organic compounds
5,5′-Bis[(2,2,2-trifluoroethoxy)methyl]-2,2′-bipyridine
aInstitute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei 106, Taiwan
*Correspondence e-mail: normanlu@ntut.edu.tw
The complete molecule of the title compound, C16H14F6N2O2, is generated by crystallographic inversion symmetry, which results in two short intramolecular C—H⋯N hydrogen-bond contacts per molecule. In the crystal, aromatic π–π stacking [centroid–centroid distance = 3.457 (2) Å] and weak C—H⋯π interactions occur. A short H⋯H [2.32 (3) Å] contact is present.
Related literature
For related structures and background to the anti-planar geometry of bpy, see: Lu, Tu, Wu et al. (2010); Iyer et al. (2005); Heirtzler et al. (2002); Maury et al. (2001); Vogtle et al. (1990). For background to the bipyridine (bpy) ligand, see: Bain et al. (1989); Chambron & Sauvage (1986, 1987); Grätzel (2001); Haga et al. (2000); Lu, Tu, Hou et al. (2010); Lu, Tu, Wen et al. (2010); Lu et al. (2007). For C—H⋯H—C interactions, see: Wolstenholme & Cameron (2006).
Experimental
Crystal data
|
Refinement
|
Data collection: APEX2 (Bruker, 2010); cell SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
10.1107/S1600536811000730/fk2030sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811000730/fk2030Isup2.hkl
5,5'-bis(CF3CH2OCH2)-2,2'-bpy, (I), was prepared according to the general procedure described in Lu et al., (2007). The crude product was further purified by vacuum
or to obtain the title compound as a colorless solid. Full characterization data are listed below.Analytical data of (I): Yield 76 %, m.p. = 393 K. 1H NMR (500 MHz, d-DMSO, room temperature), δ(ppm) Pyridine ring H: 8.66 s, H6, 2H), 8.39 (d, H4, 3JHH=8.24 Hz, 2H), 7.92 (d, H3, 3JHH=8.24 Hz, 2H), 4.77 (s, bpy-CH2, 4H), 4.17 (q, -OCH2CF3, 3JHF=9.34 Hz, 4H); 19F NMR (470.5 MHz, d-DMSO, room temperature), δ (ppm) -73.1 (t, -CH2CF3, 3JHF = 9.7 Hz, 6F); 13C NMR (126 MHz,d-DMSO, room temperature) δ (ppm) 120.3, 133.1, 136.9, 148.7, 154.7 (s, bpy, 10C), 121.1-127.8 (q, -CF3, 1JCF = 279.6 Hz, 2C), 70.6 (s, bpy-CH2, 2C), 66.8 (q, -CH2CF3, 2JCF = 33.2 Hz, 2C).
GC/MS (M/e) : M+ = 380, (M-C2H3F3O)+ = 281, [M-(C2H3F3O)2]+= 182, (C6H5N)+ = 91.
FT-IR (cm-1): 1601.5, 1553.8, 1469.4, 1360.1 (bpy-ring, m), 1155.8, 1122.6 (CF2 stretch, s).
Recrystallization proceeded with dissolution of I in DMSO to form a
to which the water overlayer (5 cm3) was added. Solvent diffusion over a period of ten days at 298 K afforded needle shaped crystals.The diffraction data were collected at 100K employing a Bruker CCD diffractometer; the structure was solved by successive Fourier maps. All H atoms were located at the end of anisotropic refinements and refined isotropically to convergence.
Data collection: APEX2 (Bruker, 2010); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).C16H14F6N2O2 | Z = 1 |
Mr = 380.29 | F(000) = 194 |
Triclinic, P1 | Dx = 1.605 Mg m−3 Dm = 1.53 Mg m−3 Dm measured by w/v |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 4.6573 (2) Å | Cell parameters from 3201 reflections |
b = 5.6842 (3) Å | θ = 2.6–27.1° |
c = 15.7273 (8) Å | µ = 0.15 mm−1 |
α = 94.298 (3)° | T = 100 K |
β = 98.473 (3)° | Prism, colourless |
γ = 105.689 (4)° | 0.2 × 0.14 × 0.12 mm |
V = 393.57 (3) Å3 |
Bruker APEXII CCD area-detector diffractometer | 1348 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.024 |
ϕ and ω scans | θmax = 26.4°, θmin = 1.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | h = −5→5 |
Tmin = 0.664, Tmax = 0.746 | k = −7→7 |
6627 measured reflections | l = −19→19 |
1577 independent reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.031 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.104 | All H-atom parameters refined |
S = 1.12 | w = 1/[σ2(Fo2) + (0.0595P)2 + 0.094P] where P = (Fo2 + 2Fc2)/3 |
1577 reflections | (Δ/σ)max < 0.001 |
146 parameters | Δρmax = 0.29 e Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
C16H14F6N2O2 | γ = 105.689 (4)° |
Mr = 380.29 | V = 393.57 (3) Å3 |
Triclinic, P1 | Z = 1 |
a = 4.6573 (2) Å | Mo Kα radiation |
b = 5.6842 (3) Å | µ = 0.15 mm−1 |
c = 15.7273 (8) Å | T = 100 K |
α = 94.298 (3)° | 0.2 × 0.14 × 0.12 mm |
β = 98.473 (3)° |
Bruker APEXII CCD area-detector diffractometer | 1577 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 1348 reflections with I > 2σ(I) |
Tmin = 0.664, Tmax = 0.746 | Rint = 0.024 |
6627 measured reflections |
R[F2 > 2σ(F2)] = 0.031 | 0 restraints |
wR(F2) = 0.104 | All H-atom parameters refined |
S = 1.12 | Δρmax = 0.29 e Å−3 |
1577 reflections | Δρmin = −0.27 e Å−3 |
146 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
F1 | 1.8989 (2) | 1.22574 (16) | 0.98212 (6) | 0.0271 (3) | |
F2 | 1.8270 (2) | 1.35589 (16) | 0.85765 (6) | 0.0299 (3) | |
F3 | 1.4537 (2) | 1.23169 (17) | 0.92410 (6) | 0.0294 (3) | |
O | 1.4170 (2) | 0.88799 (19) | 0.79273 (7) | 0.0225 (3) | |
N | 0.6609 (3) | 0.3432 (2) | 0.58189 (8) | 0.0173 (3) | |
C1 | 1.1096 (3) | 0.6201 (3) | 0.67039 (9) | 0.0160 (3) | |
C2 | 0.8935 (3) | 0.3918 (3) | 0.64727 (10) | 0.0174 (3) | |
C3 | 0.6289 (3) | 0.5286 (2) | 0.53652 (8) | 0.0144 (3) | |
C4 | 0.8268 (3) | 0.7658 (3) | 0.55708 (10) | 0.0181 (3) | |
C5 | 1.0718 (3) | 0.8098 (3) | 0.62300 (10) | 0.0189 (3) | |
C6 | 1.3693 (3) | 0.6554 (3) | 0.74291 (10) | 0.0187 (3) | |
C7 | 1.6509 (4) | 0.9271 (3) | 0.86434 (10) | 0.0214 (4) | |
C8 | 1.7066 (3) | 1.1854 (3) | 0.90685 (10) | 0.0204 (3) | |
H2 | 0.903 (4) | 0.259 (4) | 0.6804 (12) | 0.025 (5)* | |
H4 | 0.789 (4) | 0.887 (3) | 0.5248 (11) | 0.023 (4)* | |
H5 | 1.215 (4) | 0.970 (4) | 0.6343 (12) | 0.029 (5)* | |
H6A | 1.556 (4) | 0.658 (3) | 0.7197 (11) | 0.021 (4)* | |
H6B | 1.327 (4) | 0.527 (3) | 0.7796 (12) | 0.024 (4)* | |
H7A | 1.594 (4) | 0.813 (4) | 0.9065 (12) | 0.026 (5)* | |
H7B | 1.843 (4) | 0.916 (3) | 0.8461 (12) | 0.028 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1 | 0.0318 (5) | 0.0225 (5) | 0.0219 (5) | 0.0071 (4) | −0.0072 (4) | −0.0029 (4) |
F2 | 0.0381 (6) | 0.0217 (5) | 0.0283 (5) | 0.0050 (4) | 0.0051 (4) | 0.0072 (4) |
F3 | 0.0266 (5) | 0.0305 (5) | 0.0318 (5) | 0.0125 (4) | 0.0036 (4) | −0.0048 (4) |
O | 0.0264 (6) | 0.0187 (5) | 0.0205 (6) | 0.0106 (4) | −0.0067 (5) | −0.0044 (4) |
N | 0.0208 (6) | 0.0119 (6) | 0.0188 (6) | 0.0044 (5) | 0.0024 (5) | 0.0025 (5) |
C1 | 0.0161 (7) | 0.0164 (7) | 0.0168 (7) | 0.0063 (6) | 0.0046 (6) | −0.0002 (6) |
C2 | 0.0223 (8) | 0.0126 (7) | 0.0182 (7) | 0.0065 (6) | 0.0031 (6) | 0.0027 (5) |
C3 | 0.0162 (7) | 0.0125 (7) | 0.0156 (7) | 0.0044 (5) | 0.0054 (6) | 0.0023 (5) |
C4 | 0.0208 (7) | 0.0133 (7) | 0.0198 (7) | 0.0035 (6) | 0.0026 (6) | 0.0055 (6) |
C5 | 0.0187 (7) | 0.0139 (7) | 0.0217 (8) | 0.0006 (6) | 0.0028 (6) | 0.0022 (6) |
C6 | 0.0192 (7) | 0.0156 (7) | 0.0210 (8) | 0.0061 (6) | 0.0015 (6) | −0.0002 (6) |
C7 | 0.0236 (8) | 0.0205 (8) | 0.0188 (8) | 0.0084 (6) | −0.0033 (7) | 0.0004 (6) |
C8 | 0.0212 (8) | 0.0209 (8) | 0.0183 (7) | 0.0074 (6) | −0.0008 (6) | 0.0015 (6) |
F1—C8 | 1.3386 (17) | C3—C4 | 1.396 (2) |
F2—C8 | 1.3411 (18) | C3—C3i | 1.481 (3) |
F3—C8 | 1.3347 (18) | C4—C5 | 1.377 (2) |
O—C7 | 1.4053 (18) | C4—H4 | 0.926 (19) |
O—C6 | 1.4304 (17) | C5—H5 | 0.96 (2) |
N—C2 | 1.3322 (19) | C6—H6A | 0.990 (19) |
N—C3 | 1.3446 (18) | C6—H6B | 0.960 (19) |
C1—C5 | 1.390 (2) | C7—C8 | 1.505 (2) |
C1—C2 | 1.394 (2) | C7—H7A | 0.98 (2) |
C1—C6 | 1.494 (2) | C7—H7B | 1.00 (2) |
C2—H2 | 0.96 (2) | ||
C7—O—C6 | 111.24 (11) | O—C6—H6A | 108.1 (10) |
C2—N—C3 | 117.65 (12) | C1—C6—H6A | 110.2 (10) |
C5—C1—C2 | 117.07 (14) | O—C6—H6B | 109.2 (11) |
C5—C1—C6 | 122.24 (13) | C1—C6—H6B | 110.7 (11) |
C2—C1—C6 | 120.69 (13) | H6A—C6—H6B | 109.9 (14) |
N—C2—C1 | 124.41 (13) | O—C7—C8 | 107.27 (12) |
N—C2—H2 | 115.6 (11) | O—C7—H7A | 111.5 (11) |
C1—C2—H2 | 119.9 (11) | C8—C7—H7A | 108.4 (11) |
N—C3—C4 | 122.04 (13) | O—C7—H7B | 111.4 (10) |
N—C3—C3i | 117.10 (15) | C8—C7—H7B | 107.4 (11) |
C4—C3—C3i | 120.85 (15) | H7A—C7—H7B | 110.6 (16) |
C5—C4—C3 | 119.25 (13) | F3—C8—F1 | 107.01 (12) |
C5—C4—H4 | 122.6 (11) | F3—C8—F2 | 106.48 (12) |
C3—C4—H4 | 118.2 (11) | F1—C8—F2 | 107.15 (12) |
C4—C5—C1 | 119.49 (14) | F3—C8—C7 | 112.67 (13) |
C4—C5—H5 | 119.0 (11) | F1—C8—C7 | 110.74 (12) |
C1—C5—H5 | 121.5 (11) | F2—C8—C7 | 112.46 (13) |
O—C6—C1 | 108.60 (11) | ||
C3—N—C2—C1 | −1.6 (2) | C6—C1—C5—C4 | −179.74 (13) |
C5—C1—C2—N | 1.9 (2) | C7—O—C6—C1 | 177.45 (12) |
C6—C1—C2—N | −177.87 (13) | C5—C1—C6—O | 41.49 (19) |
C2—N—C3—C4 | −1.1 (2) | C2—C1—C6—O | −138.72 (14) |
C2—N—C3—C3i | 179.43 (14) | C6—O—C7—C8 | 174.02 (13) |
N—C3—C4—C5 | 3.4 (2) | O—C7—C8—F3 | 52.09 (17) |
C3i—C3—C4—C5 | −177.17 (15) | O—C7—C8—F1 | 171.89 (12) |
C3—C4—C5—C1 | −3.0 (2) | O—C7—C8—F2 | −68.27 (17) |
C2—C1—C5—C4 | 0.5 (2) |
Symmetry code: (i) −x+1, −y+1, −z+1. |
Cg is the centroid of the N,C1–C5 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—H4···Ni | 0.925 (17) | 2.464 (18) | 2.809 (2) | 102.3 (12) |
C6—H6A···Cgii | 0.990 (19) | 2.59 | 3.5089 (16) | 155 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C16H14F6N2O2 |
Mr | 380.29 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 100 |
a, b, c (Å) | 4.6573 (2), 5.6842 (3), 15.7273 (8) |
α, β, γ (°) | 94.298 (3), 98.473 (3), 105.689 (4) |
V (Å3) | 393.57 (3) |
Z | 1 |
Radiation type | Mo Kα |
µ (mm−1) | 0.15 |
Crystal size (mm) | 0.2 × 0.14 × 0.12 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2008) |
Tmin, Tmax | 0.664, 0.746 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6627, 1577, 1348 |
Rint | 0.024 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.031, 0.104, 1.12 |
No. of reflections | 1577 |
No. of parameters | 146 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.29, −0.27 |
Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
Cg is the centroid of the N,C1–C5 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—H4···Ni | 0.925 (17) | 2.464 (18) | 2.809 (2) | 102.3 (12) |
C6—H6A···Cgii | 0.990 (19) | 2.59 | 3.5089 (16) | 155 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x+1, y, z. |
hpd(Å) | hcd(Å) | sa(°) | |
C6-H6A···πiii | 2.57 (2) | 2.59 (2) | 6.4 (2) |
Symmetry code: (iii) x-1, y, z. |
Acknowledgements
NL thanks the Taiwan NSC for financial support (NSC 98-2113-M- 027-002-MY3). We also thank Mr T. S. Kuo (Department of Chemistry, National Taiwan Normal University, Taiwan) for the assistance with the structure analysis.
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Bipyridine (bpy) ligand is among the most versatile ligands in organometallics. It has been extensively used to prepare various chelating compounds with different metal ions (Haga et al., 2000; Bain et al., 1989; Grätzel, 2001; Chambron & Sauvage, 1987, 1986). Structures with the motif {[4,4'-bis(RfCH2OCH2) -2,2'-bpy]MCl2, M = Pd or Pt} are interesting and reveal the blue shifting C–H···F–C hydrogen bonding (Lu, Tu, Hou et al., 2010; Lu, Tu, Wen et al., 2010; Lu, et al., 2007). However, the X-ray crystal structure of poly-fluorinated bpy ligands still remains elusive until recent elucidation of the structure on simplest 4,4'-bis(CF3CH2OCH2)-2,2'-bpy (Lu, Tu, Wu et al., 2010). Reported here is the significantly different crystal structure on its 5,5'-isomer. They vary only on the positions of two identical substituents, yet features of packing in the solid state show little in similarity.
The title compound I is centro-symmetric and crystallizes in the space group of P-1, one half of the molecule being crystallographically independent. Two structural features of the title compound I are the planarity and the anti conformation of connected pyridyl units. The bpy exhibits a planar core and the N–C3–C3i–Ni torsion angle is 180°, similar to the values in its 4,4'-isomer (Lu, Tu, Wu et al., 2010). Also noticed is the intramolecular weak hydrogen bonding interaction on C4–H4···Ni, as suggested by the short H4···Ni distance of 2.46 (2) Å and the C4–H4···Ni angle of 102 (1)° (see Fig. 1).
Although both the title compound and its 4,4'-isomer (Lu, Tu, Wu et al., 2010) have the same molecular formula and their bpy cores are similarly planar, their identical side chains, positioned differently, show very different intermolecular interactions and packing methods. The intramolecular C–H···O and intermolecular C–H···N and C–H···F interactions, which were observed in 4,4'-bis(2,2,2-trifluoroethoxymethyl)-2,2'-bipyridine (Lu, Tu, Wu et al., 2010), are missing in I. There is almost no intramolecular C–H···O interaction in I, judged from the C5–C1–C6–O torsion angle of 41.5 (2)°, which deviates significantly from that reported for such a hydrogen-bonding system. In its 4,4'-isomer, the corresponding H3···O8 distance is 2.52 (1) Å and the C3–C4–C7–O8 torsion angle measures -21.9 (1)°.
Instead of intermolecular C–H···N and C–H···F interactions, stabilization of the structure of I is likely due to effective intermolecular C–H..π and F···F interactions. The π-π stacking is the driving force towards crystallization, with two adjacent bpy layers at a distance of 3.512 (2) Å. On top of this, the C6–H6A..π hydrogen bonding interaction has been observed between the methylene H atom and one of the adjacent bpy rings on the a-translation related direction. As shown in Table 1, the distance of H6A to bpy plane is 2.57 (2) Å, making less than 10° with the vector of H6A to centroid of the bpy ring. The terminal CF3 groups shown in Fig. 2 are then fixed in crystalline state by the F···F interaction between two adjacent stacking layers. The F1···F3' distance is 2.857 (2) Å, the C8–F1···F3' angle 101.4 (1)°, and the C8–F3···F1" angle 166.0 (1)°.
In particular, the weak C4–H4···H4'–C4' (Wolstenholme et al., 2006) interaction shown in Fig. 2 has also been identified with H4···H4' distance of 2.32 (3) Å and the C4–H4···H4' angle of 113 (2)°. The C4–H4···H4'–C4' interaction connects two neighboring π stacking piles. Inside one π stacking pile, the π..π stacking distance between consecutive layers is 3.512 (2) Å, whereas the shifting step between two neighboring π stacking piles is 1.448 (2) Å. It is believed that this rare C–H···H–C supramolecular interaction seems to be derived from the dipole-induced interactions, defined by Wolstenholme, on the symmetry-related hydrogen atoms.