AbstractThe object of the present study are BODIPY molecules obtained previously by Piskorz et al. (Dyes Pigm. 178:108322, 2020) for their antimicrobial activity. Structural analysis of the BODIPY dimers is presented in context of the aggregation influence on the photophysical properties. The thorough investigation of the nature of intermolecular interaction in the representative BODIPY dimers is provided together with the decomposition of the interaction energy into the components of well-defined origin according to SAPT procedure. For the model BODIPY systems the careful examination of the interaction nature for the dimer structure based on experimental crystal study as well as fully optimized is given. The tendencies observed in the model dimers are further on investigated for two pairs of BODIPY systems designed for biomedical application. The analyzed molecules are shown to maximize the mutual interaction by the optimization of the stacking dispersion contacts between the aromatic rings of the molecules, therefore producing stable dimers. The estimation of SAPT0 interaction energy components confirms the dominating dispersion character arising from mutual BODIPY core contacts. The influence of the dimerization process on the photophysical properties of the systems studied theoretically depends to the high extend on the dimerization mode and is significant for parallel and antiparallel dispersion-governed dimers.