A co-crystal of quabodepistat and 2,5-dihydroxybenzoic acid was obtained and the crystal structure was solved from microcrystal electron diffraction (MicroED) data.
Keywords: crystal structure; co-crystal; quabodepistat; 2,5-dihydroxybenzoic acid; microcrystal electron diffraction
Abstract
Quabodepistat [(5-{[(3R,4R)-1-(4-chloro-2,6-difluorophenyl)-3,4-dihydroxypiperidin-4-yl]methoxy}-8-fluoro-3,4-dihydroquinolin-2(1H)-one); C21H20ClF3N2O4] and 2,5-dihydroxybenzoic acid (2,5DHBA; C7H6O4) were successfully co-crystallized. Given the small size of the crystals (1 × 0.2 × 0.2 µm) the structure was solved via microcrystal electron diffraction (MicroED). The C—O and C=O bond-length ratio of the carboxylic group in 2,5DHBA is 1.08 (1.34 Å/1.24 Å), suggesting that 2,5DHBA remains protonated. Therefore, the material is a co-crystal rather than a salt. The amide group of quabodepistat participates in a cyclic hydrogen bond with the carboxylic group of the 2,5DHBA. Additional hydrogen bonds involving the quabodepistat amide and hydroxyl groups result in a three-dimensional network.
1. Chemical context
Quabodepistat (OPC-167832), discovered by Otsuka Pharmaceutical Co., Ltd. as an anti-tuberculosis drug (Hariguchi et al., 2020 ▸), has a mode of action that involves inhibiting the DprE1 enzyme of M. tuberculosis. 2,5-dihydroxybenzoic acid (2,5DHBA) – a derivative of benzoic acid or salicylic acid – is one of the hepatic metabolites of acetylsalicylic acid (aspirin) (Levy & Tsuchiya, 1972 ▸). In the pharmaceutical industry, crystal-engineering approaches such as co-crystallization have been useful techniques for modifying the physicochemical properties [e.g., solubility (Yoshimura et al., 2017 ▸) or tabletability (Wang et al., 2021 ▸)] of an active pharmaceutical ingredient. We obtained the quabodepistat co-crystal with 2,5DHBA by the anti-solvent crystallization method and then attempted to solve its crystal structure using a conventional X-ray diffractometer; however, the crystal size was too small (1 × 0.2 × 0.2 µm). Therefore, we used MicroED (XtaLAB Synergy-ED, Rigaku Corporation, Tokyo, Japan), which is a powerful tool to solve crystal structures when the crystal size is smaller than 1 µm (Ito et al., 2021 ▸). Here, we report the crystal structure of the 1:1 co-crystal between quabodepistat and 2,5DHBA, solved using MicroED.
2. Structural commentary
Quabodepistat and 2,5DHBA co-crystallize in a 1:1 stoichiometric ratio in the monoclinic system, space group P21, with Z = 2. Unusual bond lengths and angles are expected given the low crystal quality and the current limitations of the technique. A Mogul geometry analysis (Bruno et al., 2004 ▸) indicated that the bonds C8—N7, O42—C36, F30—C28, C6—N7, O1—C2, and O41—C33, are unusual (z-score > 3). The angles O21—C16—C17, F30—C28—C23, C6—N7—C8, C9—C10—C11, O1—C14—C15, and C6—C11—C2 also have z-score values greater than 3.
All rings expected to be planar due to aromaticity (C2–C6/C11, C23–C28, and C32–C37) exhibit χ2 values (PLATON; Spek, 2020 ▸) indicating good planarity. The six-membered ring formed by C15–C17/N18/C19–C20 displays a slight chair conformation. The best plane constructed through atoms C23–C28 makes an angle of 20.9 (11)° with the best plane through C2–C6/N7/C8–C11.
3. Supramolecular features
Intermolecular interactions via hydrogen bonds are observed between quabodepistat and 2,5DHBA. One of the interactions is between a carboxylic group and an amide. As shown in Fig. 1 ▸, they form the common synthon: (amide of quabodepistat) N7—H7⋯O40=C38 (carboxylic group of 2,5DHBA) and (amide of quabodepistat) C8=O12⋯H39—O39 (carboxylic group of 2,5DHBA). Moreover, the C8=O12 of the amide interacts with a hydroxyl group of a neighboring quabodepistat (O12⋯H22—O22), and the H22—O22 interacts with another hydroxyl of quabodepistat (O22⋯H21—O21). These interactions form a three-dimensional network (Figs. 2 ▸ and 3 ▸, Table 1 ▸). It is worth mentioning that the C—O:C=O bond-length ratio of the carboxylic group in 2,5DHBA is 1.08 (1.34 Å/1.24 Å), which suggests that protonation has not occurred for complex binding. Therefore, this material is a co-crystal instead of a salt. The compound TAK-020 has also been reported as a co-crystal with 2,5DHBA (Kimoto et al., 2020 ▸). Therein, a carboxylic group of 2,5DHBA interacts with an amide moiety of the triazolinone of TAK-020, which is similar to the synthon observed in the compound reported in this contribution.
Figure 1.
The molecular structure of the quabodepistat:2,5DHBA co-crystal showing the carboxylic group and amide hydrogen bond synthon. Displacement ellipsoids are drawn at the 50% probability level.
Figure 2.
Intermolecular interactions via hydrogen bonds in the quabodepistat:2,5DHBA co-crystal.
Figure 3.
Crystal packing viewed down the a axis of the quabodepistat:2,5DHBA co-crystal.
Table 1. Hydrogen-bond geometry (Å, °).
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| C3—H3⋯O42i | 0.93 | 2.71 | 3.40 (7) | 131 |
| C9—H9B⋯O22ii | 0.97 | 2.94 | 3.49 (11) | 117 |
| N7—H7⋯O40ii | 1.01 | 1.93 | 2.93 (9) | 169 |
| C34—H34⋯O42iii | 0.93 | 2.69 | 3.48 (7) | 143 |
| O42—H42⋯O41iv | 0.82 | 2.48 | 3.23 (6) | 152 |
| O39—H39⋯O12v | 0.82 | 1.92 | 2.73 (10) | 169 |
| O21—H21⋯O22vi | 0.82 | 2.02 | 2.84 (18) | 175 |
| O22—H22⋯O12v | 0.82 | 2.11 | 2.90 (7) | 164 |
Symmetry codes: (i)
; (ii)
; (iii)
; (iv)
; (v)
; (vi)
.
4. Database survey
A search for co-crystals with 2,5-dihydroxybenzoic acid (or gentisic acid) in the Cambridge Structural Database (WebCSD, accessed June 2023; Groom et al., 2016 ▸) gave a total of 55 hits. In contrast, a search for co-crystals of quabodepistat with 2,5DHBA in the SciFinder database gave a total of two hits (Sakamoto & Miyata, 2021 ▸).
5. Synthesis and crystallization
Quabodepistat was synthesized at Otsuka Pharmaceutical Co., Ltd. (Tokushima, Japan). Tetrahydrofuran (THF) and hexane were purchased from FUJIFILM Wako Pure Chemical Corporation (Osaka, Japan). 2,5DHBA was purchased from Tokyo Kasei Kogyo Co., Ltd. (Tokyo, Japan). Quabodepistat (5 g) and 2,5DHBA (16.9 g, stoichiometric ratio 1:10) were dissolved in 100 mL of THF. 250 mL of hexane were added while stirring. Precipitation occurred as soon as hexane was added. The THF/hexane was stirred at room temperature (approximately 298 K) for three days. After filtration, it was dried at room temperature for 24 h, then heated at 383 K for 20 h.
6. Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. Two data sets were merged to obtain 93.1% data completeness to 0.9 Å resolution. Crystals were illuminated at an electron dose rate of ∼0.01 e−Å−2 s−1. Contiguous diffraction frames were collected every 0.5° from each crystal by continuously rotating the sample stage at a goniometer rotation speed of 1° s−1; the sample stage was rotated from −40° to 40° for the first crystal (crystal 1) and from −60° to 60° for the second crystal (crystal 2). The structure was refined kinematically. Refinement with SHELXL was carried out using the scattering factors for electron diffraction (Saha et al., 2022 ▸). Pseudo-merohedric twinning was identified and refined as described by Parkin (2021 ▸). For absolute structure determination, dynamical refinement is required. However, it was not performed since the absolute configuration of quabodepistat, which has two stereocenters, is known. Extinction was high because of the dynamical effects of electron diffraction (Saha et al., 2022 ▸). In spite of the presence of some unusual bond lengths and angles, no unusual intermolecular contacts are observed. This indicates that the structural model presented is correct.
Table 2. Experimental details.
| Crystal data | |
| Chemical formula | C21H20ClF3N2O4·C7H6O4 |
| M r | 610.96 |
| Crystal system, space group | Monoclinic, P21 |
| Temperature (K) | 293 |
| a, b, c (Å) | 5.6 (3), 9.6 (3), 28.2 (3) |
| β (°) | 90.30 (9) |
| V (Å3) | 1516 (109) |
| Z | 2 |
| Radiation type | Electron, λ = 0.0251 Å |
| Crystal size (μm) | 1.0 × 0.2 × 0.2 |
| Data collection | |
| Diffractometer | Rigaku XtaLAB Synergy-ED |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 8548, 4096, 2030 |
| R int | 0.149 |
| θmax (°) | 0.8 |
| (sin θ/λ)max (Å−1) | 0.556 |
| Refinement | |
| R[F 2 > 2σ(F 2)], wR(F 2), S | 0.160, 0.480, 1.08 |
| No. of reflections | 4096 |
| No. of parameters | 348 |
| No. of restraints | 537 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.15, −0.15 |
Supplementary Material
Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989023006047/dj2052sup1.cif
Supporting information file. DOI: 10.1107/S2056989023006047/dj2052Isup2.cml
Deposit the raw data into Zenodo: https://doi.org/10.5281/zenodo.7156704
Deposit the raw data into CCDC: https://dx.doi.org/10.5517/ccdc.csd.cc2d19zr
CCDC reference: 2205804
Additional supporting information: crystallographic information; 3D view; checkCIF report
Acknowledgments
The authors thank Dr Yamano (Rigaku Corporation) for technical advice on microED. The authors also thank Dr Kawato (Otsuka Pharmaceutical Co., Ltd.) for helpful discussions of the single-crystal structure.
supplementary crystallographic information
Crystal data
| C21H20ClF3N2O4·C7H6O4 | F(000) = 224 |
| Mr = 610.96 | Dx = 1.338 Mg m−3 |
| Monoclinic, P21 | Electron radiation, λ = 0.0251 Å |
| a = 5.6 (3) Å | Cell parameters from 411 reflections |
| b = 9.6 (3) Å | θ = 0.1–0.8° |
| c = 28.2 (3) Å | µ = 0.000 mm−1 |
| β = 90.30 (9)° | T = 293 K |
| V = 1516 (109) Å3 | Thin platelets, colourless |
| Z = 2 | 1 × 0.2 × 0.2 mm |
Data collection
| Rigaku XtaLAB Synergy-ED diffractometer | 2030 reflections with I > 2σ(I) |
| Radiation source: thermionic-emission electron gun | Rint = 0.149 |
| Detector resolution: 10.0 pixels mm-1 | θmax = 0.8°, θmin = 0.1° |
| rotation scans | h = −6→6 |
| 8548 measured reflections | k = −10→10 |
| 4096 independent reflections | l = −31→31 |
Refinement
| Refinement on F2 | H-atom parameters constrained |
| Least-squares matrix: full | w = 1/[σ2(Fo2) + (0.2805P)2 + 0.170P] where P = (Fo2 + 2Fc2)/3 |
| R[F2 > 2σ(F2)] = 0.160 | (Δ/σ)max = 0.001 |
| wR(F2) = 0.480 | Δρmax = 0.15 e Å−3 |
| S = 1.08 | Δρmin = −0.15 e Å−3 |
| 4096 reflections | Extinction correction: 'SHELXL2018/3 (Sheldrick, 2015)', Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
| 348 parameters | Extinction coefficient: 368 (31) |
| 537 restraints | Absolute structure: All f" are zero, so absolute structure could not be determined |
| Hydrogen site location: inferred from neighbouring sites |
Special details
| Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
| Refinement. Refined as a 2-component twin. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | ||
| C2 | 0.960 (3) | 0.5589 (17) | 0.7945 (6) | 0.070 (5) | |
| C11 | 0.804 (4) | 0.6700 (17) | 0.7886 (5) | 0.068 (4) | |
| C6 | 0.660 (3) | 0.7121 (17) | 0.8261 (6) | 0.063 (4) | |
| C5 | 0.673 (3) | 0.6431 (19) | 0.8694 (6) | 0.072 (5) | |
| C4 | 0.829 (3) | 0.5320 (19) | 0.8752 (5) | 0.075 (5) | |
| H4 | 0.837583 | 0.485853 | 0.904220 | 0.090* | |
| C3 | 0.973 (3) | 0.4899 (16) | 0.8378 (6) | 0.073 (5) | |
| H3 | 1.077324 | 0.415597 | 0.841680 | 0.087* | |
| C10 | 0.796 (5) | 0.753 (2) | 0.7416 (8) | 0.069 (5) | |
| H10A | 0.957975 | 0.785032 | 0.735893 | 0.083* | |
| H10B | 0.759602 | 0.686397 | 0.716684 | 0.083* | |
| C9 | 0.631 (5) | 0.878 (3) | 0.7338 (10) | 0.075 (5) | |
| H9A | 0.528342 | 0.859999 | 0.706630 | 0.090* | |
| H9B | 0.726751 | 0.959210 | 0.726908 | 0.090* | |
| C8 | 0.476 (5) | 0.906 (3) | 0.7778 (9) | 0.068 (5) | |
| N7 | 0.479 (5) | 0.824 (2) | 0.8206 (10) | 0.067 (5) | |
| H7 | 0.359249 | 0.842859 | 0.846624 | 0.080* | |
| C32 | 0.785 (2) | 0.0552 (14) | 0.9171 (6) | 0.053 (4) | |
| C37 | 0.611 (3) | 0.1500 (15) | 0.9033 (5) | 0.054 (4) | |
| H37 | 0.608891 | 0.184541 | 0.872468 | 0.065* | |
| C36 | 0.440 (2) | 0.1933 (15) | 0.9357 (6) | 0.057 (5) | |
| C35 | 0.443 (2) | 0.1417 (17) | 0.9818 (6) | 0.059 (5) | |
| H35 | 0.327933 | 0.170661 | 1.003412 | 0.071* | |
| C34 | 0.617 (3) | 0.0469 (18) | 0.9955 (5) | 0.064 (5) | |
| H34 | 0.619200 | 0.012343 | 1.026363 | 0.076* | |
| C33 | 0.789 (2) | 0.0036 (15) | 0.9632 (6) | 0.059 (4) | |
| O40 | 1.128 (4) | −0.085 (2) | 0.8909 (11) | 0.069 (6) | |
| C15 | 1.307 (4) | 0.340 (2) | 0.7081 (11) | 0.081 (5) | |
| C38 | 0.975 (3) | 0.005 (2) | 0.8818 (8) | 0.053 (4) | |
| O42 | 0.251 (4) | 0.291 (2) | 0.9211 (10) | 0.061 (6) | |
| H42 | 0.156468 | 0.302044 | 0.943037 | 0.092* | |
| C14 | 1.241 (6) | 0.397 (3) | 0.7565 (12) | 0.082 (5) | |
| H14A | 1.151605 | 0.326933 | 0.773690 | 0.099* | |
| H14B | 1.386475 | 0.415660 | 0.774296 | 0.099* | |
| O12 | 0.319 (5) | 1.000 (2) | 0.7774 (9) | 0.075 (7) | |
| O41 | 0.958 (4) | −0.099 (2) | 0.9792 (11) | 0.076 (7) | |
| H41 | 1.043887 | −0.121798 | 0.956939 | 0.114* | |
| F13 | 0.511 (6) | 0.688 (2) | 0.9048 (10) | 0.079 (7) | |
| O1 | 1.104 (4) | 0.520 (2) | 0.7540 (12) | 0.077 (5) | |
| O39 | 0.968 (4) | 0.071 (2) | 0.8400 (11) | 0.066 (5) | |
| H39 | 1.072100 | 0.039139 | 0.822607 | 0.099* | |
| C17 | 1.138 (5) | 0.243 (2) | 0.6290 (10) | 0.090 (6) | |
| H17A | 1.232176 | 0.158593 | 0.628400 | 0.108* | |
| H17B | 0.988301 | 0.225125 | 0.612765 | 0.108* | |
| O21 | 0.972 (5) | 0.185 (3) | 0.7110 (12) | 0.098 (8) | |
| H21 | 0.828359 | 0.200591 | 0.711408 | 0.148* | |
| C20 | 1.438 (5) | 0.447 (2) | 0.6775 (10) | 0.089 (6) | |
| H20A | 1.346328 | 0.532911 | 0.678027 | 0.106* | |
| H20B | 1.591213 | 0.466927 | 0.692442 | 0.106* | |
| O22 | 1.469 (3) | 0.224 (2) | 0.7149 (14) | 0.083 (7) | |
| H22 | 1.401436 | 0.161832 | 0.729667 | 0.125* | |
| C16 | 1.087 (4) | 0.283 (2) | 0.6810 (9) | 0.083 (5) | |
| H16 | 0.976517 | 0.361826 | 0.679004 | 0.100* | |
| C23 | 1.265 (6) | 0.344 (3) | 0.5511 (9) | 0.131 (7) | |
| C28 | 1.434 (5) | 0.264 (3) | 0.5280 (10) | 0.150 (8) | |
| C27 | 1.440 (5) | 0.261 (3) | 0.4787 (10) | 0.164 (9) | |
| H27 | 1.553704 | 0.206657 | 0.463185 | 0.197* | |
| C26 | 1.277 (6) | 0.339 (4) | 0.4525 (9) | 0.170 (9) | |
| C25 | 1.108 (5) | 0.419 (3) | 0.4756 (10) | 0.162 (9) | |
| H25 | 0.998639 | 0.471406 | 0.458099 | 0.194* | |
| C24 | 1.102 (5) | 0.422 (3) | 0.5249 (10) | 0.148 (8) | |
| Cl31 | 1.268 (6) | 0.322 (4) | 0.3905 (9) | 0.215 (12) | |
| F29 | 0.929 (10) | 0.501 (5) | 0.548 (2) | 0.172 (14) | |
| F30 | 1.615 (9) | 0.176 (5) | 0.551 (2) | 0.158 (13) | |
| C19 | 1.485 (4) | 0.410 (3) | 0.6254 (10) | 0.092 (6) | |
| H19A | 1.534890 | 0.492210 | 0.608241 | 0.111* | |
| H19B | 1.612402 | 0.341921 | 0.623696 | 0.111* | |
| N18 | 1.268 (5) | 0.353 (3) | 0.6034 (11) | 0.101 (5) |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| C2 | 0.078 (9) | 0.057 (8) | 0.076 (10) | 0.029 (7) | 0.010 (9) | 0.005 (8) |
| C11 | 0.085 (9) | 0.056 (8) | 0.062 (9) | 0.030 (7) | 0.008 (8) | 0.011 (7) |
| C6 | 0.087 (9) | 0.043 (7) | 0.059 (9) | 0.034 (7) | 0.009 (8) | 0.015 (7) |
| C5 | 0.088 (10) | 0.063 (9) | 0.066 (10) | 0.037 (8) | 0.007 (9) | 0.024 (8) |
| C4 | 0.081 (11) | 0.069 (10) | 0.074 (11) | 0.037 (8) | 0.002 (10) | 0.020 (9) |
| C3 | 0.082 (11) | 0.059 (9) | 0.076 (11) | 0.032 (9) | 0.002 (10) | 0.008 (8) |
| C10 | 0.089 (10) | 0.058 (9) | 0.060 (10) | 0.031 (8) | 0.009 (10) | 0.011 (8) |
| C9 | 0.096 (11) | 0.067 (9) | 0.062 (11) | 0.040 (9) | 0.015 (10) | 0.018 (9) |
| C8 | 0.090 (10) | 0.058 (8) | 0.055 (10) | 0.045 (8) | 0.011 (9) | 0.013 (8) |
| N7 | 0.096 (10) | 0.045 (8) | 0.059 (10) | 0.040 (8) | 0.015 (9) | 0.009 (7) |
| C32 | 0.051 (7) | 0.050 (7) | 0.057 (9) | 0.005 (6) | 0.002 (7) | −0.002 (7) |
| C37 | 0.055 (8) | 0.052 (8) | 0.055 (10) | 0.010 (7) | 0.008 (8) | −0.004 (8) |
| C36 | 0.049 (8) | 0.064 (9) | 0.059 (10) | 0.015 (7) | 0.004 (8) | −0.004 (8) |
| C35 | 0.052 (9) | 0.063 (9) | 0.062 (10) | 0.001 (7) | 0.009 (9) | 0.003 (9) |
| C34 | 0.064 (9) | 0.063 (9) | 0.064 (10) | 0.000 (8) | 0.004 (9) | 0.012 (9) |
| C33 | 0.061 (8) | 0.053 (8) | 0.065 (10) | −0.004 (7) | 0.006 (8) | 0.009 (8) |
| O40 | 0.047 (10) | 0.078 (12) | 0.083 (17) | 0.016 (9) | 0.025 (12) | 0.016 (12) |
| C15 | 0.062 (8) | 0.062 (8) | 0.118 (11) | 0.038 (7) | 0.019 (9) | 0.020 (8) |
| C38 | 0.044 (8) | 0.053 (9) | 0.063 (10) | 0.001 (7) | 0.001 (8) | −0.008 (8) |
| O42 | 0.048 (10) | 0.065 (11) | 0.072 (16) | 0.022 (8) | 0.004 (12) | −0.005 (11) |
| C14 | 0.072 (10) | 0.059 (9) | 0.116 (12) | 0.033 (9) | 0.018 (10) | 0.011 (9) |
| O12 | 0.106 (15) | 0.062 (11) | 0.058 (15) | 0.059 (11) | 0.015 (13) | 0.020 (11) |
| O41 | 0.087 (14) | 0.055 (10) | 0.087 (17) | 0.001 (9) | 0.013 (14) | 0.024 (12) |
| F13 | 0.134 (17) | 0.045 (9) | 0.059 (14) | 0.041 (11) | 0.023 (13) | 0.025 (10) |
| O1 | 0.071 (9) | 0.057 (8) | 0.103 (12) | 0.030 (8) | 0.018 (10) | 0.007 (9) |
| O39 | 0.046 (10) | 0.084 (12) | 0.069 (13) | 0.001 (10) | 0.000 (11) | 0.005 (11) |
| C17 | 0.075 (10) | 0.072 (10) | 0.124 (13) | 0.041 (9) | 0.019 (11) | 0.018 (10) |
| O21 | 0.068 (12) | 0.092 (14) | 0.14 (2) | 0.016 (10) | 0.013 (15) | 0.031 (14) |
| C20 | 0.074 (10) | 0.067 (9) | 0.125 (13) | 0.034 (8) | 0.020 (11) | 0.026 (10) |
| O22 | 0.049 (10) | 0.057 (10) | 0.14 (2) | 0.036 (9) | 0.027 (13) | 0.012 (12) |
| C16 | 0.062 (9) | 0.065 (9) | 0.122 (12) | 0.039 (8) | 0.019 (10) | 0.018 (9) |
| C23 | 0.123 (13) | 0.128 (12) | 0.143 (14) | 0.041 (12) | 0.019 (14) | 0.012 (13) |
| C28 | 0.146 (15) | 0.149 (15) | 0.154 (16) | 0.043 (14) | 0.018 (16) | −0.007 (15) |
| C27 | 0.165 (16) | 0.162 (16) | 0.166 (18) | 0.041 (15) | 0.017 (18) | −0.011 (17) |
| C26 | 0.174 (16) | 0.168 (16) | 0.168 (17) | 0.040 (15) | 0.015 (18) | −0.007 (16) |
| C25 | 0.161 (16) | 0.159 (16) | 0.165 (18) | 0.040 (15) | 0.015 (18) | 0.005 (17) |
| C24 | 0.144 (15) | 0.146 (15) | 0.153 (17) | 0.045 (14) | 0.018 (16) | 0.012 (15) |
| Cl31 | 0.23 (2) | 0.22 (2) | 0.19 (2) | 0.06 (2) | 0.01 (2) | −0.01 (2) |
| F29 | 0.17 (3) | 0.18 (3) | 0.16 (3) | 0.05 (2) | 0.02 (3) | 0.02 (2) |
| F30 | 0.16 (2) | 0.14 (2) | 0.17 (3) | 0.05 (2) | 0.01 (3) | −0.05 (2) |
| C19 | 0.078 (11) | 0.072 (10) | 0.127 (13) | 0.041 (9) | 0.025 (12) | 0.030 (11) |
| N18 | 0.088 (10) | 0.090 (10) | 0.126 (12) | 0.035 (9) | 0.022 (11) | 0.023 (10) |
Geometric parameters (Å, º)
| C2—C11 | 1.3900 | C15—O22 | 1.45 (5) |
| C2—C3 | 1.3900 | C15—C16 | 1.54 (6) |
| C2—O1 | 1.45 (4) | C38—O39 | 1.34 (4) |
| C11—C6 | 1.3900 | O42—H42 | 0.8200 |
| C11—C10 | 1.55 (2) | C14—H14A | 0.9700 |
| C6—C5 | 1.3900 | C14—H14B | 0.9700 |
| C6—N7 | 1.49 (6) | C14—O1 | 1.41 (5) |
| C5—C4 | 1.3900 | O41—H41 | 0.8200 |
| C5—F13 | 1.42 (5) | O39—H39 | 0.8200 |
| C4—H4 | 0.9300 | C17—H17A | 0.9700 |
| C4—C3 | 1.3900 | C17—H17B | 0.9700 |
| C3—H3 | 0.9300 | C17—C16 | 1.54 (2) |
| C10—H10A | 0.9700 | C17—N18 | 1.47 (4) |
| C10—H10B | 0.9700 | O21—H21 | 0.8200 |
| C10—C9 | 1.53 (5) | O21—C16 | 1.42 (3) |
| C9—H9A | 0.9700 | C20—H20A | 0.9700 |
| C9—H9B | 0.9700 | C20—H20B | 0.9700 |
| C9—C8 | 1.54 (4) | C20—C19 | 1.53 (2) |
| C8—N7 | 1.44 (4) | O22—H22 | 0.8200 |
| C8—O12 | 1.26 (5) | C16—H16 | 0.9800 |
| N7—H7 | 1.0100 | C23—C28 | 1.3900 |
| C32—C37 | 1.3900 | C23—C24 | 1.3900 |
| C32—C33 | 1.3900 | C23—N18 | 1.47 (4) |
| C32—C38 | 1.53 (5) | C28—C27 | 1.3900 |
| C37—H37 | 0.9300 | C28—F30 | 1.46 (7) |
| C37—C36 | 1.3900 | C27—H27 | 0.9300 |
| C36—C35 | 1.3900 | C27—C26 | 1.3900 |
| C36—O42 | 1.47 (6) | C26—C25 | 1.3900 |
| C35—H35 | 0.9300 | C26—Cl31 | 1.75 (3) |
| C35—C34 | 1.3900 | C25—H25 | 0.9300 |
| C34—H34 | 0.9300 | C25—C24 | 1.3900 |
| C34—C33 | 1.3900 | C24—F29 | 1.40 (7) |
| C33—O41 | 1.44 (5) | C19—H19A | 0.9700 |
| O40—C38 | 1.24 (5) | C19—H19B | 0.9700 |
| C15—C14 | 1.52 (4) | C19—N18 | 1.46 (6) |
| C15—C20 | 1.54 (4) | ||
| C11—C2—C3 | 120.0 | O40—C38—C32 | 124 (3) |
| C11—C2—O1 | 117 (2) | O40—C38—O39 | 122 (2) |
| C3—C2—O1 | 123 (2) | O39—C38—C32 | 114 (2) |
| C2—C11—C10 | 120.8 (16) | C36—O42—H42 | 109.5 |
| C6—C11—C2 | 120.0 | C15—C14—H14A | 108.9 |
| C6—C11—C10 | 119.2 (19) | C15—C14—H14B | 108.9 |
| C11—C6—N7 | 122 (2) | H14A—C14—H14B | 107.7 |
| C5—C6—C11 | 120.0 | O1—C14—C15 | 113 (3) |
| C5—C6—N7 | 117.9 (18) | O1—C14—H14A | 108.9 |
| C6—C5—C4 | 120.0 | O1—C14—H14B | 108.9 |
| C6—C5—F13 | 116 (2) | C33—O41—H41 | 109.5 |
| C4—C5—F13 | 124 (2) | C14—O1—C2 | 119 (3) |
| C5—C4—H4 | 120.0 | C38—O39—H39 | 109.5 |
| C3—C4—C5 | 120.0 | H17A—C17—H17B | 107.9 |
| C3—C4—H4 | 120.0 | C16—C17—H17A | 109.1 |
| C2—C3—H3 | 120.0 | C16—C17—H17B | 109.1 |
| C4—C3—C2 | 120.0 | N18—C17—H17A | 109.1 |
| C4—C3—H3 | 120.0 | N18—C17—H17B | 109.1 |
| C11—C10—H10A | 106.6 | N18—C17—C16 | 112 (2) |
| C11—C10—H10B | 106.6 | C16—O21—H21 | 109.5 |
| H10A—C10—H10B | 106.6 | C15—C20—H20A | 107.9 |
| C9—C10—C11 | 123 (2) | C15—C20—H20B | 107.9 |
| C9—C10—H10A | 106.6 | H20A—C20—H20B | 107.2 |
| C9—C10—H10B | 106.6 | C19—C20—C15 | 117 (2) |
| C10—C9—H9A | 109.3 | C19—C20—H20A | 107.9 |
| C10—C9—H9B | 109.3 | C19—C20—H20B | 107.9 |
| C10—C9—C8 | 111 (3) | C15—O22—H22 | 109.5 |
| H9A—C9—H9B | 108.0 | C15—C16—H16 | 105.0 |
| C8—C9—H9A | 109.3 | C17—C16—C15 | 114 (3) |
| C8—C9—H9B | 109.3 | C17—C16—H16 | 105.0 |
| N7—C8—C9 | 125 (2) | O21—C16—C15 | 107 (3) |
| O12—C8—C9 | 121 (3) | O21—C16—C17 | 119 (3) |
| O12—C8—N7 | 114 (3) | O21—C16—H16 | 105.0 |
| C6—N7—H7 | 120.4 | C28—C23—C24 | 120.0 |
| C8—N7—C6 | 119 (3) | C28—C23—N18 | 120 (2) |
| C8—N7—H7 | 120.4 | C24—C23—N18 | 120 (2) |
| C37—C32—C33 | 120.0 | C23—C28—C27 | 120.0 |
| C37—C32—C38 | 121 (2) | C23—C28—F30 | 126 (3) |
| C33—C32—C38 | 119.1 (19) | C27—C28—F30 | 114 (3) |
| C32—C37—H37 | 120.0 | C28—C27—H27 | 120.0 |
| C36—C37—C32 | 120.0 | C26—C27—C28 | 120.0 |
| C36—C37—H37 | 120.0 | C26—C27—H27 | 120.0 |
| C37—C36—C35 | 120.0 | C27—C26—Cl31 | 119.7 (11) |
| C37—C36—O42 | 120 (3) | C25—C26—C27 | 120.0 |
| C35—C36—O42 | 119.6 (18) | C25—C26—Cl31 | 120.1 (13) |
| C36—C35—H35 | 120.0 | C26—C25—H25 | 120.0 |
| C34—C35—C36 | 120.0 | C26—C25—C24 | 120.0 |
| C34—C35—H35 | 120.0 | C24—C25—H25 | 120.0 |
| C35—C34—H34 | 120.0 | C23—C24—F29 | 120 (4) |
| C35—C34—C33 | 120.0 | C25—C24—C23 | 120.0 |
| C33—C34—H34 | 120.0 | C25—C24—F29 | 120 (3) |
| C32—C33—O41 | 122.8 (19) | C20—C19—H19A | 109.6 |
| C34—C33—C32 | 120.0 | C20—C19—H19B | 109.6 |
| C34—C33—O41 | 117 (3) | H19A—C19—H19B | 108.1 |
| C14—C15—C20 | 112 (3) | N18—C19—C20 | 110 (3) |
| C14—C15—C16 | 112 (3) | N18—C19—H19A | 109.6 |
| C20—C15—C16 | 110 (3) | N18—C19—H19B | 109.6 |
| O22—C15—C14 | 109 (3) | C17—N18—C23 | 116 (3) |
| O22—C15—C20 | 107 (4) | C19—N18—C17 | 118 (3) |
| O22—C15—C16 | 107 (4) | C19—N18—C23 | 117 (3) |
| C2—C11—C6—C5 | 0.0 | C14—C15—C16—C17 | 172 (2) |
| C2—C11—C6—N7 | −176 (2) | C14—C15—C16—O21 | −54 (3) |
| C2—C11—C10—C9 | −179 (2) | O12—C8—N7—C6 | −178 (2) |
| C11—C2—C3—C4 | 0.0 | F13—C5—C4—C3 | 176 (2) |
| C11—C2—O1—C14 | −172 (2) | O1—C2—C11—C6 | 179.7 (19) |
| C11—C6—C5—C4 | 0.0 | O1—C2—C11—C10 | −3 (2) |
| C11—C6—C5—F13 | −177 (2) | O1—C2—C3—C4 | −180 (2) |
| C11—C6—N7—C8 | −10 (3) | C20—C15—C14—O1 | 56 (4) |
| C11—C10—C9—C8 | −1 (4) | C20—C15—C16—C17 | 46 (3) |
| C6—C11—C10—C9 | −2 (4) | C20—C15—C16—O21 | −180 (2) |
| C6—C5—C4—C3 | 0.0 | C20—C19—N18—C17 | −48 (3) |
| C5—C6—N7—C8 | 174 (2) | C20—C19—N18—C23 | 165 (2) |
| C5—C4—C3—C2 | 0.0 | O22—C15—C14—O1 | 174 (2) |
| C3—C2—C11—C6 | 0.0 | O22—C15—C20—C19 | 69 (3) |
| C3—C2—C11—C10 | 177 (2) | O22—C15—C16—C17 | −70 (3) |
| C3—C2—O1—C14 | 8 (3) | O22—C15—C16—O21 | 65 (3) |
| C10—C11—C6—C5 | −177 (2) | C16—C15—C14—O1 | −69 (4) |
| C10—C11—C6—N7 | 7 (2) | C16—C15—C20—C19 | −46 (3) |
| C10—C9—C8—N7 | −2 (4) | C16—C17—N18—C23 | −163 (3) |
| C10—C9—C8—O12 | −176 (3) | C16—C17—N18—C19 | 51 (4) |
| C9—C8—N7—C6 | 7 (5) | C23—C28—C27—C26 | 0.0 |
| N7—C6—C5—C4 | 176 (2) | C28—C23—C24—C25 | 0.0 |
| N7—C6—C5—F13 | −1 (2) | C28—C23—C24—F29 | 178.7 (11) |
| C32—C37—C36—C35 | 0.0 | C28—C23—N18—C17 | −86 (5) |
| C32—C37—C36—O42 | −178.6 (16) | C28—C23—N18—C19 | 61 (5) |
| C37—C32—C33—C34 | 0.0 | C28—C27—C26—C25 | 0.0 |
| C37—C32—C33—O41 | 177.5 (17) | C28—C27—C26—Cl31 | −174 (3) |
| C37—C32—C38—O40 | −175.6 (19) | C27—C26—C25—C24 | 0.0 |
| C37—C32—C38—O39 | 6 (2) | C26—C25—C24—C23 | 0.0 |
| C37—C36—C35—C34 | 0.0 | C26—C25—C24—F29 | −178.7 (11) |
| C36—C35—C34—C33 | 0.0 | C24—C23—C28—C27 | 0.0 |
| C35—C34—C33—C32 | 0.0 | C24—C23—C28—F30 | −179 (3) |
| C35—C34—C33—O41 | −177.7 (17) | C24—C23—N18—C17 | 97 (5) |
| C33—C32—C37—C36 | 0.0 | C24—C23—N18—C19 | −116 (4) |
| C33—C32—C38—O40 | 4 (3) | Cl31—C26—C25—C24 | 174 (3) |
| C33—C32—C38—O39 | −174.3 (16) | F30—C28—C27—C26 | 179 (3) |
| C15—C14—O1—C2 | 159 (2) | N18—C17—C16—C15 | −49 (3) |
| C15—C20—C19—N18 | 47 (3) | N18—C17—C16—O21 | −177 (2) |
| C38—C32—C37—C36 | 179.5 (14) | N18—C23—C28—C27 | −177 (3) |
| C38—C32—C33—C34 | −179.5 (14) | N18—C23—C28—F30 | 4 (3) |
| C38—C32—C33—O41 | −2 (2) | N18—C23—C24—C25 | 177 (3) |
| O42—C36—C35—C34 | 178.6 (16) | N18—C23—C24—F29 | −5 (3) |
| C14—C15—C20—C19 | −172 (2) |
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| C3—H3···O42i | 0.93 | 2.71 | 3.40 (7) | 131 |
| C9—H9B···O22ii | 0.97 | 2.94 | 3.49 (11) | 117 |
| N7—H7···O40ii | 1.01 | 1.93 | 2.93 (9) | 169 |
| C34—H34···O42iii | 0.93 | 2.69 | 3.48 (7) | 143 |
| O42—H42···O41iv | 0.82 | 2.48 | 3.23 (6) | 152 |
| O39—H39···O12v | 0.82 | 1.92 | 2.73 (10) | 169 |
| O21—H21···O22vi | 0.82 | 2.02 | 2.84 (18) | 175 |
| O22—H22···O12v | 0.82 | 2.11 | 2.90 (7) | 164 |
Symmetry codes: (i) x+1, y, z; (ii) x−1, y+1, z; (iii) −x+1, y−1/2, −z+2; (iv) −x+1, y+1/2, −z+2; (v) x+1, y−1, z; (vi) x−1, y, z.
References
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989023006047/dj2052sup1.cif
Supporting information file. DOI: 10.1107/S2056989023006047/dj2052Isup2.cml
Deposit the raw data into Zenodo: https://doi.org/10.5281/zenodo.7156704
Deposit the raw data into CCDC: https://dx.doi.org/10.5517/ccdc.csd.cc2d19zr
CCDC reference: 2205804
Additional supporting information: crystallographic information; 3D view; checkCIF report



