Structure and bonding of a cation-pi complex and an OH-pi adduct are investigated using density functional theory with gradient-corrections for the exchange-correlation functional. Our calculations are carried out for two specific model complexes representing (i) the thymine/Arg 72 adduct in the. ternary complex of HIV-I reverse transcriptase (RT) with a DNA template primer and a deoxynucleoside triphosphate (Huang, H., et al. Science 1998, 282, 1669-1675) and (ii) the Tyr6-Thr13 adduct in mu -gluthatione transferase (mu -GST) (Xiao, G., et al. Biochemistry 1996, 35, 4753-4765). We find that electrostatic interactions play an important role and provide similar stabilization energies to the two pi complexes. In HIV-1 RT, the pi electronic density of thymine is essentially uneffected by the presence of the arginine guanidium group; on the contrary, tyrosine is significantly polarized by the interaction with the hydroxyl group and other groups present in the mu -GST enzyme. The influence of Thr13 induced-polarization on Tyr6 pK(a) is compared with that of other interacting groups at the active site.