organic compounds
(Z)-3-(1-Hydroxy-3-oxobut-1-enyl)-6-nitro-2H-chromen-2-one
aCentre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605 014, India, and bDepartment of Chemistry, Pondicherry University, Puducherry 605 014, India
*Correspondence e-mail: krishstrucbio@gmail.com
In the title compound, C13H9NO6, the coumarin system has the benzene ring aligned at 0.61 (18)° with respect to the pyrone ring. An intramolecular O—H⋯O hydrogen bond stabilizes the molecular conformation and a C—H⋯O contact also occurs. In the crystal, weak C—H⋯O interactions link the molecules, forming inversion dimers.
Related literature
For the biological importance of flavinoids and et al. (1982); Andersen et al. (2006); Murakami et al. (2001); Wu et al. (2003). For their use as fluorescent probes and triplet sensitisers, see: Wagner (2009); Takadate et al. (1995). For a related structure, see: Da & Quan (2010).
see: MurryExperimental
Crystal data
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Refinement
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Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009).
Supporting information
10.1107/S1600536812051872/sj5289sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812051872/sj5289Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812051872/sj5289Isup3.cml
A solution of 4-hydroxy-6-methyl-3-(2-(methylamino)-3,6-dinitro-4H-chromen-4-yl)-2H-pyran-2-one (0.010 g, 0.266 mmol) in ethanol (15 ml) was heated to reflux for 25 min by which time the reaction was complete (TLC; hexanes: EtOAc, 6:4). The compound was crystallized and separated by filtration with the help of cold ethanol (5 ml) to yield 93% of the product, a yellow crystalline solid, mp 121.6 °C; IR (KBr) υmax cm-1; 1H NMR (400 MHz, DMSO-D6) δ 15.71 (s, 1H), 8.70 (s, 1H), 8.58 (s, 1H), 8.49 (d, J = 9.0 Hz, 1H), 7.51 (d, J = 9.12 Hz, 1H), 6.98 (s, 1H), 2.29 (s, 3H) p.p.m.; 13C NMR (100 MHz, DMSO-D6) δ 200.2, 171.1, 157.5, 153.3, 144.0, 136.6, 131.6, 121.8, 120.1, 118.4, 117.6, 102.0, 27.8 p.p.m..
All hydrogen atoms were placed in calculated positions, with C—H = 0.93Å for aromatic and 0.96Å for methyl and 0.82Å for hydroxyl H atoms and were included in the
using a riding model with Uiso(H) = x Ueq(C/O), where x = 1.5 for methyl and OH and 1.2 for all other atoms.Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell
CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009).C13H9NO6 | Z = 2 |
Mr = 275.21 | F(000) = 284 |
Triclinic, P1 | Dx = 1.532 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.4591 (13) Å | Cell parameters from 2257 reflections |
b = 8.2178 (19) Å | θ = 3.1–29.1° |
c = 10.0087 (18) Å | µ = 0.12 mm−1 |
α = 85.202 (17)° | T = 293 K |
β = 77.346 (15)° | Plate, colorless |
γ = 89.278 (17)° | 0.4 × 0.32 × 0.2 mm |
V = 596.5 (2) Å3 |
Oxford Diffraction Xcalibur Eos diffractometer | 2093 independent reflections |
Radiation source: fine-focus sealed tube | 1395 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.033 |
Detector resolution: 15.9821 pixels mm-1 | θmax = 25.0°, θmin = 3.1° |
ω scans | h = −8→8 |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | k = −9→8 |
Tmin = 0.917, Tmax = 1.000 | l = −11→11 |
4789 measured reflections |
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)] = 0.048 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.170 | H-atom parameters constrained |
S = 0.93 | w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3 |
2093 reflections | (Δ/σ)max < 0.001 |
183 parameters | Δρmax = 0.18 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C13H9NO6 | γ = 89.278 (17)° |
Mr = 275.21 | V = 596.5 (2) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.4591 (13) Å | Mo Kα radiation |
b = 8.2178 (19) Å | µ = 0.12 mm−1 |
c = 10.0087 (18) Å | T = 293 K |
α = 85.202 (17)° | 0.4 × 0.32 × 0.2 mm |
β = 77.346 (15)° |
Oxford Diffraction Xcalibur Eos diffractometer | 2093 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | 1395 reflections with I > 2σ(I) |
Tmin = 0.917, Tmax = 1.000 | Rint = 0.033 |
4789 measured reflections |
R[F2 > 2σ(F2)] = 0.048 | 0 restraints |
wR(F2) = 0.170 | H-atom parameters constrained |
S = 0.93 | Δρmax = 0.18 e Å−3 |
2093 reflections | Δρmin = −0.20 e Å−3 |
183 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.25449 (19) | 0.17075 (18) | 0.16604 (16) | 0.0422 (5) | |
C4 | 0.5804 (3) | 0.1391 (2) | 0.1024 (2) | 0.0306 (5) | |
C2 | 0.4261 (3) | 0.3162 (2) | −0.0432 (2) | 0.0318 (5) | |
C5 | 0.7376 (3) | 0.0665 (2) | 0.1335 (2) | 0.0350 (6) | |
H5 | 0.8525 | 0.0887 | 0.0766 | 0.042* | |
C3 | 0.5812 (3) | 0.2510 (2) | −0.0161 (2) | 0.0329 (5) | |
H3 | 0.6927 | 0.2791 | −0.0757 | 0.040* | |
C9 | 0.4119 (3) | 0.1020 (3) | 0.1911 (2) | 0.0337 (5) | |
O3 | 0.6017 (2) | 0.4703 (2) | −0.23192 (17) | 0.0497 (5) | |
H3A | 0.5984 | 0.5364 | −0.2974 | 0.075* | |
O4 | 0.4619 (3) | 0.6406 (2) | −0.40237 (18) | 0.0584 (6) | |
C11 | 0.2837 (3) | 0.4849 (3) | −0.2152 (2) | 0.0417 (6) | |
H11 | 0.1660 | 0.4551 | −0.1668 | 0.050* | |
C6 | 0.7191 (3) | −0.0382 (3) | 0.2494 (2) | 0.0367 (6) | |
C8 | 0.3959 (3) | −0.0051 (3) | 0.3076 (2) | 0.0402 (6) | |
H8 | 0.2815 | −0.0284 | 0.3648 | 0.048* | |
O2 | 0.1007 (2) | 0.3272 (2) | 0.04475 (19) | 0.0620 (6) | |
C10 | 0.4319 (3) | 0.4287 (2) | −0.1671 (2) | 0.0344 (6) | |
N1 | 0.8848 (3) | −0.1149 (2) | 0.2826 (2) | 0.0474 (6) | |
C7 | 0.5514 (3) | −0.0762 (3) | 0.3373 (2) | 0.0393 (6) | |
H7 | 0.5444 | −0.1485 | 0.4149 | 0.047* | |
C1 | 0.2494 (3) | 0.2775 (3) | 0.0523 (2) | 0.0394 (6) | |
O6 | 0.8773 (3) | −0.1692 (3) | 0.3998 (2) | 0.0900 (8) | |
O5 | 1.0203 (2) | −0.1232 (2) | 0.1907 (2) | 0.0639 (6) | |
C13 | 0.1405 (4) | 0.6402 (4) | −0.3939 (3) | 0.0728 (9) | |
H13A | 0.1784 | 0.6891 | −0.4863 | 0.109* | |
H13B | 0.0716 | 0.7180 | −0.3369 | 0.109* | |
H13C | 0.0651 | 0.5462 | −0.3932 | 0.109* | |
C12 | 0.3071 (4) | 0.5893 (3) | −0.3397 (3) | 0.0474 (6) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0340 (9) | 0.0494 (10) | 0.0382 (10) | 0.0047 (7) | −0.0036 (7) | 0.0134 (7) |
C4 | 0.0345 (12) | 0.0279 (12) | 0.0291 (12) | −0.0022 (8) | −0.0071 (9) | 0.0012 (8) |
C2 | 0.0367 (12) | 0.0279 (12) | 0.0297 (13) | −0.0012 (9) | −0.0064 (10) | 0.0017 (9) |
C5 | 0.0315 (12) | 0.0373 (13) | 0.0348 (13) | −0.0012 (9) | −0.0054 (10) | 0.0014 (10) |
C3 | 0.0332 (12) | 0.0324 (12) | 0.0302 (12) | −0.0031 (9) | −0.0022 (9) | 0.0024 (9) |
C9 | 0.0344 (12) | 0.0354 (12) | 0.0308 (12) | 0.0018 (9) | −0.0076 (9) | 0.0013 (9) |
O3 | 0.0494 (11) | 0.0562 (12) | 0.0381 (11) | −0.0036 (8) | −0.0053 (8) | 0.0177 (8) |
O4 | 0.0770 (13) | 0.0554 (12) | 0.0395 (11) | −0.0030 (9) | −0.0123 (9) | 0.0143 (8) |
C11 | 0.0491 (15) | 0.0397 (14) | 0.0365 (14) | 0.0011 (10) | −0.0135 (11) | 0.0062 (10) |
C6 | 0.0406 (13) | 0.0361 (13) | 0.0363 (13) | 0.0046 (9) | −0.0156 (10) | −0.0016 (9) |
C8 | 0.0383 (13) | 0.0486 (14) | 0.0295 (13) | −0.0025 (10) | −0.0022 (10) | 0.0068 (10) |
O2 | 0.0348 (10) | 0.0816 (14) | 0.0625 (13) | 0.0106 (8) | −0.0080 (8) | 0.0261 (10) |
C10 | 0.0436 (13) | 0.0297 (12) | 0.0287 (12) | −0.0019 (9) | −0.0059 (10) | 0.0003 (9) |
N1 | 0.0478 (13) | 0.0527 (13) | 0.0445 (13) | 0.0056 (9) | −0.0198 (10) | 0.0041 (10) |
C7 | 0.0482 (14) | 0.0403 (13) | 0.0283 (13) | 0.0022 (10) | −0.0089 (10) | 0.0049 (9) |
C1 | 0.0409 (13) | 0.0405 (14) | 0.0342 (13) | 0.0030 (10) | −0.0066 (10) | 0.0065 (10) |
O6 | 0.0764 (15) | 0.142 (2) | 0.0506 (13) | 0.0326 (14) | −0.0257 (11) | 0.0264 (13) |
O5 | 0.0431 (11) | 0.0806 (14) | 0.0632 (14) | 0.0153 (9) | −0.0091 (9) | 0.0125 (10) |
C13 | 0.090 (2) | 0.078 (2) | 0.0564 (19) | 0.0096 (16) | −0.0389 (17) | 0.0148 (15) |
C12 | 0.0694 (18) | 0.0401 (14) | 0.0362 (14) | 0.0019 (12) | −0.0209 (13) | 0.0022 (11) |
O1—C9 | 1.360 (3) | C11—C12 | 1.432 (3) |
O1—C1 | 1.385 (3) | C11—H11 | 0.9300 |
C4—C9 | 1.391 (3) | C6—C7 | 1.384 (3) |
C4—C5 | 1.392 (3) | C6—N1 | 1.470 (3) |
C4—C3 | 1.438 (3) | C8—C7 | 1.370 (3) |
C2—C3 | 1.341 (3) | C8—H8 | 0.9300 |
C2—C1 | 1.470 (3) | O2—O2 | 0.0000 |
C2—C10 | 1.476 (3) | O2—C1 | 1.192 (3) |
C5—C6 | 1.368 (3) | N1—O6 | 1.210 (3) |
C5—H5 | 0.9300 | N1—O5 | 1.214 (2) |
C3—H3 | 0.9300 | C7—H7 | 0.9300 |
C9—C8 | 1.385 (3) | C1—O2 | 1.192 (3) |
O3—C10 | 1.325 (3) | C13—C12 | 1.502 (4) |
O3—H3A | 0.8200 | C13—H13A | 0.9600 |
O4—O4 | 0.000 (5) | C13—H13B | 0.9600 |
O4—C12 | 1.247 (3) | C13—H13C | 0.9600 |
C11—C10 | 1.361 (3) | C12—O4 | 1.247 (3) |
C9—O1—C1 | 123.35 (17) | O3—C10—C11 | 121.5 (2) |
C9—C4—C5 | 118.4 (2) | O3—C10—C2 | 112.69 (18) |
C9—C4—C3 | 117.68 (19) | C11—C10—C2 | 125.8 (2) |
C5—C4—C3 | 123.93 (19) | O6—N1—O5 | 123.5 (2) |
C3—C2—C1 | 119.73 (19) | O6—N1—C6 | 118.0 (2) |
C3—C2—C10 | 120.49 (19) | O5—N1—C6 | 118.4 (2) |
C1—C2—C10 | 119.77 (18) | C8—C7—C6 | 118.7 (2) |
C6—C5—C4 | 118.5 (2) | C8—C7—H7 | 120.7 |
C6—C5—H5 | 120.8 | C6—C7—H7 | 120.7 |
C4—C5—H5 | 120.8 | O2—C1—O2 | 0.00 (18) |
C2—C3—C4 | 121.97 (19) | O2—C1—O1 | 115.3 (2) |
C2—C3—H3 | 119.0 | O2—C1—O1 | 115.3 (2) |
C4—C3—H3 | 119.0 | O2—C1—C2 | 128.1 (2) |
O1—C9—C8 | 117.09 (19) | O2—C1—C2 | 128.1 (2) |
O1—C9—C4 | 120.68 (19) | O1—C1—C2 | 116.55 (18) |
C8—C9—C4 | 122.2 (2) | C12—C13—H13A | 109.5 |
C10—O3—H3A | 109.5 | C12—C13—H13B | 109.5 |
O4—O4—C12 | 0 (10) | H13A—C13—H13B | 109.5 |
C10—C11—C12 | 120.7 (2) | C12—C13—H13C | 109.5 |
C10—C11—H11 | 119.7 | H13A—C13—H13C | 109.5 |
C12—C11—H11 | 119.7 | H13B—C13—H13C | 109.5 |
C5—C6—C7 | 123.2 (2) | O4—C12—O4 | 0.0 (2) |
C5—C6—N1 | 118.6 (2) | O4—C12—C11 | 121.4 (2) |
C7—C6—N1 | 118.2 (2) | O4—C12—C11 | 121.4 (2) |
C7—C8—C9 | 119.0 (2) | O4—C12—C13 | 119.6 (2) |
C7—C8—H8 | 120.5 | O4—C12—C13 | 119.6 (2) |
C9—C8—H8 | 120.5 | C11—C12—C13 | 119.0 (3) |
O2—O2—C1 | 0 (10) | ||
C9—C4—C5—C6 | 0.2 (3) | C7—C6—N1—O6 | −20.2 (4) |
C3—C4—C5—C6 | 180.0 (2) | C5—C6—N1—O5 | −21.4 (3) |
C1—C2—C3—C4 | 2.1 (3) | C7—C6—N1—O5 | 158.3 (2) |
C10—C2—C3—C4 | −179.02 (19) | C9—C8—C7—C6 | 0.0 (4) |
C9—C4—C3—C2 | −1.2 (3) | C5—C6—C7—C8 | −0.4 (4) |
C5—C4—C3—C2 | 178.94 (19) | N1—C6—C7—C8 | 179.8 (2) |
C1—O1—C9—C8 | −178.8 (2) | O2—O2—C1—O1 | 0.00 (3) |
C1—O1—C9—C4 | 1.2 (3) | O2—O2—C1—C2 | 0.00 (10) |
C5—C4—C9—O1 | 179.40 (19) | C9—O1—C1—O2 | 179.87 (19) |
C3—C4—C9—O1 | −0.4 (3) | C9—O1—C1—O2 | 179.87 (19) |
C5—C4—C9—C8 | −0.6 (3) | C9—O1—C1—C2 | −0.4 (3) |
C3—C4—C9—C8 | 179.6 (2) | C3—C2—C1—O2 | 178.4 (2) |
C4—C5—C6—C7 | 0.3 (4) | C10—C2—C1—O2 | −0.5 (4) |
C4—C5—C6—N1 | −179.93 (18) | C3—C2—C1—O2 | 178.4 (2) |
O1—C9—C8—C7 | −179.48 (18) | C10—C2—C1—O2 | −0.5 (4) |
C4—C9—C8—C7 | 0.5 (4) | C3—C2—C1—O1 | −1.2 (3) |
C12—C11—C10—O3 | 1.0 (4) | C10—C2—C1—O1 | 179.84 (19) |
C12—C11—C10—C2 | −177.7 (2) | O4—O4—C12—C11 | 0.00 (14) |
C3—C2—C10—O3 | −8.2 (3) | O4—O4—C12—C13 | 0.00 (10) |
C1—C2—C10—O3 | 170.69 (19) | C10—C11—C12—O4 | −4.9 (4) |
C3—C2—C10—C11 | 170.6 (2) | C10—C11—C12—O4 | −4.9 (4) |
C1—C2—C10—C11 | −10.5 (3) | C10—C11—C12—C13 | 176.3 (2) |
C5—C6—N1—O6 | 160.0 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3A···O4 | 0.82 | 1.78 | 2.510 (2) | 147 |
C11—H11···O2 | 0.93 | 2.24 | 2.870 (3) | 125 |
C3—H3···O5i | 0.93 | 2.58 | 3.308 (3) | 136 |
C7—H7···O4ii | 0.93 | 2.39 | 3.304 (3) | 166 |
Symmetry codes: (i) −x+2, −y, −z; (ii) x, y−1, z+1. |
Experimental details
Crystal data | |
Chemical formula | C13H9NO6 |
Mr | 275.21 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 293 |
a, b, c (Å) | 7.4591 (13), 8.2178 (19), 10.0087 (18) |
α, β, γ (°) | 85.202 (17), 77.346 (15), 89.278 (17) |
V (Å3) | 596.5 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.4 × 0.32 × 0.2 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur Eos diffractometer |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) |
Tmin, Tmax | 0.917, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4789, 2093, 1395 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.048, 0.170, 0.93 |
No. of reflections | 2093 |
No. of parameters | 183 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.18, −0.20 |
Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 2012), PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3A···O4 | 0.82 | 1.78 | 2.510 (2) | 147.3 |
C11—H11···O2 | 0.93 | 2.24 | 2.870 (3) | 124.5 |
C3—H3···O5i | 0.93 | 2.58 | 3.308 (3) | 135.7 |
C7—H7···O4ii | 0.93 | 2.39 | 3.304 (3) | 165.9 |
Symmetry codes: (i) −x+2, −y, −z; (ii) x, y−1, z+1. |
Footnotes
‡Additional correspondence author, e-mail: hspr@yahoo.com.
Acknowledgements
RK thanks the Department of Biotechnology and the Department of Information Technology, Government of India, New Delhi, for their financial support of the Centre for Bioinformatics, Pondicherry University, Puducherry. NST [No. F. 14–2(ST)/2010 (SA-III)] thanks the UGC for a Rajiv Gandhi National Fellowship to pursue his PhD degree. HSPR and VT thank the Council for Scientific and Industrial Research (CSIR), New Delhi, for financial support.
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Coumarins are heterocyclic compounds belonging to the benzopyrone chemical class, well known to exhibit varied biological activities (Murry et al., 1982; Andersen et al., 2006). In the technological and medicinal fields, coumarins and flavones, independently, find extensive use (Murakami et al., 2001) (Wu et al., 2003), with activities reported for anti-HIV, anti-tumor, anti-cancer, anti-hypertension, anti-arrhythmia, anti-inflammatory, anti-osteoporosis, antiseptic, and analgesic uses. They are also known to be used as fluorescent probes and as triplet sensitizers, especially those having electronic push-pull characteristics (Wagner, 2009; Takadate et al., 1995). Considering the importance of coumarin derivatives, we report here the structure of the title compound. A structure related to the title compound has also been reported (Da & Quan, 2010).
The molecular structure of the title compound is shown in Fig.1. The pyrone ring and the benzene ring are essentially co-planar with a dihedral angle of 0.61 (18)° between them. The benzene ring orients in a (-)-anti-periplanar conformation with respect to the pyrone ring. The crystal packing is stabilized by intermolecular C3—H3···O5, C3—H3···O5 and C7—H7···O4 bonds as shown in Fig.2 and Fig.3.