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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2458.
Published online 2009 September 12. doi:  10.1107/S1600536809035776
PMCID: PMC2970495

5-(4-Bromo­anilinomethyl­ene)-2,2-dimethyl-1,3-dioxane-4,6-dione

Abstract

In the title compound, C13H12BrNO4, the dihedral angles between the amino­methyl­ene group and the dioxane ring and between the benzyl ring and the amino­methyl­ene unit are 7.96 (4) and 12.15 (4)°, respectively. The dioxane ring shows a half-boat conformation, in which the C atom between the dioxane ring O atoms is 0.460 (8) Å out of the plane through the remaining ring atoms. An intra­molecular N—H(...)O hydrogen bond may stabilize the planar conformation of the mol­ecule. An inter­molecular C—H(...)O inter­action is also present.

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],c [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2458-scheme1.jpg

Experimental

Crystal data

  • C13H12BrNO4
  • M r = 326.14
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2458-efi1.jpg
  • a = 13.837 (3) Å
  • b = 13.019 (3) Å
  • c = 7.4900 (15) Å
  • β = 105.24 (3)°
  • V = 1301.8 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 3.17 mm−1
  • T = 113 K
  • 0.20 × 0.18 × 0.04 mm

Data collection

  • Rigaku Saturn CCD area-detector diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005 [triangle]) T min = 0.570, T max = 0.884
  • 9108 measured reflections
  • 2279 independent reflections
  • 1063 reflections with I > 2σ(I)
  • R int = 0.113

Refinement

  • R[F 2 > 2σ(F 2)] = 0.066
  • wR(F 2) = 0.160
  • S = 0.99
  • 2279 reflections
  • 179 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.97 e Å−3
  • Δρmin = −0.96 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2005 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; 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/S1600536809035776/rk2160sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809035776/rk2160Isup2.hkl

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

supplementary crystallographic information

Comment

The 4(1H)quinolone structure plays an extremely important role in the field of pharmaceutical chemistry. The 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), that can be used as precursors foranti–malarial agents, anticancer agents, and reversible (H+/K+) ATPase inhibitors (Ruchelman et al., 2003). The conformation of the title compound is similar with those reported early by Li et al., (2009a,b,c), which is almost planar with the dihedral angles of 7.96 (4)° and 12.15 (4)° between the aminomethylene group and the dioxane ring, and between the benzyl ring and the aminomethylene unit, respectively. Besides, the dioxane ring of the title compound exhibits a half–boat conformation, in which the C atom between the dioxane oxygen atoms is -0.460 (8) Å out–of–plane. The intramolecular N—H···O hydrogen bond (Table 1) is stabilizing the planar conformation in the molecule.

Experimental

A solution 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 2.5 h, then the arylamine (1.32 g, 0.01 mol) was added into the above solution. The mixture was heated under reflux for another 4 h and then filtered. Single crystals were obtained from the filtrate after 2 days.

Refinement

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

Figures

Fig. 1.
The molecular structure of the title compound with the numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as a small spheres of arbitrary radius.
Fig. 2.
Crystal packing of the title compound, showing the intermolecular hydrogen bonds as dashed lines. H atoms not involved in these interactions have been omitted. Symmetry code: (i) -x+2, -y, -z+2.

Crystal data

C13H12BrNO4F(000) = 656
Mr = 326.14Dx = 1.664 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 4079 reflections
a = 13.837 (3) Åθ = 2.2–27.7°
b = 13.019 (3) ŵ = 3.17 mm1
c = 7.4900 (15) ÅT = 113 K
β = 105.24 (3)°Plate, colourless
V = 1301.8 (5) Å30.20 × 0.18 × 0.04 mm
Z = 4

Data collection

Rigaku Saturn CCD area-detector diffractometer2279 independent reflections
Radiation source: rotating anode1063 reflections with I > 2σ(I)
confocalRint = 0.113
Detector resolution: 7.31 pixels mm-1θmax = 25.0°, θmin = 2.2°
ω and [var phi] scansh = −16→16
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005)k = −15→15
Tmin = 0.570, Tmax = 0.884l = −7→8
9108 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.066H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.160w = 1/[σ2(Fo2) + (0.0585P)2] where P = (Fo2 + 2Fc2)/3
S = 0.99(Δ/σ)max = 0.001
2279 reflectionsΔρmax = 0.97 e Å3
179 parametersΔρmin = −0.96 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: 0.017 (3)

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
Br10.55042 (5)0.35263 (5)1.07667 (10)0.0385 (4)
O11.2599 (3)0.2261 (3)0.9075 (6)0.0281 (11)
O21.2115 (3)0.0519 (3)0.8410 (5)0.0263 (11)
O31.0562 (3)0.0009 (3)0.8058 (6)0.0335 (12)
O41.1515 (3)0.3439 (3)0.9505 (6)0.0310 (12)
N10.9664 (4)0.2768 (4)0.9800 (7)0.0235 (13)
H1N1.008 (7)0.337 (5)0.978 (11)0.08 (3)*
C11.0970 (5)0.1708 (4)0.9159 (8)0.0232 (16)
C21.1680 (5)0.2526 (5)0.9294 (8)0.0269 (16)
C31.2909 (5)0.1209 (5)0.9352 (9)0.0270 (16)
C41.1175 (5)0.0689 (5)0.8546 (8)0.0260 (16)
C51.3741 (5)0.1084 (5)0.8402 (9)0.0324 (17)
H5A1.35000.12750.71240.049*
H5B1.39550.03800.84850.049*
H5C1.42940.15160.89940.049*
C61.3222 (5)0.0959 (5)1.1391 (8)0.0351 (18)
H6A1.37250.14381.20180.053*
H6B1.34900.02751.15620.053*
H6C1.26520.10041.18900.053*
C71.0035 (5)0.1867 (5)0.9435 (8)0.0250 (16)
H70.96240.12940.93620.030*
C80.8705 (5)0.2914 (5)1.0096 (7)0.0212 (15)
C90.8101 (5)0.2096 (5)1.0358 (8)0.0294 (17)
H90.83400.14261.03880.035*
C100.7156 (5)0.2274 (5)1.0571 (8)0.0284 (16)
H100.67550.17301.07460.034*
C110.6813 (5)0.3276 (5)1.0521 (8)0.0241 (16)
C120.7412 (5)0.4097 (4)1.0325 (8)0.0259 (16)
H120.71800.47661.03390.031*
C130.8362 (5)0.3912 (5)1.0109 (8)0.0252 (16)
H130.87680.44590.99730.030*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.0334 (6)0.0385 (6)0.0460 (6)0.0036 (3)0.0148 (4)−0.0078 (3)
O10.038 (3)0.020 (2)0.031 (3)0.000 (2)0.019 (2)0.000 (2)
O20.030 (3)0.022 (2)0.032 (3)0.001 (2)0.016 (2)−0.004 (2)
O30.042 (3)0.022 (3)0.044 (3)−0.005 (2)0.024 (3)−0.001 (2)
O40.040 (3)0.018 (3)0.038 (3)0.000 (2)0.016 (2)−0.006 (2)
N10.028 (4)0.019 (3)0.025 (3)0.001 (3)0.010 (3)−0.003 (2)
C10.035 (5)0.019 (4)0.019 (3)−0.003 (3)0.013 (3)0.004 (3)
C20.037 (5)0.027 (4)0.019 (3)0.006 (3)0.012 (3)0.005 (3)
C30.029 (5)0.020 (4)0.034 (4)0.008 (3)0.012 (3)−0.003 (3)
C40.030 (4)0.023 (4)0.027 (4)0.003 (3)0.010 (3)0.006 (3)
C50.034 (5)0.023 (4)0.043 (4)0.002 (3)0.014 (4)−0.006 (3)
C60.047 (5)0.030 (4)0.024 (4)0.015 (3)0.002 (3)−0.004 (3)
C70.034 (5)0.024 (4)0.019 (3)0.002 (3)0.010 (3)0.005 (3)
C80.030 (4)0.020 (4)0.014 (3)−0.004 (3)0.008 (3)−0.002 (3)
C90.047 (5)0.018 (4)0.028 (4)0.009 (3)0.019 (3)0.000 (3)
C100.037 (5)0.030 (4)0.022 (3)−0.006 (3)0.014 (3)−0.005 (3)
C110.028 (4)0.022 (4)0.022 (4)0.001 (3)0.007 (3)−0.003 (3)
C120.042 (5)0.013 (3)0.023 (4)0.008 (3)0.010 (3)0.005 (3)
C130.041 (5)0.016 (3)0.022 (4)−0.001 (3)0.014 (3)0.000 (3)

Geometric parameters (Å, °)

Br1—C111.895 (6)C5—H5B0.9600
O1—C21.369 (7)C5—H5C0.9600
O1—C31.433 (7)C6—H6A0.9600
O2—C41.350 (7)C6—H6B0.9600
O2—C31.449 (7)C6—H6C0.9600
O3—C41.214 (7)C7—H70.9300
O4—C21.229 (6)C8—C131.385 (8)
N1—C71.338 (7)C8—C91.399 (8)
N1—C81.415 (8)C9—C101.378 (8)
N1—H1N0.98 (7)C9—H90.9300
C1—C71.378 (8)C10—C111.386 (8)
C1—C21.434 (8)C10—H100.9300
C1—C41.455 (8)C11—C121.383 (8)
C3—C61.509 (8)C12—C131.386 (8)
C3—C51.513 (8)C12—H120.9300
C5—H5A0.9600C13—H130.9300
C2—O1—C3118.4 (5)C3—C6—H6B109.5
C4—O2—C3118.9 (5)H6A—C6—H6B109.5
C7—N1—C8125.2 (6)C3—C6—H6C109.5
C7—N1—H1N117 (5)H6A—C6—H6C109.5
C8—N1—H1N118 (5)H6B—C6—H6C109.5
C7—C1—C2122.1 (6)N1—C7—C1126.0 (6)
C7—C1—C4116.9 (6)N1—C7—H7117.0
C2—C1—C4120.8 (6)C1—C7—H7117.0
O4—C2—O1118.0 (6)C13—C8—C9119.7 (6)
O4—C2—C1125.5 (6)C13—C8—N1117.7 (5)
O1—C2—C1116.4 (5)C9—C8—N1122.6 (6)
O1—C3—O2111.2 (5)C10—C9—C8120.5 (6)
O1—C3—C6110.4 (5)C10—C9—H9119.7
O2—C3—C6109.8 (5)C8—C9—H9119.7
O1—C3—C5105.7 (5)C9—C10—C11119.0 (6)
O2—C3—C5106.1 (5)C9—C10—H10120.5
C6—C3—C5113.6 (6)C11—C10—H10120.5
O3—C4—O2117.9 (6)C12—C11—C10121.3 (6)
O3—C4—C1125.5 (6)C12—C11—Br1119.5 (5)
O2—C4—C1116.4 (6)C10—C11—Br1119.2 (5)
C3—C5—H5A109.5C11—C12—C13119.5 (6)
C3—C5—H5B109.5C11—C12—H12120.3
H5A—C5—H5B109.5C13—C12—H12120.3
C3—C5—H5C109.5C8—C13—C12120.0 (6)
H5A—C5—H5C109.5C8—C13—H13120.0
H5B—C5—H5C109.5C12—C13—H13120.0
C3—C6—H6A109.5
C3—O1—C2—O4162.6 (5)C2—C1—C4—O210.3 (8)
C3—O1—C2—C1−20.6 (8)C8—N1—C7—C1−179.4 (6)
C7—C1—C2—O4−6.4 (10)C2—C1—C7—N12.0 (10)
C4—C1—C2—O4167.6 (6)C4—C1—C7—N1−172.3 (6)
C7—C1—C2—O1177.0 (5)C7—N1—C8—C13−168.0 (5)
C4—C1—C2—O1−8.9 (8)C7—N1—C8—C911.5 (9)
C2—O1—C3—O246.4 (7)C13—C8—C9—C102.0 (9)
C2—O1—C3—C6−75.7 (7)N1—C8—C9—C10−177.5 (5)
C2—O1—C3—C5161.1 (5)C8—C9—C10—C110.1 (9)
C4—O2—C3—O1−44.9 (7)C9—C10—C11—C12−2.3 (9)
C4—O2—C3—C677.5 (6)C9—C10—C11—Br1178.8 (5)
C4—O2—C3—C5−159.4 (5)C10—C11—C12—C132.3 (9)
C3—O2—C4—O3−166.3 (5)Br1—C11—C12—C13−178.7 (4)
C3—O2—C4—C117.6 (7)C9—C8—C13—C12−1.9 (8)
C7—C1—C4—O38.9 (9)N1—C8—C13—C12177.6 (5)
C2—C1—C4—O3−165.4 (6)C11—C12—C13—C8−0.2 (8)
C7—C1—C4—O2−175.3 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N···O40.98 (7)2.06 (8)2.770 (7)128 (6)
C9—H9···O3i0.932.493.345 (8)152

Symmetry codes: (i) −x+2, −y, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RK2160).

References

  • 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. (2009c). Acta Cryst. E65, o1298–o1299. [PMC free article] [PubMed]
  • Rigaku/MSC (2005). CrystalClear Rigaku/MSC Inc., The Woodlands, Texas, USA.
  • 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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