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Sadabs program

Manufactured by Bruker
Sourced in Germany

SADABS is a program developed by Bruker for absorption correction of single-crystal X-ray diffraction data. It provides an automated and reliable method for determining and applying absorption corrections to experimental data. The core function of SADABS is to improve the quality and accuracy of the collected X-ray diffraction data by accounting for the effects of absorption, which can occur when the X-ray beam interacts with the sample material.

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5 protocols using sadabs program

1

Single-Crystal X-Ray Diffraction of Compound 4

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Block crystals of compound 4 were obtained from diethyl ether-acetone solvent systems at 4 °C. Single-crystal X-ray diffraction of compound 4 (0.16 × 0.11 × 0.10 mm3) was performed on a Bruker D8 Venture diffractometer using Ga Kα radiation (λ = 1.34139 Å) at 170 K. The collected data integration and reduction were processed with SAINT software (V8.37A, 2015, Bruker AXS Inc., Karlsruhe, Germany), and multi-scan absorption corrections were performed using the SADABS program (V2016/2, 2016, Bruker AXS Inc., Karlsruhe, Germany). The structures were solved by direct methods using SHELXL (V2016/6, 2016, George M. Sheldrick) and refined on F2 by the full-matrix least-squares technique using the SHELXT-2015 program package. Crystallographic data for compound 4 in this article (Table S1) have been deposited at the Cambridge Crystallographic Data Centre (deposition numbers CCDC 2225113). Copies of these data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html (accessed on 8 December 2022) or from the Cambridge Crystallographic Data Centre (12 Union Road, Cambridge CB21EZ, UK. Fax: (+44) 1223-336-033. E-mail: deposit@ccdc.cam.ac.uk).
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2

Single-Crystal X-Ray Diffraction of Compound 1

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Block crystals of compound 1 were obtained from solvent methanol at room temperature. Single-crystal X-ray diffraction of 1 (0.18 × 0.11 × 0.05 mm3) was performed on a Bruker Apex II CCD diffractometer (Bruker AXS Inc., Karlsruhe, Germany), using Cu Kα radiation (λ = 1.54178 Å) at 170 K. The collected data integration and reduction were processed with SAINT software (V8.40A, 2016, Bruker AXS Inc., Karlsruhe, Germany), and multi-scan absorption corrections were performed by using the SADABS program (V2014/7, 2014, Bruker AXS Inc., Karlsruhe, Germany). The structures were solved by direct methods, using SHELXTL (V2018/3, 2018, George M. Sheldrick), and were refined on F2 by the full-matrix least-squares technique, using the SHELXL program package. The absolute configuration was determined on the basis of a Flack parameter of −0.06(7) (Supplementary Table S1). Crystallographic data for 1 in this article were deposited at the Cambridge Crystallographic Data Centre (deposition number CCDC 2203997). Copies of these data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html (accessed on 29 August 2022) or from the Cambridge Crystallographic Data Centre (12 Union Road, Cambridge CB21EZ, UK. Fax: (+44) 1223-336-033. E-mail: deposit@ccdc.cam.ac.uk).
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3

X-ray Crystallographic Characterization of 59b

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The X-ray crystallographic
data collection for 59b was performed on a Bruker D8-Venture
diffractometer (Photon I detector) at 169(2) K. The diffractometer
was equipped with a low-temperature device (Oxford Cryostream 800,
Oxford Cryosystems) and used mirror optic monochromated Cu Kα
radiation (λ = 1.54178 Å). Intensities were measured by
fine-slicing ϕ- and ω-scans and corrected for background,
polarization, and Lorentz effects. Semi-empirical absorption corrections
were applied for all data sets by using Bruker’s SADABS program.
The structure was solved by intrinsic phasing methods and refined
anisotropically by the least-squares procedure implemented in the
ShelX program system.59 (link),60 (link) The hydrogen atoms were included
isotropically using the riding model on the bound carbon atoms. The
Flack parameter (0.09(5)) and the Bayesian statistics on Bijvoet differences
(P2(true) = 1.000; P3(true) = 1.000; P3(rac-twin) = 0.2 × 10–182; and P3(false) = 0.000)61 (link) unambiguously confirm the absolute configuration of 59b.
CCDC 2236731 contains the supplementary crystallographic
data for this paper. The data can be obtained free of charge from
The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/getstructures.
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4

Structural Determination of AZP-TRZ Crystals

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Crystals suitable for X-ray crystallography were obtained by allowing diffusion of ether vapor onto a CH2Cl2 solution of 10 mM AZP-TRZ. Single crystals were picked from the solution by using a nylon loop (Hampton Research Co.) at room temperature. Data collection for a single crystal was conducted on a Bruker, SMART CCD diffractometer equipped with a graphite-monochromated Mo (λ = 0.71073 Å) radiation source under a nitrogen cold stream (223 K). Data collection and integration were performed with a Bruker, SAINT program. Semi-empirical absorption corrections based on equivalent reflections were applied with the Bruker SADABS program. Structures were obtained by using direct methods and refined using a full-matrix least-squares method on F2 by using SHELXL97. All non-hydrogen atoms were refined anisotropically. Hydrogen atoms were added to their geometrically ideal positions. Crystal data for AZP-TRZ: C35H26N4, monoclinic, P21/c, Z = 8, a = 19.8371(6), b = 9.7227(3), c = 26.6431(9) Å, α = 90°, β = 91.6354(12)°, γ = 90°, V = 5136.6(3) Å3, μ = 0.077 mm−1, ρcalcd = 1.300 g cm−3, R1 = 0.0481, wR2 = 0.0889 for 196332 unique reflections, 703 variables. The crystallographic data for AZP-TRZ are summarized in Supplementary Table 4. Supplementary Tables 5 and 6 list selected bond distances and angles, respectively.
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5

Single-crystal X-ray structure determination

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Diffraction data were collected using a single-crystal X-ray diffractometer (D8 VENTURE, Bruker) equipped with a complementary metal oxide semiconductor detector and Mo Kα X-ray source (50 kV, 1 mA). A single crystal with a diameter of ∼50 µm was mounted on a borosilicate glass needle using an adhesive. Lattice constants were determined using the SAINT program (Bruker, 2015 ▸ ) and multi-scan absorption correction was carried out using the SADABS program (Bruker, 2015 ▸ ). The initial structure model was calculated using the SUPERFLIP program based on the charge-flipping algorithm (Palatinus & Chapuis, 2007 ▸ ). Crystal structure analysis was carried out using the JANA2006 program package (Petricek et al., 2014 ▸ ) and the analysed crystal structure was visualized using the VESTA program (Momma & Izumi, 2011 ▸ ).
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