Crystal structure and Hirshfeld surface analysis of (±)-N'-(2-hy-droxy-3-meth-oxy-benzyl-idene)-2-(4-iso-butyl-phen-yl)propionohydrazide.

The title mol-ecule, C21H26N2O3, adopts a V-shaped conformation and is chiral at the C atom with methyl group attached at the common cut of the edges of the V-conformation and crystallizes as a racemate. It also contains an intra-molecular O-H⋯N hydrogen bond. In the crystal, N-H⋯O hydrogen bonds form chains of mol-ecules extending along the c-axis direction, together with normal van der Waals contacts. The roles of the various inter-molecular inter-actions were clarified by Hirshfeld surface analysis, which reveals that the most important contributions to the crystal packing are from H⋯H (62.6%), C⋯H/H⋯C (15.8%) and O⋯H/H⋯O (15.3%) contacts.

Insight into the Crystal Structures and Potential of Two Newly Synthesized Naproxen-Based Hydrazide Derivatives as Potent COX-2 Inhibitors.

Although nonsteroidal anti-inflammatory drugs (NSAIDs) are medicines that are widely used to relieve pain, reduce inflammation, and bring down high temperature, literature confirmed that they still have harmful side effects. Most of their side effects are in the digestive system due to the carboxylic group. As naproxen is one of the NSAIDs, in this work, we try to mask the carboxylic group in naproxen with a relatively safe functional group. So, herein, we report the synthesis of new naproxen-based hydrazones derivatives, namely, (E)-N'-1-(4-chlorophenyl)ethylidene)-2-(6-methoxynaphthalen-2-yl)propane hydrazide (4a) and (E)-N'-(4-hydroxybenzylidene)-2-(6-methoxynaphthalen-2-yl)propane hydrazide ethanol solvate (4b). The compounds were confirmed by X-ray diffraction studies. Hirshfeld surface analyses and energy frameworks of 4a and 4b have been carried out and blind molecular docking studies of them to the COX-2 enzyme were undertaken to obtain binding affinities for judging whether the compounds could act as anti-inflammatory agents. The compounds interact with the key residues: Arg120, Val349, Leu352, Tyr355, Val523, Ala527, Ser530, and Leu531 of the active enzyme pocket. Molecular dynamics studies predicted that the complexes of 4a and 4b with COX-2 are structurally stable and no major conformational changes were observed. Confirmation of the docking and simulation data was achieved by a binding free energies analysis that indicated the dominance of van der Waals energy. The compounds are drug-like molecules as they obey all prominent drug-like rules and have acceptable pharmacokinetic profiles. To investigate the relationship between their intrinsic electronic properties and their possible similarities to actual drugs, the gas-phase DFT optimizations and NBO analyses were also performed in this study.

Synthesis, crystal structure, and a molecular modeling approach to identify effective antiviral hydrazide derivative against the main protease of SARS-CoV-2.

In the fall of 2019, a new type of coronavirus took place in Wuhan city, China, and rapidly spread across the world and urges the scientific community to develop antiviral therapeutic agents. In our effort we have synthesized a new hydrazide derivative, (E)-N'-(1-(4-bromophenyl)ethylidene)-2-(6-methoxynaphthalen-2-yl)propanehydrazide for this purpose because of its potential inhibitory proprieties. The asymmetric unit of the title molecule consists of two independent molecules differing noticeably in conformation. In the crystal, the independent molecules are linked by N-H···O and C-H···O hydrogen bonds and C-H···π(ring) interactions into helical chains extending along the b-axis direction. The chains are further joined by additional C-H···π(ring) interactions into the full 3-D structure. To obtain a structure-activity relationship, the DFT-NBO analysis is performed to study the intrinsic electronic properties of the title compound. Molecular modeling studies were also conducted to examine the binding affinity of the compound for the SARS-CoV-2 main protease enzyme and to determine intermolecular binding interactions. The compound revealed a stable binding mode at the enzyme active pocket with a binding energy value of -8.1 kcal/mol. Further, stable dynamics were revealed for the enzyme-compound complex and reported highly favorable binding energies. The net MMGBSA binding energy of the complex is -37.41 kcal/mol while the net MMPBSA binding energy is -40.5 kcal/mol. Overall, the compound disclosed the strongest bond of ing the main protease enzyme and might be a good lead for further structural optimization.

Synthesis, crystal structure investigation and computational approach to discover potential hydrazide derivatives as a potent inhibitor of cyclooxygenase-2 enzyme.

This study reports the synthesis of two new hydrazide derivatives, namely, (E)-N'-(4- bromobenzylidene)-2-(4-isobutylphenyl)propanehydrazide (4a) and (E)-N'-benzylidene-2-(4-isobutylphenyl)propanehydrazide (4b), respectively. The compounds were synthesized by the reaction of benzaldehyde with Ibuprofen acid hydrazide. Their structures were confirmed by X-ray crystallography. To try to do a more detailed investigation, computational studies including Hirshfeld surface analyses, energy frameworks, density functional theory (DFT) optimizations, frontier orbital analyses, molecular electrostatic potential analyses, and natural bond orbital analyses of the studied compounds are performed. Moreover, molecular docking and dynamics simulations of complexes of the compounds with the cyclooxygenase-2 (COX-2) enzyme were performed to determine the anti-inflammatory potential of the compounds. These analyses predicted the compounds to show maximum chemical interactions and be dynamically stable during simulation time. Furthermore, estimation of binding free energies confirmed the high binding affinity of the compounds for the COX-2 enzyme.

Crystal structures of two hydrazide derivatives of mefenamic acid, 3-(2,3-di-methyl-anilino)-N'-[(E)-(furan-2-yl)methyl-idene]benzohydrazide and N'-[(E)-benzyl-idene]-2-(2,3-di-methyl-anilino)benzo-hydrazide.

The conformation about the central benzene ring in the mol-ecule of (I), C20H19N3O2, is partially determined by an intra-molecular N-H⋯O hydrogen bond. In the crystal, chains parallel to the c axis are generated by inter-molecular N-H⋯O hydrogen bonds with the chains assembled into a three-dimensional network structure by inter-molecular C-H⋯O hydrogen bonds and C-H⋯π(ring) inter-actions. The mol-ecule of (II), C22H21N3O, differs from (I) only in the substituent at the hydrazide N atom where a phenyl-methyl-ene moiety for (II) is present instead of a furan-methyl-ene moiety for (I). Hence, mol-ecules of (I) and (II) show similarities in their mol-ecular and crystal structures. The conformation of the central portion of the mol-ecule of (II) is also therefore partially determined by an intra-molecular N-H⋯O hydrogen bond and inter-molecular N-H⋯O hydrogen bonds form chains parallel to the c axis. Likewise, the chains are connected into a three-dimensional network by C-H⋯O hydrogen bonds and C-H⋯π(ring) inter-actions.

Crystal structure of 1-[2-(4-nitro-phen-yl)-4,5-diphenyl-1H-imidazol-1-yl]propan-2-ol.

The title compound, C24H21N3O3, crystallizes with two unique but closely r.m.s. overlay fit = 0.215 Å) comparable mol-ecules (1 and 2) in the asymmetric unit of the triclinic unit cell. In molecule 1, the dihedral angles between the central imidazlole ring and the benzene-ring substituents are 42.51 (9), 45.41 (9) and 56.92 (8)°, respectively. Comparable data for molecule 2 are 39.36 (10), 34.45 (11) and 60.34 (8)°, respectively. The rings at the 2-positions carry p-nitro substituents that subtend dihedral angles of 12.9 (4)° in mol-ecule 1 and 11.7 (4)° in mol-ecule 2 to their respective benzene ring planes. The imidazole rings also have propan-2-ol substituents on the 1-N atoms, which adopt extended conformations for the N-C-C-C chains. In the crystal, classical O-H⋯N hydrogen bonds combine with C-H⋯O, C-H⋯N and C-H⋯π(ring) hydrogen bonds and stack the molecules along the a-axis direction.

Crystal structure of 5-[2-(9H-carbazol-9-yl)eth-yl]-1,3,4-oxa-diazole-2(3H)-thione.

The title compound, C16H13N3OS, comprises an oxa-diazo-lethione ring bound to the N atom of an almost planar carbazole ring system (r.m.s. deviation = 0.0088 Å) through an ethyl-ene chain. The oxa-diazole ring is inclined to the the carbazole ring system by 40.71 (6)°. In the crystal, N-H⋯O, N-H⋯S, C-H⋯N and C-H⋯S hydrogen bonds combine with C-H⋯π(ring) and π-π contacts to stack the mol-ecules along the b-axis direction.

Crystal structure of 1-[2-(4-chloro-phen-yl)-4,5-diphenyl-1H-imidazol-1-yl]propan-2-ol.

The title compound, C24H21ClN2O, crystallizes with two unique mol-ecules in the asymmetric unit. In each mol-ecule, the central imidazole ring is substituted at the 2-, 4- and 5-positions by benzene rings. The 2-substituted ring carries a Cl atom at the 4-position. One of the imidazole N atoms in each mol-ecule has a propan-2-ol substituent. In the crystal, a series of O-H⋯N, C-H⋯O and C-H⋯Cl hydrogen bonds, augmented by several C-H⋯π(ring) inter-actions, generate a three-dimensional network of mol-ecules stacked along the a-axis direction.

Crystal structure of ethyl 3-amino-6-methyl-2-[(4-methyl-phen-yl)carbamo-yl]-4-[(E)-2-phenyl-ethen-yl]thieno[2,3-b]pyridine-5-carboxyl-ate monohydrate.

In the title mol-ecule, C27H25N3O3S·H2O, the dihedral angle between the planes of the thienyl ring and the pendant p-tolyl group is 39.25 (6)°, while that between the pyridine ring and the pendant phenyl ring is 44.37 (6)°. In addition, there is a slight twist in the bicyclic core, with a dihedral angle of 2.39 (4)° between the thienyl and pyridine rings. The conformation of the carbamoyl moiety is partially determined by an intra-molecular N-H⋯O hydrogen bond. In the crystal, complementary N-H⋯O hydrogen bonds form dimers which are then associated into chains parallel to the c axis through O-H⋯N hydrogen bonds involving the water mol-ecule of crystallization. Electron density associated with an additional solvent mol-ecule of partial occupancy and disordered about a twofold axis was removed with the SQUEEZE procedure in PLATON [Spek (2015 ▸). Acta Cryst. C71, 9-18]. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s).

Crystal structure of 3-methyl-1-phenyl-6-propyl-amino-1H-pyrazolo[3,4-b]pyridine-5-carbo-nitrile.

In the title compound, C17H17N5, the dihedral angle between the 1H-pyrazolo-[3,4-b]pyridine ring system (r.m.s. deviation = 0.001 Å) and the attached phenyl group is 2.56 (6)°. The propyl-amino side chain has a contorted conformation [Car-N-C-C = -77.97 (16)° and N-C-C-C = -57.37 (17)°]. An intra-molecular C-H⋯N inter-action closes an S(6) ring. In the crystal, inversion dimers linked by pairs of N-H⋯N hydrogen bonds generate R 2 (2)(12) loops. Aromatic π-π stacking inter-actions [centroid-centroid distance = 3.5726 (8) Å] are also observed.

Crystal structure of methyl (2Z)-2-[(2Z)-2-(2-cyclo-pentyl-idenehydrazin-1-yl-idene)-4-oxo-3-phenyl-1,3-thia-zolidin-5-yl-idene]ethano-ate.

In the title compound, C17H17N3O3S, the cyclo-pentane ring is disordered over two sets of sites with an occupancy ratio of 0.775 (8):0.225 (8) for the affected atoms. The thia-zolidinyl ring is planar (r.m.s. deviation = 0.024 Å) and forms a dihedral angle of 65.13 (8)° with the attached phenyl ring. The mol-ecular packing is stabilized by C-H⋯O and C-H⋯π inter-actions, forming a three-dimensional structure.

Crystal structure of tetra-ethyl 27,30-dioxo-7,12,20,25-tetra-tert-but-yl-3,16-dioxa-9,22,28,31-tetra-thia-hepta-cyclo-[21.3.1.1(1,5).1(4,8).1(10,14).1(14,18).1(17,21)]dotriaconta-4,6,8(29),10,12,17,19,21(32),23,25-deca-ene-2,2,15,15-tetra-carboxyl-ate.

The asymmetric unit of the title compound, C54H64O12S4, consists of one half of the mol-ecule, which is located on an inversion centre. The heterocyclic six-membered ring adopts a distorted envelope conformation with the spiro C atom as the flap. In the crystal, mol-ecules are linked by weak C-H⋯O hydrogen bonds with an R (2) 2(14) motif, forming a chain along the b-axis direction.

Crystal structure of the inclusion complex 25-benzo-ylmeth-oxy-5,11,17,23-tetra-tert-butyl-26,27,28-trihy-droxy-2,8,14,20-tetra-thia-calix[4]arene-tetra-ethyl-ammonium chloride (1/1).

The asymmetric unit of the title compound, C48H54O5S4·N(C2H5)4 (+)·Cl(-), contains two tetra-tert-butyl-[(benzo-yl)meth-oxy]-trihy-droxy-tetra-thia-calix[4]arene mol-ecules, two tetra-ethyl-ammonium cations and two chloride anions. The two calixarene molecules in the asymmetric unit each display a cone conformation. There are no significant differences between the two independent molecules. The guest species do not sit within the calixarene 'buckets'. In the crystal, extensive O-H⋯O, O-H⋯S and O-H⋯Cl hydrogen bonds and weak C-H⋯O, C-H⋯S and C-H⋯Cl inter-actions link the thia-calixarene mol-ecules, tetra-ethyl-ammonium cations and chloride anions, forming a three-dimensional network encompassing channels running parallel to the a-axis direction. The structure contains a solvent-accessible void of 76 (3) Å(3), but no solvent mol-ecule could reasonably be located. The crystal studied was an inversion twin with a 0.57 (8):0.43 (8) domain ratio.

Crystal structure of ethyl 2-phenyl-4-(prop-2-yn-1-yl-oxy)-5,6,7,8-tetra-hydro-pyrido[4',3':4,5]thieno[2,3-d]pyrimidine-7-carboxyl-ate.

In the title compound, C21H19N3O3S, the 5,6,7,8-tetra-hydro-pyridine ring adopts a half-chair conformation. The fused-thieno[2,3-d]pyrimidine ring system is essentially planar (r.m.s. deviation = 0.001 Å) and forms a dihedral angle of 2.66 (6)° with the attached phenyl ring. The three-dimensional crystal packing is stabilized by C-H⋯O and C-H⋯N hydrogen bonds and C-H⋯π inter-actions.

Crystal structure of 3-amino-1-(4-hy-droxy-phen-yl)-1H-benzo[f]chromene-2-carbo-nitrile.

In the title compound, C20H14N2O2, the hy-droxy-benzene ring is almost perpendicular to the mean plane of the naphthalene ring system, making a dihedral angle of 85.56 (4)°. The 4H-pyran ring fused with the naphthalene ring system has a flattened boat conformation. In the crystal, O-H⋯N and N-H⋯O hydrogen bonds link the mol-ecules into a supra-molecular layer in the bc plane; N-H⋯π inter-actions also contribute to this arrangement. The layers are linked by weak by C-H⋯π and π-π [inter-centroid separation = 3.8713 (7) Å] inter-actions.

Crystal structure of 2-amino-7-hy-droxy-4-(4-hy-droxy-phen-yl)-4H-chromene-3-carbo-nitrile.

In the title compound, C16H12N2O3, the chromene ring system is nearly planar [maximum deviation from the mean plane = 0.057 (1) Å], and is almost perpendicular to the benzene ring, with a dihedral angle of 85.29 (5)°. In the crystal, mol-ecules are linked by classical N-H⋯O, O-H⋯O and O-H⋯N hydrogen bonds, and weak C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular network. Furthermore, a weak π-π stacking inter-action is observed; the centroid-to-centroid distance is 3.7260 (7) Å.

Crystal structure of 3-amino-1-(4-meth-oxy-phen-yl)-1H-benzo[f]chromene-2-carbo-nitrile.

In the title compound, C21H16N2O2, the meth-oxy-benzene ring is almost perpendicular to the mean plane of the naphthalene ring system, making a dihedral angle of 83.62 (5)°. The 4H-pyran ring fused with the naphthalene ring system is almost planar [maximum deviation = 0.033 (1) Å]. In the crystal, mol-ecules are linked into inversion dimers by pairs of N-H⋯N hydrogen bonds. N-H⋯O hydrogen bonds connect the dimers, forming a helical supra-molecular chain along the a-axis direction. The crystal packing also features C-H⋯π inter-actions.

Crystal structure of 3-amino-1-(4-chloro-phen-yl)-1H-benzo[f]chromene-2-carbo-nitrile.

In the title compound, C20H13ClN2O, the chloro-benzene ring is almost perpendicular to the mean plane of the naphthalene ring system, making a dihedral angle of 81.26 (8)°. The 4H-pyran ring fused with the naphthalene ring system has a flattened boat conformation. In the crystal, N-H⋯N hydrogen bonds generate chains along the b-axis direction. Further N-H⋯N hydrogen bonds link these chains into sheets parallel to (010). The crystal packing also features C-H⋯π inter-actions. The crystal studied was an inversion twin with a 0.557 (16):0.443 (16) domain ratio.

Crystal structure of 2-amino-4-phenyl-4H-benzo[h]chromene-3-carbo-nitrile.

In the title compound, C20H14N2O, the plane of the phenyl ring is almost normal to that of the naphthalene ring system, forming a dihedral angle of 83.15 (8)°. The 4H-pyran ring fused with the naphthalene ring system has a flattened boat conformation. In the crystal, mol-ecules are linked by pairs of N-H⋯N hydrogen bonds, forming inversion dimers with an R 2 (2)(12) ring motif. The dimers are connected by C-H⋯π inter-actions, forming supra-molecular chains along [010].

Crystal structure of ethyl (4R)-2-amino-7-hy-droxy-4-phenyl-4H-chromene-3-carboxyl-ate.

In the title compound, C18H17NO4, the dihedral angle between the phenyl ring and the fused six-membered ring is 77.65 (4)°. The conformation of the mol-ecule is determined in part by an intra-molecular N-H⋯O hydrogen bond between the amino H atom and the carbonyl O atom, forming an S(6) motif. In the crystal, mol-ecules are linked into N-H⋯O hydrogen-bonded inversion dimers which are then connected into chains along [001], forming a two-dimensional network parallel to (100) via O-H⋯O hydrogen bonds. C-H⋯O interactions further contribute to the crystal stability. The ethyl group is disordered over two sets of sites in a 0.801 (5):0.199 (5) ratio.