Wavelet treatment of structure and thermodynamics of simple liquids

A new algorithm is developed to solve integral equations for simple liquids. The algorithm is based on the discrete wavelet transform of radial distribution functions. The Coifman 2 basis set is employed for the wavelet treatment. To solve integral equations we have applied the combined scheme in which the coarse part of the solution is calculated by wavelets, while the fine part by the direct iterations. Tests on the PY and HNC approximations have indicated that the proposed procedure is more effective than the conventional method based on the hybrid algorithm. Possibilities for application of the method to molecular liquids and mixed quantum-classical systems are discussed.     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

On the structure of simple molecular liquids SbCl5 and WCl6

Neutron diffraction measurements on liquid antimony pentachloride and tungsten hexachloride have been carried out using the Studsvik liquids and amorphous diffractometer (SLAD) at the Studsvik Neutron Research Laboratory. The corrected structure factors have been interpreted by means of reverse Monte Carlo modeling which provides large structural models, containing thousands of atoms, that are consistent with the experimental data within their uncertainties. From these models, partial structure factors and pair correlation functions can be calculated. It is demonstrated that the intramolecular structure can be determined on the basis of data extending up to 10 Angstrom (-1). SbCl(5) is found to have a trigonal bipyramidal shape in the liquid, while liquid WCl(6) consists of octahedral molecules. The intermolecular structure of liquid SbCl(5) and WCl(6) seems to be determined largely by steric effects (excluded volume and molecular shape).     

Surface-hopping dynamics and decoherence with quantum equilibrium structure

In open quantum systems, decoherence occurs through interaction of a quantum subsystem with its environment. The computation of expectation values requires a knowledge of the quantum dynamics of operators and sampling from initial states of the density matrix describing the subsystem and bath. We consider situations where the quantum evolution can be approximated by quantum-classical Liouville dynamics and examine the circumstances under which the evolution can be reduced to surface-hopping dynamics, where the evolution consists of trajectory segments exclusively evolving on single adiabatic surfaces, with probabilistic hops between these surfaces. The justification for the reduction depends on the validity of a Markovian approximation on a bath averaged memory kernel that accounts for quantum coherence in the system. We show that such a reduction is often possible when initial sampling is from either the quantum or classical bath initial distributions. If the average is taken only over the quantum dispersion that broadens the classical distribution, then such a reduction is not always possible.     

Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies

We present in this work the first molecular simulation study of an enzyme, the serine protease cutinase from Fusarium solani pisi, in two ionic liquids (ILs): 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) and 1-butyl-3-methylimidazolium nitrate ([BMIM][NO(3)]). We tested different water contents in these ILs at room temperature (298 K) and high temperature (343 K), and we observe that the enzyme structure is highly dependent on the amount of water present in the IL media. We show that the enzyme is preferentially stabilized in [BMIM][PF6] at 5-10% (w/w) (weight of water over protein) water content at room temperature. [BMIM][PF6] renders a more nativelike enzyme structure at the same water content of 5-10% (w/w) as previously found for hexane, and the system displays a similar bell-shape-like dependence with the water content in the IL media. [BMIM][PF6] is shown to increase significantly the protein thermostability at high temperatures, especially at low hydration. Our analysis indicates that the enzyme is less stabilized in [BMIM][NO(3)] relative to [BMIM][PF6] at both temperatures, most likely due to the strong affinity of the [NO(3)]- anion toward the protein main chain. These findings are in accordance with the experimental knowledge for these two ionic liquids. We also show that these ILs "strip off" most of the water from the enzyme surface in a degree similar to that found for polar organic solvents such as acetonitrile, and that the remaining waters at the enzyme surface are organized in many small clusters.     

Molecular structure and dynamics of liquids: aqueous urea solutions

In this review a multi-technical approach to the analysis of the structure and dynamics of the urea/water system is described. The reorientational movement of the solute molecule is investigated by the analysis of spectral band-shapes, as well as with the use of the optical Kerr effect (OKE) and molecular dynamics simulation (MDS). The effect of solute concentration on the structure and dynamics of the aqueous solutions (aggregation, orientational distribution, solvation...) is studied by molecular dynamics simulation and neutron scattering. The results obtained by other techniques are included to provide a critical analysis. Finally, the low-frequency Raman spectra of the system are interpreted on the basis of the semi-quantitative information obtained by molecular dynamics simulation.     

Evidence for sevenfold coordination in the first solvation shell of Hg(II) aqua ion

A quite unexpected sevenfold coordination of the hydrated Hg(II) complex in aqueous solution is revealed by an extensive study combining X-ray absorption spectroscopy (XAS) and quantum mechanics/molecular dynamics (QM/MD) calculations. As a matter of fact, the generally accepted octahedral solvation of Hg(II) ion cannot be reconciled with XAS results. Next, refined QM computations point out the remarkable stability of a heptacoordinated structure with C2 symmetry, and long-time MD simulations by new interaction potentials including many-body effects reveal that the hydrated complex has a quite flexible structure, corresponding for most of the time to heptacoordinated species. This picture is fully consistent with X-ray absorption near-edge structure experimental data which unambiguously show the preference for a sevenfold instead of a sixfold coordination.     

Quantitative link between single-particle dynamics and static structure of supercooled liquids

We present evidence via molecular simulation that the supercooled fluid states of SPC/E water as well as the "repulsive" and "attractive" supercooled fluid states of a recently introduced model for colloids with short-ranged attractions are characterized by the same functional relationship between self-diffusivity and the pair correlation function. We discuss how this simple relationship connects to an earlier finding that the temperature dependency of a supercooled fluid's single-particle dynamics tracks that of its excess entropy (relative to ideal gas). The generality of this observed structure-property relationship is supported by its ability to successfully describe the nontrivial behaviors of these very different types of model systems.     

The influence of electrostatic forces on the structure and dynamics of molecular ionic liquids

The vast majority of molecular dynamics simulations are based on nonpolarizable force fields with fixed partial charges for all atoms. The traditional way to obtain these charges are quantum-mechanical calculations performed prior to simulation. Unfortunately, the set of the partial charges heavily relies on the method and the basis set used. Therefore, investigations of the influence of charge variation on simulation data are necessary in order to validate various charge sets. This paper elucidates the consequences of different charge sets on the structure and dynamics of the ionic liquid: 1-ethyl-3-methyl-imidazolium dicyanoamide. The structural features seem to be more or less independent of the partial charge set pointing to a dominance of shape force as modeled by Lennard-Jones parameters. This can be seen in the radial distribution and orientational correlation functions. The role of electrostatic forces comes in when studying dynamical properties. Here, significant deviations between different charge sets can be observed. Overall, dynamics seems to be governed by viscosity. In fact, all dynamical parameters presented in this work can be converted from one charge set to another by viscosity scaling.     

Computational evidence for a variable first shell coordination of the cadmium(II) ion in aqueous solution

In this paper, we present a state-of-the-art 100 ns molecular dynamics simulation of a cadmium(II) aqueous solution that highlights a very flexible ion first coordination shell which transits between hexa- and heptahydrated complexes. From this investigation, a dynamical picture of the water exchange process emerges that takes place through an associative mechanism for the solvent substitution reaction. Our procedure starts from the generation of an effective two-body potential from quantum mechanical ab initio calculations in which the many-body ion-water terms are accounted for by the polarizable continuum method (PCM). This approach is computationally very efficient and has allowed us to carry out extremely long molecular dynamics simulations, indispensable to reproduce the dynamic properties of the cadmium(II) aqueous solution. Quantum mechanical ab initio calculations of the hexa- and heptahydrated complexes extracted from MD configurations have revealed stable minima for both clusters with the water molecules arranged in T(h)() and C(2) symmetries in the hexa- and heptahydrated complexes, respectively, with a slight energetic preference for the heptahydrated one. Finally, a comparison of the calculated hexa- and heptahydrated cluster IR and Raman spectra with the experimental data in the literature, has demonstrated that the IR spectroscopy is not able to distinguish between the two species, whereas the Raman spectrum of the Cd(2+)-(H(2)O)(7) cluster provides a better agreement with the experimental data.     

Free volumes in simple and polymeric liquids

Values of ε₀ν₀ the vaporization energy and volume in the hypothetical liquid state at 0°K., are derived for some simple polar and nonpolar molecules used as models for vinyl polymers. The following empirical relationship between the free volume fraction, f = (v ? v₀)/v, and the liquid compressibility coefficient β is demonstrated: ?f² ∝? This is applied to several vinyl polymer liquids near their glass transition temperatures, T_g, giving. f_g ? 0.17, if the “hard-core” volume v^* is considered to be independent of pressure and temperature, (i.e., v^* = v₀); or, f_g ?0.12, if the P,T dependence of v^* is considered to be the same as that of the glass. These agree with f_g values derived by Simha and Boyer from thermal expansion coefficients for the two analogous cases. An empirical viscosity-free volume equation of the Doolittle form: η = ATⁿe^b/f is applied to the glass transition, on assuming that this is an isoviscosity state and with the use of reported values for the expansion and compressibility coefficients and dT_g/dP for three polymers: polystyrene, poly(methyl methacrylate), and poly(vinyl acetate). Reasonable values of b/n are thus obtained. This viscosity equation is critically examined in the light of molecular theories of liquid viscosity.     

Interactions and dynamics in ionic liquids

Precise dielectric spectra have been determined at 25 degrees C over the exceptionally broad frequency range of 0.1 相似文献   

Molecular dynamics simulations of the structure and transport properties of tetra-butylphosphonium amino acid ionic liquids

Systematic molecular dynamics simulations are used to study the structure, dynamics and transport properties of the ionic liquids composed of the tetra-butylphosphonium ([TBP](+), or [P(C(4)H(9))(4)](+)) cation with six amino acid ([AA](-)) anions. The structural features of these ionic liquids were characterized by calculating the partial site-site radial distribution functions, g(r), and computing the dihedral angle distribution of n-butyl side chains in the [TBP](+) cations. The dynamics of the ionic liquids are described by studying the velocity autocorrelation function (VACF) and the mean-square displacement (MSD) for the centers of mass of the ions at different temperatures. The ionic diffusion coefficients and the electrical conductivities were evaluated from both the Einstein and Green-Kubo methods. The cross-correlation terms in the electric-current autocorrelation functions, which are an indication of the ion pair correlations, are investigated. The cationic transference numbers were also estimated to study the contributions of the anions and cations to the transport of charge in these ionic liquids. We determined the role of the amino acid anion structures on the dynamical behavior and the transport coefficients of this family of ionic liquids. In general, the MSD and self-diffusion coefficients of the relatively heavier non-planar [TBP](+) cations are smaller than those of the lighter amino acid anions. Introducing polar functional groups (acid or amide) in the side chain of [AA](-) decreases the diffusion coefficient and electrical conductivity of AAILs. The major factors for determining the magnitude of the transport coefficients are the chemical functionality and the length of the alkyl side chain of the [AA](-) anion of these [TBP][AA] ionic liquids.     

A simple method for evaluation of the self-consistency of the radial distribution functions and the orientation of water molecules in the first coordination sphere from the results of molecular dynamics calculations

A simple method for determination of the angular orientation of water molecules in the first coordination sphere from the radial distribution functions is proposed. A comparative analysis of the ability of the model potentials of pair interaction to take into account the effects of manybody interactions (MBI) was performed. The responses of the model pair potentials to the MBI effects in the first and second coordination spheres were found to be poorly correlated with each other. It was concluded that it is necessary to derive a new analytical type of potential functions of pair interaction. Published inIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 11, pp. 1842–1846. November. 2000.