research communications
and Hirshfeld surface analysis of ethyl 5-phenylisoxazole-3-carboxylate
aDepartment of Chemistry, IIT Gandhinagar, Gujarat, and bDepartment of Physics & Bio-Engineering, IIT Gandhinagar, Palaj Campus, Gandhinagar, Gujarat
*Correspondence e-mail: vijay@iitgn.ac.in
The title compound, C12H11NO3, is an intermediate used in the synthesis of many drug-like molecules. The molecule is almost planar, with the phenyl ring inclined to the isoxazole ring by 0.5 (1)°. The ester moiety has an extended conformation and is almost in the same plane with respect to the isoxazole ring, as indicated by the O—C—C—N torsion angle of −172.86 (18)°. In the crystal, molecules are linked via pairs of C—H⋯O hydrogen bonds with the same acceptor atom, forming inversion dimers with two R21(7) ring motifs. The molecules stack in layers lying parallel to (10-3). Analysis using Hirshfeld surface generation and two-dimensional fingerprint plots explores the distribution of weak intermolecular interactions in the crystal structure.
Keywords: crystal structure; isoxazole derivative; drug intermediate; Hirshfeld surface; hydrogen bonding.
CCDC reference: 1534636
1. Chemical context
Nitrogen-containing heterocyclic rings are of great importance in medicinal and organic chemistry (Dou et al., 2013). Isoxazole derivatives are important heterocyclic pharmaceuticals having a broad spectrum of biological activity, which includes antagonism of the NMDA receptor, anti-inflammatory (Panda et al., 2009), anti-tumour, anticonvulsant, anti-psychotic, anti-depressant and anti HIV activity (Conti et al., 2005; Srivastava et al., 1999). Considerable attention has been paid to isoxazole derivatives as a result of their prominent biological properties (Dou et al., 2013). Valdecoxib (Bextra), a selective cyclooxygenase-2 (COX-2) inhibitor used in the treatment of arthritis, contains an isoxazole moiety which is responsible for its biological activity (Waldo & Larock, 2007; Dadiboyena & Nefzi, 2010). In addition, isoxazole derivatives are also important intermediates in the preparation of various heterocyclic biologically active drugs (Dou et al., 2013). As part of our ongoing studies on isoxazole derivatives as kinase inhibitors, we have synthesized the title compound, and report herein on its and the quantitative analysis of intermolecular interactions using the Hirshfeld surface and 2D fingerprint plot analysis.
2. Structural commentary
The molecular structure of the title compound, (I), is illustrated in Fig. 1. The molecule consists of three almost flat units: the phenyl ring, the isoxazole ring and the ester. The phenyl (C1–C6) and isoxazole (O1/N1/C7–C9) rings are almost coplanar, as indicated by the torsion angle C5—C6—C7—O1 = 0.1 (3)°. The ester unit has an extended conformation and is almost in the same plane as the isoxazole ring, as indicated by the torsion angle O2—C10—C9—N1 = −172.86 (18)°.
3. Supramolecular features
In the crystal of (I), molecules are linked via pairs of C—H⋯O hydrogen bonds, both involving atom O2 as acceptor, forming inversion dimers with two R21(7) ring motifs (Table 1 and Fig. 2). The molecules stack in layers lying parallel to (10), as illustrated in Fig. 3.
4. Hirshfeld surface and fingerprint plot analysis
To explore the weak intermolecular interactions in (I), Hirshfeld surfaces and 2D fingerprint plots were generated using Crystal Explorer 3.1 to quantify the intermolecular interactions (McKinnon et al., 2007; Spackman & Jayatilaka, 2009). Hirshfeld surfaces are produced through the partitioning of space within a crystal where the ratio of promolecule to procrystal electron density is equal to 0.5, generating continuous, non-overlapping surfaces which are widely used to visualize and study the significance of weak interactions in the molecular packing (McKinnon et al., 2007). The Hirshfeld surface of title compound was mapped over dnorm, shape index and curvedness. The dnorm surface is the normalized function of di and de (Fig. 4a), with white-, red- and blue-coloured surfaces. The white surface indicates those contacts with distances equal to the sum of the van der Waals (vdW) radii, red indicates shorter contacts (< vdW radii) and blue the longer contact (> vdW radii). The Hirshfeld surface was also mapped over electrostatic potential (Fig. 4b) using a STO-3G basis set at the Hartee–Fock level of theory (Spackman & McKinnon, 2002; McKinnon et al., 2004). In the Hirshfeld surface, a pair of interactions between the aromatic C—H⋯O=C atoms can be seen as the bright-red area (1) in Fig. 5a. The 2D fingerprint plot analysis of the O⋯H interactions revealed significant hydrogen-bonding spikes (di = 1.3, de = 0.9 Å and de = 1.9, di = 2.6 Å); Fig. 6c.
The analysis indicates that there is a weak N⋯H intermolecular interaction between the nitrogen atom of the isoxazole ring and the methylene hydrogen atom of the phenyl ring of a neighbouring molecule (Fig. 5b). The fingerprint plot analysis of N⋯H contacts reveals a significant wing-like structure (di = 1.2, de = 1.5 Å and de = 2.2, di = 2.4 Å) Fig. 6d.
The relative contributions to the Hirshfeld surface area for each type of intermolecular contact are illustrated in Figs. 6 and 7. The H⋯H interactions appear as scattered points over nearly the entire plot and have a significant composition of 41% of the Hirshfeld surface. The H⋯O contacts comprise of 18.7% and the C⋯C interactions comprise 1.6% of the total Hirshfeld surface. The C⋯H and N⋯H interactions cover 23.2% and 9.2% of the surface, respectively. Thus, these weak interactions contribute significantly to the packing of (I).
5. Database survey
A search of the Cambridge Structural Database (CSD, V5.38; last update November 2016; Groom et al., 2016) for similar isoxazole derivatives, revealed only one hit, viz. ethyl 5-(4-aminophenyl) isoxazole-3-carboxylate (CSD refcode YAVRIY; Zhao et al., 2012). This compound crystallizes with two independent molecules in the One molecule is slightly more planar than the other, with the phenyl ring being inclined to the isoxazole ring by 1.77 (10) and 5.85 (10)°. In the title compound, (I), this dihedral angle is 0.5 (1)°.
6. Synthesis and crystallization
There are several methods available in the literature for the preparation of isoxazole derivatives. We have followed a simple preparation from a diketoester (Tourteau et al., 2013; Bastos et al., 2015). After the reaction of acetophenone with diethyoxalate in a basic solution (sodium ethoxide) of ethanol for 8 h, 1N HCl was added to neutralize the sodium ethoxide to obtain the diketoester (ethyl 2,4-dioxo-4-phenylbutanoate; see Fig. 8) as a yellow liquid. 1 g (4.5 mmol) of the diketoester in ethanol was added to hydroxyl amine hydrochloride (0.315 g, 4.5 mmol) at room temperature and the resulting mixture was stirred at 353 K for 12 h. The progress of the reaction was monitored by TLC. After the completion of starting materials, the reaction mixture was cooled to room temperature and the excess of ethanol removed. The resulting residue was dissolved in water and extracted with ethyl acetate. The organic layer was dried with Na2SO4, filtered and the concentrated under reduced pressure. The resulting residue was purified by silica gel (3% ethyl acetate: Pet-ether) to afford the title compound, (I) (yield 76.9%, 0.75 g; m.p. 325–327 K).
Colourless crystals were obtained by slow evaporation of a solution in ethyl acetate. Spectroscopic data: 1H NMR (500 MHz, chloroform-d) δ 7.80 (m, 2H), 7.50 (m, 3H), 6.92 (s, 1H), 4.47 (q, 2H), 1.44 (t, 3H). 13C NMR (126 MHz, chloroform-d) δ 171.66, 159.98, 156.96, 130.76, 129.11, 126.61, 125.89, 99.92, 62.18, 14.15.
7. Refinement
Crystal data, data collection and structure . All H atoms were positioned geometrically and refined as riding: C—H = 0.95–0.99 Å with Uiso(H) = 1.2Ueq(C).
parameters are given in Table 2Supporting information
CCDC reference: 1534636
https://doi.org/10.1107/S2056989017003127/su5350sup1.cif
contains datablocks I, Global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017003127/su5350Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989017003127/su5350Isup5.cml
Supporting information file. DOI: https://doi.org/10.1107/S2056989017003127/su5350sup3.png
Supporting information file. DOI: https://doi.org/10.1107/S2056989017003127/su5350sup4.png
Data collection: APEX2 (Bruker, 2006); cell
SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: SHELXTL (Sheldrick 2008) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick 2008).C12H11NO3 | F(000) = 456 |
Mr = 217.22 | Dx = 1.316 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
a = 5.4447 (7) Å | Cell parameters from 5392 reflections |
b = 17.180 (2) Å | θ = 2.4–30.5° |
c = 11.7603 (19) Å | µ = 0.10 mm−1 |
β = 94.508 (5)° | T = 100 K |
V = 1096.6 (3) Å3 | Blocks, colourless |
Z = 4 | 0.4 × 0.2 × 0.2 mm |
Bruker APEXII CCD diffractometer | Rint = 0.075 |
φ and ω scans | θmax = 28.7°, θmin = 2.4° |
14119 measured reflections | h = −5→7 |
2813 independent reflections | k = −23→23 |
1889 reflections with I > 2σ(I) | l = −15→14 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.064 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.177 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3 |
2813 reflections | (Δ/σ)max < 0.001 |
146 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.30 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.1048 (2) | 0.62026 (7) | 0.20002 (11) | 0.0221 (4) | |
O3 | −0.4360 (3) | 0.73867 (7) | 0.01862 (12) | 0.0230 (4) | |
O2 | −0.6161 (2) | 0.62208 (7) | −0.01700 (11) | 0.0243 (4) | |
C10 | −0.4499 (3) | 0.66119 (10) | 0.02530 (16) | 0.0184 (4) | |
C6 | 0.1914 (3) | 0.48387 (10) | 0.22525 (16) | 0.0181 (4) | |
N1 | −0.0666 (3) | 0.67215 (8) | 0.14685 (14) | 0.0225 (4) | |
C4 | 0.5520 (4) | 0.44302 (11) | 0.34137 (19) | 0.0256 (5) | |
H4 | 0.692513 | 0.455560 | 0.387897 | 0.031* | |
C7 | 0.0322 (4) | 0.54579 (9) | 0.17410 (16) | 0.0174 (4) | |
C9 | −0.2320 (3) | 0.62718 (10) | 0.09196 (15) | 0.0180 (4) | |
C5 | 0.4000 (4) | 0.50161 (10) | 0.29503 (17) | 0.0234 (5) | |
H5 | 0.438869 | 0.553372 | 0.311094 | 0.028* | |
C3 | 0.4941 (4) | 0.36559 (11) | 0.31817 (17) | 0.0249 (5) | |
H3 | 0.596502 | 0.326217 | 0.348598 | 0.030* | |
C1 | 0.1308 (4) | 0.40540 (10) | 0.20262 (16) | 0.0203 (4) | |
H1 | −0.010182 | 0.392615 | 0.156628 | 0.024* | |
C12 | −0.5855 (4) | 0.86283 (11) | −0.04174 (18) | 0.0273 (5) | |
H12A | −0.579681 | 0.880375 | 0.035929 | 0.041* | |
H12B | −0.711938 | 0.890614 | −0.086440 | 0.041* | |
H12C | −0.429204 | 0.872225 | −0.071751 | 0.041* | |
C8 | −0.1780 (3) | 0.54715 (9) | 0.10639 (16) | 0.0185 (4) | |
H8 | −0.267753 | 0.504983 | 0.075862 | 0.022* | |
C11 | −0.6410 (4) | 0.77721 (11) | −0.04635 (18) | 0.0243 (5) | |
H11A | −0.794720 | 0.766468 | −0.012878 | 0.029* | |
H11B | −0.654755 | 0.759053 | −0.124690 | 0.029* | |
C2 | 0.2846 (4) | 0.34724 (10) | 0.24996 (17) | 0.0237 (5) | |
H2 | 0.245566 | 0.295307 | 0.235394 | 0.028* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0236 (8) | 0.0114 (6) | 0.0300 (8) | 0.0009 (5) | −0.0065 (6) | 0.0016 (5) |
O3 | 0.0239 (8) | 0.0128 (6) | 0.0314 (8) | 0.0024 (5) | −0.0047 (6) | 0.0009 (5) |
O2 | 0.0233 (8) | 0.0170 (6) | 0.0319 (8) | −0.0022 (5) | −0.0028 (6) | −0.0018 (6) |
C10 | 0.0199 (10) | 0.0140 (8) | 0.0215 (10) | −0.0001 (7) | 0.0026 (8) | −0.0025 (7) |
C6 | 0.0190 (10) | 0.0150 (8) | 0.0207 (10) | 0.0016 (7) | 0.0047 (8) | 0.0019 (7) |
N1 | 0.0246 (10) | 0.0139 (7) | 0.0280 (9) | 0.0031 (6) | −0.0052 (7) | 0.0029 (7) |
C4 | 0.0195 (11) | 0.0220 (10) | 0.0345 (12) | −0.0005 (8) | −0.0036 (8) | 0.0034 (8) |
C7 | 0.0234 (11) | 0.0102 (8) | 0.0190 (10) | −0.0019 (7) | 0.0041 (8) | −0.0019 (7) |
C9 | 0.0209 (10) | 0.0131 (8) | 0.0204 (10) | −0.0019 (7) | 0.0035 (8) | 0.0001 (7) |
C5 | 0.0211 (11) | 0.0146 (9) | 0.0345 (12) | −0.0003 (7) | 0.0017 (9) | 0.0006 (8) |
C3 | 0.0224 (11) | 0.0195 (9) | 0.0331 (11) | 0.0057 (8) | 0.0038 (9) | 0.0064 (8) |
C1 | 0.0218 (11) | 0.0161 (8) | 0.0228 (10) | −0.0003 (7) | 0.0005 (8) | −0.0010 (7) |
C12 | 0.0294 (12) | 0.0197 (9) | 0.0320 (12) | 0.0047 (8) | −0.0019 (9) | 0.0042 (8) |
C8 | 0.0208 (10) | 0.0108 (8) | 0.0243 (10) | −0.0014 (7) | 0.0032 (8) | −0.0020 (7) |
C11 | 0.0219 (11) | 0.0197 (9) | 0.0300 (11) | 0.0041 (8) | −0.0055 (8) | 0.0009 (8) |
C2 | 0.0276 (11) | 0.0150 (8) | 0.0289 (11) | 0.0020 (8) | 0.0042 (8) | −0.0001 (8) |
O1—C7 | 1.366 (2) | C9—C8 | 1.413 (2) |
O1—N1 | 1.4018 (19) | C5—H5 | 0.9300 |
O3—C10 | 1.336 (2) | C3—C2 | 1.379 (3) |
O3—C11 | 1.461 (2) | C3—H3 | 0.9300 |
O2—C10 | 1.203 (2) | C1—C2 | 1.391 (3) |
C10—C9 | 1.489 (3) | C1—H1 | 0.9300 |
C6—C5 | 1.382 (3) | C12—C11 | 1.502 (2) |
C6—C1 | 1.408 (2) | C12—H12A | 0.9600 |
C6—C7 | 1.471 (2) | C12—H12B | 0.9600 |
N1—C9 | 1.317 (2) | C12—H12C | 0.9600 |
C4—C3 | 1.389 (3) | C8—H8 | 0.9300 |
C4—C5 | 1.387 (3) | C11—H11A | 0.9700 |
C4—H4 | 0.9300 | C11—H11B | 0.9700 |
C7—C8 | 1.342 (3) | C2—H2 | 0.9300 |
C7—O1—N1 | 108.98 (13) | C4—C3—H3 | 120.1 |
C10—O3—C11 | 115.97 (14) | C2—C1—C6 | 119.14 (18) |
O2—C10—O3 | 125.19 (16) | C2—C1—H1 | 120.4 |
O2—C10—C9 | 122.75 (16) | C6—C1—H1 | 120.4 |
O3—C10—C9 | 112.06 (15) | C11—C12—H12A | 109.5 |
C5—C6—C1 | 119.53 (17) | C11—C12—H12B | 109.5 |
C5—C6—C7 | 120.93 (16) | H12A—C12—H12B | 109.5 |
C1—C6—C7 | 119.54 (17) | C11—C12—H12C | 109.5 |
C9—N1—O1 | 104.55 (14) | H12A—C12—H12C | 109.5 |
C3—C4—C5 | 119.89 (19) | H12B—C12—H12C | 109.5 |
C3—C4—H4 | 120.1 | C9—C8—C7 | 104.35 (15) |
C5—C4—H4 | 120.1 | C9—C8—H8 | 127.8 |
O1—C7—C8 | 109.53 (15) | C7—C8—H8 | 127.8 |
O1—C7—C6 | 115.78 (16) | O3—C11—C12 | 106.35 (15) |
C8—C7—C6 | 134.68 (16) | O3—C11—H11A | 110.5 |
C8—C9—N1 | 112.59 (16) | C12—C11—H11A | 110.5 |
C8—C9—C10 | 126.49 (16) | O3—C11—H11B | 110.5 |
N1—C9—C10 | 120.92 (15) | C12—C11—H11B | 110.5 |
C6—C5—C4 | 120.69 (17) | H11A—C11—H11B | 108.7 |
C6—C5—H5 | 119.7 | C3—C2—C1 | 120.87 (17) |
C4—C5—H5 | 119.7 | C3—C2—H2 | 119.6 |
C2—C3—C4 | 119.87 (18) | C1—C2—H2 | 119.6 |
C2—C3—H3 | 120.1 | ||
C11—O3—C10—O2 | −0.4 (3) | O3—C10—C9—N1 | 7.3 (2) |
C11—O3—C10—C9 | 179.40 (15) | C1—C6—C5—C4 | 1.1 (3) |
C7—O1—N1—C9 | −0.10 (19) | C7—C6—C5—C4 | −178.82 (18) |
N1—O1—C7—C8 | 0.15 (19) | C3—C4—C5—C6 | −0.4 (3) |
N1—O1—C7—C6 | −179.04 (15) | C5—C4—C3—C2 | −0.6 (3) |
C5—C6—C7—O1 | 0.1 (3) | C5—C6—C1—C2 | −0.9 (3) |
C1—C6—C7—O1 | −179.73 (15) | C7—C6—C1—C2 | 179.02 (17) |
C5—C6—C7—C8 | −178.8 (2) | N1—C9—C8—C7 | 0.1 (2) |
C1—C6—C7—C8 | 1.3 (3) | C10—C9—C8—C7 | −178.89 (17) |
O1—N1—C9—C8 | 0.0 (2) | O1—C7—C8—C9 | −0.13 (19) |
O1—N1—C9—C10 | 179.04 (15) | C6—C7—C8—C9 | 178.9 (2) |
O2—C10—C9—C8 | 6.0 (3) | C10—O3—C11—C12 | 179.89 (15) |
O3—C10—C9—C8 | −173.78 (16) | C4—C3—C2—C1 | 0.8 (3) |
O2—C10—C9—N1 | −172.86 (18) | C6—C1—C2—C3 | 0.0 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C1—H1···O2i | 0.93 | 2.52 | 3.447 (2) | 171 |
C8—H8···O2i | 0.93 | 2.36 | 3.260 (2) | 163 |
Symmetry code: (i) −x−1, −y+1, −z. |
Acknowledgements
SK is grateful for a Ramanujan Fellowship. VT and AS thank the IIT Gandhinagar for laboratory facilities and infrastructure. The authors thank the IISER Bhopal for the SCXRD facility.
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