3 Dienes, C9 to C26

Wilhoit, R. C.; Marsh, Kenneth N.; Hong, Xin; Gadalla, N.; Frenkel, Michael

doi:10.1007/10544836_9

Cited by 1 publication

(2 citation statements)

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“…After optimization of the partial atom charges, MD simulations of several dienes were carried out in the NPT ensemble at 303 K for 10 ns and the computed density was compared to the experimental ones . New recomputed partial charges (shown in Figure ) and torsion potentials from ref were used in these simulations.…”

Section: Methods and Modelsmentioning

confidence: 99%

“…New recomputed partial charges (shown in Figure ) and torsion potentials from ref were used in these simulations. The density computations for several isomers of nonadiene such as 1,8-nonadiene (0.74 g/cm 3 at 25 °C), 2-butyl-1,4-pentadiene (0.747 g/cm 3 at 25 °C, 2-(1,1-dimethylethyl)-1,3-pentadiene (0.751 g/cm 3 at 25 °C), 2,4-dimethyl-1,5-heptadiene (0.746 g/cm 3 at 25 °C) showed agreement with experimental data within 1% in all cases. For cis -3, cis -6-dodecadiene we compared simulated density (0.777 g/cm 3 at 30 °C) with experimental density of isomers cis -5, cis -7-dodecadiene (0.777 g/cm 3 ) [, accessed October 18, 2016], and cis -5, cis -7-dodecadiene (0.767 g/cm 3 ) [, accessed October 18, 2016].…”

Section: Methods and Modelsmentioning

confidence: 99%

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Extension of the Slipids Force Field to Polyunsaturated Lipids

Ermilova

Lyubartsev

2016

J. Phys. Chem. B

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The all-atomic force field Slipids (Stockholm Lipids) for lipid bilayers simulations has been extended to polyunsaturated lipids. Following the strategy adopted in the development of previous versions of the Slipids force field, the parametrization was essentially based on high-level ab initio calculations. Atomic charges and torsion angles related to polyunsaturated lipid tails were parametrized using structures of dienes molecules. The new parameters of the force field were validated in simulations of bilayers composed of seven polyunsaturated lipids. An overall good agreement was found with available experimental data on the areas per lipids, volumetric properties of bilayers, deuterium order parameters, and scattering form factors. Furthermore, simulations of bilayers consisting of highly polyunsaturated lipids and cholesterol molecules have been carried out. The majority of cholesterol molecules were found in a position parallel to bilayer normal with the hydroxyl group directed to the membrane surface, while a small fraction of cholesterol was found in the bilayer center parallel to the membrane plane. Furthermore, a tendency of cholesterol molecules to form chain-like clusters in polyunsaturated bilayers was qualitatively observed.

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Section: Methods and Modelsmentioning

confidence: 99%

Section: Methods and Modelsmentioning

confidence: 99%