Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties

Patra, Michael; Karttunen, Mikko

doi:10.1002/jcc.10417

Cited by 205 publications

(219 citation statements)

References 46 publications

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“…For cross LJ interaction parameters between ions and water, and between PEG chain and CHARMM atoms, we followed Patra et al [75] and Zheng et al [76] respectively and used Lorentz-Berthelot combination rules. …”

Section: Force Field Parameters For Cross-linker and Ionsmentioning

confidence: 99%

Effect of Cross-Linking on the Diffusion of Water, Ions, and Small Molecules in Hydrogels

2009

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Understanding the diffusion of small molecules in hydrogel system is of major importance in a variety of applications including drug delivery systems, tissue engineering and contact lens. Cross-linking density of hydrogels has been commonly used to tune key parameters like mesh size and molecular weight between cross-linkers, in order to change macroscopic properties of hydrogels. In this thesis, molecular dynamics investigations of chemically-cross-linked poly(ethylene glycol) (PEG) hydrogels are reported with the aim of exploring the diffusion properties of water, ions, and rhodamine within the polymer at the molecular level.The water structure and diffusion properties were studied at various cross-linking densities with molecular weights of the chains ranging from 572 to 3400. As the cross-linking density is increased, the water diffusion decreases and the slowdown in diffusion is more severe at the polymer-water interface. The water diffusion at various cross-linking densities is correlated with the water hydrogen bonding dynamics. The diffusion of ions and rhodamine also decreased as the cross-linking density is increased. The variation of diffusion coefficient with cross-linking density is related to the variation of water content at different cross-linking densities.Comparison of simulation results and obstruction scaling theory for hydrogels showed similar trends.ii To Father and Mother.iii

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Section: Force Field Parameters For Cross-linker and Ionsmentioning

confidence: 99%

Effect of Cross-Linking on the Diffusion of Water, Ions, and Small Molecules in Hydrogels

2009

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“…32 For NaCl we employed the default set of parameters supplied within the Gromacs force field, 33,34 while being aware of the effects of different models for sodium and chloride ions. 35 The Lennard-Jones interactions were cut off at 1 nm without shift or switch functions. Since truncation of electrostatic interactions is known to lead to pronounced artifacts in simulations of lipid bilayers, [36][37][38] the long-range interactions were handled using the particle-mesh Ewald (PME) method.…”

Section: Model and Simulation Detailsmentioning

confidence: 99%

Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations

Gurtovenko

Miettinen²,

Karttunen³

et al. 2005

J. Phys. Chem. B

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An atomic-scale understanding of cationic lipid membranes is required for development of gene delivery agents based on cationic liposomes. To address this problem, we recently performed molecular dynamics (MD) simulations of mixed lipid membranes comprised of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) (Biophys. J. 2004, 86, 3461-3472). Given that salt ions are always present under physiological conditions, here we focus on the effects of monovalent salt (NaCl) on cationic (DMPC/DMTAP) membranes. Using atomistic MD simulations, we found that saltinduced changes in membranes depend strongly on their composition. When the DMTAP mole fraction is small (around 6%), the addition of monovalent salt leads to a considerable compression of the membrane and to a concurrent enhancement of the ordering of lipid acyl chains. That is accompanied by reorientation of phosphatidylcholine headgroups in the outward normal direction and slight changes in electrostatic properties. We attribute these changes to complexation of DMPC lipids with Na + ions which penetrate deep into the membrane and bind to the carbonyl region of the DMPC lipids. In contrast, at medium and high molar fractions of cationic DMTAP (50 and 75%) a substantial positive surface charge density of the membranes prevents the binding of Na + ions, making such membranes almost insensitive to monovalent salt. Finally, we compare our results to the Poisson-Boltzmann theory. With the exception of the immediate vicinity of the bilayer plane, we found excellent agreement with the theory. This is as expected since unlike in the theoretical description the surface is now structured due to its atomic scale nature.

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“…5 Geissler et al provided an interesting look into the complexity of an ionic dissociation and emphasized the importance of including explicit solvent dynamics. 4 One of the few quantum mechanical approaches to this topic was taken up by Ghosh et al 13 In their investigation of NaCl(H 2 O) [1][2][3][4][5][6] clusters and subsequent QM/EFP-MD simulation they found and described several Interionic Hydration Structures (IHS), in addition to the CIP and SSIP species.…”

Section: Introductionmentioning

confidence: 99%

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

Wiedemair

Weiss²,

Rode

2014

Phys. Chem. Chem. Phys.

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A single sodium chloride molecule in aqueous solution was simulated by the ab initio quantum mechanical charge field-molecular dynamics (QMCF-MD) approach. During a series of simulations the solvated molecule (CIP), dissociated solvated ions and -most noticeably -a solvent separated ion pair (SSIP) were observed and the structural and dynamical characteristics of these systems were investigated. In addition to a detailed structural analysis of the observed species, vibrational spectra and charge distributions were calculated to elucidate the mechanism of the NaCl dissociation.

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Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties

Cited by 205 publications

References 46 publications

Effect of Cross-Linking on the Diffusion of Water, Ions, and Small Molecules in Hydrogels

Effect of Cross-Linking on the Diffusion of Water, Ions, and Small Molecules in Hydrogels

Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation

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