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Crystal structure of (S)-5-(3-acetyl-5-chloro-2-eth­oxy-6-fluoro­phenyl)-2-oxazolidinone

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aW. M. Keck Center for Advanced Microscopy and Microanalysis, University of Delaware, Newark, DE 19716, USA, bDepartment of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA, and cDepartment of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
*Correspondence e-mail: cni@udel.edu

Edited by J. Reibenspies, Texas A & M University, USA (Received 14 November 2023; accepted 27 February 2024; online 19 March 2024)

The structure of (S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone, C13H13ClFNO4, at 100 K has monoclinic (P21) symmetry. The compound has a polymeric structure propagated by a screw axis parallel to the b axis with N—H⋯O hydrogen bonding. It is of inter­est with respect to efforts in the synthesis of a candidate anti­cancer drug, parsaclisib.

1. Chemical context

Oxazolidinones are a class of compounds containing the five-membered heterocycle 1,3-oxazolidin-2-one and were mainly used for anti­microbials acting as protein synthesis inhibitors targeting N-formyl­methionyl-tRNA to ribosome binding (Zhao et al., 2021[Zhao, Q., Xin, L., Liu, Y., Liang, C., Li, J., Jian, Y., Li, H., Shi, Z., Liu, H. & Cao, W. (2021). J. Med. Chem. 64, 10557-10580.]). Cases with elevated levels of phospho­inositide 3-kinase delta (PI3Kδ) were found associated with increased cancer susceptibility (Crank et al., 2014[Crank, M. C., Grossman, J. K., Moir, S., Pittaluga, S., Buckner, C. M., Kardava, L., Agharahimi, A., Meuwissen, H., Stoddard, J., Niemela, J., Kuehn, H. & Rosenzweig, S. D. (2014). J. Clin. Immunol. 34, 272-276.]). An oxa­zol­idinone drug candidate, (4R)-4-[3-[(1S)-1-(4-amino-3-methyl­pyrazolo­[3,4-d]pyrimidin-1-yl)eth­yl]-5-chloro-2-eth­oxy-6-fluoro­phen­yl]pyrrolidin-2-one, parsaclisib, was discovered to be a potent PI3Kδ inhibitor (Zinzani et al., 2023[Zinzani, P. L., Trněný, M., Ribrag, V., Zilioli, V. R., Walewski, J., Christensen, J. H., Delwail, V., Rodriguez, G., Venugopal, P., Coleman, M., Dartigeas, C., Patti, C., Pane, F., Jurczak, W., Taszner, M., Paneesha, S., Zheng, F., DeMarini, D. J., Jiang, W., Gilmartin, A. & Mehtas, A. (2023). EClinicalMedicine, 62, 102131.]). As part of evolving attempts to improve the synthesis of parsaclisib, we were sent samples of an inter­mediate product that required confirmation of substituents and absolute chirality determination. Our diffraction studies identified it as (S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone. Atom C-3 has been determined by our study to have S absolute chirality, which can yield the corresponding alcohol via enantioselective ketone reduction (Mao et al., 2005[Mao, J., Wan, B., Wu, F. & Lu, S. (2005). Tetrahedron Lett. 46, 7341-7344.]), which should subsequently yield parsaclisib as per the reaction scheme.

[Scheme 1]

2. Structural commentary

The asymmetric unit consisting of one complete mol­ecule of the title compound is shown in Fig. 1[link]. Consistent with similar structures (vide infra), the oxazolidinone ring is essentially planar and is twisted from the plane of the dihalophenyl ring as seen from twist angles C2—C3—C4—C9 = 70.5 (5)°. One of the two symmetry-unique mol­ecules in (R)-5-mesityloxazolidin-2-one has the closest similar twist of 73.5 (2)° (Qin et al., 2012[Qin, D.-D., Lai, W.-H., Hu, D., Chen, Z., Wu, A.-A., Ruan, Y.-P., Zhou, Z.-H. & Chen, H.-B. (2012). Chem. Eur. J. 18, 10515-10518.]). The acetate and eth­oxy groups in the title compound are almost perpendicular to the phenyl ring with torsion angles C7—C6—C12—O4 = −92.8 (6)° and C10—O3—C5—C6 = −96.8 (4)°, respectively. The absolute structure refined to nil indicating the correct handedness has been established.

[Figure 1]
Figure 1
The contents of the asymmetric unit with atom labeling. H-atom labels are omitted for clarity. Displacement ellipsoids are plotted at 50% probability.

3. Supra­molecular features

In the crystal, N—H⋯O hydrogen-bonding inter­actions (Table 1[link]) occur between neighboring mol­ecules related by −x, [{1\over 2}] + y, 1 − z, resulting in chains parallel to the b-axis direction (Fig. 2[link]). In contrast, di­chloro-{2-meth­oxy-4-[2-(pyridin-2-yl)-1,3-oxazolidin-5-yl]phenol}palladium aceto­nitrile solvate does not show this type of hydrogen bonding, perhaps because the oxazolidinone N atom is also coordinated to palladium (Denisov & Gagarskikh, 2021[Denisov, M. S. & Gagarskikh, O. N. (2021). Russ. J. Gen. Chem. 91, 1354-1360.]). Remarkably, the four other structures do display N—H⋯O hydrogen bonding; however, in each case, this leads to pair-wise dimer formation instead of a more extended structure (Chen et al., 2021[Chen, X., Huang, Z. & Xu, J. (2021). Adv. Synth. Catal. 363, 3098-3108.]; Norte et al., 1988[Norte, M., Rodriguez, M. L., Fernández, J. J., Eguren, L. & Estrada, D. M. (1988). Tetrahedron, 44, 4973-4980.]; Qin et al., 2012[Qin, D.-D., Lai, W.-H., Hu, D., Chen, Z., Wu, A.-A., Ruan, Y.-P., Zhou, Z.-H. & Chen, H.-B. (2012). Chem. Eur. J. 18, 10515-10518.]; Bresciani et al., 2020[Bresciani, G., Antico, E., Ciancaleoni, G., Zacchini, S., Pampaloni, G. & Marchetti, F. (2020). ChemSusChem, 13, 5586-5594.]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O2i 0.84 (6) 2.12 (6) 2.923 (4) 161 (5)
Symmetry code: (i) [-x, y+{\script{1\over 2}}, -z+1].
[Figure 2]
Figure 2
A view perpendicular to the c axis showing hydrogen-bonding inter­actions (dotted lines) forming a chain parallel to the b axis. Displacement ellipsoids are plotted at 50% probability.

4. Database survey

A search of the Cambridge Structural Database with WebCSD (https://www.ccdc.cam.ac.uk/structures/WebCSD, accessed November 8, 2023; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for structures containing the 5-(arene)-oxazolidine-2-one moiety yielded five additional structures: EWIPEI (Chen et al., 2021[Chen, X., Huang, Z. & Xu, J. (2021). Adv. Synth. Catal. 363, 3098-3108.]), GIGHUZ (Norte et al., 1988[Norte, M., Rodriguez, M. L., Fernández, J. J., Eguren, L. & Estrada, D. M. (1988). Tetrahedron, 44, 4973-4980.]), MAZDEN (Qin et al., 2012[Qin, D.-D., Lai, W.-H., Hu, D., Chen, Z., Wu, A.-A., Ruan, Y.-P., Zhou, Z.-H. & Chen, H.-B. (2012). Chem. Eur. J. 18, 10515-10518.]), WAFCEP (Bresciani et al., 2020[Bresciani, G., Antico, E., Ciancaleoni, G., Zacchini, S., Pampaloni, G. & Marchetti, F. (2020). ChemSusChem, 13, 5586-5594.]) and YALYUJ (Denisov & Gagarskikh, 2021[Denisov, M. S. & Gagarskikh, O. N. (2021). Russ. J. Gen. Chem. 91, 1354-1360.]).

5. Synthesis and crystallization

(S)-5-(3-Acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazol­id­inone and solvents were used as received without further purification. (S)-5-(3-Acetyl-5-chloro-2-eth­oxy-6-fluoro­phen­yl)-2-oxazolidinone (20 mg) was dissolved in a mixed solvent of methanol (3 mL) and di­chloro­methane (1 mL). The solution was allowed to evaporate slowly at room temperature until suitable crystals were deposited.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. Amide H atoms were located from difference maps and positionally refined. Other H atoms were positioned geometrically. All H atoms refined as riding with Uiso(H) = 1.2 or 1.5Ueq(C,N).

Table 2
Experimental details

Crystal data
Chemical formula C13H13ClFNO4
Mr 301.69
Crystal system, space group Monoclinic, P21
Temperature (K) 100
a, b, c (Å) 7.8729 (12), 5.5655 (8), 15.492 (2)
β (°) 101.446 (3)
V3) 665.31 (17)
Z 2
Radiation type Cu Kα
μ (mm−1) 2.80
Crystal size (mm) 0.41 × 0.10 × 0.08
 
Data collection
Diffractometer Bruker Venture Photon III
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.523, 0.754
No. of measured, independent and observed [I > 2σ(I)] reflections 12247, 2540, 2483
Rint 0.061
(sin θ/λ)max−1) 0.620
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.050, 0.136, 1.08
No. of reflections 2540
No. of parameters 186
No. of restraints 1
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.44, −0.28
Absolute structure Flack x determined using 1052 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.009 (11)
Computer programs: APEX4 (Bruker, 2021[Bruker (2021). APEX4. Bruker AXS Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2016[Bruker (2016). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT2018/2 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2019/3 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information


Computing details top

(S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone top
Crystal data top
C13H13ClFNO4F(000) = 312
Mr = 301.69Dx = 1.506 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54178 Å
a = 7.8729 (12) ÅCell parameters from 9877 reflections
b = 5.5655 (8) Åθ = 2.9–72.0°
c = 15.492 (2) ŵ = 2.80 mm1
β = 101.446 (3)°T = 100 K
V = 665.31 (17) Å3Needle, colourless
Z = 20.41 × 0.10 × 0.08 mm
Data collection top
Bruker Venture Photon III
diffractometer
2483 reflections with I > 2σ(I)
area detector profiles from φ and ω scansRint = 0.061
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)
θmax = 72.9°, θmin = 2.9°
Tmin = 0.523, Tmax = 0.754h = 99
12247 measured reflectionsk = 66
2540 independent reflectionsl = 1919
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.050 w = 1/[σ2(Fo2) + (0.0799P)2 + 0.4134P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.136(Δ/σ)max < 0.001
S = 1.08Δρmax = 0.44 e Å3
2540 reflectionsΔρmin = 0.28 e Å3
186 parametersAbsolute structure: Flack x determined using 1052 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
1 restraintAbsolute structure parameter: 0.009 (11)
Primary atom site location: dual
Special details top

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. 1. Fixed Uiso At 1.2 times of: All C(H) groups, All C(H,H) groups, All N(H) groups At 1.5 times of: All C(H,H,H) groups 2.a Ternary CH refined with riding coordinates: C3(H3) 2.b Secondary CH2 refined with riding coordinates: C2(H2A,H2B), C10(H10A,H10B) 2.c Aromatic/amide H refined with riding coordinates: C7(H7) 2.d Idealised Me refined as rotating group: C11(H11A,H11B,H11C), C13(H13A,H13B,H13C)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.46325 (14)0.0030 (2)0.91489 (7)0.0449 (3)
F10.3318 (3)0.1581 (4)0.73539 (17)0.0349 (6)
O10.4236 (3)0.2441 (5)0.57659 (19)0.0301 (6)
O20.1716 (4)0.0984 (5)0.50190 (19)0.0322 (7)
O30.8242 (3)0.6319 (5)0.70925 (19)0.0289 (6)
O40.9772 (4)0.7707 (7)0.9207 (2)0.0495 (9)
N10.1913 (5)0.4736 (7)0.5652 (2)0.0353 (8)
H10.090 (7)0.528 (11)0.557 (3)0.042*
C10.2492 (5)0.2622 (7)0.5438 (3)0.0268 (8)
C20.3247 (6)0.6254 (8)0.6146 (4)0.0493 (13)
H2A0.2988580.6690610.6725630.059*
H2B0.3399970.7737210.5816750.059*
C30.4851 (5)0.4609 (7)0.6246 (3)0.0328 (9)
H30.5737300.5393480.5958150.039*
C40.5655 (5)0.4054 (7)0.7189 (3)0.0270 (8)
C50.7273 (5)0.5032 (8)0.7582 (3)0.0275 (8)
C60.7992 (5)0.4604 (8)0.8463 (3)0.0294 (8)
C70.7180 (6)0.3066 (8)0.8952 (3)0.0321 (9)
H70.7693010.2726870.9547430.039*
C80.5617 (5)0.2021 (8)0.8570 (3)0.0304 (9)
C90.4874 (5)0.2588 (7)0.7713 (3)0.0278 (8)
C100.7841 (5)0.8849 (8)0.7014 (3)0.0353 (10)
H10A0.7667910.9495900.7585100.042*
H10B0.6765770.9111580.6569420.042*
C110.9338 (6)1.0079 (9)0.6736 (3)0.0387 (10)
H11A0.9571850.9313220.6202110.058*
H11B1.0366590.9952490.7208350.058*
H11C0.9056241.1777350.6616480.058*
C120.9720 (6)0.5739 (8)0.8859 (3)0.0345 (9)
C131.1270 (6)0.4320 (13)0.8800 (4)0.0605 (18)
H13A1.2311570.5235900.9056430.091*
H13B1.1276800.3970570.8180830.091*
H13C1.1254160.2810040.9123610.091*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0441 (6)0.0441 (6)0.0467 (6)0.0063 (5)0.0097 (5)0.0123 (5)
F10.0204 (11)0.0352 (14)0.0458 (14)0.0082 (9)0.0014 (9)0.0003 (11)
O10.0236 (13)0.0249 (14)0.0366 (15)0.0006 (11)0.0063 (11)0.0011 (11)
O20.0284 (14)0.0259 (14)0.0369 (15)0.0028 (11)0.0062 (12)0.0021 (12)
O30.0246 (13)0.0234 (14)0.0374 (15)0.0009 (11)0.0035 (11)0.0027 (12)
O40.0407 (18)0.040 (2)0.059 (2)0.0019 (15)0.0109 (16)0.0079 (16)
N10.0272 (17)0.0273 (18)0.044 (2)0.0064 (16)0.0101 (14)0.0030 (16)
C10.0214 (18)0.0269 (19)0.0282 (19)0.0005 (15)0.0043 (14)0.0061 (15)
C20.047 (3)0.023 (2)0.063 (3)0.007 (2)0.024 (2)0.003 (2)
C30.031 (2)0.023 (2)0.039 (2)0.0033 (16)0.0072 (17)0.0025 (16)
C40.0220 (17)0.0228 (17)0.033 (2)0.0010 (14)0.0024 (15)0.0008 (15)
C50.0199 (16)0.0234 (17)0.036 (2)0.0001 (15)0.0007 (14)0.0027 (17)
C60.0216 (17)0.031 (2)0.0322 (19)0.0010 (15)0.0037 (14)0.0037 (16)
C70.0283 (19)0.037 (2)0.0278 (19)0.0033 (16)0.0029 (16)0.0010 (16)
C80.0275 (19)0.027 (2)0.037 (2)0.0023 (15)0.0073 (16)0.0039 (16)
C90.0158 (16)0.0233 (18)0.041 (2)0.0003 (14)0.0035 (15)0.0026 (16)
C100.029 (2)0.025 (2)0.049 (3)0.0024 (17)0.0004 (18)0.0005 (19)
C110.041 (2)0.028 (2)0.048 (2)0.0125 (19)0.0126 (19)0.008 (2)
C120.030 (2)0.036 (2)0.032 (2)0.0060 (17)0.0048 (16)0.0022 (17)
C130.025 (2)0.077 (4)0.075 (4)0.002 (2)0.001 (2)0.039 (3)
Geometric parameters (Å, º) top
Cl1—C81.727 (4)C4—C91.379 (6)
F1—C91.361 (4)C5—C61.392 (6)
O1—C11.370 (5)C6—C71.380 (6)
O1—C31.449 (5)C6—C121.515 (5)
O2—C11.211 (5)C7—H70.9500
O3—C51.378 (5)C7—C81.383 (6)
O3—C101.443 (5)C8—C91.377 (6)
O4—C121.217 (6)C10—H10A0.9900
N1—H10.84 (6)C10—H10B0.9900
N1—C11.328 (6)C10—C111.498 (6)
N1—C21.443 (6)C11—H11A0.9800
C2—H2A0.9900C11—H11B0.9800
C2—H2B0.9900C11—H11C0.9800
C2—C31.542 (6)C12—C131.472 (7)
C3—H31.0000C13—H13A0.9800
C3—C41.505 (5)C13—H13B0.9800
C4—C51.408 (5)C13—H13C0.9800
C1—O1—C3109.7 (3)C6—C7—C8119.7 (4)
C5—O3—C10114.7 (3)C8—C7—H7120.1
C1—N1—H1130 (4)C7—C8—Cl1120.6 (3)
C1—N1—C2113.7 (4)C9—C8—Cl1120.2 (3)
C2—N1—H1116 (4)C9—C8—C7119.2 (4)
O2—C1—O1120.3 (4)F1—C9—C4118.2 (3)
O2—C1—N1129.7 (4)F1—C9—C8118.4 (4)
N1—C1—O1109.9 (3)C8—C9—C4123.3 (4)
N1—C2—H2A111.4O3—C10—H10A110.2
N1—C2—H2B111.4O3—C10—H10B110.2
N1—C2—C3101.6 (4)O3—C10—C11107.4 (4)
H2A—C2—H2B109.3H10A—C10—H10B108.5
C3—C2—H2A111.4C11—C10—H10A110.2
C3—C2—H2B111.4C11—C10—H10B110.2
O1—C3—C2105.0 (3)C10—C11—H11A109.5
O1—C3—H3109.0C10—C11—H11B109.5
O1—C3—C4111.1 (3)C10—C11—H11C109.5
C2—C3—H3109.0H11A—C11—H11B109.5
C4—C3—C2113.4 (4)H11A—C11—H11C109.5
C4—C3—H3109.0H11B—C11—H11C109.5
C5—C4—C3120.7 (4)O4—C12—C6120.2 (4)
C9—C4—C3122.9 (3)O4—C12—C13123.7 (4)
C9—C4—C5116.5 (3)C13—C12—C6116.1 (4)
O3—C5—C4121.1 (3)C12—C13—H13A109.5
O3—C5—C6117.8 (3)C12—C13—H13B109.5
C6—C5—C4121.0 (4)C12—C13—H13C109.5
C5—C6—C12118.9 (4)H13A—C13—H13B109.5
C7—C6—C5120.1 (4)H13A—C13—H13C109.5
C7—C6—C12120.9 (4)H13B—C13—H13C109.5
C6—C7—H7120.1
Cl1—C8—C9—F13.0 (5)C3—C4—C9—C8178.4 (4)
Cl1—C8—C9—C4174.5 (3)C4—C5—C6—C74.6 (6)
O1—C3—C4—C5132.4 (4)C4—C5—C6—C12178.7 (4)
O1—C3—C4—C947.5 (5)C5—O3—C10—C11161.8 (3)
O3—C5—C6—C7171.5 (4)C5—C4—C9—F1179.1 (3)
O3—C5—C6—C125.1 (6)C5—C4—C9—C81.6 (6)
N1—C2—C3—O12.5 (5)C5—C6—C7—C82.3 (6)
N1—C2—C3—C4119.0 (4)C5—C6—C12—O490.6 (5)
C1—O1—C3—C22.1 (5)C5—C6—C12—C1389.9 (6)
C1—O1—C3—C4120.9 (4)C6—C7—C8—Cl1176.6 (3)
C1—N1—C2—C32.3 (6)C6—C7—C8—C91.7 (6)
C2—N1—C1—O11.1 (5)C7—C6—C12—O492.8 (6)
C2—N1—C1—O2178.7 (5)C7—C6—C12—C1386.7 (6)
C2—C3—C4—C5109.5 (4)C7—C8—C9—F1178.7 (4)
C2—C3—C4—C970.5 (5)C7—C8—C9—C43.8 (6)
C3—O1—C1—O2179.4 (4)C9—C4—C5—O3173.4 (4)
C3—O1—C1—N10.8 (4)C9—C4—C5—C62.6 (6)
C3—C4—C5—O36.6 (6)C10—O3—C5—C487.1 (5)
C3—C4—C5—C6177.4 (4)C10—O3—C5—C696.8 (4)
C3—C4—C9—F10.9 (6)C12—C6—C7—C8178.9 (4)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.84 (6)2.12 (6)2.923 (4)161 (5)
Symmetry code: (i) x, y+1/2, z+1.
 

Acknowledgements

We thank Dr Jiacheng Zhou of Incyte Corp. for providing samples of (S)-4-{3-chloro-6-eth­oxy-2-fluoro-5-[(S)-1-hy­droxy­eth­yl]phen­yl}pyrrolidin-2-one.

Funding information

Funding for this research was provided by: National Institutes of Health (award No. S10 OD026896A to G. P. A. Yap).

References

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