The complexation of a tweezers ligand with zinc perchlorate in the absence and presence of amines in methanol solution was explored. L2Zn2(ClO4)4 was a thermodynamic product of the reaction in the absence of an amine. The complex was shown to interact with aliphatic amines resulting in the formation of a Zn–N(amine) bond. If metal–ligand complexation was carried out in the presence of an amine the formation of a trinuclear zinc complex L3Zn36+ was observed. Moreover the transformation of complex L2Zn24+ to L3Zn36+ occurred, when the former was subjected to an amine in the amount, which is sufficient to coordinate more than one amino group on each zinc atom. Complexes ligand-zinc-amine were shown to be kinetically stable, and the method of their preparation was crucial to the purity of the final complexes. L3Zn36+ was favored under kinetic control: reagent concentration 10−5M, slow addition of zinc perchlorate to the mixture of an amine and the ligand. Under thermodynamic control (fast mixing of reagents, concentration 10−2–10−3 M) formation of a mixture of complexes was observed. All pure complexes and their mixtures were characterized using UV-Vis, ROESY, PFGSE NMR and ESI-MS techniques. On the basis of DFT calculations the mechanism of influence of an amine on self-assembly was suggested.