Supernova diffractometer

Manufactured by Rigaku

Sourced in Japan

The SuperNova diffractometer is a comprehensive X-ray diffraction system designed for single-crystal analysis. It features a high-intensity micro-focus X-ray source and a fast, low-noise detector to provide efficient and reliable data collection. The SuperNova is capable of performing a range of diffraction experiments on a variety of sample types.

Automatically generated - may contain errors

Lab products found in correlation

Crysalis pro, by Rigaku (4 mentions) Cryojet, by Oxford Instruments (3 mentions) Diffraction xcalibur ccd diffractometer, by Rigaku (1 mentions) Smart 1000, by Bruker (1 mentions) Cryostream 700, by Oxford Cryosystems (1 mentions) Dip 3600, by Jasco (1 mentions) Lh 20, by Merck Group (1 mentions) Avance 600, by Bruker (1 mentions) 400 spectrometer, by JEOL (1 mentions) Uv 2600 uv vis spectrophotometer, by Shimadzu (1 mentions) Exactive mass spectrometer, by Thermo Fisher Scientific (1 mentions) Spectrum two spectrometer, by PerkinElmer (1 mentions) D max 3c x ray diffractometer, by Rigaku (1 mentions)

Close spelling variants of this product

SuperNova DualSource diffractometer Diffraction SuperNova area-detector diffractometer SuperNova X-Ray single crystal diffractometer Diffraction SuperNova CCD diffractometer Oxford Diffraction SuperNova diffractometer SuperNova

18 protocols using supernova diffractometer

Single-Crystal X-ray Diffraction Protocols

Check if the same lab product or an alternative is used in the 5 most similar protocols

Single-crystal diffraction data for 1 were collected in an Oxford Diffraction Xcalibur CCD diffractometer using graphite-monochromatic Mo-Kα radiation (λ = 0.71073 Å) at room temperature. Single-crystal diffraction data for 2 and 3 were collected in an Oxford-Diffraction SuperNova diffractometer equipped with a CCD area detector and a graphite monochromator utilising Mo-Kα (for 2) and Cu-Kα radiation (for 3). The structures were solved using SHELXT and [90 (link)] embedded in the OSCAIL software [91 (link)]. The non-H atoms were treated anisotropically, whereas the hydrogen atoms were placed in calculated, ideal positions and refined as riding on their respective carbon atoms. Molecular graphics were produced with DIAMOND [92 ]. We note that crystal twining occurs in 2, which affects the quality of the structure. We carried out many experiments in order to grow single crystals of better quality; however, this has not been achieved. We collected three sets of data using two different diffractometers and used the best set to solve the structure.
Unit cell data and structure refinement details are listed in Table 1. The crystal structures have been deposited with the Cambridge Crystallographic Data Centre (CCDC 2180525-2180527), and they can be accessed, free of charge, by filling out the application form at https://www.ccdc.cam.ac.uk/structures/.

Dimakopoulou F., Efthymiou C.G., O’Malley C., Kourtellaris A., Moushi E., Tasiopooulos A., Perlepes S.P., McArdle P., Costa-Villén E., Mayans J, & Papatriantafyllopoulou C. (2022). Novel Co5 and Ni4 Metal Complexes and Ferromagnets by the Combination of 2-Pyridyl Oximes with Polycarboxylic Ligands. Molecules, 27(15), 4701.

+ Open protocol

+ Expand

Single Crystal Structure Determination

Check if the same lab product or an alternative is used in the 5 most similar protocols

Single crystals of complexes 3, 4c, 5a, 6c, 7, 8b, and 9 (CCDC reference numbers 1589484–1589490†) suitable for X-ray diffraction were obtained by crystallization from n-hexane/CH₂Cl₂ (1 : 1). Data collection was performed on an Oxford Diffraction SuperNova diffractometer, processed with CrysalisPro, and processed with Olex2, using ShelXT as the solution program and refined with SheLX-2014/7, or on a Bruker SMART 1000, using graphite-monochromated Mo Kα radiation (ω–2θ scans, λ = 0.71073 Å). The crystal data and summary of X-ray data collection are presented in Tables S1 and S2 in the ESI.†

Chu X., Zhang S., Wang Z., Li T, & Zhu B. (2018). Aromatic alkyne insertion into six-membered cyclometalated pyridine complexes of iridium: different insertion modes and structurally novel products. RSC Advances, 8(13), 7164-7172.

+ Open protocol

+ Expand

Single Crystal X-ray Diffraction of Large Cation Structure

Check if the same lab product or an alternative is used in the 5 most similar protocols

A colorless, transparent single crystal was used in the experiment. Single crystal X-ray diffraction data were collected on an Oxford Diffraction Supernova diffractometer equipped with an Atlas CCD detector and MoKα-radiation at Aarhus University. The crystal was cooled to a temperature of 100(1) K using an Oxford Cryosystems Cryostream 700. The maximum achievable resolution was limited (sinθ/λ < 0.93 Å -1 ) due to the thermal motion of the large cations in the crystal structure. Within that resolution range, a complete data set with an average redundancy of 8.6 was collected. The data was integrated using CrysalisPro (version 39.46) and frame scale factors as well as absorption correction were applied using SCALEPACK. The integrated intensities were merged in the Laue group 2/m using SORTAV. [32] [33] A correction for low energy contamination is applied to all (3h3k3l) reflections, which led to a significant improvement of the fit. [34] [35] The structure was solved by direct methods encoded in SHELXT 36 and an independent atom model (IAM) refinement was performed with SHELXL 37 in Olex2 38 to obtain the molecular structure. Relevant crystallographic information is listed in Table 1, and an ORTEP drawing shown in Figure 1.

Gao C., Macetti G, & Overgaard J. (2019). Experimental X-ray Electron Density Study of Atomic Charges, Oxidation States, and Inverted Ligand Field in Cu(CF₃)₄. Inorganic chemistry, 58(3).

+ Open protocol

+ Expand

Single Crystal X-Ray Diffraction Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

Suitable single crystals were coated in inert oil, attached on a fine nylon loop, and mounted on the goniometer of a SuperNova diffractometer (Rigaku, Tokyo, Japan) which was equipped with dual X-ray micro-sources (Mo and Cu), an Eos CCD detector, and a tube operating at 50 kV and 0.8 mA.
Experimental diffraction intensities were collected and corrected for Lorentz, polarization, and absorption effects in the CrysAlis PRO package [15 ]. The crystal structures of GW-1 and GW-4 were solved with the SHELXS solution program [16 (link)] by Direct Methods, while GW-2 and GW-3 were solved with SHELXT [17 (link)] using Intrinsic Phasing. They were refined further via the SHELXL [18 ] refinement package using Least Squares minimization, all being implemented in the Olex2 package [19 (link)].
H atoms on carbons were located, refined, and treated by standard riding procedure, considering the isotropic displacement parameter U_iso(H) = 1.2U_eq(C) for ternary CH groups [C-H = 0.93 Å] and secondary CH₂ groups [C-H = 0.97 Å], and 1.5U_eq(C) considered for all methyl CH₃ groups [C-H = 0.96 Å].

Turza A., Pascuta P., Muresan-Pop M., Mare L., Borodi G, & Popescu V. (2024). Five Novel Polymorphs of Cardarine/GW501516 and Their Characterization by X-ray Diffraction, Computational Methods, Thermal Analysis and a Pharmaceutical Perspective. Pharmaceutics, 16(5), 623.

+ Open protocol

+ Expand

Crystal Structure Determination Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

For all structures, reflection intensities were measured at 110(2) K using a SuperNova diffractometer (equipped with Atlas detector) Cu Kα radiation (λ = 1.54178 Å) under the program CrysAlisPro (Version 1.171.39.29c, Rigaku OD, 2017). The same program was used to refine the cell dimensions and for data reduction. The structures were solved with the program SHELXS-2014/7 and refined on F^{2 (link)} with SHELXL-2014/7.^{45 (link)} The temperature of the data collection was controlled using the system Cryojet (manufactured by Oxford Instruments). An analytical numeric absorption correction method was used involving a multifaceted crystal model based on expressions derived elsewhere.⁴⁶

Alvarado J.G., Cummins D.C., Diaconescu A., Siegler M.A, & Goldberg D.P. (2021). The Selective Monobromination of a Highly Sterically Encumbered Corrole: Structural and Spectroscopic Properties of Fe(Cl)(2-Bromo-5,10,15-tris(triphenyl)phenyl corrole). Journal of porphyrins and phthalocyanines, 25(10-12), 1176-1185.

+ Open protocol

+ Expand

Recrystallization and X-ray Analysis of FBTA

Check if the same lab product or an alternative is used in the 5 most similar protocols

For crystal structure determination and NMR analysis of the solid, FBTA was recrystallized as a methanol solvate. Commercially sourced FBTA (Fluorochem Ltd) was initially purified by removal of impurities which crystallised first upon cooling of the minimum volume of hot ethanol required to dissolve the sample from hot ethanol followed by precipitation of the FBTA by addition of an equal volume of water. Crystals suitable for X-ray diffraction were then grown by repeatedly crystallising from hot methanol, removing the supernatant liquid and repeating the process 4 times. A suitable crystal was selected and mounted on a Rigaku SuperNova diffractometer with and Atlas detector. The crystal was kept at 100.01(10) K during data collection. The crystallographic data set was solved and refined using the SHELX suite of software.10

Hughes E., Griffin J.M., Coogan M.P, & Middleton D.A. (2018). Average orientation of a fluoroaromatic molecule in lipid bilayers from DFT-informed NMR measurements of 1H–19F dipolar couplings †Electronic supplementary information (ESI) available. CCDC 1584785. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c8cp01064a. Physical Chemistry Chemical Physics, 20(27), 18207-18215.

+ Open protocol

+ Expand

Characterization of Novel Organic Compounds

Check if the same lab product or an alternative is used in the 5 most similar protocols

The optical rotations were determined with a Jasco DIP-3600 digital polarimeter (Jasco, Tokyo, Japan) using a 10 mm cell. The high-resolution mass spectra were recorded using a Micromass-Q-TOF-MS (Waters, Milford, MA, USA). For the DMSO-d₆, MeOD, CDCl₃, and Acetone-d₆, the ¹H NMR and ¹³C NMR spectra were recorded using Bruker DRX (¹H NMR, 500 MHz and ¹³C NMR, 125 MHz) and Bruker Avance 600 (¹H NMR, 600 MHz, and ¹³C NMR, 150 MHz) spectrometers (Bruker, Rheinstetten, Germany), respectively. X-ray crystallography data were collected with a Rigaku Supernova diffractometer using Cu Kα (λ = 1.54184 Å) radiation. Column chromatography (CC) readings were carried out using silica gel (63–200 μm, Merck, Darmstadt, Germany), and Sephadex LH-20. A TLC analysis was performed using percolated aluminum plates backed with silica gel 60 F₂₅₄ sheets. The TLC plate was visualized under UV light (254 and 365 nm), sprayed with H₂SO₄ (10%), and then heated.

Djoumessi A.K., Nono R.N., Neumann B., Stammler H.G., Bitchagno G.T., Efange N.M., Nkenfou C.N., Ayong L., Lenta B.N., Sewald N., Nkeng-Efouet-Alango P, & Chouna J.R. (2023). Constituents of the Stem Bark of Trichilia monadelpha (Thonn.) J. J. De Wilde (Meliaceae) and Their Antibacterial and Antiplasmodial Activities. Metabolites, 13(2), 298.

+ Open protocol

+ Expand

Cocrystal Formation of cis-A Derivatives

Check if the same lab product or an alternative is used in the 5 most similar protocols

Cocrystals cis-A‧½(1,2-DCE), cis-A‧½(1,2-DBE), and cis-A‧½C₆H₁₄ were obtained via the slow evaporation of the corresponding solutions of cis-A in 1,2-dichloroethane, 1,2-dibromoethane, and a n-hexane/CHCl₃ (1:1, v/v) mixture in air at RT. Single crystals of trans-A were grown via the slow evaporation of its 1,2-dichloroethane solution in air at RT. The XRD data for cis-A‧½(1,2-DBE), cis-A‧½C₆H₁₄, and trans-A were collected using a Rigaku SuperNova diffractometer and CuKα (λ = 0.154184 nm) radiation, whereas cis-A‧½(1,2-DCE) was studied using a Xcalibur Eos diffractometer and MoKα (λ = 0.71073 nm) radiation. The structure was solved with the ShelXT [59 (link)] structure solution program using Intrinsic Phasing and refined with the ShelXL [60 (link)] refinement program incorporated into the OLEX2 program package [61 (link)] by means of Least Squares minimization. Supplementary crystallographic data for this paper have been deposited at Cambridge Crystallographic Data Centre and can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif (accessed on 8 January 2024) (CCDC numbers 2314867 (trans-A), 2314868 (cis-A‧½(1,2-DCE)), 2314869 (cis-A‧½(1,2-DBE)), 2314870 (cis-A‧½C₆H₁₄).

Baykov S.V., Semenov A.V., Presnukhina S.I., Tarasenko M.V., Shetnev A.A., Frontera A., Boyarskiy V.P, & Kukushkin V.Y. (2024). Hybrid 2D Supramolecular Organic Frameworks (SOFs) Assembled by the Cooperative Action of Hydrogen and Halogen Bonding and π⋯π Stacking Interactions. International Journal of Molecular Sciences, 25(4), 2062.

+ Open protocol

+ Expand

X-Ray Crystallography Analysis of Glycine Salicylaldehyde Complexes

Check if the same lab product or an alternative is used in the 5 most similar protocols

The data for GlySalLi-a and GlySalNa-h were collected using SuperNova diffractometer (Rigaku Oxford Diffraction, Oxford, UK) equipped with Atlas CCD detector and using Cu Kα radiation at 100 K. Unit cell parameters were determined and refined using CrysAlis^Pro program [18 ]. Additionally, the integration of the collected data was performed with the same program. Both structures were solved using direct methods with SHELXS-2013 program and then refined using SHELXL-2019/2 program [19 (link)]. Nonhydrogen atoms were refined with anisotropic displacement parameters. The hydrogen atoms were fixed at calculated distances and allowed to ride on the parent atoms using suitable constraints in SHELXL [19 (link)].
The crystal structures CIF files for GlySalLi-a and GlySalNa-h have been deposited in a Crystallography Open Database (crystallography.net) under No. 3000421 and 3000422, respectively. The crystal structures have been also deposited at the Cambridge Crystallographic Data Centre. CCDC-2220609 and 2220610 contain the supplementary crystallographic data for this paper. The data can be obtained free of charge via Cambridge Crystallographic Data Centre: www.ccdc.cam.ac.uk/structures (accessed 26 November 2022).

Tomczyk M.M., Przypis Ł., Shiraki T., Kusz J., Książek M., Janas D, & Kuźnik N. (2022). Surprising Solid-State ESIPT Emission from Apparently Ordinary Salicyliden Glycinates Schiff Bases. International Journal of Molecular Sciences, 23(23), 14955.

+ Open protocol

+ Expand

X-ray Analysis of Apremilast Forms

Check if the same lab product or an alternative is used in the 5 most similar protocols

X-ray analyses of the apremilast multicomponent forms were performed either at 95 K using a SuperNova diffractometer with a micro-focus sealed tube, mirror-collimated Cu Kα radiation (λ = 1.54184 Å) and CCD detector Atlas S2; or at 120 K on an Xcalibur, Gemini ultra diffractometer using Cu Kα radiation (λ = 1.54178 Å) from a fine-focus sealed X-ray tube with a graphite monochromator and CCD detector Atlas S2.
The data reduction and absorption correction were carried out with CrysAlisPro (Rigaku Oxford Diffraction, 2019 ▸ ). The structure was solved by charge flipping methods using the Superflip software (Palatinus & Chapuis, 2007 ▸ ) and refined by full matrix least squares on the F-squared value using the Crystals software (Betteridge et al., 2003 ▸ ). The MCE software (Rohlíček & Hušák, 2007 ▸ ) was used for visualization of residual electron density maps. According to common practice, hydrogen atoms attached to carbon atoms were assigned geometrically with U_iso (H) in the range 1.2–1.5 U_eq of the parent atom (C).

Jirát J., Babor M., Ridvan L., Skořepová E., Dušek M, & Šoóš M. (2022). Structure–property relations of a unique and systematic dataset of 19 isostructural multicomponent apremilast forms. IUCrJ, 9(Pt 4), 508-515.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!