organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

(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

(Received 17 December 2012; accepted 26 December 2012; online 23 January 2013)

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 coumarins, see: Murry et al. (1982[Murry, R. D. H., Mendez, J. & Brown, S. A. (1982). In The Natural Coumarins: Occurrence, Chemistry and Biochemistry. New York: John Wiley & Sons.]); Andersen et al. (2006[Andersen, M. & Markham, K. R. (2006). In Flavonoids: Chemistry, Biochemistry and Applications. Boca Raton: CRC Press.]); Murakami et al. (2001[Murakami, A., Yamayoshi, A., Iwase, R., Nishida, J., Yamaoka, T. & Wake, N. (2001). Eur. J. Pharm. Sci. 13, 25-34.]); Wu et al. (2003[Wu, J. Y., Fong, W. F., Zhang, J. X., Leung, C. H., Kwong, H. L. & Yang, M. S. (2003). Eur. J. Pharmacol. 473, 9-17.]). For their use as fluorescent probes and triplet sensitisers, see: Wagner (2009[Wagner, B. D. (2009). Molecules, 14, 210-237.]); Takadate et al. (1995[Takadate, A., Masuda, T., Murata, C., Tanaka, T., Irikura, M. & Goya, S. (1995). Anal. Sci. 11, 97-101.]). For a related structure, see: Da & Quan (2010[Da, Y.-X. & Quan, Z.-J. (2010). Acta Cryst. E66, o2872.]).

[Scheme 1]

Experimental

Crystal data
  • C13H9NO6

  • Mr = 275.21

  • Triclinic, [P \overline 1]

  • a = 7.4591 (13) Å

  • b = 8.2178 (19) Å

  • c = 10.0087 (18) Å

  • α = 85.202 (17)°

  • β = 77.346 (15)°

  • γ = 89.278 (17)°

  • V = 596.5 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.12 mm−1

  • T = 293 K

  • 0.4 × 0.32 × 0.2 mm

Data collection
  • Oxford Diffraction Xcalibur Eos diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]) Tmin = 0.917, Tmax = 1.000

  • 4789 measured reflections

  • 2093 independent reflections

  • 1395 reflections with I > 2σ(I)

  • Rint = 0.033

Refinement
  • R[F2 > 2σ(F2)] = 0.048

  • wR(F2) = 0.170

  • S = 0.93

  • 2093 reflections

  • 183 parameters

  • H-atom parameters constrained

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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.

Data collection: CrysAlis PRO (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis PRO. Oxford Diffraction Ltd, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

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.

Related literature top

For the biological importance of flavinoids and coumarins, see: Murry 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).

Experimental top

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..

Refinement top

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 refinement 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.

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the atom-numbering scheme with displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. View showing the weak C–H···O intermolecular interactions in compound (I).
[Figure 3] Fig. 3. Packing diagram of the title compound (I).
(Z)-3-(1-Hydroxy-3-oxobut-1-enyl)-6-nitro-2H-chromen-2-one top
Crystal data top
C13H9NO6Z = 2
Mr = 275.21F(000) = 284
Triclinic, P1Dx = 1.532 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.4591 (13) ÅCell parameters from 2257 reflections
b = 8.2178 (19) Åθ = 3.1–29.1°
c = 10.0087 (18) ŵ = 0.12 mm1
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
Data collection top
Oxford Diffraction Xcalibur Eos
diffractometer
2093 independent reflections
Radiation source: fine-focus sealed tube1395 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
Detector resolution: 15.9821 pixels mm-1θmax = 25.0°, θmin = 3.1°
ω scansh = 88
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
k = 98
Tmin = 0.917, Tmax = 1.000l = 1111
4789 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.170H-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 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C13H9NO6γ = 89.278 (17)°
Mr = 275.21V = 596.5 (2) Å3
Triclinic, P1Z = 2
a = 7.4591 (13) ÅMo Kα radiation
b = 8.2178 (19) ŵ = 0.12 mm1
c = 10.0087 (18) ÅT = 293 K
α = 85.202 (17)°0.4 × 0.32 × 0.2 mm
β = 77.346 (15)°
Data collection top
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 = 1.000Rint = 0.033
4789 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0480 restraints
wR(F2) = 0.170H-atom parameters constrained
S = 0.93Δρmax = 0.18 e Å3
2093 reflectionsΔρmin = 0.20 e Å3
183 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.25449 (19)0.17075 (18)0.16604 (16)0.0422 (5)
C40.5804 (3)0.1391 (2)0.1024 (2)0.0306 (5)
C20.4261 (3)0.3162 (2)0.0432 (2)0.0318 (5)
C50.7376 (3)0.0665 (2)0.1335 (2)0.0350 (6)
H50.85250.08870.07660.042*
C30.5812 (3)0.2510 (2)0.0161 (2)0.0329 (5)
H30.69270.27910.07570.040*
C90.4119 (3)0.1020 (3)0.1911 (2)0.0337 (5)
O30.6017 (2)0.4703 (2)0.23192 (17)0.0497 (5)
H3A0.59840.53640.29740.075*
O40.4619 (3)0.6406 (2)0.40237 (18)0.0584 (6)
C110.2837 (3)0.4849 (3)0.2152 (2)0.0417 (6)
H110.16600.45510.16680.050*
C60.7191 (3)0.0382 (3)0.2494 (2)0.0367 (6)
C80.3959 (3)0.0051 (3)0.3076 (2)0.0402 (6)
H80.28150.02840.36480.048*
O20.1007 (2)0.3272 (2)0.04475 (19)0.0620 (6)
C100.4319 (3)0.4287 (2)0.1671 (2)0.0344 (6)
N10.8848 (3)0.1149 (2)0.2826 (2)0.0474 (6)
C70.5514 (3)0.0762 (3)0.3373 (2)0.0393 (6)
H70.54440.14850.41490.047*
C10.2494 (3)0.2775 (3)0.0523 (2)0.0394 (6)
O60.8773 (3)0.1692 (3)0.3998 (2)0.0900 (8)
O51.0203 (2)0.1232 (2)0.1907 (2)0.0639 (6)
C130.1405 (4)0.6402 (4)0.3939 (3)0.0728 (9)
H13A0.17840.68910.48630.109*
H13B0.07160.71800.33690.109*
H13C0.06510.54620.39320.109*
C120.3071 (4)0.5893 (3)0.3397 (3)0.0474 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0340 (9)0.0494 (10)0.0382 (10)0.0047 (7)0.0036 (7)0.0134 (7)
C40.0345 (12)0.0279 (12)0.0291 (12)0.0022 (8)0.0071 (9)0.0012 (8)
C20.0367 (12)0.0279 (12)0.0297 (13)0.0012 (9)0.0064 (10)0.0017 (9)
C50.0315 (12)0.0373 (13)0.0348 (13)0.0012 (9)0.0054 (10)0.0014 (10)
C30.0332 (12)0.0324 (12)0.0302 (12)0.0031 (9)0.0022 (9)0.0024 (9)
C90.0344 (12)0.0354 (12)0.0308 (12)0.0018 (9)0.0076 (9)0.0013 (9)
O30.0494 (11)0.0562 (12)0.0381 (11)0.0036 (8)0.0053 (8)0.0177 (8)
O40.0770 (13)0.0554 (12)0.0395 (11)0.0030 (9)0.0123 (9)0.0143 (8)
C110.0491 (15)0.0397 (14)0.0365 (14)0.0011 (10)0.0135 (11)0.0062 (10)
C60.0406 (13)0.0361 (13)0.0363 (13)0.0046 (9)0.0156 (10)0.0016 (9)
C80.0383 (13)0.0486 (14)0.0295 (13)0.0025 (10)0.0022 (10)0.0068 (10)
O20.0348 (10)0.0816 (14)0.0625 (13)0.0106 (8)0.0080 (8)0.0261 (10)
C100.0436 (13)0.0297 (12)0.0287 (12)0.0019 (9)0.0059 (10)0.0003 (9)
N10.0478 (13)0.0527 (13)0.0445 (13)0.0056 (9)0.0198 (10)0.0041 (10)
C70.0482 (14)0.0403 (13)0.0283 (13)0.0022 (10)0.0089 (10)0.0049 (9)
C10.0409 (13)0.0405 (14)0.0342 (13)0.0030 (10)0.0066 (10)0.0065 (10)
O60.0764 (15)0.142 (2)0.0506 (13)0.0326 (14)0.0257 (11)0.0264 (13)
O50.0431 (11)0.0806 (14)0.0632 (14)0.0153 (9)0.0091 (9)0.0125 (10)
C130.090 (2)0.078 (2)0.0564 (19)0.0096 (16)0.0389 (17)0.0148 (15)
C120.0694 (18)0.0401 (14)0.0362 (14)0.0019 (12)0.0209 (13)0.0022 (11)
Geometric parameters (Å, º) top
O1—C91.360 (3)C11—C121.432 (3)
O1—C11.385 (3)C11—H110.9300
C4—C91.391 (3)C6—C71.384 (3)
C4—C51.392 (3)C6—N11.470 (3)
C4—C31.438 (3)C8—C71.370 (3)
C2—C31.341 (3)C8—H80.9300
C2—C11.470 (3)O2—O20.0000
C2—C101.476 (3)O2—C11.192 (3)
C5—C61.368 (3)N1—O61.210 (3)
C5—H50.9300N1—O51.214 (2)
C3—H30.9300C7—H70.9300
C9—C81.385 (3)C1—O21.192 (3)
O3—C101.325 (3)C13—C121.502 (4)
O3—H3A0.8200C13—H13A0.9600
O4—O40.000 (5)C13—H13B0.9600
O4—C121.247 (3)C13—H13C0.9600
C11—C101.361 (3)C12—O41.247 (3)
C9—O1—C1123.35 (17)O3—C10—C11121.5 (2)
C9—C4—C5118.4 (2)O3—C10—C2112.69 (18)
C9—C4—C3117.68 (19)C11—C10—C2125.8 (2)
C5—C4—C3123.93 (19)O6—N1—O5123.5 (2)
C3—C2—C1119.73 (19)O6—N1—C6118.0 (2)
C3—C2—C10120.49 (19)O5—N1—C6118.4 (2)
C1—C2—C10119.77 (18)C8—C7—C6118.7 (2)
C6—C5—C4118.5 (2)C8—C7—H7120.7
C6—C5—H5120.8C6—C7—H7120.7
C4—C5—H5120.8O2—C1—O20.00 (18)
C2—C3—C4121.97 (19)O2—C1—O1115.3 (2)
C2—C3—H3119.0O2—C1—O1115.3 (2)
C4—C3—H3119.0O2—C1—C2128.1 (2)
O1—C9—C8117.09 (19)O2—C1—C2128.1 (2)
O1—C9—C4120.68 (19)O1—C1—C2116.55 (18)
C8—C9—C4122.2 (2)C12—C13—H13A109.5
C10—O3—H3A109.5C12—C13—H13B109.5
O4—O4—C120 (10)H13A—C13—H13B109.5
C10—C11—C12120.7 (2)C12—C13—H13C109.5
C10—C11—H11119.7H13A—C13—H13C109.5
C12—C11—H11119.7H13B—C13—H13C109.5
C5—C6—C7123.2 (2)O4—C12—O40.0 (2)
C5—C6—N1118.6 (2)O4—C12—C11121.4 (2)
C7—C6—N1118.2 (2)O4—C12—C11121.4 (2)
C7—C8—C9119.0 (2)O4—C12—C13119.6 (2)
C7—C8—H8120.5O4—C12—C13119.6 (2)
C9—C8—H8120.5C11—C12—C13119.0 (3)
O2—O2—C10 (10)
C9—C4—C5—C60.2 (3)C7—C6—N1—O620.2 (4)
C3—C4—C5—C6180.0 (2)C5—C6—N1—O521.4 (3)
C1—C2—C3—C42.1 (3)C7—C6—N1—O5158.3 (2)
C10—C2—C3—C4179.02 (19)C9—C8—C7—C60.0 (4)
C9—C4—C3—C21.2 (3)C5—C6—C7—C80.4 (4)
C5—C4—C3—C2178.94 (19)N1—C6—C7—C8179.8 (2)
C1—O1—C9—C8178.8 (2)O2—O2—C1—O10.00 (3)
C1—O1—C9—C41.2 (3)O2—O2—C1—C20.00 (10)
C5—C4—C9—O1179.40 (19)C9—O1—C1—O2179.87 (19)
C3—C4—C9—O10.4 (3)C9—O1—C1—O2179.87 (19)
C5—C4—C9—C80.6 (3)C9—O1—C1—C20.4 (3)
C3—C4—C9—C8179.6 (2)C3—C2—C1—O2178.4 (2)
C4—C5—C6—C70.3 (4)C10—C2—C1—O20.5 (4)
C4—C5—C6—N1179.93 (18)C3—C2—C1—O2178.4 (2)
O1—C9—C8—C7179.48 (18)C10—C2—C1—O20.5 (4)
C4—C9—C8—C70.5 (4)C3—C2—C1—O11.2 (3)
C12—C11—C10—O31.0 (4)C10—C2—C1—O1179.84 (19)
C12—C11—C10—C2177.7 (2)O4—O4—C12—C110.00 (14)
C3—C2—C10—O38.2 (3)O4—O4—C12—C130.00 (10)
C1—C2—C10—O3170.69 (19)C10—C11—C12—O44.9 (4)
C3—C2—C10—C11170.6 (2)C10—C11—C12—O44.9 (4)
C1—C2—C10—C1110.5 (3)C10—C11—C12—C13176.3 (2)
C5—C6—N1—O6160.0 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3A···O40.821.782.510 (2)147
C11—H11···O20.932.242.870 (3)125
C3—H3···O5i0.932.583.308 (3)136
C7—H7···O4ii0.932.393.304 (3)166
Symmetry codes: (i) x+2, y, z; (ii) x, y1, z+1.

Experimental details

Crystal data
Chemical formulaC13H9NO6
Mr275.21
Crystal system, space groupTriclinic, 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)
V3)596.5 (2)
Z2
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.4 × 0.32 × 0.2
Data collection
DiffractometerOxford Diffraction Xcalibur Eos
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2009)
Tmin, Tmax0.917, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
4789, 2093, 1395
Rint0.033
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.170, 0.93
No. of reflections2093
No. of parameters183
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3A···O40.821.782.510 (2)147.3
C11—H11···O20.932.242.870 (3)124.5
C3—H3···O5i0.932.583.308 (3)135.7
C7—H7···O4ii0.932.393.304 (3)165.9
Symmetry codes: (i) x+2, y, z; (ii) x, y1, 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.

References

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