The results of a comprehensive structure-affinity relationship study on the effect of the quaternization (i.e., N-methylation) of structurally different ligands in the classes of tropane and quinuclidine derivatives are described. This study shows that the effects of the quaternization of the basic nitrogen of these 5-HT3 receptor ligands appear to be strictly structure-dependent suggesting that different binding modes are operative at 5-HT3 receptor binding site. The different effect of the quaternization of the basic nitrogen of structurally different ligands were rationalized in tern-is of the interaction with the receptor by means of the combined use of experimental techniques (X-ray diffraction and NMR studies) and computational simulation studies. (C) 2002 Elsevier Science Ltd. All rights reserved.