Two-dimensional infrared (2D IR) spectroscopy was used to characterize the structure of a self-assembled polycyclic aromatic hydrocarbon (PAH), violanthrone-79. A local mode basis was constructed using spectroscopic and computational results of anthrone and monomer violanthrone-79. The vibrational modes in the spectral region 1550-1700 cm(-1), carbonyl stretching and in-plane ring breathing, are used as vibrational probes. The local mode basis and an electrostatic coupling model were applied to three nanoaggregate structures: parallel, antiparallel, and a chiral configuration produced by a 28° rotation from parallel. Angular disorder within each nanoaggregate configuration was also explored. This investigation is a first approach to probe self-assembled PAHs with 2D IR spectroscopy. The experimental and calculated 2D IR spectra align best when the violanthrone-79 molecules are in an anti-parallel configuration within the nanoaggregate.