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Acta Crystallogr Sect E Struct Rep Online. 2008 September 1; 64(Pt 9): o1672.
Published online 2008 August 6. doi:  10.1107/S1600536808024057
PMCID: PMC2960520

4,4-Difluoro-1,3,5,7-tetra­methyl-4-bora-3a,4a-diaza-s-indacene

Abstract

In the title compound, C13H15BF2N2, the two pyrrole rings are almost coplanar, with a dihedral angle of 3.08 (10)°. The BF2 plane is almost perpendicular to the boron–dipyrromethene ring plane, with a dihedral angle of 89.99 (7)°.

Related literature

For related literature, see: Bergström et al. (2002 [triangle]); Kollmannsberger et al. (1998 [triangle]); Kuhn et al. (1990 [triangle]); Trieflinger et al. (2005 [triangle]).

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Object name is e-64-o1672-scheme1.jpg

Experimental

Crystal data

  • C13H15BF2N2
  • M r = 248.08
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1672-efi1.jpg
  • a = 7.6909 (8) Å
  • b = 14.3392 (15) Å
  • c = 11.8334 (10) Å
  • β = 111.108 (5)°
  • V = 1217.4 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 293 (2) K
  • 0.30 × 0.20 × 0.20 mm

Data collection

  • Rigaku Mercury2 diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 [triangle]) T min = 0.961, T max = 0.974
  • 6540 measured reflections
  • 2396 independent reflections
  • 1963 reflections with I > 2σ(I)
  • R int = 0.019

Refinement

  • R[F 2 > 2σ(F 2)] = 0.040
  • wR(F 2) = 0.126
  • S = 1.06
  • 2396 reflections
  • 167 parameters
  • H-atom parameters constrained
  • Δρmax = 0.27 e Å−3
  • Δρmin = −0.24 e Å−3

Data collection: CrystalClear (Rigaku, 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: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808024057/at2574sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808024057/at2574Isup2.hkl

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

Acknowledgments

H-JX acknowledges a Start-up Grant from Southeast University, China.

supplementary crystallographic information

Comment

Boron-dipyrromethene (BODIPY) dyes are excellent fluorophores, with a high molar extinction coefficient and high fluorescence quantum yield, which have recently received considerable attention with regard to the design of fluorescence labels and biomolecular sensors (Bergström et al., 2002; Trieflinger et al., 2005). We hope to synthesize the boron-dipyrromethene (BODIPY) dyes containing phenanthroline group by the use of the reaction of 1,10-phenanthroline-2,9-dicarbaldehyde with 2,4-dimethyl-1H-pyrrole, however we only obtained the title compound (I) unexpectedly.

As shown in Fig. 1, the BODIPY skeleton is formed by three conjugated heterocyclic rings which is nearly coplanar. The C1/C2/C3/C4/N1 and C6/C7/C8/C9/N2 rings make dihedral angles of 1.37 (8) ° and 2.37 (9) °, respectively, with the N1/C4/C5/C6/N2/B1 ring plane. The average bond lengths for B—N and B—F and the average N—B—N and F—B—F and F—B—N angles indicate a tetrahedral BF2N2 configuration and are in good agreement with previous published data (Kuhn, et al., 1990). The F1/B1/F2 plane is almost perpendicular to the BODIPY ring plane [dihedral angle = 89.99 (0.07) °].

Experimental

Compound (I) was prepared in one-pot reaction (Kollmannsberger et al., 1998). Pyrrole (4 mmol) and 1,10-phenanthroline-2,9-dicarbaldehyde (1 mmol) were dissolved in newly dry CH2Cl2 (80 ml) under argon atmosphere. One drop of trifluoroacetic acid was added and the solution was stirred at room temperature until thin layer chromatography showed complete consumption of the aldehyde. At this point, a solution of dichlorodicyanobenzoquinone (DDQ, 2 mmol) in dry CH2Cl2 (20 ml) was added, and the mixture was stirred for additional 15 min. The reaction mixture was then treated with triethylamine (3 ml) and boron trifluoride etherate (3 ml). After stirring for another 30 min, the dark brown solution was washed with water (3×50 ml) and brine (50 ml), dried over Na2SO4, and concentrated at reduced pressure. The crude product was purified by silica-gel flash column chromatography and recrystallization from CHCl3/hexane. 1H NMR (300 MHz, CDCl3): δ = 7.37(s, 1 H), 6.13 (s, 2 H), 2.43 (s, 6 H), 2.16 (s, 6 H). Esi-Mass: 229.47 [M—F]+. Single crystals of (I) were obtain from a hexane-chloroform solution.

Refinement

Positional parameters of all the H atoms were calculated geometrically with C—H = 0.93 - 0.96 Å and were allowed to ride on the C atoms to which they are bonded, with Uiso(H) = 1.2 or 1.5Ueq(C).

Figures

Fig. 1.
A view of the title compound with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.

Crystal data

C13H15B1F2N2F000 = 520
Mr = 248.08Dx = 1.353 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2682 reflections
a = 7.6909 (8) Åθ = 2.8–27.9º
b = 14.3392 (15) ŵ = 0.10 mm1
c = 11.8334 (10) ÅT = 293 (2) K
β = 111.108 (5)ºBlock, red
V = 1217.4 (2) Å30.30 × 0.20 × 0.20 mm
Z = 4

Data collection

Rigaku Mercury2 diffractometer2396 independent reflections
Radiation source: fine-focus sealed tube1963 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.019
Detector resolution: 13.6612 pixels mm-1θmax = 26.0º
T = 293(2) Kθmin = 2.3º
[var phi] and ω scansh = −8→9
Absorption correction: empirical (using intensity measurements)(CrystalClear; Rigaku, 2005)k = −17→16
Tmin = 0.961, Tmax = 0.974l = −14→12
6540 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.126  w = 1/[σ2(Fo2) + (0.0669P)2 + 0.3386P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.007
2396 reflectionsΔρmax = 0.27 e Å3
167 parametersΔρmin = −0.24 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
F10.90473 (14)−0.13462 (7)0.77523 (9)0.0416 (3)
F20.59217 (14)−0.11875 (7)0.68465 (9)0.0429 (3)
N10.77362 (17)0.01985 (9)0.76358 (11)0.0296 (3)
N20.72797 (18)−0.10054 (9)0.90212 (12)0.0302 (3)
C10.7917 (2)0.06479 (12)0.66762 (15)0.0333 (4)
C20.8203 (2)0.15979 (12)0.69475 (16)0.0368 (4)
H2A0.83710.20540.64380.044*
C30.8194 (2)0.17455 (11)0.80964 (15)0.0331 (4)
C40.7899 (2)0.08638 (11)0.85312 (14)0.0296 (4)
C50.7747 (2)0.06086 (11)0.96176 (14)0.0292 (4)
H5A0.78650.10651.01990.035*
C60.7427 (2)−0.03013 (11)0.98692 (14)0.0296 (4)
C70.7146 (2)−0.06999 (12)1.08848 (15)0.0331 (4)
C80.6836 (2)−0.16395 (12)1.06306 (16)0.0377 (4)
H8A0.6607−0.20831.11330.045*
C90.6926 (2)−0.18101 (11)0.94874 (15)0.0343 (4)
C100.7815 (3)0.01588 (13)0.55463 (16)0.0419 (4)
H10A0.8497−0.04160.57490.063*
H10B0.83460.05470.50930.063*
H10C0.65360.00300.50670.063*
C110.8416 (3)0.26491 (12)0.87641 (17)0.0411 (4)
H11A0.91680.30660.84980.062*
H11B0.90110.25390.96180.062*
H11C0.72130.29230.86060.062*
C120.7199 (2)−0.01832 (13)1.19915 (16)0.0388 (4)
H12A0.6385−0.04821.23340.058*
H12B0.67970.04481.17790.058*
H12C0.8449−0.01831.25740.058*
C130.6716 (3)−0.27203 (12)0.88435 (17)0.0426 (4)
H13A0.7826−0.28510.86800.064*
H13B0.5669−0.26900.80940.064*
H13C0.6516−0.32060.93420.064*
B10.7490 (2)−0.08597 (13)0.77801 (16)0.0310 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
F10.0484 (6)0.0363 (6)0.0467 (6)0.0106 (4)0.0251 (5)−0.0002 (4)
F20.0463 (6)0.0438 (6)0.0326 (6)−0.0101 (4)0.0070 (5)−0.0031 (4)
N10.0304 (7)0.0317 (7)0.0272 (7)0.0027 (5)0.0109 (6)0.0002 (5)
N20.0303 (7)0.0297 (7)0.0298 (7)0.0031 (5)0.0099 (6)0.0009 (5)
C10.0331 (8)0.0369 (9)0.0312 (9)0.0055 (7)0.0132 (7)0.0039 (7)
C20.0432 (9)0.0346 (9)0.0366 (9)0.0045 (7)0.0192 (8)0.0060 (7)
C30.0321 (8)0.0319 (8)0.0371 (9)0.0031 (6)0.0145 (7)0.0018 (7)
C40.0271 (8)0.0311 (8)0.0299 (8)0.0035 (6)0.0093 (6)−0.0009 (6)
C50.0257 (7)0.0311 (8)0.0301 (8)0.0031 (6)0.0094 (6)−0.0023 (6)
C60.0270 (7)0.0337 (8)0.0278 (8)0.0046 (6)0.0095 (6)−0.0005 (6)
C70.0296 (8)0.0383 (9)0.0312 (9)0.0046 (7)0.0108 (7)0.0036 (7)
C80.0418 (9)0.0367 (9)0.0364 (9)0.0023 (7)0.0163 (8)0.0081 (7)
C90.0343 (9)0.0325 (9)0.0346 (9)0.0023 (6)0.0104 (7)0.0030 (7)
C100.0510 (11)0.0448 (10)0.0336 (9)0.0035 (8)0.0197 (8)−0.0003 (7)
C110.0495 (10)0.0319 (9)0.0447 (10)−0.0003 (8)0.0204 (9)−0.0010 (7)
C120.0411 (9)0.0460 (10)0.0318 (9)0.0039 (8)0.0163 (8)0.0005 (7)
C130.0511 (11)0.0327 (9)0.0421 (10)−0.0013 (8)0.0146 (8)0.0008 (7)
B10.0326 (9)0.0312 (9)0.0287 (9)0.0011 (7)0.0105 (7)−0.0004 (7)

Geometric parameters (Å, °)

F1—B11.397 (2)C7—C81.382 (2)
F2—B11.392 (2)C7—C121.492 (2)
N1—C11.356 (2)C8—C91.401 (2)
N1—C41.3974 (19)C8—H8A0.9300
N1—B11.546 (2)C9—C131.490 (2)
N2—C91.348 (2)C10—H10A0.9600
N2—C61.399 (2)C10—H10B0.9600
N2—B11.548 (2)C10—H10C0.9600
C1—C21.399 (2)C11—H11A0.9600
C1—C101.487 (2)C11—H11B0.9600
C2—C31.378 (2)C11—H11C0.9600
C2—H2A0.9300C12—H12A0.9600
C3—C41.414 (2)C12—H12B0.9600
C3—C111.495 (2)C12—H12C0.9600
C4—C51.382 (2)C13—H13A0.9600
C5—C61.380 (2)C13—H13B0.9600
C5—H5A0.9300C13—H13C0.9600
C6—C71.416 (2)
C1—N1—C4107.60 (14)C8—C9—C13127.78 (15)
C1—N1—B1127.78 (14)C1—C10—H10A109.5
C4—N1—B1124.57 (13)C1—C10—H10B109.5
C9—N2—C6107.47 (13)H10A—C10—H10B109.5
C9—N2—B1127.51 (13)C1—C10—H10C109.5
C6—N2—B1125.02 (13)H10A—C10—H10C109.5
N1—C1—C2109.00 (14)H10B—C10—H10C109.5
N1—C1—C10122.75 (15)C3—C11—H11A109.5
C2—C1—C10128.25 (15)C3—C11—H11B109.5
C3—C2—C1108.66 (14)H11A—C11—H11B109.5
C3—C2—H2A125.7C3—C11—H11C109.5
C1—C2—H2A125.7H11A—C11—H11C109.5
C2—C3—C4106.26 (14)H11B—C11—H11C109.5
C2—C3—C11127.90 (15)C7—C12—H12A109.5
C4—C3—C11125.84 (15)C7—C12—H12B109.5
C5—C4—N1120.68 (14)H12A—C12—H12B109.5
C5—C4—C3130.84 (15)C7—C12—H12C109.5
N1—C4—C3108.48 (14)H12A—C12—H12C109.5
C6—C5—C4122.19 (14)H12B—C12—H12C109.5
C6—C5—H5A118.9C9—C13—H13A109.5
C4—C5—H5A118.9C9—C13—H13B109.5
C5—C6—N2120.14 (14)H13A—C13—H13B109.5
C5—C6—C7131.18 (15)C9—C13—H13C109.5
N2—C6—C7108.66 (14)H13A—C13—H13C109.5
C8—C7—C6106.01 (14)H13B—C13—H13C109.5
C8—C7—C12128.52 (15)F2—B1—F1108.55 (14)
C6—C7—C12125.47 (16)F2—B1—N1110.45 (13)
C7—C8—C9108.40 (15)F1—B1—N1110.32 (13)
C7—C8—H8A125.8F2—B1—N2110.53 (13)
C9—C8—H8A125.8F1—B1—N2109.77 (13)
N2—C9—C8109.46 (14)N1—B1—N2107.21 (13)
N2—C9—C13122.76 (15)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2574).

References

  • Bergström, F., Mikhalyov, L., Hägglöf, P., Wortmmann, R., Ny, T. & Johansson, L. B. (2002). J. Am. Chem. Soc.124, 196–204. [PubMed]
  • Kollmannsberger, M., Rurack, K., Resch-Genger, U. & Daub, J. (1998). J. Phys. Chem. A, 102, 10211–10220.
  • Kuhn, N., Kuhn, A., Speis, M., Blaser, D. & Boese, R. (1990). Chem. Ber.123, 1301–1303.
  • Rigaku (2005). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Trieflinger, C., Rurack, K. & Daub, J. (2005). Angew. Chem. Int. Ed.44, 2288–2291. [PubMed]

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