Structural adaptability and hydrogen bonding in a dissymmetric pyrimidine thioether ligand

Dissymmetric ligands have garnered interest due to their ability to simultaneously coordinate to multiple different acceptors. Herein, we report the synthesis of a dissymmetric thioether N,N'-bidentate ligand, namely, 2-[(6-chloropyrimidin-4-yl)sulfanyl]pyrimidine-4,6-diamine (C₈H₇ClN₆S, L1), along with its hydrated form (C₈H₇ClN₆S·H₂O). In addition, we describe the structure of a nitrate salt of the protonated ligand {4,6-diamino-2-[(6-chloropyrimidin-4-yl)sulfanyl]pyrimidin-1-ium nitrate, C₈H₈ClN₆S⁺·NO₃^-} and a cobalt(II) complex of L1 (dichlorido{2-[(6-chloropyrimidin-4-yl-κN³)sulfanyl]pyrimidine-4,6-diamine-κN³}cobalt(II), [CoCl₂(C₈H₇ClN₆S)]). The structures of all four compounds were determined by single-crystal X-ray diffraction and Hirshfeld surface analyses were performed. These analyses reveal unengaged hydrogen-bond donors and acceptors in both the neutral ligand and its water solvate, while protonation or metal coordination induces a conformational change that enables full engagement of hydrogen-bond donors. These structural insights have implications for the molecular design of ligands in ion-sensing applications.