Proteins can adopt helical and sheet-type secondary structures that depend on their primary sequence of amino acids, Nonnatural foldamers have been developed to emulate these protein structures as well as investigate various types of noncovalent interactions. Here we report a strategy to access two distinct folding topologies in aqueous solutions using the inherent recognition properties of aromatic donor/acceptor interactions. These oligomers are constructed of electron-rich 1,5-dialkoxynaphthalene (Dan) and electron-deficient 1,4,5,8-naphthalenetetracarboxylic diimide (Ndi) units. A trimer of the sequence Dan-Ndi-Dan was shown to adopt a pleated fold in solution, while its constitutional isomer, Dan-Dan-Ndi, adopted an intercalative or turn-type fold. UV-vis and NOESY spectroscopy analyses were consistent with the two different conformations. This study illustrates the designability of folding naphthyl oligomers and encourages the use of directed aromatic interactions to construct larger and more complex assemblies in water.