We have performed two molecular-dynamics simulations to study the structural and dynamical properties of water at the interface with phospholipid bilayers. In one of the simulations the bilayer contained neutral phospholipid molecules, dioleoylphosphatidylcholine (DOPC); in the second simulation the bilayer contained charged lipid molecules, dioleoylphosphatidylserine (DOPS). From the density profile of water we observe that water next to the DOPS bilayer is more perturbed as compared to water near the DOPC bilayer. Using an energetic criterion for the determination of hydrogen bonding we find that water molecules create strong hydrogen bonds with the headgroups of the phospholipid molecules. Due to the presence of these bonds and also due to the confinement of water, the translational and orientational dynamics of water at the interface are slowed down. The degree of slowing down of the dynamics depends upon the location of water molecules near a lipid headgroup.

With a view towards optimizing gas storage and separation in crystalline and disordered nanoporous carbon-based materials, we use ab initio density functional theory calculations to explore the effect of chemical functionalization on gas binding to exposed edges within model carbon nanostructures. We test the geometry, energetics, and charge distribution of in-plane and out-of-plane binding of CO(2) and CH(4) to model zigzag graphene nanoribbons edge-functionalized with COOH, OH, NH(2), H(2)PO(3), NO(2), and CH(3). Although different choices for the exchange-correlation functional lead to a spread of values for the binding energy, trends across the functional groups are largely preserved for each choice, as are the final orientations of the adsorbed gas molecules. We find binding of CO(2) to exceed that of CH(4) by roughly a factor of two. However, the two gases follow very similar trends with changes in the attached functional group, despite different molecular symmetries. Our results indicate that the presence of NH(2), H(2)PO(3), NO(2), and COOH functional groups can significantly enhance gas binding, making the edges potentially viable binding sites in materials with high concentrations of edge carbons. To first order, in-plane binding strength correlates with the larger permanent and induced dipole moments on these groups. Implications for tailoring carbon structures for increased gas uptake and improved CO(2)/CH(4) selectivity are discussed.

We performed six molecular dynamics simulations: three on hydrated bilayers containing pure phospholipids and three on hydrated bilayers containing mixtures of these phospholipids with cholesterol. The phospholipids in our simulations were SSM (sphingomyelin containing a saturated 18:0 acyl chain), OSM (sphingomyelin with an unsaturated 18:1 acyl chain), and POPC (palmitoyloleoylphosphatidylcholine containing one saturated and one unsaturated chain). Data from our simulations were used to study systematically the effect of cholesterol on phospholipids that differed in their headgroup and tail composition. In addition to the structural analysis, we performed an energetic analysis and observed that energies of interaction between cholesterol and neighboring SM molecules are similar to the energies of interaction between cholesterol and POPC. We also observed that the interaction energy between cholesterol and neighboring lipids cannot be used for the determination of which lipids are involved in the creation of a complex.

We studied the effects of confinement and the head group motion on the behavior of the reorientational correlation functions for water molecules at the water/lipid bilayer interface. The correlation functions were calculated from the data obtained from two molecular dynamics simulations: one with a flexible bilayer and the other with a frozen bilayer. In our present analysis the water molecules were separated into spatial regions according to their distance from the bilayer surface and into population groups, according to the length of their stay in the corresponding regions. We estimate that for most of the water molecules that are in a strongly confined environment of the transition region between the head groups and tails, and that solvate carbonyl groups, the decay time of their reorientational correlation functions is of the order of a few tens of picoseconds. Water molecules that stay inside the transition region for long periods of time can display longer time decay (of the order of hundreds of picoseconds). This latter long time decay is determined by the dynamics of the phospholipids, it is substantially reduced when the bilayer is frozen. The decay of the correlation functions for the interfacial water molecules that are solvating the head groups is also slowed down when compared to bulk, but just by factors of 3-4.

Molecular dynamics investigation of benzene in one-dimensional channel systems AlPO4-5, VPI-5, and carbon nanotube is reported. The results suggest that, in all the three host systems, the plane of benzene is almost perpendicular to the channel axis when the molecule is near the center of the channel and the plane of benzene is parallel to the channel axis when the molecule is near the wall of the channel. The density distribution of benzene as a function of channel length, z, and the radial distance, r, from the channel axis is also different in the three host structures. Anisotropy in translational diffusion coefficient, calculated in body-fixed frame of benzene, suggests that benzene prefers to move with its plane parallel to the direction of motion in AlPO4-5 and VPI-5 whereas in carbon nanotube the motion occurs predominantly with the plane of the benzene perpendicular to the direction of motion. Anisotropy associated with the rotational motion is seen to alter significantly in confinement as compared to liquid benzene. In AlPO4-5, the rotational anisotropy is reversed as compared to liquid benzene thereby suggesting that anisotropy arising out of molecular geometry can be reduced. Reorientational correlation times for C 6 and C 2 axes of benzene are reported. Apart from the inertial decay of reorientational correlation function due to free rotation, two other distinct regimes of decay are observed in narrower channels (AlPO4-5 and carbon nanotube): (i) an initial fast decay (0.5−2 ps) and (ii) a slower decay (>2 ps) of reorientational correlation function where C 6 decays slower than C 2 similar to what is observed in liquid benzene. In the initial fast decay, it is seen that the decay for C 6 is faster than C 2 which is in contrast to what is observed in liquid benzene or for benzene confined in VPI-5.