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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

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

aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
*Correspondence e-mail: xuhj@seu.edu.cn

(Received 12 June 2008; accepted 29 July 2008; online 6 August 2008)

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[Bergström, F., Mikhalyov, L., Hägglöf, P., Wortmmann, R., Ny, T. & Johansson, L. B. (2002). J. Am. Chem. Soc. 124, 196-204.]); Kollmannsberger et al. (1998[Kollmannsberger, M., Rurack, K., Resch-Genger, U. & Daub, J. (1998). J. Phys. Chem. A, 102, 10211-10220.]); Kuhn et al. (1990[Kuhn, N., Kuhn, A., Speis, M., Blaser, D. & Boese, R. (1990). Chem. Ber. 123, 1301-1303.]); Trieflinger et al. (2005[Trieflinger, C., Rurack, K. & Daub, J. (2005). Angew. Chem. Int. Ed. 44, 2288-2291.]).

[Scheme 1]

Experimental

Crystal data
  • C13H15BF2N2

  • Mr = 248.08

  • Monoclinic, P 21 /c

  • 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[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.961, Tmax = 0.974

  • 6540 measured reflections

  • 2396 independent reflections

  • 1963 reflections with I > 2σ(I)

  • Rint = 0.019

Refinement
  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 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[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalClear; 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: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

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) °].

Related literature top

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

Experimental top

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 top

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).

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. A view of the title compound with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
4,4-Difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene top
Crystal data top
C13H15BF2N2F(000) = 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 = 2.8–27.9°
b = 14.3392 (15) ŵ = 0.10 mm1
c = 11.8334 (10) ÅT = 293 K
β = 111.108 (5)°Block, red
V = 1217.4 (2) Å30.30 × 0.20 × 0.20 mm
Z = 4
Data collection top
Rigaku Mercury2
diffractometer
2396 independent reflections
Radiation source: fine-focus sealed tube1963 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
Detector resolution: 13.6612 pixels mm-1θmax = 26.0°, θmin = 2.3°
ϕ and ω scansh = 89
Absorption correction: empirical (using intensity measurements)
(CrystalClear; Rigaku, 2005)
k = 1716
Tmin = 0.961, Tmax = 0.974l = 1412
6540 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)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.126H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0669P)2 + 0.3386P]
where P = (Fo2 + 2Fc2)/3
2396 reflections(Δ/σ)max = 0.007
167 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = 0.24 e Å3
Crystal data top
C13H15BF2N2V = 1217.4 (2) Å3
Mr = 248.08Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.6909 (8) ŵ = 0.10 mm1
b = 14.3392 (15) ÅT = 293 K
c = 11.8334 (10) Å0.30 × 0.20 × 0.20 mm
β = 111.108 (5)°
Data collection top
Rigaku Mercury2
diffractometer
2396 independent reflections
Absorption correction: empirical (using intensity measurements)
(CrystalClear; Rigaku, 2005)
1963 reflections with I > 2σ(I)
Tmin = 0.961, Tmax = 0.974Rint = 0.019
6540 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0400 restraints
wR(F2) = 0.126H-atom parameters constrained
S = 1.06Δρmax = 0.27 e Å3
2396 reflectionsΔρmin = 0.24 e Å3
167 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
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)
H8A0.66070.20831.11330.045*
C90.6926 (2)0.18101 (11)0.94874 (15)0.0343 (4)
C100.7815 (3)0.01588 (13)0.55463 (16)0.0419 (4)
H10A0.84970.04160.57490.063*
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)
H12A0.63850.04821.23340.058*
H12B0.67970.04481.17790.058*
H12C0.84490.01831.25740.058*
C130.6716 (3)0.27203 (12)0.88435 (17)0.0426 (4)
H13A0.78260.28510.86800.064*
H13B0.56690.26900.80940.064*
H13C0.65160.32060.93420.064*
B10.7490 (2)0.08597 (13)0.77801 (16)0.0310 (4)
Atomic displacement parameters (Å2) top
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, º) top
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)

Experimental details

Crystal data
Chemical formulaC13H15BF2N2
Mr248.08
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)7.6909 (8), 14.3392 (15), 11.8334 (10)
β (°) 111.108 (5)
V3)1217.4 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.30 × 0.20 × 0.20
Data collection
DiffractometerRigaku Mercury2
diffractometer
Absorption correctionEmpirical (using intensity measurements)
(CrystalClear; Rigaku, 2005)
Tmin, Tmax0.961, 0.974
No. of measured, independent and
observed [I > 2σ(I)] reflections
6540, 2396, 1963
Rint0.019
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.126, 1.06
No. of reflections2396
No. of parameters167
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.27, 0.24

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

 

Acknowledgements

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

References

First citationBergström, F., Mikhalyov, L., Hägglöf, P., Wortmmann, R., Ny, T. & Johansson, L. B. (2002). J. Am. Chem. Soc. 124, 196–204.  Web of Science PubMed Google Scholar
First citationKollmannsberger, M., Rurack, K., Resch-Genger, U. & Daub, J. (1998). J. Phys. Chem. A, 102, 10211–10220.  Web of Science CrossRef CAS Google Scholar
First citationKuhn, N., Kuhn, A., Speis, M., Blaser, D. & Boese, R. (1990). Chem. Ber. 123, 1301–1303.  CrossRef CAS Web of Science Google Scholar
First citationRigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationTrieflinger, C., Rurack, K. & Daub, J. (2005). Angew. Chem. Int. Ed. 44, 2288–2291.  Web of Science CrossRef CAS Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds