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Diffraction xcalibur ccd diffractometer

Manufactured by Rigaku
Sourced in United Kingdom

The Diffraction Xcalibur CCD diffractometer is a laboratory instrument designed for single-crystal X-ray diffraction analysis. It features a CCD (Charge-Coupled Device) detector for data collection and analysis. The core function of this equipment is to determine the crystal structure of materials by measuring the diffraction pattern of X-rays interacting with the sample.

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4 protocols using diffraction xcalibur ccd diffractometer

1

Single-crystal X-ray Structural Analysis of Complexes

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Single-crystal data for the complexes were collected on an Oxford Diffraction Xcalibur CCD diffractometer (MoKα radiation, λ = 0.71073Å). The program CrysAlis [33 ] was used for collecting frames of data, cell refinement and data reduction. A multi-scan absorption correction was applied. Crystal data, data collection and structure refinement details are summarized in Table 1. The structures were solved by direct methods using SHELXS-2018 and refined by the full-matrix least-squares on F2 using the SHELXL-2018 [34 (link)] (both programs implemented in WinGX software [35 (link)]). All the non-hydrogen atoms were refined with anisotropic displacement parameters. The H-atoms attached to carbon were positioned geometrically and refined applying the riding model [C–H = 0.93–0.99 Å and with Uiso(H) = 1.2 or 1.5 Ueq(C)]. The O-bound H atoms were located on a difference Fourier map and refined freely or with O–H distances restrained to 0.82 Å using DFIX command. The following programs were used to prepare the molecular graphics: ORTEP3 [35 (link)] and Mercury [36 (link)]. The geometrical calculations were performed using PLATON program [37 (link)].
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2

Single-Crystal X-Ray Structural Analysis

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The single-crystal X-ray analysis was performed on an Oxford Diffraction Xcalibur CCD diffractometer (Abingdon, Oxfordshire, UK) using the graphite-monochromated MoKα radiation (λ = 0.71073 Å). The CrysAlis software56 was applied for data collection, integration and data reduction. The crystal was kept at 293 K during data collection. Using WinGX57 , the structure was solved by direct method using SHELXS-2018 and refined with the SHELXL-201858 (link). The CrysAlis software was used for multi-scan absorption correction. All non-H atoms were refined with the anisotropic displacement parameters. The H-atoms attached to carbon were positioned geometrically and allowed to ride on the parent atoms with Uiso(H) = 1.2–1.5Ueq(C). The nitrogen-bound hydrogen atoms were located from the different Fourier maps and refined isotropically except H8N. The final data collection parameters and refinement are reported in Table S3 (Supplementary Information). The molecular plots were drawn with OLEX259 and Mercury60 (link). The PLATON program61 was used for geometrical calculations. The CIF file refinement can be retrieved from the Cambridge Crystallographic Data Centre (CCDC).
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3

Single-Crystal X-ray Diffraction Protocols

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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/.
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4

Single Crystal Diffraction Analysis of Compounds 1-5

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Single crystal diffraction data for 1–5 were collected in an Oxford Diffraction Xcalibur CCD diffractometer using graphite-monochromatic Mo Ka radiation (λ = 0.71073 Å) at room temperature. The structures were solved using SHELXT [94 (link)], embedded in the OSCAIL software [95 (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. The hydrogen atoms on water molecules cannot be calculated accurately and are best located in difference maps and then refined. In the case of compound 1•2H2O, it was not possible to locate the water H atoms in difference maps. Molecular graphics were produced with DIAMOND [96 ].
Unit cell data and structure refinement details are listed in Table 1. CIF files can be obtained free of charge at www.ccdc.camac.uk/retrieving.html or from the Cambridge Crystallographic Data Centre, Cambridge, UK with the REF codes 2,054,509–2,054,513 for 15.
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