Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions

Simulating DNA by molecular dynamics: aims, methods, and validation

The structure and dynamics of the B-DNA double helix involves subtle sequence-dependent effects which are decisive for its function, but difficult to characterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics simulations with the major force fields in use today. We explain why a critical analysis of the MD trajectories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood.

A comparison of methods for melting point calculation using molecular dynamics simulations

Accurate and efficient prediction of melting points for complex molecules is still a challenging task for molecular simulation, although many methods have been developed. Four melting point computational methods, including one free energy-based method (the pseudo-supercritical path (PSCP) method) and three direct methods (two interface-based methods and the voids method) were applied to argon and a widely studied ionic liquid 1-n-butyl-3-methylimidazolium chloride ([BMIM][Cl]). The performance of each method was compared systematically. All the methods under study reproduce the argon experimental melting point with reasonable accuracy. For [BMIM][Cl], the melting point was computed to be 320 K using a revised PSCP procedure, which agrees with the experimental value 337-339 K very well. However, large errors were observed in the computed results using the direct methods, suggesting that these methods are inappropriate for large molecules with sluggish dynamics. The strengths and weaknesses of each method are discussed.

On the interaction of aliphatic amines and ammonium ions with carboxylic acids in solution and in receptor pockets

Association energies of the acetate ion with cationic amines bearing one to three methyl groups were calculated in the range of -14 to -17 kcal/mol in aqueous solution by means of the IEF-PCM method at the CCSD(T)/CBS//MP2/aug-cc-pvdz and DFT/B97D/CBS//B97D/aug-cc-pvtz levels. The main stabilization factor for the association is the possibility for the formation of an ionic intermolecular hydrogen bond between the elements of the complex. For a quaternary ammonium ion, the favorable electrostatic interaction energy is the only driving force, and the stabilization energy for the complex is reduced to -4 kcal/mol. The internal free energies of the ion-pair tautomers of the studied species are higher by 10-15 kcal/mol in water than those for the neutral, hydrogen-bonded forms. Monte Carlo free energy perturbation calculations at T = 298 K and p = 1 atm predict -11 to -16 kcal/mol relative solvation free energy in favor of the corresponding ionic form. As a result, the ion-pair tautomer is the prevailing form in aqueous solution and on the extracellular surface of a receptor. Modeling the complex of a protonated ligand interacting with an Asp/Glu carboxylate side-chain in the binding cavity of a receptor, two strongly bound water molecules were considered so as to form hydrogen-bonded water bridges between the elements of the ion-pair. Nonetheless, the low polarity environment mimicked by a chloroform solvent cannot stabilize the ionic tautomer. A proton jump was predicted, which suggests that acetylcholine, an inherent cation by structure, might have evolved as the natural agonist for muscarinic receptors because a quaternary ammonium system assures the maintenance of the ion-pair form with a carboxylate side-chain in a protein cavity, the latter perhaps then being needed for receptor activation.

Hydration force between mica surfaces in aqueous KCl electrolyte solution

Liquid-vapor molecular dynamics simulations are performed to study the interaction forces between two mica surfaces in an aqueous KCl electrolyte solution. Strong repulsive hydration force is obtained within a distance of ~2 nm between the two mica surfaces, which cannot be explained by the continuum theory of double-layer repulsion. We find that this short-range repulsive hydration force is much stronger than the double-layer force between mica surfaces. Whereas the simulation system is much smaller than the surface force measurement system, fundamental mechanisms of repulsive hydration force are revealed. In particular, important features of the step-like force oscillatory behavior during normal compression and force hysteresis during retraction are observed. Detailed analysis of the ionic density distributions shows that the "forced adsorption" of diffusive K(+) ions onto mica surfaces during compression and the subsequent "slow desorption" of the absorbed K(+) ions from mica surfaces upon retraction are responsible for the hysteresis phenomenon. From a mechanics point of view, we attribute the load bearing capacity of the dense electrolyte to the very hard hydration shells of K(+) metal ions under confinement. We find that the hydrated K(+) ions and Cl(-) co-ions remain very diffusive in the aqueous film. Water molecules in the hydration layer are also very fluidic, in the sense that the diffusion constant of water molecules is less than its bulk value by at most 3 orders of magnitude under the extreme confinement.

Pairwise long-range compensation for strongly ionic systems

We propose a pairwise compensation method for long-range electrostatics, as an alternative to traditional infinite lattice sums. The approach represents the third generation in a series beginning with the shifted potential corresponding to counterions surrounding a cutoff sphere. That simple charge compensation scheme resulted in pairwise potentials that are continuous at the cutoff, but forces that are not. A second-generation approach modified both the potential and the force such that both are continuous at the cutoff. Here we introduce another layer of softening such that the derivative of the force is also continuous at the cutoff. In strongly ionic liquids, this extension removes structural artifacts associated with the earlier pairwise compensation schemes, and provides results that compare well with Ewald sums.

Liquid-liquid coexistence in NaCl aqueous solutions: a simulation study of concentration effects

In this paper we investigate by means of molecular dynamics computer simulations how the hypothesized liquid-liquid critical point of water shifts in supercooled aqueous solutions of salt as a function of concentration. We study sodium chloride solutions in TIP4P water, NaCl(aq), for concentrations c = 1.36 mol/kg and c = 2.10 mol/kg. The liquid-liquid critical point is found up to the highest concentration investigated, and its position in the P-T plane shifts to higher temperatures and lower pressures upon increasing concentration. For c = 2.10 mol/kg it is also located very close to the temperature of maximum density line of the system. The results are discussed and compared with previous results for bulk TIP4P water and for c = 0.67 mol/kg NaCl(aq) and with experimental findings. We observe a progressive shrinkage of the low-density liquid region when the concentration of salt increases; this suggests an eventual disappearance of the liquid-liquid coexistence upon further increase of NaCl concentration.

New theoretical method for rapid prediction of solvation free energy in water

We present a new theoretical method for rapid calculation of the solvation free energy in water by combining molecular simulation and the classical density functional theory (DFT). The DFT calculation is based on an accurate free-energy functional for water that incorporates the simulation results for long-range correlations and the fundamental measure theory for the molecular excluded-volume effects. The numerical performance of the theoretical method has been validated with simulation results and experimental data for the solvation free energies of halide (F(-), Cl(-), Br(-), and I(-)) and alkali (Li(+), Na(+), K(+), Rb(+), and Cs(+)) ions in water at ambient conditions. Because simulation is applied only to the particular thermodynamic condition of interest, the hybrid method is computationally much more efficient than conventional ways of solvation free energy calculations.

A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides

A classical nonpolarizable force field is presented for the simulation of aqueous alkali halide solutions (MX), where M = Li(+), Na(+), K(+), Rb(+), Cs(+) and X = F(-), Cl(-), Br(-), I(-), and their interactions with biomolecules. The models are specifically designed to reproduce the experimental Kirkwood-Buff integrals, and thereby the solution salt activities, as a function of salt concentration. Additionally, we demonstrate that these models reasonably reproduce other experimental properties including ion diffusion constants, dielectric decrements, and the excess heats of mixing. The parameters are developed by considering the properties of aqueous NaX and MCl solutions using a previously established model for NaCl. Transferability of the parameters to other salts is then established by the successful simulation of additional aqueous salt solutions, KI and CsBr, not originally included in the parameterization procedure.

Mapping the importance of four factors in creating monovalent ion selectivity in biological molecules

The ability of macrocycles, enzymes, ion channels, transporters, and DNA to differentiate among ion types is often crucial to their function. Using molecular dynamics simulations on both detailed systems and simple models, we quantify the importance of several factors which affect the ion selectivity of such molecules, including the number of coordinating ligands, their dipole moment, and their vibrational motion. The information resulting from our model systems is distilled into a series of selectivity maps that can be used to read off the relative free energy associated with binding of different ions, and to provide an estimate of the importance of the various factors. Although our maps cannot capture all elements of real systems, it is remarkable that they produce differential site-binding energies that are in line with experiment and more-detailed simulations for a variety of systems-making them useful for understanding the origins of selective binding and transport. The chemical nature of the coordinating ligands is essential for creating thermodynamic ion selectivity in flexible molecules (such as 18c6), but as the binding site becomes more rigid, the number of ligands (as in ion channels) and the reduction of thermal fluctuations (as in amino-acid transporters) can become important. In the future, our maps could aid in the determination of the local structure from binding energies and assist in the design of novel ion selective molecules.

A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide

Most current biomolecular simulations are based on potential energy functions that treat the electrostatic energy as a sum of pairwise Coulombic interactions between effective fixed atomic charges. This approximation, in which many-body induced polarization effects are included in an average way, is expected to be satisfactory for a wide range of systems, but less accurate for processes involving the transfer and partition of ions among heterogeneous environments. The limitations of these potential energy functions are perhaps most obvious in studies of ion permeation through membrane channels. In many cases, the pore is so narrow that the permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with protein atoms. Interactions of cations with protein backbone carbonyl oxygens, in particular, play a critical role in several important biological channels. As a first step toward meeting the challenge of developing an accurate explicit accounting for induced polarization effects, the present work combines experiments and computation to characterize the interactions of alkali and halide ions with N-methylacetamide chosen to represent the peptide bond. From solubility measurements, we extract the solvation free energies of KCl and NaCl in liquid N-methylacetamide. Polarizable models based on the Drude oscillator are then developed and compared with available experimental and ab initio data. The good agreement for a range of structural and thermodynamic properties in the gas and condensed phases suggests that the polarizable models provide an accurate representation of ion-amide interactions in biological systems.

Hydration of lanthanide chloride salts: a quantum chemical and classical molecular dynamics simulation study

We present the results of a quantum chemical and classical molecular dynamics simulation study of some solutions containing chloride salts of La(3+), Gd(3+), and Er(3+) at various concentrations (from 0.05 to 5 M), with the purpose of understanding their structure and dynamics and analyzing how the coordination varies along the lanthanide series. In the La-Cl case, nine water molecules surround the central La(3+) cation in the first solvation shell, and chloride is present only in the second shell for all solutions but the most concentrated one (5 M). In the Gd(3+) case, the coordination number is ∼8.6 for the two lowest concentrations (0.05 and 0.1 M), and then it decreases rapidly. In the Er(3+) case, the coordination number is 7.4 for the two lowest concentrations (0.05 and 0.1 M), and then it decreases. The counterion Cl(-) is not present in the first solvation shell in the La(3+) case for most of the solutions, but it becomes progressively closer to the central cation in the Gd(3+) and Er(3+) cases, even at low concentrations.

Structure and dynamics of hydrated ion pairs in a hydrophobic environment

The structure, energetics, and dynamics of different alkali halide ion pairs hydrated in a hydrophobic medium are studied using molecular dynamics computer simulations. One or two water molecules hydrating NaCl, NaI, KCl, KI, and KF in bulk carbon tetrachloride are considered. The ion pairs remain in contact throughout the simulations, so the structure of the hydration complex is well characterized. The ions' interaction energy and hydration structure are examined and correlated with the ion sizes and charges. For the first four salts, the stronger interaction of the water molecules with the cation than with the anion of the ion pair is in agreement with recent experiments. However, when the anion is significantly smaller than the cation (as in the case of KF, which was not studied experimentally), the opposite behavior is found. The asymmetry of interaction with the cation and the anion are further elucidated by examining hypothetical ion pairs made from equal-sized cations and anions and by defining an asymmetry hydration parameter, which is found to correlate well with the structural characteristics, as well as with the water molecules' reorientation dynamics.