New 2,4-dihydro-1H-1,2,4-triazole-3-selones and 3,3'-di(4H-1,2,4-triazolyl)diselenides. Synthesis, biological evaluation, and in silico studies as antibacterial and fungicidal agents.

The reaction of aromatic ring-substituted isoselenocyanates with 2-thiopheacetic and 4-pyridinecarboxylic acid hydrazides yielded selenosemicarbazides which were further converted into previously unknown 1,2,4-triazole-3-selones and 3,3'-di(4H-1, 2,4-triazolyl)diselenides. The structures of the obtained compounds were studied by NMR spectroscopy, IR spectroscopy, and high-resolution mass spectroscopy (HR-MS). The bactericidal and fungicidal activity of some obtained compounds was evaluated in molecular modeling studies such as docking and simulation studies. The compound 3ba was reported as the most promising compound to show robust binding energy with different antibacterial and antifungal compounds. The compounds were observed in strong hydrophilic and hydrophobic interactions and remained in stable binding conformation with the receptor enzymes. Furthermore, the interatomic interaction energies were dominated by Van der Waals and electrostatic energies indicating the formation of stable complexes.

Crystal structure, Hirshfeld surface analysis and DFT study of (5E,5'E,6Z,6'Z)-6,6'-[ethane-1,2-diyl-bis(aza-nylyl-idene)]bis-{5-[2-(4-fluoro-phen-yl)hydra-zono]-3,3-di-methyl-cyclo-hexa-none} 2.5-hydrate.

The title compound, C30H34F2N6O2·2.5H2O, was obtained by condensation of 2-[2-(4-fluoro-phen-yl)hydrazono]-5,5-di-methyl-cyclo-hexan-1,3-dione with ethyl-enedi-amine in ethanol and crystallized as a 1:2.5 hydrate in space group C2/c. The two independent mol-ecules, with approximate crystallographic C 2 symmetries, have different conformations and packing environments, are stabilized by intra-molecular N-H⋯N hydrogen bonds and linked by O-H⋯O hydrogen bonds involving the water mol-ecules. A Hirshfeld surface analysis showed that H⋯H contacts make by far the largest (48-50%) contribution to the crystal packing. From DFT calculations, the LUMO-HOMO energy gap of the mol-ecule is 0.827 eV.

Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA.

In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.

Facile Access to 2-Selenoxo-1,2,3,4-tetrahydro-4-quinazolinone Scaffolds and Corresponding Diselenides via Cyclization between Methyl Anthranilate and Isoselenocyanates: Synthesis and Structural Features.

A practical method for the synthesis of 2-selenoxo-1,2,3,4-tetrahydro-4-quinazolinone was reported. The latter compounds were found to undergo facile oxidation with H2O2 into corresponding diselenides. Novel organoselenium derivatives were characterized by the 1H, 77Se, and 13C NMR spectroscopies, high-resolution electrospray ionization mass spectrometry, IR, elemental analyses (C, H, N), and X-ray diffraction analysis for several of them. Novel heterocycles exhibited multiple remarkable chalcogen bonding (ChB) interactions in the solid state, which were studied theoretically.

Complexes of 1-(2-R(F, CH3, Cl)-phenyl)-1,4-dihydro-5H-tetrazole-5-thiones with cadmium chloride: Synthesis, molecular, crystal structures and computational investigation approach.

New complex compounds (I) - (IV) were synthesized by the reaction of 1-(2-fluorofluorophenyl) -1,4-dihydro-5H-tetrazole-5-thione (HL1), 1-(2-methylphenyl)-1,4-dihydro-5H-tetrazole-5-thione (HL2) and 1-(2-chlorochlorophenyl)-1,4-dihydro-5H-tetrazole-5-thione (HL3) with cadmium chloride. By X-ray diffraction analysis, molecular and crystal structures of complexes (I), (II), (III) and (IV) are determined. (CIF files CCDC № 2,003,797 (I), 1,993,454 (II), 2,151,359 (III), 2,098,997 (IV)). Hirshfeld surface analysis, frontier orbital analysis, atomic charges, electrostatic potential, nonlinear optical properties, and natural bond analysis of all three­cadmium metal-organic complexes were discussed. A molecular docking study was used to investigate compounds' binding and interactions with DNA molecules, which predicted compound I as the best binder at the DNA minor groove and demonstrated closed distance interactions. In a long run of molecular dynamics simulations, the compound I complex was also depicted with good dynamics.

Crystal structure and Hirshfeld surface analysis of 3-[2-(3,5-di-methyl-phen-yl)hydrazinyl-idene]benzo-furan-2(3H)-one.

In the title compound, C16H14N2O2, the 2,3-di-hydro-1-benzo-furan ring system is essentially planar and makes a dihedral angle of 3.69 (7)° with the di-methyl-phenyl ring. The mol-ecular conformation is stabilized by an intra-molecular N-H⋯O hydrogen bond with an S(6) ring motif. In the crystal, mol-ecules are connected by C-H⋯π and π-π stacking inter-actions, forming a layer lying parallel to the (11) plane. One methyl group is disordered over two orientations, with occupancies of 0.67 (4) and 0.33 (4). Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (51.2%), O⋯H/H⋯O (17.9%), C⋯H/H⋯C (15.2%) and C⋯C (8.1%) contacts.

Crystal structure and Hirshfeld surface analysis of (3Z)-7-meth-oxy-3-(2-phenyl-hydrazinyl-idene)-1-benzo-furan-2(3H)-one.

In the title compound, C15H12N2O3, pairs of mol-ecules are linked into dimers by N-H⋯O hydrogen bonds, forming an R 2 2(12) ring motif, with the dimers stacked along the a axis. These dimers are connected through π-π stacking inter-actions between the centroids of the benzene and furan rings of their 2,3-di-hydro-1-benzo-furan ring systems. Furthermore, there exists a C-H⋯π inter-action that consolidates the crystal packing. A Hirshfeld surface analysis indicates that the most important contacts are H⋯H (40.7%), O⋯H/H⋯O (24.7%), C⋯H/H⋯C (16.1%) and C⋯C (8.8%).

Crystal structure and Hirshfeld surface analysis of (E)-1-[2,2-di-chloro-1-(4-methyl-phen-yl)ethen-yl]-2-(4-meth-oxy-phen-yl)diazene.

The asymmetric unit of the title compound, C16H14Cl2N2O, comprises two similar mol-ecules, A and B, in which the dihedral angles between the two aromatic rings are 70.1 (3) and 73.2 (2)°, respectively. The crystal structure features short C-H⋯Cl and C-H⋯O contacts and C-H⋯π and van der Waals inter-actions. The title compound was refined as a two-component non-merohedral twin, BASF 0.1076 (5). The Hirshfeld surface analysis and two-dimensional fingerprint plots show that H⋯H (38.2% for mol-ecule A; 36.0% for mol-ecule B), Cl⋯H/H⋯Cl (24.6% for mol-ecule A; 26.7% for mol-ecule B) and C⋯H/H⋯C (20.0% for mol-ecule A; 20.2% for mol-ecule B) inter-actions are the most important contributors to the crystal packing.

Crystal structure and Hirshfeld surface analysis of 1,3-bis-{2,2-di-chloro-1-[(E)-phenyl-diazen-yl]ethen-yl}benzene.

In the mol-ecule of the title compound, C22H14Cl4N4, the central benzene ring makes dihedral angles of 77.03 (9) and 81.42 (9)° with the two approximately planar 2,2-di-chloro-1-[(E)-phenyl-diazen-yl]vinyl groups. In the crystal, mol-ecules are linked by C-H⋯π, C-Cl⋯π, Cl⋯Cl and Cl⋯H inter-actions, forming a three-dimensional network. The Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (30.4%), C⋯H/H⋯C (20.4%), Cl⋯H/H⋯Cl (19.4%), Cl⋯Cl (7.8%) and Cl⋯C/C⋯Cl (7.3%) inter-actions.

Crystal structure and Hirshfeld surface analysis of 1-(2-fluoro-phen-yl)-1H-tetra-zole-5(4H)-thione.

In the crystal of the title compound, C7H5FN4S, the mol-ecules are non-planar, with dihedral angle formed by least-squares planes of tetra-zole and benzene rings of 59.94 (8) °. The crystal packing is formed by N-H⋯S hydrogen bonds, which link the mol-ecules into centrosymmetric dimers with an R 2 2(8) ring motif, and by the offset face-to-face π-π stacking inter-actions between the benzene rings, which join the dimers into layers parallel to (100). The Hirshfeld surface analysis shows that the most important contributions to the surface contacts are from N⋯H/H⋯N (21.9%), S⋯H/H⋯S (21.1%), H⋯H (14.6%), F⋯H/H⋯F (11.8%) and C⋯H/H⋯C (9.5%) inter-actions.

Crystal structure and Hirshfeld surface analysis of 6-benzoyl-3,5-di-phenyl-cyclo-hex-2-en-1-one.

In the title compound, C25H20O2, the central cyclo-hexenone ring adopts an envelope conformation. The mean plane of the cyclo-hexenone ring makes dihedral angles of 87.66 (11) and 23.76 (12)°, respectively, with the two attached phenyl rings, while it is inclined by 69.55 (11)° to the phenyl ring of the benzoyl group. In the crystal, the mol-ecules are linked by C-H⋯O and C-H⋯π inter-actions, forming a three-dimensional network.

Crystal Structure and Hirshfeld Surface Analysis of Acetoacetanilide Based Reaction Products.

We report an unprecedented multicomponent reaction of acetoacetanilide with malononitrile leading to a structurally novel bicyclic product (9) in a high yield. The structure has been confirmed by X-ray crystallography and comparative Hirshfeld surface analysis of 5-cyano-2-hydroxy-2-methyl-N-phenyl-4-(yridine-4-yl)-6-(thiophen-2-yl)-3,4-dihydro-2H-pyran-3-carboxamide 2, 5-cyano-2-hydroxy-2-methyl-6-oxo-N-phenyl-4-(thiophen-2-yl)piperidine-3-carboxamide 4 and 2-(8-amino-7,8a-dicyano-1-imino-4a-methyl-3-oxo-2-phenyl-1,3,4,4a,5,8a-hexahydroisoquinolin-6(2H)-ylidene)-N-phenylacetamide 9.

The synthesis and crystal structure of 2-(chloro-selan-yl)pyridine 1-oxide: the first monomeric organoselenenyl chloride stabilized by an intra-molecular secondary Se⋯O inter-action.

The title compound, C5H4ClNOSe, is the product of the reaction of sulfuryl chloride and 2-selanyl-1-pyridine 1-oxide in di-chloro-methane. The mol-ecule has an almost planar geometry (r.m.s. deviation = 0.012 Å), and its mol-ecular structure is stabilized by an intra-molecular secondary Se⋯O inter-action of 2.353 (3) Å, closing a four-membered N-C-Se⋯O ring. The title compound represents the first monomeric organoselenenyl chloride stabilized intra-molecularly by an inter-action of this type. The non-valent attractive Se⋯O inter-action results in a substantial distortion of the geometry of the ipso-carbon atom. The endo-cyclic N-C-Se [102.1 (3)°] and exo-cyclic C-C-Se [136.9 (3)°] bond angles deviate significantly from the ideal value of 120° for an sp2-hybridized carbon atom, the former bond angle being much smaller than the latter. In the crystal, mol-ecules are linked by C-H⋯O hydrogen bonds, forming zigzag chains propagating along [010]. The chains, which stack along the a-axis direction, are linked by offset π-π inter-actions [inter-centroid distance = 3.960 (3) Å], forming corrugated sheets parallel to the ab plane.

Crystal structure of rac-(3aR*,9aS*)-4,4,4-tri-chloro-1,2,3,3a,4,9a-hexa-hydro-4λ(5),9λ(4)-cyclo-penta-[4,5][1,3]tellurazolo[3,2-a]pyridine.

The title compound, C10H12Cl3NTe, crystallizes with two crystallographically independent mol-ecules (A and B) in the asymmetric unit. In each case, the coordination around the Te atom is distorted square-pyramidal, with the equatorial plane composed of the three Cl atoms and the C atom of the pyridinium ring. The Te atom is displaced from the mean-square plane by 0.1926 (7) and 0.1981 (8) Å, in mol-ecules A and B, respectivly, away from the apical C atom. The bond lengths from the Te atom to the two Cl atoms arranged trans to each other [2.5009 (7)/2.5145 (7) and 2.5184 (7)/2.5220 (8) Šin mol-ecules A and B, respectivly] are substan-ti-ally shorter than the third Te-Cl distance [2.8786 (7) and 2.8763 (7) Šin mol-ecules A and B, respectivly]. The 1,3-tellurazole ring is almost planar (r.m.s. deviations of 0.042 and 0.045 Šin mol-ecules A and B, respectivly). The cyclopentane rings in both molecules A and B adopt envelope conformations with the carbon atom opposed to the (Te)C-C(N) bond as the flap. In the crystal, mol-ecules form centrosymmetric 2 + 2 associates via Te⋯Cl inter-actions [3.3993 (7) and 3.2030 (7) Å]. As a result of these secondary inter-actions, the Te atom attains a strongly distorted 5 + 1 octa-hedral environment. Further, the 2 + 2 associates are bound by weak C-H⋯Cl hydrogen bonds into a three-dimensional framework.

(1R*,2R*,3S*,4R*)-Diethyl 4-hy-droxy-4-methyl-2-(4-methyl-phen-yl)-6-oxo-cyclo-hexane-1,3-di-carboxyl-ate.

The title compound, C20H26O6, is chiral and crystallizes as a racemate: the relative configuration of the stereogenic centres is 1R*,2R*,3S*,4R*. The cyclo-hexane ring has a chair conformation. The ethyl fragment of the eth-oxy-carbonyl group in the 3-position is disordered over two sets of sites in a 0.650 (6):0.350 (6) ratio. The hy-droxy group acts as a bifurcated hydrogen-bond donor, forming both intra- and inter-molecular hydrogen bonds with ester carbonyl O atoms. The inter-molecular hydrogen bonds form inversion dimers in the crystal.

rac-Ethyl 2-hy-droxy-2,7,7-trimethyl-4-(4-nitro-phen-yl)-5-oxo-3,4,5,6,7,8-hexa-hydro-2H-chromene-3-carboxyl-ate.

The title mol-ecule, C21H25NO7, has four stereogenic centres and crystallized as a racemate. It consists of enanti-omeric pairs with the relative configuration rac-(1R*,2S*,3R*). The cyclo-hexenone ring adopts an envelope conformation; the dimethyl-substituted C atom lies 0.640 (1) Šout of the mean plane formed by the rest of the ring atoms (r.m.s. deviation = 0.016 Å). The oxacyclo-hexene ring adopts a half-chair conformation, the hy-droxy- and carboxyl-substituted C atoms lying -0.336 (1) and 0.419 (1) Å, respectively, out of the mean plane formed by the rest of the ring atoms (r.m.s. deviation = 0.002 Å). In the crystal, O-H⋯O hydrogen bonds link the mol-ecules into a chain along the c-axis direction.

rac-1-[6-Hy-droxy-4-(4-meth-oxy-phen-yl)-3,6-dimethyl-4,5,6,7-tetra-hydro-2H-indazol-5-yl]ethanone.

The title compound, C(18)H(22)N(2)O(3), represents a (4S,5R,6S)-stereoisomer, crystallizing as a racemate in a centrosymmetric space group. The six-membered aliphatic ring adopts a half-chair conformation, with the hy-droxy- and acetyl-substituted C atoms deviating by 0.458 (2) and -0.366 (2) Å, respectively, from the plane defined by other four ring atoms. The pyrazole ring is essentially planar [r.m.s deviation = 0.004 (2) Å]. In the crystal, the mol-ecules are linked into chains along the b axis by N-H⋯N hydrogen bonds. The chains are linked by O-H⋯N hydrogen bonds into layers parallel to the bc plane.

1,4-Bis[2-(prop-1-en-yl)phen-oxy]butane.

The mol-ecule of the title compound, C(22)H(26)O(2), exhibits C(i) mol-ecular symmetry with a crystallographic inversion centre at the mid-point of the central C-C bond. A kink in the mol-ecule is defined by the torsion angle of 66.7 (2)° about this central bond of the alkyl bridge.

rac-Ethyl 6-hy-droxy-6-methyl-3-oxo-4-phenyl-1,3,4,5,6,7-hexa-hydro-benzo[c][1,2]oxazole-5-carboxyl-ate.

In the title compound, C(17)H(19)NO(5), the cyclo-hexene ring is in a half-chair conformation and the isoxazole ring in an envelope conformation with the N atom as the flap. The C atoms in the 4- and 6-positions are of the same absolute configuration, whereas the C atom in the 5-position is of the opposite configuration, i.e. (4S*,5R*,6S*). The methyl fragment of the eth-oxy-carbonyl group at position 5 is disordered over two sets of sites in a 0.60:0.40 ratio. The crystal packing displays inter-molecular N-H⋯O and O-H⋯O hydrogen bonds.

Self-assembly of a palladium complex formed from two U-shaped calixsalen molecules.

U-shaped calixsalens can be efficient building blocks for the construction of molecular boxes or cavitands. The first example of a calixsalen complex that has no coordination between the metal ion and phenolic oxygen atom was provided by X-ray. The resulting molecular structure has a high thermal stability, but completely degrades after the addition of DMSO.