Synthesis, anticancer activity, and molecular docking of half-sandwich iron(II) cyclopentadienyl complexes with maleimide and phosphine or phosphite ligands.

In these studies, we designed and investigated the potential anticancer activity of five iron(II) cyclopentadienyl complexes bearing different phosphine and phosphite ligands. All complexes were characterized with spectroscopic analysis viz. NMR, FT-IR, ESI-MS, UV-Vis, fluorescence, XRD (for four complexes) and elemental analyses. For biological studies, we used three types of cells-normal peripheral blood mononuclear (PBM) cells, leukemic HL-60 cells and non-small-cell lung cancer A549 cells. We evaluated cell viability and DNA damage after cell incubation with these complexes. We observed that all iron(II) complexes were more cytotoxic for HL-60 cells than for A549 cells. The complex CpFe(CO)(P(OPh)3)(η1-N-maleimidato) 3b was the most cytotoxic with IC50 = 9.09 µM in HL-60 cells, IC50 = 19.16 µM in A549 and IC50 = 5.80 µM in PBM cells. The complex CpFe(CO)(P(Fu)3)(η1-N-maleimidato) 2b was cytotoxic only for both cancer cell lines, with IC50 = 10.03 µM in HL-60 cells and IC50 = 73.54 µM in A549 cells. We also found the genotoxic potential of the complex 2b in both types of cancer cells. However, the complex CpFe(CO)2(η1-N-maleimidato) 1 which we studied previously, was much more genotoxic than complex 2b, especially for A549 cells. The plasmid relaxation assay showed that iron(II) complexes do not induce strand breaks in fully paired ds-DNA. The DNA titration experiment showed no intercalation of complex 2b into DNA. Molecular docking revealed however that complexes CpFe(CO)(PPh3) (η1-N-maleimidato) 2a, 2b, 3b and CpFe(CO)(P(OiPr)3)(η1-N-maleimidato) 3c have the greatest potential to bind to mismatched DNA. Our studies demonstrated that the iron(II) complex 1 and 2b are the most interesting compounds in terms of selective cytotoxic action against cancer cells. However, the cellular mechanism of their anticancer activity requires further research.

(3+2)-Cycloadditions of Levoglucosenone (LGO) with Fluorinated Nitrile Imines Derived from Trifluoroacetonitrile: An Experimental and Computational Study.

The in situ-generated N-aryl nitrile imines derived from trifluoroacetonitrile smoothly undergo (3+2)-cycloadditions onto the enone fragment of the levoglucosenone molecule, yielding the corresponding, five-membered cycloadducts. In contrast to the 'classic' C(Ph),N(Ph) nitrile imine, reactions with fluorinated C(CF3),N(Ar) analogues lead to stable pyrazolines in a chemo- and stereoselective manner. Based on the result of X-ray single crystal diffraction analysis, their structures were established as exo-cycloadducts with the location of the N-Ar terminus of the 1,3-dipole at the α-position of the enone moiety. The DFT computation demonstrated that the observed reaction pathway results from the strong dominance of kinetic control over thermodynamic control.

1-(Pyridin-4-yl)-4-thiopyridine (PTP) in the crystalline state - pure PTP and a cocrystal and salt.

The first in situ preparation and single-crystal structure identification of pure 1-(pyridin-4-yl)-4-thiopyridine (PTP), C10H8N2S, a simple and basic derivative of mercaptopyridine, from a crystallization mixture is described. The same PTP was found in two multicomponent crystal forms with 3,5-dinitrobenzoic acid as a classic two-component cocrystal, namely, 1-(pyridin-4-yl)-4-thiopyridine-3,5-dinitrobenzoic acid (1/1), C7H4N2O6·C10H8N2S, and with 2-hydroxy-3,5-dinitrobenzoic acid as a salt formed via proton transfer from the hydroxy group of the acid to the pyridyl N atom of PTP, namely, 4-(4-sulfanylidene-1,4-dihydropyridin-1-yl)pyridin-1-ium 1-carboxy-3,5-dinitrophenolate, C10H9N2S+·C7H3N2O7-. The protonation energy of PTP is 944.64 kJ mol-1, indicating slightly greater N-basicity compared to pyridine, a well characterized and very basic chemical reference. A variety of molecular interactions can be observed in the three new crystal structures of PTP, which are all discussed in detail. Our findings confirm those of previous studies, indicating that PTP and 4-mercaptopyridine may, under suitable conditions, be chemically converted to one another, and that this process can be stimulated by light (UV-Vis).

In Vitro Evaluation and In Silico Calculations of the Antioxidant and Anti-Inflammatory Properties of Secondary Metabolites from Leonurus sibiricus L. Root Extracts.

Leonurus sibiricus L. has great ethnobotanical and ethnomedicinal significance. This study aimed to assess the antioxidant and anti-inflammatory properties of Leonurus sibiricus L. transgenic roots extracts transformed by Rhizobium rhizogenes, with and without the AtPAP1 transcriptional factor. The study determined the total phenolic and flavonoid contents, as well as in vitro antioxidant assays, including hydrogen peroxide and nitric oxide scavenging activity. In addition, in silico computational studies and molecular docking were conducted to evaluate the antioxidant and anti-inflammatory potential of the identified compounds. The ligands were docked to NADPH oxidase, cyclooxygenase 2,5-lipoxygenase, inducible nitric synthase and xanthine oxidase: enzymes involved in the inflammatory process. The total phenolic and flavonoid contents ranged from 85.3 ± 0.35 to 57.4 ± 0.15 mg/g GAE/g and 25.6 ± 0.42 to 18.2 ± 0.44 mg/g QUE/g in hairy root extracts with and without AtPAP1, respectively. H2O2 scavenging activity (IC50) was found to be 29.3 µg/mL (with AtPAP1) and 37.5 µg/mL (without AtPAP1 transcriptional factor), and NO scavenging activity (IC50) was 48.0 µg/mL (with AtPAP1) and 68.8 µg/mL (without AtPAP1 transcriptional factor). Leonurus sibiricus L. transformed root extracts, both with and without AtPAP1, are a source of phytochemicals belonging to different classes of molecules, such as flavonoids (catechin and rutin), phenolic compounds (caffeic acid, coumaric acid, chlorogenic acid, ferulic acid) and phenylpropanoid (verbascoside). Among the radicals formed after H removal from the different -OH positions, the lowest bond dissociation enthalpy was observed for rutin (4'-OH). Rutin was found to bind with cyclooxygenase 2, inducible nitric synthases and xanthine oxidase, whereas chlorogenic acid demonstrated optimal binding with 5-lipoxygenase. Therefore, it appears that the Leonurus sibiricus L. transformed root extract, both with and without the AtPAP1 transcriptional factor, may serve as a potential source of active components with antioxidant and anti-inflammatory potential; however, the extract containing AtPAP1 demonstrates superior activities. These properties could be beneficial for human health.

One-Pot Synthesis of 1-Aryl-3-trifluoromethylpyrazoles Using Nitrile Imines and Mercaptoacetaldehyde As a Surrogate of Acetylene.

A synthetically useful approach for one-pot preparation of 1-aryl-3-trifluoromethylpyrazoles using in situ generated nitrile imines and mercaptoacetaldehyde applied as 1 equiv of acetylene is presented. This protocol comprises (3 + 3)-annulation of the mentioned reagents to form 5,6-dihydro-5-hydroxy-4H-1,3,4-thiadiazine, followed by cascade dehydration/ring contraction reactions with p-TsCl. In addition, representative nonfluorinated analogues functionalized with Ph, Ac, and CO2Et groups at the C(3)-position of the pyrazole ring were also prepared by the devised method.

Comparative study of the antioxidant capability of EDTA and Irganox.

Oxidative stress makes it difficult to preserve food and negatively affect the applicability of polymeric packaging. It is typically caused by an excess of free radicals, and it is dangerous to human health, resulting in the onset and development of diseases. The antioxidant ability and activity of ethylenediaminetetraacetic acid (EDTA) and Irganox (Irg) as synthetic antioxidant additives were studied. Three different antioxidant mechanisms were considered and compared by calculating bond dissociation enthalpy (BDE), ionization potential (IP), proton dissociation enthalpy (PDE), proton affinity (PA), and electron transfer enthalpy (ETE) values. Two density functional theory (DFT) methods were used, M05-2X and M06-2X with the 6-311++G(2d,2p) basis set in gas phase. Both additives can be used to protect pre-processed food products and polymeric packaging from oxidative stress related material deterioration. By comparing the two studied compounds, it was found that EDTA has a higher antioxidant potential than Irganox. To the best of our knowledge several studies have been carried out to understand the antioxidant potential of various natural and synthetic species, but EDTA and Irganox were not compared and investigated before. These additives can be used to protect pre-processed food products and polymeric packaging and prevent material deterioration caused by oxidative stress.

Higher-order [8+2]-cycloadditions of tropothione with levoglucosenone (LGO) and structurally similar exo-cyclic enones derived from cyrene.

Levoglucosenone (LGO) and structurally similar exo-cyclic enones derived from cyrene (dihydrolevoglucosenone) react with tropothione following the higher-order [8 + 2]-cycloaddition pathway. Reactions were performed at room temperature in CH2Cl2 solutions in absence of any activating reagent. Whereas reaction of tropothione with LGO occurred with complete stereoselectivity, leading to a single, sterically favored exo cycloadduct, identified as polycylic thiophene derivative, reactions performed with exo-cyclic enones yielded in some instances mixtures of two isomeric exo and endo cycloadducts, derived from spiro-tetrahydrothiophene as major and minor components, respectively, of the studied reaction mixtures. Exo and endo [8 + 2] cycloadducts differ in absolute configuration at the newly created chiral centers. Structures of exo and endo cycloadducts were confirmed by single crystal X-ray diffraction analysis.

(3+2)-Cyclization Reactions of Unsaturated Phosphonites with Aldehydes and Thioketones.

By exploiting the unique reactivity of ethynyl-phosphonites we obtain novel P(V)-containing five-membered heterocycles via (3+2)-cyclization reactions with aldehydes or cycloaliphatic thioketones in satisfactory to excellent yields. Whereas reactions with thioketones to yield 1,3-thiaphospholes-3-oxides occur smoothly at room temperature with equimolar amounts of the starting materials in absence of any catalyst, the analogous conversions with aldehydes to generate 3-oxides of 1,3-oxaphospholes require addition of triethylamine as a base. We postulate a step-wise (3+2)-cyclization mechanism for the formation of the 1,3-thiaphosphole ring based on DFT quantum chemical calculations. With this study, we introduce new cyclization reactions originating from unsaturated phosphonites as central synthetic building blocks to yield previously inaccessible stable phosphorus-containing heterocycles with unexplored potential for the molecular sciences.

Effect of a Substituent on the Properties of Salicylaldehyde Hydrazone Derivatives.

The present study investigates the effect of the substitution of salicylaldehyde hydrazones at two selected positions, i.e., the para-position with regard to the proton-donating and proton-accepting centers forming the hydrogen bridge. A detailed analysis of structural data obtained by theoretical approaches and X-ray experiments, together with original resonance Hammett's constants, indicates that the strength of the intramolecular hydrogen bonding present in salicylaldehyde hydrazones can be selectively modulated by substitution of the parent molecular system with the chemical group of known π-electron-donating or -accepting properties. Our findings provide an insight into planning synthesis pathways for salicylaldehyde hydrazone species and predicting their result with regard to their H-bonding and related physical and chemical properties.

Testing of Exchange-Correlation Functionals of DFT for a Reliable Description of the Electron Density Distribution in Organic Molecules.

Researchers carrying out calculations using the DFT method face the problem of the correct choice of the exchange-correlation functional to describe the quantities they are interested in. This article deals with benchmark calculations aimed at testing various exchange-correlation functionals in terms of a reliable description of the electron density distribution in molecules. For this purpose, 30 functionals representing all rungs of Jacob's Ladder are selected and then the values of some QTAIM-based parameters are compared with their reference equivalents obtained at the CCSD/aug-cc-pVTZ level of theory. The presented results show that the DFT method undoubtedly has the greatest problems with a reliable description of the electron density distribution in multiple strongly polar bonds, such as C=O, and bonds associated with large electron charge delocalization. The performance of the tested functionals turned out to be unsystematic. Nevertheless, in terms of a reliable general description of QTAIM-based parameters, the M11, SVWN, BHHLYP, M06-HF, and, to a slightly lesser extent, also BLYP, B3LYP, and X3LYP functionals turned out to be the worst. It is alarming to find the most popular B3LYP functional in this group. On the other hand, in the case of the electron density at the bond critical point, being the most important QTAIM-based parameter, the M06-HF functional is especially discouraged due to the very poor description of the C=O bond. On the contrary, the VSXC, M06-L, SOGGA11-X, M06-2X, MN12-SX, and, to a slightly lesser extent, also TPSS, TPSSh, and B1B95 perform well in this respect. Particularly noteworthy is the overwhelming performance of double hybrids in terms of reliable values of bond delocalization indices. The results show that there is no clear improvement in the reliability of describing the electron density distribution with climbing Jacob's Ladder, as top-ranked double hybrids are also, in some cases, able to produce poor values compared to CCSD.

A novel hydrogen-bonding N-oxide-sulfonamide-nitro N-H...O synthon determining the architecture of benzenesulfonamide cocrystals.

The structures of novel cocrystals of 4-nitropyridine N-oxide with benzenesulfonamide derivatives, namely, 4-nitrobenzenesulfonamide-4-nitropyridine N-oxide (1/1), C5H4N2O3·C6H6N2O4S, and 4-chlorobenzenesulfonamide-4-nitropyridine N-oxide (1/1), C6H6ClNO2S·C5H4N2O3, are stabilized by N-H...O hydrogen bonds, with the sulfonamide group acting as a proton donor. The O atoms of the N-oxide and nitro groups are acceptors in these interactions. The latter is a double acceptor of bifurcated hydrogen bonds. Previous studies on similar crystal structures indicated competition between these functional groups in the formation of hydrogen bonds, with the priority being for the N-oxide group. In contrast, the present X-ray studies indicate the existence of a hydrogen-bonding synthon including N-H...O(N-oxide) and N-H...O(nitro) bridges. We present here a more detailed analysis of the N-oxide-sulfonamide-nitro N-H...O ternary complex with quantum theory computations and the Quantum Theory of Atoms in Molecules (QTAIM) approach. Both interactions are present in the crystals, but the O atom of the N-oxide group is found to be a more effective proton acceptor in hydrogen bonds, with an interaction energy about twice that of the nitro-group O atoms.

Ionic cocrystals of dithiobispyridines: the role of I...I halogen bonds in the building of iodine frameworks and the stabilization of crystal structures.

It has been confirmed that mercaptopyridines undergo spontaneous condensation in redox reaction with iodine-forming dithiopyridines. In the solid state, these compounds are protonated at the N atoms and cocrystallize with iodine forming salt structures, namely, 2-[(pyridin-2-yl)disulfanyl]pyridinium triiodide sesquiiodine, C10H9N2S2+·I3-·1.5I2, and 4,4'-(disulfanediyl)dipyridinium pentaiodide triiodide, C10H10N2S22+·I5-·I3-. Dithiopyridine cations are packed among three-dimensional frameworks built from iodide anions and neutral iodine molecules, and are linked by hydrogen, halogen and chalcogen interactions. Quantum chemical computations indicated that dithiopyridines exhibit anomalously high nitrogen basicity which qualify them as potential proton sponges.

A rare case of a 2:2:1 ternary cocrystal of pyridine sulfides and trithiocyanuric acid.

We report a rare case of a 2:2:1 ternary cocrystal consisting of two trithiocyanuric acid molecules, two bis(pyridin-4-yl) sulfide molecules and 1,4-bis(pyridin-4-yl)tetrasulfane, namely, 1,3,5-triazinane-2,4,6-trithione-4-(pyridin-4-ylsulfanyl)pyridine-1,4-bis(pyridin-4-yl)tetrasulfane (2/2/1), 2C3H3N3S3·2C10H8N2S·C10H8N2S4. This interesting crystal structure with five neutral molecules per asymmetric unit was synthesized and characterized by means of X-ray diffraction (XRD) experiments and quantum-chemical modelling. Among various specific interactions, hydrogen and halogen bridges have a significant role in stabilizing the crystal structure. In particular, the role played by stacking interactions has been revealed by structure analysis and theoretical calculations. Crystallization was spontaneous and reproducible. One of the components, 1,4-bis(pyridin-4-yl)tetrasulfane, has been characterized by XRD for the first time.

A straightforward conversion of 1,4-quinones into polycyclic pyrazoles via [3 + 2]-cycloaddition with fluorinated nitrile imines.

In-situ-generated N-aryl nitrile imines derived from trifluoroacetonitrile efficiently react with polycyclic 1,4-quinones, yielding fused pyrazole derivatives as the exclusive products. The reactions proceed via the initially formed [3 + 2]-cycloadducts, which undergo spontaneous aerial oxidation to give aromatized heterocyclic products. Only for 2,3,5,6-tetramethyl-1,4-benzoquinone, the expected [3 + 2]-cycloadduct exhibited fair stability and could be isolated in moderate yield (53%). The presented method offers a straightforward access to hitherto little known trifluoromethylated polycyclic pyrazoles. All products were isolated as pale colored solids with medium-intensity absorption maxima in the range of 310-340 nm for naphthoquinone-derived products and low-intensity bands in the visible region (≈400 nm) for the anthraquinone series.

Trithiocyanuric acid: novel cocrystals and analysis of its tautomeric forms.

Cocrystals of trithiocyanuric acid with 2,2'-bipyridyl [1,3,5-triazinane-2,4,6-trithione-2,2'-bipyridine (2/1), 2C3H3N3S3·C10H8N2, (I)] and 4-methylbenzohydrazide [1,3,5-triazinane-2,4,6-trithione-4-methylbenzohydrazide (1/1), C8H10N2O·C3H3N3S3, (II)] crystallize in the monoclinic crystal system. In the crystals, molecules of both components are linked by hydrogen bonds. The trithiocyanuric acid molecules are connected by N-H...S hydrogen bonds forming R22(8) synthons, which are further organized into chain motifs. Computations based on quantum chemistry methods have been performed for a more detailed description of the observed tautomerism of trithiocyanuric acid.

Resonance-Assisted Hydrogen Bond-Revisiting the Original Concept in the Context of Its Criticism in the Literature.

In the presented research, we address the original concept of resonance-assisted hydrogen bonding (RAHB) by means of the many-body interaction approach and electron density delocalization analysis. The investigated molecular patterns of RAHBs are open chains consisting of two to six molecules in which the intermolecular hydrogen bond stabilizes the complex. Non-RAHB counterparts are considered to be reference systems. The results show the influence of the neighbour monomers on the unsaturated chains in terms of the many-body interaction energy contribution. Exploring the relation between the energy parameters and the growing number of molecules in the chain, we give an explicit extrapolation of the interaction energy and its components in the infinite chain. Electron delocalization within chain motifs has been analysed from three different points of view: three-body delocalization between C=C-C, two-body hydrogen bond delocalization indices and also between fragments (monomers). A many-body contribution to the interaction energy as well as electron density helps to establish the assistance of resonance in the strength of hydrogen bonds upon the formation of the present molecular chains. The direct relation between interaction energy and delocalization supports the original concept, and refutes some of the criticisms of the RAHB idea.

C-Br...S halogen bonds in novel thiourea N-oxide cocrystals: analysis of energetic and QTAIM parameters.

Cocrystals of thiourea with 4-nitropyridine N-oxide, C5H4N2O3·2CH4N2S, (I), and 3-bromopyridine N-oxide, C5H4BrNO·CH4N2S, (II), crystallize in the monoclinic space group P21/c. In the crystals, molecules of both components are linked by N-H...O hydrogen bonds, creating R21(6) synthons. The bromine substituent of the N-oxide component in (II) is a centre for C-Br...S halogen bonding to the thiourea molecule. Computations based on quantum chemistry methods (quantum theory of atoms in molecules, QTAIM) and atoms in molecules (AIM) theory were performed for a more detailed description of the observed type of halogen-bonding interaction.

Crystal structure of 3,6-bis-(pyridin-2-yl)-1,4-di-hydro-1,2,4,5-tetra-zine.

The structure of the title compound, C12H10N6, at 100 K has monoclinic (P21/n) symmetry. Crystals were obtained as a yellow solid by reduction of 3,6-bis-(pyridin-2-yl)-1,2,4,5-tetra-zine. The structure displays inter-molecular hydrogen bonding of the N-H⋯N type, ordering mol-ecules into infinite ribbons extending along the [100] direction.

Extremely Strong Halogen Bond. The Case of a Double-Charge-Assisted Halogen Bridge.

The stable model of a double (±)charge-assisted halogen bridge has been built on the basis of searches of the Crystal Structure Database. The model, investigated by DFT theory, consists of quinuclidine-like cation derivatives and a set of simple anions. These charged fragments form halogen-bonded complexes of which the energy of complexation in some cases reaches 100 kcal/mol. Even for such strong interactions, the QTAIM characteristics are similar to those of the more classic, relatively weak halogen bonds. An important effect of complexation is the charge transfer measured by means of QTAIM and NBO. It can also be supposed, on the basis of detailed structural and QTAIM analysis, that the delocalization of the charge in a quinuclidine moiety occurs through space and not necessarily along formal bonds. The analysis of only partially charged and fully neutral counterparts of a double (±)charge-assisted halogen bridge shows significantly weaker bonding, being less than 10 kcal/mol.

N-Oxide-N-oxide interactions and Cl...Cl halogen bonds in pentachloropyridine N-oxide: the many-body approach to interactions in the crystal state.

Pentachloropyridine N-oxide, C5Cl5NO, crystallizes in the monoclinic space group P21/c. In the crystal structure, molecules are linked by C-Cl...Cl halogen bonds into infinite ribbons extending along the crystallographic [100] direction. These molecular aggregates are further stabilized by very short intermolecular N-oxide-N-oxide interactions into herringbone motifs. Computations based on quantum chemistry methods allowed for a more detailed description of the N-oxide-N-oxide interactions and Cl...Cl halogen bonds. For this purpose, Hirshfeld surface analysis and the many-body approach to interaction energy were applied.