supplementary materials


zl2539 scheme

Acta Cryst. (2013). E69, o647    [ doi:10.1107/S1600536813008027 ]

10-(3,5-Dinitrophenyl)-5,5-difluoro-1,3,7,9-tetramethyl-5H-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-4-ium-5-uide

A.-J. Cui, Y. Wang, J. He, X. Li and M.-Y. He

Abstract top

In an effort to discover new potential boron-dipyrromethene (BODIPY) dyes, the title compound, C19H17BF2N4O4, was prepared from 2,4-dimethylpyrrole, 3,5-dinitrobenzaldehyde and boron trifluoride in a one-pot reaction. The BODIPY fragment is nearly planar, with a maximum deviation from the least-squares plane of 0.251 (2) Å, and the benzene ring is inclined at a dihedral angle of 86.8 (6)° to the BODIPY mean plane. In the crystal, pairs of C-H...F hydrogen bonds connect neighbouring molecules into inversion dimers, which are linked by further strong C-H...F interactions, forming a supramolecular layered array parallel to the bc plane.

Comment top

In the past decades, many novel boron-dipyrromethene (BODIPY) dyes were developed for fluorescence analysis (Weiner et al., 2001; Gabe et al., 2004) and their crystal structures were investigated at the same time (Euler et al., 2002a,b). As part of our ongoing studies of the substituent effect on the solid-state structures of BODIPY derivatives (Cui et al., 2006), we report herein the crystal strcuture of the title compound, 4,4-difluoro-1,3,5,7-tetramethyl-8-(3',5'-dinitro-phenyl)-4-bora-3a,4a-diaza-s-indacene, (I).

A perspective view of (I), including the atomic numbering scheme, is shown in Fig. 1. The bond lengths and angles are within normal ranges. In the asymmetric unit, the BODIPY fragment is nearly planar, with a maximum deviation from the least-squares plane of 0.251 (2) Å. Owing to the steric hindrance, the benzene ring is almost perpendicular to the boron-dipyrromethene mean plane with a dihedral angle of 86.8 (6)° between the mean planes of the BODIPY fragment and the benzene ring. Intermolecular C5—H5···F2 (Table 1) hydrogen bonding connects two neighbouring molecules into a centrosymmetric dimer, which is further linked by another strong C—H···F interaction (C13—H13A···F1, Table 1) to form a supramolecular layered array, as depicted in Fig. 2.

Related literature top

For the use of related compounds for fluorescence analysis, see: Weiner et al. (2001); Gabe et al. (2004). For the structural characterization of related compounds, see: Euler et al. (2002a,b); Cui et al. (2006). For the synthetic procedure, see: Kollmannsberger et al. (1998).

Experimental top

Compound (I) was synthesized by the reaction of 2,4-dimethylpyrrole with 3,5-dinitro-benzaldehyde and boron trifluoride in a one-pot reaction (Kollmannsberger et al., 1998). General procedure: 4.2 mmol of 2,4-dimethylpyrrole and 2 mmol of the aldehyde were dissolved in 200 ml of absolute methylene chloride under nitrogen atmosphere. One drop of trifluoroacetic acid was added and the solution was stirred at room temperature until TLC-control showed complete consumption of the aldehyde. At this point, 2 mmol dichlorodicyanobenzoquinone (DDQ) was added, and stirring was continued for 30 min followed by quick addition of 4 ml of triethylamine and 4 ml of boron trifluoride etherate. After stirring for another 3 h, the reaction mixture was washed with water and dried, and the solvent was evaporated. The residue was chromatographed twice on a silica column (a mixture of dichloromethane and hexane, v:v: 1:1, was used as the eluting solvent). Total yield: 42%. Purple crystals. 1H NMR (CDCl3): δ 1.46 (s, 6H, CH3), 1.96 (s, 6H, CH3), 5.62 (s, 2H, CH), 8.65 (s, 2H, CH), 8.90 (s, H, CH). MS (ESI), m/z: 414.1 [M—H]-. HRMS: [M—H]- calculated: 414.176, measured: 414.143.

Purple single crystals suitable for X-ray analysis were obtained by dissolving (I) (0.15 g) in a hexane/dichloromethane (15 ml, v:v: 1:3) mixture and slowly evaporating the solvent at room temperature for a period of about one month.

Refinement top

All H atoms bound to C atoms were assigned to calculated positions, with C—H = 0.96 Å (methyl) and 0.93 Å (aromatic), and refined using a riding model, with Uiso(H)=1.2Ueq (C).

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: APEX2 and SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. Hydrogen atoms are omitted for clarity.
[Figure 2] Fig. 2. View of the two-dimensional supramolecular layered structure constructed via intermolecular C—H···F hydrogen bonding interactions. Nitro groups and irrelevant hydrogen atoms are omitted for clarity.
10-(3,5-Dinitrophenyl)-5,5-difluoro-1,3,7,9-tetramethyl-5H-dipyrrolo[1,2-c:2',1'-f][1,3,2]diazaborinin-4-ium-5-uide top
Crystal data top
C19H17BF2N4O4F(000) = 1712
Mr = 414.18Dx = 1.434 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2164 reflections
a = 29.016 (3) Åθ = 2.4–24.3°
b = 9.1763 (9) ŵ = 0.11 mm1
c = 16.8294 (16) ÅT = 295 K
β = 121.086 (2)°Block, purple
V = 3837.4 (7) Å30.21 × 0.21 × 0.16 mm
Z = 8
Data collection top
Bruker APEXII CCD
diffractometer
3767 independent reflections
Radiation source: fine-focus sealed tube2276 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
φ and ω scansθmax = 26.0°, θmin = 1.6°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 3435
Tmin = 0.973, Tmax = 0.985k = 911
11322 measured reflectionsl = 2018
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)] = 0.045Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0507P)2]
where P = (Fo2 + 2Fc2)/3
3767 reflections(Δ/σ)max < 0.001
275 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.19 e Å3
Crystal data top
C19H17BF2N4O4V = 3837.4 (7) Å3
Mr = 414.18Z = 8
Monoclinic, C2/cMo Kα radiation
a = 29.016 (3) ŵ = 0.11 mm1
b = 9.1763 (9) ÅT = 295 K
c = 16.8294 (16) Å0.21 × 0.21 × 0.16 mm
β = 121.086 (2)°
Data collection top
Bruker APEXII CCD
diffractometer
3767 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
2276 reflections with I > 2σ(I)
Tmin = 0.973, Tmax = 0.985Rint = 0.035
11322 measured reflectionsθmax = 26.0°
Refinement top
R[F2 > 2σ(F2)] = 0.045H-atom parameters constrained
wR(F2) = 0.114Δρmax = 0.19 e Å3
S = 1.04Δρmin = 0.19 e Å3
3767 reflectionsAbsolute structure: ?
275 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
B10.21971 (10)0.3620 (3)0.35983 (14)0.0507 (6)
N10.02477 (8)0.7770 (2)0.44115 (15)0.0721 (5)
N20.10066 (8)0.3996 (2)0.68190 (12)0.0618 (5)
N30.16759 (6)0.29249 (18)0.34430 (10)0.0501 (4)
N40.24400 (6)0.45079 (17)0.45002 (10)0.0481 (4)
O10.00805 (8)0.8018 (2)0.46364 (14)0.1030 (6)
O20.02809 (8)0.8443 (2)0.38261 (15)0.1074 (7)
O30.07160 (8)0.44618 (19)0.70880 (11)0.0898 (6)
O40.12896 (7)0.2925 (2)0.71305 (11)0.0828 (5)
C10.06408 (8)0.5895 (2)0.56281 (13)0.0539 (5)
H10.04190.62010.58430.065*
C20.06252 (8)0.6547 (2)0.48802 (13)0.0519 (5)
C30.09496 (8)0.6107 (2)0.45427 (13)0.0513 (5)
H3A0.09260.65620.40290.062*
C40.13103 (7)0.4974 (2)0.49844 (11)0.0445 (5)
C50.13404 (8)0.4307 (2)0.57523 (12)0.0468 (5)
H50.15860.35620.60640.056*
C60.09981 (8)0.4773 (2)0.60432 (12)0.0474 (5)
C70.16365 (7)0.4434 (2)0.45850 (11)0.0451 (5)
C80.13997 (8)0.3386 (2)0.38813 (12)0.0493 (5)
C90.21486 (8)0.4977 (2)0.49101 (12)0.0450 (5)
C100.24901 (8)0.5908 (2)0.56652 (12)0.0478 (5)
C110.29708 (8)0.5971 (2)0.56926 (13)0.0544 (5)
H110.32730.64920.61210.065*
C120.29309 (8)0.5123 (2)0.49699 (13)0.0524 (5)
C130.23721 (9)0.6657 (2)0.63311 (13)0.0596 (6)
H13A0.23560.59490.67350.089*
H13B0.20330.71550.59920.089*
H13C0.26520.73490.66930.089*
C140.04881 (9)0.2612 (3)0.37558 (16)0.0758 (7)
H14A0.02980.35200.35550.114*
H14B0.06510.25210.44160.114*
H14C0.02410.18210.34540.114*
C150.09174 (8)0.2570 (2)0.35092 (13)0.0563 (5)
C160.09160 (9)0.1637 (3)0.28651 (13)0.0636 (6)
H160.06500.09560.25150.076*
C170.13746 (9)0.1876 (2)0.28228 (13)0.0572 (5)
C180.15291 (10)0.1167 (3)0.21963 (14)0.0707 (7)
H18A0.15440.18870.17970.106*
H18B0.12670.04400.18270.106*
H18C0.18760.07160.25610.106*
C190.33455 (9)0.4896 (3)0.47106 (15)0.0665 (6)
H19A0.34630.39000.48240.100*
H19B0.36470.55270.50760.100*
H19C0.31930.51160.40650.100*
F10.20797 (5)0.45458 (14)0.28592 (7)0.0708 (4)
F20.25531 (5)0.25610 (13)0.36548 (8)0.0695 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
B10.0537 (15)0.0672 (15)0.0426 (12)0.0197 (12)0.0330 (11)0.0136 (11)
N10.0556 (12)0.0716 (13)0.0916 (15)0.0124 (10)0.0396 (11)0.0006 (11)
N20.0609 (13)0.0867 (14)0.0507 (10)0.0185 (11)0.0379 (10)0.0127 (10)
N30.0512 (10)0.0681 (11)0.0365 (8)0.0141 (9)0.0266 (8)0.0045 (8)
N40.0472 (10)0.0679 (11)0.0399 (8)0.0095 (8)0.0302 (8)0.0095 (8)
O10.0840 (13)0.1048 (15)0.1403 (16)0.0355 (11)0.0721 (13)0.0046 (12)
O20.0984 (15)0.1041 (15)0.1317 (16)0.0395 (12)0.0679 (13)0.0494 (14)
O30.1098 (15)0.1162 (14)0.0872 (12)0.0138 (11)0.0820 (11)0.0146 (10)
O40.0828 (12)0.1060 (14)0.0694 (10)0.0068 (11)0.0462 (9)0.0238 (10)
C10.0446 (12)0.0673 (14)0.0607 (12)0.0095 (10)0.0349 (10)0.0200 (11)
C20.0401 (11)0.0577 (12)0.0586 (12)0.0029 (10)0.0259 (10)0.0053 (10)
C30.0438 (12)0.0643 (13)0.0493 (11)0.0043 (10)0.0265 (10)0.0031 (10)
C40.0372 (11)0.0629 (12)0.0381 (10)0.0010 (9)0.0227 (9)0.0028 (9)
C50.0422 (11)0.0621 (12)0.0385 (10)0.0014 (9)0.0226 (9)0.0045 (9)
C60.0443 (12)0.0645 (13)0.0398 (10)0.0092 (10)0.0263 (9)0.0097 (10)
C70.0426 (11)0.0635 (12)0.0334 (10)0.0109 (10)0.0227 (9)0.0072 (9)
C80.0438 (12)0.0721 (13)0.0368 (10)0.0096 (10)0.0242 (9)0.0019 (10)
C90.0465 (12)0.0617 (12)0.0359 (9)0.0090 (10)0.0278 (9)0.0091 (9)
C100.0517 (12)0.0574 (12)0.0416 (10)0.0060 (10)0.0293 (9)0.0102 (9)
C110.0486 (13)0.0685 (14)0.0502 (11)0.0013 (10)0.0285 (10)0.0064 (10)
C120.0475 (13)0.0694 (14)0.0489 (11)0.0071 (10)0.0310 (10)0.0171 (11)
C130.0604 (14)0.0709 (14)0.0540 (12)0.0030 (11)0.0342 (11)0.0046 (11)
C140.0470 (13)0.1140 (19)0.0679 (14)0.0121 (13)0.0308 (11)0.0276 (14)
C150.0429 (12)0.0824 (15)0.0398 (10)0.0061 (11)0.0186 (9)0.0057 (10)
C160.0509 (14)0.0831 (16)0.0476 (12)0.0036 (12)0.0189 (10)0.0102 (11)
C170.0602 (14)0.0725 (14)0.0369 (10)0.0164 (12)0.0235 (10)0.0029 (11)
C180.0807 (17)0.0867 (16)0.0507 (12)0.0180 (14)0.0381 (12)0.0042 (12)
C190.0601 (14)0.0842 (16)0.0769 (14)0.0077 (12)0.0508 (12)0.0157 (13)
F10.0903 (10)0.0893 (9)0.0471 (6)0.0167 (7)0.0457 (6)0.0206 (6)
F20.0640 (8)0.0823 (8)0.0780 (8)0.0215 (7)0.0478 (7)0.0026 (6)
Geometric parameters (Å, º) top
B1—F21.385 (2)C7—C81.400 (3)
B1—F11.396 (2)C8—C151.416 (3)
B1—N31.534 (3)C9—C101.423 (3)
B1—N41.536 (3)C10—C111.373 (3)
N1—O21.208 (2)C10—C131.497 (2)
N1—O11.214 (2)C11—C121.397 (3)
N1—C21.480 (3)C11—H110.9300
N2—O41.213 (2)C12—C191.491 (3)
N2—O31.222 (2)C13—H13A0.9600
N2—C61.477 (2)C13—H13B0.9600
N3—C171.356 (3)C13—H13C0.9600
N3—C81.405 (2)C14—C151.503 (3)
N4—C121.345 (2)C14—H14A0.9600
N4—C91.407 (2)C14—H14B0.9600
C1—C61.369 (3)C14—H14C0.9600
C1—C21.373 (3)C15—C161.380 (3)
C1—H10.9300C16—C171.386 (3)
C2—C31.387 (2)C16—H160.9300
C3—C41.387 (3)C17—C181.492 (3)
C3—H3A0.9300C18—H18A0.9600
C4—C51.392 (2)C18—H18B0.9600
C4—C71.500 (2)C18—H18C0.9600
C5—C61.383 (2)C19—H19A0.9600
C5—H50.9300C19—H19B0.9600
C7—C91.385 (3)C19—H19C0.9600
F2—B1—F1108.56 (15)N4—C9—C10107.70 (17)
F2—B1—N3110.77 (18)C11—C10—C9106.38 (16)
F1—B1—N3109.62 (16)C11—C10—C13125.20 (19)
F2—B1—N4111.02 (16)C9—C10—C13128.40 (18)
F1—B1—N4109.52 (18)C10—C11—C12108.75 (18)
N3—B1—N4107.34 (14)C10—C11—H11125.6
O2—N1—O1124.3 (2)C12—C11—H11125.6
O2—N1—C2118.27 (19)N4—C12—C11109.37 (17)
O1—N1—C2117.4 (2)N4—C12—C19122.61 (19)
O4—N2—O3124.47 (19)C11—C12—C19128.0 (2)
O4—N2—C6118.18 (17)C10—C13—H13A109.5
O3—N2—C6117.3 (2)C10—C13—H13B109.5
C17—N3—C8107.57 (17)H13A—C13—H13B109.5
C17—N3—B1127.84 (16)C10—C13—H13C109.5
C8—N3—B1124.36 (17)H13A—C13—H13C109.5
C12—N4—C9107.79 (16)H13B—C13—H13C109.5
C12—N4—B1127.57 (16)C15—C14—H14A109.5
C9—N4—B1124.17 (16)C15—C14—H14B109.5
C6—C1—C2116.96 (17)H14A—C14—H14B109.5
C6—C1—H1121.5C15—C14—H14C109.5
C2—C1—H1121.5H14A—C14—H14C109.5
C1—C2—C3122.70 (19)H14B—C14—H14C109.5
C1—C2—N1118.96 (18)C16—C15—C8106.07 (18)
C3—C2—N1118.34 (18)C16—C15—C14124.5 (2)
C2—C3—C4118.85 (18)C8—C15—C14129.41 (18)
C2—C3—H3A120.6C15—C16—C17109.2 (2)
C4—C3—H3A120.6C15—C16—H16125.4
C3—C4—C5119.71 (16)C17—C16—H16125.4
C3—C4—C7118.93 (15)N3—C17—C16109.11 (17)
C5—C4—C7121.26 (17)N3—C17—C18123.0 (2)
C6—C5—C4118.72 (18)C16—C17—C18127.9 (2)
C6—C5—H5120.6C17—C18—H18A109.5
C4—C5—H5120.6C17—C18—H18B109.5
C1—C6—C5123.04 (18)H18A—C18—H18B109.5
C1—C6—N2118.49 (17)C17—C18—H18C109.5
C5—C6—N2118.45 (19)H18A—C18—H18C109.5
C9—C7—C8122.66 (16)H18B—C18—H18C109.5
C9—C7—C4120.02 (17)C12—C19—H19A109.5
C8—C7—C4117.32 (16)C12—C19—H19B109.5
C7—C8—N3119.15 (17)H19A—C19—H19B109.5
C7—C8—C15132.72 (17)C12—C19—H19C109.5
N3—C8—C15108.06 (17)H19A—C19—H19C109.5
C7—C9—N4119.35 (17)H19B—C19—H19C109.5
C7—C9—C10132.80 (16)
F2—B1—N3—C1747.3 (2)C9—C7—C8—C15172.3 (2)
F1—B1—N3—C1772.5 (2)C4—C7—C8—C158.1 (3)
N4—B1—N3—C17168.62 (16)C17—N3—C8—C7177.55 (16)
F2—B1—N3—C8138.92 (17)B1—N3—C8—C77.6 (3)
F1—B1—N3—C8101.31 (19)C17—N3—C8—C150.4 (2)
N4—B1—N3—C817.6 (2)B1—N3—C8—C15175.24 (16)
F2—B1—N4—C1248.5 (3)C8—C7—C9—N42.4 (3)
F1—B1—N4—C1271.4 (2)C4—C7—C9—N4177.16 (15)
N3—B1—N4—C12169.67 (17)C8—C7—C9—C10172.43 (19)
F2—B1—N4—C9140.44 (17)C4—C7—C9—C108.0 (3)
F1—B1—N4—C999.7 (2)C12—N4—C9—C7176.52 (16)
N3—B1—N4—C919.2 (2)B1—N4—C9—C710.9 (3)
C6—C1—C2—C30.4 (3)C12—N4—C9—C100.5 (2)
C6—C1—C2—N1179.64 (17)B1—N4—C9—C10173.08 (16)
O2—N1—C2—C1171.6 (2)C7—C9—C10—C11175.1 (2)
O1—N1—C2—C19.3 (3)N4—C9—C10—C110.2 (2)
O2—N1—C2—C38.4 (3)C7—C9—C10—C133.3 (3)
O1—N1—C2—C3170.7 (2)N4—C9—C10—C13178.58 (18)
C1—C2—C3—C40.9 (3)C9—C10—C11—C120.8 (2)
N1—C2—C3—C4179.11 (17)C13—C10—C11—C12179.24 (18)
C2—C3—C4—C50.0 (3)C9—N4—C12—C111.0 (2)
C2—C3—C4—C7176.17 (17)B1—N4—C12—C11173.25 (17)
C3—C4—C5—C61.5 (3)C9—N4—C12—C19178.41 (17)
C7—C4—C5—C6174.66 (17)B1—N4—C12—C196.1 (3)
C2—C1—C6—C51.1 (3)C10—C11—C12—N41.1 (2)
C2—C1—C6—N2176.91 (16)C10—C11—C12—C19178.22 (19)
C4—C5—C6—C12.1 (3)C7—C8—C15—C16176.2 (2)
C4—C5—C6—N2175.98 (16)N3—C8—C15—C160.4 (2)
O4—N2—C6—C1173.66 (18)C7—C8—C15—C141.6 (4)
O3—N2—C6—C14.6 (3)N3—C8—C15—C14178.3 (2)
O4—N2—C6—C54.5 (3)C8—C15—C16—C171.0 (2)
O3—N2—C6—C5177.23 (17)C14—C15—C16—C17179.0 (2)
C3—C4—C7—C994.5 (2)C8—N3—C17—C161.0 (2)
C5—C4—C7—C989.4 (2)B1—N3—C17—C16175.65 (17)
C3—C4—C7—C885.2 (2)C8—N3—C17—C18177.46 (18)
C5—C4—C7—C891.0 (2)B1—N3—C17—C182.8 (3)
C9—C7—C8—N34.0 (3)C15—C16—C17—N31.3 (2)
C4—C7—C8—N3175.56 (16)C15—C16—C17—C18177.1 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5···F2i0.932.513.307 (2)144
C13—H13A···F1ii0.962.453.287 (2)146
Symmetry codes: (i) x+1/2, y+1/2, z+1; (ii) x, y+1, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C5—H5···F2i0.932.513.307 (2)143.7
C13—H13A···F1ii0.962.453.287 (2)146.0
Symmetry codes: (i) x+1/2, y+1/2, z+1; (ii) x, y+1, z+1/2.
Acknowledgements top

We gratefully acknowledge the financial support from the Open Foundation of Jiangsu Province Key Laboratory of Fine Petrochemical Technology (KF1005) and the Analysis Center of Changzhou University.

references
References top

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