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

Reversal of Salt Concentration Dependencies of Salt and Water Diffusivities in Polymer Electrolyte Membranes

Recent experimental results have shown that transport properties of salt ions and water in charged polymer membranes exhibit an intriguing dependence on salt concentration that is opposite to that seen in electrolyte solutions. Motivated by such observations, in this study we have used atomistic molecular dynamics simulations to investigate the molecular level mechanisms underlying the transport properties of salt solutions in charged polymer membranes. Our results are in qualitative agreement with experimental results and suggest that the mobility of the salt ions is influenced by electrostatic interactions with the charged groups in the polymer membrane. The mobility of water molecules is shown to arise as a consequence of the influence of salt on the hydration characteristics in solution and polymer electrolyte systems.

RNA force field with accuracy comparable to state-of-the-art protein force fields

The complex and often highly dynamic 3D structures of RNA molecules are central to their diverse cellular functions. Molecular dynamics (MD) simulations have played a major role in characterizing the structure and dynamics of proteins, but the physical models (“force fields”) used for simulating nucleic acids are substantially less accurate overall than those used in protein simulations, creating a major challenge for MD studies of RNA. Here, we report an RNA force field capable of describing the structural and thermodynamic properties of RNA molecules with accuracy comparable to state-of-the-art protein force fields. This force field should facilitate the use of MD simulation as a tool for the study of biologically significant RNA molecules and protein–RNA complexes.

Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models (“force fields”) available for MD simulations of RNA molecules are substantially less accurate in many respects than those currently available for proteins. Here, we introduce an extensive revision of a widely used RNA force field in which the parameters have been modified, based on quantum mechanical calculations and existing experimental information, to more accurately reflect the fundamental forces that stabilize RNA structures. We evaluate these revised parameters through long-timescale MD simulations of a set of RNA molecules that covers a wide range of structural complexity, including single-stranded RNAs, RNA duplexes, RNA hairpins, and riboswitches. The structural and thermodynamic properties measured in these simulations exhibited dramatically improved agreement with experimentally determined values. Based on the comparisons we performed, this RNA force field appears to achieve a level of accuracy comparable to that of state-of-the-art protein force fields, thus significantly advancing the utility of MD simulation as a tool for elucidating the structural dynamics and function of RNA molecules and RNA-containing biological assemblies.

Density Functional Computations and Molecular Dynamics Simulations of the Triethylammonium Triflate Protic Ionic Liquid

Systematic molecular dynamics simulations based on an empirical force field have been carried out for samples of triethylammonium trifluoromethanesulfonate (triethylammonium triflate, [TEA][Tf]), covering a wide temperature range 200 K ≤ T ≤ 400 K and analyzing a broad set of properties, from self-diffusion and electrical conductivity to rotational relaxation and hydrogen-bond dynamics. The study is motivated by recent quasi-elastic neutron scattering and differential scanning calorimetry measurements on the same system, revealing two successive first order transitions at T ≈ 230 and 310 K (on heating), as well as an intriguing and partly unexplained variety of subdiffusive motions of the acidic proton. Simulations show a weakly discontinuous transition at T = 310 K and highlight an anomaly at T = 260 K in the rotational relaxation of ions that we identify with the simulation analogue of the experimental transition at T = 230 K. Thus, simulations help identifying the nature of the experimental transitions, confirming that the highest temperature one corresponds to melting, while the one taking place at lower T is a transition from the crystal, stable at T ≤ 260 K, to a plastic phase (260 ≤ T ≤ 310 K), in which molecules are able to rotate without diffusing. Rotations, in particular, account for the subdiffusive motion seen at intermediate T both in the experiments and in the simulation. The structure, distribution, and strength of hydrogen bonds are investigated by molecular dynamics and by density functional computations. Clustering of ions of the same sign and the effect of contamination by water at 1% wgt concentration are discussed as well.

Force Field Parametrization of Metal Ions from Statistical Learning Techniques

A novel statistical procedure has been developed to optimize the parameters of nonbonded force fields of metal ions in soft matter. The criterion for the optimization is the minimization of the deviations from ab initio forces and energies calculated for model systems. The method exploits the combination of the linear ridge regression and the cross-validation techniques with the differential evolution algorithm. Wide freedom in the choice of the functional form of the force fields is allowed since both linear and nonlinear parameters can be optimized. In order to maximize the information content of the data employed in the fitting procedure, the composition of the training set is entrusted to a combinatorial optimization algorithm which maximizes the dissimilarity of the included instances. The methodology has been validated using the force field parametrization of five metal ions (Zn²⁺, Ni²⁺, Mg²⁺, Ca²⁺, and Na⁺) in water as test cases.

Two Cl Ions and a Glu Compete for a Helix Cage in the CLC Proton/Cl- Antiporter

The ubiquitously expressed CLC chloride transporters are involved in a great variety of physiological functions. The CLC protein fold is shared by Cl^- channels and 2Cl^-:1H⁺ antiporters. The antiporters pump three charges per cycle across the membrane with two Cl ions moving in the opposite direction of one proton. Multiconformational continuum electrostatics was used to calculate the coupled thermodynamics of the protonation of the extracellular-facing gating Glu (E_x) and Cl^- binding to the external (S_x) and central (S_c) sites in CLC-ec1, the Escherichia coli exchanger. S_x, S_c, and E_x are buried within the protein where the intersection of two helix N-termini creates a region with a strong, localized positive potential for anion binding. Our chemical potential titrations describe the thermodynamic linkage for binding the Cl^- to each site and protons to E_x. We find that the 2Cl^-:1H⁺ binding stoichiometry is a result of Cl^- binding to S_x requiring H⁺ binding to E_x, whereas Cl^- binding to S_c does not lead to proton uptake. When S_x binds a Cl^-, the protonated E_x moves upward, out of the positive helix cage. The increasing E_x proton affinity on binding the first Cl^- reduces the cost of binding the second Cl^- at either S_x or S_c. Despite the repulsion among the anions, the lowest energy states have two anions bound in the helix cage. The state with no Cl^- is not favored electrostatically, but relies on E_x blocking S_x and on the central residues Y445 and S107 blocking S_c.

Surface Polarization Effects on Ion-Containing Emulsions

Surface polarization in ion-containing heterogeneous dielectric media such as cell media and emulsions is determined by and determines the positions of the ions. We compute the surface polarization self-consistently as the ions move and analyze their effects on the interactions between electro-neutral, ion-containing droplets using coarse-grained molecular dynamics simulations based on the true energy functional. For water droplets immersed in oil, the interdroplet interaction is attractive, and the surface polarization makes the major contribution. By contrast, for oil droplets in water, the ion-surface induced charge interaction is repulsive and counteracts the attraction between the ions, leading to a small attractive interaction between the droplets. This research improves our understanding of self-assembly in mixed phases such as metal extraction for recovering rare earth elements and nuclear waste as well as water purification.

Understanding the molecular mechanism of pulse current charging for stable lithium-metal batteries

High energy and safe electrochemical storage are critical components in multiple emerging fields of technologies. Rechargeable lithium-metal batteries are considered to be promising alternatives for current lithium-ion batteries, leading to as much as a 10-fold improvement in anode storage capacity (from 372 to 3860 mAh g-1). One of the major challenges for commercializing lithium-metal batteries is the reliability and safety issue, which is often associated with uneven lithium electrodeposition (lithium dendrites) during the charging stage of the battery cycling process. We report that stable lithium-metal batteries can be achieved by simply charging cells with square-wave pulse current. We investigated the effects of charging period and frequency as well as the mechanisms that govern this process at the molecular level. Molecular simulations were performed to study the diffusion and the solvation structure of lithium cations (Li+) in bulk electrolyte. The model predicts that loose association between cations and anions can enhance the transport of Li+ and eventually stabilize the lithium electrodeposition. We also performed galvanostatic measurements to evaluate the cycling behavior and cell lifetime under pulsed electric field and found that the cell lifetime can be more than doubled using certain pulse current waveforms. Both experimental and simulation results demonstrate that the effectiveness of pulse current charging on dendrite suppression can be optimized by choosing proper time- and frequency-dependent pulses. This work provides a molecular basis for understanding the mechanisms of pulse current charging to mitigating lithium dendrites and designing pulse current waveforms for stable lithium-metal batteries.

Analysis of Prepeak Structure of Concentrated Organic Lithium Electrolyte by Means of Neutron Diffraction with Isotopic Substitution and Molecular Dynamics Simulation

The prepeak structure of a 3 mol/kg solution of LiClO₄ in propylene carbonate (PC) was studied by both neutron diffraction with isotopic substitution (NDIS) and molecular dynamics (MD) simulation. The NDIS data showed that the intensity of the prepeak decreases experimentally with an increase in the scattering length of the lithium atom from ⁷Li to ⁶Li in PC-d₆. On the other hand, although the prepeak was observed in solutions of both PC-d₆ and PC-h₆, it disappears when the 1:1 mixture of PC-d₆ and PC-h₆ was used as the solvent. The prepeak structure and its variation with the isotope substitution were reproduced well by MD simulation, and they were explained in terms of the contrast of the scattering length densities of the ionic and nonpolar domains.

Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data

Force-field parameters are developed for a multisite model of Ni(II) ions to be used in molecular dynamics simulations combined to enhanced sampling methods. The performances of two charge-partitioning schemes are validated by taking into account structural, thermodynamic, and kinetic observables. One of the two models, featuring partial charges on the dummy atoms only, matches both Ni(II) free energy of solvation and water exchange rates. Such model is particularly suited to study complexation events at a fully dynamic description. © 2017 Wiley Periodicals, Inc.

Metal Ion Modeling Using Classical Mechanics

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

Collective dynamic dipole moment and orientation fluctuations, cooperative hydrogen bond relaxations, and their connections to dielectric relaxation in ionic acetamide deep eutectics: Microscopic insight from simulations

The paper reports a detailed simulation study on collective reorientational relaxation, cooperative hydrogen bond (H-bond) fluctuations, and their connections to dielectric relaxation (DR) in deep eutectic solvents made of acetamide and three uni-univalent electrolytes, lithium nitrate (LiNO3), lithium bromide (LiBr), and lithium perchlorate (LiClO4). Because cooperative H-bond fluctuations and ion migration complicate the straightforward interpretation of measured DR timescales in terms of molecular dipolar rotations for these conducting media which support extensive intra- and inter-species H-bonding, one needs to separate out the individual components from the overall relaxation for examining the microscopic origin of various timescales. The present study does so and finds that reorientation of ion-complexed acetamide molecules generates relaxation timescales that are in sub-nanosecond to nanosecond range. This explains in molecular terms the nanosecond timescales reported by recent giga-Hertz DR measurements. Interestingly, the simulated survival timescale for the acetamide-Li(+) complex has been found to be a few tens of nanosecond, suggesting such a cation-complexed species may be responsible for a similar timescale reported by mega-Hertz DR measurements of acetamide/potassium thiocyanate deep eutectics near room temperature. The issue of collective versus single particle relaxation is discussed, and jump waiting time distributions are determined. Dependence on anion-identity in each of the cases has been examined. In short, the present study demonstrates that assumption of nano-sized domain formation is not required for explaining the DR detected nanosecond and longer timescales in these media.

Ion-Specific Effects on the Elongation Dynamics of a Nanosized Water Droplet in Applied Electric Fields

We report an all-atom molecular dynamics study of the structures and dynamics of salty water droplets on a silicon surface under the influence of applied electric field. Our simulation results support ion-specific effects on the elongation dynamics of salty nanodroplets, induced by the field. This feature has not been explored up to now in monovalent salts. Nevertheless, the importance of ion-specific effects is widely confirmed in biological and colloidal systems. In particular, the increase of salt concentration enhances the effect of the nature of ions on the wetting properties of droplets. In the presence of electric field (0.05 V Å^-1), a complete spreading is implemented in a short time for different droplets at a concentration of 1 M, and the droplet morphology is stable, observed at long time scales. However, a higher salt concentration of 4 M considerably suppresses the spreading process owing to the increase of surface tension. It was found that the NaCl droplet shows deformation oscillations along the external field, but cannot fully wet the substrate surface. By contrast, the CsCl droplet reaches complete elongation rapidly and adopts a steady strip shape. The KCl droplet undergoes frequent transitions between breakup and connection. Additionally, the droplets can be elongated only when the electric field strength exceeds a threshold value. The dipole orientation of interfacial water and the ionic diffusion exhibit ion-specific dependences, but the hydrogen bond network is scarcely disturbed, excluding a concentration-dependent effect.

Electronic and relativistic contributions to ion-pairing in polyoxometalate model systems

Experiment and theory delineate covalency, electrostatic association, and relativistic effect contributions to polyoxometalate-alkali ion-pairs in water.

Developing multisite empirical force field models for Pt(II) and cisplatin

We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water. Comparison has been made with experimental and quantum mechanical results. We have demonstrated that both versions are generally capable of reproducing key properties of the system, but the second-order polarizable POSSIM formalism permits more accurate quantitative results to be obtained. For example, the energy of formation of cisplatin as calculated with the modified OPLS-AA exhibited an error of 9.9%, while the POSSIM error for the same quantity was 6.2%. The produced parameter sets are transferable and suitable to be used in protein-metal binding simulations in which position or even coordination of the ion does not have to be constrained using preexisting knowledge. © 2016 Wiley Periodicals, Inc.

The effects of replacing the water model while decoupling water-water and water-solute interactions on computed properties of simple salts

The effects of decoupling the water-water and water-solute interactions are studied with selected mono-valent ions as the solute. Using the ion-water cross terms developed for the BLYPSP-4F water model, we replaced the water potential with WAIL, TIP4P, and TIP3P without changing the ion-water parameters. When the adaptive force matching (AFM) derived BLYPSP-4F model is replaced by the other AFM derived WAIL model, the difference in ion properties, such as hydration free energies, radial distribution functions, relative diffusion constants, is negligible, demonstrating the feasibility for combining AFM parameters from different sources. Interestingly, when the AFM-derived ion-water cross-terms are used with a non-AFM based water model, only small changes in the ion properties are observed. The final combined models with TIP3P or TIP4P water reproduce the salt hydration free energies within 6% of experiments. The feasibility of combining AFM models with other non-AFM models is of significance since such combinations allow more complex systems to be studied without specific parameterization. In addition, the study suggests an interesting prospect of reusing the cross-terms when a part of a general force field is replaced with a different model. The prevailing practice, which is to re-derive all cross-terms with combining rules, may not have been optimal.

Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching

Simple non-polarizable potentials were developed for Na(+), K(+), Cl(-), and Br(-) using the adaptive force matching (AFM) method with ab initio MP2 method as reference. Our MP2-AFM force field predicts the solvation free energies of the four salts formed by the ions with an error of no more than 5%. Other properties such as the ion-water radial distribution functions, first solvation shell water tilt angle distributions, ion diffusion constants, concentration dependent diffusion constant of water, and concentration dependent surface tension of the solutions were calculated with this potential. Very good agreement was achieved for these properties. In particular, the diffusion constants of the ions are within 6% of experimental measurements. The model predicts bromide to be enriched at the interface in the 1.6M KBr solution but predicts the ion to be repelled for the surface at lower concentration.

Long-timescale dynamics of the Drew-Dickerson dodecamer

We present a systematic study of the long-timescale dynamics of the Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC)₂) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na⁺Cl⁻ or K⁺Cl⁻. The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

A classical force field for tetrahedral oxyanions developed using hydration properties: The examples of pertechnetate (TcO4(-)) and sulfate (SO4(2-))

Radioactive pertechnetate, (99)TcO4(-), is one of the most problematic ionic species in the context of the clean up and storage of nuclear waste. Molecular simulations can be used to understand the behavior of TcO4(-) in dilute aqueous solutions, providing reliable potentials are available. This work outlines the development of a new potential model for TcO4(-) and competing SO4(2-), optimized using their hydration properties, such as the Gibbs hydration free energy (calculated using Bennett's acceptance ratio method). The findings show that the TcO4(-) oxyanion has a very low hydration free energy (-202 kJ mol(-1)) compared to other anions (Cl(-), I(-), SO4(2-)) leading to fast water exchange dynamics and explaining its observed high mobility in the aqueous environment. Its hydrated structure, investigated using ion-water radial distribution functions, shows that it is unique amongst the other anions in that it does not possess well-defined hydration shells. Since contaminants and ubiquitous species in the aqueous environment are often present as tetrahedral oxyanions, it is proposed that the approach could easily be extended to a whole host of other species.

Nuclear quantum effects in water exchange around lithium and fluoride ions

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell is found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.

Effect of interionic interactions on the structure and dynamics of ionic solvation shells in aqueous electrolyte solutions

Molecular dynamics (MD) simulations to explore the structure and dynamics of the ionic solvation shell of alkali ions and halide ions in aqueous solution.