A series of N-pyridyl ureas bearing 1,2,4- (1a, 2a, and 3a) and 1,3,4-oxadiazole moiety (1b, 2b, 3b) was prepared and characterized by HRMS, 1H and 13C NMR spectroscopy, as well as X-ray diffraction. The inspection of the crystal structures of (1–3)a,b and the Hirshfeld surface analysis made possible the recognition of the (oxadiazole)···(pyridine) and (oxadiazole)···(oxadiazole) interactions. The presence of these interactions was confirmed theoretically by DFT calculations, including NCI analysis for experimentally determined crystal structures as well as QTAIM analysis for optimized equilibrium structures. The preformed database survey allowed the verification of additional examples of relevant (oxadiazole)···π interactions both in Cambridge Structural Database and in Protein Data Bank, including the cocrystal of commercial anti-HIV drug Raltegravir.
Co-crystallization of dithiocarbamate complexes [MII(S2CNEt2)2] (M = Cu 1, Ni 2, Pd 3, Pt 4) and 1,3,5-triiodotrifluorobenzene (FIB) gives an isomorphic series of (1–4)·2FIB co-crystals exhibiting quadruple Cu/Ni/Pd/Pt isostructural exchange. In the structures of (1–4)·2FIB, the halogen-bonded C–I⋯M (Ni, Pd, Pt) and semicoordination M⋯I–C (Cu) metal-involving contacts were identified by X-ray diffractometry and their nature was verified theoretically. The directionality of the Iσ-hole⋯d2zMII and MII⋯Ielectron belt interactions depends on the identity of a metal center: on going from a rather electrophilic CuII to substantially more nucleophilic NiII, PdII, and PtII centers, we observed the electron belt-to-σ-hole switch of a noncovalently bound iodine(I) of FIB and, correspondingly, its shift from semicoordination to halogen bonding. The negative values of the electrostatic potentials (given in parentheses) were estimated for all metal centers and they decrease in the order CuII (−8.8) > NiII (−24.5) > PdII (−28.6) > PtII (−33.3 kcal mol−1). Despite the negative potentials at all MIIs, the semicoordinative contact Cu⋯I was established by the recognition of the LP(I) → LP*(Cu) charge transfer using natural bond orbital (NBO) analysis and the comparison of electron density (ED) and electrostatic potential (ESP) minima positions along the I⋯Cu bond paths. In the case of the rather nucleophilic (although positively charged) PdII and PtII centers, the contacts C–I⋯d2z[Pd] and C–I⋯d2z[Pt] can be attributed to the unconventional metal-involving halogen bonding; these contacts are among the strongest (4.30 and 5.42 kcal mol−1, correspondingly) between any metal center and iodine(I)-based σ-hole donors.
1 February 2019 in European Journal of Medicinal Chemistry