In this work, the collective structure of aqueous solutions of ionic liquids was studied by means of molecular dynamics simulations. Various concentrations of 1-butyl-3-methyl-imidazolium tetrafluoroborate and TIP3P water were simulated at the very same size of the simulation box. For the analysis, the ternary system cation/anion/water was subdivided into binary networks. The local structure of each of these six networks is investigated by atom-atom radial distribution functions as well as by the so-called g coefficients, which reveal the mutual orientation of the network constituting partners. Furthermore, the collective structure of the whole samples was characterized by the contribution of each species to the static dielectric constant epsilon(omega=0) and to the Kirkwood G(K) factor. The combination of the analysis tools mentioned above provides knowledge about the cross-linking of the ionic species with the dipolar water. Thereby, the interplay between charge-charge and hydrogen bond networks is analyzed in detail.

Three different mixtures of 1-butyl-3-methyl-imidazolium tetrafluoroborate with water have been studied by means of molecular dynamics simulations. Based on the classical Lopes-Padua force field trajectories of approximately 60 ns were computed. This is the third part of a series concerning the collective network of 1-butyl-3-methyl-imidazolium tetrafluoroborate/water mixtures. The first part [C. Schröder et al., J. Chem. Phys. 127, 234503 (2007)] dealt with the orientational structure and static dielectric constants. The second part [C. Schröder et al., J. Chem. Phys. 129, 184501 (2008)] was focused on the decomposition of the dielectric spectrum of these mixtures. In this work the focus lies on the characterization of the neighborhood of ionic liquids by means of the Voronoi decomposition. The Voronoi algorithm is a rational tool to uniquely decompose the space around a reference molecule without using any empirical parameters. Thus, neighborhood relations, direct and indirect ones, can be extracted and were used in combination with g-coefficients. These coefficients represent the generalization of the traditional radial distribution function in order to include the mutual positioning and orientation of anisotropic molecules. Furthermore, the Voronoi method provides, as a by-product, the mutual coordination numbers of molecular species.

The complex ionic network of 1-butyl-3-methyl-imidazolium trifluoroacetate was simulated by means of the molecular dynamics methods over a time period of 100 ns. The influence of the anisotropy of the shape and charge distribution of both the cations and the anions on the local (molecular) and global (collective) structure and dynamics is analyzed. The distance-dependent g coefficients of the orientational probability function g(r,Omega) were found to be an excellent way to interpret local structure. Thereby, the combination and interrelation of individual g coefficients elucidate the mutual orientation. Dynamics at the molecular level is characterized by the time correlation function of the center-of-mass corrected molecular dipole moment mucm. Upon uniting the set of molecular dipoles to a single collective rotational dipole moment, MD, dynamics on a global level is studied. Decomposing into subsets of cations and anions respective self terms as well as the prominent cross term can be extracted. This decomposition also enables a detailed peak assignment in dielectric spectra.

The relaxation of solvation shells is studied following a twofold strategy based on a direct analysis of simulated data as well as on a solution of a Markovian master equation. In both cases solvation shells are constructed by Voronoi decomposition or equivalent Delaunay tessellation. The theoretical framework is applied to two types of hydrated molecular ionic liquids, 1-butyl-3-methyl-imidazolium tetrafluoroborate and 1-ethyl-3-methyl-imidazolium trifluoromethylsulfonate, both mixed with water. Molecular dynamics simulations of both systems were performed at various mole fractions of water. A linear relationship between the mean residence time and the system's viscosity is found from the direct analysis independent of the system's type. The complex time behavior of shell relaxation can be modeled by a Kohlrausch-Williams-Watts function with an almost universal stretching parameter of 1/2 indicative of a square root time law. The probabilistic model enables an intuitive interpretation of essential motional parameters otherwise not accessible by direct analysis. Even more, incorporating the square root time law into the probabilistic model enables a quantitative prediction of shell relaxation from very short simulation studies. In particular, the viscosity of the respective systems can be predicted.

This paper presents the structure and dynamics of hydration shells for the three proteins: ubiquitin, calbindin, and phospholipase. The raw data derived from molecular dynamics simulations are analyzed on the basis of fully atomistic Delaunay tesselations. In order to cope with the high numerical effort for the computation of these Voronoi shells, we have implemented and optimized an intrinsically periodic algorithm. Based on this highly efficient Voronoi decomposition, a variety of properties is presented: three dimensional water and ion nuclear densities as well as the geometrical packing of water molecules are discussed. Thereby, we develop Voronoi interface surface area, the Voronoi analog of the well known solvent accessible surface area. The traditional radial distribution functions are resolved into Voronoi shells as a transient device to the new concept of shell-grained orientational order. Thus, we analyze the donor-acceptor property as well as the amount of dielectric screening. Shell dynamics is described in terms of mean residence times. In this way, a retardation factor for different shells can be derived and was compared to experimental values. All these results and properties are presented both at the global protein level as well as at the local residue level.