Parameter sets for alkane, alkene, aliphatic fluorine and pyridine derivatives were developed for empirical force field calculations. Parameters were designed to be compatible with CHARMM22 all hydrogen parameter sets for proteins, nucleic acids and lipids. A novel methodology for optimizing Lennard-Jones parameters was developed by including ab initio interaction energies and geometries between helium or neon and model compounds as goal data. Membrane permeability of pyridine derivatives were studied by developing a quantitative structure-activity relationship (QSAR). Physicochemical parameters used in QSAR were obtained from empirical force field calculations and quantum mechanics calculations.