Synthesis, crystal structures, antiproliferative activities and reverse docking studies of eight novel Schiff bases derived from benzil.

Eight novel Schiff bases derived from benzil dihydrazone (BDH) or benzil monohydrazone (BMH) and four fused-ring carbonyl compounds (3-formylindole, FI; 3-acetylindole, AI; 3-formyl-1-methylindole, MFI; 1-formylnaphthalene, FN) were synthesized and characterized by elemental analysis, ESI-QTOF-MS, 1H and 13C NMR spectroscopy, as well as single-crystal X-ray diffraction. They are (1Z,2Z)-1,2-bis{(E)-[(1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethane (BDHFI), C32H24N6, (1Z,2Z)-1,2-bis{(E)-[1-(1H-indol-3-yl)ethylidene]hydrazinylidene}-1,2-diphenylethane (BDHAI), C34H28N6, (1Z,2Z)-1,2-bis{(E)-[(1-methyl-1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethane (BMHMFI) acetonitrile hemisolvate, C34H28N6·0.5CH3CN, (1Z,2Z)-1,2-bis{(E)-[(naphthalen-1-yl)methylidene]hydrazinylidene}-1,2-diphenylethane (BDHFN), C36H26N4, (Z)-2-{(E)-[(1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethanone (BMHFI), C23H17N3O, (Z)-2-{(E)-[1-(1H-indol-3-yl)ethylidene]hydrazinylidene}-1,2-diphenylethanone (BMHAI), C24H19N3O, (Z)-2-{(E)-[(1-methyl-1H-indol-3-yl)methylidene]hydrazinylidene}-1,2-diphenylethanone (BMHMFI), C24H19N3O, and (Z)-2-{(E)-[(naphthalen-1-yl)methylidene]hydrazinylidene}-1,2-diphenylethanone (BMHFN) C25H18N2O. Moreover, the in vitro cytotoxicity of the eight title compounds was evaluated against two tumour cell lines (A549 human lung cancer and 4T1 mouse breast cancer) and two normal cell lines (MRC-5 normal lung cells and NIH 3T3 fibroblasts) by MTT assay. The results indicate that four (BDHMFI, BDHFN, BMHMFI and BMHFN) are inactive and the other four (BDHFI, BDHAI, BMHFI and BMHAI) show severe toxicities against human A549 and mouse 4T1 cells, similar to the standard cisplatin. All the compounds exhibited weaker cytotoxicity against normal cells than cancer cells. The Swiss Target Prediction web server was applied for the prediction of protein targets. After analyzing the differences in frequency hits between these active and inactive Schiff bases, 18 probable targets were selected for reverse docking with the Surflex-dock function in SYBYL-X 2.0 software. Three target proteins, i.e. human ether-á-go-go-related (hERG) potassium channel, the inhibitor of apoptosis protein 3 and serine/threonine-protein kinase PIM1, were chosen as the targets. Finally, the ligand-based structure-activity relationships were analyzed based on the putative protein target (hERG) docking results, which will be used to design and synthesize novel hERG ion channel inhibitors.

Structural and theoretical study of four novel norcantharidine derivatives: two new cases of conditional isomorphism.

Structural and theoretical studies of four novel 5,6-dehydronorcantharidine (DNCA)/norcantharidine (NCA) derivatives, namely (3aR,4S,7R,7aS)-2-phenyl-3a,4,7,7a-tetrahydro-4,7-epoxy-1H-isoindole-1,3(2H)-dione, C14H11NO3 (DNCA-A), (3aR,4S,7R,7aS)-2-(4-nitrophenyl)-3a,4,7,7a-tetrahydro-4,7-epoxy-1H-isoindole-1,3(2H)-dione, C14H10N2O5 (DNCA-NA), (3aR,4S,7R,7aS)-2-(4-nitrophenyl)-3a,4,5,6,7,7a-hexahydro-1H-4,7-epoxyisoindole-1,3(2H)-dione, C14H12N2O5 (NCA-NA), and (3aR,4S,7R,7aS)-2-(2-hydroxyethyl)-3a,4,5,6,7,7a-hexahydro-1H-4,7-epoxyisoindole-1,3(2H)-dione, C10H13NO4 (NCA-AE), are reported. The supramolecular interactions and single-crystal structural characteristics of these molecules, together with the crystal structures of four other similar molecules, i.e. NCA-A (the 4-phenyl derivative of NCA-NA), DNCA-AE (the 5,6-unsaturated derivative of NCA-AE), DNCA and NCA, were analysed. Surprisingly, DNCA-A and NCA-A, as well as DNCA-NA and NCA-NA, proved to be isomorphic, while DNCA-AE and NCA-AE, as well as DNCA and NCA, have very different crystal structures. These are very rare isostructural examples between unsaturated and saturated oxanorbornene/oxanorbornane derivatives. To further explore how noncovalent interactions (NCIs) affect the degree of isomorphism in this particular series of rigid molecules where there is a fairly limited conformational degree of freedom, all four pairs of crystal structures were analyzed in parallel. The differentiation in NCIs which entails the packing mode of similar molecules is supported by energy calculations based on real or exchanged crystal structures. Our results show that minor structural differences may result in very different supramolecular interactions, and so lead to altered packing modes in the crystalline solids. Even if isostructurality sometimes occurs, the possibility of various molecular packing types cannot be ruled out. On the other hand, isomorphism may just be the result of kinetic possibilities instead of relative thermodynamic stabilities. Though crystal structure prediction is formidable, the comparison method based on existing crystal structures and quantum calculations can be used to predict the probability of isomorphism. This understanding will help us to design new norbornene derivatives with specified structures.

Synthesis, structure and antiproliferative and optical activities of two new biphenyl-derived Schiff bases.

Two novel Schiff bases derived from indole and biphenyl have been designed and synthesized, namely 3-((E)-{(E)-[1-(biphenyl-4-yl)ethylidene]hydrazinylidene}methyl)-1-methyl-1H-indole (3-BEHMI) acetonitrile monosolvate, C24H21N3·CH3CN, and 3-((E)-{(E)-[1-(biphenyl-4-yl)ethylidene]hydrazinylidene}methyl)-1-methyl-1H-indole (3-BEHEI) acetonitrile monosolvate, C24H21N3·CH3CN. Their structures were characterized by elemental analysis, quadrupole time-of-flight MS, NMR and UV-Vis spectroscopy. The single-crystal packing structure of 3-BEHMI is largely dominated by C-H...π interactions and weak van der Waals interactions. The in vitro cytotoxicity of the two title compounds have been evaluated against two tumour cell lines (A549 human lung cancer and 4T1 mouse breast cancer) and two normal cell lines (MRC-5 normal lung cells and NIH 3T3 fibroblasts) by MTT assay. The results indicate that 3-BEHEI exhibits a slightly weaker antiproliferative capability (IC50 = ∼50 µM) than the previously reported similar Schiff base 3-BEHI (IC50 = ∼20 µM). This is in line with docking results. 3-BEHMI demonstrates a weak cytotoxic activity, with IC50 values around 110 µM, which disagrees with its docking results. Overall, the tested compounds manifest relevant cytotoxicities on the selected cancer cell lines and normal cell lines. The UV-Vis and fluorescence spectra were recorded and reproduced through the TD-DFT method with four types of hybrid density functionals, including B3LYP, M062X, PBE1PBE and WB97XD.

Order and disorder in (E)-[1-(biphenyl-4-yl)ethylidene]hydrazine: a structural, spectroscopic and theoretical study.

An unexpected global disorder (co-existing rotational disorder and glide disorder) has been observed during an X-ray investigation of the crystal structure of (E)-[1-(biphenyl-4-yl)ethylidene]hydrazine, C14H14N2, at room temperature. When the temperature decreases to 273 K, the disorder disappears, but the quality of the data set is low. The diffraction data were collected again at 110 K. Differential scanning calorimetry (DSC) analysis and polarizing-microscopy experiments, as well as a fourth set of single-crystal data collected at 283 K, proved that the order-disorder transformation occurs continuously. The analyses of these crystal structures and full-range relaxed potential energy surface scans showed that this kind of global disorder is not very difficult to achieve inside the crystal. Experimental and theoretical studies via UV-Vis and fluorescence spectra impart an understanding on the prediction methods of optical properties, which are essential for the rational design of biphenyl-based materials with pre-defined properties.

Theoretical insight into the disordered structure of (Z)-2-[(E)-(4-methoxybenzylidene)hydrazinylidene]-1,2-diphenylethanone: the role of noncovalent interactions.

A global glide disorder has been discovered during an X-ray investigation of the crystal structure of (Z)-2-[(E)-(4-methoxybenzylidene)hydrazinylidene]-1,2-diphenylethanone (MHDE, C22H18N2O2) at room temperature. In another crystal, however, such disorder disappears (still at room temperature). Even though the disorder may be partly due to the poor quality of the harvested crystal, the structure can shed light on the nature of disorder. With the help of quantum chemical calculations, it is found that the global disorder seems to be connected with the need for stabilization of the somewhat rigid but mobile and unstable molecular structure. The most relevant feature driving the packing of the disordered structure concerns the slight perturbations (such as glide) of two or more disorder components (fractional occupancies) distributed throughout the crystal.

Design, synthesis, crystal structure and in vitro cytotoxic properties of a novel Schiff base derived from indole and biphenyl.

A novel and potentially active dihydroorotate dehydrogenase (DHODH) inhibitor, namely 3-({(E)-[(E)-1-(biphenyl-4-yl)ethylidene]hydrazinylidene}methyl)-1H-indole (BEHI) acetonitrile disolvate, C23H19N3·2CH3CN, has been designed and synthesized. The structure of BEHI was characterized by elemental analysis, Q-TOF (quadrupole time-of-flight) MS, NMR, UV-Vis and single-crystal X-ray diffraction. The antitumour activity of the target molecule was evaluated by the MTT method. Results indicated that BEHI exhibited rather potent cytotoxic activity against human A549 (IC50 = 20.5 µM) and mouse breast 4T1 (IC50 = 18.5 µM) cancer cell lines. Meanwhile, to rationalize its potencies in the target, BEHI was docked into DHODH and the interactions with the active site residues were analyzed. Single-crystal structure analysis indicated that hydrogen bonds are present only between BEHI and acetonitrile solvent molecules in the asymmetric unit. The interplay of weak π-π stacking and weak C(N)-H...π interactions between neighbouring BEHI molecules play crucial roles in the formation of the final supramolecular frameworks.

Experimental and theoretical studies of the products of addition-elimination reactions between benzil dihydrazone and three isomeric chlorobenzaldehydes.

A series of mono- and di-Schiff bases formed between benzil dihydrazone {BDH; systematic name: (1Z)-[(2E)-2-hydrazinylidene-1,2-diphenylethylidene]hydrazine} and three isomeric chlorobenzaldehydes were designed and synthesized to be used as model compounds to help to explain the reaction mechanisms for the formation of Schiff bases. These compounds are 1-(2-chlorobenzylidene)-2-{2-[2-(2-chlorobenzylidene)hydrazin-1-ylidene]-1,2-diphenylethylidene}hydrazine (BDHOCB), and the 3-chloro (BDHMCB) and 4-chloro (BDHPCB) analogues, all having the formula C28H20Cl2N4. Surprisingly, only di-Schiff bases were obtained; our attempts to push the reaction in favour of the mono-Schiff bases all failed. Density functional theory (DFT) calculations were performed to explain the trend in the experimental results. In the case of the systems studied, the type of Schiff base produced exhibits a clear dependence on the HOMO-LUMO energy gaps (ΔE(HOMO-LUMO)), i.e. the product is mainly governed by its stability. The compounds were characterized by single-crystal X-ray diffractometry, elemental analysis, melting point, (1)H NMR and (13)C NMR spectroscopy. The structural features of the three new Schiff bases are similar. For instance, they have the same chemical formula, all the molecules have a symmetrical double helix structure, with each Ph-C=N-N=C-Ph arm exhibiting an anti conformation, and their supramolecular interactions include intermolecular π-π and weak C-H...π stacking interactions. The crystal systems are different, however, viz. triclinic (space group P1¯) for BDHPCB, monoclinic (space group P2(1)/n) for BDHOCB and orthorhombic (space group Pnna) for BDHMCB.

1-(2-Hy-droxy-eth-yl)pyrrole-2,5-dione.

The asymmetric unit of the title compound, C(6)H(7)NO(3), contains two mol-ecules (A and B) related by a non-crystallographic twofold pseudo-axis. The mol-ecules are joined in the (AABB)(n) manner by O-H⋯O hydrogen bonds between their hy-droxy groups, thus forming C(2) chains along the a-axis direction. Neighboring mol-ecules of the same kind (A and A, or B and B) are related by inversion centers, so that all hy-droxy H atoms are disordered other two sets of sites with half occupancies (superimposed O-H⋯O and O⋯H-O fragments). The mol-ecules are further linked by C-H⋯O inter-actions, which can be considered to be weak hydrogen bonds.

exo,exo-4-(2-Hy-droxy-eth-yl)-10-oxa-4-aza-tricyclo-[5.2.1.0]dec-8-ene-3,5-dione.

In the crystal of the title compound, C(10)H(11)NO(4), the hy-droxy group forms an O-H⋯O(carbon-yl) hydrogen bond with an adjacent molecule, so forming chains which extend along (010). Further weak C-H⋯O hydrogen-bonding associations give an infinite three-dimensional network structure.

A two-dimensional undulating Ag(I) coordination polymer constructed of Ag-C and Ag-O bonds: poly[[[µ3-(5,6-η):κO(2):κO(2)-(±)-(1S,2S,3R,4R)-3-carboxy-7-oxabicyclo[2.2.1]hept-5-ene-2-carboxylato]silver(I)] monohydrate].

The title coordination polymer, {[Ag(C(8)H(7)O(5))]·H(2)O}(n), is built from Ag(+) cations and singly protonated dehydronorcantharidin (SP-DNC) anions, with a distorted trigonal-planar geometry at the metal centre. The coordination number of Ag(I) is three (with one Ag-π bond and two Ag-O bonds, one from each of three different SP-DNC ligands), if only formal Ag-ligand bonds are considered, but can be regarded as five if longer weak Ag···O interactions are also included. The two-dimensional corrugated-sheet coordination polymer forms a non-interpenetrating framework with (4.8(2)) topology. Disordered water molecules are sandwiched between the sheets.

4,4'-(Phenyl-imino)dibenzaldehyde.

The asymmetric unit of the title compound, C(20)H(15)NO(2), contains one half-molecule with the central N atom and two C atoms of the benzene moiety lying on a twofold rotation axis. Weak C-H⋯O inter-actions join the mol-ecules together into an infinite three-dimensional network.

Methyl pyrazine-2-carboxyl-ate.

The title compound, C(6)H(6)N(2)O(2), is approximately planar [r.m.s. deviation = 0.0488 (3) Å]. In the crystal, weak inter-molecular C-H⋯O and C-H⋯N inter-actions join the mol-ecules into an infinite three-dimensional network.