Molecular dynamics simulations with an all-atom model were carried out to study the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate, [bmim][PF(6)]. Analysis was carried out to characterize a number of structural and dynamic properties. It is found that the hydrogen bonds are weaker than expected, as indicated by their short lifetimes, which is due to the fast rotational motion of anions. Transport properties such as ion diffusion coefficients and ionic conductivity were also measured on the basis of long trajectories, and good agreement was obtained with experimental results. The phenomenon that electrical conductivity of ionic liquids deviates from the Nernst-Einstein relation was well reproduced in our work. On the basis of our analysis, we suggest that this deviation results from the correlated motion of cations and anions over time scales up to nanoseconds. In contrast, we find no evidence for long-lived ion-pairs migrating together.

Anionic palmitoyloleoylphosphatidylglycerol (POPG) is one of the most abundant lipids in nature, yet its atomic-scale properties have not received significant attention. Here we report extensive 150-ns molecular dynamics simulations of a pure POPG lipid membrane with sodium counterions. It turns out that the average area per lipid of the POPG bilayer under physiological conditions is approximately 19% smaller than that of a bilayer built from its zwitterionic phosphatidylcholine analog, palmitoyloleoylphosphatidylcholine. This suggests that there are strong attractive interactions between anionic POPG lipids, which overcome the electrostatic repulsion between negative charges of PG headgroups. We demonstrate that interlipid counterion bridges and strong intra- and intermolecular hydrogen bonding play a key role in this seemingly counterintuitive behavior. In particular, the substantial strength and stability of ion-mediated binding between anionic lipid headgroups leads to complexation of PG molecules and ions and formation of large PG-ion clusters that act in a concerted manner. The ion-mediated binding seems to provide a possible molecular-level explanation for the low permeability of PG-containing bacterial membranes to organic solvents: highly polar interactions at the water/membrane interface are able to create a high free energy barrier for hydrophobic molecules such as benzene.

We carried out classical molecular dynamics simulations with a standard and two quantum chemistry based charge sets to study the ionic liquid 1-n-butyl-3-methylimidazolium bromide, [C(4)C(1)im][Br]. We split the cation up into different charge groups and found that the total charge and the charge distribution in the imidazolium ring are completely different in the three systems while the total charge of the butyl chain is much better conserved between the methods. For comparison, the spatial distribution functions and the radial distribution functions as well as different time correlation functions were calculated. For the structural properties we obtained a good agreement between the standard and one of the two quantum chemistry based sets, while the results from the second quantum chemistry based set led to a completely different picture. The opposite was observed for the dynamic properties, which agree well between the standard set and the second quantum chemistry based set, whereas the dynamics in the first charge set obtained by quantum chemistry calculations proceeded much too slow, which is not obvious from the total charge. We observed, that the structure of the butyl chain is mostly unaffected by the choice of the charge set. This is an indirect proof for separation into ionic parts and nonpolar domains. A second focus of the article is the investigation of dynamical heterogeneity and the ion cages. Therefore, we analyzed the reorientational dynamics in the three systems and at five different temperatures in system with the standard charge set. Generally speaking, we detected four different time domains. The fastest movement can be found for the continuous hydrogen bond and the nearest neighbor ion pair dynamics. In the second time domain the movement of the butyl chain took place. The third time domain consisted in the increasing movement of the imidazolium ring as well as in the continuous distortion of an ion cage, i.e., the departure of one of the several counterions from the central ion's first shell, and the intermittent hydrogen bond dynamics. The remaining domain involves the translational displacement of the ions.