Crystal structure of 9-(di­bromo­meth­yl)-1,1-di­fluoro-3,7-dimethyl-1H-[1,3,5,2]oxadi­aza­borinino[3,4-a][1,8]naphthyridin-11-ium-1-uide

Wang, B.Z.; Zhou, J.P.; Zhou, Y.; Luo, J.S.; Chi, S.M.

doi:10.1107/S2056989016016704

research communications

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 72| Part 11| November 2016| Pages 1642-1644

https://doi.org/10.1107/S2056989016016704

Open

access

Crystal structure of 9-(dibromomethyl)-1,1-difluoro-3,7-dimethyl-1H-[1,3,5,2]oxadiazaborinino[3,4-a][1,8]naphthyridin-11-ium-1-uide

Bang Zhong Wang,^a Jun Ping Zhou,^a Yong Zhou,^a Jian Song Luo ^a and Shao Ming Chi ^a ^*

^aCollege of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, People's Republic of China
^*Correspondence e-mail: chishaoming@gmail.com

Edited by M. Weil, Vienna University of Technology, Austria (Received 9 September 2016; accepted 18 October 2016; online 25 October 2016)

The molecule of the title 1,8-naphthyridine-BF₂ derivative, C₁₂H₁₀BBr₂F₂N₃O, is located on a mirror plane running parallel to the entire ring system and the attached methyl C atoms. Individual molecules are stacked along the b-axis direction. The cohesion in the crystal structure is accomplished by C—H⋯F hydrogen bonds and additional off-set π–π interactions [centroid-to-centroid distance = 3.6392 (9) Å, slippage 0.472 Å], leading to the formation of a three-dimensional supramolecular network.

Keywords: crystal structure; 1,8-naphthyridine BF₂ complex; hydrogen bonding.

CCDC reference: 1510400

1. Chemical context

1,8-Naphthyridines are one of the most widely studied naphthyridine derivatives (Quan et al., 2012 ). They can exhibit diverse coordination modes and have excellent optical properties or biological activities. They are also widely employed in the synthesis of metal complexes, e.g. for the identification of small molecules (Liang et al., 2012 ; Tanaka et al., 2012 ) or metal cations (Liu et al., 2014 ), as luminescent materials and in biomedical fields (Eweas et al., 2014 ; Di Braccio et al., 2014 ). BF₂ compounds based on 1,8-naphthyridine ligands are used as fluorescent dyes due to their high fluorescence quantum yields (Zheng et al., 2015 ) and high photochemical stabilities. Their characteristic absorption and emission spectra (Wu et al., 2013 ; Li et al., 2010 ) can be applied in many fields, such as cell imaging, as molecular probes, solar cells and so on (Boens et al., 2012 ; Loudet & Burgess, 2007 ). However, only a few BF₂ compounds based on the 1,8-naphthyridine moiety have been described in the literature. In view of their importance, the title compound, 9-(dibromomethyl)-1,1-difluoro-3,7–dimethyl-1H-[1,3,5,2]oxadiazaborinino[3,4-a][1,8]naphthyridin-11-ium-1-uide, was synthesized and structurally characterized by single crystal X-ray diffraction.

2. Structural commentary

The molecular structure of the title compound is shown in Fig. 1. The 1,8-naphthyridine ring system is fused with a mixed difluororoxadiazaborinino unit. The entire oxadiazaborininonaphthyridine ring system is planar due to its location on a mirror plane running parallel to the ring system. In addition, the C atoms of the two methyl groups (C8 and C1) as well as the C atom (C12) of the dibromomethyl group are located on the mirror plane, hence only two pairs of the methyl H atoms, the two Br atoms and the two F atoms are above and below this plane. The F1—B1—F1ⁱ and Br1ⁱ—C12—Br1 angles [symmetry code: (i) x, −y + $[{1\over 2}]$ , z] are 113.6 (7) and 110.3 (3)°, and the distances of the Br and F atoms to the plane are 1.5916 (6) and 1.141 (3) Å, respectively. The individual F—B bond length is 1.364 (5) Å and the Br—C bond length 1.940 (4) Å. Compared with the molecular structure of a related compound (Wu et al., 2012 ), the difference between the F1—B1—F1ⁱ angles is 2.16°, while the bond lengths and angles in the oxadiazaborine ring moiety of the two structures are almost the same.

Figure 1
The molecular structure of the title compound, with displacement ellipsoids drawn at the 50% probability level. [Symmetry code: (A) x, −y + $[{1\over 2}]$ , z.]

3. Supramolecular features

In the crystal structure of the title compound, the molecules are stacked along the b-axis direction and linked into a three-dimensional network through C—H⋯F hydrogen bonds involving one of the methyl groups as acceptor H atoms (Fig. 2, Table 1). The cohesion in this network is reinforced via off-set π–π interactions [Cg2⋯Cg2ⁱ = 3.6392 (9) Å, interplanar distance = 3.6085 (1) Å, slippage = 0.472 Å; Cg2 is the centroid of the N2/C3–C6/C11 ring; symmetry code: (i) −x, − $[{1\over 2}]$ + y, 2 − z] (Fig. 3).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C1—H1B⋯F1ⁱ	0.96	2.41	3.163 (6)	135
Symmetry code: (i) $[-x+{\script{1\over 2}}, -y, z+{\script{1\over 2}}]$ .

Figure 2
A view along the a axis of the crystal packing of the title compound. Hydrogen bonds are shown as dashed lines.

Figure 3
A view along the b axis of the crystal packing of the title compound. Hydrogen bonds are shown as dashed lines.

4. Database survey

Owing to the shortage of BF₂ compounds based on 1,8-naphthyridine derivatives, there are only a few examples of similar compounds in the literature. A search of the Cambridge Structural Database (CSD version 5.37; August 19, 2016; Groom et al., 2016 ) revealed the structure of another very similar compound, viz. [N-(5,7-dimethyl-1,8-naphthyridin-2-yl)ethanimidato](difluoro)borate (CSD code MONGED; Du et al., 2014 ).

5. Synthesis and crystallization

BF₃·OEt₂ (2 ml, 16 mmol) was added dropwise to an ice-cooled solution of 2,6-lutidine (1 ml) and N-[7-(dibromomethyl)-5-methyl-1,8-naphthyridin-2-yl]acetamide (0.37 g, 1 mmol) in anhydrous CH₂Cl₂ (80 ml) under a nitrogen atmosphere. After the mixture had been stirred for 24 h under ambient temperature, the reaction was quenched with 20 ml distilled water. The aqueous layer was extracted with CH₂Cl₂ (3 × 50 ml); the organic layer was dried with anhydrous Na₂SO₄ and the solvent removed under reduced pressure. The residue was purified by silica gel chromatography using CH₂Cl₂ as eluent to give the pure product as a bright white powder (yield 0.19 g, 45%). Yellow crystals of the title compound were obtained from its CH₂Cl₂ solution by slow evaporation at room temperature.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were placed in calculated positions and included in the final cycles of refinement using a riding-model approximation with C—H = 0.96 Å and with U_iso(H) = 1.2U_eq(C) for aromatic and U_iso(H) = 1.5U_eq(C) for methyl H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₁₀BBr₂F₂N₃O
M_r	420.86
Crystal system, space group	Orthorhombic, Pnma
Temperature (K)	293
a, b, c (Å)	17.161 (3), 7.2169 (14), 11.678 (2)
V (Å³)	1446.3 (5)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	5.63
Crystal size (mm)	0.32 × 0.30 × 0.28

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995 )
T_min, T_max	0.266, 0.302
No. of measured, independent and observed [I > 2σ(I)] reflections	13517, 1765, 937
R_int	0.139
(sin θ/λ)_max (Å⁻¹)	0.647

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.054, 0.120, 0.95
No. of reflections	1765
No. of parameters	122
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.50, −0.37
Computer programs: PROCESS-AUTO (Rigaku, 1998 ), CrystalStructure (Rigaku/MSC, 2006 ), SHELXS97, SHELXL97 and XP in SHELXTL (Sheldrick, 2008 ).

Supporting information

CCDC reference: 1510400

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989016016704/wm5325sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016016704/wm5325Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989016016704/wm5325Isup3.cml

checkCIF report

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku/MSC, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

9-(Dibromomethyl)-1,1-difluoro-3,7-dimethyl-1H-[1,3,5,2]oxadiazaborinino[3,4-a][1,8]naphthyridin-11-ium-1-uide top

Crystal data top

C₁₂H₁₀BBr₂F₂N₃O	F(000) = 816
M_r = 420.86	D_x = 1.933 Mg m⁻³
Orthorhombic, Pnma	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2n	Cell parameters from 1765 reflections
a = 17.161 (3) Å	θ = 3.1–26.0°
b = 7.2169 (14) Å	µ = 5.63 mm⁻¹
c = 11.678 (2) Å	T = 293 K
V = 1446.3 (5) Å³	Block, yellow
Z = 4	0.32 × 0.30 × 0.28 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	1765 independent reflections
Radiation source: fine-focus sealed tube	937 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.139
ω scans	θ_max = 27.4°, θ_min = 3.3°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −22→22
T_min = 0.266, T_max = 0.302	k = −8→9
13517 measured reflections	l = −15→15

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.054	H-atom parameters constrained
wR(F²) = 0.120	w = 1/[σ²(F_o²) + (0.0519P)²] where P = (F_o² + 2F_c²)/3
S = 0.95	(Δ/σ)_max < 0.001
1765 reflections	Δρ_max = 0.50 e Å⁻³
122 parameters	Δρ_min = −0.37 e Å⁻³
0 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0042 (6)

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

	x	y	z	U_iso*/U_eq
Br1	0.11449 (3)	0.02946 (8)	0.57510 (5)	0.0624 (3)
B1	0.1752 (5)	0.2500	0.9765 (7)	0.041 (2)
F1	0.19639 (16)	0.0919 (4)	0.9205 (3)	0.0585 (8)
N1	0.1041 (4)	0.2500	1.2022 (6)	0.0524 (16)
N2	0.0835 (3)	0.2500	1.0005 (5)	0.0349 (13)
N3	0.0640 (3)	0.2500	0.8049 (5)	0.0385 (14)
O1	0.2143 (3)	0.2500	1.0882 (5)	0.0558 (14)
C1	0.2326 (5)	0.2500	1.2869 (8)	0.063 (2)
H1A	0.2025	0.2500	1.3562	0.095*
H1B	0.2649	0.1414	1.2847	0.095*
C2	0.1794 (5)	0.2500	1.1872 (7)	0.0450 (19)
C3	0.0572 (4)	0.2500	1.1095 (7)	0.0408 (18)
C4	−0.0249 (5)	0.2500	1.1303 (8)	0.055 (2)
H4A	−0.0433	0.2500	1.2079	0.065*
C5	−0.0760 (4)	0.2500	1.0421 (8)	0.049 (2)
H5A	−0.1309	0.2500	1.0579	0.059*
C6	−0.0513 (4)	0.2500	0.9274 (8)	0.0417 (18)
C7	−0.1003 (4)	0.2500	0.8304 (7)	0.0435 (19)
C8	−0.1880 (4)	0.2500	0.8438 (8)	0.060 (2)
H8A	−0.2125	0.2500	0.7698	0.089*
H8B	−0.2036	0.1414	0.8854	0.089*
C9	−0.0662 (4)	0.2500	0.7256 (7)	0.0463 (19)
H9A	−0.0981	0.2500	0.6580	0.056*
C10	0.0160 (4)	0.2500	0.7152 (7)	0.0424 (18)
C11	0.0314 (4)	0.2500	0.9079 (6)	0.0349 (17)
C12	0.0518 (4)	0.2500	0.5979 (7)	0.050 (2)
H12A	0.0104	0.2500	0.5425	0.059*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.0685 (4)	0.0646 (4)	0.0542 (5)	0.0055 (3)	0.0040 (3)	−0.0122 (3)
B1	0.037 (5)	0.055 (5)	0.029 (5)	0.000	−0.010 (4)	0.000
F1	0.0538 (17)	0.0646 (18)	0.057 (2)	0.0161 (15)	−0.0013 (15)	−0.0145 (17)
N1	0.062 (4)	0.059 (4)	0.037 (4)	0.000	0.004 (4)	0.000
N2	0.042 (3)	0.033 (3)	0.030 (4)	0.000	−0.002 (3)	0.000
N3	0.040 (3)	0.044 (3)	0.032 (4)	0.000	0.000 (3)	0.000
O1	0.055 (3)	0.076 (4)	0.036 (4)	0.000	−0.006 (3)	0.000
C1	0.079 (6)	0.068 (5)	0.042 (6)	0.000	−0.016 (5)	0.000
C2	0.073 (6)	0.031 (4)	0.031 (5)	0.000	−0.003 (4)	0.000
C3	0.056 (5)	0.033 (3)	0.034 (5)	0.000	0.004 (4)	0.000
C4	0.065 (5)	0.053 (4)	0.046 (6)	0.000	0.023 (5)	0.000
C5	0.044 (4)	0.051 (4)	0.053 (6)	0.000	0.011 (4)	0.000
C6	0.037 (4)	0.035 (3)	0.053 (5)	0.000	0.008 (4)	0.000
C7	0.040 (4)	0.036 (4)	0.055 (6)	0.000	−0.002 (4)	0.000
C8	0.036 (4)	0.063 (5)	0.080 (7)	0.000	0.004 (4)	0.000
C9	0.047 (4)	0.047 (4)	0.045 (6)	0.000	−0.009 (4)	0.000
C10	0.043 (4)	0.040 (4)	0.044 (5)	0.000	−0.004 (4)	0.000
C11	0.046 (4)	0.024 (3)	0.035 (5)	0.000	0.004 (3)	0.000
C12	0.046 (4)	0.063 (5)	0.039 (6)	0.000	−0.006 (4)	0.000

Geometric parameters (Å, º) top

Br1—C12	1.940 (4)	C4—C5	1.353 (11)
B1—F1	1.364 (5)	C4—H4A	0.9600
B1—F1ⁱ	1.364 (5)	C5—C6	1.406 (11)
B1—O1	1.467 (9)	C5—H5A	0.9600
B1—N2	1.599 (10)	C6—C7	1.410 (11)
N1—C2	1.303 (9)	C6—C11	1.437 (9)
N1—C3	1.349 (9)	C7—C9	1.357 (10)
N2—C3	1.351 (9)	C7—C8	1.514 (9)
N2—C11	1.403 (9)	C8—H8A	0.9600
N3—C11	1.327 (8)	C8—H8B	0.9600
N3—C10	1.332 (9)	C9—C10	1.416 (9)
O1—C2	1.302 (9)	C9—H9A	0.9600
C1—C2	1.481 (11)	C10—C12	1.501 (10)
C1—H1A	0.9600	C12—Br1ⁱ	1.940 (4)
C1—H1B	0.9600	C12—H12A	0.9600
C3—C4	1.431 (10)

F1—B1—F1ⁱ	113.6 (7)	C6—C5—H5A	118.7
F1—B1—O1	107.7 (4)	C5—C6—C7	125.8 (6)
F1ⁱ—B1—O1	107.7 (4)	C5—C6—C11	116.7 (7)
F1—B1—N2	110.2 (4)	C7—C6—C11	117.5 (7)
F1ⁱ—B1—N2	110.2 (4)	C9—C7—C6	117.8 (7)
O1—B1—N2	107.1 (6)	C9—C7—C8	121.5 (7)
C2—N1—C3	118.9 (7)	C6—C7—C8	120.7 (7)
C3—N2—C11	120.9 (6)	C7—C8—H8A	110.0
C3—N2—B1	119.6 (6)	C7—C8—H8B	109.2
C11—N2—B1	119.5 (6)	H8A—C8—H8B	109.5
C11—N3—C10	116.9 (6)	C7—C9—C10	120.5 (7)
C2—O1—B1	125.4 (6)	C7—C9—H9A	119.7
C2—C1—H1A	109.3	C10—C9—H9A	119.8
C2—C1—H1B	109.5	N3—C10—C9	123.2 (7)
H1A—C1—H1B	109.5	N3—C10—C12	117.7 (6)
N1—C2—O1	125.2 (7)	C9—C10—C12	119.1 (7)
N1—C2—C1	120.4 (8)	N3—C11—N2	115.5 (6)
O1—C2—C1	114.4 (7)	N3—C11—C6	124.0 (7)
N2—C3—N1	123.9 (7)	N2—C11—C6	120.5 (7)
N2—C3—C4	119.2 (7)	C10—C12—Br1ⁱ	110.6 (3)
N1—C3—C4	116.9 (7)	C10—C12—Br1	110.6 (3)
C5—C4—C3	120.7 (8)	Br1ⁱ—C12—Br1	110.3 (3)
C5—C4—H4A	120.4	C10—C12—H12A	108.2
C3—C4—H4A	119.0	Br1ⁱ—C12—H12A	108.5
C4—C5—C6	122.0 (7)	Br1—C12—H12A	108.5
C4—C5—H5A	119.3

Symmetry code: (i) x, −y+1/2, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1B···F1ⁱⁱ	0.96	2.41	3.163 (6)	135

Symmetry code: (ii) −x+1/2, −y, z+1/2.

Acknowledgements

Support from `Spring Sunshine' Plan of the Ministry of Education of China (grant No. Z2011125) and the National Natural Science Foundation of China (grant No. 21262049) is gratefully acknowledged.

References

Boens, N., Leen, V. & Dehaen, W. (2012). Chem. Soc. Rev. 41, 1130–1172. Web of Science CrossRef CAS PubMed Google Scholar
Di Braccio, M., Grossi, G., Alfei, S., Ballabeni, V., Tognolini, M., Flammini, L., Giorgio, C., Bertoni, S. & Barocelli, E. (2014). Eur. J. Med. Chem. 86, 394–405. CrossRef CAS PubMed Google Scholar
Du, M. L., Hu, C. Y., Wang, L. F., Li, C., Han, Y. Y., Gan, X., Chen, Y., Mu, W. H., Huang, M. L. & Fu, W. F. (2014). Dalton Trans. 43, 13924–13931. Web of Science CSD CrossRef CAS PubMed Google Scholar
Eweas, A. F., Khalifa, N. M., Ismail, N. S., Al-Omar, M. A. & Soliman, A. M. M. (2014). Med. Chem. Res. 23, 76–86. CrossRef CAS Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Li, H. J., Fu, W. F., Li, L., Gan, X., Mu, W. H., Chen, W. Q., Duan, X. M. & Song, H. B. (2010). Org. Lett. 12, 2924–2927. Web of Science CSD CrossRef CAS PubMed Google Scholar
Liang, F., Lindsay, S. & Zhang, P. (2012). Org. Biomol. Chem. 10, 8654–8659. Web of Science CrossRef CAS PubMed Google Scholar
Liu, X. J., Chen, M. X., Liu, Z. P., Yu, M. M., Wei, L. H. & Li, Z. X. (2014). Tetrahedron, 70, 658–663. Web of Science CSD CrossRef CAS Google Scholar
Loudet, A. & Burgess, K. (2007). Chem. Rev. 107, 4891–4932. Web of Science CrossRef PubMed CAS Google Scholar
Quan, L., Chen, Y., Lv, X. J. & Fu, W. F. (2012). Chem. Eur. J. 18, 14599–14604. Web of Science CSD CrossRef CAS PubMed Google Scholar
Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku/MSC (2006). CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Tanaka, K., Murakami, M., Jeon, J.-H. & Chujo, Y. (2012). Org. Biomol. Chem. 10, 90–95. CrossRef CAS PubMed Google Scholar
Wu, Y. Y., Chen, Y., Gou, G. Z., Mu, W. H., Lv, X. J., Du, M. L. & Fu, W. F. (2012). Org. Lett. 14, 5226–5229. Web of Science CSD CrossRef CAS PubMed Google Scholar
Wu, Y. Y., Chen, Y., Mu, W. H., Lv, X. J. & Fu, W. F. (2013). J. Photochem. Photobiol. Chem. 272, 73–79. Web of Science CSD CrossRef CAS Google Scholar
Zheng, J., Huang, F., Li, Y. J., Xu, T. W., Xu, H., Jia, J. H., Ye, Q. & Gao, J. R. (2015). Dyes Pigments, 113, 502–509. Web of Science CSD CrossRef CAS Google Scholar

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.