Crystal structure of 9-(di-bromo-meth-yl)-1,1-di-fluoro-3,7-dimethyl-1H-[1,3,5,2]oxadi-aza-borinino[3,4-a][1,8]naphthyridin-11-ium-1-uide.

The mol-ecule 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 mol-ecules 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 inter-actions [centroid-to-centroid distance = 3.6392 (9) Å, slippage 0.472 Å], leading to the formation of a three-dimensional supra-molecular network.

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.

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 + , 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 + , z.]

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, − + y, 2 − z] (Fig. 3 ▸).

Figure 2

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

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) .

Figure 3

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

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 ▸).

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.

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, P n m a
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[F 2 > 2σ(F 2)], wR(F 2), S	0.054, 0.120, 0.95
No. of reflections	1765
No. of parameters	122
H-atom treatment	H-atom parameters constrained
Δρmax, Δρmin (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 ▸).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989016016704/wm5325sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016016704/wm5325Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989016016704/wm5325Isup3.cml

CCDC reference: 1510400

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

C12H10BBr2F2N3O	F(000) = 816
Mr = 420.86	Dx = 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

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

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(Fo2) + (0.0519P)2] where P = (Fo2 + 2Fc2)/3
S = 0.95	(Δ/σ)max < 0.001
1765 reflections	Δρmax = 0.50 e Å−3
122 parameters	Δρmin = −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)

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
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*

	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

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

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