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Multinanosecond molecular dynamics (MD) simulations have been employed to characterize the interaction of an integral membrane protein (IMP), the leucine transmitter from Aquifex aeolicus(Yamashita et al., Nature2005, 437, 215−223), with hydrated lipid bilayer membranes in their physiologically relevant liquid crystalline phases. Analysis of the MD trajectories for dimyristoyl phosphatidylcholine (DMPC), 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE) focused on the contacts between aromatic and basic side chains of the IMP with the lipid head groups and water. Structural fluctuations of the IMP were investigated as well as the contact dynamics of neighboring lipids. In characterizing the IMP−membrane systems, the behaviors of the protein’s cytoplasmic and periplasmic parts are considered separately. All three lipid membranes show a rather similar overall level of association with the IMP. However, for DMPC there is a better matching of the membrane core to the hydrophobic transmembrane portion of the IMP. The closed cytoplasmic end of the IMP exhibits a higher degree of association with lipids than the more open periplasmic end, an observation which correlates with the more compact structure and a slower dynamics of surrounding lipids. [ABSTRACT FROM AUTHOR]

The structure of an aqueous 1-n-decyl-3-methylimidazolium bromide solution and its vapor−liquid interface has been studied using molecular dynamics (MD) simulations. Starting from an isotropic solution, spontaneous self-assembly of cations into small micellar aggregates has been observed. The decyl chains are buried inside the micelle to avoid unfavorable interactions with water, leaving the polar headgroups exposed to water. The cation aggregation numbers, ranging from 15 to 24 compare favorably with experimental estimates. Results are presented for the organization of solvent around the cations. The structure of the aggregates as determined from the present MD simulations does not support the staircase model proposed on the basis of nuclear magnetic resonance studies on similar aqueous ionic-liquid solutions. The distribution of ions in bulk solutions and at an air/water interface is also discussed. [ABSTRACT FROM AUTHOR]

Using first principles molecular dynamics simulation, we have studied a fluoride anion embedded in a periodically replicated water slab composed of 215 water molecules to mimic both bulk and interfacial solvation. In contrast to some recent experiments, our findings suggest that there are only small structural changes for fluoride and its first solvation shell in the bulk. Moreover, the presence of fluoride does not significantly alter the rotational dynamics of nearby water. In addition, we have computed the molecular dipole moments using Wannier centers. At the interface, the presence of fluoride increases the molecular dipole moments of nearby water molecules, whereas in the bulk, the dipole moments for water appear to be essentially invariant to the presence of fluoride in the vicinity. Previous studies of the air−water interface have showed interfacial water to have higher average HOMO energies and, thus, likely to be more prone to electrophilic attack. With the addition of fluoride, the most likely reactive site for electrophilic reactions shifts to the anion. This finding could explain the known large increase in reaction rates for heterogeneous process of interest in atmospheric science. The reactive properties of other anions near the air−water interface are of general interest in heterogeneous chemistry and can be elucidated using a similar type of analysis, as performed here for the fluoride anion. [ABSTRACT FROM AUTHOR]