4,4-Di­fluoro-2,3;5,6-bis­(tetra­methylene)-4-bora-3a,4a-di­aza-s-indacene (LD540)

Kirsi Salorinne; Tiia-Riikka Tero; Tanja Lahtinen

doi:10.1107/S1600536813033448

. 2013 Dec 18;70(Pt 1):o74. doi: 10.1107/S1600536813033448

4,4-Difluoro-2,3;5,6-bis(tetramethylene)-4-bora-3a,4a-diaza-s-indacene (LD540)

Kirsi Salorinne ^a, Tiia-Riikka Tero ^a, Tanja Lahtinen ^a,^*

PMCID: PMC3914101 PMID: 24527006

Abstract

The title compound, C₁₈H₂₁BF₂N₂, is a lipophilic dye based on a BODIPY fluorophore backbone, which was developed for microscopic imaging of lipid droplets; the molecule has a planar BODIPY core [dihedral angle between the pyrrole rings = 2.3 (3)°] and two tetramethylene substituents at the 2,3- and 5,6-positions in a half-chair conformation. One of the tetramethylene substituents is disordered over two two sets of sites with site occupancies of 0.5. In the crystal, pairs of C—H⋯F interactions link the molecules into inversion dimers. Neighbouring dimers are linked by further C—H⋯F interactions, forming an infinite array. C—H⋯π and π–π [centroid–centroid distance = 4.360 (3) Å] interactions are observed between the BODIPY core and the tetramethylene substituents of neighbouring dimer pairs.

Related literature

For lipid droplets and fluorescence imaging with LD540, see: Beller et al. (2010 ▶); Bickel et al. (2009 ▶); Spandl et al. (2009 ▶). For related BODIPY structures, see: Uppal et al. (2012 ▶). graphic file with name e-70-00o74-scheme1.jpg

Experimental

Crystal data

C₁₈H₂₁BF₂N₂
M _r = 314.18
Monoclinic,
a = 8.8836 (4) Å
b = 16.467 (1) Å
c = 11.4865 (6) Å
β = 111.271 (3)°
V = 1565.84 (15) Å³
Z = 4
Cu Kα radiation
μ = 0.77 mm⁻¹
T = 173 K
0.1 × 0.1 × 0.04 mm

Data collection

Nonius KappaCCD diffractometer with APEXII detector
Absorption correction: multi-scan (SADABS; Bruker, 2004 ▶) T _min = 0.840, T _max = 1
7413 measured reflections
2511 independent reflections
1902 reflections with I > 2σ(I)
R _int = 0.054

Refinement

R[F ² > 2σ(F ²)] = 0.047
wR(F ²) = 0.125
S = 1.03
2511 reflections
227 parameters
H-atom parameters constrained
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.30 e Å⁻³

Data collection: COLLECT (Bruker, 2004 ▶); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 ▶); data reduction: DENZO (Otwinowski & Minor, 1997 ▶) and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: OLEX2 (Dolomanov et al., 2009 ▶); software used to prepare material for publication: OLEX2.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813033448/vm2201sup1.cif

e-70-00o74-sup1.cif^{(276.1KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813033448/vm2201Isup2.hkl

e-70-00o74-Isup2.hkl^{(138KB, hkl)}

Click here for additional data file.^{(5.2KB, mol)}

Supporting information file. DOI: 10.1107/S1600536813033448/vm2201Isup3.mol

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

Cg1 and Cg2 are the centroids of the N4,C5,C10–C12 and N22,C21,C14–C16 rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C23—H23B⋯F3ⁱ	0.96	2.66	3.621 (3)	178
C8—H8B⋯F2ⁱⁱ	0.97	2.56	3.252 (3)	129
C17—H17A⋯Cg2ⁱⁱⁱ	0.97	3.10	3.879 (3)	138

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) .

Acknowledgments

Professor Kari Rissanen is gratefully acknowledged for his help with the data collection and structure refinement. Dr Arto Valkonen and Filip Topic are acknowledged for their help with preparing the CIF file.

supplementary crystallographic information

1. Comment

Lipid droplets are metabolically active organelles (Beller et al., 2010; Bickel et al., 2009), which function as intracellular storehouses of lipid esters found inside almost all cells. LD540 is one of the dyes that can be used for multicolor fluorescence imaging for lipid droplets in both fixed and living cells (Spandl et al., 2009). In the structure of the title compound, the BODIPY core is planar having the average dihedral angle formed between the two pyrrole rings of 2.3 (3)° (Fig. 1). The two tetramethylene substituents on either side of the BODIPY core at the 2,3- and 5,6-positions are in a half-chair conformation. Intermolecular F···H—C interactions (distance of 2.661 (3) Å) between the fluoride (F3) and methyl (C23) groups of the opposite facing molecules connect the two LD540 molecules to form a dimer (Fig.2, Table 2). In a similar manner, the second fluoride (F2) atom forms an intermolecular F···H—C interaction (distance of 2.555 (3) Å) to one of the CH₂ (C8) groups of the tetramethylene unit connecting the neighbouring dimer pairs in an infinite array through the crystal lattice (Fig. 3, Table 2). In addition to the F···H—C interactions, intermolecular C—H···π interactions [C18A—H18A···Cg1ⁱ = 2.812 Å and C17—H17A···Cg2ⁱⁱ = 3.103 Å; Cg1 and Cg2 are the centroids of rings N4,C5,C10-C12 and N22,C21,C14-C16, respectively; symmetry codes: (i) x + 1, y, z; (ii) -x, -y + 1, -z + 1] and π···π interactions [Cg2···Cg2ⁱⁱⁱ = 4.360 (3) Å; symmetry code: (iii) -x + 1, -y + 1, -z +1] are observed between the BODIPY core and the tetramethylene substituents of the neighbouring dimer pairs.

2. Experimental

The title compound was synthesized by a known method described by Christoph Thiele and co-workers (Spandl et al., 2009) using tetrahydropyrrole, acetylchloride and BF₃-etherate as the starting material. For single-crystal X-ray analysis the crude product was recrystallized from dichloromethane yielding greenish red prism crystals.