Oxford diffraction supernova

Manufactured by Rigaku

The Oxford Diffraction SuperNova is a high-performance X-ray diffraction system designed for single-crystal structure determination. It features a microfocus X-ray source and a high-performance CCD or CMOS detector, providing efficient data collection and high-quality results.

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Lab products found in correlation

Hypix arc 100, by Rigaku (2 mentions) Cryostream 700 low temperature device, by Oxford Cryosystems (1 mentions) X pert pro, by Malvern Panalytical (1 mentions) Nitrogen gas flow device, by Oxford Cryosystems (1 mentions) Atlass2 ccd, by Rigaku (1 mentions) Oxford diffraction xcalibur, by Rigaku (1 mentions) Crysalis pro, by Rigaku (1 mentions)

Close spelling variants of this product

Oxford Diffraction Supernova Dual Source Oxford Diffraction SuperNova diffractometer Diffraction SuperNova Oxford Diffraction SuperNova

13 protocols using oxford diffraction supernova

Structural Analysis of Crystalline Samples

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Diffraction data for samples 1-4 were collected using Bruker SMART APEXII (1) or Rigaku Oxford Diffraction SuperNova (2-4) diffractometers with MoK α (1, 2 & 4) and CuK α (3) radiation, and are given in Table S1 in the ESI. ‡ An Oxford Cryosystems Cryostream 700+ low temperature device was used to maintain a crystal temperature of 120.0 K for all experiments. The structures were solved using ShelXT and refined with ShelXL interfaced through Olex2. 33, 34 All non-hydrogen atoms were refined using anisotropic displacement parameters. H atoms were placed in calculated positions geometrically and refined using the riding model. Unit cell parameters for 2 were also obtained at T = 3.4 Ksee the ESI ‡ for details. CCDC: 1819131-1819134. ‡

Fraser H.W.L., Nichol G.S., Uhrín D., Nielsen U.G., Evangelisti M., Schnack J, & Brechin E.K. (2018). Order in disorder: solution and solid-state studies of [MM] wheels (M^III = Cr, Al; M^II = Ni, Zn). Dalton transactions (Cambridge, England : 2003), 47(34).

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Crystallization and Structure Determination

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3 and its chloro-substituted derivative, 4, were crystallized using MeOH under room temperature for about 7 days at a controlled evaporation rate. Yellowish plates were observed at the bottom of the glass tube. Powder diffractograms were obtained on single-crystal powders at room temperature using Cu-Kα radiation on the PANAlytical X’Pert PRO diffractometer with a 1D X’celerator detector or the PANAlytical Aeris benchtop powder X-ray diffractometer. The single-crystal X-ray structures of 3 and 4 were determined at 100 K on the Rigaku Oxford Diffraction Supernova operating with a microfocus Cu-Kα source and the Atlas detector. Their absolute stereochemistries were confirmed using the refined Flack parameter value.

She W., Ye W., Cheng A., Liu X., Tang J., Lan Y., Chen F, & Qian P.Y. (2021). Discovery, Bioactivity Evaluation, Biosynthetic Gene Cluster Identification, and Heterologous Expression of Novel Albofungin Derivatives. Frontiers in Microbiology, 12, 635268.

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Crystallization and Structure Determination of THB4

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THB4 crystals were grown at room temperature using the hanging drop vapor diffusion method, with 0.5 mL of solution in the reservoir. 3 μL of 33 mg/mL THB4 in the ferric state was mixed with 1 μL of reservoir solution, consisting of 0.2 M ammonium sulfate, 0.1 M Bis-tris pH 5.5, and 20% PEG 3350. Red crystals, measuring ~0.35 × 0.35 × 0.2 mm³, appeared within 12 h. Single crystals were looped and coated in Paratone oil prior to flash-cooling in a chilled nitrogen stream. Data were collected at 110 K on a Rigaku Oxford Diffraction SuperNova X-ray diffractometer using CuKα radiation. CrysAlisPro was used for data indexing, integration and scaling.
Phenix.autosol, phenix.refine, [36 (link)] and coot [37 (link)] were used for phasing, refinement, and model building, respectively. Initial phasing was solved by SAD using the anomalous signal of the heme iron. NCS restraints were used for the two polypeptide chains in the asymmetric unit during the initial rounds of refinement and released after three rounds of refinement. TLS was incorporated into the final two rounds of refinement, using two TLS groups (the A chain and the B chain). Crystal contact interfaces were analyzed using the standalone PISA software from the CCP4 suite [38 (link)]. MOLEonline v.2.5 was used for cavity calculation [39 (link)].

Johnson E.A., Russo M.M., Nye D.B., Jamie L. S.c.h.l.e.s.s.m.a.n, & Lecomte J.T. (2018). Lysine as a heme iron ligand: A property common to three truncated hemoglobins from Chlamydomonas reinhardtii. Biochimica et biophysica acta. General subjects, 1862(12), 2660-2673.

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Crystallization and Diffraction of C6F6:C4H5N

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After mounting on the SCXRD instrument, the capillary containing the C₆F₆:C₄H₅N was cooled rapidly in situ to 230 K resulting in the formation of numerous white crystals. The temperature was then raised until the crystals fully melted, before subsequent cooling back to 230 K. The temperature was then increased to 260 K, (just below the melting point at 266 K) in order to encourage annealing of single crystals present. The sample was held at 260 K for 2 h before cooling to 254 K for data acquisition. Initially, a full sphere of data was collected to ca 0.84 Å resolution using an Agilent Oxford Diffraction Supernova diffractometer upgraded with a Rigaku HyPix Arc-100 detector (Fig. S1 of the supporting information) in about 2.5 h. Subsequently, the sample was cooled to 150 K and a further full sphere of data was collected. Further details are given in the supporting information.

Bear J.C., Terzoudis N, & Cockcroft J.K. (2023). Single-crystal quality data from polycrystalline samples: finding the needle in the haystack. IUCrJ, 10(Pt 6), 720-728.

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Crystallization and Diffraction of C6F6:C4H5N

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Bear J.C., Terzoudis N, & Cockcroft J.K. (2023). Single-crystal quality data from polycrystalline samples: finding the needle in the haystack. IUCrJ, 10(Pt 6), 720-728.

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Single-Crystal X-Ray Diffraction of Lactones

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The single crystal X-ray diffraction for lactones was carried out on a Rigaku Oxford Diffraction SuperNova diffractometer equipped with a micro focus Cu X-ray source. The crystals were maintained at 100 K by using an Oxford Cryosystems nitrogen gas-flow device. Data collection strategies were optimized using CrysAlisPro software package [41 ]. The crystal structures of lactones were solved using the charge-flipping method implemented in SUPERFLIP and refined with the JANA package [42 ]. The crystal data, data collection, and refinement parameters for lactones are given in Table 6. Crystallographic data, as CIF files, have been deposited with the Cambridge Crystallographic Data Centre. The solid-state structure of lactone was determined by single-crystal X-ray diffraction. The lactones 5a (Figure 8), 7a (Figure 9), and 13a (Figure 10) crystallized in the centrosymmetric space group

P 2_{1 / c}

while lactones 12b (Figure 11) and 12c (Figure 12) in the orthorhombic space group Pbca. Only one molecule is present in the asymmetric unit. Experimental details of the crystallographic analysis are given in Table 5.

Kamizela A., Gawdzik B., Urbaniak M., Lechowicz Ł., Białońska A., Kutniewska S.E., Gonciarz W, & Chmiela M. (2019). New γ-Halo-δ-lactones and δ-Hydroxy-γ-lactones with Strong Cytotoxic Activity. Molecules, 24(10), 1875.

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Crystallization and Structural Characterization of Compound 1

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After many attempts with various solvent systems,
we successfully obtained the colorless orthorhombic crystals of compound 1 by culturing the compound in a mixture of methanol/water
(10:1) at room temperature for several days. The intensity data were
collected on a diffractometer Rigaku Oxford Diffraction SuperNova,
Dual, Cu at zero, equipped with an AtlasS2 CCD using Cu Kα radiation.
The crystal of 1 was kept at 150.00 (10) K during data
collection. The crystallographic data of 1 have been
deposited in the Cambridge Crystallographic Data Center database (CCDC
2172881).

Wu X.J., Cao D., Chen F.L., Shen R.S., Gao J., Bai L.P., Zhang W., Jiang Z.H, & Zhu G.Y. (2022). Chlorfortunones A and B, Two Sesquiterpenoid Dimers, Possessing Dispiro[4,2,5,2]pentadecane-6,10,14-tren Moiety from Chloranthus fortunei. ACS Omega, 7(39), 35063-35068.

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Single-crystal X-ray Structure of 1-(Sa)

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Single-crystal X-ray data for 1-(S_a) (CCDC number: ; 1818253†) were collected at 173 K with Cu Kα radiation (λ = 1.54178 Å) on a Rigaku Oxford Diffraction SuperNova diffractometer. The selected crystal was mounted onto a nylon loop in polyisobutene and immersed in a low-temperature (173 K) stream of dry nitrogen gas during data collection. The structure was solved by direct methods, and non-hydrogen atoms were located from difference Fourier maps. Non-hydrogen atoms, except three carbon atoms of the diethyl ether solvent molecule, were subjected to anisotropic refinement by full-matrix least-squares on F² by using the SHELXTL program19 and Olex² program.20 All figures were drawn by using the X-seed program.21 Crystal data for 1-(S_a): C₁₃₂H₁₁₂Au₆B₂F₈N₂OP₆, M = 3283.56, orthorhombic, space group P2₁2₁2₁, a = 13.7644(1) Å, b = 24.8987(2) Å, c = 35.6022(2) Å, V = 12 201.43(15) Å³, Z = 4, T = 173 K, D_c = 1.788 g cm^–3. The structure, refined on F², converged for 25 357 unique reflections (R_int = 0.0862) and 24 837 observed reflections with I > 2σ(I) to give R₁ = 0.0605 and wR₂ = 0.1554 and a goodness-of-fit = 1.062. A tetrafluoroborate anion is disordered at two positions with the occupancy ratio of 0.65 : 0.35.

Guo P., Yang B., Zhang L, & Zhao L. (2018). Temperature dependent chiroptical response of sigmoidal gold clusters: probing the stability of chiral metal clusters †Electronic supplementary information (ESI) available: Supporting figures, high-resolution ESI-MS, NMR, crystal refinement details and computational results. CCDC 1818253. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c8sc00344k. Chemical Science, 9(25), 5614-5622.

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Structural Determination via Single-Crystal X-ray Diffraction

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Data were obtained on Rigaku Oxford Diffraction SuperNova (1, 2, 4) and Rigaku Oxford Diffraction XCalibur (3) X-ray diffractometers using Mo-K α radiation. Structures were solved with olex2.solve (2, 3) 30 or ShelXS (1, 4) 31 and refined by full-matrix least-squares on F-squared using ShelXL, interfaced through Olex2. 32 All non-hydrogen atoms were refined anisotropically.
Hydrogen atom parameters were constrained. For full details see Table S1. † CCDC 1557650-1557653. †

Pedersen A.H., Julve M., Martínez-Lillo J., Cano J, & Brechin E.K. (2017). Magneto-structural correlations in dirhenium(iv) complexes possessing magnetic pathways with even or odd numbers of atoms. Dalton transactions (Cambridge, England : 2003), 46(35).

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Temperature and Pressure X-ray Diffraction

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Temperature-dependent X-ray diffraction measurements in the range 240–400 K were performed on a Rigaku Oxford Diffraction SuperNova single-crystal diffractometer with a Mo Kα X-ray source. The temperatures were set using an Oxford Instruments nitrogen flow gas jet cryostat/heater. Diffraction data were integrated with the CrysAlisPRO (v171.40.53; Rigaku Oxford Diffraction, 2019 ▸ ) program and the structure refinements were carried out with Jana2006 (Petříček et al., 2014 ▸ ).
Exploratory high-pressure X-ray diffraction measurements to 7.3 GPa at room temperature were performed on a Stoe IPDS-II single-crystal diffractometer with a Mo Kα X-ray source using a Boehler Almax diamond anvil cell loaded with a CrAs crystal, a ruby chip and a 4:1 methanol–ethanol mixture as a pressure-transmitting medium. The diffraction data were integrated with the X-Area (v1.62; Stoe & Cie, 2011 ▸ ) software.

Eich A., Grzechnik A., Paulmann C., Müller T., Su Y., Wolf T, & Friese K. (2021). Comparison of the temperature- and pressure-dependent behavior of the crystal structure of CrAs. Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials, 77(Pt 4), 594-604.

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