Computer simulations of aqueous electrolyte solutions

Atomic structure and electrical property of ionic liquids at the MoS2 electrode with varying interlayer spacing

Understanding the structure and properties at the electrolyte-electrode interface is vital for the rational design of the supercapacitors or other electrochemical devices. In this work, we explored the influence of interlayer spacing of the MoS₂ electrode on the interfacial structure and electrical properties of sodium-ionic liquids (ILs) electrolytes via performing the all-atom molecular dynamics simulations. From the number density, charge density, and electrical potential distribution near the surface, the Mo- and S-terminal edges possess positive and negative features when the interlayer spacing is less than 8.5 Å. Meanwhile, the strength of the first density layer of ILs increases with the increase of the interlayer spacing of MoS₂ for both Mo- and S- terminal surfaces in the neutral or charging state. Furthermore, the coordination number of sodium ion at the electrode surface was analyzed, and it was shown that the S-terminal surface has a larger coordination number than that on the Mo-terminal surface. Interestingly, the coordination number of MoS₂ with the interlayer spacing of 8.0 Å is the lowest in the ranges of 6.5~8.5 Å. The electrolyte's charge screening factor also reflects the opposite electrical state of Mo- and S-terminal surfaces and weakens with increasing the interlayer spacing and surface charge density. The obtained understanding of ILs at electrode interfaces with different layer spacings in this work will provide insight into the molecular mechanisms of ILs-based sodium supercapacitors or other electrochemical devices in critical chemical engineering processes.

Solvation structure around ruthenium(II) tris(bipyridine) in lithium halide solutions

The solvation of the ruthenium(II) tris(bipyridine) ion ([Ru(bpy)3](2+)) is investigated with molecular dynamics simulations of lithium halide solutions in polar solvents. The anion distribution around the [Ru(bpy)3](2+) complex exhibits a strong solvent dependence. In aqueous solution, the iodide ion forms a solvent shared complex with [Ru(bpy)3](2+), but not in the other solvents. Between Cl(-) and [Ru(bpy)3](2+), the strong hydration of the chloride ion results in a solvent separated complex where more than one solvent molecule separates the anion from the metal center. Hence, tailored solvation properties in electrolytes is a route to influence ion-ion interactions and related electron transfer processes.

Solvation shell resolved THz spectra of simple aqua ions – distinct distance- and frequency-dependent contributions of solvation shells

Spatial decomposition schemes for infrared spectra reveal the importance of both dipolar couplings and correlations in particle motion in aqueous solutions of Na⁺and Cl⁻.

Competition between Na⁺ and Rb⁺ in the minor groove of DNA

The competition between Na⁺ and Rb⁺ ions in the minor groove of a synthetic B-DNA dodecamer d (CGCGAATTCGCG) is studied using molecular dynamics simulations as the ratio of these two ions changing from 9:1 to 1:9 with the DNA merged into the solvent of water molecule at 298 K. When the concentration of Rb⁺ ions increases, from minority to majority, Na⁺ ions are gradually released from the A tract, and the binding sites in the minor groove are occupied by Rb⁺ ions, extending from the A tract to the whole minor groove. Comparing Na⁺ with Rb⁺ ions, the conformation of the minor groove is influenced strongly by Na⁺ ions.

H4 histone tail mediated DNA-DNA interaction and effects on DNA structure, flexibility, and counterion binding. A molecular dynamics study

All-atom molecular dynamics (MD) simulations were performed during 30-45 ns for a system of three identical DNA 22-mers, 14 short fragments of the charged H4 histone tail peptide fragment (amino acids 5-12, KGGKGLGK) with K(+) counterions, and explicit water. The simulation setup mimics the crowded conditions of DNA in eukaryotic chromatin. To assess the influence of tail fragments on DNA structure and dynamics, a "control" 20 ns MD simulation was carried for a system with the same DNA and water content but in the absence of oligopeptides. Results of DNA interaction with the histone tail fragments, K(+), and water is presented. DNA structure and dynamics and its interplay with the histone tail fragments binding are described. The charged side chains of the lysines play a major role in mediating DNA-DNA attraction by forming bridges and coordinating to phosphate groups and electronegative sites in the minor groove. Binding of all species to DNA is dynamic. Some of the tail fragments while being flexible and mobile in each of its functional groups remain associated near certain locations of the DNA oligomer. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction, and dynamics.

Computer modeling demonstrates that electrostatic attraction of nucleosomal DNA is mediated by histone tails

We conducted molecular dynamics computer simulations of charged histone tail-DNA interactions in systems mimicking nucleosome core particles (NCP) . In a coarse-grained model, the NCP is modeled as a negatively charged spherical particle with flexible polycationic histone tails attached to it in a dielectric continuum with explicit mobile counterions and added salt. The size, charge, and distribution of the tails relative to the core were built to mimick real NCP. In this way, we incorporate attractive ion-ion correlation effects due to fluctuations in the ion cloud and the attractive entropic and energetic tail-bridging effects. In agreement with experimental data, increase of monovalent salt content from salt-free to physiological concentration leads to the formation of NCP aggregates; likewise, in the presence of MgCl2, the NCPs form condensed systems via histone-tail bridging and accumulation of counterions. More detailed mechanisms of the histone tail-DNA interactions and dynamics have been obtained from all-atom molecular dynamics simulations (including water), comprising three DNA 22-mers and 14 short fragments of the H4 histone tail (amino acids 5-12) carrying three positive charges on lysine+ interacting with DNA. We found correlation of the DNA-DNA distance with the presence and association of the histone tail between the DNA molecules.

Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study

Four 20 ns molecular dynamics simulations have been performed with two counterions, K⁺ or Na⁺, at two water contents, 15 or 20 H₂O per nucleotide. A hexagonal simulation cell comprised of three identical DNA decamers [d(5′-ATGCAGTCAG) × d(5′-TGACTGCATC)] with periodic boundary condition along the DNA helix was used. The simulation setup mimics the DNA state in oriented DNA fibers or in crystals of DNA oligomers. Variation of counterion nature and water content do not alter averaged DNA structure. K⁺ and Na⁺ binding to DNA are different. K⁺ binds to the electronegative sites of DNA bases in the major and the minor grooves, while Na⁺ interacts preferentially with the phosphate groups. Increase of water causes a shift of both K⁺ and Na⁺ from the first hydration shell of O1P/O2P and of the DNA bases in the minor groove with lesser influence for the cation binding to the bases in the major groove. Mobility of both water and cations in the K–DNA systems is faster than in the Na–DNA systems: Na⁺ organizes and immobilizes water structure around itself and near DNA while for K⁺ water is less organized and more dynamic.

Study of Lithium Cation in Water Clusters: Based on Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.

Hydration of Li+-ion in atom-bond electronegativity equalization method–7P water: A molecular dynamics simulation study

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric

We have extended an earlier Brownian dynamics simulation algorithm for simulating the structural dynamics of ions around biomolecules to accommodate dielectric inhomogeneity. The electrostatic environment of a biomolecule immersed in water was obtained by numerically solving the Poisson equation with the biomolecule treated as a low dielectric region and the solvent treated as a high dielectric region. Instead of using the mean-field type approximations of ion interactions as in the Poisson-Boltzmann model, the ions were treated explicitly by allowing them to evolve dynamically under the electrostatic field of the biomolecule. This model thus accounts for ion-ion correlations and the finite-size effects of the ions. For a 13-residue alpha-helical polyalanine and a 12-base-pair bp B-form DNA, we found that the choice of the dielectric constant of the biomolecule has much larger effects on the mean ionic structure around the biomolecule than on the fluctuational and dynamical properties of the ions surrounding the biomolecule.

Determination of solvation free energies by adaptive expanded ensemble molecular dynamics

A new method of calculating absolute free energies is presented. It was developed as an extension to the expanded ensemble molecular dynamics scheme and uses probability density estimation to continuously optimize the expanded ensemble parameters. The new method is much faster as it removes the time-consuming and expertise-requiring step of determining balancing factors. Its efficiency and accuracy are demonstrated for the dissolution of three qualitatively very different chemical species in water: methane, ionic salts, and benzylamine. A recently suggested optimization scheme by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)] was also implemented and found to be computationally less efficient than the proposed adaptive expanded ensemble method.

Molecular dynamics estimates of ion diffusion in model hydrophobic and KcsA potassium channels

Molecular dynamics simulations are carried out to obtain estimates of diffusion coefficients of biologically important Na+, K+, Ca2+ and Cl- ions in hydrophobic cylindrical channels with varying radii and large reservoirs. Calculations for the cylindrical channels are compared to those for the KcsA potassium channel, for which the protein structure has recently been determined from X-ray diffraction experiments. Our results show that ion diffusion is maintained at reasonably high levels even within narrow channels, and does not support the very small diffusion coefficients used in some continuum models in order to fit experimental data. The present estimates of ion diffusion coefficients are useful in the calculation of channel conductance using the Poisson-Nernst-Planck theory, or Brownian dynamics.

Molecular dynamics simulations of DNA in solutions with different counter-ions

Molecular dynamics simulations of the [d(ATGCAGTCAG]2 fragment of DNA, in water and in the presence of three different counter-ions (Li+, Na+ and Cs+) are reported. Three-dimensional hydration structure and ion distribution have been calculated using spatial distribution functions for a detailed picture of local concentrations of ions and water molecules around DNA. According to the simulations, Cs+ ions bind directly to the bases in the minor groove, Na+ ions bind prevailing to the bases in the minor groove through one water molecule, whereas Li+ ions bind directly to the phosphate oxygens. The different behavior of the counter-ions is explained by specific hydration structures around the DNA and the ions. It is proposed how the observed differences in the ion binding to DNA may explain different conformational behavior of DNA. Calculated self-diffusion coefficients for the ions agree well with the available NMR data.