Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution.

Research output: Contribution to journalArticle

Abstract

Sodium dodecyl sulfate (SDS) is a well-known anionic detergent widely used in both experimental and theoretical investigations. Many molecular dynamics (MD) simulation have been performed on the SDS molecule at coarse-grained (CG), united-atom (UA), and all-atom (AA) resolutions. However, these simulations are usually based on general parameters determined from large sets of molecules, and as a result, peculiar molecular specificities are often poorly represented. In addition, the parameters (ideal bond lengths, angles, dihedrals and charge distribution) differ according to the resolution, highlighting a lack of coherence. We therefore propose a new set of parameters for CG, UA, and AA resolutions based on a high quantum mechanics (QM) level optimization of the detergent structure and the charge distribution. For the first time, QM-optimized parameters were directly applied to build the AA, UA, and CG model of the SDS molecule, leading to a more coherent description. As a test case, MD simulations were then performed on SDS preformed micelles as previous experimental and theoretical investigations allow direct comparison with our new sets of parameters. While all three models yield similar macromolecular properties (size, shape, and accessible surface) perfectly matching previous results, the attribution of more coherent parameters to SDS enables the description of the specific interactions inside and outside the micelle. These more consistent parameters can now be used to accurately describe new multi-scale systems involving the SDS molecule.

Original languageEnglish
Article number20
Pages (from-to)2469-2477
Number of pages8
JournalJournal of Molecular Modeling
Volume20
Issue number10
DOIs
Publication statusPublished - 10 Oct 2014

Fingerprint

Sodium dodecyl sulfate
Micelles
sodium sulfates
Sodium Dodecyl Sulfate
Molecular dynamics
micelles
molecular dynamics
Atoms
Computer simulation
atoms
Molecules
simulation
Quantum theory
Charge distribution
Detergents
detergents
charge distribution
quantum mechanics
molecules
Bond length

Keywords

  • All-atom
  • Coarse-grained
  • GROMOS
  • Molecular dynamics
  • Parameters
  • Sodium dodecyl sulfate
  • United-atom

Cite this

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title = "Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution.",
abstract = "Sodium dodecyl sulfate (SDS) is a well-known anionic detergent widely used in both experimental and theoretical investigations. Many molecular dynamics (MD) simulation have been performed on the SDS molecule at coarse-grained (CG), united-atom (UA), and all-atom (AA) resolutions. However, these simulations are usually based on general parameters determined from large sets of molecules, and as a result, peculiar molecular specificities are often poorly represented. In addition, the parameters (ideal bond lengths, angles, dihedrals and charge distribution) differ according to the resolution, highlighting a lack of coherence. We therefore propose a new set of parameters for CG, UA, and AA resolutions based on a high quantum mechanics (QM) level optimization of the detergent structure and the charge distribution. For the first time, QM-optimized parameters were directly applied to build the AA, UA, and CG model of the SDS molecule, leading to a more coherent description. As a test case, MD simulations were then performed on SDS preformed micelles as previous experimental and theoretical investigations allow direct comparison with our new sets of parameters. While all three models yield similar macromolecular properties (size, shape, and accessible surface) perfectly matching previous results, the attribution of more coherent parameters to SDS enables the description of the specific interactions inside and outside the micelle. These more consistent parameters can now be used to accurately describe new multi-scale systems involving the SDS molecule.",
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