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

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)°.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.041
• wR factor = 0.126
• Data-to-parameter ratio = 14.3

checkCIF/PLATON results

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Alert level G
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   0 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. 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) °].

Related literature

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

S2. 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.

S3. 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 U_iso(H) = 1.2 or 1.5U_eq(C).

Computing details

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

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

Crystal data

C13H15BF2N2	F(000) = 520
Mr = 248.08	Dx = 1.353 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2682 reflections
a = 7.6909 (8) Å	θ = 2.8–27.9°
b = 14.3392 (15) Å	µ = 0.10 mm^−1
c = 11.8334 (10) Å	T = 293 K
β = 111.108 (5)°	Block, red
V = 1217.4 (2) Å^3	0.30 × 0.20 × 0.20 mm
Z = 4

Data collection

Rigaku Mercury2 diffractometer	2396 independent reflections
Radiation source: fine-focus sealed tube	1963 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.019
Detector resolution: 13.6612 pixels mm^-1	θmax = 26.0°, θmin = 2.3°
ϕ and ω scans	h = −8→9
Absorption correction: empirical (using intensity measurements) (CrystalClear; Rigaku, 2005)	k = −17→16
Tmin = 0.961, Tmax = 0.974	l = −14→12
6540 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.126	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0669P)^2 + 0.3386P] where P = (Fo^2 + 2Fc^2)/3
2396 reflections	(Δ/σ)max = 0.007
167 parameters	Δρmax = 0.27 e Å^−3
0 restraints	Δρmin = −0.24 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq
F1	0.90473 (14)	−0.13462 (7)	0.77523 (9)	0.0416 (3)
F2	0.59217 (14)	−0.11875 (7)	0.68465 (9)	0.0429 (3)
N1	0.77362 (17)	0.01985 (9)	0.76358 (11)	0.0296 (3)
N2	0.72797 (18)	−0.10054 (9)	0.90212 (12)	0.0302 (3)
C1	0.7917 (2)	0.06479 (12)	0.66762 (15)	0.0333 (4)
C2	0.8203 (2)	0.15979 (12)	0.69475 (16)	0.0368 (4)
H2A	0.8371	0.2054	0.6438	0.044*
C3	0.8194 (2)	0.17455 (11)	0.80964 (15)	0.0331 (4)
C4	0.7899 (2)	0.08638 (11)	0.85312 (14)	0.0296 (4)
C5	0.7747 (2)	0.06086 (11)	0.96176 (14)	0.0292 (4)
H5A	0.7865	0.1065	1.0199	0.035*
C6	0.7427 (2)	−0.03013 (11)	0.98692 (14)	0.0296 (4)
C7	0.7146 (2)	−0.06999 (12)	1.08848 (15)	0.0331 (4)
C8	0.6836 (2)	−0.16395 (12)	1.06306 (16)	0.0377 (4)
H8A	0.6607	−0.2083	1.1133	0.045*
C9	0.6926 (2)	−0.18101 (11)	0.94874 (15)	0.0343 (4)
C10	0.7815 (3)	0.01588 (13)	0.55463 (16)	0.0419 (4)
H10A	0.8497	−0.0416	0.5749	0.063*
H10B	0.8346	0.0547	0.5093	0.063*
H10C	0.6536	0.0030	0.5067	0.063*
C11	0.8416 (3)	0.26491 (12)	0.87641 (17)	0.0411 (4)
H11A	0.9168	0.3066	0.8498	0.062*
H11B	0.9011	0.2539	0.9618	0.062*
H11C	0.7213	0.2923	0.8606	0.062*
C12	0.7199 (2)	−0.01832 (13)	1.19915 (16)	0.0388 (4)
H12A	0.6385	−0.0482	1.2334	0.058*
H12B	0.6797	0.0448	1.1779	0.058*
H12C	0.8449	−0.0183	1.2574	0.058*
C13	0.6716 (3)	−0.27203 (12)	0.88435 (17)	0.0426 (4)
H13A	0.7826	−0.2851	0.8680	0.064*
H13B	0.5669	−0.2690	0.8094	0.064*
H13C	0.6516	−0.3206	0.9342	0.064*
B1	0.7490 (2)	−0.08597 (13)	0.77801 (16)	0.0310 (4)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
F1	0.0484 (6)	0.0363 (6)	0.0467 (6)	0.0106 (4)	0.0251 (5)	−0.0002 (4)
F2	0.0463 (6)	0.0438 (6)	0.0326 (6)	−0.0101 (4)	0.0070 (5)	−0.0031 (4)
N1	0.0304 (7)	0.0317 (7)	0.0272 (7)	0.0027 (5)	0.0109 (6)	0.0002 (5)
N2	0.0303 (7)	0.0297 (7)	0.0298 (7)	0.0031 (5)	0.0099 (6)	0.0009 (5)
C1	0.0331 (8)	0.0369 (9)	0.0312 (9)	0.0055 (7)	0.0132 (7)	0.0039 (7)
C2	0.0432 (9)	0.0346 (9)	0.0366 (9)	0.0045 (7)	0.0192 (8)	0.0060 (7)
C3	0.0321 (8)	0.0319 (8)	0.0371 (9)	0.0031 (6)	0.0145 (7)	0.0018 (7)
C4	0.0271 (8)	0.0311 (8)	0.0299 (8)	0.0035 (6)	0.0093 (6)	−0.0009 (6)
C5	0.0257 (7)	0.0311 (8)	0.0301 (8)	0.0031 (6)	0.0094 (6)	−0.0023 (6)
C6	0.0270 (7)	0.0337 (8)	0.0278 (8)	0.0046 (6)	0.0095 (6)	−0.0005 (6)
C7	0.0296 (8)	0.0383 (9)	0.0312 (9)	0.0046 (7)	0.0108 (7)	0.0036 (7)
C8	0.0418 (9)	0.0367 (9)	0.0364 (9)	0.0023 (7)	0.0163 (8)	0.0081 (7)
C9	0.0343 (9)	0.0325 (9)	0.0346 (9)	0.0023 (6)	0.0104 (7)	0.0030 (7)
C10	0.0510 (11)	0.0448 (10)	0.0336 (9)	0.0035 (8)	0.0197 (8)	−0.0003 (7)
C11	0.0495 (10)	0.0319 (9)	0.0447 (10)	−0.0003 (8)	0.0204 (9)	−0.0010 (7)
C12	0.0411 (9)	0.0460 (10)	0.0318 (9)	0.0039 (8)	0.0163 (8)	0.0005 (7)
C13	0.0511 (11)	0.0327 (9)	0.0421 (10)	−0.0013 (8)	0.0146 (8)	0.0008 (7)
B1	0.0326 (9)	0.0312 (9)	0.0287 (9)	0.0011 (7)	0.0105 (7)	−0.0004 (7)

Geometric parameters (Å, º)

F1—B1	1.397 (2)	C7—C8	1.382 (2)
F2—B1	1.392 (2)	C7—C12	1.492 (2)
N1—C1	1.356 (2)	C8—C9	1.401 (2)
N1—C4	1.3974 (19)	C8—H8A	0.9300
N1—B1	1.546 (2)	C9—C13	1.490 (2)
N2—C9	1.348 (2)	C10—H10A	0.9600
N2—C6	1.399 (2)	C10—H10B	0.9600
N2—B1	1.548 (2)	C10—H10C	0.9600
C1—C2	1.399 (2)	C11—H11A	0.9600
C1—C10	1.487 (2)	C11—H11B	0.9600
C2—C3	1.378 (2)	C11—H11C	0.9600
C2—H2A	0.9300	C12—H12A	0.9600
C3—C4	1.414 (2)	C12—H12B	0.9600
C3—C11	1.495 (2)	C12—H12C	0.9600
C4—C5	1.382 (2)	C13—H13A	0.9600
C5—C6	1.380 (2)	C13—H13B	0.9600
C5—H5A	0.9300	C13—H13C	0.9600
C6—C7	1.416 (2)
C1—N1—C4	107.60 (14)	C8—C9—C13	127.78 (15)
C1—N1—B1	127.78 (14)	C1—C10—H10A	109.5
C4—N1—B1	124.57 (13)	C1—C10—H10B	109.5
C9—N2—C6	107.47 (13)	H10A—C10—H10B	109.5
C9—N2—B1	127.51 (13)	C1—C10—H10C	109.5
C6—N2—B1	125.02 (13)	H10A—C10—H10C	109.5
N1—C1—C2	109.00 (14)	H10B—C10—H10C	109.5
N1—C1—C10	122.75 (15)	C3—C11—H11A	109.5
C2—C1—C10	128.25 (15)	C3—C11—H11B	109.5
C3—C2—C1	108.66 (14)	H11A—C11—H11B	109.5
C3—C2—H2A	125.7	C3—C11—H11C	109.5
C1—C2—H2A	125.7	H11A—C11—H11C	109.5
C2—C3—C4	106.26 (14)	H11B—C11—H11C	109.5
C2—C3—C11	127.90 (15)	C7—C12—H12A	109.5
C4—C3—C11	125.84 (15)	C7—C12—H12B	109.5
C5—C4—N1	120.68 (14)	H12A—C12—H12B	109.5
C5—C4—C3	130.84 (15)	C7—C12—H12C	109.5
N1—C4—C3	108.48 (14)	H12A—C12—H12C	109.5
C6—C5—C4	122.19 (14)	H12B—C12—H12C	109.5
C6—C5—H5A	118.9	C9—C13—H13A	109.5
C4—C5—H5A	118.9	C9—C13—H13B	109.5
C5—C6—N2	120.14 (14)	H13A—C13—H13B	109.5
C5—C6—C7	131.18 (15)	C9—C13—H13C	109.5
N2—C6—C7	108.66 (14)	H13A—C13—H13C	109.5
C8—C7—C6	106.01 (14)	H13B—C13—H13C	109.5
C8—C7—C12	128.52 (15)	F2—B1—F1	108.55 (14)
C6—C7—C12	125.47 (16)	F2—B1—N1	110.45 (13)
C7—C8—C9	108.40 (15)	F1—B1—N1	110.32 (13)
C7—C8—H8A	125.8	F2—B1—N2	110.53 (13)
C9—C8—H8A	125.8	F1—B1—N2	109.77 (13)
N2—C9—C8	109.46 (14)	N1—B1—N2	107.21 (13)
N2—C9—C13	122.76 (15)