Micelles molecular dynamics

Figure C2.3.7. Snapshot of micelle of sodium octanoate obtained during molecular dynamics simulation. The darkest shading is for sodium counter-ions, the lightest shading is for oxygens and the medium shading is for carbon atoms. Reproduced by pennission from figure 2 of [36].

Mesoscale simulations model a material as a collection of units, called beads. Each bead might represent a substructure, molecule, monomer, micelle, micro-crystalline domain, solid particle, or an arbitrary region of a fluid. Multiple beads might be connected, typically by a harmonic potential, in order to model a polymer. A simulation is then conducted in which there is an interaction potential between beads and sometimes dynamical equations of motion. This is very hard to do with extremely large molecular dynamics calculations because they would have to be very accurate to correctly reflect the small free energy differences between microstates. There are algorithms for determining an appropriate bead size from molecular dynamics and Monte Carlo simulations. 

M. Kroger, R. Makhloufi. Wormlike micelles under shear flow A microscopic model studied by nonequihbrium molecular dynamics computer simulations. Phys Rev E 55 2531-2536, 1996. 

MacKerell, Jr., A. D. (1995) Molecular dynamics simulation analysis of a sodium dodecyl sulfate micelle in aqueous solution decreased fluidity of the micelle hydrocarbon interior. J. Phys. Chem. 99, 1846-1855. 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

I. Benjamin, Chemical reactions and solvation at liquid interfaces a microscopic perspective, Chem. Rev. (Washington, D. C.), 96 (1996) 1449-75 I. Benjamin, Theory and computer simulations of solvation and chemical reactions at liquid interfaces, Acc. Chem. Res., 28 (1995) 233-9 L. R. Martins, M. S. Skaf and B. M. Ladanyi, Solvation dynamics at the water/zirconia interface molecular dynamics simulations, J. Phys. Chem. B, 108 (2004) 19687-97 J. Faeder and B. M. Ladanyi, Solvation dynamics in reverse micelles the role of headgroup-solute interactions, J. Phys. Chem. B, 109 (2005) 6732 10 W. H. Thompson, Simulations of time-dependent fluorescence in nano-confined solvents, J. Chem. Phys., 120 (2004) 8125-33. 

There are presently several groups around the world conducting molecular dynamics simulations of micellization and liquid crystallization of more or less realistic models of water, hydrocarbon, and surfactants. The memory and speed of a supercomputer required to produce reliably equilibrated microstructures constitute a challenge not yet met, in my opinion. By taking advantage of identified or hypothesized elemental structures one can, however, hope to learn a great deal about the dynamics and stability of the various identified microstructures. 

We shall consider only some results of investigation of complex polymer systems by method of EPR-spectroscopy obtained recently (results obtained earlier were considered in details in works [2, 3]). We shall discuss possibilities of method of EPR-spectroscopy of spin marks and probes for determination of macromolecules conformation in solid state, and also the results of investigation of molecular dynamics and organization of micelle systems -complexes polyelectrolyte-SAS. We shall also discuss some results obtained with the use of method of EPR-spectroscopy and its modification - the method of EPR-tomography for revealing of particularities of spatial distribution of active sites resulted from process of thermo-oxidative destruction of solid polymers. 

At room temperature, these molecules occupy well-defined locations in their respective crystal lattices. However, they tumble freely and isotropically (equally in all directions) in place at their lattice positions. As a result, their solid phase NMR spectra show features highly reminiscent of liquids. We will see an illustration of this point shortly. Other molecules may reorient anisotropically (as in solid benzene). Polymer segmental motions in the melt may cause rapid reorientation about the chain axis but only relatively slow reorientation of the chain axes themselves. Large molecular aggregates in solution (such as surfactant micelles or protein complexes or nucleic acids) may appear to have solidlike spectra if their tumbling rates are sufficiently slow. There are numerous other instances in which our macroscopic motions of solid and liquid may be at odds with the molecular dynamics. Nuclear magnetic resonance is one of the foremost ways of investigating these situations. 

Yoshii, N., and Okazaki, S. (2006), A molecular dynamics study of structural stability of spherical SDS micelle as a function of its size, Chem. Phys. Left., 425(1-3), 58-61. 

Clarke gives a review on molecular dynamics of liquids and solids composed of short-chain molecules as possible models for polymers.In addition, he provides another review with a more applied flavor and with an emphasis on the prediction of the properties of the bulk.23 Because important industrial materials may contain liquid hydrocarbons, polymers, and/or micelles, this review is a welcome addition to the literature aiming at popularizing polymer modeling. 

Phospholamban is a homopentameric membrane protein involved in muscle contraction through regulation of the calcium pump in cardiac muscle cells. The stmcture of the unphospho-rylated protein solved in DPC micelles reveals a symmetric pentamer of phospholamban monomers (Fig. 2g) stabilized by leucine/isoleucine zipper motifs along the transmembrane domains (51). Notably, another stmcture was produced for phospholamban (Fig. 2h) that used a variant of the traditional simulated annealing and molecular dynamics protocol that reduced the chances of entrapment in local minima (52). 

Model calculations of interface-solute electrostatic interactions reproduce well the view of microenvironment polarities of micelles and bilayers obtained from experimental data [57]. According to molecular dynamics simulations, at 1.2 nm from a bilayer interface, water has the properties of bulk water. At shorter distances, water movement slows as individual water molecules become attracted to the interface. At the true interface, which is a region containing both H2O molecules and the surfactant polar head groups, the water molecules are oriented with... 

Kyoko Watanabe (University of Pennsylvania) and Michael L. Klein Molecular Dynamics Study of a Sodium Octanoate Micelle in Aqueous Solution. ... 

Marrink SJ and Mark AE. Molecular Dynamics Simulations of Mixed Micelles Modeling Human Bile. Biochemistry 2002 41 5375-5382. 

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