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.

Solvent-Induced Formation of Novel Ni(II) Complexes Derived from Bis-Thiosemicarbazone Ligand: An Insight from Experimental and Theoretical Investigations

In this work, we report solvent-induced complexation properties of a new N₂S₂ tetradentate bis-thiosemicarbazone ligand (H₂L^I), prepared by the condensation of 4-phenylthiosemicarbazide with bis-aldehyde, namely 2,2'-(ethane-1,2-diylbis(oxy)dibenzaldehyde, towards nickel(II). Using ethanol as a reaction medium allowed the isolation of a discrete mononuclear homoleptic complex [NiL^I] (1), for which its crystal structure contains three independent molecules, namely 1-I, 1-II, and 1-III, in the asymmetric unit. The doubly deprotonated ligand L^I in the structure of 1 is coordinated in a cis-manner through the azomethine nitrogen atoms and the thiocarbonyl sulfur atoms. The coordination geometry around metal centers in all the three crystallographically independent molecules of 1 is best described as the seesaw structure. Interestingly, using methanol as a reaction medium in the same synthesis allowed for the isolation of a discrete mononuclear homoleptic complex [Ni(L^II)₂] (2), where L^II is a monodeprotonated ligand 2-(2-(2-(2-(dimethoxymethyl)phenoxy)ethoxy)benzylidene)-N-phenylhydrazine-1-carbothioamide (HL^II). The ligand L^II was formed in situ from the reaction of L^I with methanol upon coordination to the metal center under synthetic conditions. In the structure of 2, two ligands L^II are coordinated in a trans-manner through the azomethine nitrogen atom and the thiocarbonyl sulfur atom, also yielding a seesaw coordination geometry around the metal center. The charge and energy decomposition scheme ETS-NOCV allows for the conclusion that both structures are stabilized by a bunch of London dispersion-driven intermolecular interactions, including predominantly N-H∙∙∙S and N-H∙∙∙O hydrogen bonds in 1 and 2, respectively; they are further augmented by less typical C-H∙∙∙X (where X = S, N, O, π), CH∙∙∙HC, π∙∙∙π stacking and the most striking, attractive long-range intermolecular C-H∙∙∙Ni preagostic interactions. The latter are found to be determined by both stabilizing Coulomb forces and an exchange-correlation contribution as revealed by the IQA energy decomposition scheme. Interestingly, the analogous long-range C-H∙∙∙S interactions are characterized by a repulsive Coulomb contribution and the prevailing attractive exchange-correlation constituent. The electron density of the delocalized bonds (EDDB) method shows that the nickel(II) atom shares only ~0.8|e| due to the σ-conjugation with the adjacent in-plane atoms, demonstrating a very weak σ-metalloaromatic character.

Tetrel Bonding and Other Non-Covalent Interactions Assisted Supramolecular Aggregation in a New Pb(II) Complex of an Isonicotinohydrazide

A new supramolecular Pb(II) complex [PbL(NO₂)]_n was synthesized from Pb(NO₃)₂, N’-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and NaNO₂. [PbL(NO₂)]_n is constructed from discrete [PbL(NO₂)] units with an almost ideal N₂O₃ square pyramidal coordination environment around Pb(II). The ligand L⁻ is coordinated through the 2-pyridyl N-atom, one aza N-atom, and the carbonyl O-atom. The nitrite ligand binds in a κ²-O,O coordination mode through both O-atoms. The Pb(II) center exhibits a hemidirected coordination geometry with a pronounced coordination gap, which allows a close approach of two additional N-atoms arising from the N=C(O) N-atom of an adjacent molecule and from the 4-pyridyl N-atom from the another adjacent molecule, yielding a N₄O₃ coordination, constructed from two Pb–N and three Pb–O covalent bonds, and two Pb⋯N tetrel bonds. Dimeric units in the structure of [PbL(NO₂)]_n are formed by the Pb⋯N=C(O) tetrel bonds and intermolecular electrostatically enforced π⁺⋯π⁻ stacking interactions between the 2- and 4-pyridyl rings and further stabilized by C–H⋯π intermolecular interactions, formed by one of the methyl H-atoms and the 4-pyridyl ring. These dimers are embedded in a 2D network representing a simplified uninodal 3-connected fes (Shubnikov plane net) topology defined by the point symbol (4∙8²). The Hirshfeld surface analysis of [PbL(NO₂)] revealed that the intermolecular H⋯X (X = H, C, N, O) contacts occupy an overwhelming majority of the molecular surface of the [PbL(NO₂)] coordination unit. Furthermore, the structure is characterized by intermolecular C⋯C and C⋯N interactions, corresponding to the intermolecular π⋯π stacking interactions. Notably, intermolecular Pb⋯N and, most interestingly, Pb⋯H interactions are remarkable contributors to the molecular surface of [PbL(NO₂)]. While the former contacts are due to the Pb⋯N tetrel bonds, the latter contacts are mainly due to the interaction with the methyl H-atoms in the π⋯π stacked [PbL(NO₂)] molecules. Molecular electrostatic potential (MEP) surface calculations showed marked electrostatic contributions to both the Pb⋯N tetrel bonds and the dimer forming π⁺⋯π⁻ stacking interactions. Quantum theory of atoms in molecules (QTAIM) analyses underlined the tetrel bonding character of the Pb⋯N interactions. The manifold non-covalent interactions found in this supramolecular assembly are the result of the proper combination of the polyfunctional multidentate pyridine-hydrazide ligand and the small nitrito auxiliary ligand.

Exploring catecholase activity in dinuclear Mn(ii) and Cu(ii) complexes: an experimental and theoretical approach

Two dinuclear Mn(ii) and Cu(ii) complexes were prepared, characterised and assessed for non-covalent interactions and catecholase oxidase properties. The catecholase activity of2is further corroborated by theoretical calculations using DFT.

Solvent induced mononuclear and dinuclear mixed ligand Cu(ii) complex: structural diversity, supramolecular packing polymorphism and molecular docking studies

Phenolate bridged dinuclear and solvent induced mononuclear supramolecular isomers of Cu(ii) complex have been reported to explore the structural diversity and their antibacterial activity supported by molecular docking studies.

Different effects in the selective detection of aniline and Fe3+ by lanthanide-based coordination polymers containing multiple reactive sites

Isostructural Ln-CPs (1-Eu and 2-Tb) show almost the same high detection ability for Fe³⁺ and different detection abilities for aniline. The detection difference was studied through PXRD, UV-vis, luminescence lifetimes and Hirshfeld surface analysis.

M, Ahmad M, Shahid M. Synthesis, characterization, theoretical studies and catecholase like activities of [MO6] type complexes

Co(ii) and Zn(ii) complexes are prepared and characterized through spectral, crystallographic and theoretical studies. The Co(ii) complex is shown to be a catechol oxidase mimic and the activity is corroborated by DFT results.

Cu(I) complexes regulated by N-heterocyclic ligands: Syntheses, structures, fluorescence and electrochemical properties

Three mononuclear Cu(I) complexes, namely, [Cu(2-PBO)(PPh₃)₂]·ClO₄·2CH₂Cl₂ (1), [Cu(3-PBO)(PPh₃)₂(ClO₄)]·CH₂Cl₂ (2) and [Cu(PBM)(PPh₃)₂]·ClO₄ (3) (2-PBO = 2-(2'-Pyridyl)benzoxazole, 3-PBO = 2-(3'-Pyridyl)benzoxazole, PBM = 2-(2'-Pyridyl)benzimidazole, PPh₃ = triphenylphosphine) have been synthesized and characterized by elemental analyses, IR, ¹H NMR, ¹³C NMR, X-ray single crystal diffraction and thermal analysis. Photoluminescent investigation shows that complexes 1-3 exhibit distinct tunable light green (512 nm)-to-yellow (557 nm) photoluminescence by varying the N-heterocyclic ligands. Three complexes show intense 2-PBO-based yellow, 3-PBO-based light green and intense PBM-based bright green luminescence upon irradiation with a standard UV lamp (λ_ex = 254 nm) at room temperature. Moreover, the electrochemical properties of 1-3 have been investigated by cyclic voltammetry. The results suggest the frontier molecular orbits and the HOMO-LUMO energy gaps of these cuprous complexes are effectively adjusted through the introduction of different N-heterocyclic ligands, thus achieving the selective luminescence of the cuprous complexes.

Addressing the role of triphenylphosphine in copper catalyzed ATRP

A new Atom Transfer Radical Polymerization (ATRP) process with triphenylphosphine (PPh₃) and [Cu^IIMe₆TREN]²⁺ as the catalyst system is reported.

Crystal structure of bromido(4,4′-dimethoxy-2,2′-bipyridine-κ2N,N′)(isopropyl(diphenyl)phosphane-κP)copper(I), C27H29BrCuN2O2P

C27H29BrCuN2O2P, monoclinic, Cc (no. 9), a = 15.5806(10) Å, b = 10.5071(10) Å, c = 16.9748(15) Å, β = 110.729(2)°, V = 2599.0(4) Å3, Z = 4, Rgt(F) = 0.0186 , wRref(F2) = 0.0445, T = 120 K.

Solvent-driven azide-induced mononuclear discreteversusone-dimensional polymeric aromatic Möbius cadmium(ii) complexes of an N6tetradentate helical ligand

We report on a solvent-driven formation of discrete[Cd(N₃)₂(L)(MeOH)]·MeOHand a one-dimensional coordination polymer[Cd3(N3)6(L)]n.

Design, structures and study of non-covalent interactions of mono-, di-, and tetranuclear complexes of a bifurcated quadridentate tripod ligand, N-(aminopropyl)-diethanolamine

Supramolecular non-covalent interactions in novel mono-, di- and tetranuclear complexes are explored.