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1 This is an electronic reprint of the original article. This reprint may differ from the original in pagination and typographic detail. Author(s): Salorinne, Kirsi; Tero, Tiia-Riikka; Lahtinen, Tanja Title: 4,4-Difluoro-2,3;5,6-bis(tetramethylene)-4-bora-3a,4a-diaza-s-indacene (LD540) Year: Version: 2014 Publisher's PDF Please cite the original version: Salorinne, K., Tero, T.-R., & Lahtinen, T. (2014). 4,4-Difluoro-2,3;5,6- bis(tetramethylene)-4-bora-3a,4a-diaza-s-indacene (LD540). Acta Crystallographica Section E : Structure Reports Online, 70 (1), o74. doi: /s All material supplied via JYX is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user.

2 organic compounds Acta Crystallographica Section E Structure Reports Online ISSN ,4-Difluoro-2,3;5,6-bis(tetramethylene)- 4-bora-3a,4a-diaza-s-indacene (LD540) Kirsi Salorinne, Tiia-Riikka Tero and Tanja Lahtinen* Department of Chemistry, Nanoscience Center, University of Jyväskylä, PO Box 35, FIN University of Jyväskylä, Finland Correspondence tanja.m.lahtinen@jyu.fi Received 20 November 2013; accepted 10 December 2013 = (3) V = (15) Å 3 Z =4 Cu K radiation Data collection Nonius KappaCCD diffractometer with APEXII detector Absorption correction: multi-scan (SADABS; Bruker, 2004) T min = 0.840, T max =1 Refinement R[F 2 >2(F 2 )] = wr(f 2 ) = S = reflections = 0.77 mm 1 T = 173 K mm 7413 measured reflections 2511 independent reflections 1902 reflections with I > 2(I) R int = parameters H-atom parameters constrained max = 0.17 e Å 3 min = 0.30 e Å 3 Key indicators: single-crystal X-ray study; T = 173 K; mean (C C) = Å; disorder in main residue; R factor = 0.047; wr factor = 0.125; data-to-parameter ratio = The title compound, C 18 H 21 BF 2 N 2, 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 HF interactions link the molecules into inversion dimers. Neighbouring dimers are linked by further C HF interactions, forming an infinite array. C H and [centroid centroid distance = (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). 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 HA D H HA DA D HA C23 H23BF3 i (3) 178 C8 H8BF2 ii (3) 129 C17 H17ACg2 iii (3) 138 Symmetry codes: (i) x; y þ 1; z; (ii) x 1 2 ; y þ 1 2 ; z 1 2 ; (iii) x þ 1; y þ 1; z þ 1. 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. 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 data and figures for this paper are available from the IUCr electronic archives (Reference: VM2201). Experimental Crystal data C 18 H 21 BF 2 N 2 M r = Monoclinic, P2 1 =n a = (4) Å b = (1) Å c = (6) Å References Beller, M., Thiel, K., Thul, P. J. & Jäckle, H. (2010). FEBS Lett. 584, Bickel, P. E., Tansey, J. T. & Welte, M. A. (2009). Biochim. Biophys. Acta, 1791, Bruker (2004). COLLECT. Bruker AXS Inc., Madison, Wisconsin, USA. Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter & R. M. Sweet, pp New York: Academic Press. Sheldrick, G. M. (2008). Acta Cryst. A64, Spandl, J., White, D. J., Peychl, J. & Thiele, C. (2009). Traffic, 10, Uppal, T., Hu, C., Fronczek, F. R., Maschek, S., Bobadova-Parvanova, P. & Vicente, M. G. H. (2012). Chem. Eur. J. 18, o74 Salorinne et al. doi: /s

3 supporting information [doi: /s ] 4,4-Difluoro-2,3;5,6-bis(tetramethylene)-4-bora-3a,4a-diaza-s-indacene (LD540) Kirsi Salorinne, Tiia-Riikka Tero and Tanja Lahtinen S1. 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 (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 (3) Å) to one of the CH 2 (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 Cg1 i = Å and C17 H17A Cg2 ii = 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 Cg2 iii = (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. S2. 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 BF 3 -etherate as the starting material. For single-crystal X-ray analysis the crude product was recrystallized from dichloromethane yielding greenish red prism crystals. S3. Refinement All H atoms were visible in the electron density maps, but those bonded to C were ideally positioned and allowed to ride on their parent atoms with U iso (H) of 1.2 (or 1.5 for methyl) times U eq (C). One of the tetramethylene substituent is disordered over two positions (C18 C19) having fixed site occupation factors of 0.5. sup-1

4 Figure 1 Molecular structure of the title compound with atom labels and 50% probability displacement ellipsoids for non-h atoms. Figure 2 Dimer pair formed by the intermolecular F H C interactions (black dotted line) between the opposite facing molecules. sup-2

5 Figure 3 Packing diagram showing the infinite array of dimer pairs in the crystal lattice connected by the intermolecular F H C interactions viewed along a) the a axis and b) from a view highlighting the aromatic interactions formed between the molecule layers. Intermolecular F H C interactions forming the dimer pairs have been marked with red and the ones between the dimer pairs have been marked with blue color. 4,4-Difluoro-2,3;5,6-bis(tetramethylene)-4-bora-3a,4a-diaza-s-indacene Crystal data C 18 H 21 BF 2 N 2 M r = Monoclinic, P2 1 /n a = (4) Å b = (1) Å c = (6) Å β = (3) V = (15) Å 3 Z = 4 F(000) = 664 D x = Mg m 3 Cu Kα radiation, λ = Å Cell parameters from 2349 reflections θ = sup-3

6 µ = 0.77 mm 1 T = 173 K Data collection Nonius KappaCCD diffractometer with APEXII detector Radiation source: Enraf Nonius FR590 Horizonally mounted graphite crystal monochromator Detector resolution: 9 pixels mm -1 CCD rotation images, thick slices scans Absorption correction: multi-scan (SADABS; Bruker, 2004) Refinement Refinement on F 2 Least-squares matrix: full R[F 2 > 2σ(F 2 )] = wr(f 2 ) = S = reflections 227 parameters 0 restraints Primary atom site location: structure-invariant direct methods Prism, green red mm T min = 0.840, T max = measured reflections 2511 independent reflections 1902 reflections with I > 2σ(I) R int = θ max = 63.3, θ min = 4.9 h = k = l = Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ 2 (F o2 ) + (0.0626P) P] where P = (F o 2 + 2F c2 )/3 (Δ/σ) max < Δρ max = 0.17 e Å 3 Δρ min = 0.30 e Å 3 Special details Experimental. SADABS v.2.03 (Bruker, 2004) was used for absorption correction. R(int) was before and after correction. The Ratio of minimum to maximum transmission is The λ/2 correction factor is 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. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 ) x y z U iso */U eq Occ. (<1) C (3) (12) (19) (5) C (3) (12) (2) (5) H6A * H6B * C (3) (13) (2) (6) H7A * H7B * C (3) (13) (2) (6) H8A * H8B * C (3) (13) (2) (5) H9A * H9B * C (2) (12) (19) (5) C (3) (12) (19) (5) sup-4

7 H * C (3) (12) (19) (5) C (2) (12) (18) (5) C (3) (12) (19) (5) C (3) (13) (19) (5) H * C (3) (13) (2) (5) C (3) (14) (2) (6) H17A * 0.5 H17B * 0.5 H17C * 0.5 H17D * 0.5 C18A (8) (5) (6) (15) 0.5 H18A * 0.5 H18B * 0.5 C19A (6) (3) (5) (12) 0.5 H19A * 0.5 H19B * 0.5 C18B (9) (5) (6) (17) 0.5 H18C * 0.5 H18D * 0.5 C19B (7) (4) (6) (14) 0.5 H19C * 0.5 H19D * 0.5 C (3) (14) (2) (5) H20A * 0.5 H20B * 0.5 H20C * 0.5 H20D * 0.5 C (2) (13) (19) (5) C (3) (12) (2) (5) H23A * H23B * H23C * B (3) (14) (2) (6) N (2) (10) (15) (4) N (2) (10) (15) (4) F (15) (7) (12) (4) F (15) (7) (12) (4) Atomic displacement parameters (Å 2 ) U 11 U 22 U 33 U 12 U 13 U 23 C (12) (11) (11) (9) (9) (8) C (12) (11) (12) (9) (10) (9) C (13) (12) (15) (10) (11) (10) C (12) (12) (15) (10) (11) (11) C (12) (12) (13) (9) (10) (10) sup-5

8 C (11) (11) (11) (9) (9) (9) C (12) (10) (11) (9) (10) (9) C (12) (10) (11) (9) (9) (9) C (12) (11) (11) (9) (9) (9) C (11) (11) (11) (9) (9) (9) C (12) (11) (12) (9) (10) (9) C (12) (12) (12) (9) (10) (9) C (12) (14) (14) (10) (11) (11) C18A (3) (3) (4) (2) (3) (4) C19A (3) (3) (3) (2) (2) (2) C18B (3) (4) (4) (2) (3) (4) C19B (3) (3) (4) (2) (3) (3) C (12) (12) (13) (10) (10) (10) C (11) (12) (11) (9) (9) (9) C (12) (12) (12) (9) (10) (9) B (14) (12) (13) (10) (11) (11) N (10) (9) (9) (7) (8) (7) N (10) (9) (9) (7) (8) (7) F (8) (7) (8) (6) (6) (6) F (7) (7) (8) (5) (6) (6) Geometric parameters (Å, º) C5 C (3) C17 H17C C5 C (3) C17 H17D C5 N (3) C17 C18A (7) C6 H6A C17 C18B (8) C6 H6B C18A H18A C6 C (3) C18A H18B C7 H7A C18A C19A (10) C7 H7B C19A H19A C7 C (3) C19A H19B C8 H8A C19A C (6) C8 H8B C18B H18C C8 C (3) C18B H18D C9 H9A C18B C19B (10) C9 H9B C19B H19C C9 C (3) C19B H19D C10 C (3) C19B C (6) C11 H C20 H20A C11 C (3) C20 H20B C12 C (3) C20 H20C C12 N (3) C20 H20D C13 C (3) C20 C (3) C13 C (3) C21 N (3) C14 C (3) C23 H23A C14 N (3) C23 H23B C15 H C23 H23C sup-6

9 C15 C (3) B1 N (3) C16 C (3) B1 N (3) C16 C (3) B1 F (3) C17 H17A B1 F (3) C17 H17B H18A Cg(1) i Cg(2) Cg(2) iii (3) H17A Cg(2) ii C10 C5 C (19) C18B C17 H17D N4 C5 C (19) C17 C18A H18A N4 C5 C (18) C17 C18A H18B C5 C6 H6A H18A C18A H18B C5 C6 H6B C19A C18A C (4) C5 C6 C (18) C19A C18A H18A H6A C6 H6B C19A C18A H18B C7 C6 H6A C18A C19A H19A C7 C6 H6B C18A C19A H19B C6 C7 H7A H19A C19A H19B C6 C7 H7B C20 C19A C18A (4) H7A C7 H7B C20 C19A H19A C8 C7 C (18) C20 C19A H19B C8 C7 H7A C17 C18B H18C C8 C7 H7B C17 C18B H18D C7 C8 H8A H18C C18B H18D C7 C8 H8B C19B C18B C (5) C7 C8 C (19) C19B C18B H18C H8A C8 H8B C19B C18B H18D C9 C8 H8A C18B C19B H19C C9 C8 H8B C18B C19B H19D C8 C9 H9A C18B C19B C (5) C8 C9 H9B H19C C19B H19D H9A C9 H9B C20 C19B H19C C10 C9 C (17) C20 C19B H19D C10 C9 H9A C19A C20 H20A C10 C9 H9B C19A C20 H20B C5 C10 C (18) C19B C20 H20C C11 C10 C (18) C19B C20 H20D C11 C10 C (19) H20A C20 H20B C10 C11 H H20C C20 H20D C10 C11 C (18) C21 C20 C19A (3) C12 C11 H C21 C20 C19B (3) C13 C12 C (19) C21 C20 H20A C13 C12 N (18) C21 C20 H20B N4 C12 C (17) C21 C20 H20C C12 C13 C (19) C21 C20 H20D C14 C13 C (19) C16 C21 C (2) C14 C13 C (18) N22 C21 C (18) sup-7

10 C13 C14 C (19) N22 C21 C (19) C13 C14 N (18) C13 C23 H23A N22 C14 C (18) C13 C23 H23B C14 C15 H C13 C23 H23C C16 C15 C (19) H23A C23 H23B C16 C15 H H23A C23 H23C C15 C16 C (2) H23B C23 H23C C15 C16 C (19) N4 B1 N (16) C21 C16 C (19) F2 B1 N (18) C16 C17 H17A F2 B1 N (18) C16 C17 H17B F2 B1 F (17) C16 C17 H17C F3 B1 N (18) C16 C17 H17D F3 B1 N (18) C16 C17 C18A (3) C5 N4 C (17) H17A C17 H17B C5 N4 B (17) H17C C17 H17D C12 N4 B (17) C18A C17 H17A C14 N22 B (17) C18A C17 H17B C21 N22 C (17) C18B C17 C (3) C21 N22 B (17) C18B C17 H17C C5 C6 C7 C (2) C17 C16 C21 C (3) C5 C10 C11 C (2) C17 C16 C21 N (19) C6 C5 C10 C9 0.7 (3) C17 C18A C19A C (6) C6 C5 C10 C (19) C17 C18B C19B C (8) C6 C5 N4 C (18) C18A C17 C18B C19B 49.4 (9) C6 C5 N4 B1 1.1 (3) C18A C19A C20 C19B 41.9 (6) C6 C7 C8 C (3) C18A C19A C20 C (5) C7 C8 C9 C (3) C19A C20 C21 C (4) C8 C9 C10 C (3) C19A C20 C21 N (3) C8 C9 C10 C (2) C18B C17 C18A C19A 50.6 (10) C9 C10 C11 C (2) C18B C19B C20 C19A 55.1 (7) C10 C5 C6 C (3) C18B C19B C20 C (6) C10 C5 N4 C (2) C19B C20 C21 C (4) C10 C5 N4 B (19) C19B C20 C21 N (3) C10 C11 C12 C (2) C20 C21 N22 C (2) C10 C11 C12 N4 0.7 (2) C20 C21 N22 B1 1.6 (3) C11 C12 C13 C (2) C21 C16 C17 C18A 15.2 (4) C11 C12 C13 C (3) C21 C16 C17 C18B 12.2 (4) C11 C12 N4 C5 0.8 (2) C23 C13 C14 C (3) C11 C12 N4 B (19) C23 C13 C14 N (19) C12 C13 C14 C (2) N4 C5 C6 C (19) C12 C13 C14 N (3) N4 C5 C10 C (18) C13 C12 N4 C (18) N4 C5 C10 C (2) C13 C12 N4 B1 2.2 (3) N4 C12 C13 C (3) C13 C14 C15 C (2) N4 C12 C13 C (18) C13 C14 N22 C (18) N4 B1 N22 C (3) C13 C14 N22 B1 1.8 (3) N4 B1 N22 C (17) sup-8

11 C14 C15 C16 C (2) N22 C14 C15 C (2) C14 C15 C16 C (2) N22 B1 N4 C (18) C15 C14 N22 C (2) N22 B1 N4 C (3) C15 C14 N22 B (18) F2 B1 N4 C (3) C15 C16 C17 C18A (3) F2 B1 N4 C (2) C15 C16 C17 C18B (3) F2 B1 N22 C (2) C15 C16 C21 C (2) F2 B1 N22 C (3) C15 C16 C21 N (2) F3 B1 N4 C (3) C16 C17 C18A C19A 49.1 (5) F3 B1 N4 C (2) C16 C17 C18B C19B 40.7 (7) F3 B1 N22 C (2) C16 C21 N22 C (2) F3 B1 N22 C (3) C16 C21 N22 B (19) Symmetry codes: (i) x+1, y, z; (ii) x, y+1, z+1; (iii) x+1, y+1, z+1. Hydrogen-bond geometry (Å, º) 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 F3 iv (3) 178 C8 H8B F2 v (3) 129 C17 H17A Cg2 iii (3) 138 Symmetry codes: (iii) x+1, y+1, z+1; (iv) x, y+1, z; (v) x 1/2, y+1/2, z 1/2. sup-9