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Apex 2 d8 venture area diffractometer

Manufactured by Bruker
Sourced in Germany

The APEX-II D8 Venture is an area diffractometer designed for single-crystal X-ray diffraction analysis. It features a high-performance rotating anode X-ray source and a state-of-the-art PHOTON II CMOS detector for rapid data collection. The system is optimized for a wide range of crystallographic applications, including chemical, pharmaceutical, and materials science research.

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10 protocols using apex 2 d8 venture area diffractometer

1

X-ray Structural Analysis of Compound

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The compound of 5g was obtained as single crystals by slow evaporation from ethanol solution of the pure compound at room temperature. Data were collected on a Bruker APEX‐II D8 Venture area diffractometer, equipped with graphite monochromatic Mo Kα radiation, λ=0.71073 Å at 293 (2) K. Cell refinement and data reduction were carried out by Bruker SAINT. SHELXT15 was used to solve structure. The final refinement was carried out by full‐matrix least‐squares techniques with anisotropic thermal data for non‐hydrogen atoms on. CCDC 1877313 contains the supplementary crystallographic data for this compound can be obtained free of charge from the Cambridge Crystallographic Data Centre viawww.ccdc.cam.ac.uk/data_request/cif.
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2

Characterization of Chemical Compounds

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The NMR spectra were measured on a Bruker AMX 500 spectrometer (Bruker, Billerica, MA, USA) in deuterated dimethyl sulfoxide (DMSO-d6) and reported as δ (ppm) values relative to tetramethylsilane (TMS) at 500 and 125 MHz for 1H and 13C NMR, respectively. J values were recorded in Hz. The electrospray ionization mass spectrometry (ESI-MS) spectra were recorded using a Micromass Quattro micro™ triple-quadruple tandem mass spectrometer (Waters Corp., Milford, MA, USA). The X-ray data were collected on a Bruker APEX-II D8 Venture area diffractometer using graphite monochromatic Mo Kα radiation (λ = 0.71073 Å) at 100(2) K. The uncorrected melting point (mp) values were determined using a Stuart SMP10 melting point apparatus with open glass capillaries. The reactions were followed, and the product purity was checked by thin layer chromatography (TLC) on a DC-Mikrokarten Polygram® SIL G/UV254, TLC plate (Thickness: 0.25 mm; Macherey-Nagel, Düren, Germany).
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3

X-ray Diffraction Analysis of Compound 3

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Slow evaporation of ethanol solution of pure compound 3 yielded colorless crystals. A crystal of dimensions, 0.67 × 0.27 × 0.16 mm was selected for X-ray diffraction analysis. Data were collected on a Bruker APEX-II D8 Venture area diffractometer, equipped with graphite monochromatic Mo Kα radiation at 100 °K. Cell refinement and data reduction were carried out by Bruker SAINT. SHELXS-97 [49 (link), 50 ] was used to solve structure. The final refinement was carried out by full-matrix least-squares techniques with anisotropic thermal data for non-hydrogen atoms on F2. All the hydrogen atoms were placed in calculated positions (Tables 1, 2 and 3). The asymmetric unit of the crystal structure is shown in Fig. 1 and the crystal packing is shown in Fig. 2.
The structure of 3 was confirmed by X-ray crystal structure analysis (Bruker AXS GmbH). CCDC- 1026251 contains the supplementary crystallographic data for this compound. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
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4

Slow Evaporation of Compound 3 Crystals

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Compound 3 was obtained as single crystals by slow evaporation of diethyl ether solution of the pure compound 3 in dichloromethane at room temperature for 24 h. Data were collected on a Bruker APEX-II D8 Venture area diffractometer (Bruker AXS GmbH, Karlsruhe, Germany), equipped with graphite monochromatic Mo Kα radiation at 150(2) °K. Cell refinement and data reduction were carried out by Bruker SAINT. SHELXS-97 [43 (link),44 (link),45 ] was used to solve structure. The final refinement was carried out by full-matrix least-squares techniques with anisotropic thermal data for nonhydrogen atoms on F2.
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5

Characterization of Organic Compounds

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Melting points were determined on open glass capillaries using a STUART Melting point SMP 10 apparatus and are uncorrected. NMR spectra were recorded on a Bruker AMX 500 spectrometer in DMSO-d6 and reported as δ ppm values relative to TMS at 500/700 and 125/176 MHz for 1H and 13C NMR, respectively. J values were recorded in Hz. HREI-MS spectra were measured on a JEOL MStation JMS-700 system. X-ray data were collected on a Bruker APEX-II D8 Venture area diffractometer, equipped with graphite monochromatic Mo Kα radiation, λ = 0.71073 Å at 100 (2) K. Follow-up of the reactions and checking the purity of compounds was made by TLC on DC-Mikrokarten polygram SIL G/UV254, from the Macherey–Nagel Firm, Duren Thickness: 0.25 mm.
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6

X-ray Crystal Structure Determination

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X-ray crystal data were collected on a Bruker APEX-II D8 Venture area diffractometer. Crystal data, data collection, and structure refinement details are summarized in Table S1 (Supplementary data). All H atoms were found in the difference Fourier maps.
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7

Single-crystal X-ray diffraction analysis

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SCXRD data for the harvested crystals were collected on a Bruker APEX-II D8 Venture area diffractometer (Bruker, Germany). The crystal structures were solved via direct methods and refined by a full-matrix least-squares procedure against F2 using OLEX2 (Dolomanov et al., 2009 ▸ ) and SHELXTL (Sheldrick, 2008 ▸ ) with anisotropic displacement parameters (ADPs) for non-hydrogen atoms. Hydrogen atoms bonded to nitrogen or oxygen were determined by the experimental electron density map, and their isotropic displacement parameters and positions were refined freely. All other hydrogen atoms were located in geometrically calculated positions and refined using a riding model.
Hirshfeld surfaces formed by the equal electron density point between the investigated molecule and its surrounding molecules were obtained by Crystal Explorer (version 3.1; McKinnon et al., 2004 ▸ ) based on the SCXRD data. After, various intermolecular interactions among the different crystal structures were quantitatively explored and compared.
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8

Characterization of Compound IIb

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All the solvents were purchased from Merck (Kenilworth, NJ, USA). To check the purity of compounds, thin layer chromatography (TLC), was performed on silica gel 60 F254 coated plates (Merck). For performing FTIR, Perkin Elmer (Waltham, MA, USA) FT-IR spectrophotometer was used. Melting points were measured by Gallenkamp melting point apparatus. 1H and 13C NMR were recorded in Bruker (Billerica, MA, USA) NMR 500/700 MHz and 125/176 MHz spectrophotometer. The samples were run in DMSO-d6 with tetramethyl silane (TMS) as an internal standard. Molecular weights of compounds were determined in mass spectroscopy. The elemental analysis of compounds was performed by CHN Elementar (Analysensysteme GmbH, Langenselbold, Germany). The compound (IIb) was obtained as single crystal by reported method. Data were collected on a Bruker APEX-II D8 Venture area diffractometer. SHELXT was used to solve structure [41 (link),42 ]. CCDC 1532829 contains the supplementary crystallographic data for the compound (IIb). These data can be obtained free of charge via http://www.ccdc.cam.ac.uk/conts/retrieving.html (or from the CCDC, 12 Union Road, Cambridge CB2 1EZ, UK; Fax: +44 1223 336033; E-mail: deposit@ccdc.cam.ac.uk).
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9

Characterization of Compound 8 Crystal

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Melting points were recorded on a Barnstead 9100 electrothermal melting apparatus. IR spectra (KBr) were recorded on an FT-IR Perkin-Elmer spectrometer (ν cm−1). 1H and 13C NMR spectra were recorded on Bruker 500 or 700 MHz spectrometers using DMSO-d6 as the solvent. Microanalytical data (C, H, and N) were obtained using a Perkin-Elmer 240 analyser and the proposed structures were within ±0.4% of the theoretical values. Mass spectra were recorded on a Varian TQ 320 GC/MS/MS mass spectrometer. Data of compound 8 were collected on a Bruker APEX-II D8 Venture area diffractometer (Billerica, MA), equipped with graphite monochromatic Mo Kα radiation, λ = 0.71073 Å at 296 (2) K. Cell refinement and data reduction were carried out by Bruker SAINT. SHELXT35 ,36 was used to solve the structure.
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10

Single Crystal X-ray Diffraction of Compound 5o

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Compound 5o was obtained as single crystals by slow evaporation from ethanol solution of the pure compound at room temperature. Data were collected on a Bruker APEX-II D8 Venture area diffractometer, equipped with graphite monochromatic Mo Kα radiation, λ=0.71073 Å at 293 (2) K. Cell refinement and data reduction were carried out by Bruker SAINT. SHELXT14 was used to solve the structure. The final refinement was carried out by full-matrix least-squares techniques with anisotropic thermal data for non-hydrogen atoms on F. CCDC 1875757 contains the supplementary crystallographic data for this compound and can be obtained free of charge from the Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
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