to the translational entropy of the solvent, and that the large activation barrier is arising from the weak attraction between the solute and the solvent. The comparison between the SPCE model and the LJ solvent model suggests that the qualitative description of the hydrophobic interaction is possible by using the LJ solvent model. On the other hand, the dewetting tendency on the surface of the apolar solute in a room condition is observed only on the SPCE model. These results indicate that the characteristics of water such as the hydrogen bond affect rather the hydrophobic hydration than the hydrophobic interaction.

Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: Application to solvatochromic shift calculations

The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

Solubility of KF and NaCl in water by molecular simulation

The solubility of two ionic salts, namely, KF and NaCl, in water has been calculated by Monte Carlo molecular simulation. Water has been modeled with the extended simple point charge model (SPC/E), ions with the Tosi-Fumi model and the interaction between water and ions with the Smith-Dang model. The chemical potential of the solute in the solution has been computed as the derivative of the total free energy with respect to the number of solute particles. The chemical potential of the solute in the solid phase has been calculated by thermodynamic integration to an Einstein crystal. The solubility of the salt has been calculated as the concentration at which the chemical potential of the salt in the solution becomes identical to that of the pure solid. The methodology used in this work has been tested by reproducing the results for the solubility of KF determined previously by Ferrario et al. [J. Chem. Phys. 117, 4947 (2002)]. For KF, it was found that the solubility of the model is only in qualitative agreement with experiment. The variation of the solubility with temperature for KF has also been studied. For NaCl, the potential model used predicts a solubility in good agreement with the experimental value. The same is true for the hydration chemical potential at infinite dilution. Given the practical importance of solutions of NaCl in water the model used in this work, whereas simple, can be of interest for future studies.

Molecular dynamics simulations of water droplets on polymer surfaces

Molecular dynamics simulations were used to study the wetting of polymer surfaces with water. Contact angles of water droplets on crystalline and two amorphous polyethylene (PE) and poly(vinyl chloride) (PVC) surfaces were extracted from atomistic simulations. Crystalline surfaces were produced by duplicating the unit cell of an experimental crystal structure, and amorphous surfaces by pressing the bulk polymer step by step at elevated temperature between two repulsive grid surfaces to a target density. Different-sized water droplets on the crystalline PE surface revealed a slightly positive line tension on the order of 10(-12)-10(-11) N, whereas droplets on crystalline PVC did not yield a definite line tension. Microscopic contact angles produced by the simple point charge (SPC) water model were mostly a few degrees smaller than those produced by the extended SPC model, which, as the model with lowest bulk energy, presents an upper boundary for contact angles. The macroscopic contact angle for the SPC model was 94 degrees on crystalline PVC and 113 degrees on crystalline PE. Amorphicity of the surface increased the water contact angle on PE but decreased it on PVC, for both water models. If the simulated contact angles on crystalline and amorphous surfaces are combined in proportion to the crystallinity of the polymer in question, simulated values in relatively good agreement with measured values are obtained.

Feynman-Kleinert Linearized Path Integral (FK-LPI) Algorithms for Quantum Molecular Dynamics, with Application to Water and He(4).

The Feynman-Kleinert Linearized Path Integral (FK-LPI) representation of quantum correlation functions is extended in applications and algorithms. Diffusion including quantum effects for a flexible simple point charge model of liquid water is explored, including new tests of internal consistency. An ab initio quantum correction factor (QCF) is also obtained to correct the far-infrared spectrum of water. After correction, a spectrum based on a classical simulation is in good agreement with the experiment. The FK-LPI QCF is shown to be superior to the so-called harmonic QCF. New computational algorithms are introduced so that the quantum Boltzmann Wigner phase-space density, the central object in the implementation, can be obtained for arbitrary potentials. One scheme requires only that the standard classical force routine be replaced when turning from one molecular problem to another. The new algorithms are applied to the calculation of the Van Hove spectrum of liquid He(4) at 27 K. The spectrum moments are in very good agreement with the experiment. These observations indicate that the FK-LPI approach can be broadly effective for molecular problems involving the dynamics of light nuclei.

Molecular dynamics simulation of ion selectivity traits of nickel hexacyanoferrate thin films

The ion selectivity of nickel hexacyanoferrate thin film to alkali cations in ESIX (electrochemically switched ion exchange) processes was investigated using molecular dynamics(MD) techniques; water and cation (Na + and Cs +) intercalation, configuration, and dynamics in reduced nickel hexacyanoferrate structures with different cation combinations were studied and compared with the experimental results. In the simulations, water was represented by an extended simple point-charge(SPC/E) model, and all other atomic interactions were represented by a universal force field(UFF). The potential energies of various cations combination (Cs + and Na +) in reduced i-NiHCF and 1 mol/L Cs/NaCl mixed solution were obtained. In most cases, the total potential energy of the solid is reduced when water is intercalated into the various reduced NiHCF structures. Combining the solid and the solution simulation results, it is shown that the solid composition of 3Cs +/lNa + is the stablest structure form (NaCs 3Ni 4[Fe(CN) 6] 3) over a range of solution compositions.

Effect of an external electric field on liquid water using molecular dynamics simulation with a flexible potential

Molecular dynamics simulations of liquid water were performed at 258 K and density of 1.0 g/cm3 under different strengths of an external electric field, ranging from 0 to 8.0×109 V/m, to investigate the influence of an external field on structural and dynamic properties of water. The flexible simple point charge model is used for water molecules. An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bond structure. With increasing field strength, water system has a more perfect structure, which is similar to ice structure. However, the electrofreezing phenomenon of liquid water has not been detected because of a too large self-diffusion coefficient. The self-diffusion coefficient decreases remarkably with increasing strength of electric field, and the self-diffusion coefficient is anisotropic.

Monte Carlo Simulation Study of Water Adsorption in Activated Carbon

We present a Monte Carlo simulation study of adsorption and desorption for two molecular models of water in activated carbon, focusing on the temperature range for which the system exhibits hysteresis. The activated carbon is modeled using an adaptation of the platelet model developed by Segarra and Glandt (Chem. Eng. Sci. 1994, 49 (17), 2953−2965). The active sites in the carbon are modeled by placing interaction sites at the periphery of the platelets. To model water we have used two model potentials: the simple point charge (SPC) model and adaptation of the primitive model of water developed by Kolafa and Nezbeda (Mol. Phys. 1987, 61 (1), 161−175). We find that both models considered yield quite good qualitative agreement with the experimental data for water in BPL carbon obtained by Levan and co-workers (Ind. Eng. Chem. Res. 1992, 31 (4), 1122−1130). In particular both the shape of the hysteresis loops and their temperature dependence are correctly described by the simulation results. The sensitivity...

Surface Tension Prediction Using Characteristics of the Density Profile Through the Interfacial Region

A simple surface tension estimation technique is described that is based solely upon the characteristics of the density profile in the interfacial region and the physical properties of the molecules in the fluid. This method, denoted free energy integration (FEI), links interfacial tension to known interfacial region density profile characteristics obtained via experiment or simulation. The general FEI methodology is provided here, and specific relations are derived for a methodology that incorporates the Redlich–Kwong fluid model. The Redlich–Kwong based FEI method was used to predict interfacial tension using the density profile characteristics of molecular dynamics (MD) simulations of argon using the Lennard–Jones potential, diatomic nitrogen using the two-center Lennard–Jones potential, and water using the extended simple point-charge (SPC/E) model. These results for argon compare favorably to values calculated by the traditional virial approach, known values from the literature using the finite-size scaling technique, and ASHRAE recommended values. In addition, the FEI predictions agree well with ASHRAE values and predictions using the virial method for nitrogen for the simulated range of temperatures in this study, and for water for reduced temperatures above 0.7. In addition, the FEI method results agree well with other established theoretical techniques for predictions of the surface tension of sulfur hexafluoride close to the critical point.

Simulated water adsorption in chemically heterogeneous carbon nanotubes

Grand canonical Monte Carlo simulations are used to study the adsorption of water in single-walled (10:10), (12:12), and (20:20) carbon nanotubes at 298 K. Water is represented by the extended simple point charge model and the carbon atoms as Lennard-Jones spheres. The nanotubes are decorated with different amounts of oxygenated sites, represented as carbonyl groups. In the absence of carbonyl groups the simulated isotherms are characterized by negligible amounts of water uptake at low pressures, sudden and complete pore filling once a threshold pressure is reached, and wide adsorption-desorption hysteresis loops. In the presence of a few carbonyl groups the simulated adsorption isotherms are characterized by pore filling at lower pressures and by narrower adsorption-desorption hysteresis loops compared to the results obtained in the absence of carbonyl groups. Our results show that the distribution of the carbonyl groups has a strong effect on the adsorption isotherms. For carbonyl groups localized in a narrow section the adsorption of water may be gradual because a cluster of adsorbed water forms at low pressures and grows as the pressure increases. For carbonyl groups distributed along the nanotube the adsorption isotherm is of type V.

Relation between Rotational and Translational Dynamic Heterogeneities in Water

We use molecular dynamics simulations to probe the rotational dynamics of the extended simple point charge model of water for a range of temperatures down to 200 K, 6 K above the mode coupling temperature. We find that rotational dynamics is spatially heterogeneous; i.e., there are clusters of molecules that rotate significantly more than the average for a given time interval, and we study the size and the temporal behavior of these clusters. We find that the position of a rotational heterogeneity is strongly correlated with the position of a translational heterogeneity, and that the fraction of molecules belonging to both kinds of heterogeneities increases with decreasing temperature. We further find that although the two types of heterogeneities are not identical, they are related to the same physical picture.

Flexible simple point-charge water model with improved liquid-state properties

In order to introduce flexibility into the simple point-charge (SPC) water model, the impact of the intramolecular degrees of freedom on liquid properties was systematically studied in this work as a function of many possible parameter sets. It was found that the diffusion constant is extremely sensitive to the equilibrium bond length and that this effect is mainly due to the strength of intermolecular hydrogen bonds. The static dielectric constant was found to be very sensitive to the equilibrium bond angle via the distribution of intermolecular angles in the liquid: A larger bond angle will increase the angle formed by two molecular dipoles, which is particularly significant for the first solvation shell. This result is in agreement with the work of Hochtl et al. [J. Chem. Phys. 109, 4927 (1998)]. A new flexible simple point-charge water model was derived by optimizing bulk diffusion and dielectric constants to the experimental values via the equilibrium bond length and angle. Due to the large sensitivities, the parametrization only slightly perturbs the molecular geometry of the base SPC model. Extensive comparisons of thermodynamic, structural, and kinetic properties indicate that the new model is much improved over the standard SPC model and its overall performance is comparable to or even better than the extended SPC model.

Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions.

Absolute free energies of hydration (ΔGhyd) for more than 500 neutral and charged compounds have been computed, using Poisson-Boltzmann (PB) and Generalized Born (GB) continuum methods plus a solvent-accessible surface area (SA) term, to evaluate the accuracy of eight simple point-charge models used in molecular modeling. The goal is to develop improved procedures and protocols for protein-ligand binding calculations and virtual screening (docking). The best overall PBSA and GBSA results, in comparison with experimental ΔGhyd values for small molecules, were obtained using MSK, RESP, or ChelpG charges obtained from ab initio calculations using 6-31G* wave functions. Correlations using semiempirical (AM1BCC, AM1CM2, and PM3CM2) or empirical (Gasteiger-Marsili and MMFF94) methods yielded mixed results, particularly for charged compounds. For neutral compounds, the AM1BCC method yielded the best agreement with experimental results. In all cases, the PBSA and GBSA results are highly correlated (overall r(2) = 0.94), which highlights the fact that various partial charge models influence the final results much more than which continuum method is used to compute hydration free energies. Overall improved agreement with experimental results was demonstrated using atom-based constants in place of a single surface area term. Sets of optimized SA constants, suitable for use with a given charge model, were derived by fitting to the difference in experimental free energies and polar continuum results. The use of optimized atom-based SA constants for the computation of ΔGhyd can fine-tune already reasonable agreement with experimental results, ameliorate gross deficiencies in any particular charge model, account for nonoptimal radii, or correct for systematic errors.