Synthesis of catenane 6 has been successfully achieved by the combination of Pd complex 1 and pyridines 2 and 3 at a molar ratio of 2:1:1 in D2O. A mixture of square molecule 4 (prepared from 1 and 2) and macrocycle 5 (obtained from 1 and 3), in which the final ratio of 1, 2, and 3 was kept 2:1:1 reorganizes in D2O/CD3OD (1:1) to form 6 within one day. However, the same mixture in D2O shows the formation of novel catenane 7 along with the catenane. In order to make 7, the theoretical ratio of components 1, 2, and 3 should be 3:1:2. Thus, deliberately maintaining such ratio of the above-mentioned molecules, a higher proportion of the catenane is observed in D2O as found from 1H NMR spectra of the system. Reorganization of the twelve components to form catenane is supported by studies with the DOSY method. This method is a first attempt to separate, from a mixture, either catenanes or any other supramolecular self-assembly structures. CSI-MS studies further support the assigned catenane super structures 6 and 7. All the results indicate that the catenane is thermodynamically the most stable structure, while the catenane is a meta-stable self-assembly.