Quantum-mechanical calculations, at HF level, were performed to gain chemical–physical basis information on the 2,4-dinitro-toluene hydrogenation occurring over palladium catalysts. To investigate the surface characteristics of the species involved in the reaction system, simplified molecular models including small metal clusters were considered. Remarkable findings, useful to elucidate the reaction mechanism and important parameters, working in time dependent Monte-Carlo simulations of the title reaction, were obtained; inter alia: the molar standard free energies of the molecules involved in the reaction, the volume occupied by the species in solution phase and the qualitative order of the desorption activation energy values, of the nitro, amino and hydroxylamino groups of the toluene fragments interacting with the Pd surface.The molecular level interaction modes of the different toluene derivatives on Pd clusters, mimicking the catalyst surface, were visualized. The results have been discussed in terms of microscopic (energetic, structural and steric hindering) factors driving the observed macroscopic reaction.