Crystal structure and Hirshfeld surface analysis of ethyl 2-(7-chloro-3-methyl-2-oxo-1,2-di-hydro-quinoxalin-1-yl)acetate.

The quinoxaline moiety in the title mol-ecule, C13H13ClN2O3, is almost planar (r.m.s. deviation of the fitted atoms = 0.033 Å). In the crystal, C-H⋯O hydrogen bonds plus slipped π-stacking and C-H⋯π(ring) inter-actions generate chains of mol-ecules extending along the b-axis direction. The chains are connected by additional C-H⋯O hydrogen bonds. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (37.6%), H⋯O/O⋯H (22.7%) and H⋯Cl/Cl⋯H (13.1%) inter-actions.

Synthesis, crystal structure, DFT, Hirshfeld surface analysis, energy frameworks and in-Silico drug-targeting PFKFB3 kinase of novel triazolequinoxalin derivative (TZQ) as a therapeutic Strategy against cancer.

Overall, drug design is a dynamic and evolving field, with researchers constantly working to improve their understanding of molecular interactions, develop new computational methods, and explore innovative techniques for creating effective and safe medications. The process can involve steps such as the identification of targets, the discovery of lead compounds, lead optimization, preliminary testing, human trials, regulatory approval and finally post-marketing surveillance, all aimed at bringing a new drug from concept to market. In this article, the synthesis of the novel triazolequinoxalin (TZQ) 1-((1-hexyl-1H-1,2,3-triazol-5-yl)methyl)-3-phenylquinoxalin-2(1H)-one (4) is reported. The structure has been identified with a variety of spectroscopic methods (1H, 13C NMR, and LC-MS) and finally, the structure has been determined by X-ray diffraction (XRD) studies. The TZQ molecule has crystallized in the monoclinic space C2/c group with unit cell dimensions a = 41.201(2) Å, b = 10.6339(6) Å, c = 9.4997(4) Å, ß = 93.904(4). The crystal structure is stabilized by intermolecular interactions (N-H ⋯ O and N-H … Cg) occurring within the molecule. The presence of these intermolecular interactions is evaluated through analysis of Hirshfeld surfaces (HS) and two-dimensional (2D) chemical fingerprints map. Additionally, energy frameworks were employed to identify the prevailing interaction energy influencing the molecular arrangement. Density Functional Theory (DFT) calculations were computed to establish concurrence between theoretical and experimental results. Furthermore, the HOMO-LUMO energy levels were determined using the B3LYP/6-31+G(d, p) level of theory. Finally, molecular docking was used to predict the anti-cancer activity of the compound (4) against PFKFB3 kinase and presented noticeable hydrophilic and hydrophobic interactions at the active site region.

CuII Pyrazolyl-Benzimidazole Dinuclear Complexes with Remarkable Antioxidant Activity.

Three dinuclear coordination complexes generated from 1-n-butyl-2-((5-methyl-1H-pyrazole-3-yl)methyl)-1H-benzimidazole (L), have been synthesized and characterized spectroscopically and structurally by single crystal X-ray diffraction analysis. Reaction with iron(II) chloride and then copper(II) nitrate led to a co-crystal containing 78 % of [Cu(NO3 )(µ-Cl)(L')]2 (C1 ) and 22 % of [Cu(NO3 )(µ-NO3 )(L')]2 (C2 ), where L was oxidized to a new ligand L' . A mechanism is provided. Reaction with copper chloride led to the dinuclear complex [Cu(Cl)(µ-Cl)(L)]2 (C3 ). The presence of N-H⋅⋅⋅O and C-H⋅⋅⋅O intermolecular interactions in the crystal structure of C1 and C2 , and C-H⋅⋅⋅N and C-H⋅⋅⋅Cl hydrogen bonding in the crystal structure of C3 led to supramolecular structures that were confirmed by Hirshfeld surface analysis. The ligands and their complexes were tested for free radical scavenging activity and ferric reducing antioxidant power. The complex C1 /C2 shows remarkable antioxidant activities as compared to the ligand L and reference compounds.

Crystal structure, Hirshfeld surface analysis and DFT calculations of (E)-3-[1-(2-hy-droxy-phenyl-anilino)ethyl-idene]-6-methyl-pyran-2,4-dione.

The asymmetric unit of the title compound, C14H13NO4, contains three independent mol-ecules, which differ slightly in conformation. Each contains an intra-molecular N-H⋯O hydrogen bond. In the crystal, O-H⋯O hydrogen bonds form chains of mol-ecules, which are linked into corrugated sheets parallel to (03) plane by C-H⋯O hydrogen bonds together with π inter-actions between the carbonyl groups and the 2-hy-droxy-phenyl rings. The layers are linked by further C-H⋯O hydrogen bonds. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (49.0%), H⋯O/O⋯H (28.3%) and H⋯C/C⋯H (10.9%) inter-actions. van der Waals inter-actions are the dominant inter-actions in the crystal packing. Moreover, density functional theory (DFT) optimized structures at the B3LYP/ 6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behavior was elucidated to determine the energy gap of 4.53 eV.

Coordination complexes constructed from pyrazole-acetamide and pyrazole-quinoxaline: effect of hydrogen bonding on the self-assembly process and antibacterial activity.

Two mononuclear coordination complexes of N-(2-aminophenyl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide (L1), namely [Cd(L1)2Cl2] (C1) and [Cu(L1)2(C2H5OH)2](NO3)2 (C2) and one mononuclear complex [Fe(L2)2(H2O)2](NO3)2·2H2O (C3), obtained after in situ oxidation of L1, have been synthesized and characterized spectroscopically. As revealed by single-crystal X-ray diffraction, each coordination sphere made of two heterocycles is completed either by two chloride anions (in C1), two ethanol molecules (in C2) or two water molecules (in C3). The crystal packing analysis of C1, C2 and C3, revealed 1D and 2D supramolecular architectures, respectively, via various hydrogen bonding interactions, which are discussed in detail. Furthermore, evaluation in vitro of the ligands and their metal complexes for their antibacterial activity against Escherichia coli (ATCC 4157), Pseudomonas aeruginosa (ATCC 27853), Staphylococcus aureus (ATCC 25923) and Streptococcus fasciens (ATCC 29212) strains of bacteria, revealed outstanding results compared to chloramphenicol, a well-known antibiotic, with a normalized minimum inhibitory concentration as low as 5 µg mL-1.

Crystal structure, Hirshfeld surface analysis and density functional theory study of 1-nonyl-3-phenyl-quinoxalin-2-one.

In the title mol-ecule, C23H28N2O, the phenyl ring is inclined to the quinoxaline ring system at a dihedral angle of 20.40 (9)°. In the crystal, C-H⋯O inter-actions between neighbouring mol-ecules form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (70.6%), H⋯C/C⋯H (15.5%) and H⋯O/O⋯H (4.6%) inter-actions. The optimized structure calculated using density functional theory at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied mol-ecular orbital (HOMO) and lowest unoccupied mol-ecular orbital (LUMO) energy gap is 3.8904 eV. Part of the n-nonyl chain attached to one of the nitro-gen atoms of the quinoxaline ring system shows disorder and was refined with a double conformation with occupancies of 0.604 (11) and 0.396 (11).

Crystal structure, Hirshfeld surface analysis and density functional theory study of benzyl 2-oxo-1-(prop-2-yn-1-yl)-1,2-di-hydro-quinoline-4-carboxyl-ate.

The title mol-ecule, C20H15NO3, adopts a Z-shaped conformation with the carboxyl group nearly coplanar with the di-hydro-quinoline unit. In the crystal, corrugated layers are formed by C-H⋯O hydrogen bonds and are stacked by C-H⋯π(ring) inter-actions. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (43.3%), H⋯C/C⋯H (26.6%) and H⋯O/O⋯H (16.3%) inter-actions. The optimized structure calculated using density functional theory at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO-LUMO energy gap is 4.0319 eV.

Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-amino-5-methyl-phen-yl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide.

The title mol-ecule, C13H16N4O, adopts an angular conformation. In the crystal a layer structure is generated by N-H⋯O and N-H⋯N hydrogen bonds together with C-H⋯π(ring) inter-actions. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (53.8%), H⋯C/C⋯H (21.7%), H⋯N/N⋯H (13.6%), and H⋯O/O⋯H (10.8%) inter-actions. The optimized structure calculated using density functional theory (DFT) at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO-LUMO energy gap is 5.0452 eV.

Crystal structure, Hirshfeld surface analysis and density functional theory study of 6-methyl-2-[(5-methyl-isoxazol-3-yl)meth-yl]-1H-benzimidazole.

In the title mol-ecule, C13H13N3O, the isoxazole ring is inclined to the benzimidazole ring at a dihedral angle of 69.28 (14)°. In the crystal, N-H⋯N hydrogen bonds between neighboring benzimidazole rings form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.8%), H⋯C/C⋯H (20.9%) and H⋯N/N⋯H (19.3%) inter-actions. The optimized structure calculated using density functional theory at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied mol-ecular orbital (HOMO) and lowest unoccupied mol-ecular orbital (LUMO) energy gap is 4.9266 eV.

Crystal structure, Hirshfeld surface analysis and DFT study of 1-ethyl-3-phenyl-1,2-di-hydro-quinoxalin-2-one.

In the title mol-ecule, C16H14N2O, the di-hydro-quinoxaline moiety is not planar as there is a dihedral angle of 4.51 (5)° between the constituent rings. In the crystal, C-H⋯O hydrogen bonds form helical chains about the crystallographic 21 screw axis in the b-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (51.7%), H⋯C/C⋯H (26%) and H⋯O/O⋯H (8.5%) inter-actions. The optimized structure calculated using density functional theory (DFT) at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO-LUMO energy gap is 3.8918 eV.

Crystal structure, Hirshfeld surface analysis, inter-action energy and DFT studies of 4-[(4-allyl-2-meth-oxy-phen-oxy)meth-yl]-1-(4-meth-oxy-phen-yl)-1H-1,2,3-triazole.

In the title mol-ecule, C20H21N3O3, the allyl substituent is rotated out of the plane of its attached phenyl ring [torsion angle 100.66 (15)°]. In the crystal, C-HMthphn⋯OMthphn (Mthphn = meth-oxy-phen-yl) hydrogen bonds lead to the formation of (100) layers that are connected into a three-dimensional network by C-H⋯π(ring) inter-actions, together with π-π stacking inter-actions [centroid-to-centroid distance = 3.7318 (10) Å] between parallel phenyl rings. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.7%) and H⋯C/C⋯H (23.3%) inter-actions. Computational chemistry reveals that the C-HMthphn⋯OMthphn hydrogen bond energy is 47.1 kJ mol-1. The theoretical structure, optimized by density functional theory (DFT) at the B3LYP/ 6-311 G(d,p) level, is compared with the experimentally determined mol-ecular structure. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Solvent induced supramolecular polymorphism in Cu(II) coordination complex built from 1,2,4-triazolo[1,5-a]pyrimidine: Crystal structures and anti-oxidant activity.

Two Cu(II) coordination complexes, C1 and C2 of the formula [Cu(4)2(H2O)2], have been prepared by reaction between CuCl2·2H2O and 7-ethoxycarbonylmethyl-5-methyl-1,2,4[1,5-a]pyrimidine (L) in a 1:2 M:L molar ratio. The L molecule decomposes during the reaction process into 7-carboxy-5-methyl-[1,2,4]-triazolo[1,5-a]pyrimidine (4) through an intermediate, ethyl 2,2-dihydroxy-2-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)acetate (5), which has been isolated and its crystal structure determined by X-ray diffraction. The X-ray analysis of the single crystals of [Cu(4)2(H2O)2] obtained from the slow evaporation of EtOH and MeOH, separately, revealed the formation of "solvent induced" polymorphs C1 and C2, respectively. The primary supramolecular synthon for C1 and C2 are six membered ring, and square shaped hydrogen bonded architecture, respectively. The self-assembly of such synthons resulted in a two dimensional hydrogen bonded sheet supported by OH⋯O interactions. In addition, the antioxidant properties of the ligands and its complexes were evaluated in vitro using 1,1-diphenyl-2-picrylhydrazyl acid, 2,2'-azino-bis (3-ethylbenzothiazoline-6 sulfonic acid radical scavenging methods and ferric reducing antioxidant power.

Crystal structure and Hirshfeld surface analysis of N-{2-[(E)-(4-methyl-benzyl-idene)amino]-phen-yl}-2-(5-methyl-1-H-pyrazol-3-yl)acetamide hemihydrate.

The asymmetric unit of the title compound, C20H20N4O·0.5H2O, contains two independent organic mol-ecules (1 and 2) and a water mol-ecule of crystallization. The two mol-ecules differ primarily in the dihedral angles between the aromatic rings, which are 7.79 (7) and 29.89 (7)° in mol-ecules 1 and 2, respectively. In each mol-ecule there is intra-molecular C-H⋯O hydrogen bond forming an S(6) ring motif. In mol-ecule 1 there is an intra-molecular N-H⋯π(pyrazole) inter-action and an intra-molecular C-H⋯π(pyrazole) inter-action present. Mol-ecule 1 is linked to mol-ecule 2 by a C-H⋯π(benzene ring) inter-action. An intra-molecular N-H⋯N hydrogen bond and an intra-molecular C-H⋯N hydrogen bond are also present in mol-ecule 2. In the crystal, the three components are linked by Owater-H⋯N, N-H⋯Owater and N-H⋯N hydrogen bonds, forming chains along the [100] direction. The chains are linked by C-H⋯O and C-H⋯N hydrogen bonds, forming layers parallel to the ab plane. Finally, the layers are linked by C-H⋯π inter-actions, forming a three-dimensional structure.

Crystal structure and Hirshfeld surface analysis of a new benzodiazepine derivative: 4-di-chloro-methyl-2,3-di-hydro-1H-1,5-benzodiazepin-2-one.

In the title compound, C10H8Cl2N2O, the seven-membered diazepine ring adopts a boat-shaped conformation. The mean planes of the two rings of the benzodiazepine unit are inclined to each other by 22.05 (6)°. In the crystal, mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 2(8) ring motif. The dimers are linked by C-H⋯π inter-actions, forming layers lying parallel to (10). The roles of the inter-molecular inter-actions in the crystal packing were clarified using Hirshfeld surface analysis; the most important contributions are from Cl⋯H/H⋯Cl (30.5%) and H⋯H (22.5%) inter-actions.

Novel Co(II) and Cu(II) coordination complexes constructed from pyrazole-acetamide: Effect of hydrogen bonding on the self assembly process and antioxidant activity.

In the present study, two pyrazole-acetamide derivatives namely N­(2­aminophenyl)­2­(5­methyl­1H­pyrazol­3­yl) acetamide (L1) and (E)­N­(2­(1­(2­hydroxy­6­methyl­4­oxo­4H­pyran­3­yl)ethylideneamino)phenyl)­2­(5­methyl­1H­pyrazol­3­yl) acetamide (L2) have been synthesized and characterized by infrared spectrophotometry (IR), nuclear magnetic resonance spectroscopy (NMR) and electrospray ionization-mass spectrometry (ESI-MS). Two coordination complexes of L1 and L2, namely [Co(L1)2(EtOH)2]·Cl2 (1) and [Cu(L2)]·H2O (2), respectively have been synthesized and characterized by elemental analysis and spectroscopic studies. The solid state structure of these two complexes was established by single crystal X-ray crystallography. In complex 1, the amide O and pyrazole N atoms of two molecules of L1 take part in coordination with octahedral Co(II) ions, the remaining two coordination sites being occupied by two EtOH molecules leading to a N2O4 coordination environment. On the other hand, the imine N atoms, pyrazole N and O atoms of the 2­hydroxy­6­methyl­4H­pyran­4­one function present in L2 are involved in coordination with Cu(II) ions, resulting in a distorted square planar geometry displaying a N2O4 chromophore, in complex 2. The crystal packing analysis of 1 and 2, revealed 1D and 2D supramolecular architectures respectively, via various hydrogen bonding interactions, which are discussed in the present account. Furthermore, the antioxidant activity of the ligands and their complexes were determined in vitro by 1,1­diphenyl­2­picrylhydrazyl (DPPH), 2,2'­azino­bis(3­ethylbenzothiazoline­6­sulphonic acid (ABTS) and ferric reducing antioxidant power(FRAP), showing that the ligands L1 and L2 and complexes 1 and 2 present significant antioxidant activity.

Crystal structure and Hirshfeld surface analysis of 5-methyl-1,2,4-triazolo[1,5-a]pyrimidine.

The nine-membered ring system of the title compound, C6H6N4, is essentially planar. In the crystal, mol-ecules are linked via C-HTrz⋯NTrz and C-HPyrm⋯NTrz (Trz = triazole and Pyrm = pyrimidine) hydrogen bonds together with weaker C-HPyrm⋯NPyrm hydrogen bonds to form layers parallel to (02). The layers are further connected by π-π-stacking inter-actions between the nine-membered ring system [centroid-centroid = 3.7910 (8) Å], forming oblique stacks along the a-axis direction. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯N/N⋯H (40.1%), H⋯H (35.3%), H⋯C/C⋯H (9.5%), N⋯C/C⋯N (9.0%), N⋯N (3.1%) and C⋯C (3.0%) inter-actions and that hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. No significant C-H⋯π inter-actions are observed.

Crystal structure and Hirshfeld surface analysis of (4Z)-1-butyl-4-(2-oxo-propyl-idene)-2,3,4,5-tetra-hydro-1H-1,5-benzodiazepin-2-one.

The asymmetric unit of the title compound, C16H20N2O2, consists of two independent mol-ecules differing slightly in the conformations of the seven-membered rings and the butyl substituents, where the benzene rings are oriented at a dihedral angle of 34.56 (3)°. In the crystal, pairwise inter-molecular C-H⋯O and complementary intra-molecular C-H⋯O hydrogen bonds form twisted strips extending parallel to (012). These strips are connected into layers parallel to (111) by additional inter-molecular C-H⋯O hydrogen bonds. The layers are further joined by C-H⋯π inter-actions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (65.5%), H⋯C/C⋯H (16.0%) and H⋯O/O⋯H (15.8%) inter-actions.