Ab initio molecular orbital (MO) calculations were performed on the adsorption bond energies between the main sulfur compounds and the Cu+ on CuCl and CuY zeolite, for desulfurization of transportation fuels by pi-complexation sorbents. The relative adsorption bond energies of these compounds were measured by the elution order, based on the breakthrough curves of these compounds, from a column of CuY zeolite using commercial diesel and gasoline as the influents. The order from the elution followed: 4,6-dimethyldibenzothiophene greater than or equal to dibenzothiophene > benzothiophene greater than or equal to 2-methylthiophene > thiophene. The order is in agreement with that predicted from the calculations. The calculated values for benzene and thiophene were also in excellent agreement with the measured values that we reported earlier. The methyl and benzo groups have an electron-donating effect on the aromatic rings that undergo pi-complexation. For the sulfur compounds, the thiophene ring was bonded to Cu+. For pi-complexation on both CuY and CuCl, the amount of electron forward donation was more than that of electron back donation for thiophenic adsorbates, but the reverse was true for benzene and toluene.