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In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r-6 term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations. [ABSTRACT FROM AUTHOR]

We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules and n = 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ∼ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain. [ABSTRACT FROM AUTHOR]

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been carried out to investigate structural and dynamical characteristics of NaCl aqueous solutions confined within silica nanopores in contact with a 'bulk-like' reservoir. Two types of pores, with diameters intermediate between 20 Å and 37.5 Å, were investigated: The first one corresponded to hydrophobic cavities, in which the prevailing wall-solution interactions were of the Lennard-Jones type. In addition, we also examined the behavior of solutions trapped within hydrophilic cavities, in which a set of unsaturated O-sites at the wall were transformed in polar silanol Si-OH groups. In all cases, the overall concentrations of the trapped electrolytes exhibited important reductions that, in the case of the narrowest pores, attained 50% of the bulk value. Local concentrations within the pores also showed important fluctuations. In hydrophobic cavities, the close vicinity of the pore wall was coated exclusively by the solvent, whereas in hydrophilic pores, selective adsorption of Na+ ions was also observed. Mass and charge transport were also investigated. Individual diffusion coefficients did not present large modifications from what is perceived in the bulk; contrasting, the electrical conductivity exhibited important reductions. The qualitative differences are rationalized in terms of simple geometrical considerations. [ABSTRACT FROM AUTHOR]

Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method. We also show how to reduce the computational overhead for evaluating the dipoles, introducing to the state-of-the-art methods: the extended Lagrangian method and the always stable predictor corrector method. Finally we discuss the importance of screening the electrostatic interactions at short range, defending this technique against simpler approximations usually made. We compare results of density functional theory and classical force field-based Molecular Dynamics simulations of chloride in water. [ABSTRACT FROM AUTHOR]

We report molecular dynamics simulation results of equilibrium and dynamical characteristics pertaining to the solvation of the dye coumarin 153 (C153) trapped within hydrophobic cavities of di- and trimethylated beta-cyclodextrins (CD) in aqueous solutions. We found that stable configurations of the encapsulated probe are characterized by a slanted docking, in which the plane of the C153 lies mostly parallel to one of the glucose units of the CD. "In and out" dynamical modes of the encapsulated probe present very small amplitudes. The rotational dynamics of the trapped coumarin can be cast in terms of a simple model that includes diffusive motions within a local restrictive environment coupled to the overall rotational motion of the CD. We have examined the early stages of the solvation response of the environment following a vertical excitation of the probe. Regardless of the degree of CD methylation, the water dynamical response seems to be completed within 2-3 ps and does not differ substantially from that observed for nonencapsulated probes. The CD response is characterized by a single, subpicosecond relaxation that involves intramolecular motions. We also explored dynamical modes that could account for the recently reported persistence of Stokes shifts in the nanosecond time domain. In all cases, the only sources of ultraslow dynamics that we detected were those associated with gauche-trans interconversions in primary hydroxyl chains of the CD, which do not seem to be directly connected to the electronic excitation of the probe.