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The heat of isodesmic (formal) reaction Q is systematically used as a measure of deviations from the additivity of bond energies. For molecules these Q values are applied to quantification of strain energies in cyclic compounds, to evaluation of aromaticity of benzene, to explanation of the reasons for deviation from additivity in the heats of formation for disubstituted benzenes and some alkenes. The isodesmic reactions are further used for quantification of structure-stability relationships for cations and free radicals as reactive intermediates in many organic reactions. The scales of relative thermodynamic stabilities comprising 31 cations and 33 free radicals are represented with the range of Q values ca. 225 and 90 kcal/mol respectively. The evaluated energies of aromaticity for benzene, tropylium cation, cyclopentadienyl cation are 30.5, 21.8, 20.3, and -26.8 kcal/mol, respectively.