Isomeric nitro substituted symmetrical benzamides: Crystal Structures, Hirshfeld surface analysis, 3D energy frameworks, DNA binding and cell line studies

Synthesis, single crystal X-ray structure determination, Hirshfeld surface analysis, interaction energies, and density functional theory calculations of N,N'-(cyclohexane-1,4-dicarbonothioyl)bis(4-methylbenzamide)

N-Benzoyl-morpholine-4-carbothioamides: Crystal structures, Hirshfeld surface analysis, and Density functional theory calculations

In the title compound, C12H10ClNO3, the di-hydro-quinoline moiety is not planar with a dihedral angle between the two ring planes of 1.61 (6)°. An intra-molecular C-H⋯O hydrogen bond helps to establish the rotational orientation of the carboxyl group. In the crystal, sheets of mol-ecules parallel to (10) are generated by C-H⋯O and C-H⋯Cl hydrogen bonds, and are stacked through slipped π-stacking inter-actions between inversion-related di-hydro-quinoline units. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (34.2%), H⋯O/O⋯H (19.9%), H⋯Cl/Cl⋯H (12.8%), H⋯C/C⋯H (10.3%) and C⋯C (9.7%) inter-actions. Computational chemistry indicates that in the crystal, the C-H⋯Cl hydrogen-bond energy is -37.4 kJ mol-1, while the C-H⋯O hydrogen-bond energies are -45.4 and -29.2 kJ mol-1. An evaluation of the electrostatic, dispersion and total energy frameworks revealed that the stabilization is dominated via the dispersion energy contribution. 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, and the HOMO-LUMO behaviour was elucidated to determine the energy gap.

The title compound, C19H14N2O3, features competition and inter-play of a range of weak inter-actions, which actualize under the absence of conventional hydrogen-bond donors. Two kinds of stacking inter-actions, namely slipped anti-parallel inter-actions of cyano-phenyl groups as well as quinoline and carb-oxy groups, are primarily important. In combination with relatively short tetrel OCH3⋯N≡C bonds [C⋯N = 3.146 (3) Å] they are responsible for the generation of the layers, while the inter-layer bonding occurs via C-H⋯O and C-H⋯N weak hydrogen bonds. These findings are consistent with the results of Hirshfeld surface analysis and calculated inter-action energies. Contributions of the C⋯C, C⋯N/N⋯C and C⋯O/O⋯C contacts originating in the stacking inter-actions account for 17.0% to the surface area. The largest inter-actions energies are associated with the two kinds of stacks (-45.8 and -24.3 kJ mol-1) and they are superior to the energies of weak hydrogen bond and tetrel inter-actions (-12.4 to -22.4 kJ mol-1). Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the consolidation is dominated via the dispersion energy contributions.

The title mol-ecule, C17H26N2O, adopts an L-shaped conformation, with the straight n-decyl chain positioned nearly perpendicular to the di-hydro-benzimidazole moiety. The di-hydro-benzimidazole portion is not quite planar as there is a dihedral angle of 1.20 (6)° between the constituent planes. In the crystal, N-H⋯O hydrogen bonds form inversion dimers, which are connected into the three-dimensional structure by C-H⋯O hydrogen bonds and C-H⋯π(ring) inter-actions. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (75.9%), H⋯C/C⋯H (12.5%) and H⋯O/O⋯H (7.0%) inter-actions. Based on computational chemistry using the CE-B3LYP/6-31 G(d,p) energy model, C-H⋯O hydrogen bond energies are -74.9 (for N-H⋯O) and -42.7 (for C-H⋯O) kJ mol-1.

α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-D-2'-deoxyadenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydrogen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydrogen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydrogen bonds formed by the conformers. The formation of the supramolecular assembly of α-dA is controlled by hydrogen bonding and stacking interactions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydrogen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydrogen bonds involving the sugar moieties to form a sheet. A comparison of the solid-state structures of the anomeric 2'-deoxyadenosines revealed significant differences of their conformational parameters.

New polymorph of N-benzoyl-morpholine-4-carbothioamide with ten crystallographically independent molecules in the asymmetric unit: Crystal structure, Hirshfeld surface analysis and Density functional theory calculations

A new Cd(II) complex, bis(N,N-diethylenediamine)cadmium(II)] dichloride, C12H32CdCl2N4, was synthesized by the reaction between cadmium(II) chloride hexahydrate, sodium hydroxide, and N,N-diethylenediamine in aqueous methanol. The crystal structure was characterized by single-crystal X-ray diffraction analysis technique. The crystal structure is monoclinic, space group P21/c with parameters a=6.8959(3) Å, b=16.0795(10) Å, c=16.4406(8) Å, α=90°, β=100.23(4)°, γ=90°, V=1794(16) Å3, Z=4. The X-ray structure analysis reveals that the Cd(II) cation coordinated by four N atoms of the N,N-diethylenediamine units and two Cl atoms, giving it a octahedral geometry. In the crystal, the molecules are linked by N−H···Cl hydrogen bond, forming a three-dimensional supramolecular architecture. A Hirshfeld surface analysis was performed to record various intermolecular interactions, indicating the stabilization of the Cd(II) complex structure by the intermolecular weak N−H···Cl hydrogen bonds. The major interactions are H···H (80.2%) and Cl···H (19.8%) interactions for the title complex.

Synthesis, characterization, crystal structures, Hirshfeld surface analysis and DFT computational studies of new Schiff Bases derived from Phenylhydrazine

The complexes (1–3) of an amidothiourea receptor L with three different types of organic bases have been synthesized, and their crystal structures were solved using single crystal X-ray diffraction data. A detailed structural analysis of the complexes reveals that the complexes are primarily stabilized by a strong hydrogen bonding interaction between the amide oxygen of the deprotonated receptor and N–H proton of the protonated bases. Close inspection of the hydrogen bond parameters of the complexes shows that the receptor significantly forms a low barrier hydrogen bond with imidazole and hexamine, whereas no obvious low barrier hydrogen bond has been found in case of triethylamine. The Hirshfeld surface and fingerprint plot analysis of the complexes have been carried out, and reveal that the complexes are stabilized O–H⋯O, C–H⋯O, N–H⋯S and N–H⋯O, hydrogen bonds. Additionally, the nitro groups of the receptor are involved in different types of charge transfer or electron donor acceptor interactions, which also have a prominent effect in the solid state stabilization of the complexes (1–3).

The crystal structure of {3-[2-(1,3-benzodioxol-5-yl)-7-methoxy-1-benzofuran-5-yl] propyl} diethylamine hydrohloride hydrate [C23H28NO4]+•[H2OCl]– is determined. The molecular geometrical parameters, frontier molecular orbital energies (HOMO, LUMO), their energy gap (ΔE), molecular electrostatic potential analysis of the compound are calculated by DFT/B3LYP at the 6-311G(d,p) level. The benzofuran and benzodioxo ring systems, except the diethylamine group, are essentially planar and a dihedral angle between the ring systems is 7.38(14)°. The compound crystallizes in the monoclinic space group P21/c, with a = 15.230(4) A, b = 11.418(2) A, c = 12.880(3) A, β = 94.56(3)°, V = 2232.8(9) A3, D calc = 1.297g/cm3, Z = 4. The hydrogen bonded Cl and H2O are self-assembled to form a supramolecular array of strong N–H…Cl and O–H…Cl bifurcated hydrogen bonds making tetramers which consist of a fused four-membered ring with a graph-set descriptor and a pseudo cyclic centrosymmetric R 2 2(8) ring motif. The hybrid dihalide-dihydrate clusters of [Cl2(H2O)2]2– are observed, too. The supramolecular crystal packing is consolidated by these bifurcated hydrogen bonds and the stacking of the sheet through strong π…π interactions. Moreover, the intra chain hydrogen bonds form intermolecular and intramolecular C–H…O hydrogen bonds, and the 1D supramolecular array is organized by C–H…π interactions. The contacts in the crystal structure are analyzed using the Hirshfeld surfaces computational method. The calculated geometrical parameters are in good agreement with the single crystal XRD data.

Synthesis, crystallographic structure, DFT computational studies and Hirschfeld surface analysis of a new tetranuclear anionic bromobismuthate(III): [C12H20N2]2Bi4Br16•2H2O

The title compound, C15H16N2O2, consists of pyrrole and benzodiazepine units linked to an allyl moiety, where the pyrrole and diazepine rings adopt half-chair and boat conformations, respectively. In the crystal, weak C—HBnz···ODiazp (Bnz = benzene and Diazp = diazepine) hydrogen bonds link the molecules into infinite chains along the c-axis direction with the corrugated 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 ··· H (60.6%), H ··· C/C ··· H (18.0%) and H ··· O/O ··· H (17.4%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, C—H···O hydrogen bond energy is 32.9 (for C—HBnz···ODiazp) kJ mol-1. Density functional theory (DFT) optimized structures at the B3LYP/ 6–311G(d,p) level are compared with the experimentally determined molecular structure in the solid state. The HOMO—LUMO behaviour was elucidated to determine the energy gap..

Synthesis, crystal structure, Hirshfeld surface analysis, In-Silico assessment of druggability and molecular docking studies of Schiff base compound

In the title mol-ecule, C7H6N4O3, the bicyclic ring system is planar with the carb-oxy-methyl group inclined by 81.05 (5)° to this plane. In the crystal, corrugated layers parallel to (010) are generated by N-H⋯O, O-H⋯N and C-H⋯O hydrogen-bonding inter-actions. The layers are associated through C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯O/O⋯H (34.8%), H⋯N/N⋯H (19.3%) and H⋯H (18.1%) inter-actions. The volume of the crystal voids and the percentage of free space were calculated to be 176.30 Å3 and 10.94%, showing that there is no large cavity in the crystal packing. Computational methods revealed O-H⋯N, N-H⋯O and C-H⋯O hydrogen-bonding energies of 76.3, 55.2, 32.8 and 19.1 kJ mol-1, respectively. Evaluations of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via dispersion energy contributions. Moreover, the optimized mol-ecular structure, using density functional theory (DFT) at the B3LYP/6-311G(d,p) level, was compared with the experimentally determined one. The HOMO-LUMO energy gap was determined and the mol-ecular electrostatic potential (MEP) surface was calculated at the B3LYP/6-31G level to predict sites for electrophilic and nucleophilic attacks.