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

The structure of the title compound (TM-BODIPY), C₁₃H₁₅BF₂N₂, which can be used to synthesize mol­ecular probes for labelling DNA and proteins, has been determined using a very small single crystal employing Cu Kα radiation and a two-dimensional multi-wire proportional detector. The mol­ecules stack perpendicular to (90), forming a corrugated sheet-like structure when viewed along (3,0,10).

Key indicators

• Single-crystal X-ray study
• T = 110 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.047
• wR factor = 0.119
• Data-to-parameter ratio = 10.4

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT027_ALERT_3_A _diffrn_reflns_theta_full (too) Low ............      59.48 Deg.

Author Response: We have used a combination of CuK\a radiation along with multiwire proportional counter. Thus the instrumental geometry restricts the maximum theta angle to theta = 60 degrees.

Alert level B
THETM01_ALERT_3_B  The value of sine(theta_max)/wavelength is less than 0.575
            Calculated sin(theta_max)/wavelength =    0.5587
PLAT023_ALERT_3_B Resolution (too) Low [sin(th)/Lambda < 0.6].....      59.48 Deg.

Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.98
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?

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

   1 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
   4 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: FRAMBO (Bruker–Nonius, 2003); cell refinement: Cell_Now (Sheldrick, 2003) and SAINT (Bruker–Nonius, 2003); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2001); program(s) used to refine structure: SHELXL97 (Sheldrick, 2001); molecular graphics: X-SEED (Barbour, 2001) and DIAMOND (Brandenbourg, 2001); software used to prepare material for publication: SHELXL97, PLATON (Spek 2004) as incorporated in WinGX (Farrugia, 1999)'.

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/n	Cu Kα radiation, λ = 1.54178 Å
a = 7.6932 (13) Å	Cell parameters from 739 reflections
b = 14.379 (2) Å	θ = 5.1–51.4°
c = 11.5295 (16) Å	µ = 0.84 mm^−1
β = 107.245 (8)°	T = 110 K
V = 1218.0 (3) Å^3	Block, red
Z = 4	0.08 × 0.03 × 0.01 mm

Data collection

Bruker GADDS D8 Discover diffractometer	1736 independent reflections
Radiation source: fine-focus sealed tube	1035 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.085
φ and ω scans	θmax = 59.5°, θmin = 5.1°
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)	h = −8→8
Tmin = 0.936, Tmax = 0.992	k = −16→16
7569 measured reflections	l = −12→12

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)] = 0.047	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.119	H-atom parameters constrained
S = 1.06	w = [exp{2(sinθ/λ)^2}]/[σ^2(Fo^2) + (0.061P)^2] where P = 0.333Fo^2 + 0.667Fc^2
1736 reflections	(Δ/σ)max < 0.001
167 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.22 e Å^−3

Special details

Experimental. For data collection a BRUKER GADDS D8 Discover instrument equipped with a combination of monochromated (with Graphite) CuKα radiation, and a HI-STAR multi-wire proportional counter area detector was used.

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
B1	0.0294 (5)	0.4137 (3)	0.7772 (3)	0.0294 (9)
F1	−0.1296 (2)	0.36472 (11)	0.77587 (15)	0.0360 (5)
F2	0.0918 (2)	0.38121 (12)	0.68269 (14)	0.0369 (5)
N1	0.1754 (3)	0.39915 (16)	0.9023 (2)	0.0266 (6)
N2	−0.0104 (3)	0.51964 (16)	0.7635 (2)	0.0261 (6)
C1	0.2589 (4)	0.3182 (2)	0.9488 (3)	0.0287 (8)
C2	0.3815 (4)	0.3355 (2)	1.0637 (3)	0.0322 (8)
H7	0.4563	0.2904	1.1154	0.039*
C3	0.3752 (4)	0.4301 (2)	1.0892 (3)	0.0290 (8)
C4	0.2465 (4)	0.4700 (2)	0.9868 (3)	0.0266 (7)
C5	0.1875 (4)	0.5613 (2)	0.9625 (3)	0.0250 (7)
H5	0.2339	0.6076	1.0226	0.030*
C6	0.0637 (4)	0.5869 (2)	0.8537 (2)	0.0248 (7)
C7	−0.0115 (4)	0.6745 (2)	0.8098 (3)	0.0287 (8)
C8	−0.1277 (4)	0.6598 (2)	0.6946 (3)	0.0310 (8)
H2	−0.1973	0.7062	0.6424	0.037*
C9	−0.1254 (4)	0.5642 (2)	0.6676 (3)	0.0286 (8)
C10	0.2156 (5)	0.2276 (2)	0.8843 (3)	0.0370 (8)
H12A	0.0846	0.2156	0.8645	0.055*
H12B	0.2829	0.1778	0.9366	0.055*
H12C	0.2507	0.2299	0.8093	0.055*
C11	0.4836 (4)	0.4812 (2)	1.2015 (3)	0.0337 (8)
H11A	0.4194	0.4783	1.2632	0.051*
H11B	0.4982	0.5463	1.1811	0.051*
H11C	0.6037	0.4522	1.2332	0.051*
C12	0.0327 (5)	0.7657 (2)	0.8769 (3)	0.0346 (8)
H10A	0.1446	0.7914	0.8658	0.052*
H10B	0.0498	0.7553	0.9636	0.052*
H10C	−0.0677	0.8095	0.8450	0.052*
C13	−0.2291 (4)	0.5161 (2)	0.5535 (3)	0.0354 (8)
H9A	−0.1503	0.5075	0.5013	0.053*
H9B	−0.3347	0.5539	0.5108	0.053*
H9C	−0.2704	0.4553	0.5734	0.053*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
B1	0.032 (2)	0.032 (2)	0.0245 (19)	−0.0053 (17)	0.0084 (17)	−0.0017 (16)
F1	0.0328 (11)	0.0334 (10)	0.0398 (10)	−0.0079 (8)	0.0075 (8)	−0.0011 (9)
F2	0.0455 (12)	0.0390 (11)	0.0266 (9)	0.0049 (9)	0.0111 (8)	−0.0029 (8)
N1	0.0264 (14)	0.0295 (15)	0.0247 (13)	−0.0035 (12)	0.0088 (12)	0.0006 (12)
N2	0.0239 (14)	0.0285 (15)	0.0253 (14)	−0.0023 (11)	0.0061 (12)	−0.0005 (11)
C1	0.0304 (19)	0.0277 (19)	0.0296 (18)	0.0024 (14)	0.0116 (16)	0.0047 (14)
C2	0.0319 (19)	0.033 (2)	0.0297 (18)	0.0034 (15)	0.0063 (16)	0.0074 (14)
C3	0.0266 (18)	0.034 (2)	0.0292 (18)	−0.0054 (14)	0.0129 (15)	0.0028 (14)
C4	0.0233 (17)	0.0336 (19)	0.0229 (16)	−0.0043 (14)	0.0066 (14)	0.0022 (14)
C5	0.0242 (17)	0.0283 (18)	0.0255 (16)	−0.0058 (13)	0.0117 (15)	−0.0022 (13)
C6	0.0216 (17)	0.0286 (17)	0.0261 (17)	−0.0030 (14)	0.0100 (14)	−0.0018 (14)
C7	0.0261 (18)	0.0282 (18)	0.0319 (18)	−0.0035 (14)	0.0089 (15)	0.0013 (14)
C8	0.0300 (19)	0.0324 (19)	0.0292 (18)	0.0023 (15)	0.0064 (16)	0.0070 (14)
C9	0.0210 (17)	0.037 (2)	0.0300 (18)	−0.0030 (14)	0.0109 (15)	0.0036 (14)
C10	0.045 (2)	0.0309 (19)	0.0346 (19)	−0.0001 (17)	0.0118 (17)	0.0016 (15)
C11	0.0332 (19)	0.039 (2)	0.0271 (17)	−0.0020 (16)	0.0059 (15)	0.0008 (15)
C12	0.036 (2)	0.0280 (18)	0.0389 (19)	−0.0006 (15)	0.0091 (17)	−0.0024 (15)
C13	0.035 (2)	0.041 (2)	0.0273 (18)	−0.0008 (16)	0.0038 (16)	0.0016 (15)

Geometric parameters (Å, º)

B1—F2	1.395 (4)	C7—C8	1.379 (4)
B1—F1	1.407 (4)	C7—C12	1.508 (4)
B1—N2	1.553 (4)	C8—C9	1.411 (4)
B1—N1	1.557 (4)	C8—H2	0.9500
N1—C1	1.360 (4)	C9—C13	1.492 (4)
N1—C4	1.403 (4)	C10—H12A	0.9800
N2—C9	1.354 (4)	C10—H12B	0.9800
N2—C6	1.411 (4)	C10—H12C	0.9800
C1—C2	1.401 (4)	C11—H11A	0.9800
C1—C10	1.488 (4)	C11—H11B	0.9800
C2—C3	1.396 (4)	C11—H11C	0.9800
C2—H7	0.9500	C12—H10A	0.9800
C3—C4	1.418 (4)	C12—H10B	0.9800
C3—C11	1.507 (4)	C12—H10C	0.9800
C4—C5	1.390 (4)	C13—H9A	0.9800
C5—C6	1.381 (4)	C13—H9B	0.9800
C5—H5	0.9500	C13—H9C	0.9800
C6—C7	1.416 (4)
F2—B1—F1	108.9 (3)	C6—C7—C12	125.7 (3)
F2—B1—N2	110.6 (3)	C7—C8—C9	108.3 (3)
F1—B1—N2	110.2 (3)	C7—C8—H2	125.8
F2—B1—N1	111.0 (3)	C9—C8—H2	125.8
F1—B1—N1	109.2 (2)	N2—C9—C8	109.2 (3)
N2—B1—N1	107.0 (2)	N2—C9—C13	123.3 (3)
C1—N1—C4	107.8 (2)	C8—C9—C13	127.5 (3)
C1—N1—B1	127.3 (2)	C1—C10—H12A	109.5
C4—N1—B1	124.8 (2)	C1—C10—H12B	109.5
C9—N2—C6	107.5 (2)	H12A—C10—H12B	109.5
C9—N2—B1	127.5 (2)	C1—C10—H12C	109.5
C6—N2—B1	124.9 (2)	H12A—C10—H12C	109.5
N1—C1—C2	109.2 (3)	H12B—C10—H12C	109.5
N1—C1—C10	122.8 (3)	C3—C11—H11A	109.5
C2—C1—C10	128.0 (3)	C3—C11—H11B	109.5
C3—C2—C1	108.4 (3)	H11A—C11—H11B	109.5
C3—C2—H7	125.8	C3—C11—H11C	109.5
C1—C2—H7	125.8	H11A—C11—H11C	109.5
C2—C3—C4	106.1 (3)	H11B—C11—H11C	109.5
C2—C3—C11	127.7 (3)	C7—C12—H10A	109.5
C4—C3—C11	126.2 (3)	C7—C12—H10B	109.5
C5—C4—N1	120.6 (3)	H10A—C12—H10B	109.5
C5—C4—C3	130.9 (3)	C7—C12—H10C	109.5
N1—C4—C3	108.4 (2)	H10A—C12—H10C	109.5
C6—C5—C4	122.0 (3)	H10B—C12—H10C	109.5
C6—C5—H5	119.0	C9—C13—H9A	109.5
C4—C5—H5	119.0	C9—C13—H9B	109.5
C5—C6—N2	120.4 (3)	H9A—C13—H9B	109.5
C5—C6—C7	131.3 (3)	C9—C13—H9C	109.5
N2—C6—C7	108.2 (2)	H9A—C13—H9C	109.5
C8—C7—C6	106.7 (3)	H9B—C13—H9C	109.5
C8—C7—C12	127.6 (3)
F2—B1—N1—C1	−54.9 (4)	C2—C3—C4—C5	−179.4 (3)
F1—B1—N1—C1	65.1 (4)	C11—C3—C4—C5	0.0 (5)
N2—B1—N1—C1	−175.6 (3)	C2—C3—C4—N1	0.9 (3)
F2—B1—N1—C4	123.8 (3)	C11—C3—C4—N1	−179.8 (3)
F1—B1—N1—C4	−116.1 (3)	N1—C4—C5—C6	−2.7 (4)
N2—B1—N1—C4	3.1 (4)	C3—C4—C5—C6	177.6 (3)
F2—B1—N2—C9	57.4 (4)	C4—C5—C6—N2	1.2 (4)
F1—B1—N2—C9	−63.0 (4)	C4—C5—C6—C7	−178.8 (3)
N1—B1—N2—C9	178.4 (3)	C9—N2—C6—C5	−179.6 (3)
F2—B1—N2—C6	−125.6 (3)	B1—N2—C6—C5	2.9 (4)
F1—B1—N2—C6	114.0 (3)	C9—N2—C6—C7	0.4 (3)
N1—B1—N2—C6	−4.6 (4)	B1—N2—C6—C7	−177.1 (3)
C4—N1—C1—C2	1.0 (3)	C5—C6—C7—C8	179.6 (3)
B1—N1—C1—C2	179.9 (3)	N2—C6—C7—C8	−0.4 (3)
C4—N1—C1—C10	179.2 (3)	C5—C6—C7—C12	0.7 (5)
B1—N1—C1—C10	−1.9 (5)	N2—C6—C7—C12	−179.2 (3)
N1—C1—C2—C3	−0.4 (3)	C6—C7—C8—C9	0.3 (3)
C10—C1—C2—C3	−178.6 (3)	C12—C7—C8—C9	179.1 (3)
C1—C2—C3—C4	−0.3 (3)	C6—N2—C9—C8	−0.2 (3)
C1—C2—C3—C11	−179.7 (3)	B1—N2—C9—C8	177.2 (3)
C1—N1—C4—C5	179.1 (3)	C6—N2—C9—C13	179.5 (3)
B1—N1—C4—C5	0.2 (4)	B1—N2—C9—C13	−3.1 (5)
C1—N1—C4—C3	−1.1 (3)	C7—C8—C9—N2	0.0 (4)
B1—N1—C4—C3	179.9 (3)	C7—C8—C9—C13	−179.8 (3)