Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

Yu, Haibo; Whitfield, Troy W.; Harder, Edward; Lamoureux, Guillaume; Vorobyov, Igor; Anisimov, Victor M.; MacKerell, Alexander D.; Roux, Benoı̂t

doi:10.1021/ct900576a

Cited by 421 publications

(670 citation statements)

References 94 publications

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“…The parameters in these models were optimized to reproduce the binding energies of gas-phase monohydrates and the hydration free energies in the bulk liquid. These models have since been updated and extended with additional ions (36), yielding confidence that further computational investigations on airborne chemicals can be done in order to advance knowledge of atmospheric chemicals and their interactions.…”

Section: Methodsmentioning

confidence: 99%

Atomistic simulation of ion solvation in water explains surface preference of halides

Caleman

Hub

Maaren

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

209

316

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Water is a demanding partner. It strongly attracts ions, yet some halide anions-chloride, bromide, and iodide-are expelled to the air/water interface. This has important implications for chemistry in the atmosphere, including the ozone cycle. We present a quantitative analysis of the energetics of ion solvation based on molecular simulations of all stable alkali and halide ions in water droplets. The potentials of mean force for Cl − , Br − , and I − have shallow minima near the surface. We demonstrate that these minima derive from more favorable water-water interaction energy when the ions are partially desolvated. Alkali cations are on the inside because of the favorable ion-water energy, whereas F − is driven inside by entropy. Models attempting to explain the surface preference based on one or more ion properties such as polarizability or size are shown to lead to qualitative and quantitative errors, prompting a paradigm shift in chemistry away from such simplifications.ozone layer | GROMACS | aerosol | thermodynamics S ea water becomes airborne in the form of droplets formed at the sea surface by the action of waves (1). These droplets can be carried by the wind, and they interact with other constituents of the atmosphere (Fig. 1A). On the surface of the small water droplets, halide anions can be converted into halogen atoms by absorption of light (2, 3), and the air-water interface serves to increase certain reaction probabilities (4, 5). One example is the oxidation of Cl − and Br − by OH radicals or O 3 that can occur at the air-water interface, with mechanisms different from those in the bulk phase (6), leading to natural ozone depletion in the stratosphere.Both theoretical and experimental studies have shown that Cl − , Br − and I − prefer to be at the surface of water droplets (Fig. 1A), whereas F − and alkali cations strive to become fully solvated in the bulk of water droplets (7-12). The Br − concentration is enhanced more at the surface than the Cl − concentration (13), an effect that may be enhanced in mixtures containing both Br − and Cl − , such as seawater (14). Because Br − is more reactive than Cl − , the surface preference has an impact on the chemistry in the atmosphere, despite the fact that the content of Cl − in bulk sea water is about three orders of magnitude higher than that of Br − (15). The energetic and structural mechanisms underlying the surface preference of large halide anions have been studied in quite some detail (16-18), but the phenomenon is still not understood quantitatively (10). Only very recently has the surface absorption free energy of one halide anion, Br − , been determined experimentally (19). Recent progress in development of force fields for water (20) and ions (21) finally allows establishment of the surface preferences for all halide and alkali ions quantitatively.Here we present the energetics of ion solvation in a water droplet with a radius of approximately 1.1 nm for all stable halide anions (F − , Cl − , Br − , I − ) and alkali cations (Li þ , Na þ , K þ...

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Section: Methodsmentioning

confidence: 99%

Atomistic simulation of ion solvation in water explains surface preference of halides

Caleman

Hub

Maaren

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

209

316

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“…22,27 Ever since, force field parameters based on Drude oscillator models have been developed for water, 22,28 alkanes, 29 alcohols, 30 ethers, 31 amides, 32 aromatics, 33 nitrogen-containing heteroaromatics, 34 sulfur-containing compounds, 35,36 and ions. 37,38 Those for biomolecules, such as proteins, nucleic acids, lipids, and carbohydrates, 39 are under active development. While these models have shown improvements in many properties as compared with their additive counterparts, it is of interest to see how they will perform in describing the behavior of liquid mixtures when compared to the additive force field.…”

Section: Introductionmentioning

confidence: 99%

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Lin

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

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Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.

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“…Second, parameters for acetate were included in the forcefield. Ion parameters in the Drude-2013 forcefield were developed by matching single-ion properties such as geometries and energies of monohydrates, and the solvation free energy at the infinite dilution limit 20 . The parameters were thereafter optimized to reproduce osmotic pressure data, in order to enable simulations of concentrated solutions 46 .…”

Section: Approachmentioning

confidence: 99%

“…Also, more complex inter-atomic potentials make such forcefields less transferable between software packages. Different polarizable forcefields are available for ions, including Drude or 'particle on a spring' type forcefields 20 , forcefields that rely on induced dipoles 21 , forcefields that use a multipole approach 22 , and forcefields that allow charge-transfer [23][24][25][26] .…”

Section: Introductionmentioning

confidence: 99%

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

Ahlstrand

Schpector

Friedman

2017

The Journal of Chemical Physics

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When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions is available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields, and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1 M). In addition, quantummechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li + and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved, but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.

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Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

Cited by 421 publications

References 94 publications

Atomistic simulation of ion solvation in water explains surface preference of halides

Atomistic simulation of ion solvation in water explains surface preference of halides

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations

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