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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2017 Mar 17;73(Pt 4):531–534. doi: 10.1107/S2056989017003127

Crystal structure and Hirshfeld surface analysis of ethyl 5-phenyl­isoxazole-3-carboxyl­ate

Althaf Shaik a, Sivapriya Kirubakaran a, Vijay Thiruvenkatam b,*
PMCID: PMC5382615  PMID: 28435714

In the title isoxazole derivative, the phenyl and isoxazole rings are in the same plane, as indicated by the C—C—C—O torsion angle of 0.1 (3)°. The ester group 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)°.

Keywords: crystal structure, isoxazole derivative, drug inter­mediate, Hirshfeld surface, hydrogen bonding

Abstract

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 R 2 1(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.

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 crystal structure and the qu­anti­tative analysis of inter­molecular inter­actions using the Hirshfeld surface and 2D fingerprint plot analysis.graphic file with name e-73-00531-scheme1.jpg

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)°.

Figure 1.

Figure 1

The mol­ecular structure of compound (I), with the atom labelling and displacement ellipsoid drawn at the 50% probability level.

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 Inline graphic(7) ring motifs (Table 1 and Fig. 2). The mol­ecules stack in layers lying parallel to (10Inline graphic), as illustrated in Fig. 3.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA 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) Inline graphic.

Figure 2.

Figure 2

Crystal packing of compound (I), viewed along the a axis. Hydrogen bonds are shown as dashed lines (see Table 1).

Figure 3.

Figure 3

Crystal packing of compound (I) viewed along the b axis. Hydrogen bonds are shown as dashed lines and, for clarity, H atoms have been omitted.

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 d norm, shape index and curvedness. The d norm surface is the normalized function of d i and d e (Fig. 4 a), 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. 4 b) 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. 5 a. The 2D fingerprint plot analysis of the O⋯H inter­actions revealed significant hydrogen-bonding spikes (d i = 1.3, d e = 0.9 Å and d e = 1.9, d i = 2.6 Å); Fig. 6 c.

Figure 4.

Figure 4

Hirshfeld surface mapped over (a) d norm and (b) electrostatic potential.

Figure 5.

Figure 5

Hirshfeld surface mapped over (a) d norm highlighting the regions of C—H⋯O hydrogen bonding and (b) d norm highlighting the region of C—H⋯N hydrogen bonding.

Figure 6.

Figure 6

Two-dimensional fingerprint plot analysis (a) all inter­actions, (b) H⋯H contacts, (c) O⋯H contacts, (d) N⋯H contacts, (e) C⋯H contacts and (f) C⋯C contacts.

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. 5 b). The fingerprint plot analysis of N⋯H contacts reveals a significant wing-like structure (d i = 1.2, d e = 1.5 Å and d e = 2.2, d i = 2.4 Å) Fig. 6 d.

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).

Figure 7.

Figure 7

Relative contribution of each inter­action in the two-dimensional fingerprint analysis.

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 asymmetric unit. 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)°.

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 column chromatography (3% ethyl acetate: Pet-ether) to afford the title compound, (I) (yield 76.9%, 0.75 g; m.p. 325–327 K).

Figure 8.

Figure 8

Synthesis of the title compound, (I).

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.

Refinement  

Crystal data, data collection and structure refinement parameters are given in Table 2. All H atoms were positioned geometrically and refined as riding: C—H = 0.95–0.99 Å with U iso(H) = 1.2U eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula C12H11NO3
M r 217.22
Crystal system, space group Monoclinic, P21/n
Temperature (K) 100
a, b, c (Å) 5.4447 (7), 17.180 (2), 11.7603 (19)
β (°) 94.508 (5)
V3) 1096.6 (3)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.4 × 0.2 × 0.2
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction
No. of measured, independent and observed [I > 2σ(I)] reflections 14119, 2813, 1889
R int 0.075
(sin θ/λ)max−1) 0.676
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.064, 0.177, 1.09
No. of reflections 2813
No. of parameters 146
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.27, −0.30

Computer programs: APEX2 and SAINT (Bruker, 2006), SHELXS97 and SHELXTL (Sheldrick 2008), SHELXL2014 (Sheldrick, 2015), and Mercury (Macrae et al., 2008).

Supplementary Material

Crystal structure: contains datablock(s) I, Global. DOI: 10.1107/S2056989017003127/su5350sup1.cif

e-73-00531-sup1.cif (427KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017003127/su5350Isup2.hkl

e-73-00531-Isup2.hkl (225KB, hkl)

Supporting information file. DOI: 10.1107/S2056989017003127/su5350Isup5.cml

Supporting information file. DOI: 10.1107/S2056989017003127/su5350sup3.png

Supporting information file. DOI: 10.1107/S2056989017003127/su5350sup4.png

CCDC reference: 1534636

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Crystal data

C12H11NO3 F(000) = 456
Mr = 217.22 Dx = 1.316 Mg m3
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 mm1
β = 94.508 (5)° T = 100 K
V = 1096.6 (3) Å3 Blocks, colourless
Z = 4 0.4 × 0.2 × 0.2 mm

Data collection

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

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 Å3
0 restraints Δρmin = −0.30 e Å3

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

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*

Atomic displacement parameters (Å2)

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)

Geometric parameters (Å, º)

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)

Hydrogen-bond geometry (Å, º)

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.

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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) I, Global. DOI: 10.1107/S2056989017003127/su5350sup1.cif

e-73-00531-sup1.cif (427KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017003127/su5350Isup2.hkl

e-73-00531-Isup2.hkl (225KB, hkl)

Supporting information file. DOI: 10.1107/S2056989017003127/su5350Isup5.cml

Supporting information file. DOI: 10.1107/S2056989017003127/su5350sup3.png

Supporting information file. DOI: 10.1107/S2056989017003127/su5350sup4.png

CCDC reference: 1534636

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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