Synthesis, X-ray, Hirshfeld, and AIM Studies on Zn(II) and Cd(II) Complexes with Pyridine Ligands

The synthesis and crystal structures of three heteroleptic complexes of Zn(II) and Cd(II) with pyridine ligands (ethyl nicotinate (EtNic), N,N-diethylnicotinamide (DiEtNA), and 2-amino-5-picoline (2Ampic) are presented. The complex [Zn(EtNic)2Cl2] (1) showed a distorted tetrahedral coordination geometry with two EtNic ligand units and two chloride ions as monodentate ligands. Complexes [Zn(DiEtNA)(H2O)4(SO4)]·H2O (2) and [Cd(OAc)2(2Ampic)2] (3) had hexa-coordinated Zn(II) and Cd(II) centers. In the former, the Zn(II) was coordinated with three different monodentate ligands, which were DiEtNA, H2O, and SO42−. In 3, the Cd(II) ion was coordinated with two bidentate acetate ions and two monodentate 2Ampic ligand units. The supramolecular structures of the three complexes were elucidated using Hirshfeld analysis. In 1, the most important interactions that governed the molecular packing were O···H (15.5–15.6%), Cl···H (13.6–13.8%), Cl···C (6.3%), and C···H (10.3–10.6%) contacts. For complexes 2 and 3, the H···H, O···H, and C···H contacts dominated. Their percentages were 50.2%, 41.2%, and 7.1%, respectively, for 2 and 57.1%, 19.6%, and 15.2%, respectively, for 3. Only in complex 3, weak π-π stacking interactions between the stacked pyridines were found. The Zn(II) natural charges were calculated using the DFT method to be 0.8775, 1.0559, and 1.2193 for complexes 1–3, respectively. A predominant closed-shell character for the Zn–Cl, Zn–N, Zn–O, Cd–O, and Cd–N bonds was also concluded from an atoms in molecules (AIM) study

Synthesis, Supramolecular Structural Investigations of Co(II) and Cu(II) Azido Complexes with Pyridine-Type Ligands

Two new Co(II) and Cu(II) azido complexes with 4-picoline (4-Pic) and pyridine-2-carboxaldoxime (HAld) were synthesized by self-assembly of the organic ligand and the M(II) nitrate in the presence of azide as a co-ligand. Their structures were determined to be [Co(4-Pic)4(H2O)(N3)]NO3*H2O*4-Pic (1) and [Cu(HAld)(Ald)(N3)] (2) using X-ray single crystal diffraction. In complex 1, the coordination geometry is a slightly distorted octahedron with a water molecule and azide ion located trans to one another. On the other hand, complex 2 has a distorted square pyramid CuN5 coordination sphere with N-atoms of the organic ligand as a basal plane and azide ion as apical. All types of intermolecular contacts and their contributions in the molecular packing were analyzed using Hirshfeld analysis. The intermolecular contacts, H…H (53.9%), O…H (14.1%), N…H (11.0%) and H…C (18.8%) in 1, and H…H (27.4%), N…H (27.7%), O…H (14.7%) and H…C (13.6%) in 2 have the largest contributions. Of all the contacts, the O…H, N…H and C…C interactions in 2 and the O…H, N…H and H…C in 1 are apparently shorter than the van der Waals radii sum of the interacting atoms. Atoms in molecules (AIM) topological parameters explained the lower symmetry of the coordinated azide in 1 than 2

Synthesis and Structure Elucidation of Novel Spirooxindole Linked to Ferrocene and Triazole Systems via [3 + 2] Cycloaddition Reaction

In the present work, a novel heterocyclic hybrid of a spirooxindole system was synthesized via the attachment of ferrocene and triazole motifs into an azomethine ylide by [3 + 2] cycloaddition reaction protocol. The X-ray structure of the heterocyclic hybrid (1″R,2″S,3R)-2″-(1-(3-chloro-4-fluorophenyl)-5-methyl-1H-1,2,3-triazole-4-carbonyl)-5-methyl-1″-(ferrocin-2-yl)-1″,2″,5″,6″,7″,7a″-hexahydrospiro[indoline-3,3″-pyrrolizin]-2-one revealed very well the expected structure, by using different analytical tools (FTIR and NMR spectroscopy). It crystallized in the triclinic-crystal system and the P-1-space group. The unit cell parameters are a = 9.1442(2) Å, b = 12.0872(3) Å, c = 14.1223(4) Å, α = 102.1700(10)°, β = 97.4190(10)°, γ = 99.1600(10)°, and V = 1484.81(7) Å3. There are two molecules per unit cell and one formula unit per asymmetric unit. Hirshfeld analysis was used to study the molecular packing of the heterocyclic hybrid. H···H (50.8%), H···C (14.2%), Cl···H (8.9%), O···H (7.3%), and N···H (5.1%) are the most dominant intermolecular contacts in the crystal structure. O···H, N···H, H···C, F···H, F···C, and O···O are the only contacts that have the characteristic features of short and significant interactions. AIM study indicated predominant covalent characters for the Fe–C interactions. Also, the electron density (ρ(r)) at the bond critical point correlated inversely with the Fe–C distances

Synthesis, Molecular and Supramolecular Structure Aspects, and Antimicrobial Activity of the Centrosymmetric [Ag(5-Nitroquinoline)2]ClO4 Complex

The new homoleptic [Ag(5-nitroquinoline)2]ClO4 centrosymmetric complex was synthesized and its structure aspects were investigated. It crystallized in the monoclinic space group C2/c with a = 10.0279(2) Å, b = 13.2295(3) Å, c = 14.7552(3) Å and β = 102.1050(10)° while V = 1913.96(7) Å3 and half molecule as asymmetric formula. The Ag(I) is coordinated with two symmetrically related 5-nitroquinoline ligand units via the heterocyclic nitrogen atom with Ag-N distance of 2.146(6) Å and N1-Ag-N1 angle of 173.0(3)°. The two coordinated 5-nitroquinoline have anti configuration to one another and the perchlorate anion is set freely uncoordinated. The only Ag…O interactions are Ag1…O2 (3.110 Å) and Ag1…O1 (3.189 Å) which occur between the Ag(I) in one complex unit and the O-atoms from the NO2 groups in the neighbouring complex units. Hence, Ag(I) has coordination number 2 and its coordination geometry is slightly bent. Hirshfeld analysis indicated that the O…H (51.1%), C…H (11.8%), H…H (10.8%) and C…C (8.9%) contacts are the most common. Exclusively, the O…H, C…O, N…O, O…O and Ag…O contacts are the only shorter contacts than the vdWs radii sum of the interacting atoms. The studied Ag(I) complex showed good antimicrobial activity. It has comparable antibacterial activity against P. vulgaris (MIC = 9.7 μg/mL) and S. aureus (39.1 μg/mL) to Gentamycin (4.8 and 9.7 μg/mL, respectively) while better antifungal activity against A. fumigatus (MIC = 39.1 μg/mL) than Ketoconazole (156.2 μg/mL)

Synthesis of a Novel Hydrazone of Thieno[2,3-d]pyrimidine Clubbed with Ninhydrin : X-ray Crystal Structure and Computational Investigations

The novel hydrazone-containing thieno[2,3-d]pyrimidine, namely, N′-(1,3-dioxo-1,3-dihydro-2H-inden-2-ylidene)-2-(4-oxo-5,6,7,8-tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidin-3(4H)-yl)acetohydrazide 4 was synthesized in a very good yield from the reaction of the triketoester 1 or ninhydrin 2 with the exocyclic acetohydrazide 3 in methanol. Good-quality crystals of 4 were obtained by recrystallization of the compound from the DMF/MeOH solvent mixture. The target product 4 crystallized in the triclinic crystal system and P-1 space group. The topology analysis of molecular packing indicated that the H…H (30.4%), O…H (22.0%) and H…C (17.0%) contacts are the most dominant intermolecular interactions in the crystal of 4, while the O…H, N…H, H…C, N…C, O…C, C…C and O…O are the only contacts which have shorter interaction distances than the vdWs radii sum of the interacting atoms. The structure of 4 is optimized and the calculated structure showed good agreement with the experimental one. Additionally, MEP, HOMO, LUMO and the reactivity descriptors were calculated.peerReviewe

Vibrational spectral analysis, XRD-structure, computation, exo⇔endo isomerization and non-linear optical crystal of 5-((5-chloro-1H-indol-2-yl)methylene)-1,3-diethyl-2-thioxodihy-dropyrimidine-4,6 (1H,5H)-dione

Abstract This work deals with the synthesis and characterization of the novel 5-((5-chloro-1H-indol-2-yl)methylene)-1,3-diethyl-2-thioxodihydro-pyrimidine-4,6(1H,5H)-dione π-bridge (D–A–D) donor–acceptor–donor compound. Its exo-isomer structure has been proven by XRD-single-crystal analysis for the first time. The IR, UV–Vis., MS, CHN-, 1H and 13C NMR analysis were also carried out. The DFT-optimized structural-parameters were matched with the XRD-crystallographic data. The experimental-XRD-interactions in the lattice were compared to the computed Hirshfeld analysis (HSA), MEP map and Mulliken charge population. The DFT/6-311G(d) calculations like IR/B3LYP, TD-SCF, HOMO–LUMO, GRD and GIAO-NMR have been compared to their corresponding experimental parameters. Non-linear optical (NLO) crystal theoretical-analysis was carried out then compared to urea reference. The compound thermal activity was evaluated in an open-atmosphere by TG/DTG analysis

Synthesis of Unexpected Dimethyl 2-(4-Chlorophenyl)-2,3-dihydropyrrolo[2,1-a]isoquinoline-1,3-dicarboxylate via Hydrolysis/Cycloaddition/Elimination Cascades : Single Crystal X-ray and Chemical Structure Insights

Hydrolysis/[3 + 2] cycloaddition/elimination cascades employed for the synthesis of unexpected tricyclic compound derived from isoquinoline. Reaction of ethylene derivative 1 with the isoquinoline ester iminium ion 2 in alkaline medium (MeOH/NEt3) under reflux for 1 h resulted in the formation of the fused pyrrolo[2,1-a]isoquinoline derivative 3. Its structure was elucidated by X-ray single crystal and other spectrophotometric tools. Hirshfeld calculations for 3 and its crystal structure analysis revealed the importance of the short O…H (19.1%) contacts and the relatively long H…C (17.1%), Cl…H (10.6%) and C…C (6.1%) interactions in the molecular packing. DFT calculations were used to compute the electronic and spectroscopic properties of the studied system. The studied compound has polar nature (3.5953 Debye). TD-DFT calculations assigned the shortest wavelength band (220 nm) to the HOMO−1→LUMO+2 (57%), HOMO−1→LUMO+4 (14%) mixed excitations. The calculated NMR chemical shifts correlated very well with the experimental data (R2 = 0.93–0.94).peerReviewe

Stereoselective Synthesis of New 4-Aryl-5-indolyl-1,2,4-triazole S- and N-β-Galactosides : Characterizations, X-ray Crystal Structure and Hirshfeld Surface Analysis

5-(1H-Indol-2-yl)-4-phenyl-2,4-dihydro-3H-1,2,4-triazole-3-thione 1a and 4-(4-chlorophenyl)-5-(1H-indol-2-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione 1b were galactosylated in the presence of NaHCO3 in ethanol to produce S-galactosides 3,4, whereas, in the presence of K2CO3 in acetone they produced a mixture of S- and N-galactosides 3-6 with a higher yield of S-galactosides over the respective N-galactosides. Improvement in the yields of N-galactosides was produced by thermal migration of the galactosyl moiety from sulfur to nitrogen using fusion. β-Stereoselectivity of galactosylation was determined using the coupling constant value 3J1,2, which exceeded 9.0 Hz in all prepared galactosides. The precursors 1a and 1b alkylated with 3-bromopropan-1-ol 7 in K2CO3 and acetone produced the S-alkylated products 8 and 9, respectively. Structural determinations of new compounds 5 and 9 are presented. The phenyl and indole moieties were found to be twisted from the triazole ring mean in both compounds. For compound 5, the twist angles were 66.24° and 18.86°, respectively, while the corresponding values for 9 were in the ranges of 73.15–77.29° and 13.96–20.70°, respectively. Hence, the crystal system of 9 is triclinic while the space group is P-1. Detailed analysis of the intermolecular interactions in the crystal structure of 5 is presented using Hirshfeld calculations. The O…H, N…H, C…H, and S…H contacts appeared as red spots in the dnorm Hirshfeld surface indicating short distance intermolecular interactions. Their percentages were estimated based on the decomposition of the fingerprint plot to be 25.6, 2.4, 14.0, and 6.3%, respectively.peerReviewe

[3+2] Cycloaddition Reaction for the Stereoselective Synthesis of a New Spirooxindole Compound Grafted Imidazo[2,1-b]thiazole Scaffold : Crystal Structure and Computational Study

A new spirooxindole hybrid engrafted imidazo[2,1-b]thiazole core structure was designed and achieved via [3+2] cycloaddition reaction approach. One multi-component reaction between the ethylene derivative based imidazo[2,1-b]thiazole scaffold with 6-Cl-isatin and the secondary amine under heat conditions afforded the desired compound in a stereoselective manner. The relative absolute configuration was assigned based on single-crystal X-ray diffraction analysis. Hirshfeld calculations for 4 revealed the importance of the H . . . H (36.8%), H . . . C (22.9%), Cl . . . H (10.4%) and S . . . H (6.6%), as well as the O . . . H (4.7%), N . . . H (5.3%), Cl . . . C (1.6%), Cl . . . O (1.0%) and N . . . O (0.5%) contacts in the crystal stability. DFT calculations showed excellent straight-line correlations (R2 = 0.9776–0.9962) between the calculated and experimental geometric parameters. The compound has polar nature (3.1664 Debye). TD-DFT and GIAO calculations were used to assign and correlate the experimental UV-Vis and NMR spectra, respectively.peerReviewe

Synthesis of a New Ag(I)-Azine Complex via Ag(I)-Mediated Hydrolysis of 2-(((1-(Pyridin-2-yl)ethylidene)hydrazineylidene) Methyl)phenol with AgClO₄; X-ray Crystal Structure and Biological Studies

A new Ag(I)-azine complex of the formula [Ag(La)]2(ClO4)2.1/2(Lb) was synthesized and characterized using elemental analysis, FTIR, XPS and single-crystal X-ray diffraction. The [Ag(La)]2(ClO4)2.1/2(Lb) complex was obtained via Ag(I)-mediated hydrolysis of 2-(((1-(pyridin-2-yl)ethylidene)hydrazineylidene)methyl)phenol (L) with AgClO4 leading to the formation of the azines (1E,2E)-1,2-bis(1-(pyridin-2-yl)ethylidene)hydrazine (La) and 2,2’-((1E,1’E)-hydrazine-1,2-diylidene bis(methanylylidene)) diphenol (Lb). The former underwent complexation with AgClO4, while the latter was co-crystallized with the resulting Ag(I) complex, leading to the complex formula [Ag(La)]2(ClO4)2.1/2(Lb). In this complex, the azine La is acting as a bridged bidentate chelate connecting the two Ag(I) sites, leading to a tetra-coordinated Ag(I) with a distorted square planar coordination environment. Hirshfeld analysis indicated the importance of the H…H (38.4%), O…H (17.9%), H…C (13.2%), C…C (9.0%) and N…H (8.9%) interactions in the molecular packing. The antimicrobial, antioxidant and cytotoxic activities of the [Ag(La)]2(ClO4)2.1/2(Lb) complex were examined and compared with those of [Ag(La)]2(ClO4)2. The former was found to have lower bioactivity than the latter, which shed light on the lowering of biological actions as a consequence of the incorporation of the azine Lb within the Ag(I) complex. In other words, lowering the %Ag decreases the biological actions. The [Ag(La)]2(ClO4)2.1/2(Lb) complex (ΜIC = 39 μg/mL) has higher activity against the fungus A. fumigatus than the control Ketoconazole (ΜIC =156 μg/mL). This complex also has good cytotoxic activity against colon carcinoma and weak antioxidant activity