Molecular modeling of four different reagent systems shows that the (free) energies of supramolecular interactions in the gas phase and in solution can explain the different reaction products (i.e., various sized macrocycles, catenanes, and linear oligomers) that are formed in classic amide-catenane-forming reactions. Self-assembly of the catenanes requires the formation of ordered intertwined chains and is driven by bifurcated hydrogen bonds, with pi stacking only playing a lesser role. The understanding gained from the computational study was used to predict the possibility of a new rotaxane-forming system that does not permit catenane formation. The predictions were confirmed by the successful synthesis and characterization (including X-ray crystallography) of two novel rotaxanes.