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This study reports on the supramolecular assemblies formed between planar carbon systems (PCSs) such as thermally reduced graphene oxide (TRGO) and its small-molecule model system coronene and a series of d- and l-α amino acid derivatized naphthalenediimides (NDIs) where the halogen substituents (X = F, Cl, Br, I) are varied systematically. Confocal fluorescence microscopy of NDIs, NDI•coronene, and NDI•TRGO complexes is performed proving the uptake and stability of such complexes in the cellular environment and suggesting their potential as prostate cancer imaging agents. 1H NMR and UV-vis spectroscopy studies support the formation of charge transfer complexes whereby the increasing polarizability and general electronegativity of the aryl halide substituted at the NDI periphery influence the magnitude of the association constants in the ground state between NDI and coronene. Complexation between NDIs and PCSs also results in stable photoexcited assemblies within the solution (coronene) as well as the dispersed phased (TRGO). Fluorescence emission titrations and 2-photon time correlated single photon counting measurements suggest the existence of dynamic quenching mechanisms upon the excitation of the fluorophore in the presence of the carbon substrates, as these methods are sensitive proves for the subtle changes in the NDI environment. The series of halogenated species used exerts supramolecular control over the degree of surface assembly on the TRGO and over the interactions with the coronene molecule, and this is of relevance to the assembly of future biosensing platforms as these materials can both be viewed as congeners of graphene. Finally, MTT assays carried out in PC-3 cells demonstrate that the stable noncovalent functionalization of TRGO and coronene with either l or d NDIs remarkably improves the cellular viability in the presence of such graphene-like materials. These phenomena are of particular relevance for the understanding of the direct donor-acceptor interactions in solutions which govern the design of nanomaterials with future biosensing and bioimaging applications.