The hypothesis that the activity of cimetidine, a member of a family o
f anti-ulcer drugs, may depend on the protonation ability of the unsat
urated nitrogens of its guanidine arm is studied quantitatively on the
basis of energies and charge distributions determined by the PM3 meth
od. At variance of histamine, whose two sites susceptible of proton ac
tivity are more or less energetically equivalent, in cimetidine proton
ation at the imidazole cycle is favoured. However, the ability of the
cyano-guanidine arm to fur a proton depends on the conformation of the
whole molecule and, in certain cases, it becomes comparable with that
of the imidazole nitrogen. These points may provide a key to a better
understanding of the mechanism of action of drugs of the cimetidine g
roup.