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

Li, V.; Yap, G.P.A.; Ni, C.

doi:10.1107/S2056989024001920

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Volume 80| Part 4| April 2024| Pages 375-377

https://doi.org/10.1107/S2056989024001920

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

Victor Li,^a Glenn P. A. Yap ^b and Chaoying Ni ^c ^*

^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.

Keywords: crystal structure; oxazolidinone; parsaclib; pharmaceutical; kinase inhibitor; anti-cancer; drug.

CCDC reference: 2306123

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 ). Cases with elevated levels of phosphoinositide 3-kinase delta (PI3Kδ) were found associated with increased cancer susceptibility (Crank et al., 2014 ). 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 ). 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 ), which should subsequently yield parsaclisib as per the reaction scheme.

2. Structural commentary

The asymmetric unit consisting of one complete molecule of the title compound is shown in Fig. 1. 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 ). 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
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) occur between neighboring molecules related by −x, $[{1\over 2}]$ + y, 1 − z, resulting in chains parallel to the b-axis direction (Fig. 2). 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 ). 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 ; Norte et al., 1988 ; Qin et al., 2012; Bresciani et al., 2020 ).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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
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 ) for structures containing the 5-(arene)-oxazolidine-2-one moiety yielded five additional structures: EWIPEI (Chen et al., 2021), GIGHUZ (Norte et al., 1988), MAZDEN (Qin et al., 2012), WAFCEP (Bresciani et al., 2020) and YALYUJ (Denisov & Gagarskikh, 2021).

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. Amide H atoms were located from difference maps and positionally refined. Other H atoms were positioned geometrically. All H atoms refined as riding with U_iso(H) = 1.2 or 1.5U_eq(C,N).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₃ClFNO₄
M_r	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)
V (Å³)	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 )
T_min, T_max	0.523, 0.754
No. of measured, independent and observed [I > 2σ(I)] reflections	12247, 2540, 2483
R_int	0.061
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.28
Absolute structure	Flack x determined using 1052 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	0.009 (11)
Computer programs: APEX4 (Bruker, 2021 ), SAINT (Bruker, 2016 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2019/3 (Sheldrick, 2015b ), and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 2306123

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989024001920/jy2039sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024001920/jy2039Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989024001920/jy2039Isup3.cml

checkCIF report

Computing details top

(S)-5-(3-acetyl-5-chloro-2-ethoxy-6-fluorophenyl)-2-oxazolidinone top

Crystal data top

C₁₃H₁₃ClFNO₄	F(000) = 312
M_r = 301.69	D_x = 1.506 Mg m⁻³
Monoclinic, P2₁	Cu Kα radiation, λ = 1.54178 Å
a = 7.8729 (12) Å	Cell parameters from 9877 reflections
b = 5.5655 (8) Å	θ = 2.9–72.0°
c = 15.492 (2) Å	µ = 2.80 mm⁻¹
β = 101.446 (3)°	T = 100 K
V = 665.31 (17) Å³	Needle, colourless
Z = 2	0.41 × 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 scans	R_int = 0.061
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 72.9°, θ_min = 2.9°
T_min = 0.523, T_max = 0.754	h = −9→9
12247 measured reflections	k = −6→6
2540 independent reflections	l = −19→19

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.050	w = 1/[σ²(F_o²) + (0.0799P)² + 0.4134P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.136	(Δ/σ)_max < 0.001
S = 1.08	Δρ_max = 0.44 e Å⁻³
2540 reflections	Δρ_min = −0.28 e Å⁻³
186 parameters	Absolute structure: Flack x determined using 1052 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
1 restraint	Absolute 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

	x	y	z	U_iso*/U_eq
Cl1	0.46325 (14)	−0.0030 (2)	0.91489 (7)	0.0449 (3)
F1	0.3318 (3)	0.1581 (4)	0.73539 (17)	0.0349 (6)
O1	0.4236 (3)	0.2441 (5)	0.57659 (19)	0.0301 (6)
O2	0.1716 (4)	0.0984 (5)	0.50190 (19)	0.0322 (7)
O3	0.8242 (3)	0.6319 (5)	0.70925 (19)	0.0289 (6)
O4	0.9772 (4)	0.7707 (7)	0.9207 (2)	0.0495 (9)
N1	0.1913 (5)	0.4736 (7)	0.5652 (2)	0.0353 (8)
H1	0.090 (7)	0.528 (11)	0.557 (3)	0.042*
C1	0.2492 (5)	0.2622 (7)	0.5438 (3)	0.0268 (8)
C2	0.3247 (6)	0.6254 (8)	0.6146 (4)	0.0493 (13)
H2A	0.298858	0.669061	0.672563	0.059*
H2B	0.339997	0.773721	0.581675	0.059*
C3	0.4851 (5)	0.4609 (7)	0.6246 (3)	0.0328 (9)
H3	0.573730	0.539348	0.595815	0.039*
C4	0.5655 (5)	0.4054 (7)	0.7189 (3)	0.0270 (8)
C5	0.7273 (5)	0.5032 (8)	0.7582 (3)	0.0275 (8)
C6	0.7992 (5)	0.4604 (8)	0.8463 (3)	0.0294 (8)
C7	0.7180 (6)	0.3066 (8)	0.8952 (3)	0.0321 (9)
H7	0.769301	0.272687	0.954743	0.039*
C8	0.5617 (5)	0.2021 (8)	0.8570 (3)	0.0304 (9)
C9	0.4874 (5)	0.2588 (7)	0.7713 (3)	0.0278 (8)
C10	0.7841 (5)	0.8849 (8)	0.7014 (3)	0.0353 (10)
H10A	0.766791	0.949590	0.758510	0.042*
H10B	0.676577	0.911158	0.656942	0.042*
C11	0.9338 (6)	1.0079 (9)	0.6736 (3)	0.0387 (10)
H11A	0.957185	0.931322	0.620211	0.058*
H11B	1.036659	0.995249	0.720835	0.058*
H11C	0.905624	1.177735	0.661648	0.058*
C12	0.9720 (6)	0.5739 (8)	0.8859 (3)	0.0345 (9)
C13	1.1270 (6)	0.4320 (13)	0.8800 (4)	0.0605 (18)
H13A	1.231157	0.523590	0.905643	0.091*
H13B	1.127680	0.397057	0.818083	0.091*
H13C	1.125416	0.281004	0.912361	0.091*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0441 (6)	0.0441 (6)	0.0467 (6)	−0.0063 (5)	0.0097 (5)	0.0123 (5)
F1	0.0204 (11)	0.0352 (14)	0.0458 (14)	−0.0082 (9)	−0.0014 (9)	0.0003 (11)
O1	0.0236 (13)	0.0249 (14)	0.0366 (15)	−0.0006 (11)	−0.0063 (11)	−0.0011 (11)
O2	0.0284 (14)	0.0259 (14)	0.0369 (15)	−0.0028 (11)	−0.0062 (12)	−0.0021 (12)
O3	0.0246 (13)	0.0234 (14)	0.0374 (15)	−0.0009 (11)	0.0035 (11)	−0.0027 (12)
O4	0.0407 (18)	0.040 (2)	0.059 (2)	−0.0019 (15)	−0.0109 (16)	−0.0079 (16)
N1	0.0272 (17)	0.0273 (18)	0.044 (2)	0.0064 (16)	−0.0101 (14)	−0.0030 (16)
C1	0.0214 (18)	0.0269 (19)	0.0282 (19)	0.0005 (15)	−0.0043 (14)	0.0061 (15)
C2	0.047 (3)	0.023 (2)	0.063 (3)	0.007 (2)	−0.024 (2)	−0.003 (2)
C3	0.031 (2)	0.023 (2)	0.039 (2)	−0.0033 (16)	−0.0072 (17)	0.0025 (16)
C4	0.0220 (17)	0.0228 (17)	0.033 (2)	0.0010 (14)	−0.0024 (15)	0.0008 (15)
C5	0.0199 (16)	0.0234 (17)	0.036 (2)	0.0001 (15)	−0.0007 (14)	−0.0027 (17)
C6	0.0216 (17)	0.031 (2)	0.0322 (19)	0.0010 (15)	−0.0037 (14)	−0.0037 (16)
C7	0.0283 (19)	0.037 (2)	0.0278 (19)	0.0033 (16)	−0.0029 (16)	−0.0010 (16)
C8	0.0275 (19)	0.027 (2)	0.037 (2)	0.0023 (15)	0.0073 (16)	0.0039 (16)
C9	0.0158 (16)	0.0233 (18)	0.041 (2)	−0.0003 (14)	−0.0035 (15)	−0.0026 (16)
C10	0.029 (2)	0.025 (2)	0.049 (3)	0.0024 (17)	0.0004 (18)	−0.0005 (19)
C11	0.041 (2)	0.028 (2)	0.048 (2)	−0.0125 (19)	0.0126 (19)	−0.008 (2)
C12	0.030 (2)	0.036 (2)	0.032 (2)	−0.0060 (17)	−0.0048 (16)	−0.0022 (17)
C13	0.025 (2)	0.077 (4)	0.075 (4)	−0.002 (2)	0.001 (2)	−0.039 (3)

Geometric parameters (Å, º) top

Cl1—C8	1.727 (4)	C4—C9	1.379 (6)
F1—C9	1.361 (4)	C5—C6	1.392 (6)
O1—C1	1.370 (5)	C6—C7	1.380 (6)
O1—C3	1.449 (5)	C6—C12	1.515 (5)
O2—C1	1.211 (5)	C7—H7	0.9500
O3—C5	1.378 (5)	C7—C8	1.383 (6)
O3—C10	1.443 (5)	C8—C9	1.377 (6)
O4—C12	1.217 (6)	C10—H10A	0.9900
N1—H1	0.84 (6)	C10—H10B	0.9900
N1—C1	1.328 (6)	C10—C11	1.498 (6)
N1—C2	1.443 (6)	C11—H11A	0.9800
C2—H2A	0.9900	C11—H11B	0.9800
C2—H2B	0.9900	C11—H11C	0.9800
C2—C3	1.542 (6)	C12—C13	1.472 (7)
C3—H3	1.0000	C13—H13A	0.9800
C3—C4	1.505 (5)	C13—H13B	0.9800
C4—C5	1.408 (5)	C13—H13C	0.9800

C1—O1—C3	109.7 (3)	C6—C7—C8	119.7 (4)
C5—O3—C10	114.7 (3)	C8—C7—H7	120.1
C1—N1—H1	130 (4)	C7—C8—Cl1	120.6 (3)
C1—N1—C2	113.7 (4)	C9—C8—Cl1	120.2 (3)
C2—N1—H1	116 (4)	C9—C8—C7	119.2 (4)
O2—C1—O1	120.3 (4)	F1—C9—C4	118.2 (3)
O2—C1—N1	129.7 (4)	F1—C9—C8	118.4 (4)
N1—C1—O1	109.9 (3)	C8—C9—C4	123.3 (4)
N1—C2—H2A	111.4	O3—C10—H10A	110.2
N1—C2—H2B	111.4	O3—C10—H10B	110.2
N1—C2—C3	101.6 (4)	O3—C10—C11	107.4 (4)
H2A—C2—H2B	109.3	H10A—C10—H10B	108.5
C3—C2—H2A	111.4	C11—C10—H10A	110.2
C3—C2—H2B	111.4	C11—C10—H10B	110.2
O1—C3—C2	105.0 (3)	C10—C11—H11A	109.5
O1—C3—H3	109.0	C10—C11—H11B	109.5
O1—C3—C4	111.1 (3)	C10—C11—H11C	109.5
C2—C3—H3	109.0	H11A—C11—H11B	109.5
C4—C3—C2	113.4 (4)	H11A—C11—H11C	109.5
C4—C3—H3	109.0	H11B—C11—H11C	109.5
C5—C4—C3	120.7 (4)	O4—C12—C6	120.2 (4)
C9—C4—C3	122.9 (3)	O4—C12—C13	123.7 (4)
C9—C4—C5	116.5 (3)	C13—C12—C6	116.1 (4)
O3—C5—C4	121.1 (3)	C12—C13—H13A	109.5
O3—C5—C6	117.8 (3)	C12—C13—H13B	109.5
C6—C5—C4	121.0 (4)	C12—C13—H13C	109.5
C5—C6—C12	118.9 (4)	H13A—C13—H13B	109.5
C7—C6—C5	120.1 (4)	H13A—C13—H13C	109.5
C7—C6—C12	120.9 (4)	H13B—C13—H13C	109.5
C6—C7—H7	120.1

Cl1—C8—C9—F1	3.0 (5)	C3—C4—C9—C8	178.4 (4)
Cl1—C8—C9—C4	−174.5 (3)	C4—C5—C6—C7	4.6 (6)
O1—C3—C4—C5	132.4 (4)	C4—C5—C6—C12	−178.7 (4)
O1—C3—C4—C9	−47.5 (5)	C5—O3—C10—C11	161.8 (3)
O3—C5—C6—C7	−171.5 (4)	C5—C4—C9—F1	−179.1 (3)
O3—C5—C6—C12	5.1 (6)	C5—C4—C9—C8	−1.6 (6)
N1—C2—C3—O1	2.5 (5)	C5—C6—C7—C8	−2.3 (6)
N1—C2—C3—C4	−119.0 (4)	C5—C6—C12—O4	90.6 (5)
C1—O1—C3—C2	−2.1 (5)	C5—C6—C12—C13	−89.9 (6)
C1—O1—C3—C4	120.9 (4)	C6—C7—C8—Cl1	176.6 (3)
C1—N1—C2—C3	−2.3 (6)	C6—C7—C8—C9	−1.7 (6)
C2—N1—C1—O1	1.1 (5)	C7—C6—C12—O4	−92.8 (6)
C2—N1—C1—O2	−178.7 (5)	C7—C6—C12—C13	86.7 (6)
C2—C3—C4—C5	−109.5 (4)	C7—C8—C9—F1	−178.7 (4)
C2—C3—C4—C9	70.5 (5)	C7—C8—C9—C4	3.8 (6)
C3—O1—C1—O2	−179.4 (4)	C9—C4—C5—O3	173.4 (4)
C3—O1—C1—N1	0.8 (4)	C9—C4—C5—C6	−2.6 (6)
C3—C4—C5—O3	−6.6 (6)	C10—O3—C5—C4	87.1 (5)
C3—C4—C5—C6	177.4 (4)	C10—O3—C5—C6	−96.8 (4)
C3—C4—C9—F1	0.9 (6)	C12—C6—C7—C8	−178.9 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.84 (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).

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Volume 80| Part 4| April 2024| Pages 375-377

https://doi.org/10.1107/S2056989024001920

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

Funding information

References

research communications

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

3. Supramolecular features