Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer

We report the results of a constant pressure and temperature molecular dynamics simulation of a gel-phase dipalmitoylphosphatidylcholine bilayer with n(W) = 11.8 water molecules/lipid at 19 degrees C. The results of the simulation were compared in detail with a variety of x-ray and neutron diffraction data. The average positions of specific carbon atoms along the bilayer normal and the interlamellar spacing and electron density profile were in very good agreement with neutron and x-ray diffraction results. The area per lipid and the details of the in-plane hydrocarbon chain structure were in excellent agreement with wide-angle x-ray diffraction results. The only significant deviation is that the chains met in a pleated arrangement at the bilayer center, although they should be parallel. Novel discoveries made in the present work include the observation of a bimodal headgroup orientational distribution. Furthermore, we found that there are a significant number of gauche conformations near the ends of the hydrocarbon chains and, in addition to verifying a previous suggestion that there is partial rotational ordering in the hydrocarbon chains, that the two chains in a given molecule are inequivalent with respect to rotations. Finally, we have investigated the lipid/water interface and found that the water penetrates beneath the headgroups, but not as far as the carbonyl groups, that the phosphates are strongly hydrated almost exclusively at the nonesterified oxygen atoms, and that the hydration of the ammonium groups is more diffuse, with some water molecules concentrated in the grooves between the methyl groups.