Molecular dynamics study of polarizable point dipole models for molten sodium iodide

The structure, the ionic transport properties, and the dynamics of long-wavelength charge-density fluctuations, for two polarizable point dipole models of molten NaI, have been studied by molecular dynamics simulations. These models are based on a rigid ion potential to which the induced dipole polarization of the anions is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and short-range damping interactions that oppose the electrically induced dipole moments. The two polarizable ion models differ only in the range of the damping polarization interactions. The influence of the induced anion polarization on the different properties of simulated molten NaI is discussed.     

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short‐range penetration correction up to quadrupoles

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short‐range charge penetration correction modifying the charge‐charge, charge‐dipole and charge‐quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry‐Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono‐ and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER‐HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration‐corrected polarizable force fields highlighting the mandatory need of non‐spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short‐range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio‐ or bioinorganic systems in periodic boundary conditions. © 2016 Wiley Periodicals, Inc.     

Effect of repulsive interaction on the structural and dynamic features of liquid water. The role of molecular polarizability

The effect of variation of the potential function on the structural and dynamic properties of model water when the surface of pair interactions is invariant is studied by the molecular dynamics method. Variations for the rigid and polarizable models are compared. Translated fromZhurnal Strukturnoi Khimii, Vol.40, No. 2, pp. 296–303, March–April, 1999.     

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

Vibrational analysis of free and hydrogen bonded complexes of nicotinamide and picolinamide

Harmonic and anharmonic vibrations of free nicotinamide (NIA) and picolinamide (PIA) molecules together with their hydrogen bonded complexes H₂O–NIA and H₂O–PIA have been studied by means of density functional method. The calculation results of the vibrational spectra of free molecules have been investigated and are compared to the available experimental spectra. The vibrational wavenumbers of both molecules have also been calculated by polarizable continuum model (PCM) that represents the solvent as a polarizable continuum and places the solute in a cavity within the solvent (water is chosen as the solvent in this study). The results of PCM calculations and the H₂O–NIA, H₂O–PIA complexes, are used to investigate the H-bonding interactions of both molecules with the water molecule. The harmonic wavenumbers have been scaled by proper factors obtained by comparing the observed versus calculated wavenumbers and it is shown that anharmonic corrections on the vibrational spectra provided a better agreement between the observed and calculated wavenumbers compared to the results obtained by scaling factor method.     

Temperature Dependence of Physical Properties of Imidazolium Based Ionic Liquids: Internal Pressure and Molar Refraction

Density, speed of sound and refractive index of the imidazolium-based ionic liquids (ILs), 1-methyl-3-octylimidazolium chloride [C₈mim][Cl], 1-butyl-3-methylimidazolium methyl sulfate [C₄mim][C₁OSO₃], and 1-butyl-3-methylimidazolium octyl sulfate [C₄mim][C₈OSO₃], have been measured in the temperature range from 283.15 to 343.15 K. Experimental density and speed of sound have been used to calculate the internal pressure p _i of the ILs. The p _i values were found to be higher than those of water and molecular organic liquids, but lower than those of classical molten salts. We also calculated molar refraction R _M from the measured refractive index n _D in the temperature range from 288.15 to 343.15 K. Refractive indices of ILs were also higher than those of normal organic liquids, but comparable to long-chain hydrocarbon organic solvents. The structure-property correlation of the ILs has been discussed and the results have been compared to our earlier studies (Kumar in J. Solution Chem. 37:203–214, 2008).     

Kinetic Monte Carlo study of binary diffusion in silicalite

We report a Kinetic Monte Carlo (KMC) study of the diffusion of linear n-hexane (nC6) and 2,2-dimethylbutane (22DMB) mixture in zeolite silicalite. We first investigated the loading dependences of single component self- and corrected diffusivities of nC6 at 300 K. Anisotropic transition rates are implemented to account for the distribution of the molecules within the zeolite framework. Repulsive guest-guest interactions are modeled using the parameter introduced by Reed and Ehrlich (Surf. Sci. 102:588–601, 1981). The results are in good agreement with recent experimental Quasi Elastic Neutron Scattering data of Jobic et al. (J. Phys. Chem. B 110:2195–2201, 2006), although the influence of the adsorption isotherm inflection is not reproduced. The binary diffusion study of nC6/22DMB mixtures was performed by implementing the nC6 transition rates used for the single component study while 22DMB molecules propagate via intersection-intersection hops. This KMC model allows for different saturation capacities and accounts for interactions between molecules by introducing f _ij parameters. Results show the large impact of guest-guest interactions between nC6 and 22DMB on both self- and corrected diffusivities of the two components. Molecule-size effects are found to be predominant near 22DMB saturation capacity. Acceleration/deceleration effects already described in the literature are confirmed.     

Hydrogen-Bond Structure and Low-Frequency Dynamics of Electrolyte Solutions: Hydration Numbers from ab Initio Water Reorientation Dynamics and Dielectric Relaxation Spectroscopy

We present an atomistic simulation scheme for the determination of the hydration number (h) of aqueous electrolyte solutions based on the calculation of the water dipole reorientation dynamics. In this methodology, the time evolution of an aqueous electrolyte solution generated from ab initio molecular dynamics simulations is used to compute the reorientation time of different water subpopulations. The value of h is determined by considering whether the reorientation time of the water subpopulations is retarded with respect to bulk-like behavior. The application of this computational protocol to magnesium chloride (MgCl₂) solutions at different concentrations (0.6–2.8 mol kg⁻¹) gives h values in excellent agreement with experimental hydration numbers obtained using GHz-to-THz dielectric relaxation spectroscopy. This methodology is attractive because it is based on a well-defined criterion for the definition of hydration number and provides a link with the molecular-level processes responsible for affecting bulk solution behavior. Analysis of the ab initio molecular dynamics trajectories using radial distribution functions, hydrogen bonding statistics, vibrational density of states, water-water hydrogen bonding lifetimes, and water dipole reorientation reveals that MgCl₂ has a considerable influence on the hydrogen bond network compared with bulk water. These effects have been assigned to the specific strong Mg-water interaction rather than the Cl-water interaction.     

An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: application to water

An efficient parallelization scheme for classical molecular dynamics simulations with flexible, polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during molecular dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128 to 512 molecules employing two flexible polarizable water models [DC(F) and TTM2.1-F] containing 1 and 3 polarizable sites, respectively. The time-to-solution for these two polarizable models is compared with the one for a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculation of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed. To the best of our knowledge, this is the first reported results of parallel scaling and performance for simulations of liquid water with a polarizable potential under periodic boundary conditions.     

Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.     

Infrared and molecular-dynamics studies of the rotational dynamics of water highly diluted in supercritical CO2

Far-infrared (FIR) and mid-infrared (MIR) profiles of D2O infinitely dilute in supercritical CO2 have been studied using molecular-dynamics simulations. For this purpose, we have proposed an intermolecular potential model taking implicitly into account electron donor-acceptor (EDA) interactions between water and CO2 evaluated from ab initio calculations of the intermolecular potential-energy surface (IPS). Interaction-induced dipole mechanisms have been also taken into account in addition to the water permanent dipole to evaluate the simulated FIR profiles of water and CO2 polarizable molecules. They were found to play a minor role in the genesis of the FIR profiles of water/CO2 under supercritical conditions. The analysis of the reorientational dynamics of D2O shows that the rotational dynamics of water is weakly anisotropic due to the EDA interactions which affect more specifically the reorientational motions of the C2 symmetry axis of solute. These results have been used to assess the contribution of the vibrational relaxation in the experimental mid-infrared profiles associated with the nu1 symmetric and nu3 antisymmetric stretching and nu2 bending modes of D2O. It was found that the rotational dynamics mainly contribute to the broadening of the infrared (IR) profiles. Nevertheless, the vibrational processes play a role in the frequency shifts of the band centers and the relative intensity enhancements of the nu1 and nu3 modes of D2O. In particular, the EDA interactions between water and CO2 lead to the appearance of a well-defined IR band of the nu1 mode of D2O. Finally, a comparison with another model taking only into account dipole-quadrupole electrostatic interactions between water and CO2 molecules clearly reveals that EDA interactions have to be considered to reproduce both MIR and FIR measurements. From this point of view CO2 can be classified on a hydrophilic solvent scale based upon the solubility criterion as an intermediate solvent between "inert" xenon and carbon tetrachloride.     

The Conformations of Amino Acids on a Gold(111) Surface

The interactions of amino acids with inorganic surfaces are of interest for biologists and biotechnologists alike. However, the structural determinants of peptide–surface interactions have remained elusive, but are important for a structural understanding of the interactions of biomolecules with gold surfaces. Molecular dynamics simulations are a tool to analyze structures of amino acids on surfaces. However, such an approach is challenging due to lacking parameterization for many surfaces and the polarizability of metal surfaces. Herein, we report DFT calculations of amino acid fragments in vacuo and molecular dynamics simulations of the interaction of all amino acids with a gold(111) surface in explicit solvent, using the recently introduced polarizable gold force field GolP. We describe preferred orientations of the amino acids on the metal surface. We find that all amino acids preferably interact with the gold surface at least partially with their backbone, underlining an unfolding propensity of gold surfaces.     

A multiscale coarse‐grained polarizable solvent model for handling long tail bulk electrostatics

A multiscale coarse‐grained approach able to handle efficiently the solvation of microscopic solutes in extended chemical environment is described. That approach is able to compute readily and efficiently very long‐range solute/solvent electrostatic microscopic interactions, up to the 1‐μm scale, by considering a reduced amount of computational resources. All the required parameters are assigned to reproduce available data concerning the solvation of single ions. Such a strategy makes it possible to reproduce with good accuracy the solvation properties concerning simple ion pairs in solution (in particular, the asymptotic behavior of the ion pair potentials of mean force). This new method represents an extension of the polarizable pseudoparticle solvent model, which has been recently improved to account for the main features of hydrophobic effects in liquid water (Masella et al., J. Comput. Chem. 2011 , 32, 2664). This multiscale approach is well suited to be used for computing the impact of charge changes in free energy computations, in terms of both accuracy and efficiency. © 2013 Wiley Periodicals, Inc.