Structure-property relationship in thioxotriaza-spiro derivative: Crystal structure and molecular docking analysis against SARS-CoV-2 main protease

Detailed structural and non-covalent interactions in thioxotriaza-spiroderivative (DZ2) are investigated by single crystal structure anslysis and computational approaches. Its results were compared with the previously reported spiroderivative (DZ1). The crystal structure analysis revealed various C–H…O, N–H…O, C–H…N and N–H…S hydrogen bonds involved in constructing several dimeric motifs to stabilize the crystal packing. The differences and similarities in the relative contribution of non-covalent interactions in DZ1 and DZ2 compounds are compared using the Hirshfeld surface analysis and 2D fingerprint plots. The binding energies of specific molecular pairs and homodimers have been obtained using molecule–molecule interaction energy calculation. The hierarchy and topology of pair-wise intermolecular interactions are visualized through energy frameworks. The nature and strength of intra and intermolecular interactions were characterized using non-covalent interaction index analysis and the quantum theory of atoms in molecule approach. Further, molecular docking of compounds (DZ1 and DZ2) with SARS-CoV-2 main protease for COVID-19 is performed. And the superposition of these ligands and inhibitor N3, which is docked into the binding pocket of 7BQY, is presented. The binding affinity of −6.7 kcal/mol is observed, attributed to hydrogen bonding and hydrophobic interactions between the ligand and the amino acid residues of the receptor.

Synthesis and structural study of some new phosphorus(v) hydrazide compounds: spectroscopic evidence and a theoretical approach

New phosphorus(v) hydrazides based on methyl and t-butyl carbazates are reported. Experimental trends are elucidated using DFT calculations.

Di- and Trinuclear Complexes Derived from Hexakis(2-pyridyloxy)cyclotriphosphazene. Unusual P−O Bond Cleavage in the Formation of [{(L‘CuCl)2(Co(NO3)}Cl] (L‘ = N3P3(OC5H4N)5(O))

Hexakis(2-pyridyloxy)cyclotriphosphazene (L) is an efficient multisite coordination ligand which binds with transition metal ions to produce dinuclear (homo- and heterometallic) complexes [L(CuCl)(CoCl3)], [L(CuCl)(ZnCl3)], [L(CoCl)(ZnCl3)], and [L(ZnCl2)2]. In these dinuclear derivatives the cyclophosphazene ligand utilizes from five to six nitrogen coordination sites out of the maximum of nine available sites. Further, the spacer oxygen that separates the pyridyl moiety from the cyclophosphazene ring ensures minimum steric strain to the cyclophosphazene ring upon coordination. This is reflected in the near planarity of the cyclophosphazene ring in all the dinuclear derivatives. In the dinuclear heterobimetallic derivatives one of the metal ions [Cu(II) or Co(II)] is hexacoordinate and is bound by the cyclophosphazene in a eta5-gem-N5 mode. The other metal ion in these heterobimetallic derivatives [Co(II) or Zn(II)] is tetracoordinate and is bound in an eta(1)-N(1) fashion. In the homobimetallic derivative, [L(ZnCl2)2], one of the zinc ions is five-coordinate (eta3-nongem-N3), while the other zinc ion is tetracoordinate(eta2-gem-N2). The reaction of L with CuCl2 followed by Co(NO3)2.6H2O yields a trinuclear heterobimetallic complex [{(L'CuCl)2Co(NO3)}Cl] [L' = N3P3(OC5H4N)5(O)]. In the formation of this compound an unusual P-O bond cleavage involving one of the phosphorus-pyridyloxy bonds is observed. The molecular structure of [{(L'CuCl)2Co(NO3)}Cl] [L' = N3P3(OC5H4N)5(O)] reveals that each of the two the P-O-cleaved L' ligands is involved in binding to Cu(II) to generate the motif L'CuCl. Two such units are bridged by a Co(II) ion. The coordination environment around the bridging Co(II) ion contains four oxygen (two P-O units, one chelating nitrate) and two nitrogen atoms (pyridyloxy nitrogens).

Cyclotriphosphazene Hydrazides as Efficient Multisite Coordination Ligands. η3-fac-non-geminal-N3 Coordination of spiro-N3P3[O2C12H8][N(Me)NH2]4 (L) in L2CoCl3 and L2M(NO3)2 (M = Ni, Zn, Cd)

The cyclophosphazene tetrahydrazide spiro-N(3)P(3)[O(2)C(12)H(8)][N(Me)NH(2)](4) (L) functions as a multisite coordination ligand and affords L(2)CoCl(3).2CH(3)OH (4), L(2)Ni(NO(3))(2).2CHCl(3).2.5H(2)O (5), L(2)Zn(NO(3))(2).2CH(3)CN.2H(2)O (6), and L(2)Cd(NO(3))(2) (7). Each of the cyclophosphazene ligands that is involved in coordination to the metal functions as a non-geminal-N(3) donor coordinating through one ring nitrogen atom and two non-geminal-NH(2) nitrogen atoms. The coordination geometry around the metal ion in 4-6 is approximately octahedral while it is severely distorted in the case of 7.