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Benzimidazole derivatives are of substantial importance because of their wide array of pharmacological activities. These nitrogen-containing heterocycles are used as therapeutic agents in medicinal chemistry. The title compound has been prepared using click chemistry (Copper-Catalyzed Azide-Alkyne Cycloaddition (CuAAC)) involving 1-propargyl-6-methoxy benzimidazolone as the dipolarophile and benzylazide as the dipole. The crystallographic study showed that the compound with formula C18H17N5O2 adopts a "pincer-like" conformation in the crystal. Inversion-related N H⋯O hydrogen bonds form dimers which are elaborated into layers parallel to (10–2) by C H⋯O and C H⋯N hydrogen bonds and C H⋯π(ring) and π-stacking interactions. The Hirshfeld surface analysis of the title compound was performed using the Crystal Explorer program while the density functional theory (DFT) calculation was performed by the hybrid B3LYP method. more...

The asymmetric unit of the title compound, C14H11N3O3, consists of two independent molecules having very similar conformations in which the indazole moieties are planar. The independent molecules are distinguished by small differences in the rotational orientations of the nitro groups. In the crystal, N—H...O and C—H...O hydrogen bonds form zigzag chains along the b-axis direction. Additional C—H...O hydrogen bonds link the chains into layers parallel to (10\overline{1}). These are connected by slipped π-stacking and C—H...π(ring) interactions. more...

Imidazopyrimidine derivatives are organic synthesized compounds with a pyrimido[1,2-a]benzimidazole as basic skeleton. They are known for their various biological properties and as an important class of compounds in medicinal chemistry. A new 1,4-dimethyl-2-oxo-pyrimido[1,2-a]benzimidazole hydrate derivative of the tilted group has been synthesized and characterized by spectroscopic techniques NMR and FT-IR; and by a single crystal X-ray diffraction. The X-ray results showed that the tricyclic core of the title compound, C12H11N3O·H2O, is almost planar. The molecules stack along the a-axis direction in head-to- tail fashion through π-stacking interactions involving all three rings. The stacks are tied together by direct C H⋯O hydrogen bonds and by O H⋯O, O N⋯N and C H⋯O hydrogen bonds with the lattice water. DFT calculations at B3LYP/6-311++G(d,p) in gas phase an polarizable continuum model have been carried out to predict the spectral and geometrical data of the tilted compound. The obtained results showed relatively good correlations between the predicted and experimental data with correlation coefficients higher than 98%. more...

The di­hydro­indole portion is planar and the nonyl substituent is in an ‘extended’ conformation. In the crystal, the nonyl chains inter­calate aided by pairwise C—H⋯O hydrogen bonds and the di­hydro­indole­dione units are associated through additional C—H⋯O hydrogen bonds to form micellar blocks. The blocks are linked through π-stacking inter­actions between the six-membered rings of the di­hydro­indole units., In the title mol­ecule, C17H23NO2, the di­hydro­indole portion is planar (r.m.s. deviation = 0.0157 Å) and the nonyl substituent is in an ‘extended’ conformation. In the crystal, the nonyl chains inter­calate and the di­hydro­indole­dione units are associated through C—H⋯O hydrogen bonds to form micellar blocks. Based on the Hirshfeld surface analysis, the most important inter­molecular inter­action is the H⋯H inter­action. more...

A ring transformation of 6-methyl-7H[1,2,4]triazolo [4,3-b][1,2,4] triazepine-8(9H)-ones (thiones) in the presence of acetic anhydride give rise to a new series of 17 condensed 1,2,4-triazole derivatives (1–17). Plausible mechanisms are proposed and show the formation of a beta fused β-lactam moiety. The compounds were tested for their (i) inhibitory potential on digestive enzymes (α-amylase and α-glucosidase), and (ii) antioxidant activity using radical scavenging (DPPH and ABTS radicals) and ferric reducing power assays. The compounds showed interesting and promising antidiabetic activities compared to the reference drug Acarbose. Molecular docking study has been carried out to determine the binding mode interactions between these derivatives and the targeted enzymes. The results showed the strength of intermolecular hydrogen bonding in ligand-receptor complexes as an important descriptor in rationalizing the observed inhibition results. Moreover, molecular dynamics simulations are also performed for the best protein-ligand complex to understand the stability of small molecule in a protein environment. To shed light on the antioxidant activity of the synthesized compounds and the mechanism involved in DPPH free radical, DFT calculations were performed at the B3P86/6-311++G(d,p) level using the polarizable continuum model. The effect of aprotic solvent on bond dissociation enthalpies (BDEs) is investigated by calculating and comparing BDEs of 1 in methanol and dimethylsulfoxide as solvents using PCM. The obtained results show that the mechanism of action depends on the basic skeleton and the presence of substituted functional groups in these derivatives. BDEs are found to be slightly influenced by the aprotic solvent of less than 0.01 kcal/mol compared with those obtained in methanol. more...

The present article describes the synthesis of the new compound 2-methylbenzimidazo[1,2-a]pyrimidin-4(1H)-one. The electronic and spatial structure of this molecule was studied theoretically and experimentally. The title molecule, C11H9N3O, is slightly twisted and bowed based on the recent crystallographic study, while the DFT-B3LYP study shows that the title compound is fully planar in the gas phase. This discrepancy between the experimentally determined geometry and the B3LYP optimized one may be due to the crystal packing. In the crystal, a layer structure is formed by N—H•••N and C—H•••O hydrogen bonds together with π-stacking and C—H•••π(ring) interactions. However, the Hirshfled surface analysis showed that the most important intermolecular interaction for the title compound is the H•••H contact. Based on the wide biological interest, molecular docking and molecular dynamics studies were performed for the above titled compound with the poly(ADP-ribose)polymerase (PARP) enzyme target and the result shows that there is a good binding affinity and stability in PARP complex system. more...

The tetrahydrodiazepine ring in the title molecule, C11H12N2O, adopts a twisted envelope conformation. In the crystal, inversion dimers are formed by N H⋯O hydrogen bonds which are connected into corrugated layers by N H⋯O hydrogen bonds and C H⋯π(ring) interactions. However, the Hirshfeld surface analysis indicated that the most important intermolecular interaction for the title compound is the H⋯H contact. Moreover, the DFT-B3LYP study showed that the title compound should have a slightly different geometry in the gas phase with respect to that in the solid phase. The antitumor activity of the novel tetrahydrodiazepine derivative is investigated by investigating its binding affinity into the active site of Checkpoint Kinase Chk1/SB218078. Docking outputs reveal moderate Checkpoint Kinase inhibition by tetrahydrodiazepine derivative. more...

The organic molecule in the title hydrate, C12H13NO3S·H2O, is folded across the S...N vector. Chains two molecules thick extending along the a-axis direction are formed by N—H...O and O—H...O hydrogen bonds. These interactions are reinforced by C—H...S hydrogen bonds and offset π-stacking interactions between centrosymmetrically related benzene rings. The chains are associated through C—H...O hydrogen bonds. more...

In the title compound, C22H32N2O3, the tetrahydroquinoxaline unit is planar. The ester substituent is nearly coplanar with this ring system as a result of an intramolecular N—H...O hydrogen bond. In the crystal, C—H...O hydrogen bonds and π-stacking interactions form oblique stacks which are connected into pairs by additional C—H...O hydrogen bonds. These pairs are further linked into thick sheets, with the n-decyl chains extending out from both surfaces as a result of a third set of C—H...O hydrogen bonds. Intercalation of the n-decyl chains completes the crystal packing. more...

The asymmetric unit of the title compound, C17H14N2O2, consists of two independent molecules differing mainly in the orientations of the phenyl and oxirane substituents. In the first molecule, the dihedral angle between the dihydroquinoxaline ring system and phenyl ring is 28.4 (2)° and the N—C—C—O torsion angle is 87.8 (5)°; corresponding data for the second molecule are 23.1 (2) and −85.6 (5)°, respectively. In the crystal, offset π-stacking interactions between the dihydroquinoxaline moieties form oblique stacks, which are connected into layers parallel to the bc plane by C—H...O hydrogen bonds and C—H...π(ring) interactions. Additional C—H...π(ring) interactions tie the layers together. The model was refined as a two-component twin. more...

The asymmetric unit of the title compound, C16H14N2O, contains three independent molecules differing primarily in the orientations of the benzyl groups. Each independent molecule forms inversion related dimersviaoffset π-stacking interactions. For two of these dimers, stacks are formed approximately along thea-axis direction by a combinations of C—H...N and C—H...π(ring) contacts, in addition to the offset π-stacking interactions. The third set of dimers are also stacked in the same direction but only by pairwise C—H...N hydrogen bonds. more...

In the title compound, C14H11N3O2, the indazole portion is planar to within 0.022 (2) Å and subtends a dihedral angle of 65.87 (7)° with the pendant benzene ring. In the crystal, oblique stacks of molecules extending along the a-axis direction are generated by π–π stacking interactions between the five- and six-membered rings [centroid–centroid separation = 3.6743 (19) Å] and the stacks are cross-linked by C—H...O hydrogen bonds. more...

The asymmetric unit of the title compound, C9H6ClN3O3, contains one full molecule in a general position and a half molcule sitting on a crystallographic mirror plane. In the crystal, molecules form stacks extending along theb-axis direction through a combination of offset π–π stacking between indazole units and C—Cl...π(ring) interactions with the six-membered rings of the same units. Elaboration of the C—Cl...π(ring) interactions along thea-axis direction forms slabs of molecules parallel to [001]. The stacks are joined by a combination of C—H...O and C—H...N hydrogen bonds. more...

The title compound, C20H30N2O2, has crystallographically imposed C 2 symmetry; the hexyl side chain adopts a tttg (t = trans and g = gauche) conformation. In the crystal, C—H...O hydrogen bonds link the molecules into chains extending along the b-axis direction. These chains pack to form zigzag sheets lying parallel to (101). more...

In the title molecule, C9H7N3O3, the indazole moiety is essentially planar and the mean plane of the acetyl substituent is twisted by 5.3 (1)° from its plane. In the crystal, weak C—H...O and C—H...N hydrogen bonds form layers parallel to (102), which are associated through π-stacking interactions to form a three-dimensional network. The structure was refined as a two-component twin. more...

In the title compound, C15H11NO, the anthracene unit is slightly bowed. Inversion-related pairs of O—H...N hydrogen bonds form dimers that are stacked along theb-axis direction by offset π–π stacking interactions between the anthracene units. more...

In the title compound, C14H14N2O2, the dihydroquinoxaline moiety deviates slightly from planarity. In the crystal, zigzag chains are formed by inversion-related C—H...O hydrogen bonds. Adjacent chains are associated through pairwise C—H...π(ring) and π-stacking interactions. more...

In the title compound, C10H10ClN3O3, the side chain is oriented nearly perpendicular to the mean plane of the indazole ring system. In the crystal, complementary sets of O—H...N and C—H...O hydrogen bonds form chains of molecules stacked along thea-axis direction more...

In the title compound, C18H20N2O2, the diazepin-2-one ring adopts a tub conformation. The conformation of the acetyl group is partially determined by an intramolecular N—H...O hydrogen bond. In the crystal, pairwise C—H...O hydrogen bonds form inversion dimers. more...

The asymmetric unit of the title compound, C11H11N3O4, comprises two independent molecules, both of which display positional disorder of their ethyl chains in 0.868 (4):0.132 (4) and 0.839 (4):0.161 (4) ratios. The packing is directed by a combination of C—H...O hydrogen bonds and N—O...π interactions between nitro groups and the aromatic rings. more...

The asymmetric unit of the title complex, [ZnCl2(C12H12N4)], contains two independent molecules having similar conformations. The coordination about the ZnIIatom is distorted tetrahedral, with the geometrical constraints of the chelating ligand responsible for the observed distortion. Each of the independent molecules forms chains in the crystal through pairs of N—H...Cl hydrogen bonds, using the pyrazole and benzimidazole N—H groups as donors. The first molecule forms chains running parallel to thebaxis, while the other molecule affords the same kind of one-dimensional supramolecular structure parallel to theaaxis. The structure was refined as a two-component twin with BASF = 0.0437 (4). more...

In the title compound, C16H11N3O, the molecular conformation is partially determined by an intramolecular C—H...π(ring) interaction. In the crystal, pairwise N—H...N hydrogen bonds form dimers, which associate into stacks through a combination of C—H...O, C—H...π(ring) and offset π–π stacking interactions. more...

In the title compound, C8H11N5O, the triazepine ring displays a boat conformation. Its mean plane is inclined to the triazole ring by 22.10 (9)°. In the crystal, molecules are linked by C—H...O hydrogen bonds to form chains parallel to theb-axis direction. Inversion-related chains are linkedviaoffset π–π interactions between the triazole rings, forming ribbons propagating in theb-axis direction. The terminal CH3group is disordered over two sets of sites, with a refined occupancy ratio of 0.48 (6):0.52 (6). more...

In the crystal of the title compound, C16H16N2O3, weak C—H...O hydrogen bonds involving the nitro group as acceptor form chains extending in theb-axis direction. The chains are arranged into layers by π–π stacking interactions along thec-axis direction between the substituted pyridine rings, separated by 3.624 (1) Å. more...

In the crystal of the title molecular salt, C16H34N5+·Cl−, (100) bilayers arise in which the tetradecylamino `tails' (which adopt extended conformations) interdigitate and the triazolium `heads' associate with the chloride anions through N—H...Cl hydrogen bonds. more...

In the title compound, C24H36N2O2, the orientation of the 2-oxopropylidene substituent is determined by the formation of an intramolecular N—H...O hydrogen bond. The benzodiazepine seven-membered ring adopts a slightly twisted boat conformation. The molecules pack in a bilayer fashion with the dodecyl chains intercalated to form the inner portion, and the benzodiazepine moieties on the outer surfaces. more...

In the title compound, C15H14N2O2, the seven-membered benzodiazepine ring adopts a twist-boat conformation and the two aromatic rings are inclined to one another by 81.06 (15)°. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming chains propagating along the [10-1] direction. The chains are linked by C—H...O hydrogen bonds, forming sheets parallel to theacplane. Within the sheets, there are N—H...π interactions present, and C—H...π interactions link the sheets to form a three-dimensional structure. more...

In the title omeprazole derivative, C20H21N3O3S, the benzimidazole ring is inclined to the pyridine ring by 21.21 (8)°. In the crystal, neighbouring molecules are linked by C—H...O hydrogen bonds, forming chains along thea-axis direction. Within the chains, there are offset π–π interactions [intercentroid distance = 3.880 (2) Å] involving neighbouring benzimidazole rings. There are no other significant intermolecular interactions present. more...

The title compound, C30H55N5O, forms a micellar structure in the crystal with the dodecyl chains intercalating and the bicyclic cores forming dimers across centres of symmetry, via weak C—H...N hydrogen bonds, and slipped π-stacking interactions between the five-membered rings. more...

In the molecule of the title compound, C6H7N5S, the triazole ring is planar, while the triazepine ring displays a boat conformation. The dihedral angle between the mean plane through the triazole and triazepine rings is 18.48 (8)°. In the crystal, molecules are linked into centrosymmetric dimers by N—H...N hydrogen bondsviaeight-membered {...HNCN}2synthons. Supramolecular layers in theabplane are sustained by C—H...N and π–π interactions [inter-centroid separation between triazole rings = 3.2880 (16) Å]. Connections along thecaxis occur between S atoms [S...S = 3.5972 (16) Å]. more...