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Acta Crystallogr Sect E Struct Rep Online. 2009 September 1; 65(Pt 9): o2171.
Published online 2009 August 15. doi:  10.1107/S1600536809031535
PMCID: PMC2970156

2,2-Dimethyl-5-[(3-nitro­anilino)methyl­ene]-1,3-dioxane-4,6-dione

Abstract

The benzene ring of the title compound, C13H12N2O6, is twisted away from the planes of the amino­methyl­ene unit and the dioxane ring by 30.13 (4) and 35.89 (4)°, respectively. The dioxane ring exhibits a half-boat conformation, in which the C atom between the dioxane O atoms is 0.553 (8) Å out-of-plane. An intra­molecular N—H(...)O hydrogen bond stabilizes the conformation of the dioxane ring with the amino­methyl­ene group [the dihedral angle between the mean planes of the dioxane ring and the amino­methyl­ene group is 11.61 (4)°]. In the crystal, a three-dimensional framework is built via weak inter­molecular N—H(...)O and C—H(...)O inter­actions.

Related literature

For the synthesis of related compounds, see: Cassis et al. (1985 [triangle]). For the synthesis of related anti­tumor precursors, see Ruchelman et al. (2003 [triangle]). For the crystal structures of related 5-aryl­amino­methyl­ene-2,2-dimethyl-1,3-dioxane-4,6-dione deriv­atives, see Li et al. (2009a [triangle],b [triangle]); Li, Shi et al. (2009 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2171-scheme1.jpg

Experimental

Crystal data

  • C13H12N2O6
  • M r = 292.25
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2171-efi1.jpg
  • a = 11.7900 (13) Å
  • b = 8.7699 (9) Å
  • c = 14.0614 (15) Å
  • β = 113.8640 (10)°
  • V = 1329.6 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 153 K
  • 0.20 × 0.10 × 0.10 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: none
  • 8116 measured reflections
  • 3052 independent reflections
  • 2572 reflections with I > 2σ(I)
  • R int = 0.014

Refinement

  • R[F 2 > 2σ(F 2)] = 0.036
  • wR(F 2) = 0.101
  • S = 1.05
  • 3052 reflections
  • 197 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.18 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809031535/zq2002sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809031535/zq2002Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This research was supported financially by the State Key Laboratory of Drug Research (Shanghai Institute of Materia Medica, Chinese Academy of Sciences).

supplementary crystallographic information

Comment

The 4(1H)quinolone structure have long attracted pharmacological interest as anticancer agents, anti-malarial agents and reversible (H+/K+) ATPase inhibitors (Ruchelman et al., 2003). 5-Arylaminomethylene-2,2-dimethyl-1,3-dioxane-4,6-diones are the key intermediates which can be used to synthesize the 4(1H)quinolone derivatives by thermolysis (Cassis et al., 1985).

The molecular structure of the title compound is shown in Fig. 1. The dihedral angle between the mean planes formed by the benzyl and aminomethylene units is 30.13 (4)°, while the angle between the mean planes of the dioxane ring and the aminomethylene group is only 11.61 (4)° due to the intramolecular N1—H1···O3 hydrogen bond (Table 1). Apart from that, the dioxane ring exhibits a half-boat conformation, in which the C atom between the dioxane oxygen atoms is 0.553 (8) Å out-of-plane.

The three-dimensional framework is built by the weak intermolecular N1—H1···O3i, C7—H7···O4ii, C13—H13···O4ii and C11—H11···O4iii interactions (Fig. 2).

Experimental

An ethanol solution (50 ml) of 2,2-dimethyl-1,3-dioxane-4,6-dione (1.44 g, 0.01 mol) and methylorthoformate (1.27 g, 0.012 mol) was heated to reflux for 1 h, then the 3-nitrobenzenamine (1.38 g, 0.01 mol) was added into the solution. The mixture was heated under reflux for another 8 h and then filtered. Single crystals were obtained from the filtrate after 3 days.

Refinement

The imino H atom was located in a difference Fourier map and refined isotropically. The other H atoms were positioned geometrically and refined using a riding model, with C—H = 0.93 Å and Uiso(H) = 1.2Ueq(C) for aromatic, C—H = 0.96 Å and Uiso(H) = 1.5Ueq(C) for methyl H atoms.

Figures

Fig. 1.
The molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level. The intramolecular hydrogen bond is shown as a dashed line.
Fig. 2.
Crystal packing of the title compound, showing the intermolecular hydrogen bonds as dashed lines. [Symmetry codes: (i) -x + 1, -y, -z + 2; (ii) -x, -y, -z + 2].

Crystal data

C13H12N2O6F(000) = 608
Mr = 292.25Dx = 1.460 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 11.7900 (13) ÅCell parameters from 4305 reflections
b = 8.7699 (9) Åθ = 2.3–27.6°
c = 14.0614 (15) ŵ = 0.12 mm1
β = 113.864 (1)°T = 153 K
V = 1329.6 (2) Å3Block, colourless
Z = 40.20 × 0.10 × 0.10 mm

Data collection

Bruker SMART CCD area-detector diffractometer2572 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.014
graphiteθmax = 27.6°, θmin = 2.8°
[var phi] and ω scansh = −15→14
8116 measured reflectionsk = −11→10
3052 independent reflectionsl = −18→18

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.036H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.101w = 1/[σ2(Fo2) + (0.045P)2 + 0.3157P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
3052 reflectionsΔρmax = 0.22 e Å3
197 parametersΔρmin = −0.18 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0195 (18)

Special details

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)

xyzUiso*/Ueq
O10.45433 (8)−0.09916 (10)1.23372 (6)0.0370 (2)
O30.47419 (8)−0.05487 (12)1.08661 (7)0.0440 (2)
O20.25826 (8)−0.13984 (11)1.23681 (6)0.0401 (2)
C40.40464 (11)−0.06725 (13)1.13054 (9)0.0322 (2)
N10.26298 (10)0.01843 (13)0.91248 (8)0.0359 (2)
C80.19585 (11)0.06369 (14)0.80763 (9)0.0342 (3)
C90.24224 (11)0.02544 (14)0.73506 (9)0.0347 (3)
H90.3148−0.03120.75380.042*
C30.37852 (11)−0.07324 (14)1.29110 (9)0.0337 (3)
O40.08565 (9)−0.12773 (15)1.09442 (8)0.0584 (3)
C70.21114 (11)−0.01291 (14)0.97781 (9)0.0350 (3)
H70.1252−0.00550.95190.042*
O50.30012 (13)−0.07262 (15)0.57581 (10)0.0684 (3)
C60.19637 (11)−0.10611 (15)1.13438 (9)0.0381 (3)
C50.27159 (11)−0.05534 (14)1.08029 (9)0.0333 (3)
C100.17796 (12)0.07365 (16)0.63388 (9)0.0403 (3)
C130.08587 (14)0.14495 (19)0.77793 (11)0.0510 (4)
H130.05450.17050.82680.061*
C20.43836 (14)−0.16096 (17)1.39116 (10)0.0459 (3)
H2A0.3876−0.15391.42990.069*
H2B0.5188−0.11891.43150.069*
H2C0.4468−0.26601.37590.069*
N20.22862 (12)0.03454 (17)0.55739 (9)0.0535 (3)
C10.36712 (15)0.09463 (15)1.30692 (11)0.0481 (3)
H1A0.32850.14401.24060.072*
H1B0.44810.13721.34440.072*
H1C0.31740.10991.34590.072*
C110.06978 (15)0.1552 (2)0.60191 (11)0.0586 (4)
H110.02930.18740.53340.070*
O60.19778 (16)0.1124 (2)0.47934 (10)0.0992 (6)
C120.02320 (15)0.1877 (2)0.67512 (13)0.0672 (5)
H12−0.05180.23930.65500.081*
H10.3441 (15)0.0100 (18)0.9339 (12)0.051 (4)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0341 (4)0.0496 (5)0.0266 (4)0.0047 (4)0.0115 (3)0.0028 (3)
O30.0338 (5)0.0665 (6)0.0354 (5)0.0021 (4)0.0177 (4)0.0058 (4)
O20.0413 (5)0.0500 (5)0.0306 (4)−0.0094 (4)0.0164 (4)0.0009 (4)
C40.0350 (6)0.0351 (6)0.0270 (5)0.0005 (4)0.0130 (5)0.0007 (4)
N10.0313 (5)0.0478 (6)0.0274 (5)0.0026 (4)0.0106 (4)0.0029 (4)
C80.0332 (6)0.0396 (6)0.0279 (5)−0.0008 (5)0.0105 (5)0.0033 (5)
C90.0328 (6)0.0388 (6)0.0302 (6)0.0001 (5)0.0106 (5)0.0030 (5)
C30.0375 (6)0.0384 (6)0.0263 (5)−0.0019 (5)0.0140 (5)−0.0011 (4)
O40.0353 (5)0.0966 (9)0.0440 (6)−0.0133 (5)0.0167 (4)0.0000 (5)
C70.0312 (6)0.0427 (6)0.0295 (6)−0.0006 (5)0.0108 (5)−0.0006 (5)
O50.0855 (9)0.0756 (8)0.0587 (7)0.0112 (7)0.0443 (6)−0.0031 (6)
C60.0352 (6)0.0482 (7)0.0324 (6)−0.0042 (5)0.0152 (5)−0.0021 (5)
C50.0315 (6)0.0409 (6)0.0283 (5)−0.0007 (5)0.0128 (5)−0.0004 (5)
C100.0420 (7)0.0496 (7)0.0294 (6)−0.0030 (5)0.0146 (5)0.0032 (5)
C130.0479 (8)0.0687 (10)0.0417 (7)0.0176 (7)0.0235 (6)0.0123 (7)
C20.0555 (8)0.0499 (8)0.0300 (6)−0.0003 (6)0.0147 (6)0.0052 (5)
N20.0583 (8)0.0716 (9)0.0339 (6)−0.0037 (7)0.0218 (5)0.0014 (6)
C10.0629 (9)0.0392 (7)0.0427 (7)0.0011 (6)0.0219 (7)−0.0044 (6)
C110.0521 (9)0.0833 (12)0.0349 (7)0.0148 (8)0.0118 (6)0.0209 (7)
O60.1211 (13)0.1419 (14)0.0516 (7)0.0380 (11)0.0524 (8)0.0415 (8)
C120.0509 (9)0.0965 (13)0.0529 (9)0.0351 (9)0.0197 (7)0.0271 (9)

Geometric parameters (Å, °)

O1—C41.3560 (14)C7—H70.9300
O1—C31.4441 (14)O5—N21.2183 (18)
O3—C41.2147 (14)C6—C51.4524 (16)
O2—C61.3580 (15)C10—C111.370 (2)
O2—C31.4348 (15)C10—N21.4665 (17)
C4—C51.4401 (17)C13—C121.383 (2)
N1—C71.3219 (15)C13—H130.9300
N1—C81.4190 (15)C2—H2A0.9600
N1—H10.882 (16)C2—H2B0.9600
C8—C91.3800 (17)C2—H2C0.9600
C8—C131.3875 (18)N2—O61.2164 (17)
C9—C101.3802 (17)C1—H1A0.9600
C9—H90.9300C1—H1B0.9600
C3—C11.5030 (18)C1—H1C0.9600
C3—C21.5053 (17)C11—C121.378 (2)
O4—C61.2092 (16)C11—H110.9300
C7—C51.3754 (16)C12—H120.9300
C4—O1—C3117.92 (9)C4—C5—C6119.70 (10)
C6—O2—C3117.84 (9)C11—C10—C9123.24 (12)
O3—C4—O1118.31 (11)C11—C10—N2118.87 (12)
O3—C4—C5124.71 (11)C9—C10—N2117.88 (12)
O1—C4—C5116.96 (10)C12—C13—C8119.52 (13)
C7—N1—C8124.04 (10)C12—C13—H13120.2
C7—N1—H1119.2 (10)C8—C13—H13120.2
C8—N1—H1116.7 (10)C3—C2—H2A109.5
C9—C8—C13120.26 (11)C3—C2—H2B109.5
C9—C8—N1118.62 (11)H2A—C2—H2B109.5
C13—C8—N1121.12 (11)C3—C2—H2C109.5
C8—C9—C10118.11 (11)H2A—C2—H2C109.5
C8—C9—H9120.9H2B—C2—H2C109.5
C10—C9—H9120.9O6—N2—O5123.59 (14)
O2—C3—O1109.91 (9)O6—N2—C10117.94 (14)
O2—C3—C1110.44 (11)O5—N2—C10118.46 (12)
O1—C3—C1110.45 (10)C3—C1—H1A109.5
O2—C3—C2106.13 (10)C3—C1—H1B109.5
O1—C3—C2106.25 (10)H1A—C1—H1B109.5
C1—C3—C2113.48 (11)C3—C1—H1C109.5
N1—C7—C5126.51 (11)H1A—C1—H1C109.5
N1—C7—H7116.7H1B—C1—H1C109.5
C5—C7—H7116.7C10—C11—C12117.54 (13)
O4—C6—O2118.33 (11)C10—C11—H11121.2
O4—C6—C5125.30 (12)C12—C11—H11121.2
O2—C6—C5116.25 (10)C11—C12—C13121.26 (14)
C7—C5—C4122.25 (10)C11—C12—H12119.4
C7—C5—C6117.66 (11)C13—C12—H12119.4
C3—O1—C4—O3163.48 (11)O3—C4—C5—C6165.88 (12)
C3—O1—C4—C5−18.46 (15)O1—C4—C5—C6−12.04 (17)
C7—N1—C8—C9−149.73 (12)O4—C6—C5—C77.2 (2)
C7—N1—C8—C1330.4 (2)O2—C6—C5—C7−176.78 (11)
C13—C8—C9—C101.64 (19)O4—C6—C5—C4−165.75 (14)
N1—C8—C9—C10−178.26 (11)O2—C6—C5—C410.23 (18)
C6—O2—C3—O1−50.49 (14)C8—C9—C10—C11−1.1 (2)
C6—O2—C3—C171.61 (13)C8—C9—C10—N2179.15 (11)
C6—O2—C3—C2−164.99 (10)C9—C8—C13—C12−0.1 (2)
C4—O1—C3—O248.46 (13)N1—C8—C13—C12179.74 (15)
C4—O1—C3—C1−73.64 (14)C11—C10—N2—O622.6 (2)
C4—O1—C3—C2162.88 (10)C9—C10—N2—O6−157.58 (15)
C8—N1—C7—C5−179.14 (12)C11—C10—N2—O5−158.17 (16)
C3—O2—C6—O4−161.51 (12)C9—C10—N2—O521.6 (2)
C3—O2—C6—C522.23 (16)C9—C10—C11—C12−1.0 (3)
N1—C7—C5—C41.6 (2)N2—C10—C11—C12178.78 (16)
N1—C7—C5—C6−171.23 (12)C10—C11—C12—C132.5 (3)
O3—C4—C5—C7−6.8 (2)C8—C13—C12—C11−2.0 (3)
O1—C4—C5—C7175.30 (11)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O30.882 (16)2.150 (15)2.7705 (14)126.8 (13)
N1—H1···O3i0.882 (16)2.308 (16)3.1101 (14)151.2 (13)
C7—H7···O40.932.482.8026 (18)101
C7—H7···O4ii0.932.583.4527 (18)156
C11—H11···O4iii0.932.393.242 (2)152
C13—H13···O4ii0.932.363.205 (2)151

Symmetry codes: (i) −x+1, −y, −z+2; (ii) −x, −y, −z+2; (iii) −x, y+1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZQ2002).

References

  • Bruker (2000). SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2001). SMART Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cassis, R., Tapia, R. & Valderrama, J. A. (1985). Synth. Commun.15, 125–133.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Li, R., Ding, Z.-Y., Wei, Y.-Q. & Ding, J. (2009a). Acta Cryst. E65, o1296. [PMC free article] [PubMed]
  • Li, R., Ding, Z.-Y., Wei, Y.-Q. & Ding, J. (2009b). Acta Cryst. E65, o1297. [PMC free article] [PubMed]
  • Li, R., Shi, J.-Y., Ding, Z.-Y., Wei, Y.-Q. & Ding, J. (2009). Acta Cryst. E65, o1298–o1299. [PMC free article] [PubMed]
  • Ruchelman, A. L., Singh, S. K., Ray, A., Wu, X. H., Yang, J. M., Li, T. K., Liu, A., Liu, L. F. & LaVoie, E. J. (2003). Bioorg. Med. Chem.11, 2061–2073. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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