Ionic and dipolar solvation dynamics in liquid water

The solvation time correlation function for solvation in liquid water was measured recently. The solvation was found to be very fast, with a time constant equal to 55 fs. In this article we present theoretical studies on solvation dynamics of ionic and dipolar solutes in liquid water, based on the molecular hydrodynamic approach developed earlier. The molecular hydrodynamic theory can successfully predict the ultrafast dynamics of solvation in liquid water as observed from recent experiments. The present study also reveals some interesting aspects of dipolar solvation dynamics, which differs significantly from that of ionic solvation. Dedicated to Prof. C N R Rao on his 60th birthday     

Dielectric friction and solvation dynamics: Novel results on relaxation in dipolar liquids

In this article we present a new, general but simple, microscopic expression for time-dependent solvation energy of an ion. This expression is surprisingly similar to the expression for the time-dependent dielectric friction on a moving ion. We show that both the Chandra-Bagchi and the Fried-Mukamel formulations of solvation dynamics can be easily derived from this expression. This expression leads to an almost perfect agreement of the theory with all the available computer simulation results. Second, we show here for the first time that the mobility of a light solute ion can significantly accelerate its own solvation, specially in the underdamped limit. The latter result is also in excellent agreement with the computer simulations.     

Histidine as a dipolar eluent in ion chromatography of aliphatic amines

Summary Acidified L-histidine was found to be a suitable eluent in membrane-suppressed cation chromatography for the separation of aliphatic mono-amines (methyl, ethyl, trimethyl, triethyl, tripropylamines). Based on the protonation equilibrium of amines with the histidine eluent, a simplified separation method was developed, in which the eluent can act as a source of diprotic cations and analytes as monoprotic amines. On detection, the suppressor converts the eluent by deprotonation to its dipolar form with minimum conductivity at the pH of the isoelectric point of histidine, (pl 7.56). Efficient separations were observed under isocratic development with an eluent concentration of C_HIS≤2 mM and a pH below 2.0. The effect of eluent concentration and number of carbon atoms in the aliphatic chain on the retention and the resolution was determined. Selectivity data of the separation system are also presented. Presented at Balaton Symposium '01 on High-Performance Separation Methods, Siófok, Hungary, September 2–4, 2001     

Molecular Dynamics Simulation of Aqueous Solutions Using Interaction Energy Components: Application to the Solvation Gibbs Energy

Molecular dynamics simulations of aqueous solutions of the solutes acetamide (AcNH₂), acetic acid (AcOH), and acetaldehyde (AcH) were made using Lennard–Jones 12-6-1 potentials to describe the solute–solvent interactions. The Morokuma decomposition scheme and the ESIE solute atomic charges were used to reproduce the exchange, polarization, and electrostatic components of the solute–water interaction energy. A nonlinear perturbation was incorporated into the “slow-growth” technique in order to improve the results for the solvation Gibbs energy that were found to be in agreement with the available experimental and theoretical values.     

Efficient treatment of solvation shells in 3D molecular theory of solvation

We developed a technique to decrease memory requirements when solving the integral equations of three‐dimensional (3D) molecular theory of solvation, a.k.a. 3D reference interaction site model (3D‐RISM), using the modified direct inversion in the iterative subspace (MDIIS) numerical method of generalized minimal residual type. The latter provides robust convergence, in particular, for charged systems and electrolyte solutions with strong associative effects for which damped iterations do not converge. The MDIIS solver (typically, with 2 × 10 iterative vectors of argument and residual for fast convergence) treats the solute excluded volume (core), while handling the solvation shells in the 3D box with two vectors coupled with MDIIS iteratively and incorporating the electrostatic asymptotics outside the box analytically. For solvated systems from small to large macromolecules and solid–liquid interfaces, this results in 6‐ to 16‐fold memory reduction and corresponding CPU load decrease in MDIIS. We illustrated the new technique on solvated systems of chemical and biomolecular relevance with different dimensionality, both in ambient water and aqueous electrolyte solution, by solving the 3D‐RISM equations with the Kovalenko–Hirata (KH) closure, and the hypernetted chain (HNC) closure where convergent. This core–shell‐asymptotics technique coupling MDIIS for the excluded volume core with iteration of the solvation shells converges as efficiently as MDIIS for the whole 3D box and yields the solvation structure and thermodynamics without loss of accuracy. Although being of benefit for solutes of any size, this memory reduction becomes critical in 3D‐RISM calculations for large solvated systems, such as macromolecules in solution with ions, ligands, and other cofactors. © 2012 Wiley Periodicals, Inc.     

Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions

ERmod is a software package to efficiently and approximately compute the solvation free energy using the method of energy representation. Molecular simulation is to be conducted at two condensed‐phase systems of the solution of interest and the reference solvent with test‐particle insertion of the solute. The subprogram ermod in ERmod then provides a set of energy distribution functions from the simulation trajectories, and another subprogram slvfe determines the solvation free energy from the distribution functions through an approximate functional. This article describes the design and implementation of ERmod, and illustrates its performance in solvent water for two organic solutes and two protein solutes. Actually, the free‐energy computation with ERmod is not restricted to the solvation in homogeneous medium such as fluid and polymer and can treat the binding into weakly ordered system with nano‐inhomogeneity such as micelle and lipid membrane. ERmod is available on web at http://sourceforge.net/projects/ermod . © 2014 Wiley Periodicals, Inc.     

A comparative theoretical study of dipeptide solvation in water

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).     

Enhanced stability of the model mini‐protein in amino acid ionic liquids and their aqueous solutions

Using molecular dynamics simulations, the structure of model mini‐protein was thoroughly characterized in the imidazolium‐based amino acid ionic liquids and their aqueous solutions. Complete substitution of water by organic cations and anions further results in hindered conformational flexibility of the mini‐protein. This observation suggests that amino acid‐based ionic liquids are able to defend proteins from thermally induced denaturation. We show by means of radial distributions that the mini‐protein is efficiently solvated by both solvents due to a good mutual miscibility. Amino acid‐based anions prevail in the first coordination sphere of positively charged sites of the mini‐protein whereas water molecules prevail in the first coordination sphere of negatively charged sites of the mini‐protein. © 2015 Wiley Periodicals, Inc.     

Al3+ solvation in solutions of aluminum nitrate in a protic ionic liquid: Nuclear magnetic resonance verification of the solvation shell composition

The closest environment of Al³⁺ cations was analyzed in detail in solutions of aluminum nitrate in the prototypical protic ionic liquid ethyl ammonium nitrate (EAN) using ¹H and ¹⁴N nuclear magnetic resonance (NMR) spectra. For Al (NO₃)₃–EAN mixtures with different water content, a quantitative analysis of the integral intensities of the ¹H and ¹⁴N signals was carried out and the composition of the first solvation shell of the aluminum cation was refined.     

New approach to free energy of solvation applying continuum models to molecular dynamics simulation

A new approach to the calculation of the free energy of solvation from trajectories obtained by molecular dynamics simulation is presented. The free energy of solvation is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent nonpolar (repulsion and dispersion) interactions, and the electrostatic solvation of the solute. The electrostatic term is calculated based on ideas developed for the broadly used continuum models, the cavitational contribution from the excluded volume by the Claverie-Pierotti model, and the Van der Waals term directly from the molecular dynamics simulation. The proposed model is tested for diluted aqueous solutions of simple molecules containing a variety of chemically important functions: methanol, methylamine, water, methanethiol, and dichloromethane. These solutions were treated by molecular dynamics simulations using SPC/E water and the OPLS force field for the organic molecules. Obtained free energies of solvation are in very good agreement with experimental data.     

Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra—Theory Meets Experiment

The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide.     

Dynamics in ferro- and antiferroelectric phases of a liquid crystal with fluorinated molecules as studied by dielectric spectroscopy

For 1-[3-fluoro-4-(1-methylheptyloxycarbonyl)phenyl]-2-[4-2,2,3,3,4,4,4-heptafluorobutoxybutoxy)biphenyl-4-yl]ethane (1F7), built of chiral molecules, results of dielectric measurements of liquid-crystalline and solid phases are presented. Rich polymorphism of liquid-crystalline (SmC*, SmC*_A and SmI*_A) phases as well as of solid (Cr1 and Cr2) phases were observed down to –130°C. At a frequency range from 0.1 Hz to 3 MHz, the relaxation processes were detected in ferroelectric SmC*, antiferroelectric SmC*_A and highly ordered SmI*_A smectic phases. The mechanism of complex dynamics (moleculear and collective) was identified with the help of the bias field. Vitrification of conformationally disordered crystal phase Cr2 was found in accordance with calorimetric observations.     

Correlation of gas–liquid partition coefficients using a generalized linear solvation energy relationship

In a number of previous communications, we reported on the utility of the solvatochromic linear solvation energy relationship (LSER) method for the correlation of a number of solute and solvent-dependent properties. In those studies, it was our practice to examine the effect of a variety of solvents on a given solute or a number of solutes in a given solvent. Here we report on a novel generalized LSER in which the solute and solvent were both simultaneously varied so as to assess the validity of the entire LSER concept and define its limits. The Hildebrand solubility parameter, δ_H, the Kamlet–Taft solvatochromic parameters, π*, α, β and the solute molar volume, V₂, were used as the explanatory variables. The gas–liquid partition coefficient (K) was the property of interest. We have found that the correlation using the generalized linear solvation energy relationship is statistically as good as the previous LSER correlations despite the use of a far smaller number of freely adjustable parameters. Furthermore, the new approach is able to give reasonable predictions of K values of systems not included in the data set upon which the regression is based.     

Electrostatic contribution to the ion solvation energy: cavity effects

Ion solvation process has been analysed for the spherically symmetrical system where an ion is located inside a cavity surrounded by an isotropic nonlocal dielectric medium. It has been proven that for any dielectric properties of the medium, the electric field outside the cavity as well as the ion solvation energy depend only on the total ion charge but not of the particular distribution of the ion charge density inside the cavity. These characteristics remain unchanged if the charge is displaced from the external boundary of the cavity into it. Analytical formulas for them have been derived for a particular model of the nonlocal dielectric function. Comparison of results for the solvation energy on the basis of this new theory and of the conventional approach (disregarding the existence of the cavity) shows a significant difference between their predictions if the ion charge is displaced inside the ion cavity.     

Simulation studies on mixtures of dipolar with nonpolar linear molecules II. A mixing rule for the dipolar contribution to the Helmholtz energy

In recent equations of state an explicit expression for the dipolar contribution to the Helmholtz energy F_D is used. If such equations are applied to mixtures the problem of mixing rules for F_D arises. As a solution, a “one-fluid dipole moment μ_x” is introduced which is based on perturbation theory. The accuracy of the approach is tested by simulation results for mixtures of dipolar with nonpolar linear molecules. In addition to the simulation runs from Part I (Müller et al. (1994)), results from 97 new NVT simulations are presented. Comparisons of pressures, internal energies, dipole energies and excess free energies from simulations with those obtained from the equation for F_D in combination with the one-fluid dipole moment μ_x shows good to excellent agreement.     

Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models

Implicit solvent models for biomolecular simulations have been developed to use in place of more expensive explicit models; however, these models make many assumptions and approximations that are likely to affect accuracy. Here, the changes in free energies of solvation upon folding of several fast folding proteins are calculated from previously run μs–ms simulations with a number of implicit solvent models and compared to the values needed to be consistent with the explicit solvent model used in the simulations. In the majority of cases, there is a significant and substantial difference between the values calculated from the two approaches that is robust to the details of the calculations. These differences could only be remedied by selecting values for the model parameters—the internal dielectric constant for the polar term and the surface tension coefficient for the nonpolar term—that were system‐specific or physically unrealistic. We discuss the potential implications of our findings for both implicit and explicit solvent simulations. © 2015 Wiley Periodicals, Inc.     

Effect of ion solvation on the diffuse layer structure in mixed electrolytes

A “solvionic” model of a multicomponent electrochemical system (mixed electrolyte) is considered. An ion in the solution is considered as a point charge rigidly fixed inside its solvation shell. The corresponding equations for the diffuse layer on an ideally polarizable electrode are derived, and an effective method of their numerical solution is formulated. The calculations are performed in order to follow the changes in the diffuse layer structure with variations in the electrode charge and electrolyte composition. Far from the zerocharge potential of solution, the dependences of distributions of solution components over the diffuse layer on the electrode charge radically differ from those within the classic Gouy-Chapman theory. Analytical equations (asymptotics at large electrode charges) for concentrations of solvated ions in the plane of their maximum approach and for their “surface excesses” (diffuse adsorption) are determined. Results of numerical calculations for a 0.2 M LiCl + 0.05 M BaCl₂ solution are plotted.     

气液界面上阴离子表面活性剂单层膜的分子动力学模拟

用分子动力学方法研究了阴离子表面活性剂十二烷基硫酸钠(SDS)在气液界面上的结构和动力学性质. 选择单分子占有面积分别为0.45和0.68 nm²的两个模拟体系, 通过径向分布函数表征了单层膜的厚度, 并根据疏水链中碳原子与极性头中硫原子之间组成的矢量分布和取向函数, 对比了不同界面单层膜的有序排列情况. 结果表明在分子占有面积较小达到饱和吸附的情况下, 界面上的SDS具有较好的有序性. 通过计算气液界面附近水分子的扩散系数发现: 由于氢键和静电作用的影响, 界面区域内的水分子较本体溶液中的水分子有较弱的迁移能力.