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Toxicity and reactivity of nitro polycyclics have been correlated with their molecular structure and electronic properties, in particular with the nitro substituent orientation. Experimental data are scarce for mononitro derivatives of benzo[a]pyrene (BaP) and benzo[e]pyrene (BeP), so density functional B3LYP/6-311++G(d,p) calculations have been performed on all of the isomers of nitro-BaP and nitro-BeP in their singlet and triplet states. The most stable configurations are planar ones in which NO2 interacts with the aromatic π-electron system, although the majority of structures are non-planar. Nitro substitution in the bay region of both BaP and BeP results in two stable singlet structures with very different geometries; the higher energy states show a strong O–C interaction that induces sp3 hybridization in the aromatic carbon atom. The calculated IR spectra display differences between planar and non-planar structures that can be used to predict the nitro group orientation and thereby the potential toxicity of each isomer.