Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field

Stachura, Sławomir S.; Malajczuk, Chris J.; Mancera, Ricardo L.

doi:10.1007/s00894-018-3720-x

Cited by 13 publications

(12 citation statements)

References 66 publications

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“…Many experimental and theoretical investigations have been made into the structure of liquid solutions of DMSO, particularly around the 1:2 composition where the meltingpoint depression is greatest (e.g. Soper & Luzar, 1992;Vishnyakov et al, 2001;Bordallo et al, 2004;McLain et al, 2007;Wallace et al, 2015;Oh et al, 2017;Stachura et al, 2018;Wei et al, 2018;Yang et al, 2020). The prevailing interpretation of DMSO-water liquid data is in terms of 1:3 and 1:2 DMSOwater clusters and possible association into DMSO-(water) n -DMSO chains (Zhang et al, 2009;Idrissi et al, 2015;Verstakov et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

On the crystal structures and phase transitions of hydrates in the binary dimethyl sulfoxide–water system

Fortes¹,

Ponsonby²,

Kirichek³

et al. 2020

Acta Crystallogr Sect B

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Neutron powder diffraction data have been collected from a series of flash-frozen aqueous solutions of dimethyl sulfoxide (DMSO) with concentrations between 25 and 66.7 mol% DMSO. These reveal the existence of three stoichiometric hydrates, which crystallize on warming between 175 and 195 K. DMSO trihydrate crystallizes in the monoclinic space group P21/c, with unit-cell parameters at 195 K of a = 10.26619 (3), b = 7.01113 (2), c = 10.06897 (3) Å, β = 101.5030 (2)° and V = 710.183 (3) Å3 (Z = 4). Two of the symmetry-inequivalent water molecules form a sheet of tiled four- and eight-sided rings; the DMSO molecules are sandwiched between these sheets and linked along the b axis by the third water molecule to generate water–DMSO–water tapes. Two different polymorphs of DMSO dihydrate have been identified. The α phase is monoclinic (space group P21/c), with unit-cell parameters at 175 K of a = 6.30304 (4), b = 9.05700 (5), c = 11.22013 (7) Å, β = 105.9691 (4)° and V = 615.802 (4) Å3 (Z = 4). Its structure contains water–DMSO–water chains, but these are polymerized in such a manner as to form sheets of reniform eight-sided rings, with the methyl groups extending on either side of the sheet. On warming above 198 K, α-DMSO·2H2O undergoes a solid-state transformation to a mixture of DMSO·3H2O + anhydrous DMSO, and there is then a stable eutectic between these two phases at ∼203 K. The β-phase of DMSO dihydrate has been observed in a rapidly frozen eutectic melt and in very DMSO-rich mixtures. It is observed to be unstable with respect to the α-phase; above ∼180 K, β-DMSO·2H2O converts irreversibly to α-DMSO·2H2O. At 175 K, the lattice parameters of β-DMSO·2H2O are a = 6.17448 (10), b = 11.61635 (16), c = 8.66530 (12) Å, β = 101.663 (1)° and V = 608.684 (10) Å3 (Z = 4), hence this polymorph is just 1.16% denser than the α-phase under identical conditions. Like the other two hydrates, the space group appears likely, on the basis of systematic absences, to be P21/c, but the structure has not yet been determined. Our results reconcile 60 years of contradictory interpretations of the phase relations in the binary DMSO–water system, particularly between mole fractions of 0.25–0.50, and confirm empirical and theoretical studies of the liquid structure around the eutectic composition (33.33 mol% DMSO).

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Section: Introductionmentioning

confidence: 99%

On the crystal structures and phase transitions of hydrates in the binary dimethyl sulfoxide–water system

Fortes¹,

Ponsonby²,

Kirichek³

et al. 2020

Acta Crystallogr Sect B

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“…Theoretical calculations 25,24 have shown that there is a 20% increase of binding energy of H 2 with SiCNTs compared to pure CNTs. Computational modeling has already been successfully utilized to investigate a wide range of biologically significant phenomena such as the behavior of organic solvents in water, 26,27 the insulin signaling system, 28 β amyloid protein interaction with the membrane, 29 the antioxidant properties of nanostructures, 30,31 or the interaction of human immunodeficiency virus-binding peptide with the biomembrane. 32 Needless to say that by taking into account the available computational power and the level of the complexity of the systems composed of the heterogeneous nanotube and the phospholipid bilayer, only the classical molecular dynamics (MD) technique can be applied.…”

Section: ■ Introductionmentioning

confidence: 99%

Modeling the Impact of Silicon-Carbide Nanotube on the Phospholipid Bilayer Membrane: Study of Nanoindentation and Removal Processes via Molecular Dynamics Simulation

et al. 2019

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The molecular dynamics simulation technique was extensively used to explore systematically the nanoindentation of a phospholipid bilayer by a silicon-carbide nanotube. Three different indentation speeds were examined. In addition, the process of removal of the silicon-carbide nanotube from the membrane was investigated. Throughout the simulation, the mean force, work, and deflection of the bilayer were estimated and analyzed for both processes. It is found that the silicon-carbide nanotube does not destroy the phospholipid bilayer, and the self-sealing process is quite effective when the removal process is completed. Our study suggests that the silicon-carbide nanotube might be considered as a potential tool to deliver specific molecular cargo to the cells and to work as an artificial trans-membrane channel between the interior of the cell and the external environment.

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“…The solvent was described with the TIP3P water model . With respect to the AMBER parameter set for DMSO, we have recently shown that it faithfully reproduces a number of important experimental properties of DMSO in TIP3P water …”

Section: Methodsmentioning

confidence: 99%

“…While this methodology and these model systems are not especially unique, recent force-field advancements and the ability to explore longer simulation timescales gave us some confidence that we could elucidate some of the inconsistencies observed across earlier studies. For instance, we have previously demonstrated that the AMBER parameter set for DMSO faithfully reproduces a number of important experimental properties of DMSO in water . In terms of lipid force fields, Lipid14 was developed with updated Lennard-Jones and torsion parameters as well as refined partial charges compared with its predecessor Lipid11 in order to better reproduce a wide range of experimentally characterized membrane properties for several lipid types including DOPC .…”

Section: Introductionmentioning

confidence: 99%

Redefining the Molecular Interplay between Dimethyl Sulfoxide, Lipid Bilayers, and Dehydration

et al. 2022

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The potentially damaging action of dimethyl sulfoxide (DMSO) on phospholipid bilayers remains a matter of controversy. We have conducted a series of long-scale molecular dynamics simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers at various levels of hydration in the presence of variable quantities of DMSO. These simulations provide evidence for a non-destructive dehydrating mechanism of action for DMSO on DOPC bilayers across a wide concentration range and levels of hydration. Specifically, under full- and low-hydration conditions, the bilayer underwent a minor lateral contraction, coinciding with surface dehydration in the presence of dilute DMSO solutions (X DMSO < 0.3). At higher DMSO concentrations, this bilayer structure was retained despite a progressive deterioration of the hydration structure at the interface. A similar convergence of bilayer structural properties was observed under dehydration conditions for 0.3 < X DMSO < 0.7. Destabilization occurred for dehydrated bilayers in the presence of X DMSO ≥ 0.7, suggesting the existence of a DMSO concentration and/or dehydration threshold. However, such DMSO concentrations far exceed those established as toxic to other cellular components. Our findings represent a computational model for DMSO–DOPC interactions that is consistent with a range of experimental characterizations, offering new molecular insights into the cryoprotective mechanisms of action of DMSO.

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Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field

Cited by 13 publications

References 66 publications

On the crystal structures and phase transitions of hydrates in the binary dimethyl sulfoxide–water system

On the crystal structures and phase transitions of hydrates in the binary dimethyl sulfoxide–water system

Modeling the Impact of Silicon-Carbide Nanotube on the Phospholipid Bilayer Membrane: Study of Nanoindentation and Removal Processes via Molecular Dynamics Simulation

Redefining the Molecular Interplay between Dimethyl Sulfoxide, Lipid Bilayers, and Dehydration

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