Nozomu Kamiya

MOLECULAR DYNAMICS SIMULATION OF AN ANTIFERROELECTRIC LIQUID CRYSTALLINE MOLECULE MHPOBC: CONFORMATIONAL TRANSITION IN SMECTIC PHASES

Molecular dynamics (MD) simulation was carried out for an antiferroelectric liquid crystalline molecule, (S)-4-[(1-methylheptyloxycarbonyl]phenyl 4′-octyloxybiphenyl-4′-carboxylate (MHPOBC), to analyze its conformational property in smectic liquid crystalline phases. The MD simulation reproduces a “solid–SmCx–SmA–isotropic” phase transition. The MHPOBC molecules in the SmCx phase are packed in a tilted layered structure, while in the SmA phase the molecular tilt disappears. The chiral alkyl chain in the crystalline phase has a larger gauche population at the C*–C bond, which gives rise to a “highly bent structure”. In smectic phases, the conformation of both chiral and achiral alkyl chains is almost fully liberated, and the average molecular shape changes into a “moderately bent structure”. Comparison of the results of MD simulation and molecular orbital calculation indicates that the smectic phases of MHPOBC can be distinguished from the solid phase in terms of the alkyl chain conformation, and the SmCx and SmA phases are distinguished from each other in terms of molecular packing structure.

A new lipid force field (FUJI)

To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method was applied without a traditional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrank when using LJ-PME method. A new lipid force field (FUJI) was developed on the basis of the AMBER force field scheme including the Lipid14 van der Waals parameters. Point charges were calculated by the restrained electrostatic potentials of many lipid conformers. The torsion energy profiles were calculated by high level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ); then, the molecular mechanical dihedral parameters were derived by means of a fast Fourier transform. Incorporating these parameters into a new lipid force field without any fittings to experimental data, desirable lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained by GROMACS molecular dynamics simulations using the LJ-PME method and hydrogen virtual sites. The stability and structures of large membranes with undulatory fluctuations were studied by a multidrug efflux transporter (AcrABZ-TolC) with inner and outer membranes.