2-(Pyridin-4-yl)-2,3-di­hydro-1H-naphtho­[1,8-de][1,3,2]di­aza­borinine

Ryo Yamamoto; Shu Hashimoto; Tsunehisa Okuno

doi:10.1107/S2414314624006151

. 2024 Jun 28;9(Pt 6):x240615. doi: 10.1107/S2414314624006151

2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]diazaborinine

Ryo Yamamoto ^a, Shu Hashimoto ^a, Tsunehisa Okuno ^a,^*

Editor: I Brito^b

PMCID: PMC11223678 PMID: 38974848

In the title compound, the pyridyl ring and the Bdan (dan = 1,8-diaminonaphto) group subtend a dihedral angle of 24.57 (5)°. In the crystal, the molecules make Inline graphic (28) hydrogen-bonding networks around the fourfold inversion axis, giving a cyclic tetramer. The molecules form columnar stacks along the c axis.

Keywords: crystal structure, pyridine derivative, tetrameric structure, dan

Abstract

The title compound, C₁₅H₁₂BN₃, is a type of diazaborinane featuring substitution at 1, 2, and 3 positions in the nitrogen–boron six-membered heterocycle. It is comprised of two almost planar units, the pyridyl ring and the Bdan (dan = 1,8-diaminonaphtho) group, which subtend a dihedral angle of 24.57 (5)°. In the crystal, the molecules are linked into R₄⁴(28) hydrogen-bonding networks around the fourfold inversion axis, giving cyclic tetramers. The molecules form columnar stacks along the c axis.

Structure description

The title compound, C₁₅H₁₂BN₃, is a type of diazaborinane that is substituted at the 1, 2, and 3 positions in the nitrogen–boron six-membered heterocycle. Recently, diazaborinanes have been found to stabilize organic radicals (LaPorte et al., 2023 ▸).

The title molecule (Fig. 1 ▸) is comprised of two almost planar units, the N1/C1–C5 pyridyl ring and the N2/N3/C6–C15/B1 group, which subtend a dihedral angle of 24.57 (5)°. This is slightly larger than those in related compounds that have almost planar structures (Akerman et al., 2011 ▸; Slabber et al., 2011 ▸).

The title compound with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.

In the crystal, the molecules make Inline graphic (28) hydrogen-bonding (Table 1 ▸) networks around the fourfold inversion axis, giving a cyclic tetramer as shown in Fig. 2 ▸. The formation of this tetrameric structure is thought to increase the dihedral angle. The molecules also stack along the c axis, as shown in Fig. 3 ▸, forming columnar stacks in which the B1⋯C6ⁱⁱ, B1⋯C7ⁱⁱ, and B1⋯C8ⁱⁱ distances are 3.656 (3), 3.513 (3) and 3.573 (3) Å, respectively [symmetry code:(ii) x, y, z − 1].

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯N1ⁱ	0.93 (2)	2.21 (2)	3.113 (2)	162 (2)

Open in a new tab

Symmetry code: (i) Inline graphic .

The hydrogen-bonding network of the title compound. [Symmetry code: (i) y + , −x + , −z − .]

The stacking structure along the c axis. [Symmetry codes:(ii) x, y, z − 1; (iii) x, y, z + 1.]

Synthesis and crystallization

The title compound was prepared according to the literature method (Hashimoto & Okuno, 2024 ▸). Single crystals of sufficient quality were obtained by recrystallization from chloroform solution.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸.

Table 2. Experimental details.

Crystal data
Chemical formula	C₁₅H₁₂BN₃
M _r	245.09
Crystal system, space group	Tetragonal, I
Temperature (K)	100
a, c (Å)	21.5659 (3), 5.0863 (1)
V (Å³)	2365.58 (8)
Z	8
Radiation type	Cu Kα
μ (mm⁻¹)	0.65
Crystal size (mm)	0.20 × 0.05 × 0.05

Data collection
Diffractometer	XtaLAB Synergy R, DW system, HyPix
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2024 ▸)
T_min, T_max	0.807, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	7772, 2268, 2125
R _int	0.036
(sin θ/λ)_max (Å⁻¹)	0.626

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.031, 0.083, 1.06
No. of reflections	2268
No. of parameters	180
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.15, −0.16
Absolute structure	Flack x determined using 840 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 ▸)
Absolute structure parameter	−0.2 (3)

Open in a new tab

Computer programs: CrysAlis PRO (Rigaku OD, 2024 ▸), SHELXS (Sheldrick, 2008 ▸), SHELXL2013/2 (Sheldrick, 2015 ▸) and OLEX2 (Dolomanov et al., 2009 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2414314624006151/bx4031sup1.cif

x-09-x240615-sup1.cif^{(243KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314624006151/bx4031Isup2.hkl

x-09-x240615-Isup2.hkl^{(182.2KB, hkl)}

x-09-x240615-Isup3.cml^{(5.1KB, cml)}

Supporting information file. DOI: 10.1107/S2414314624006151/bx4031Isup3.cml

CCDC reference: 2364937

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

full crystallographic data

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Crystal data

C₁₅H₁₂BN₃	D_x = 1.376 Mg m⁻³
M_r = 245.09	Cu Kα radiation, λ = 1.54184 Å
Tetragonal, I4	Cell parameters from 5132 reflections
a = 21.5659 (3) Å	θ = 2.9–75.0°
c = 5.0863 (1) Å	µ = 0.65 mm⁻¹
V = 2365.58 (8) Å³	T = 100 K
Z = 8	Block, clear colourless
F(000) = 1024	0.2 × 0.05 × 0.05 mm

Open in a new tab

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Data collection

XtaLAB Synergy R, DW system, HyPix diffractometer	2268 independent reflections
Radiation source: Rotating-anode X-ray tube, Rigaku (Cu) X-ray Source	2125 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.036
Detector resolution: 10.0000 pixels mm^-1	θ_max = 75.0°, θ_min = 2.9°
ω scans	h = −25→26
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2024)	k = −26→27
T_min = 0.807, T_max = 1.000	l = −5→6
7772 measured reflections

Open in a new tab

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Refinement

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.031	w = 1/[σ²(F_o²) + (0.0502P)² + 0.1789P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.083	(Δ/σ)_max < 0.001
S = 1.06	Δρ_max = 0.15 e Å⁻³
2268 reflections	Δρ_min = −0.15 e Å⁻³
180 parameters	Absolute structure: Flack x determined using 840 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
0 restraints	Absolute structure parameter: −0.2 (3)
Primary atom site location: structure-invariant direct methods

Open in a new tab

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Special details

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. The positions of the N-bound H atoms were obtained from difference Fourier maps and were refined isotropically. The C-bound H atoms were placed at ideal positions and were refined as riding on their parent C atoms. U_iso(H) values of the H atoms were set at 1.2U_eq(parent atom for Csp²).

Open in a new tab

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²)

	x	y	z	U_iso*/U_eq
N3	0.20041 (7)	0.03150 (8)	−0.0041 (4)	0.0233 (4)
C7	0.28868 (9)	0.15497 (9)	0.5132 (4)	0.0252 (4)
H7	0.3324	0.1604	0.5071	0.030*
C1	0.39265 (9)	−0.01777 (9)	−0.5063 (4)	0.0270 (4)
H1	0.4315	−0.0032	−0.5689	0.032*
N2	0.29394 (8)	0.07934 (7)	0.1587 (3)	0.0217 (3)
C13	0.10022 (9)	0.05895 (9)	0.1820 (4)	0.0267 (4)
H13	0.0797	0.0324	0.0611	0.032*
C10	0.15895 (9)	0.14042 (9)	0.5376 (4)	0.0255 (4)
C15	0.19455 (9)	0.10642 (8)	0.3491 (4)	0.0219 (4)
C5	0.31573 (9)	−0.08947 (9)	−0.5129 (4)	0.0273 (4)
H5	0.2989	−0.1270	−0.5796	0.033*
C6	0.26012 (9)	0.11421 (8)	0.3414 (4)	0.0218 (4)
C14	0.16387 (9)	0.06513 (9)	0.1728 (4)	0.0231 (4)
C11	0.09363 (10)	0.13134 (9)	0.5452 (4)	0.0288 (5)
H11	0.0693	0.1527	0.6721	0.035*
B1	0.26579 (10)	0.03753 (10)	−0.0181 (4)	0.0220 (4)
C3	0.30411 (9)	−0.00146 (9)	−0.2242 (4)	0.0220 (4)
C4	0.28147 (9)	−0.05701 (9)	−0.3271 (4)	0.0262 (4)
H4	0.2426	−0.0727	−0.2700	0.031*
C12	0.06564 (9)	0.09191 (9)	0.3700 (4)	0.0286 (5)
H12	0.0219	0.0868	0.3758	0.034*
N1	0.37087 (8)	−0.07118 (8)	−0.6036 (3)	0.0268 (4)
C2	0.36184 (9)	0.01756 (9)	−0.3191 (4)	0.0246 (4)
H2A	0.3801	0.0547	−0.2555	0.030*
C9	0.19006 (10)	0.18127 (9)	0.7109 (4)	0.0277 (5)
H9	0.1670	0.2039	0.8380	0.033*
C8	0.25310 (10)	0.18841 (9)	0.6969 (4)	0.0279 (4)
H8	0.2732	0.2164	0.8132	0.033*
H3	0.1804 (12)	0.0058 (12)	−0.125 (6)	0.042 (7)*
H2	0.3364 (11)	0.0870 (10)	0.167 (5)	0.028 (6)*

Open in a new tab

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Atomic displacement parameters (Å²)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N3	0.0236 (8)	0.0238 (8)	0.0225 (8)	0.0017 (6)	−0.0004 (7)	−0.0003 (7)
C7	0.0272 (9)	0.0252 (9)	0.0233 (10)	0.0016 (8)	−0.0001 (8)	0.0025 (8)
C1	0.0229 (9)	0.0263 (9)	0.0317 (10)	0.0004 (8)	0.0016 (9)	0.0004 (9)
N2	0.0203 (8)	0.0225 (7)	0.0223 (8)	0.0012 (6)	0.0012 (7)	0.0008 (7)
C13	0.0254 (10)	0.0260 (9)	0.0287 (10)	−0.0001 (8)	0.0002 (9)	0.0042 (9)
C10	0.0313 (10)	0.0235 (9)	0.0216 (10)	0.0058 (8)	0.0042 (8)	0.0068 (8)
C15	0.0262 (9)	0.0202 (8)	0.0193 (9)	0.0045 (7)	0.0022 (8)	0.0053 (7)
C5	0.0272 (10)	0.0245 (9)	0.0301 (10)	−0.0008 (8)	−0.0020 (9)	−0.0043 (8)
C6	0.0270 (9)	0.0200 (8)	0.0183 (9)	0.0027 (7)	0.0016 (8)	0.0050 (8)
C14	0.0271 (9)	0.0209 (9)	0.0214 (9)	0.0025 (7)	0.0018 (8)	0.0057 (8)
C11	0.0301 (10)	0.0283 (10)	0.0278 (11)	0.0088 (8)	0.0094 (9)	0.0068 (8)
B1	0.0254 (10)	0.0194 (9)	0.0212 (10)	0.0027 (8)	0.0001 (9)	0.0041 (9)
C3	0.0227 (9)	0.0228 (9)	0.0204 (9)	0.0030 (7)	−0.0033 (7)	0.0017 (7)
C4	0.0223 (9)	0.0274 (9)	0.0290 (10)	−0.0008 (8)	−0.0003 (8)	0.0000 (9)
C12	0.0248 (9)	0.0290 (10)	0.0319 (11)	0.0044 (8)	0.0051 (9)	0.0092 (9)
N1	0.0272 (9)	0.0263 (8)	0.0270 (9)	0.0038 (7)	−0.0015 (7)	−0.0034 (7)
C2	0.0253 (9)	0.0210 (9)	0.0276 (10)	−0.0009 (8)	−0.0009 (8)	−0.0012 (8)
C9	0.0383 (11)	0.0243 (10)	0.0205 (10)	0.0092 (8)	0.0042 (9)	0.0014 (8)
C8	0.0387 (11)	0.0223 (9)	0.0226 (10)	0.0035 (8)	−0.0019 (9)	0.0010 (8)

Open in a new tab

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Geometric parameters (Å, º)

N3—C14	1.399 (3)	C10—C9	1.416 (3)
N3—B1	1.418 (3)	C15—C6	1.425 (3)
N3—H3	0.93 (3)	C15—C14	1.426 (3)
C7—H7	0.9500	C5—H5	0.9500
C7—C6	1.384 (3)	C5—C4	1.389 (3)
C7—C8	1.408 (3)	C5—N1	1.335 (3)
C1—H1	0.9500	C11—H11	0.9500
C1—N1	1.339 (3)	C11—C12	1.372 (3)
C1—C2	1.389 (3)	B1—C3	1.578 (3)
N2—C6	1.401 (2)	C3—C4	1.396 (3)
N2—B1	1.411 (3)	C3—C2	1.397 (3)
N2—H2	0.93 (2)	C4—H4	0.9500
C13—H13	0.9500	C12—H12	0.9500
C13—C14	1.380 (3)	C2—H2A	0.9500
C13—C12	1.405 (3)	C9—H9	0.9500
C10—C15	1.431 (3)	C9—C8	1.370 (3)
C10—C11	1.423 (3)	C8—H8	0.9500

C14—N3—B1	123.02 (17)	C13—C14—N3	122.15 (18)
C14—N3—H3	118.1 (17)	C13—C14—C15	120.03 (18)
B1—N3—H3	118.8 (17)	C10—C11—H11	119.9
C6—C7—H7	119.9	C12—C11—C10	120.23 (18)
C6—C7—C8	120.13 (18)	C12—C11—H11	119.9
C8—C7—H7	119.9	N3—B1—C3	120.36 (18)
N1—C1—H1	118.0	N2—B1—N3	117.04 (18)
N1—C1—C2	123.90 (18)	N2—B1—C3	122.60 (17)
C2—C1—H1	118.0	C4—C3—B1	121.57 (17)
C6—N2—B1	122.82 (16)	C4—C3—C2	115.74 (18)
C6—N2—H2	112.8 (15)	C2—C3—B1	122.68 (17)
B1—N2—H2	124.4 (15)	C5—C4—C3	120.12 (18)
C14—C13—H13	119.9	C5—C4—H4	119.9
C14—C13—C12	120.1 (2)	C3—C4—H4	119.9
C12—C13—H13	119.9	C13—C12—H12	119.3
C11—C10—C15	118.62 (19)	C11—C12—C13	121.46 (18)
C9—C10—C15	118.83 (18)	C11—C12—H12	119.3
C9—C10—C11	122.54 (18)	C5—N1—C1	116.03 (17)
C6—C15—C10	119.37 (18)	C1—C2—C3	120.15 (17)
C6—C15—C14	121.14 (17)	C1—C2—H2A	119.9
C14—C15—C10	119.49 (17)	C3—C2—H2A	119.9
C4—C5—H5	118.0	C10—C9—H9	119.7
N1—C5—H5	118.0	C8—C9—C10	120.51 (19)
N1—C5—C4	124.06 (18)	C8—C9—H9	119.7
C7—C6—N2	121.89 (17)	C7—C8—H8	119.4
C7—C6—C15	119.97 (17)	C9—C8—C7	121.19 (19)
N2—C6—C15	118.14 (16)	C9—C8—H8	119.4
N3—C14—C15	117.81 (16)

N3—B1—C3—C4	−23.9 (3)	C11—C10—C15—C6	−179.01 (17)
N3—B1—C3—C2	154.92 (19)	C11—C10—C15—C14	0.7 (3)
N2—B1—C3—C4	156.09 (19)	C11—C10—C9—C8	179.81 (19)
N2—B1—C3—C2	−25.1 (3)	B1—N3—C14—C13	179.50 (19)
C10—C15—C6—C7	−0.8 (3)	B1—N3—C14—C15	−1.1 (3)
C10—C15—C6—N2	178.65 (16)	B1—N2—C6—C7	179.99 (18)
C10—C15—C14—N3	−178.38 (17)	B1—N2—C6—C15	0.5 (3)
C10—C15—C14—C13	1.0 (3)	B1—C3—C4—C5	178.49 (18)
C10—C11—C12—C13	0.9 (3)	B1—C3—C2—C1	−178.13 (18)
C10—C9—C8—C7	−0.8 (3)	C4—C5—N1—C1	−0.6 (3)
C15—C10—C11—C12	−1.7 (3)	C4—C3—C2—C1	0.7 (3)
C15—C10—C9—C8	0.5 (3)	C12—C13—C14—N3	177.53 (17)
C6—C7—C8—C9	0.3 (3)	C12—C13—C14—C15	−1.8 (3)
C6—N2—B1—N3	−0.3 (3)	N1—C1—C2—C3	−1.1 (3)
C6—N2—B1—C3	179.77 (16)	N1—C5—C4—C3	0.3 (3)
C6—C15—C14—N3	1.4 (3)	C2—C1—N1—C5	0.9 (3)
C6—C15—C14—C13	−179.24 (18)	C2—C3—C4—C5	−0.4 (3)
C14—N3—B1—N2	0.6 (3)	C9—C10—C15—C6	0.3 (3)
C14—N3—B1—C3	−179.47 (17)	C9—C10—C15—C14	−179.93 (16)
C14—C13—C12—C11	0.9 (3)	C9—C10—C11—C12	179.00 (18)
C14—C15—C6—C7	179.45 (17)	C8—C7—C6—N2	−178.96 (17)
C14—C15—C6—N2	−1.1 (3)	C8—C7—C6—C15	0.5 (3)

Open in a new tab

\ 2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]\ diazaborinine . Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···N1ⁱ	0.93 (2)	2.21 (2)	3.113 (2)	162 (2)

Open in a new tab

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

References

Akerman, M. P., Robinson, R. S. & Slabber, C. A. (2011). Acta Cryst. E67, o1873. [DOI] [PMC free article] [PubMed]
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst.42, 339–341.
Hashimoto, S. & Okuno, T. (2024). IUCrData, 9, x240362. [DOI] [PMC free article] [PubMed]
LaPorte, A. J., Feldner, J. E., Spies, J. C., Maher, T. J. & Burke, M. D. (2023). Angew. Chem. Int. Ed.62, e202309566. [DOI] [PubMed]
Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. [DOI] [PMC free article] [PubMed]
Rigaku OD (2024). CrysAlis PRO. Rigaku Corporation, Tokyo, Japan.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8.
Slabber, C. A., Grimmer, C., Akerman, M. P. & Robinson, R. S. (2011). Acta Cryst. E67, o1995. [DOI] [PMC free article] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2414314624006151/bx4031sup1.cif

x-09-x240615-sup1.cif^{(243KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314624006151/bx4031Isup2.hkl

x-09-x240615-Isup2.hkl^{(182.2KB, hkl)}

x-09-x240615-Isup3.cml^{(5.1KB, cml)}

Supporting information file. DOI: 10.1107/S2414314624006151/bx4031Isup3.cml

CCDC reference: 2364937

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

[bb1] Akerman, M. P., Robinson, R. S. & Slabber, C. A. (2011). Acta Cryst. E67, o1873. [DOI] [PMC free article] [PubMed]

[bb2] Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst.42, 339–341.

[bb5] Hashimoto, S. & Okuno, T. (2024). IUCrData, 9, x240362. [DOI] [PMC free article] [PubMed]

[bb6] LaPorte, A. J., Feldner, J. E., Spies, J. C., Maher, T. J. & Burke, M. D. (2023). Angew. Chem. Int. Ed.62, e202309566. [DOI] [PubMed]

[bb7] Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259. [DOI] [PMC free article] [PubMed]

[bb8] Rigaku OD (2024). CrysAlis PRO. Rigaku Corporation, Tokyo, Japan.

[bb9] Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]

[bb10] Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8.

[bb11] Slabber, C. A., Grimmer, C., Akerman, M. P. & Robinson, R. S. (2011). Acta Cryst. E67, o1995. [DOI] [PMC free article] [PubMed]

PERMALINK

2-(Pyridin-4-yl)-2,3-dihydro-1H-naphtho[1,8-de][1,3,2]diazaborinine

Ryo Yamamoto

Shu Hashimoto

Tsunehisa Okuno

Roles

Abstract

Structure description