Monte Carlo studies of the structure of dilute aqueous sclutions of Li+, Na+, K+, F−, and Cl−

Structure and dynamics of the Li+ ion in water, methanol and acetonitrile solvents: ab initio molecular dynamics simulations

Fundamental understanding of the structure and dynamics of the Li+ ion in solution is of utmost importance in different fields of science and technology, especially in the field of ion batteries. In view of this, ab initio molecular dynamics (AIMD) simulations of the LiCl salt in water, methanol and acetonitrile were performed to elucidate structural parameters such as radial distribution function and coordination number, and dynamical properties like diffusion coefficient, limiting ion conductivity and hydrogen bond correlation function. In the present AIMD simulation, one LiCl in water is equivalent to 0.8 M, which is close to the concentration of the lithium salt used in the Li-ion battery. The first sphere of coordination number of the Li+ ion was reaffirmed to be 4. The radial distribution function for different pairs of atoms is seen to be in good agreement with the experimental results. The calculated potential of mean force indicates the stronger interaction of the Li+ ion with methanol over water followed by acetonitrile. The dynamical parameters convey quite high diffusion and limiting ionic conductivity of the Li+ ion in acetonitrile compared to that in water and methanol which has been attributed to the transport of the Li-Cl ion pair in a non-dissociated form in acetonitrile. The AIMD results were found to be in accordance with the experimental findings, i.e. the limiting ion conductivity was found to follow the order acetonitrile > methanol > water. This study shows the importance of atomistic level simulations in evaluating the structural and dynamical parameters and in implementing the results for predicting and synthesizing better next generation solvents for lithium ion batteries (LIBs).

Failure of molecular dynamics to provide appropriate structures for quantum mechanical description of the aqueous chloride ion charge-transfer-to-solvent ultraviolet spectrum

The lowest band in the charge-transfer-to-solvent ultraviolet absorption spectrum of aqueous chloride ion is studied by experiment and computation. Interestingly, the experiments indicate that at concentrations up to at least 0.25 M, where calculations indicate ion pairing to be significant, there is no notable effect of ionic strength on the spectrum. The experimental spectra are fitted to aid comparison with computations. Classical molecular dynamic simulations are carried out on dilute aqueous Cl-, Na+, and NaCl, producing radial distribution functions in reasonable agreement with experiment and, for NaCl, clear evidence of ion pairing. Clusters are extracted from the simulations for quantum mechanical excited state calculations. Accurate ab initio coupled-cluster benchmark calculations on a small number of representative clusters are carried out and used to identify and validate an efficient protocol based on time-dependent density functional theory. The latter is used to carry out quantum mechanical calculations on thousands of clusters. The resulting computed spectrum is in excellent agreement with experiment for the peak position, with little influence from ion pairing, but is in qualitative disagreement on the width, being only about half as wide. It is concluded that simulation by classical molecular dynamics fails to provide an adequate variety of structures to explain the experimental CTTS spectrum of aqueous Cl-.

Correlation between Computed Ion Hydration Properties and Experimental Values of Sugar Transfer through Nanofiltration and Ion Exchange Membranes in Presence of Electrolyte

The widespread use of nanofiltration and electrodialysis membrane processes is slowed down by the difficulties in predicting the membrane performances for treating streams of variable ionic compositions. Correlations between ion hydration properties and solute transfer can help to overcome this drawback. This research aims to investigate the correlation between theoretically evaluated hydration properties of major ions in solution and experimental values of neutral organic solute fluxes. In particular, ion hydration energies, coordination and hydration number and the average ion-water distance of Na+, Ca2+, Mg2+, Cl− and SO42− were calculated at a high quantum mechanics level and compared with experimental sugar fluxes previously reported. The properties computed by simple and not computationally expensive models were validated with information from the literature. This work discusses the correlation between the hydration energies of ions and fluxes of three saccharides, measured through nanofiltration and ionic-exchange membranes. In nanofiltration, the sugar flux increases with the presence of ions of increasing hydration energy. Instead, inverse linear correlations were found between the hydration energy and the sugar fluxes through ion exchange membranes. Finally, an empirical model is proposed for a rough evaluation of the variation in sugar fluxes as function of hydration energy for the ion exchange membranes in diffusion experiments.

Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields

Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.

Analyzing ion distributions around DNA

We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.

Atomistic Monte Carlo simulation of lipid membranes

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.

Hydration structure of salt solutions from ab initio molecular dynamics

The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the observed water and ion atmosphere around the DNA sequences is the MD simulation is in good agreement with experimental observations.

Hydration of sodium(I) and potassium(I) revisited: a comparative QM/MM and QMCF MD simulation study of weakly hydrated ions

Quantum mechanical/molecular mechanical (QM/MM) and quantum mechanical charge field (QMCF) molecular (MD) simulations have been performed to describe structural and dynamical properties of Na(I) and K(I) in water and to compare the two approaches. The first and second hydration shells were treated by ab initio quantum mechanics at the restricted Hartree-Fock (RHF) level. The structural data are in good agreement with previously published experimental and theoretical results. A considerable number of water exchange reactions were observed within the first shell during the simulation time of 12 ps. The number of exchange events in both shells is higher in the case of K(I) than Na(I) reflecting the weaker ion-ligand bond strength of K(I). Comparison of the "conventional" QM/MM framework with the QMCF method clearly indicates the latter to be advantageous, as ambiguities arising from the coupling of the subregions occurring in the QM/MM MD simulations did not evolve when the QMCF ansatz was applied.

Self-assembly and function of primitive cell membranes

We describe possible pathways for separating amphiphilic molecules from organic material on the early earth to form membrane-bound structures required for the start of cellular life. We review properties of the first membranes and their function as permeability barriers. Finally, we discuss the emergence of protein-mediated ion transport across membranes, which facilitated many other cellular functions.