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19 protocols using smart apex

1

Comprehensive Spectroscopic Analysis of Novel Compounds

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IR absorption spectra were recorded in the range of 4000–230 cm−1 as KBr pellets on a BRUKER Tensor 27 spectrophotometer. 1H and 13C NMR spectra were recorded in dimethyl sulfoxide (DMSO-d6) on a Bruker Fourier 300 MHz and Varian Unity Inova 500 MHz spectrometer using TMS as internal reference. The EPR spectra were recorded in DMF at liquid nitrogen temperature (77 K) on an Electron Paramagnetic Resonance Spectrometer JEOL, JES-TE300, ITC Cryogenic System, Oxford. Magnetic moments were determined using a Johnson-Matthey magnetic susceptibility balance type msb model mk II 13094-3002, with the Gouy method at room temperature. Mass spectra were recorded in a JEOL, SX 102 A spectrometer on Bruker Microflex equipped with MALDI-Flight time. Single-crystal X-ray diffractions (SCXRD) were obtained in a Bruker diffractometer, model Smart Apex, equipped with Mo radiation (λ = 0.71073Å), CCD two-dimensional detector and low-temperature device. Data collection and data reduction were performed by APEX and SAINT-Plus programs [31 ]. These structures were solved by direct methods using SHELX-2013 software and refined by Full-matrix least-squares procedure on F2 using SHELX-2008 program [32 (link)].
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2

Single Crystal X-Ray Diffraction Protocol

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Single crystals with suitable dimensions were selected under an optical microscope and mounted onto a glass fiber for data collection. Intensity data for all crystals were collected at 220 K on a Bruker SMART APEX diffracto- meter equipped with a CCD area detector and a Mo-Kα (λ = 0.71073 Å) radiation source. The data integration and reduction were processed using the SAINT software44 . An empirical absorption correction was applied to the collected reflections with SADABS45 . The structures were solved by direct methods using SHELXTL and were refined on F2 by the full-matrix least-squares method using the program SHELXL-9746 ,47 .
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3

Single Crystal X-ray Diffraction Protocol

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X-ray diffraction data were obtained at 90(2) K with a Bruker SMART APEX equipped with CCD detector with graphite-monochromated Mo Kα radiation (λ = 0.71073 Å). A single crystal was mounted with a glass capillary and flash-cooled with a cold N2 gas stream. Data were processed using the SMART software packages. Structures were solved using the intrinsic phasing methods employing the SHELXT software packages and refined on F2 (with all independent reflections).58,59 (link) The non-hydrogen atoms were refined anisotropically. All H atoms at C–H bonds were located using a riding model, and H atoms at N–H bonds were located from the electron-density difference maps and refined isotropically.
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4

X-ray Crystallography of Compounds I and II

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Example 7

The present example describes X-ray crystallography of Crystals of Compound I and Compound II.

Crystals of Compound I and Compound II were mounted on Mitegen loops with a drop of Paratone oil and placed in a cold nitrogen stream on the Bruker Smart APEX diffractometer. Full spheres of data were collected under control of the APEX2 program suite with data treatment, structure solution and refinement performed as described elsewhere. (See Bhat, et al., Eur J Inorg Chem, 3949-3958 (2015)). Relevant crystallographic data are listed in Tables 1-4.

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5

Crystal Structure Determination Procedure

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The data were collected with a Bruker AXS Smart Apex2 CCD (Bruker, Ettlingen, Germany) diffractometer, operating at 179(2) K and using graphite monochromated Mo-Kα radiation (λ = 0.71073 Å). Cell refinement, indexing, and scaling of the datasets were performed, using the program Bruker Smart Apex and Saint packages [55 ]. The structure was solved by direct methods and refined by full-matrix least-squares on F2 with anisotropic displacement parameters for all non-hydrogen atoms, using the program SHELXL [56 (link)]. The H atoms were included as riding contributions with fixed isotropic displacement parameters in idealized positions. All the calculations were carried out by using the WinGX System, V2013.3 [57 (link)]. Crystal structure determination and refinement data are given in Table 5. CCDC-2014301 contains the supplementary crystallographic data for this paper (Supplementary Materials). 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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6

Synthesis and Structural Analysis of Crystalline Compounds

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Single crystals of D were obtained by the slow recrystallization from the DCM/heptane solution; crystals of D1 and FHPMOCl were obtained by the slow recrystallization from their DCM/octane solutions, and crystals of D2 and FHPMO2 were obtained by the slow evaporation of their acetonitrile/water solutions. Single crystal X-ray analyses were performed on a SMART APEX equipped with CCD detector (Bruker) using MoKα (graphite, monochromated, λ = 0.71073 Å) radiation or CuKα (graphite, monochromated, λ = 1.54178 Å) radiation. The structures were solved by the direct method of SHELXS-97/2014/2018 and refined using the SHELXL-97/2014 or Olex2 1.2 program49 ,67 (link),68 . The positional parameters and thermal parameters of non-hydrogen atoms were refined anisotropically on F2 by the full-matrix least-squares method. Hydrogen atoms were placed at calculated positions and refined riding on their corresponding carbon atoms. Detailed crystallographic data are provided in Supplementary Tables 2 and 3.
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7

Comprehensive Spectroscopic Analysis of Complexes

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1H NMR spectroscopy
was performed on a JEOL-400 MHz spectrometer.
Infrared spectra were recorded in the solid-state (KBr pellets) using
a PerkinElmer FT-IR spectrometer in the 400–4000 cm–1 range. Bruker SMART APEX performed elemental analysis (C, H, N)
and X-ray crystallography. UV–visible spectrophotometer (Shimadzu
UV-1800) was used to analyze the electronic spectrum of complexes.
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8

X-ray Structural Analysis of Calix[4]arene Ionophore

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Appropriate crystal was selected for ionophore I, dipped in paratone oil, and mounted on cryo loop. Crystal data were collected at 100 K using graphite monochromatic MoKα (λ = 0.71073 Å) radiation on a Bruker SMART APEX diffractometer equipped CCD area detector. The SAINT software37 was used for data integration and reduction. Empirical absorption correction was applied to the collected reflections with SADABS.38 SHELXTL39 was used to solve the structures by direct methods using and refined on F2 by the full-matrix least-squares technique using the SHELXL-97 (ref. 40 ) package. Non-hydrogen atoms were refined anisotropically till convergence is reached. The MERCURY 3.8 (ref. 41 ) is used to generate graphics. The X-ray structure of ionophore I is shown in Fig. S17, wherein chloroform and water molecules have been omitted for clarity. The phenolic OH of the alternate phenyl rings of the calix moiety are substituted by amide-linked chains. The presence of hydrogen bonding between amide NHs and phenolic oxygen atoms is also observed. Crystallographic parameters for the ionophore I are given in Table S1.
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9

Single Crystal X-Ray Diffraction Protocol

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A crystal of suitable size was selected and mounted on the tip of a glass fiber and cemented using epoxy resin. Intensity data for the crystal was collected using Mo-Kα (l=0.71073 Å) radiation on a Bruker SMART APEX diffractometer equipped with CCD area detector. The hydrogen atom H1N, which is bound to the nitrogen atom N1, was located in the difference Fourier synthesis, and was refined semifreely with the help of a distance restraint, while constraining its U-value to 1.2 times the U(eq) value of N1. All other hydrogen atoms were placed in calculated positions and refined by using a riding model.
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10

Single-crystal X-ray Diffraction Analysis

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Crystals suitable for single-crystal X-ray diffraction were selected, coated in perfluoropolyether oil, and mounted on MiTeGen sample holders. Diffraction data were collected on a Bruker Smart-Apex (compounds 5, 6, 7) or a Bruker X8 Apex II (compounds 1, 2, 4) 4-circle diffractometer with a CCD area detector using graphite-monochromated Mo-Kα radiation. The crystals were cooled using a home-made nitrogen gas jet or Bruker Kryoflex low-temperature device. Data were collected at 168 K (5, 6, 7) or 100 K (1, 2, 4). The images were processed and corrected for Lorentz-polarization effects and absorption as implemented in the Bruker software packages. The structures were solved using the intrinsic phasing method (SHELXT)30 and Fourier expansion technique. All non-hydrogen atoms were refined in anisotropic approximation, with hydrogen atoms ‘riding’ in idealized positions, by full-matrix least squares against F2 of all data, using SHELXL software.30 Diamond31 software was used for graphical representation. Crystal data and experimental details are listed in Table S9 in the ESI; full structural information has been deposited with Cambridge Crystallographic Data Centre. CCDC-2056492 (1), 2056493 (2), 2056494 (4), 2056495 (5), 2056496 (6), and 2056497 (7).
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