Perylenebisdicarboxiimides exhibit potential as optical and semi-conductive materials due to the aromatic core. The self-organization of the chromonic phases that these molecules exhibit can produce direction-dependent materials. Subtle changes in the flexible side chain or counter ion used to make the molecule water soluble can result in dramatic changes in liquid crystalline behavior as seen by polarizing light microscopy. ²H and ³⁵Cl NMR are used to further explore these changes in phase behavior. The formation of a ribbon-like phase from isotropic solution is utilized in making micro- and nano-scale patterns using a template guide.