An unexpected single crystal structure of nickel(II) complex: Spectral, DFT, NLO, magnetic and molecular docking studies.

This work explores the study of a synthesized nickel complex as a possible inhibitor against the main protease (Mpro) of the recent emerging coronavirus disease (COVID-19). Overall, the template reaction of 3-acetyl-2-hydroxy-6-methyl-4H-pyran-4-one with nickel(II) chloride hexahydrate in N,N-dimethylformamide (DMF) medium leads to the formation of neutral nickel complex. This resulting complex is formulated as [Ni(DHA)2(DMF)2] on the basis of FT-IR, UV-Vis., single-crystal X-ray diffraction analysis, magnetic susceptibility and CV measurements as well as DFT quantum chemical calculations. Its single crystal suggests was found to be surrounded by the both pairs of molecules of DHA and DMF through six oxygen atoms with octahedral coordination sphere. The obtained magnetic susceptibilities are positive and agree with its paramagnetic state. In addition to the experimental investigations, optimized geometry, spectroscopic and electronic properties were also performed using DFT calculation with B3LYP/6-31G(d,p) level of theory. The nonlinear optical (NLO) properties of this complex are again examined. Some suitable quantum descriptors (EHOMO, ELUMO, Energy gap, Global hardness), Milliken atomic charge, Electrophilic potion and Molecular Electrostatic Potential) have been elegantly described. Molecular docking results demonstrated that the docked nickel complex displayed remarkable binding energy with Mpro. Besides, important molecular properties and ADME pharmacokinetic profiles of possible Mpro inhibitors were assessed by in silico prediction.

Synthesis, in silico study (DFT, ADMET) and crystal structure of novel sulfamoyloxy-oxazolidinones: Interaction with SARS-CoV-2.

A new series of sulfamoyloxyoxazolidinone (SOO) derivatives have been synthesized and characterized by single-crystal X-ray diffraction, NMR, IR, MS and EA. Chemical reactivity and geometrical characteristics of the target compounds were investigated using DFT method. The possible binding mode between SOO and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that SOO crystallizes in a monoclinic system with P 2 1 space group. The binding energy of the SARS-CoV-2/Mpro-SOO complex and the calculated inhibition constant using docking simulation showed that the active SOO molecule has the ability to inhibit SARS-CoV2. We studied the prediction of absorption, distribution, properties of metabolism, excretion and toxicity (ADMET) of the synthesized molecules.

Highly Luminescent Europium-Based Heteroleptic Coordination Polymers with Phenantroline and Glutarate Ligands.

Isostructural lanthanide-based coordination polymers with general chemical formula [Ln(phen)(glu)(NO3)]∞ with Ln = La-Tm (except Ce and Pm) have been synthesized by hydrothermal methods (H2glu stands for glutaric acid and phen stands for 1,10-phenantroline). They crystallize in the monoclinic system with the P21/c (no. 14) space group. The crystal structure has been solved on the basis of the La derivative. It can be described as the superimposition of molecular chains of dimeric La(phen)(NO3)-La(phen)(NO3) units bridged by glutarate ligands. Luminescent properties have been explored and show that the Eu derivative exhibits the highest luminance observed for Eu-based coordination polymers (85 to 105 cd·m-2). Effects of the dilution of the Eu3+ and Tb3+ luminescent ions by Gd3+ optically inactive ions are unexpected and to the best of our knowledge unprecedented. This could be related to the different intermetallic energy-transfer mechanisms in competition and to the nonisotropic distribution of the lanthanide ions in these molecular alloys. The investigation of molecular alloys with general chemical formula [Eu1-xTbx(phen)(glu)(NO3)]∞ with 0 ≤ x ≤ 1 highlights a very sizable and constant Eu3+ luminescence whatever the x value, which further confirms the existence of very strong intermetallic energy transfers in this family of compounds. It is also noticeable that some coordination polymers based on weakly emissive lanthanide ions exhibit very well defined emission spectra.

Synthesis, X-ray structure, in silico calculation, and carbonic anhydrase inhibitory properties of benzylimidazole metal complexes.

Three coordination compounds of formula {M(bmim)2Cl2} were synthetised (M = Co, Zn, and Hg) and fully characterised. Each complex incorporates 1-benzyl-2-methylimidazole (bmim) as ligand. The coordination polyhedron around the metal center for all complexes has a quasi-regular tetragonal geometry. Density functional theory calculations were carried out on the title compounds and as well on hypothetical complexes (Cu, Ni), in order to elucidate their electronic and molecular structure. The calculations reproduced the Co, Zn, and Hg experimental structures and could predict stable complexes in the case of Ni(II) and Cu(II) ions. The carbonic anhydrase (CA, EC 4.2.1.1) inhibitory effects of the three complexes were investigated. Only compound {Hg(bmim)2Cl2} (3) exhibited a modest inhibitory effect against hCA I, probably due to the affinity of Hg(II) for His residues at the entrance of the active site cavity.

Crystal structure of 3,5-bis-(4-chloro-phen-yl)-1-propyl-1,3,5-tri-aza-cyclo-hexane.

In the title mol-ecule, C18H21Cl2N3, the tri-aza-cyclo-hexane ring adopts a chair conformation with both 4-chloro-phenyl substituents in axial positions and the propyl group in an equatorial site. The dihedral angle between the planes of the benzene rings is 49.5 (1)°. In the crystal, mol-ecules are arranged in a head-to-tail fashion, forming columns along [010], and pairs of weak C-H⋯π inter-actions form inversion dimers between columns.

Crystal structure of ethyl 2-chloro-6-methyl-quinoline-3-carboxyl-ate.

In the title compound, C13H12ClNO2, the dihedral angle between the planes of the quinoline ring system (r.m.s. deviation = 0.029 Å) and the ester group is 54.97 (6)°. The C-O-C-Cm (m = meth-yl) torsion angle is -140.62 (16)°. In the crystal, mol-ecules inter-act via aromatic π-π stacking [shortest centroid-centroid separation = 3.6774 (9) Å] generating (010) sheets.

Crystal structure of 1-methyl-2-[(E)-2-(4-methyl-phen-yl)ethen-yl]-4-nitro-1H-imidazole.

In the title mol-ecule, C13H13N3O2, the planes of the benzene and imidazole rings form a dihedral angle of 7.72 (5)°. In the crystal, mol-ecules are linked by weak C-H⋯N and C-H⋯O hydrogen bonds, forming layers parallel to (100). A weak C-H⋯π inter-action connects these layers into a three-dimensional network. A π-π stacking inter-action, with a centroid-centroid distance of 3.5373 (9) Å, is also observed.

Crystal structure of ethyl 2-chloro-5,8-di-meth-oxy-quinoline-3-carboxyl-ate.

In the title compound, C14H14ClNO4, the dihedral angle between the quinoline ring system (r.m.s. deviation = 0.0142 Å) and ester planes is 18.99 (3)°. The C-O-C-Cm (m = meth-yl) torsion angle is -172.08 (10)°, indicating a trans conformation. In the crystal, the mol-ecules are linked by C-H⋯O and C-H⋯N inter-actions, generating layers lying parallel to (101). Aromatic π-π stacking [centroid-centroid distances = 3.557 (2) and 3.703 (2)Å] links the layers into a three-dimensional network.

Crystal structure of (E)-1-methyl-2-[2-(2-methoxphen-yl)ethen-yl]-4-nitro-1H-imidazole.

In the asymmetric unit of the title compound, C13H13N3O3, the 2-(2-methoxphen-yl)ethenyl unit is connected to the methyl-nitro-imidazole 1-methyl-4-nitro-1H-imidazole moiety. The mol-ecule is quasi-planar and the planes of the two rings form a dihedral angle of 0.92 (11)°. The crystal packing can be described as layers parallel to the (011) plane, stabilized by inter-molecular C-H⋯O hydrogen bonding, resulting in the formation of an infinite three-dimensional network linking these layers. Strong π-π stacking inter-actions are observed, viz. benzene-benzene, imidazole-imidazole and benzene-imidazole rings, with centroid-centroid distances of 3.528 (2), 3.457 (2) and 3.544 (2) Å, respectively. Intensity statistics indicated twinning by non-merohedry, with refined weighs of the twin components of 0.3687:0.6313.

Bis(4-amino-benzene-sulfonamide-κN (4))di-chlorido-zinc.

In the title compound, [ZnCl2(C6H8N2O2S)2], the Zn(II) ion lies on a twofold rotation axis and has a slightly distorted tetra-hedral coordination geometry, involving two Cl atoms and two N atoms from the amino groups attached directly to the benzene rings [Zn-Cl = 2.2288 (16) Šand Zn-N = 2.060 (5) Å]. The dihedral angle between the benzene rings is 67.1 (3)°. The crystal packing can be describe as layers in a zigzag arrangement parallel to (001). The amine H atoms act as donor atoms and participate in inter-molecular N-H⋯O and N-H⋯Cl hydrogen bonds, forming a three-dimensional network.

catena-Poly[[trans-bis-(1,3-benzo-thia-zole-κN)manganese(II)]-di-µ-chlorido].

In the title coordination polymer, [MnCl2(C7H5NS)2] n , the Mn(II) ion is located on the inter-section of a twofold rotation axis and a mirror plane and adopts an octa-hedral coordination geometry defined by two mutually trans N atoms from benzo-thia-zole ligands which occupy the axial positions, and four Cl atoms which form the equatorial sites. The Mn(II) ions are connected by two bridging Cl atoms, forming chains parallel to the c axis. The crystal packing can be descibed as alternating layers parallel to (001) featuring π-π stacking inter-actions with a centroid-centroid distance of 3.6029 (15) Å.

4-(2-Nitro-benz-yl)-3-phenyl-3,4-di-hydro-2H-1,4-benzoxazin-2-ol.

The title compound, C21H18N2O4, crystallizes with two independent mol-ecules (A and B) in the asymmetric unit. In both mol-ecules the oxazine ring has an envelope conformation with the hydroxyl-substituted C atom as the flap. The nitro-benzyl ring and the phenyl ring are almost normal to the mean plane of the benzooxazine ring system with dihdral angles of 85.72 (15) and 82.69 (15)°, respectively, in mol-ecule A, and 85.79 (15) and 87.72 (15)°, respectively, in mol-ecule B. The main difference in the conformation of the two mol-ecules concerns the dihedral angle between the nitro-benzyl ring and the phenyl ring, viz. 79.67 (18) in mol-ecule A and 71.13 (18)° in mol-ecule B. In the crystal, the A and B mol-ecules are linked by an O-H⋯O hydrogen bond. These units are then linked via C-H⋯O hydrogen bonds, forming sheets lying parallel to (010). Further C-H⋯O hydrogen bonds link the sheets to form a three-dimensional network. There are also O-H⋯π and C-H⋯π inter-actions present, reinforcing the three-dimensional structure.

7-Meth-oxy-2-phenyl-quinoline-3-carbaldehyde.

In the title mol-ecule, C17H13NO2, the phenyl ring is inclined to the quinoline ring system by 43.53 (4)°. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds, forming double-stranded chains propagating along [011]. These chains are linked via π-π inter-actions involving inversion-related quinoline rings; the shortest centroid-centroid distance is 3.6596 (17) Å.

2-(4-Chloro-phen-yl)-2,3-di-hydro-quinolin-4(1H)-one.

The title mol-ecule, C15H12ClNO, features a di-hydro-quinolin-4(1H)-one moiety attached to a chloro-benzene ring. The heterocyclic ring has a half-chair conformation with the methine C atom lying 0.574 (3) Šabove the plane of the five remaining atoms (r.m.s. deviation = 0.0240 Å). The dihedral angles between the terminal benzene rings is 77.53 (9)°, indicating a significant twist in the mol-ecule. In the crystal, supra-molecular zigzag chains along the c-axis direction are sustained by N-H⋯O hydrogen bonds. These are connected into double chains by C-H⋯π inter-actions.

2-p-Tolyl-2,3-di-hydro-quinolin-4(1H)-one.

In the title mol-ecule, C16H15NO, the tetra-hydro-pyridine ring is in a sofa conformation with the methine C atom forming the flap. The dihedral angle between the benzene rings is 80.85 (8)°. In the crystal, mol-ecules are arranged in alternating double layers parallel to (100) and are connected along [001] by N-H⋯O hydrogen bonds. In addition, weak C-H⋯π inter-actions are observed.

3-Anilino-5,5-di-methyl-cyclo-hex-2-enone.

In the title mol-ecule, C14H17NO, the 5,5-di-methyl-cyclo-hex-2-enone moiety is attached to an aniline group, the dihedral angle subtended [54.43 (3)°] indicating a significant twist. The hexaneone ring has a half-chair conformation with the C atom bearing two methyl groups lying 0.6384 (8) Šabove the plane of the five remaining atoms (r.m.s. deviation = 0.0107 Å). The crystal packing can be described as alternating layers parallel to (-101), which are consolidated by N-H⋯O hydrogen bonds and C-H⋯π inter-actions.

Synthesis, crystal structure and antibacterial activity of new highly functionalized ionic compounds based on the imidazole nucleus.

Several new highly functionalized imidazolium derivatives were synthesized, via appropriate synthetic routes, using imidazole, 1-methylimidazole and 2-phenyl-1-methylimidazole as key intermediates. The antibacterial activity of the prepared compounds was evaluated against: Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella thipymurium using disk-diffusion and MIC methods. Crystal X-ray structures are reported for six compounds.

2-(2-Nitro-phenyl-sulfin-yl)acetonitrile.

In the title compound, C8H6N2O3S, the dihedral angle between the nitro group and the benzene ring is 6.76 (9)°. The bond-angle sum at the S atom is 308.1°. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds to generate (010) sheets. The crystal studied was found to be a racemic twin.

2,2'-(Disulfanedi-yl)dianilinium dichloride dihydrate.

In the title hydrated mol-ecular salt, C12H14N2S2 (2+)·2Cl(-)·2H2O, the dihedral angle between the benzene rings in the dication is 9.03 (17)° and the C-S-S-C torsion angle is 96.8 (2)°. The crystal packing can be described as alternating organic and anionic water layers lying parallel to (100), which are linked by N-H⋯Cl and N-H⋯O hydrogen bonds. O-H⋯Cl hydrogen bonds and aromatic π-π stacking inter-actions [centroid-centroid separation = 3.730 (3) Å] are also observed.

Bis(3-amino-pyrazine-2-carboxyl-ato-κ(2)N(1),O)diaqua-cobalt(II).

In the title compound, [Co(C(5)H(4)N(3)O(2))(2)(H(2)O)(2)], the Co(II) atom is situated on a twofold rotation axis and is N,O-chelated by two 3-amino-pyrazine-2-carboxyl-ate anions and additionally bonded to the O atoms of two water mol-ecules, leading to a slightly distorted octa-hedral coordination environment. The crystal packing is dominated by inter-molecular O-H⋯O, O-H⋯N and N-H⋯O hydrogen bonding involving the water mol-ecules and amino groups as donors and carboxyl-ate O atoms, as well as the non-coordinating heterocyclic N atoms as acceptors, resulting in a three-dimensional network. An intra-molecular N-H⋯O hydrogen bond is also observed.