Self-consistent field modeling of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to molecular dynamics simulations

A molecular-level self-consistent-field (SCF) theory is applied to model the lipid bilayer structures composed of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (18:0/18:1omega9cis PC) and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (18:0/22:6omega3cis PC). As compared to earlier attempts to model (saturated) PC membranes several additional features are implemented: (i) A water model is used which correctly leads to low water concentration in the bilayers. (ii) Free volume is allowed for, which is important to obtain bilayers in the fluid state. (iii) A polarization term is included in the segment potentials; this new feature corrects for a minor thermodynamic inconsistency present in (all) earlier results for charged bilayers. (iv) The CH3 groups in the lipid molecules are assumed to have twice the volume of a CH2 group; this leads to stable noninterdigitated bilayers. (v) A cis double bond is simulated by forcing gauche conformations along the sn-2 acyl chain. Results of an all-atom molecular dynamics (MD) simulation, using the collision dynamics method, on the same system are presented. Both SCF and MD prove, in accordance with experimental facts, that acyl unsaturation effectively reduces the length of the chain which counteracts interdigitation. It is also found that the phosphatidylcholine head group is lying almost flat on the membrane surface and the water penetrates into the bilayer upto the glycerol backbone units. From the SCF results it further followed that the free volume is not exactly evenly distributed over the bilayer. There is a small increase in free volume in the center of the bilayer as well as in the glycerol backbone region

Plastic deformation of glassy polymethylene : computer-aided molecular-dynamic simulation

Molecular-dynamic simulation of low-temperature plastic deformation (T def = 50 K, T def/T g = 0.3) is studied for glassy polymethylene under the regime of active uniaxial compression and tension for a cell composed of 64 chains containing 100 -CH2 groups in each (as united atoms) and with periodic boundary conditions. Thirty-two such cells are created, and, in each cell, polymethylene chains in the statistical coil conformation are independently constructed. The cells are subjected to isothermal uniaxial compression at T def = 50 K by ¿ = 30% and by ¿ = 70% under uniaxial tension. In the course of loading, a s-¿ diagram is recorded, while the mechanical work spent on deformation, the changes in the overall potential energy of the system, and the contributions from various potential interactions (noncovalent van der Waals bonds, chemical links, valence and torsional angles) are estimated. The results are averaged over all 32 cells. The relaxation of stored potential energy and residual strain after complete unloading of the deformed sample is studied. The relaxation of stored energy and residual strain is shown to be incomplete. Most of this energy and strain is stored in the sample at the deformation temperature for long period. The conformational composition of chains and the average density of polymer glass during loading are analyzed. Simulation results show that inelastic deformations commence not with the conformational unfolding of coils but with the nucleation of strain-bearing defects of a nonconformational nature. The main contribution to the energy of these defects is provided by van der Waals interactions. Strain-bearing defects are nucleated in a polymer glass during tension and compression primarily as short-scale positive volume fluctuations in the sample. During tension, the average density of the glass decreases; during compression, this parameter slightly increases to ¿ ˜ 8% and then decreases. An initial increase in the density indicates that, during compression and at ¿ <8%, coils undergo compactization via an increase in chain packing. During compression, the concentration of trans conformers remains unchanged below ¿ ˜ 8% and then decreases. During compression, it means that in a glass, coils do not increase their sizes at strains below ¿ ˜ 8%. During tensile drawing, coils remain unfolded below ¿ ˜ 35%; at higher strains, coils become enriched with trans conformers or unfold. At this stage, the concentration of trans conformers linearly increases. The development of a strain-induced excess volume (strain-bearing defects) entails an increase in the potential energy of the sample. Under the given conditions of deformation, nucleation of strain-bearing defects and an increase in their concentration are found to be the only processes occurring at the initial stage of loading of glassy polymethylene. The results of computer-aided simulation are compared with the experimental data reported in the literature

Molecular dynamics simulations of hydrated unsaturated lipid bilayers in the liquid-crystal phase and comparison to self-consistent field modeling

Molecular dynamics simulations, using the collision dynamics method, were carried out for hydrated bilayers of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (18:0/18:1¿9cis PC, SOPC) and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (18:0/22:6¿3cis PC, SDPC). The simulation cells of the two bilayers consisted of 96 SOPC (or SDPC) molecules and 2304 water molecules: 48 lipid molecules per layer and 24 H2O molecules per lipid. The water was modeled by explicit TIP3P water molecules. The C¿H bond-order-parameter -SCH profiles of the hydrocarbon tails, the bond orientation distribution functions and the root-mean-square values of the positional fluctuations of the lipid chain carbons were calculated. Simulation results are compared to the available experimental data and to other computer investigations of these lipid molecules. Several results of molecular-level self-consistent field calculations of these bilayers are also presented. Both theoretical methods reveal the same main characteristic features of the order-parameter profiles for the given bilayers. Some aspects of the physical properties of unsaturated lipids and their biological significance are discussed

Glass-Transition Temperature of Cyclic Polystyrene: A Computational Study

Abstract: Molecular-dynamics simulations are employed to study the glass transition of cyclic polystyrene melts. Gibbs and DiMarzio’s theory predict an increase in glass transition temperature, Tg upon lowering the length of cyclic polymer chains, which is opposite to the well-known trend for linear polymers. Their theory has been confirmed by some experiments; however, others observe a decrease in Tg upon lowering the chain length instead. When volumetric methods are employed to obtain the glass transition temperature in simulated cyclic polystyrene, a slight increase with decreasing cyclic polystyrene chain length is obtained. This increase is more pronounced when glass transition temperatures are obtained from dynamics. Both the glass transition temperature Tg obtained from diffusion data and the ideal glass transition temperature T0 obtained from the decay of the orientational autocorrelation function of the phenyl bond show a clear upturn

Properties of unsaturated phospholipid bilayers: effect of cholesterol

Properties of hydrated unsaturated phosphatidylcholine (PC) lipid bilayers containing 40 mol % cholesterol and of pure PC bilayers have been studied. Various methods were applied, including molecular dynamics simulations, self-consistent field calculations, and the pulsed field gradient nuclear magnetic resonance technique. Lipid bilayers were composed of 18:0/18:1(n-9)cis PC, 18:0/18:2(n-6)cis PC, 18:0/18:3(n-3)cis PC, 18:0/20:4(n-6)cis PC, and 18:0/22:6(n-3)cis PC molecules. Lateral self-diffusion coefficients of the lipids in all these bilayers, mass density distributions of atoms and atom groups with respect to the bilayer normal, the C-H and C-C bond order parameter profiles of each phospholipid hydrocarbon chain with respect to the bilayer normal were calculated. It was shown that the lateral self-diffusion coefficient of PC molecules of the lipid bilayer containing 40 mol % cholesterol is smaller than that for a corresponding pure PC bilayer; the diffusion coefficients increase with increasing the degree of unsaturation of one of the PC chains in bilayers of both types (i.e., in pure bilayers or in bilayers with cholesterol). The presence of cholesterol in a bilayer promoted the extension of saturated and polyunsaturated lipid chains. The condensing effect of cholesterol on the order parameters was more pronounced for the double C=C bonds of polyunsaturated chains than for single C-C bonds of saturated chains

Properties of unsaturated phospholipid bilayers: effect of cholesterol = SVOISTVA BISLOEV NENASYShchENNYKh FOSFOLIPIDOV: VLIYaNIE KhOLESTERINA

Theoretical and experimental study of the liquid crystalline phase of five different hydrated unsaturated phosphatidylcholine (PC) lipid bilayers built up by 18:0/18:2(n-9)cis PC, 18:0/18:2(n-6)cis PC, 18:0/18:3(n-3)cis PC, 18:0/20:4(n-6)cis PC, and 18:0/22:6(n-3)cis PC molecules with 40 mol% cholesterol, and the same five pure PC bilayers have been performed at 303 K. Molecular dynamics (MD) computer simulations and self-consistent field (SCF) calculations for the study of model pure unsaturated PC and PC/cholesterol membrane systems, and the pulsed field gradient nuclear magnetic resonance (pfg NMR) technique for the study of corresponding real pure PC and PC/cholesterol membranes have been used. The lateral diffusion coefficients of the lipids in these systems, atom mass density distributions with respect to the bilayer normal, the C-H and C-C bond order parameter profiles of the lipid hydrocarbon chains have been analyzed. It has been found that mobility of PC molecules increases as the degree of their unsaturation increases (i.e., the lateral diffusion coefficients of PC molecules increase with increasing a number of double bonds in one of the lipid chains), both in pure bilayers and in bilayers with cholesterol. It has been found as well that the lateral diffusion coefficient of PC molecules of a lipid bilayer with 40 mol% cholesterol is smaller than that for the corresponding pure PC bilayer. The presence of cholesterol in a bilayer is found to promote extending of both saturated and polyunsaturated lipid chains. The effect of cholesterol on the order parameters of the double C=C bonds of polyunsaturated chains is found to be more appreciable than that for single C-C bonds of saturated chains. The theoretical (MD and SCF) results are in agreement with the results of the pfg NMR experimental study

Effects of strong confinement on the glass-transition temperature in simulated atactic polystyrene films

We have performed molecular dynamics simulations to explore the influence of confinement on the glass-transition temperature Tg for supported atactic-polystyrene (aPS) thin films of different thickness (1-10 nm) and different strengths of attraction to the substrate (0.1-3.0 kcal/mol). The aPS films have been equilibrated in a melt at 540 K and further cooled down with a constant cooling velocity of 0.01 K/ps below Tg to room temperature, 300 K. On the basis of the density measurements, we have defined three different (substrate, middle, and surface) layers for each film. We found that the monomers close to the surface and in the substrate layer are partially oriented, which leads to more effective monomer packing. For the whole film the average density-based Tg value remains almost constant for films down to 2 nm thickness, where the middle layer vanishes. For the middle layer itself Tg does not depend on the total film thickness, while an increase up to 70 K is measured for the substrate layer depending on the strength of attraction to the actual substrate. The surface layer remains liquidlike in the whole temperature range (300-540 K). We claim that the redistribution of mass in the three film layers may explain the change with film thickness of the average Tg, if the latter is determined from linear fits of the average glass and melt densities

Interfacial and topological effects on the glass transition in free-standing polystyrene films

United-atom molecular-dynamics computer simulations of atactic polystyrene (PS) were performed for the bulk and free-standing films of 2 nm – 20 nm thickness, for both linear and cyclic polymers comprised of 80 monomers. Simulated volumetric glass-transition temperatures (Tg) show a strong dependence on the film thickness below 10 nm. The glass-transition temperature of linear PS is 13% lower than that of the bulk for 2.5 nm-thick films, as compared to less than 1% lower for 20 nm films. Our studies reveal that the fraction of the chain-end groups is larger in the interfacial layer with its outermost region approx. 1 nm below the surface than it is in the bulk. The enhanced population of the end groups is expected to result in a more mobile interfacial layer and the consequent dependence of Tg on the film thickness. In addition, the simulations show an enrichment of backbone aliphatic carbons and concomitant deficit of phenyl aromatic carbons in the interfacial film layer. This deficit would weaken the strong phenyl-phenyl aromatic (-) interactions and, hence, lead to a lower film-averaged Tg in thin films, as compared to the bulk sample. To investigate the relative importance of the two possible mechanisms (increased chain ends at the surface or weakened - interactions in the interfacial region), the data for linear PS are compared with those for cyclic PS. For the cyclic PS the reduction of the glass-transition temperature is also significant in thin films, albeit not as much as for linear PS. Moreover, the deficit of phenyl carbons in the film interface is comparable to that observed for linear PS. Therefore, chain-end effects alone cannot explain the observed pronounced Tg dependence on the thickness of thin PS films; the weakened phenyl-phenyl interactions in the interfacial region seems to be an important cause as well