Amphiphiles, molecular dynamics simulation

For recent reviews on molecular dynamics simulations of amphiphilic systems, see D. J. Tobias, K. Tu, M. L. Klein. In K. Binder, G. Ciccotti, eds. Monte Carlo and Molecular Dynamics of Condensed Matter Systems. Bologna SIF, 1996, pp. 327-344. S. Bandyapadhyay, M. Tarek, M. L. Klein. Curr Opin Coll Interf Sci 3-.242-146, 1998. 

Fig. 8 Proposed model for gramicidin S in a membrane according to the orientational constraints obtained from and N-NMR. The upright backbone alignment (r 80°) and slant of the /3-sheets (p -45°) are compatible with the formation of an oligomeric /3-barrel that is stabilized by hydrogen bonds (dotted lines). A The oligomer is depicted sideways from within the lipid bilayer interior (showing only backbone atoms for clarity, but with hydrophobic side chains added to one of the monomers). Atomic coordinates of GS were taken from a monomeric structure [4], and the two DMPC lipid molecules are drawn to scale (from a molecular dynamics simulation coordinate file). The bilayer cross-section is coloured yellow in its hydrophobic core, red in the amphiphilic regions, and light blue near the aqueous surface. B Illustrates a top view of the putative pore, although the number of monomers remains speculative...

Tolpekina, T.V., den Otter, W.K., Briels, W.J. Nucleation free energy of pore formation in an amphiphilic bilayer studied by molecular dynamics simulations. J. Chem. Phys. 2004, 121, 12060-6. 

A different influence on membrane order and dynamics was reported for an amphiphilic peptide in two investigations employing both 2H-NMR measurements and molecular dynamics simulations [80]. Two model peptides were studied having the sequence... 

Methylated cyclodextrins promote the hydroformylation of higher olefins, too. Molecular dynamics simulations show that the reaction takes place right at the interface and that cyclodextrins act as both surfactants and receptors that favour the meeting of the catalyst and the olefin. The methylated cyclodextrin adopts specific amphiphilic orientations at the interface, with the wide rim pointing towards the water phase. This orientation makes easier the formation of inclusion complexes with the reactant (1-decene), the key reaction intermediate [Rh(H)CO(TPPTS)2-decene)] and the reaction product (undecanal). ... 

D. W. R. Gruen, /. Phys. Chem., 89, 146 (1985). A Model for the Chains in Amphiphilic Aggregates. 1. Comparison with a Molecular Dynamics Simulation of a Bilayer. 

Gruen D W R 1984 A model for the ohains in amphiphilic aggregates I. Comparison with a molecular dynamics simulation of a bilayer J. Phys. Chem. 89 645... 

The result of the interactions of some copolymer mimics of AMP with model bacterial membranes has been studied via atomistic molecular dynamics simulation (Figure 3.2). The model bacterial membrane expands homogeneously in a lateral manner in the membrane thickness profile compared with the polymer-free system. The individual polymers taken together are released into the bacterial membrane in a phased manner and the simulations propose that the most possible location of the partitioned polymers is near the l-palmitoyl-2-oleoyl-phosphatidylglycerol clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at the lipid-water interface, although lack intrinsic secondary structures, such as an a-helix or P-sheet, found in naturally occurring AMP [23]. 

Recently, Miller and Cacciuto explored the self-assembly of spherical amphiphilic particles using molecular dynamics simulations [46]. They found that, as well as spherical micellar-type structures and wormlike strings, also bilayers and faceted polyhedra were possible as supracolloidal structures. Whitelam and Bon [47] used computer simulations to investigate the self-assembly of Janus-like peanut-shaped nanoparticles and found phases of clusters, bilayers, and non-spherical and spherical micelles, in accordance with a packing parameter that is used conventionally and in analogy to predict the assembled structures for molecular surfactants. They also found faceted polyhedra, a structure not predicted by the packing parameter (see Fig. 8). In both studies, faceted polyhedra and bilayers coexist, a phenomenon that is still unexplained. 

Other models for ternary amphiphilic systems are based on mixtures of hard spheres and ellipsoids with Lennard-Jones interactions [58] or on mixtures of hard spheres and diatomic hard-sphere molecules [59]. Such models have been studied by molecular dynamics simulations. 

Abstract Computer simulations are used to study the aggregation phenomena of volatile amphiphiles in a system displaying liquid/vapor coexistence. These molecular dynamics simulations are based on a simple, yet versatile, model used previously to study oil/water/amphiphile systems amphiphiles are nothing more than water and oil particles connected together by stiff springs. We observe a highly regulated self-assembly process wherein amphiphiles form bilayers within the liquid phase. The density of amphiphiles in a bilayer varies from a well-defined lower to upper limit as the overall concen-... 

By variation of these factors it is possible to drive amphiphile association in the direction spheres cylinders bilayers/vesicles. Detailed theoretical investigations have recently been performed by molecular dynamics simulations (106). Further factors involve temperature and added homopolymer, which affects the stretching energy of the core chains. The variation of these factors and their effects on aggregate morphology have been reviewed (29,32-36,107-110) and are summarized in Table 3. 

Figure 6 Pearl-necklace structure In amphiphilic graft copolymer under poor solvent strength conditions for the main chain and good solvent strength conditions for the side chains m-4, n-40, and M-320). Molecular dynamics simulations snapshot kindly provided by P. Kosovan.

Huang P, Loew GH (1995) Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study. J Biomol Struct Dyn 12(5) 937-956 Bemeche S, Nina M, Roux B (1998) Molecular dynamics simulations of melittin in a dimy-ristoylphosphatidylcholine bilayer membrane. Biophys J 75(4) 1603 1618 Woolf TB, Roux B (1994) Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. PNAS 91(24) 11631 11635... 

A stern test of our single-chain model is to compare results derived from it with results derived from a recent molecular dynamics simulation [23]. This simulation explicitly considers the interactions of 128 G-(CH2)8CH3 amphiphiles in a bilayer (G is a model headgroup). To date, this simulation is by far the most reliable attempt to model the short time and short distance properties of the chains in a bilayer. It is therefore of considerable interest to compare the results of this simulation with any prospective model of the interior of amphiphilic aggregates. 

Fig. 1. C - D bond order parameters for different segments in the amphiphile chain. Carbon number 2 is the CHj (or CDj) group bonded to the headgroup while number 10 is the terminal CH, group. Scq = (jCos 6- ), where 0 is the angle between the C - D bond vector and the bilayer normal. , experimental order parameters [24] down the de-canoate chain in a 32 wt% sodium decanoate, 38 wt% deca-nol, 30 wt% water lamellar phase.-----, from the molecular dynamics simulation.-------, from our single chain...

Fig. 3. Probability distribution of molecular tilt, P(cosfl). Molecular tilt is defined by the vector joining the middle of the first to the middle of the sixth bond in the amphiphile. The tilt angle, 6, is then the angle between this vector and the bilayer normal. The data points and the dashed line display P cos6) for the single chain model and the molecular dynamics simulation respectively...

Abstract Amphiphilic polymers have the ability to self-assemble into supramolec-ular structures of great complexity and utility. Nowadays, molecular dynamics simulations can be employed to investigate the self-assembly of modestly sized natural and synthetic macromolecules into structures, such as micelles, worms (cylindrical micelles), or vesicles composed of membrane bilayers organized as single or multilamellar structures. This article presents a perspective on the use of large-scale computer simulation studies that have been used to xmderstand the formation of such structures and their interaction with nanoscale solutes. Advances in this domain of research have been possible due to relentless progress in computer power plus the development of so-called coarse-grained intermolecular interaction models that encode the basic architecture of the amphiphUic macromolecules of interest. 

B. Smit, Phys. Rev. A., 37, 3431 (1988). Molecular Dynamics Simulation of Amphiphilic Molecules at a Liquid-Liquid Interface. 

Liu et al. [14] functionalized DWCNTs as artificial water channel proteins. For the first time, molecular dynamics simulations showed that the bilayer structure of DWCNTs is advantageous for CNT-based transmembrane channels. Shielding of the amphiphilic outer layer could guarantee biocompatibility of the synthetic channel and protect the inner tube (functional part) from disturbance of the membrane environment. This novel design could promote more sophisticated nanobiodevices, which could function in a bioenvironment with high biocompatibility. 

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