The crystal structure of the title compound obtained from the reduction of its nitro precursor, methyl 3-methoxy-4-nitroisoxazole-5-carboxylate, is described.
Keywords: crystal structure, isoxazole, hydrogen-bonded chain
Abstract
The title compound, C6H8N2O4, a new derivative of isoxazole, has been synthesized and structurally characterized. The crystal structure shows the molecule to be almost planar (r.m.s. deviation for the non-hydrogen atoms = 0.029 Å), this conformation being supported by an intramolecular N—H⋯O hydrogen bond. In the extended structure, the molecules are linked by N—H⋯O hydrogen bonds into chains propagating along [010].
Structure description
Isoxazoles, five-membered heterocyclic compounds containing adjacent nitrogen and oxygen atoms, have many applications including in photochromic components (Pu et al., 2011 ▸), liquid crystals (Kauhanka et al., 2006 ▸), solar cells (Yoon et al., 2022 ▸), high energy materials (Lal et al., 2023 ▸), pesticides and insecticides (Wang et al., 2022 ▸) and pharmaceuticals (Zhu et al., 2018 ▸). In a continuation of our previous work on isoxazole derivatives (Abdul Manan et al., 2023 ▸), we now present the synthesis and structure of the title compound.
The title compound, C6H8N2O4, crystallizes in space group P21/c with one molecule in the asymmetric unit (Fig. 1 ▸). All of the non-hydrogen atoms lie almost in the same plane, with an r.m.s. deviation of 0.029 Å and a maximum deviation of 0.060 (1) Å for C8. An intramolecular N—H⋯Oe (e = ester) hydrogen bond (Table 1 ▸) helps to ensure the near co-planarity of the isoxazole and ester moieties. This whole-molecule planarity, assisted by an intramolecular hydrogen bond, is similar to what was observed in the related compounds ethyl 5-amino-3-methylisoxazole-4-carboxylate (Sony et al., 2005 ▸), ethyl 5-amino-3-(difluoromethyl)isoxazole-4-carboxylate (Schmitt et al., 2015 ▸) and 5-amino-3-methylisoxazole-4-carbohydrazide (Regiec et al., 2018 ▸). The relative orientation of the ester and amine groups, allowing the formation of the intramolecular hydrogen bond to the ester oxygen atom rather than the carbonyl oxygen atom, is, however, different to what is seen in ethyl 5-amino-3-methylisoxazole-4-carboxylate (Sony et al., 2005 ▸), ethyl 5-amino-3-(difluoromethyl)isoxazole-4-carboxylate (Schmitt et al., 2015 ▸), ethyl 5-amino-3-[fluoro(trifluoromethoxy)methyl]isoxazole-4-carboxylate (Schmitt et al., 2017 ▸) and 1-(cyclohexylcarbamoyl)cyclohexyl 5-amino-3-methylisoxazole-4-carboxylate (Bąchor et al., 2019 ▸).
Figure 1.
The molecular structure of the title compound, showing displacement ellipsoids drawn at the 50% probability level.
Table 1. Hydrogen-bond geometry (Å, °).
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| N4—H4A⋯O6i | 0.89 (1) | 2.30 (2) | 2.9765 (16) | 133 (1) |
| N4—H4B⋯O1i | 0.91 (1) | 2.31 (2) | 3.0233 (15) | 136 (1) |
| N4—H4B⋯O7 | 0.91 (1) | 2.30 (2) | 2.8734 (16) | 121 (1) |
Symmetry code: (i)
.
In the crystal of the title compound, adjacent molecules are linked by N—H⋯Oc (c = carbonyl) and N—H⋯Oi (i = isoxazole) hydrogen bonds, forming an
(7) loop, which generates chains of molecules running along the crystallographic b-axis direction (Fig. 2 ▸). No additional directional interactions exist between chains. This combination of hydrogen bonds leading to chain formation is not seen in related isoxazole compounds as a result of the different relative position of the amine group on the isoxazole ring. While the combination of two inter- and one intramolecular hydrogen bond has been seen previously in related isoxazoles (Sony et al., 2005 ▸; Regiec et al., 2018 ▸; Bąchor et al., 2019 ▸), the pattern of hydrogen bonds is either different or has additional hydrogen bonds contributing to it, and the resulting supramolecular motifs differ as well. One-dimensional chain motifs have been seen in two of the related isoxazoles (Schmitt et al., 2015 ▸, 2017 ▸), although the pattern of hydrogen bonds that leads to the chains is different.
Figure 2.
View down the [101] axis of the [010] chain formed by N—H⋯O hydrogen bonds, which are shown as dashed lines.
Synthesis and crystallization
Synthesis of the methyl 3-methoxy-4-nitroisoxazole-5-carboxylate precursor
The starting material, methyl 3-methoxyisoxazole-5-carboxylate, was prepared according to the previously described literature procedure with minor modifications (Melikian et al., 1992 ▸). K2CO3 (2.9 g, 21.0 mmol, 1.5 eq) and CH3I (1.3 ml, 21.0 mmol, 1.5 eq) were added to a solution of methyl 3-hydroxyisoxazole-5-carboxylate (2.0 g, 13.9 mmol, 1.0 eq) in dimethylformamide (DMF) (10 ml) at 0°C. After 14 h stirring at room temperature, the mixture was poured into an ice-cold aqueous solution of HCl (0.5 M, 100 ml) and extracted into Et2O (5 × 80 ml). The combined organic layers were washed with a saturated aqueous solution of Na2CO3 (80 ml), dried over MgSO4, filtered and concentrated under reduced pressure to afford a light yellow crystalline solid, which was purified by silica gel column chromatography (petroleum ether/Et2O, 80:20), affording methyl 3-methoxyisoxazole-5-carboxylate (1.45 g, 66%) as a colourless crystalline solid.
Triflic anhydride (5.9 g, 21.0 mmol, 3.0 eq) was added to a solution of tetramethylammonium nitrate (2.9 g, 21.0 mmol, 3.0 eq) in DCM (3 ml) at room temperature. The suspension was stirred for 2 h, then a solution of methyl 3-methoxyisoxazole-5-carboxylate (1.1 g, 7.0 mmol, 1.0 eq) in dichloromethane (DCM) (10 ml) was added. After 48 h stirring under reflux, the mixture was cooled to room temperature and partitioned between water (30 ml) and DCM (40 ml). The organic layer was separated and washed with water (50 ml). The aqueous layer was extracted with DCM (3 × 50 ml). The combined organic layers were washed with brine (50 ml), dried over MgSO4, filtered and concentrated under reduced pressure. The resulting yellow residue was purified by silica gel column chromatography (petroleum ether/DCM, 50:50) to afford methyl 3-methoxy-4-nitroisoxazole-5-carboxylate (0.9 g, 70%) as yellowish oil: R f = 0.41 (petroleum ether/Et2O, 80:20, UV/KMnO4); 1H (500 MHz, CDCl3), δ: (p.p.m): 4.14 (3H, s), 4.02 (3H, s); 13C (125 MHz, CDCl3), δ: (p.p.m): 164.0, 157.4, 155.0, 127.7, 58.9, 54.2; HRMS m/z (APCI+), found: [M + H]+ 203.0295, C6H7N2O6 requires [M + H]+ 203.0299.
Synthesis of methyl 4-amino-3-methoxyisoxazole-5-carboxylate
Iron powder (267 mg, 4.86 mmol, 5.0 eq) was added to a solution of methyl 3-methoxy-4-nitroisoxazole-5-carboxylate (196 mg, 0.97 mmol, 1.0 eq) in AcOH/H2O (AcOH = acetic acid) (3:1 v/v mixture, 12 ml). After stirring at 50°C for 2 h, the solution was cooled to room temperature and the solvent was removed under reduced pressure. The residue was partitioned between water (20 ml) and ethyl acetate (EtOAc) (20 ml). The mixture was basified with a saturated aqueous solution of Na2CO3 and further extracted with EtOAc (3 × 20 ml). The combined organic layers were washed with brine (20 ml), dried over MgSO4, filtered and concentrated under reduced pressure to afford a pale-yellow solid, which was purified by silica gel column chromatography (DCM, 100), affording methyl 4-amino-3-methoxyisoxazole-5-carboxylate (139 mg, 83%) as a colourless crystalline solid: R f = 0.74 (DCM/EtOAc, 90:10, UV/ninhydrin); m.p. 111–112°C; 1H (500 MHz, CDCl3), δ: (p.p.m): 4.15 (br s, 2H), 4.05 (3H, s), 3.92 (3H, s); 13C (125 MHz, CDCl3), δ: (p.p.m): 164.5, 159.1, 138.4, 125.6, 57.5, 51.9; HRMS m/z (ESI+), found: [M + Na]+ 195.0373, C6H8N2O4Na requires [M + Na]+ 195.0382.
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸.
Table 2. Experimental details.
| Crystal data | |
| Chemical formula | C6H8N2O4 |
| M r | 172.14 |
| Crystal system, space group | Monoclinic, P21/c |
| Temperature (K) | 173 |
| a, b, c (Å) | 7.0425 (18), 11.555 (3), 9.654 (2) |
| β (°) | 106.629 (6) |
| V (Å3) | 752.7 (3) |
| Z | 4 |
| Radiation type | Mo Kα |
| μ (mm−1) | 0.13 |
| Crystal size (mm) | 0.27 × 0.06 × 0.06 |
| Data collection | |
| Diffractometer | Rigaku XtaLAB P200 |
| Absorption correction | Multi-scan (CrystalClear; Rigaku, 2014 ▸) |
| T min, T max | 0.695, 0.992 |
| No. of measured, independent and observed [F 2 > 2.0σ(F 2)] reflections | 9048, 1388, 1223 |
| R int | 0.051 |
| (sin θ/λ)max (Å−1) | 0.604 |
| Refinement | |
| R[F 2 > 2σ(F 2)], wR(F 2), S | 0.030, 0.083, 1.09 |
| No. of reflections | 1388 |
| No. of parameters | 119 |
| No. of restraints | 2 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
| Δρmax, Δρmin (e Å−3) | 0.17, −0.20 |
Supplementary Material
Crystal structure: contains datablock(s) I. DOI: 10.1107/S2414314623006235/hb4437sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314623006235/hb4437Isup2.hkl
Supporting information file. DOI: 10.1107/S2414314623006235/hb4437Isup3.mol
Supporting information file. DOI: 10.1107/S2414314623006235/hb4437Isup4.cml
CCDC reference: 2281787
Additional supporting information: crystallographic information; 3D view; checkCIF report
full crystallographic data
Crystal data
| C6H8N2O4 | F(000) = 360.00 |
| Mr = 172.14 | Dx = 1.519 Mg m−3 |
| Monoclinic, P21/c | Mo Kα radiation, λ = 0.71075 Å |
| a = 7.0425 (18) Å | Cell parameters from 2384 reflections |
| b = 11.555 (3) Å | θ = 2.8–25.4° |
| c = 9.654 (2) Å | µ = 0.13 mm−1 |
| β = 106.629 (6)° | T = 173 K |
| V = 752.7 (3) Å3 | Prism, colorless |
| Z = 4 | 0.27 × 0.06 × 0.06 mm |
Data collection
| Rigaku XtaLAB P200 diffractometer | 1388 independent reflections |
| Radiation source: Rotating Anode, Rigaku FR-X | 1223 reflections with F2 > 2.0σ(F2) |
| Rigaku Osmic Confocal Optical System monochromator | Rint = 0.051 |
| Detector resolution: 11.628 pixels mm-1 | θmax = 25.4°, θmin = 2.8° |
| ω scans | h = −8→8 |
| Absorption correction: multi-scan (CrystalClear; Rigaku, 2014) | k = −13→13 |
| Tmin = 0.695, Tmax = 0.992 | l = −11→11 |
| 9048 measured reflections |
Refinement
| Refinement on F2 | Secondary atom site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.030 | Hydrogen site location: mixed |
| wR(F2) = 0.083 | H atoms treated by a mixture of independent and constrained refinement |
| S = 1.09 | w = 1/[σ2(Fo2) + (0.0426P)2 + 0.1362P] where P = (Fo2 + 2Fc2)/3 |
| 1388 reflections | (Δ/σ)max < 0.001 |
| 119 parameters | Δρmax = 0.17 e Å−3 |
| 2 restraints | Δρmin = −0.20 e Å−3 |
| Primary atom site location: structure-invariant direct methods |
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. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 sigma(F2) is used only for calculating R-factor (gt).Carbon-bound H atoms were included in calculated positions (C—H = 0.98 Å) and refined as riding atoms with Uiso(H) = 1.2Ueq(C). The nitrogen-bound hydrogen atoms were located from difference Fourier maps and refined isotropically subject to a distance restraint. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | ||
| O1 | −0.02039 (14) | 0.26697 (7) | 0.62559 (10) | 0.0332 (3) | |
| O3 | 0.32430 (13) | 0.09325 (8) | 0.53449 (10) | 0.0333 (3) | |
| O6 | −0.30018 (14) | 0.23906 (8) | 0.77949 (11) | 0.0376 (3) | |
| O7 | −0.19751 (14) | 0.05355 (8) | 0.82206 (10) | 0.0355 (3) | |
| N2 | 0.12840 (17) | 0.25137 (9) | 0.55608 (12) | 0.0321 (3) | |
| N4 | 0.11557 (19) | −0.02825 (9) | 0.71104 (14) | 0.0380 (3) | |
| H4A | 0.201 (2) | −0.0715 (13) | 0.6805 (17) | 0.044 (4)* | |
| H4B | 0.039 (2) | −0.0582 (14) | 0.7641 (17) | 0.046 (4)* | |
| C3 | 0.18521 (18) | 0.14406 (10) | 0.58185 (13) | 0.0275 (3) | |
| C4 | 0.08233 (18) | 0.08329 (10) | 0.66715 (13) | 0.0271 (3) | |
| C5 | −0.04431 (18) | 0.16376 (10) | 0.69055 (14) | 0.0289 (3) | |
| C6 | −0.19340 (18) | 0.16034 (10) | 0.76742 (14) | 0.0297 (3) | |
| C7 | −0.3398 (2) | 0.03562 (12) | 0.90147 (17) | 0.0396 (4) | |
| H7A | −0.313327 | 0.089774 | 0.982892 | 0.048* | |
| H7B | −0.329201 | −0.043968 | 0.937968 | 0.048* | |
| H7C | −0.473727 | 0.048846 | 0.837561 | 0.048* | |
| C8 | 0.4105 (2) | 0.16335 (12) | 0.44464 (16) | 0.0375 (3) | |
| H8A | 0.471816 | 0.232123 | 0.498567 | 0.045* | |
| H8B | 0.306859 | 0.187186 | 0.357868 | 0.045* | |
| H8C | 0.511435 | 0.118384 | 0.416398 | 0.045* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| O1 | 0.0415 (5) | 0.0222 (4) | 0.0413 (5) | 0.0044 (4) | 0.0205 (4) | 0.0028 (4) |
| O3 | 0.0375 (5) | 0.0275 (5) | 0.0410 (6) | 0.0027 (4) | 0.0211 (4) | 0.0030 (4) |
| O6 | 0.0383 (5) | 0.0303 (5) | 0.0495 (6) | 0.0026 (4) | 0.0209 (5) | −0.0031 (4) |
| O7 | 0.0399 (5) | 0.0281 (5) | 0.0451 (6) | −0.0013 (4) | 0.0227 (4) | 0.0007 (4) |
| N2 | 0.0385 (6) | 0.0262 (6) | 0.0360 (6) | 0.0012 (4) | 0.0178 (5) | 0.0013 (4) |
| N4 | 0.0473 (7) | 0.0223 (6) | 0.0534 (8) | 0.0053 (5) | 0.0291 (6) | 0.0077 (5) |
| C3 | 0.0299 (6) | 0.0245 (6) | 0.0291 (7) | −0.0004 (5) | 0.0102 (5) | −0.0018 (5) |
| C4 | 0.0294 (7) | 0.0231 (6) | 0.0283 (6) | −0.0013 (5) | 0.0077 (5) | −0.0013 (5) |
| C5 | 0.0340 (7) | 0.0224 (6) | 0.0309 (7) | −0.0018 (5) | 0.0104 (6) | −0.0006 (5) |
| C6 | 0.0316 (7) | 0.0260 (6) | 0.0318 (7) | −0.0026 (5) | 0.0098 (5) | −0.0042 (5) |
| C7 | 0.0421 (8) | 0.0377 (8) | 0.0469 (9) | −0.0057 (6) | 0.0252 (7) | 0.0002 (6) |
| C8 | 0.0398 (8) | 0.0368 (7) | 0.0427 (8) | 0.0006 (6) | 0.0227 (6) | 0.0057 (6) |
Geometric parameters (Å, º)
| O1—C5 | 1.3801 (15) | N4—H4B | 0.910 (14) |
| O1—N2 | 1.4083 (15) | C3—C4 | 1.4275 (18) |
| O3—C3 | 1.3302 (15) | C4—C5 | 1.3514 (17) |
| O3—C8 | 1.4417 (16) | C5—C6 | 1.4493 (19) |
| O6—C6 | 1.2070 (15) | C7—H7A | 0.9800 |
| O7—C6 | 1.3456 (16) | C7—H7B | 0.9800 |
| O7—C7 | 1.4403 (17) | C7—H7C | 0.9800 |
| N2—C3 | 1.3048 (16) | C8—H8A | 0.9800 |
| N4—C4 | 1.3560 (17) | C8—H8B | 0.9800 |
| N4—H4A | 0.893 (13) | C8—H8C | 0.9800 |
| C5—O1—N2 | 108.07 (9) | O6—C6—O7 | 124.71 (12) |
| C3—O3—C8 | 115.92 (10) | O6—C6—C5 | 126.27 (12) |
| C6—O7—C7 | 115.91 (10) | O7—C6—C5 | 109.01 (10) |
| C3—N2—O1 | 105.08 (10) | O7—C7—H7A | 109.5 |
| C4—N4—H4A | 120.1 (11) | O7—C7—H7B | 109.5 |
| C4—N4—H4B | 117.4 (11) | H7A—C7—H7B | 109.5 |
| H4A—N4—H4B | 122.2 (15) | O7—C7—H7C | 109.5 |
| N2—C3—O3 | 124.73 (11) | H7A—C7—H7C | 109.5 |
| N2—C3—C4 | 113.51 (11) | H7B—C7—H7C | 109.5 |
| O3—C3—C4 | 121.76 (11) | O3—C8—H8A | 109.5 |
| C5—C4—N4 | 131.68 (12) | O3—C8—H8B | 109.5 |
| C5—C4—C3 | 103.07 (11) | H8A—C8—H8B | 109.5 |
| N4—C4—C3 | 125.24 (11) | O3—C8—H8C | 109.5 |
| C4—C5—O1 | 110.27 (11) | H8A—C8—H8C | 109.5 |
| C4—C5—C6 | 132.56 (12) | H8B—C8—H8C | 109.5 |
| O1—C5—C6 | 117.18 (11) | ||
| C5—O1—N2—C3 | −0.22 (13) | N4—C4—C5—C6 | −1.7 (2) |
| O1—N2—C3—O3 | 179.64 (11) | C3—C4—C5—C6 | 179.23 (13) |
| O1—N2—C3—C4 | −0.08 (14) | N2—O1—C5—C4 | 0.46 (14) |
| C8—O3—C3—N2 | −2.12 (18) | N2—O1—C5—C6 | −179.30 (10) |
| C8—O3—C3—C4 | 177.58 (11) | C7—O7—C6—O6 | −0.80 (19) |
| N2—C3—C4—C5 | 0.35 (14) | C7—O7—C6—C5 | −179.66 (10) |
| O3—C3—C4—C5 | −179.38 (11) | C4—C5—C6—O6 | −179.16 (14) |
| N2—C3—C4—N4 | −178.81 (12) | O1—C5—C6—O6 | 0.53 (19) |
| O3—C3—C4—N4 | 1.45 (19) | C4—C5—C6—O7 | −0.32 (19) |
| N4—C4—C5—O1 | 178.61 (13) | O1—C5—C6—O7 | 179.37 (10) |
| C3—C4—C5—O1 | −0.48 (13) |
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| N4—H4A···O6i | 0.89 (1) | 2.30 (2) | 2.9765 (16) | 133 (1) |
| N4—H4B···O1i | 0.91 (1) | 2.31 (2) | 3.0233 (15) | 136 (1) |
| N4—H4B···O7 | 0.91 (1) | 2.30 (2) | 2.8734 (16) | 121 (1) |
Symmetry code: (i) −x, y−1/2, −z+3/2.
Funding Statement
The authors acknowledge Universiti Teknologi MARA for financial support.
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) I. DOI: 10.1107/S2414314623006235/hb4437sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314623006235/hb4437Isup2.hkl
Supporting information file. DOI: 10.1107/S2414314623006235/hb4437Isup3.mol
Supporting information file. DOI: 10.1107/S2414314623006235/hb4437Isup4.cml
CCDC reference: 2281787
Additional supporting information: crystallographic information; 3D view; checkCIF report