Coordination of a triazine ligand with Cu^II and Ag^I investigated by spectral, structural, theoretical and docking studies

Abstract

Two complexes of 5‐phenyl‐3‐(pyridin‐2‐yl)‐1,2,4‐triazine (PPTA), namely (ethanol‐κO)bis(nitrato‐κO)[5‐phenyl‐3‐(pyridin‐2‐yl‐κN)‐1,2,4‐triazine‐κN2]copper(II), [Cu(NO3)2(C14H10N4)(C2H6O)] or [Cu(NO3)2(PPTA)(EtOH)] (1), and bis[μ‐5‐phenyl‐3‐(pyridin‐2‐yl)‐1,2,4‐triazine]‐κ3N1:N2,N3;κ3N2,N3:N1‐bis[(nitrato‐κO)silver(I)], [Ag2(NO3)2(C14H10N4)2] or [Ag2(NO3)2(μ‐PPTA)2] (2), were prepared and characterized by elemental analysis, FT–IR spectroscopy and single‐crystal X‐ray diffraction. The X‐ray structure analysis of 1 revealed a copper complex with square‐pyramdial geometry containing two O‐donor nitrate ligands along with an N,N′‐donor PPTA ligand and one O‐donor ethanol ligand. In the binuclear structure of 2, formed by the bridging of two PPTA ligands, each Ag atom has an AgN3O environment and square‐planar geometry. In addition to the four dative interactions, each Ag atom interacts with two O atoms of two nitrate ligands on adjacent complexes to complete a pseudo‐octahedral geometry. Density functional theory (DFT) calculations revealed that the geometry around the Cu and Ag atoms in 1opt and 2opt (opt is optimized) for an isolated molecule is the same as the experimental results. In 1, O—H…O hydrogen bonds form R12(4) motifs. In the crystal network of the complexes, in addition to the hydrogen bonds, there are π–π stacking interactions between the aromatic rings (phenyl, pyridine and triazine) of the ligands on adjacent complexes. The ability of the ligand and complexes 1 and 2 to interact with ten selected biomacromolecules (BRAF kinase, CatB, DNA gyrase, HDAC7, rHA, RNR, TrxR, TS, Top II and B‐DNA) was investigated by docking studies. The results show that the studied compounds can interact with proteins better than doxorubicin (except for TrxR and Top II).

The Coordination Behavior of Two New Complexes, [(C7H10NO2)CdCl3]n(I) and [(C7H9NO2)CuCl2] (II), Based on 2,6-Dimethanolpyridine; Elaboration of the Structure and Hirshfeld Surface, Optical, Spectroscopic and Thermal Analysis

“…Furthermore, the pyridyl N atoms are considered strongly coordinated to the metal with a bond length of Cu–N of 1.9356(12) Å, while the oxygen and chlorine atoms of the equatorial plane form weaker connections with the central metal with a distance ranging from 2.0305(12) to 2.2228(4) Å ( Table S1 ). All of these values are consistent with those found for other comparable systems [ 52 , 53 , 54 , 55 , 56 ]. To differentiate between trigonal bipyramidal and square pyramidal coordination centers, Addison et al suggested the “ τ 5 ” parameter using the following Equation [ 57 ]: where β > α represents the coordination center’s two largest valence angles.…”

Coordination of an amino alcoholic Schiff base ligand toward the zinc(II) ion: spectral, structural, theoretical, and docking studies

“…The best predicted protein target for ligand and complexes 1-3 is HDAC7. Based on the calculated fitness values, in each case, the binding ability of one, two or three complexes is higher than that of the free ligand [57]. Docking calculations revealed that all studied compounds have higher fitness scores compared to doxorubicin in binding toward CatB and HDAC7.…”

A binuclear Cd(II) complex containing bridging pyrimidine-based ligands

“…1) -donor toward two cadmium atoms and forms an almost planar five-membered chelate ring (maximum deviation from a mean plane through the chelate ring: 0.087 Å for C5 and C7 atoms) around each cadmium atom. A six-membered 2L:2M 1,4 ring (1 and 4 refer to the positions of the cadmium atoms in the ring) forms by participation of two APPH and two cadmium atoms [20].…”