4,4-Difluoro-1,3,5,7-tetra­methyl-8-penta­fluoro­phenyl-4-bora-3a,4a-diaza-s-indacene

In the title dye compound, C₁₉H₁₄BF₇N₂, the boron-dipyrromethene core lies on a crystallographic mirror plane which bis­ects the BF₂ and penta­fluoro­phenyl groups. The dihedral angle between the penta­fluoro­phenyl ring and the tricyclic system is thus 90° by symmetry. The sp³-hybridized B atom has a slightly distorted tetra­hedral coordination.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.056
• wR factor = 0.162
• Data-to-parameter ratio = 11.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT222_ALERT_3_C Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       3.16 Ratio
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for        C17
PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) .....          2
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L=  0.600          2
PLAT913_ALERT_3_C Missing # of Very Strong Reflections in FCF ....          1
PLAT147_ALERT_1_C su on Symmetry Constrained Cell Angle(s) .......          ?

Alert level G
PLAT180_ALERT_4_G Check Cell Rounding: # of Values Ending with 0 =          3
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported   _diffrn_ambient_temperature        293 K
PLAT380_ALERT_4_G Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C10
PLAT380_ALERT_4_G Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C11
PLAT380_ALERT_4_G Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C13
PLAT380_ALERT_4_G Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C12

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

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   4 ALERT type 3 Indicator that the structure quality may be low
   5 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 and famous 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). Here, the synthesis and the crystal structure of the title compound are reported. The observed geometric parameters are generally comparable with the reported values for other BODIPY-based compounds (Picou et al., 1990; Wang et al., 2007).

As shown in Fig. 1, the BODIPY skeleton of the molecule, which is formed from three fused heterocyclic rings, is planar, as this system lies on a mirror plane. The sp³-hybridized B centre appears as a slightly distorted tetrahedron, with N—B—N and F—B—F angles of 107.5 (2) and 109.8 (3)°. The two B—N distances are almost identical, implying the usual delocalization of the positive charge. The average bond lengths for B—N and B—F and the average N—B—N, F—B—F and F—B—N bond angles indicate a tetrahedral BF₂N₂ configuration and are in good agreement with previous published data (Kuhn, et al., 1990; Picou et al., 1990; Wang et al., 2007). No unusual values are observed in the molecular structure. Perhaps due to the steric repulsion from the C11 and C13 methyl groups, the pentafluorophenyl ring is perpendicular to the BODIPY ring plane, with a dihedral angle constrained by symmetry to be 90°.

Related literature

For boron–dipyrromethene (BODIPY) dyes, see: Bergström et al. (2002); Trieflinger et al. (2005). For geometrical parameters in other BODIPY-based compounds, see: Picou et al.(1990); Wang et al.(2007); Kuhn et al. (1990).

S2. Experimental

Pentafluorobenzaldehyde (2 mmol) and 2,4-dimethyl-1H-pyrrole (4 mmol) were dissolved in 50 ml of dry CH₂Cl₂ under an Ar atmosphere. One drop of trifluoroacetic acid (TFA) was added, and the solution was stirred at room temperature overnight. Thin layer chromatography (TLC) monitoring (silica; CH₂Cl₂) 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 N,N-diisopropylethylamine (DIEA, 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 under reduced pressure. The crude product was purified by silica-gel flash column chromatography and recrystallization from CHCl₃/hexane. Single crystals suitable for X-ray analysis were obtained from an acetonitrile solution by slow evaporation.

S3. Refinement

Positional parameters of all the H atoms were calculated geometrically and were allowed to ride on the C atoms to which they are bonded. Isotropic displacement parameters for H atoms were refined.

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 for non-H atoms are drawn at the 30% probability level. 'A' labeled atoms are generated by symmetry code x, 1-y, z.

4,4-Difluoro-1,3,5,7-tetramethyl-8-pentafluorophenyl-4-bora-3a,4a-diaza- s-indacene

Crystal data

C19H14BF7N2	F(000) = 840
Mr = 414.13	Dx = 1.501 Mg m^−3
Monoclinic, C2/m	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2y	Cell parameters from 2191 reflections
a = 12.4060 (5) Å	θ = 3.1–27.5°
b = 7.5490 (9) Å	µ = 0.14 mm^−1
c = 19.720 (3) Å	T = 293 K
β = 97.12 (2)°	Prism, red
V = 1832.6 (4) Å^3	0.2 × 0.2 × 0.2 mm
Z = 4

Data collection

Rigaku SCXmini diffractometer	1936 independent reflections
Radiation source: fine-focus sealed tube	1585 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.032
Detector resolution: 13.6612 pixels mm^-1	θmax = 26.0°, θmin = 3.1°
ω scans	h = −15→15
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −9→9
Tmin = 0.973, Tmax = 0.979	l = −24→24
8232 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)] = 0.056	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.162	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.091P)^2 + 0.8854P] where P = (Fo^2 + 2Fc^2)/3
1936 reflections	(Δ/σ)max < 0.001
170 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.23 e Å^−3
0 constraints

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
F1	0.12945 (15)	0.3502 (3)	0.07469 (8)	0.1040 (7)
F3	0.28302 (13)	0.18847 (16)	0.34101 (7)	0.0721 (5)
F4	0.35839 (14)	0.1888 (2)	0.47541 (8)	0.0928 (6)
F5	0.39356 (18)	0.5000	0.54333 (9)	0.0988 (9)
N1	0.08602 (19)	0.5000	0.17499 (11)	0.0486 (6)
N2	0.2747 (2)	0.5000	0.14360 (11)	0.0523 (6)
C1	−0.0234 (2)	0.5000	0.17144 (15)	0.0564 (7)
C2	−0.0523 (2)	0.5000	0.23784 (16)	0.0597 (8)
H2A	−0.1229	0.5000	0.2490	0.104 (14)*
C3	0.0406 (2)	0.5000	0.28399 (14)	0.0489 (7)
C4	0.1291 (2)	0.5000	0.24405 (12)	0.0446 (6)
C5	0.2418 (2)	0.5000	0.26194 (12)	0.0422 (6)
C6	0.3151 (2)	0.5000	0.21363 (13)	0.0475 (6)
C7	0.4316 (2)	0.5000	0.21939 (16)	0.0563 (7)
C8	0.4565 (3)	0.5000	0.15330 (17)	0.0682 (9)
H8A	0.5263	0.5000	0.1408	0.080 (11)*
C9	0.3606 (3)	0.5000	0.10769 (15)	0.0627 (8)
C10	−0.0981 (3)	0.5000	0.10532 (18)	0.0783 (11)
H10A	−0.0559	0.5000	0.0677	0.16 (2)*
H10B	−0.1430	0.6038	0.1031	0.23 (3)*
C11	0.0428 (3)	0.5000	0.36050 (15)	0.0629 (9)
H11A	−0.0302	0.5000	0.3719	0.079 (11)*
H11B	0.0801	0.6038	0.3792	0.093 (9)*
C12	0.3492 (4)	0.5000	0.03121 (18)	0.0875 (13)
H12A	0.2735	0.5000	0.0135	0.25 (4)*
H12B	0.3833	0.3962	0.0156	0.172 (19)*
C13	0.5127 (3)	0.5000	0.28225 (19)	0.0693 (9)
H13A	0.5847	0.5000	0.2693	0.126 (17)*
H13B	0.5027	0.3962	0.3089	0.129 (13)*
C14	0.2846 (2)	0.5000	0.33641 (13)	0.0425 (6)
C15	0.30342 (16)	0.3443 (3)	0.37278 (10)	0.0490 (5)
C16	0.34105 (17)	0.3429 (3)	0.44160 (11)	0.0602 (6)
C17	0.3592 (2)	0.5000	0.47584 (15)	0.0638 (9)
B1	0.1532 (3)	0.5000	0.11399 (17)	0.0612 (9)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
F1	0.0923 (11)	0.1505 (17)	0.0710 (10)	−0.0214 (11)	0.0177 (8)	−0.0597 (10)
F3	0.0976 (11)	0.0457 (7)	0.0730 (9)	0.0076 (7)	0.0110 (7)	0.0018 (6)
F4	0.1028 (12)	0.1033 (12)	0.0732 (10)	0.0309 (10)	0.0147 (8)	0.0448 (9)
F5	0.0785 (14)	0.177 (3)	0.0379 (10)	0.000	−0.0059 (9)	0.000
N1	0.0560 (13)	0.0546 (13)	0.0346 (11)	0.000	0.0027 (9)	0.000
N2	0.0601 (14)	0.0615 (14)	0.0377 (12)	0.000	0.0155 (10)	0.000
C1	0.0547 (17)	0.0633 (18)	0.0491 (16)	0.000	−0.0017 (12)	0.000
C2	0.0491 (16)	0.079 (2)	0.0516 (16)	0.000	0.0085 (13)	0.000
C3	0.0495 (15)	0.0576 (16)	0.0405 (14)	0.000	0.0086 (11)	0.000
C4	0.0520 (15)	0.0477 (14)	0.0337 (12)	0.000	0.0041 (10)	0.000
C5	0.0507 (14)	0.0386 (13)	0.0380 (13)	0.000	0.0081 (11)	0.000
C6	0.0535 (15)	0.0490 (15)	0.0408 (14)	0.000	0.0089 (11)	0.000
C7	0.0541 (16)	0.0601 (17)	0.0570 (17)	0.000	0.0157 (13)	0.000
C8	0.0590 (19)	0.087 (2)	0.064 (2)	0.000	0.0271 (16)	0.000
C9	0.075 (2)	0.071 (2)	0.0468 (16)	0.000	0.0246 (15)	0.000
C10	0.069 (2)	0.108 (3)	0.0514 (19)	0.000	−0.0157 (16)	0.000
C11	0.0517 (16)	0.095 (3)	0.0437 (15)	0.000	0.0130 (13)	0.000
C12	0.099 (3)	0.121 (4)	0.0486 (19)	0.000	0.033 (2)	0.000
C13	0.0507 (17)	0.088 (3)	0.069 (2)	0.000	0.0068 (15)	0.000
C14	0.0428 (13)	0.0479 (14)	0.0375 (13)	0.000	0.0077 (10)	0.000
C15	0.0507 (10)	0.0498 (11)	0.0474 (10)	0.0060 (9)	0.0099 (8)	0.0030 (8)
C16	0.0533 (11)	0.0795 (16)	0.0488 (11)	0.0128 (11)	0.0104 (9)	0.0208 (11)
C17	0.0490 (16)	0.104 (3)	0.0380 (14)	0.000	0.0051 (12)	0.000
B1	0.068 (2)	0.082 (2)	0.0346 (15)	0.000	0.0083 (14)	0.000

Geometric parameters (Å, º)

B1—F1	1.382 (3)	C7—C8	1.376 (4)
B1—N1	1.546 (4)	C7—C13	1.497 (5)
B1—N2	1.548 (5)	C8—C9	1.400 (5)
F3—C15	1.342 (3)	C8—H8A	0.9301
F4—C16	1.345 (3)	C9—C12	1.497 (4)
F5—C17	1.346 (3)	C10—H10A	0.9598
N1—C1	1.350 (4)	C10—H10B	0.9600
N1—C4	1.400 (3)	C11—H11A	0.9601
N2—C9	1.350 (4)	C11—H11B	0.9600
N2—C6	1.409 (4)	C12—H12A	0.9600
C1—C2	1.400 (4)	C12—H12B	0.9601
C1—C10	1.503 (4)	C13—H13A	0.9600
C2—C3	1.377 (4)	C13—H13B	0.9600
C2—H2A	0.9298	C14—C15	1.382 (2)
C3—C4	1.428 (4)	C14—C15^i	1.382 (2)
C3—C11	1.506 (4)	C15—C16	1.379 (3)
C4—C5	1.398 (4)	C16—C17	1.370 (3)
C5—C6	1.397 (4)	C17—C16^i	1.370 (3)
C5—C14	1.498 (3)	B1—F1^i	1.382 (3)
C6—C7	1.435 (4)
C1—N1—C4	108.1 (2)	C8—C9—C12	127.9 (3)
C1—N1—B1	126.5 (2)	C1—C10—H10A	109.6
C4—N1—B1	125.4 (2)	C1—C10—H10B	109.4
C9—N2—C6	107.8 (3)	H10A—C10—H10B	109.5
C9—N2—B1	126.6 (3)	C3—C11—H11A	109.5
C6—N2—B1	125.5 (2)	C3—C11—H11B	109.5
N1—C1—C2	108.9 (3)	H11A—C11—H11B	109.5
N1—C1—C10	123.6 (3)	C9—C12—H12A	109.5
C2—C1—C10	127.6 (3)	C9—C12—H12B	109.5
C3—C2—C1	109.2 (3)	H12A—C12—H12B	109.5
C3—C2—H2A	125.5	C7—C13—H13A	109.4
C1—C2—H2A	125.4	C7—C13—H13B	109.5
C2—C3—C4	105.8 (2)	H13A—C13—H13B	109.5
C2—C3—C11	124.9 (3)	C15—C14—C15^i	116.6 (2)
C4—C3—C11	129.2 (3)	C15—C14—C5	121.69 (13)
N1—C4—C5	119.6 (2)	C15^i—C14—C5	121.69 (13)
N1—C4—C3	108.0 (2)	F3—C15—C14	119.56 (18)
C5—C4—C3	132.3 (2)	F3—C15—C16	118.27 (19)
C6—C5—C4	122.9 (2)	C14—C15—C16	122.2 (2)
C6—C5—C14	119.1 (2)	F4—C16—C17	119.9 (2)
C4—C5—C14	118.0 (2)	F4—C16—C15	120.6 (2)
C5—C6—N2	119.1 (2)	C17—C16—C15	119.5 (2)
C5—C6—C7	132.9 (3)	F5—C17—C16	119.99 (14)
N2—C6—C7	108.0 (2)	F5—C17—C16^i	119.99 (14)
C8—C7—C6	105.5 (3)	C16—C17—C16^i	120.0 (3)
C8—C7—C13	125.3 (3)	F1—B1—F1^i	109.8 (3)
C6—C7—C13	129.2 (3)	N1—B1—N2	107.5 (2)
C7—C8—C9	109.6 (3)	F1—B1—N1	109.8 (2)
C7—C8—H8A	125.2	F1^i—B1—N1	109.8 (2)
C9—C8—H8A	125.1	F1—B1—N2	110.0 (2)
N2—C9—C8	109.0 (3)	F1^i—B1—N2	110.0 (2)
N2—C9—C12	123.1 (3)

Symmetry code: (i) x, −y+1, z.