Several physico-chemical properties of alkanes, polyaromatic hydrocarbons, alkylbenzenes, polychlorobenzenes, polymethylphenols and polychlorophenols were determined using the Sony-Tektronix CAChe program and molecular orbital software packages, for the calculation of molecular mechanics, molecular dynamics, extended Huckel, MOPAC, and MOPAC-BlogP. The calculations were used to examine the difference between the measured and predicted capacity ratios of isomers. The ionization potential energy calculated by MOPAC was the most suitable property with which to adjust the capacity ratios of polychlorobenzene, polymethylphenol, and polychlorophenol isomers.