The influence of flexible walls on the self-diffusion of CH 4 in an isolated single walled carbon nanotube, as an example, is studied by molecular dynamics simulations. By simulating the carbon nanotube as a flexible framework we demonstrate that the flexibility has a crucial influence on selfdiffusion at low loadings. We show how this influence can be incorporated in a simulation of a rigid nanotube by using a Lowe-Andersen thermostat which works on interface-fluid collisions. The reproduction of the results of a flexible carbon nanotube by a rigid nanotube simulation is excellent. DOI: 10.1103/PhysRevLett.95.044501 PACS numbers: 47.55.Mh, 66.30.Pa, 83.10.Rs Carbon nanotubes (CNTs) can be aligned in a polymer film to form a well-ordered nanoporous membrane structure [1] which can be incorporated in a macroscopic structure [2] for separation devices. It is therefore of practical interest to understand the diffusive behavior of molecules adsorbed in these materials [3][4][5][6][7]. A particularly interesting observation is the remarkable increase of the diffusion coefficient of simple molecules at low densities observed by Skoulidas et al. [3]. These molecular simulations predict a diffusion coefficient higher than the corresponding gas phase value, resulting in fluxes that are orders of magnitude greater than in crystalline zeolitic membranes [3]. These results have subsequently been reproduced by other groups [8,9] and are explained in terms of the smoothness of the nanotube [3].From a computational point of view, simulations at the low density limit are surprisingly expensive; one needs an increasingly long nanotube to reach the low density limit. This poses no difficulty if one assumes a rigid substrate. However, if one has a material in which the flexibility cannot be ignored and a full atom simulation of the material is required, the calculation becomes many orders of magnitude more expensive and is completely dominated by the substrate. Therefore, most simulation studies use a rigid lattice.A novel algorithm that takes the most important aspects of flexibility into account at a fraction of the costs of a fully flexible CNT simulation is presented, resulting in effectively the same diffusivities and other effects as obtained from the flexible CNT simulations. This algorithm can be applied to other confined systems (zeolites, ion channels, membranes, etc.).Interestingly, whether or not it is reasonable to assume a rigid lattice in adsorption [10] or diffusion studies [11] is far from being understood. An obvious hypothesis would be that only in the case of narrow passages is flexibility very important, while in the case of gas molecules in carbon nanotubes, or other nanoporous materials, a rigid lattice is a very reasonable assumption. As we will show in this Letter, this assumption is the explanation of the remarkable increase of the diffusion coefficient at low loading. Molecular dynamics simulations of a fully flexible nanotube give a diffusion coefficient that is more than 1 order of magnitude lower ...

The importance of membrane-water partition coefficients led to the recent extension of the conductor-like screening model for realistic solvation (COSMO-RS) to micelles and biomembranes termed COSMOmic. Compared to COSMO-RS, this new approach needs structural information to account for the anisotropy of colloidal systems. This information can be obtained from molecular dynamics (MD) simulations. In this work, we show that this combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies. However, there is a discrepancy between the amount of data generated by MD simulations and the structural information needed for COSMOmic. Therefore, a new scheme is presented to extract data from MD trajectories for COSMOmic calculations. In particular, we show how to calculate the system structure from MD, the influence of lipid conformers, the relation to the COSMOmic layer size, and the water/lipid ratio impact. For a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer, 66 partition coefficients for various solutes were calculated. Further, 52 partition coefficients for a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer system were calculated. All these calculations were compared to experimental data.

No abstract

Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.

No abstract