Molecular dynamics simulation of solution structure and dynamics of aqueous sodium chloride solutions from dilute to supersaturated concentration

Uchida, Hirohisa; Matsuoka, Masakuni

doi:10.1016/j.fluid.2004.01.013

Cited by 61 publications

(47 citation statements)

References 38 publications

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“…5, at longrange the 0.0M concentration PMF is the lowest in energy followed by 0.1 and 0.3M PMFs, and finally by the 1.0M PMF. Interestingly, although there is pronounced difference between PMFs for the 0.0 and 0.1M concentrations as well as between those for the 0.3 and 1.0M concentrations, the PMFs for the 0.1 and 0.3M solutions are practically indistinguishable ͑within the specified accuracy͒ over the whole 16.0 Å range. The latter two concentrations correspond to physiological conditions.…”

Section: F Concentration Dependence Of the Na + -Cl − Pmfsmentioning

confidence: 91%

“…The nontrivial structural features arise from the interplay of the Coulomb and van der Waals forces between the ions and the water molecules and cannot be reproduced by simple models. [1][2][3][4][5][6][7][8][9] The parameters of the structural features to some extent depend on the ionic composition and concentration of the electrolytes in solution [10][11][12][13][14][15][16][17] and also on the size of the ions involved. 4,15,18 Importantly, in certain cases, the effective interactions between two ions of the same charge may become weakly attractive, seemingly defying the Coulomb repulsion.…”

Section: Introductionmentioning

confidence: 99%

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Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method

Khavrutskii

Dzubiella

McCammon

2008

The Journal of Chemical Physics

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We establish the accuracy of the novel generalized gradient-augmented harmonic Fourier beads ͑ggaHFB͒ method in computing free-energy profiles or potentials of mean force ͑PMFs͒ through comparison with two independent conventional techniques. In particular, we employ umbrella sampling with one dimensional weighted histogram analysis method ͑WHAM͒ and free molecular dynamics simulation of radial distribution functions to compute the PMF for the Na + -Cl − ion-pair separation to 16 Å in 1.0M NaCl solution in water. The corresponding ggaHFB free-energy profile in six dimensional Cartesian space is in excellent agreement with the conventional benchmarks. We then explore changes in the PMF in response to lowering the NaCl concentration to physiological 0.3 and 0.1M, and dilute 0.0M concentrations. Finally, to expand the scope of the ggaHFB method, we formally develop the free-energy gradient approximation in arbitrary nonlinear coordinates. This formal development underscores the importance of the logarithmic Jacobian correction to reconstruct true PMFs from umbrella sampling simulations with either WHAM or ggaHFB techniques when nonlinear coordinate restraints are used with Cartesian propagators. The ability to employ nonlinear coordinates and high accuracy of the computed free-energy profiles further advocate the use of the ggaHFB method in studies of rare events in complex systems.

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Section: F Concentration Dependence Of the Na + -Cl − Pmfsmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method

Khavrutskii

Dzubiella

McCammon

2008

The Journal of Chemical Physics

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“…A large ensemble of MD studies of aqueous ionic solutions using various parameter sets and particle mesh Ewald (PME) summation methods for the treatment of long-range electrostatic interactions have been published, including simulations of LiF, 27 LiCl, [33][34][35] NaCl, 7,[36][37][38][39][40][41][42][43][44][45] KCl, 15,40,45,46 RbCl, 35,45 CsCl, 45 NaBr, KBr, RbBr, CsBr, 45 and CsI. 35 Polarizable force-fields have also been used in other force-fields.…”

mentioning

confidence: 99%

“…As reported here, no ion aggregation has been reported in simulations using the Dang parameters even under high and supersaturated salt conditions. 38,42,43 AMBER parameters are rarely used in simulations of ionic aqueous solutions, 7,45 while they are recurrently used in MD simulations of biomolecular systems. [9][10][11][12][13] In one study, a comparison of calculated properties of a ∼1.0 M NaCl aqueous solution generated by using six different parameter sets revealed some level of aggregation for various force-fields including AMBER and GROMOS, while as expected, the Dang parameters did not lead to any detectable formation of ion clusters during 2 ns MD simulations.…”

mentioning

confidence: 99%

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

Auffinger

Cheatham

Vaiana

2007

J. Chem. Theory Comput.

162

177

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Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field parameters. Because similar results were obtained with two different water parameter sets, the simulations exclude a water model dependency in the formation of anomalous ionic clusters. Overall, the results strongly suggest that for accurate modeling of ions in biomolecular systems, great care should be taken in choosing balanced ionic parameters even when using the most popular force-fields. These results invite a reexamination of older data obtained using available force-fields and a thorough check of the quality of current parameters sets by performing simulations at finite (>0.25 M) instead of minimal salt conditions.

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“…For example, obstruction is a many-body problem and in general a numerical solution of the obstruction factor is the only practicable approach. MD simulations for these systems can provide valuable information on the solute-solute, solvent-solvent and solute-solvent interactions at the atomic level [37,38,[74][75][76].…”

Section: Obstructionmentioning

confidence: 99%

Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

et al. 2015

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Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance (NMR) measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

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Molecular dynamics simulation of solution structure and dynamics of aqueous sodium chloride solutions from dilute to supersaturated concentration

Cited by 61 publications

References 38 publications

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

Macromolecular crowding studies of amino acids using NMR diffusion measurements and molecular dynamics simulations

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