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Acta Crystallogr Sect E Struct Rep Online. 2008 December 1; 64(Pt 12): o2425.
Published online 2008 November 22. doi:  10.1107/S1600536808028158
PMCID: PMC2959852

1-(4,5-Dinitro-10-aza­tricyclo­[6.3.1.02,7]dodeca-2,4,6-trien-10-yl)-2,2,2-trifluoro­ethanone

Abstract

In the title compound, C13H10F3N3O5, a derivative of andrographolide, the five-membered ring adopts an envelope conformation, while the non-planar six-membered ring has a chair conformation. An intra­molecular C—H(...)F hydrogen bond results in the formation of a non-planar six-membered ring adopting a twisted conformation. In the crystal structure, inter­molecular C—H(...)O hydrogen bonds link the mol­ecules into centrosymmetric dimers.

Related literature

For bond-length data, see: Allen et al. (1987 [triangle]). For ring puckering parameters, see: Cremer & Pople (1975 [triangle]).

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Object name is e-64-o2425-scheme1.jpg

Experimental

Crystal data

  • C13H10F3N3O5
  • M r = 345.24
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o2425-efi1.jpg
  • a = 9.6400 (19) Å
  • b = 7.7430 (15) Å
  • c = 18.687 (4) Å
  • β = 96.98 (3)°
  • V = 1384.5 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.15 mm−1
  • T = 294 (2) K
  • 0.30 × 0.20 × 0.10 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: ψ scan (North et al., 1968 [triangle]) T min = 0.955, T max = 0.985
  • 2673 measured reflections
  • 2513 independent reflections
  • 1592 reflections with I > 2σ(I)
  • R int = 0.052
  • 3 standard reflections frequency: 120 min intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.061
  • wR(F 2) = 0.183
  • S = 1.02
  • 2513 reflections
  • 217 parameters
  • H-atom parameters constrained
  • Δρmax = 0.33 e Å−3
  • Δρmin = −0.35 e Å−3

Data collection: CAD-4 Software (Enraf–Nonius, 1989 [triangle]); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]) and PLATON (Spek, 2003 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808028158/hk2521sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808028158/hk2521Isup2.hkl

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

Acknowledgments

The authors thank the Center for Testing and Analysis, Nanjing University, for support.

supplementary crystallographic information

Comment

Some derivatives of andrographolide are important chemical materials. We report herein the crystal structure of the title compound.

In the molecule of the title compound, (Fig. 1), the bond lengths (Allen et al., 1987) and angles are generally within normal ranges. Ring A (C8–C13) is, of course, planar. Ring B (N1/C3–C7) is not planar, having total puckering amplitude, QT, of 0.626 (3) and chair conformation [[var phi] = -175.64 (3)° and θ = 36.12 (3)°] (Cremer & Pople, 1975), while ring C (C4–C6/C8/C13) adopts envelope conformation, with C5 atom displaced by -0.707 (3) Å from the plane of the other ring atoms. The intramolecular C—H···F hydrogen bond (Table 1) results in the formation of a nonplanar six-membered ring D (F2/C1/C2/N1/C7/H7B), having total puckering amplitude, QT, of 0.651 (3) and twisted conformation [[var phi] = 34.96 (3)° and θ = 76.80 (2)°] (Cremer & Pople, 1975)

In the crystal structure, intermolecular C—H···O hydrogen bonds (Table 1) link the molecules into centrosymmetric dimers (Fig. 2), in which they may be effective in the stabilization of the structure.

Experimental

For the preparation of the title compound, 1-(4,5-diamino-10-aza-tricyclo- [6.3.1.0]dodeca-2,4,6-trien-10-yl)-2,2,2-trifluoro-ethanone (3.0 g) was hydrogenated in methanol (30 ml, 95%) under hydrogen (45 psi) over Pd-carbon catalysts (300 mg of 20wt%/C,10%wt). After 2.5 h, the reaction was filtered through a celite pad and rinsed with methanol (30 ml, 95%). The solution was concentrated to a light brown oil that crystallized. An X-ray grade crystal of the title compound (500 mg) was grown from ethyl acetate (10 ml) at room temperature.

Refinement

H atoms were positioned geometrically, with C—H = 0.93, 0.98 and 0.97 Å for aromatic, methine and methylene H, respectively, and constrained to ride on their parent atoms with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. Hydrogen bond is shown as dashed line.
Fig. 2.
A partial packing diagram of the title compound. Hydrogen bonds are shown as dashed lines.

Crystal data

C13H10F3N3O5F000 = 704
Mr = 345.24Dx = 1.656 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 25 reflections
a = 9.6400 (19) Åθ = 10–13º
b = 7.7430 (15) ŵ = 0.15 mm1
c = 18.687 (4) ÅT = 294 (2) K
β = 96.98 (3)ºRed, colorless
V = 1384.5 (5) Å30.30 × 0.20 × 0.10 mm
Z = 4

Data collection

Enraf–Nonius CAD-4 diffractometerRint = 0.052
Radiation source: fine-focus sealed tubeθmax = 25.3º
Monochromator: graphiteθmin = 2.1º
T = 294(2) Kh = −11→11
ω/2θ scansk = 0→9
Absorption correction: ψ scan(North et al., 1968)l = 0→22
Tmin = 0.955, Tmax = 0.9853 standard reflections
2673 measured reflections every 120 min
2513 independent reflections intensity decay: none
1592 reflections with I > 2σ(I)

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.061H-atom parameters constrained
wR(F2) = 0.183  w = 1/[σ2(Fo2) + (0.05P)2 + 4P] where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
2513 reflectionsΔρmax = 0.33 e Å3
217 parametersΔρmin = −0.35 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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
F10.3302 (4)0.7803 (5)0.23330 (19)0.1036 (13)
F20.1596 (3)0.6268 (5)0.25814 (17)0.0907 (12)
F30.3030 (3)0.5239 (4)0.19179 (13)0.0702 (9)
O10.4775 (4)0.6527 (5)0.34298 (19)0.0681 (10)
O20.1222 (4)0.4522 (5)0.6478 (2)0.0812 (12)
O30.0247 (4)0.2030 (5)0.65267 (18)0.0733 (11)
O4−0.2298 (3)0.1740 (6)0.4660 (2)0.0772 (12)
O5−0.1736 (4)0.3629 (5)0.5498 (2)0.0749 (11)
N10.3630 (3)0.3999 (5)0.34108 (16)0.0398 (8)
N20.0824 (4)0.3155 (6)0.6213 (2)0.0512 (10)
N3−0.1427 (4)0.2615 (5)0.5031 (2)0.0532 (10)
C10.2916 (5)0.6217 (7)0.2505 (2)0.0557 (12)
C20.3865 (4)0.5564 (6)0.3165 (2)0.0446 (10)
C30.4621 (4)0.3471 (7)0.4042 (2)0.0486 (11)
H3A0.47140.44060.43900.058*
H3B0.55320.32720.38870.058*
C40.4159 (4)0.1853 (6)0.4403 (2)0.0442 (10)
H4A0.48720.14430.47840.053*
C50.3737 (5)0.0456 (7)0.3846 (3)0.0569 (12)
H5A0.3600−0.06490.40720.068*
H5B0.44190.03310.35090.068*
C60.2364 (4)0.1203 (6)0.3485 (2)0.0476 (11)
H6A0.17990.03230.32080.057*
C70.2679 (5)0.2734 (7)0.3008 (2)0.0524 (12)
H7A0.31050.23100.25980.063*
H7B0.18110.33040.28270.063*
C80.2766 (4)0.2163 (5)0.4683 (2)0.0393 (9)
C90.2468 (4)0.2693 (5)0.5352 (2)0.0398 (10)
H9A0.31810.29680.57150.048*
C100.1095 (4)0.2805 (5)0.5470 (2)0.0391 (9)
C110.0006 (4)0.2439 (5)0.4922 (2)0.0381 (9)
C120.0337 (4)0.1944 (6)0.4239 (2)0.0417 (10)
H12A−0.03650.17370.38610.050*
C130.1695 (4)0.1778 (5)0.4143 (2)0.0418 (10)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
F10.150 (3)0.070 (2)0.083 (2)0.000 (2)−0.017 (2)0.0327 (19)
F20.0614 (19)0.134 (3)0.076 (2)0.042 (2)0.0060 (15)0.020 (2)
F30.0736 (19)0.102 (2)0.0356 (14)0.0003 (17)0.0089 (12)−0.0006 (15)
O10.072 (2)0.053 (2)0.074 (2)−0.0176 (19)−0.0145 (18)0.0037 (18)
O20.100 (3)0.075 (3)0.068 (2)−0.011 (2)0.005 (2)−0.030 (2)
O30.095 (3)0.076 (3)0.056 (2)−0.005 (2)0.0403 (19)0.009 (2)
O40.0338 (17)0.108 (3)0.087 (3)−0.016 (2)−0.0066 (17)−0.001 (2)
O50.054 (2)0.078 (3)0.098 (3)0.0127 (19)0.029 (2)−0.007 (2)
N10.0348 (17)0.053 (2)0.0291 (16)−0.0060 (16)−0.0073 (13)−0.0019 (15)
N20.050 (2)0.056 (3)0.045 (2)0.007 (2)−0.0007 (17)−0.003 (2)
N30.043 (2)0.055 (3)0.060 (2)0.0015 (19)0.0023 (19)0.018 (2)
C10.054 (3)0.067 (3)0.046 (3)0.004 (3)0.008 (2)0.014 (2)
C20.045 (2)0.051 (3)0.039 (2)0.002 (2)0.0101 (18)0.007 (2)
C30.033 (2)0.069 (3)0.042 (2)−0.007 (2)−0.0008 (17)0.009 (2)
C40.033 (2)0.058 (3)0.042 (2)0.007 (2)0.0055 (17)0.010 (2)
C50.061 (3)0.052 (3)0.063 (3)0.004 (2)0.027 (2)0.003 (2)
C60.049 (2)0.053 (3)0.041 (2)−0.013 (2)0.0063 (19)−0.007 (2)
C70.053 (3)0.071 (3)0.033 (2)−0.016 (2)0.0025 (19)−0.009 (2)
C80.041 (2)0.038 (2)0.037 (2)0.0014 (18)−0.0044 (17)0.0045 (18)
C90.036 (2)0.045 (2)0.034 (2)−0.0047 (19)−0.0095 (16)0.0003 (18)
C100.041 (2)0.039 (2)0.035 (2)−0.0009 (18)−0.0026 (17)0.0051 (18)
C110.0318 (19)0.038 (2)0.042 (2)0.0017 (17)−0.0023 (16)0.0104 (18)
C120.038 (2)0.045 (3)0.039 (2)−0.0061 (19)−0.0050 (17)0.0008 (19)
C130.047 (2)0.039 (2)0.038 (2)−0.0066 (19)−0.0014 (18)0.0015 (19)

Geometric parameters (Å, °)

F1—C11.334 (6)C4—C51.521 (6)
F2—C11.298 (5)C4—H4A0.9800
F3—C11.348 (6)C5—C61.525 (6)
O1—C21.210 (5)C5—H5A0.9700
O2—N21.211 (5)C5—H5B0.9700
O3—N21.221 (5)C6—C131.523 (6)
O4—N31.227 (5)C6—C71.535 (6)
O5—N31.236 (5)C6—H6A0.9800
N1—C21.325 (6)C7—H7A0.9700
N1—C31.482 (5)C7—H7B0.9700
N1—C71.483 (5)C8—C91.379 (6)
N2—C101.470 (5)C8—C131.385 (5)
N3—C111.427 (5)C9—C101.370 (5)
C1—C21.530 (6)C9—H9A0.9300
C3—C41.516 (6)C10—C111.403 (5)
C3—H3A0.9700C11—C121.407 (6)
C3—H3B0.9700C12—C131.349 (6)
C4—C81.519 (5)C12—H12A0.9300
C2—N1—C3114.0 (3)C4—C5—H5B111.7
C2—N1—C7123.4 (3)C6—C5—H5B111.7
C3—N1—C7121.4 (4)H5A—C5—H5B109.5
O2—N2—O3124.6 (4)C13—C6—C5100.5 (3)
O2—N2—C10117.6 (4)C13—C6—C7112.1 (4)
O3—N2—C10117.8 (4)C5—C6—C7109.1 (4)
O4—N3—O5122.9 (4)C13—C6—H6A111.5
O4—N3—C11118.3 (4)C5—C6—H6A111.5
O5—N3—C11118.8 (4)C7—C6—H6A111.5
F2—C1—F1107.7 (4)N1—C7—C6111.6 (3)
F2—C1—F3106.5 (4)N1—C7—H7A109.3
F1—C1—F3105.6 (4)C6—C7—H7A109.3
F2—C1—C2114.8 (4)N1—C7—H7B109.3
F1—C1—C2110.0 (4)C6—C7—H7B109.3
F3—C1—C2111.8 (4)H7A—C7—H7B108.0
O1—C2—N1124.6 (4)C9—C8—C13120.4 (4)
O1—C2—C1117.3 (4)C9—C8—C4130.6 (4)
N1—C2—C1118.1 (4)C13—C8—C4109.1 (4)
N1—C3—C4112.7 (3)C10—C9—C8118.4 (3)
N1—C3—H3A109.0C10—C9—H9A120.8
C4—C3—H3A109.0C8—C9—H9A120.8
N1—C3—H3B109.0C9—C10—C11121.5 (4)
C4—C3—H3B109.0C9—C10—N2116.7 (3)
H3A—C3—H3B107.8C11—C10—N2121.6 (4)
C3—C4—C8110.0 (4)C10—C11—C12119.0 (4)
C3—C4—C5110.6 (3)C10—C11—N3121.9 (4)
C8—C4—C5100.0 (3)C12—C11—N3119.0 (4)
C3—C4—H4A111.9C13—C12—C11118.4 (4)
C8—C4—H4A111.9C13—C12—H12A120.8
C5—C4—H4A111.9C11—C12—H12A120.8
C4—C5—C6100.3 (4)C12—C13—C8122.2 (4)
C4—C5—H5A111.7C12—C13—C6130.3 (4)
C6—C5—H5A111.7C8—C13—C6107.5 (4)
C3—N1—C2—O1−1.8 (6)C4—C8—C9—C10−177.4 (4)
C7—N1—C2—O1−169.0 (4)C8—C9—C10—C11−1.7 (6)
C3—N1—C2—C1178.8 (4)C8—C9—C10—N2172.3 (4)
C7—N1—C2—C111.6 (6)O2—N2—C10—C963.6 (5)
F2—C1—C2—O1−121.0 (5)O3—N2—C10—C9−114.5 (5)
F1—C1—C2—O10.6 (6)O2—N2—C10—C11−122.3 (5)
F3—C1—C2—O1117.5 (5)O3—N2—C10—C1159.5 (6)
F2—C1—C2—N158.5 (6)C9—C10—C11—C120.1 (6)
F1—C1—C2—N1−179.9 (4)N2—C10—C11—C12−173.6 (4)
F3—C1—C2—N1−63.0 (5)C9—C10—C11—N3−177.6 (4)
C2—N1—C3—C4168.3 (4)N2—C10—C11—N38.7 (6)
C7—N1—C3—C4−24.2 (5)O4—N3—C11—C10−154.4 (4)
N1—C3—C4—C8−61.6 (5)O5—N3—C11—C1025.1 (6)
N1—C3—C4—C548.0 (5)O4—N3—C11—C1228.0 (6)
C3—C4—C5—C6−71.8 (4)O5—N3—C11—C12−152.6 (4)
C8—C4—C5—C644.2 (4)C10—C11—C12—C132.4 (6)
C4—C5—C6—C13−44.6 (4)N3—C11—C12—C13−179.8 (4)
C4—C5—C6—C773.4 (4)C11—C12—C13—C8−3.4 (6)
C2—N1—C7—C6−167.6 (4)C11—C12—C13—C6177.3 (4)
C3—N1—C7—C626.0 (5)C9—C8—C13—C121.8 (7)
C13—C6—C7—N158.8 (5)C4—C8—C13—C12−179.6 (4)
C5—C6—C7—N1−51.7 (5)C9—C8—C13—C6−178.8 (4)
C3—C4—C8—C9−93.2 (5)C4—C8—C13—C6−0.2 (5)
C5—C4—C8—C9150.4 (5)C5—C6—C13—C12−152.3 (5)
C3—C4—C8—C1388.4 (4)C7—C6—C13—C1291.9 (5)
C5—C4—C8—C13−28.0 (4)C5—C6—C13—C828.3 (5)
C13—C8—C9—C100.8 (6)C7—C6—C13—C8−87.5 (4)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C7—H7B···F20.972.343.002 (6)124
C9—H9A···O1i0.932.413.338 (5)173

Symmetry codes: (i) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HK2521).

References

  • Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  • Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc 97, 1354–1358.
  • Enraf–Nonius (1989). CAD-4 Software Enraf–Nonius, Delft, The Netherlands.
  • Harms, K. & Wocadlo, S. (1995). XCAD4 University of Marburg, Germany.
  • North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography