We describe here the assembly of new types of donor-acceptor catenanes from dynamic combinatorial libraries (DCL) in water. These new catenanes contain both the donor and acceptor components in at least one of the interlocked rings, thereby possessing unusual and unexpected DAAD or DADD stacking sequences of the it units in their structures. The efficiency of the catenane assembly process can be enhanced by manipulating the DCL equilibrium in a variety of ways: adding a guest. changing the building block stoichiometries, or increasing the library concentration or the ionic strength of the solvent. The formation of catenanes and their constitutions are found to be dependent on subtle differences in the geometry, dimension, and flexibility of the donor building blocks.