Single-crystal Diffraction Research Articles

Functionalized Metal-organic Frameworks for White Light Emission and Highly Sensitive Sensing of PA and Fe3+/Al3+①

Three isomorphic Ln-MOFs [Ln(bcbob)(H2O)(DMF)] (Ln = Tb for 1, Eu for 2, Gd for 3; DMF = N,N-dimethylformamide) have been constructed from a semi-rigid V-shaped organic linker 3,5-bis((4΄-carboxylbenzyl)oxy)benzoilate acid (H3bcbob) under solvothermal conditions. X-ray single-crystal diffraction analysis reveals that they exhibit a two-dimensional (2D) layered structure. Compounds 1~3 show the characteristic green and red emissions of Ln3+ and blue emission arising from the organic ligand, respectively. Based on their photoluminescence properties, the white-light emitting materials 4 and 5 with longer fluorescence lifetime (ms grade) and higher quantum yield (e.g. 40.61% for 4) are fabricated. Remarkably, 1 exhibits good sensing ability on nitroaromatic compounds, especially for picric acid (PA). In addition, 1 is still a highly selective sensing material for Fe3+ and Al3+.

Psidials L and M and Psipinene, three novel meroterpenoids with significant protective activity toward cisplatin-damaged HK2 cells from the leaves of Psidium guajava

Psidials L and M (1 and 2), two sesquiterpene-based meroterpenoids with unknown skeletons, and Psipinene (3), one novel monoterpene-based meroterpenoid, had been isolated from the leaves of Psidium guajava. Their structures were determined by spectroscopic data and calculated ECD spectra. The absolute structure of compound 1 was also determined by X-ray single crystal diffraction analysis. A plausible biosynthetic pathway for 1–2 was postulated. Compound 1 showed significant protective activity toward cisplatin-damaged HK2 cells.

Synthesis, crystal structure and DFT study of methyl 2-(1H-indol-3-yl)-2-oxoacetate

Indoles are heterocyclic compounds which exist widely in natural products. The title compound was synthesized by a two-step reaction and characterized by 1H NMR, 13C NMR, IR, and MS. Then, the single crystal structure of the target compound was determined by X-ray diffraction analysis, and the optimal crystal structure was determined by density functional theory calculation. The results show that the molecular structure of the optimized DFT is basically consistent with the crystal structure determined by X-ray single crystal diffraction. In addition, the geometric parameters, MEP, FMOS, Hirschfeld analysis and infrared spectral characteristics of the target compound were analyzed.

New secondary metabolites with cytotoxicity from fungus Penicillium roqueforti

Two novel compounds including a cyclohelminthol type polyketide (namely oxaleimide K, 1) and a maleimide derivative (namely peniroquefortine A, 2), and a new natural product (namely 2-(acetylamino)-N-[(1E)-2-phenylethenyl]-acetamide, 3), together with four known compounds (4–7), were isolated and identified from fungus Penicillium roqueforti, which was separated from the root soil of Hypericum beanii N. Robson collected from the Shennongjia Forestry District, Hubei Province. Their structures including absolute configurations were mainly established by the NMR spectroscopy analyses and single-crystal X-ray diffraction experiment. Compound 1 represents the second example of a cyclohelminthol type polyketide, which features a rare 6/6/5/5 tetracyclic system and a branched aliphatic chain containing a terminal olefin (oct-1-en-3-yl) moiety, and compound 2 possesses an unprecedented carbon skeleton that is uniquely defined by a maleimide moiety linked to the respective 4-methylene-2-(3-methylbut-2-en-1-yl)-phenol and para-substituted aromatic moieties via the carbon-carbon bonds. Remarkably, the absolute configuration of a cyclohelminthol type polyketide as exemplified by compound 1 is determined by the single-crystal diffraction analysis for the first time, highlighting an E-configuration for the linkage of a succinimide moiety and a tetrahydrofuran moiety for 1 rather than a Z-configuration as previously reported in the biosynthesis study, which gives a new insight into the structural elucidation of this category of polyketides. Additionally, compound 1 exhibited significant cytotoxic activity against multiple tumor cells, especially against the Farage and SU-DHL-2 cells (IC50 < 20 µM, 48 h). Further mechanism study revealed that compound 1 significantly induced cell cycle arrest in Farage and SU-DHL-2 cells by causing abnormal ROS level and triggering oxidative stress.Graphical

A method for improving the properties of famotidine

According to crystal engineering, the pharmaceutical intermediate m-nitrobenzoic acid (MNBA), which contains a carboxylic acid group, was selected as a coformer (CCF) for drug cocrystallization with famotidine (FMT), and a new stable FMT salt cocrystal was synthesized. The salt cocrystals were characterized by scanning electron microscopy, differential scanning calorimetry, thermogravimetric analysis, infrared spectroscopy, powder X-ray diffraction and X-ray single crystal diffraction. A single crystal structure of FMT–MNBA (1:1) was successfully obtained, and then the solubility and permeability of the newly synthesized salt cocrystal were studied. The results showed that, compared with free FMT, the FMT from the FMT–MNBA cocrystal showed improved permeability. This study provides a synthetic method to improve the permeability of BCS III drugs, which will contribute to the development of low-permeability drugs.

Bifusicoumarins A-D: Cytotoxic 3S-dihydroisocoumarins from the entomopathogenic fungus Cordyceps bifusispora (NBRC 108997)

Cordyceps is a genus of ascomycete fungi with some of them being edible and/or having a long tradition in Chinese medicine. The chemical characterization of a solvent extract of the entomopathogenic fungus Cordyceps bifusispora afforded four undescribed coumarins, bifusicoumarin A-D (1–4), along with previously reported metabolites (5–8). Structural elucidation was performed via NMR, UV and HRMS analyses, X-ray single crystal diffraction and experimental ECD. A high throughput resazurin reduction assay, that measures cell viability, indicated that 5 has a IC50 between 1 and 15 μM for several assayed tumor lines. Moreover, a protein-interaction network indicated that C. bifusispora is a promising source of additional antitumor metabolites based on SwissTargetPrediction software predictions.

Study of Hydrolysis of Nitrile Derivatives of closo-Dodecaborate Anion (Et4N)[B12H11N≡C–R] (R = Me, Et, nPr, iPr)

The reaction of nitrile derivatives of closo-dodecaborate anion (Et4N)[B12H11N≡C–R] (R = Me, Et, nPr, iPr) with water has yielded a series of (Et4N)[B12H11NH=C(OH)–R] iminols. It has been demonstrated that the hydrolysis products are in acid–base iminol–amide equilibrium, which can be controlled by changing the pH of a medium. The reaction products have been identified by 11В, 1Н, 13С NMR, IR spectroscopy, and ESI mass spectrometry. The structures of the [B12H11(Z-NH=C(OH)nC3H7)]− and [B12H11(E-NH–C(O)nC3H7)]2− anions have been determined by X-ray single-crystal diffraction.

Absolute Configuration, Enantioselective Bioactivity, and Mechanism Study of the Novel Chiral Fungicide Benzovindiflupyr.

Benzovindiflupyr has gained increasing attention as a new chiral succinate dehydrogenase inhibitor fungicide; however, its determination, bioactivity, and mechanism at the enantiomeric level are very limited. In the present study, optical rotation determination and X-ray single-crystal diffraction results identified that the absolute configurations were (+)-(1R,4S)-benzovindiflupyr and (-)-(1S,4R)-benzovindiflupyr. A quantitative determination method for enantiomers was established using high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) for pesticide detection. The stereoselective bioactivity assay indicated that (-)-(1S,4R)-benzovindiflupyr exhibited greater potency than (+)-(1R,4S)-benzovindiflupyr against seven phytopathogenic fungi. Molecular docking analysis showed that (-)-(1S,4R)-benzovindiflupyr possessed a stronger binding affinity to succinate dehydrogenase than (+)-(1R,4S)-benzovindiflupyr. The binding modes between enantiomers and the mutant with H272(B) predicted that the phytopathogenic fungi with H272(B) of succinate dehydrogenase mutation would not be resistant to benzovindiflupyr enantiomers. This study provides a basis for residue evaluation, risk assessment, and the safe application of benzovindiflupyr at the enantiomer level.

Metal organic frameworks based on mixed ligands: Syntheses, structures and selective detection of nitro explosive TNP, metal ions Fe3+ Cu2+ and CrO42-

Three new MOFs [Cd(2,5-bipi)(5-hip)]n (1), [Mn(2,5-bipi)(1,3-bdc)]n (2), and [Co(2,5-bipi)(1,3-bdc)(DMF)]n (3) (2,5-bipi = 2,5-bis(1-imidazoly)pyridine, 5-H2hip = 5-hydroxyisophthalic acid, 1,3-H2bdc = isophthalic acid) have been successfully synthesized under solvothermal conditions. They were characterized by elemental analysis, FT-IR spectra, X-ray single-crystal diffraction, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA). The results suggest that the linkage of different ligands with metal ions affords a 4-connected layer. And these 2D networks are extended to the final 3D supramolecular architectures by CH∙∙∙π stacking interactions. Fluorescence sensing measurements showed that MOF 1 can detect TNP, Fe3+, Cu2+ and CrO42− ions with high selectivity and sensitivity. In addition, their possible quenching mechanisms were studied in detail.

Highly Stereoselective Synthesis of Bis-C-ferrocenyl Glycosides via Palladium-Catalyzed Directed C-H Glycosylation.

Conjugation of carbohydrates to ferrocene scaffolds is of great value in drug design, given the nontoxic and lipophilic nature of ferrocene. However, the efficient and stereoselective synthesis of C-ferrocenyl glycosides remains a challenge. Herein, we developed a Pd-catalyzed stereoselective C-H glycosylation to provide rapid access to sole bis-C-ferrocenyl glycosides in good to high yields (up to 98% yield) with exclusive stereoselectivity. A diverse range of glycosyl chlorides were well tolerated, including d-mannose, d-glucose, l-xylose, l-rhamnose, d-mannofuranose, and d-ribofuranose. Additionally, a mononuclear PdII intermediate was characterized by X-ray single-crystal diffraction, and might participate in the C-H palladation step.

The manganese(II) and cobalt(II) complexes of enrofloxacin showed comparable antibacterial activity: Synthesis, crystal structure and antibacterial activity

Enrofloxacin (EFX) is a third-generation fluoroquinolone drug especially used for animals world wide, which shows broad-spectrum and significant antibacterial activities. In this study, EFX was selected as the ligand to synthesize two transition metal complexes, EFX-Mn and EFX-Co, in which the bio-active metal ions, manganese(II) and cobalt(II), was set to be the active metal center. Their crystal structures were reported and characterized by X-ray single crystal diffraction analysis. Both the crystal structures of EFX-Mn and EFX-Co belong to the same monoclinic crystal system with P21/c space group. Viewed from the crystal structure of EFX-Mn or EFX-Co, the central Mn(II)/Co(II) adapted a six-coordinated octahedral configuration, respectively by two EFX ligands and two H2O co-ligands. The characteristic UV-Vis absorption peaks of both complexes were examined in tris-saline buffer solution in a time-dependent mode in 24 h, which suggested that the coordination status of EFX-Mn and EFX-Co in the solid state still maintained under near-physiological condition. In vitro antibacterial activity tests demonstrated that EFX-Mn and EFX-Co showed similar and significant growth inhibitory effects towards five typical pathogenic bacteria, compared with EFX itself. While for two gram-negative bacterial strains, E. coli and S. typhi, EFX-Mn and EFX-Co showed higher bactericidal effects than EFX, the bactericidal concentration of which was only a half as low as that of EFX.

A Highly Selective and Sensitive Sequential Recognition Probe Zn2+ and H2PO4- Based on Chiral Thiourea Schiff Base.

A series of novel chiral thiourea fluorescent probes HL1-HL6 were designed and synthesized from (1R,2R)-1,2-diphenylethylenediamine, phenyl isothiocyanate, and different substituted salicylic aldehydes. All of the compounds were confirmed by 1H NMR, 13C NMR, and HRMS. They exhibit high selectivity and sensitivity to Zn2+ in the presence of nitrate ions with the detection limit of 2.3 × 10-8 M (HL5). Meanwhile, their zinc (II) complexes (L-ZnNO3) showed continuous response to H2PO4- in acetonitrile solution. The identification processes could further be verified by supramolecular chemistry data analysis, X-ray single-crystal diffraction analysis, and theoretical study. The research provides reliable evidence for an explanation of the mechanism of action of thiourea involved in coordination, which is important for the application of thiourea fluorescent probes. In short, the sensors HL1-HL6 based on chiral thiourea Schiff base will be promising detection devices for Zn2+ and H2PO4-.

Two new 3D Supramolecular Frameworks as Photocatalysts for Degradation of Methyl Blue.

We successfully synthesized two new supramolecular frameworks, namely {[Cu2(L1)(H2O)2]·(H2O)}n (1) and {[Ag(L2)(bpp)]2n·2(H2O)}n (2) (H2L1 = 2-hydroxy-5-sulfobenzoic acid, HL2 = 8-hydroxyquinoline-2-sulfonic acid) under hydrothermal condition. These single-crystal structures were determined via X-ray single crystal diffraction analyses. Solids 1 and 2 acted as photocatalysts and performed good photocatalytic activities for MB degradation under UV light irradiation.

3D Lanthanide Neodymium Porphyrin Metal–Organic Framework for Photocatalytic Oxidation of Styrene

A novel three-dimensional lanthanide porphyrin-based MOF (Nd-PMOFs) was synthesized by using tetracarboxyphenyl porphyrin as the ligand and the lanthanide Nd as the coordination metal. Its specific crystal structure information was obtained by single-crystal diffraction with the space group C2/c and the empirical formula C72H45N6Nd2O15.25. This new Nd porphyrin-based MOF with an organic framework formed by a unique coordination method enables the effective separation of photogenerated electrons and holes under photoluminescence, giving it excellent photocatalytic property which could be verified by the characterization data. The photocatalytic performance was examined by taking tert-butyl hydroperoxide as the oxidant and Nd-PMOFs as the catalyst for photocatalytic oxidation of styrene to benzaldehyde with 91.4% conversion and 81.2% benzaldehyde selectivity under optimal reactions, which surpasses most of the results reported in the literature. Several styrenes with other substituents were screened to explore the general applicability of Nd-PMOF for photocatalysis of styrene, among which Nd-PMOFs also exhibited excellent photocatalytic performance. This work offers the possibility to apply lanthanide organometallic frameworks, which are widely used in fluorescent materials, to photocatalysis. In addition, it also provides a new method for the catalytic generation of benzaldehyde from styrene that is consistent with the needs of modern green development.

Synthesis, characterization, crystal structure, and DFT study of 3,4-Diphenyl -1H-pyrrolo[2,3-b]pyridine

3,4-Diphenyl-1H-pyrrolo[2,3-b]pyridine, a useful organic building block, was obtained via a four-step reaction and the structure was determined using FT-IR, 1H NMR, 13C NMR, and mass spectrometry, and the single crystals were characterized using X-ray diffraction analysis. The optimal molecular structure, 1-2 (49.95%), was calculated using density functional theory, and was consistent with the structure determined based on single-crystal diffraction; the relative Gibbs free energy of conformer 1-2 was 0.001255 kcal mol−1. In addition, the molecular electrostatic potentials and frontier molecular orbitals of the title compound were investigated, and surface analysis was performed to further reveal its physicochemical properties.

Antibacterial Metabolites from Kiwi Endophytic Fungus Fusarium tricinctum, a Potential Biocontrol Strain for Kiwi Canker Disease

Pseudomonas syringae pv. actinidiae (Psa) is a Gram-negative bacterium causing the kiwifruit canker disease, resulting in serious economic losses to the kiwifruit industry. This study investigated the use of an endophytic fungus, Fusarium tricinctum, obtained from the kiwi plant (Actinidia chinesis) as a potential biocontrol strain against the Psa. F. tricinctum showed an inhibition rate of 59.5% in vitro against Psa. Bioassay-guided isolation was conducted on the cultural broth of F. tricinctum and seven new imidazole alkaloids, (±)-fusaritricine J ((±)-1) and fusaritricines K-P (2-7), and four enniatins (8-11) were identified. Their absolute configurations were established through extensive spectroscopic methods, quantum chemical calculations, and X-ray single crystal diffraction. Compounds 1, 4, 5, and 8-11 showed comparable anti-bacterial activities against Psa as positive control, with MIC values of 25-50 μg/mL. Further cell membrane permeability assay suggested that the most active compound 4 could destroy the bacterial cell wall structure. Hence, F. tricinctum metabolites could be applied as potential anti-Psa agents, and F. tricinctum could be considered a biocontrol strain for the control of the kiwifruit canker disease.

Anti-isostructural phase transition and twinning in CrAs at low temperatures and high pressures

Chromium arsenide CrAs (Pnma, Z = 4) is studied with synchrotron single-crystal diffraction in diamond anvil cells at high-pressures and low temperatures to examine its structural evolution across the boundary (TN) between the antiferromagnetic (AF) and paramagnetic (PM) states. Compressing CrAs across TN at low temperatures is equivalent to warming up the material from the AF to PM phases at atmospheric pressure. The phase transition at different conditions is determined from the abrupt changes of the lattice parameters, unit-cell volumes, axial ratios, and interatomic distances. Although, the space group symmetry does not change at TN, the transition is associated with the formation of twin domains. All experimental observations are rationalized with the concept of an anti-isostructural phase transition, in which both orthorhombic phases have the same space group symmetry, but different distortions of the parent hexagonal structure of the NiAs type (P63/mmc, Z = 2). The magneto-structural phase transformation in CrAs is the first example of the anti-isostructural phase transition, in which twinning, as a signature of lost higher rotational symmetry, has been detected.

Reversible Pressure-Magnetic Modulation in a Tetrathiafulvalene-Based Dyad Piezochromic Dysprosium Single-Molecule Magnet.

The extreme sensitivity of trivalent lanthanide ions to crystal field variations led to the emergence of single-molecule magnetic switching under various stimuli. The use of pressure as an external stimulus instead of classic light irradiation, oxidation or any chemical reactions allows a fine tuning of the magnetic modulation. Here the well-known pure isotopically enriched [162 Dy(tta)3 (L)]⋅C6 H14 (162 Dy) Single-Molecule Magnet (SMM) (tta- =2-2-thenoyltrifluoroacetonate and L=4,5-bis(propylthio)-tetrathiafulvalene-2-(2-pyridyl)benzimidazole-methyl-2-pyridine) was experimentally investigated by single-crystal diffraction and squid magnetometry under high applied pressures. Both reversible piezochromic properties and pressure modulation of the slow magnetic relaxation behavior were demonstrated and supported by ab initio calculations. The magnetic study of the diluted sample [162 Dy0.05 Y0.95 (tta)3 (L)]⋅C6 H14 (162 Dy@Y) indicated that variations in the electronic structure have mainly intermolecular origin with weak intramolecular contribution. Quantitative magnetic interpretation concludes to a deterioration of the Orbach process for the benefit of both Raman and QTM mechanisms under applied pressure.

Anomalous Hall effect and magnetic structure of the topological semimetal ( Mn0.78Fe0.22)Ge3

Me$_{3+\delta}$Ge, being a Weyl semimetal, shows a large anomalous Hall effect (AHE), which decreases slowly with an increase in $\delta$ from 0.1 to 0.4. However, AHE in this compound remains significantly large in the whole range of $\delta$ because of the robust nature of the topology of bands. To explore the possibility of tuning the anomalous transport effects in Weyl semimetals, we have studied the single-crystal hexagonal-(Mn$_{0.78}$Fe$_{0.22}$)$_3$Ge compound. Magnetization of this compound shows two magnetic transitions at 242 K ($T_{\text{N1}}$) and 120 K ($T_{\text{N2}}$). We observed that the AHE persists between $T_{\text{N2}}$ - $T_{\text{N1}}$ and vanishes below $T_{\text{N2}}$. Further, we performed single-crystal neutron diffraction experiments (using spherical neutron polarimetry and unpolarized neutron diffraction) to determine the magnetic structures of (Mn$_{0.78}$Fe$_{0.22}$)$_3$Ge at different temperatures. Our neutron diffraction results show that the sample possesses a collinear antiferromagnetic structure below $T_{\text{N2}}$. However, the magnetic structure of the sample remains noncollinear antiferromagnetic, the same as Mn$_3$Ge, between $T_{\text{N1}}$ to $T_{\text{N2}}$. The presence of AHE, and noncollinear magnetic structure in (Mn$_{0.78}$Fe$_{0.22}$)$_3$Ge, between $T_{\text{N1}}$ and $T_{\text{N2}}$, suggest the existence of Weyl points in this temperature regime. Below $T_{\text{N2}}$, AHE is absent, and the magnetic structure also changes to a collinear antiferromagnetic structure. These observations signify a strong link between the magnetic structure of the sample and AHE.

Crystal Structures of a Series of Hydroxamic Acids

The structure of four hydroxamic acids (HA) that show antifungal activities in complexes with several metals is revealed by single crystal diffraction. The structures of HA with C2, C6, C10, and C12 hydrocarbon chains are reported. The smallest member of the series, N-hydroxyacetamide (HA2), crystallizes in the centrosymmetric space group P21/c while those with longer chain lengths N-hydroxyhexanamide (HA6), N-hydroxydecanamide (HA10), and N-hydroxydodecanamide (HA12) crystallize in the space group P21, and display remarkable packing.