The crystal structure of danofloxacin (DFX) as a zwitterionic dihydrate [systematic name: (1S,4S)-5-(3-carboxylato-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)-2-methyl-2,5-diazabicyclo[2.2.1]heptan-2-ium dihydrate], C19H20FN3O3·2H2O, has been determined for the first time. The stability of the crystal structure is ensured by N-H...O and O-H...O hydrogen bonds, some of which are assisted by charge. The zwitterionic molecules of DFX are packed in stacks and this structural motif can be defined as a basic one from a supramolecular and energetic point of view. Hirshfeld surface analysis was used for an additional interpretation of the close contacts. The nature of the intermolecular interactions was evaluated in a pairwise manner. Destabilizing interactions were also discussed. In the context of our study on danofloxacin, we addressed the question: how common is a zwitterionic form for fluoroquinolones (FQ) in the crystalline state? A survey of the Cambridge Structural Database limited to anhydrous/hydrated/solvated forms of the most typical FQs revealed that neutral molecules are preferred, while zwitterions are less common.
Keywords: Hirshfeld surface analysis; antibacterial agent; antibiotic; crystal structure; danofloxacin dihydrate; destabilizing interactions; fluoroquinolone; stacking interactions; zwitterionic structure.