The distributions and transfer energies of several molecules and atomic groups between water and a structured hydrophobic phase were calculated by the molecular dynamics method. The coefficients of oxygen diffusion in a tetradecane membrane were estimated. The transfer energy of charged atomic groups was found to correlate with changes in the Born solvation energy. The contributions of atoms to the transfer energy of functional groups were shown to be non-additive. The steered dynamics method for estimating the kinetic parameters of the penetration of molecules through interphase boundaries was developed. Heterogeneous microviscosity of a membrane was calculated for a hydrated l-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine bilayer. Effects of the chemical properties of penetrant molecule on its translocation through the membrane were studied.