We applied the Terahertz time - domain technique for investigations of homeotropically aligned liquid crystal samples by studying of the temperature dependencies and phase transitions. A standard setup for terahertz time-domain spectroscopic measurement was used for study of 4'-pentyl-4-cyanobiphenil (5CB) and 4'-octyl-4-cyanobiphenyl (8CB). For calculation of energies, structures and vibrational frequencies of these liquid crystalline molecules we used GAUSSIAN 03. We show the results of low frequency absorption for different temperatures in compliance with phase transitions from crystalline to isotropic states via smectic and nematic mesophases. The interesting features associated with liquid crystal molecular configurations and conformational mobility are discussed.