Crystal structure of 2,6-bis­[(1H-pyrazol-1-yl)meth­yl]pyridine

Son, K.; Woo, J.O.; Kim, D.; Kang, S.K.

doi:10.1107/S1600536814017474

organic compounds

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ISSN: 2056-9890

Volume 70| Part 9| September 2014| Page o973

doi:10.1107/S1600536814017474

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Crystal structure of 2,6-bis[(1H-pyrazol-1-yl)methyl]pyridine

Kyung-sun Son,^a Jeong Oh Woo,^a Daeyoung Kim ^a and Sung Kwon Kang ^a ^*

^aDepartment of Chemistry, Chungnam National University, Daejeon 305-764, Republic of Korea
^*Correspondence e-mail: skkang@cnu.ac.kr

Edited by H. Ishida, Okayama University, Japan (Received 25 July 2014; accepted 30 July 2014; online 6 August 2014)

In the title compound, C₁₃H₁₃N₅, the planes of the pyrazolyl groups are nearly perpendicular to that of the central pyridine ring, making dihedral angles of 87.77 (8) and 85.73 (7)°. In the crystal, weak C—H⋯N hydrogen bonds link the molecules into layers extending parallel to (10-1).

Keywords: crystal structure; pyridine; purazole; tridentate ligand; catalysis.

CCDC reference: 1016859

1. Related literature

For the synthesis of the title compound, see: Reger et al. (2005 ). For metal complexes with similar ligands, see: Sharma et al. (2011 ); Ojwach et al. (2007 ); Manikandan et al. (2000 , 2001 ); Halcrow & Kilner (2002 ). For potential applications of the ligand in catalysis, see: Karam et al. (2005 ).

2. Experimental

2.1. Crystal data

C₁₃H₁₃N₅
M_r = 239.28
Monoclinic, P 2₁ /n
a = 7.481 (3) Å
b = 9.076 (4) Å
c = 19.021 (8) Å
β = 95.471 (5)°
V = 1285.7 (9) Å³
Z = 4
Mo Kα radiation
μ = 0.08 mm⁻¹
T = 296 K
0.26 × 0.2 × 0.15 mm

2.2. Data collection

Bruker SMART CCD area-detector diffractometer
25319 measured reflections
3136 independent reflections
2260 reflections with I > 2σ(I)
R_int = 0.040

2.3. Refinement

R[F² > 2σ(F²)] = 0.060
wR(F²) = 0.149
S = 1.09
3136 reflections
163 parameters
H-atom parameters constrained
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.28 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C4—H4⋯N15ⁱ	0.93	2.62	3.550 (3)	178
C6—H6B⋯N12ⁱⁱ	0.97	2.54	3.430 (2)	152
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ ; (ii) -x+1, -y+2, -z.

Data collection: SMART (Bruker, 2002 ); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ); software used to prepare material for publication: WinGX (Farrugia, 2012).

Supporting information

CCDC reference: 1016859

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536814017474/is5371sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814017474/is5371Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814017474/is5371Isup3.cml

checkCIF report

Related literature top

For the synthesis of the title compound, see: Reger et al. (2005). For metal complexes with similar ligands, see: Sharma et al. (2011); Ojwach et al. (2007); Manikandan et al. (2000, 2001); Halcrow & Kilner (2002). For potential applications of the ligand in catalysis, see: Karam et al. (2005).

Experimental top

To a stirred solution of 2,6-pyridinedimethanol (0.28 g, 2 mmol) and NaOH (0.8 g, 20 mmol) in THF/water (7.5/7.5 ml) was added a solution of p-toluenesulfonyl chloride (0.761 g, 4 mmol) in THF (7.5 ml) at 0 °C. After 4 h of stirring, the mixture was poured into 20 ml of water and extracted with methylene chloride. The organic phase was washed with saturated aqueous NaCl solution and distilled water and dried over Na₂SO₄, and the solvent was removed in vacuo to afford 2,6-pyridine-dimethylene-ditosylate (0.788 g, 88%) as a white powder. In a separate flask under a nitrogen atmosphere, a solution of pyrazole (0.22 g, 3.2 mmol) in dry THF (5 ml) was added dropwise to a suspension of NaH (0.08 g, 3.2 mmol) in dry THF (5 ml) at 0 °C. After 15 min of stirring, a clear solution of NaPz was obtained. A solution of 2,6-pyridine-dimethylene-ditosylate (0.73 g, 1.6 mmol) in dry THF (7.5 ml) was added to this solution; the mixture was stirred overnight and filtered, and the solvent was removed. The crude product was purified by column chromatography on silica gel with ethyl acetate as eluent to afford 0.30 g (76%) of pure ligand as a white solid. Single crystals of the title compound were obtained by slow diffusion of hexane into a concentrated solution of the white solid in THF at room temperature within 1–2 days.

Computing details top

Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); program(s) used to solve structure: SHELXS2013 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012).

Figures top

	Fig. 1. Molecular structure of the title compound, showing the atom-numbering scheme and 30% probability ellipsoids.
	Fig. 2. Part of the crystal structure of the title compound, showing molecules linked by intermolecular C—H···N hydrogen bonds (dashed lines).

2,6-Bis[(1H-pyrazol-1-yl)methyl]pyridine top

Crystal data top

C₁₃H₁₃N₅	F(000) = 504
M_r = 239.28	D_x = 1.236 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 5271 reflections
a = 7.481 (3) Å	θ = 2.2–25.5°
b = 9.076 (4) Å	µ = 0.08 mm⁻¹
c = 19.021 (8) Å	T = 296 K
β = 95.471 (5)°	Block, colourless
V = 1285.7 (9) Å³	0.26 × 0.2 × 0.15 mm
Z = 4

Data collection top

Bruker SMART CCD area-detector diffractometer	R_int = 0.040
Radiation source: fine-focus sealed tube	θ_max = 28.2°, θ_min = 2.2°
ϕ and ω scans	h = −9→9
25319 measured reflections	k = −12→12
3136 independent reflections	l = −25→25
2260 reflections with I > 2σ(I)

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.060	H-atom parameters constrained
wR(F²) = 0.149	w = 1/[σ²(F_o²) + (0.0539P)² + 0.4331P] where P = (F_o² + 2F_c²)/3
S = 1.09	(Δ/σ)_max < 0.001
3136 reflections	Δρ_max = 0.24 e Å⁻³
163 parameters	Δρ_min = −0.28 e Å⁻³

Crystal data top

C₁₃H₁₃N₅	V = 1285.7 (9) Å³
M_r = 239.28	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 7.481 (3) Å	µ = 0.08 mm⁻¹
b = 9.076 (4) Å	T = 296 K
c = 19.021 (8) Å	0.26 × 0.2 × 0.15 mm
β = 95.471 (5)°

Data collection top

Bruker SMART CCD area-detector diffractometer	2260 reflections with I > 2σ(I)
25319 measured reflections	R_int = 0.040
3136 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.060	0 restraints
wR(F²) = 0.149	H-atom parameters constrained
S = 1.09	Δρ_max = 0.24 e Å⁻³
3136 reflections	Δρ_min = −0.28 e Å⁻³
163 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
N1	−0.0152 (2)	0.79070 (17)	0.01406 (8)	0.0502 (4)
C2	−0.1286 (3)	0.7141 (2)	−0.02875 (11)	0.0576 (5)
H2	−0.2403	0.6823	−0.0172	0.069*
C3	−0.0626 (3)	0.6867 (2)	−0.09235 (11)	0.0637 (6)
H3	−0.1184	0.6351	−0.1306	0.076*
C4	0.1019 (3)	0.7512 (2)	−0.08738 (10)	0.0569 (5)
H4	0.1821	0.7522	−0.1218	0.068*
N5	0.12629 (18)	0.81324 (15)	−0.02326 (8)	0.0438 (4)
C6	0.2836 (2)	0.88545 (19)	0.01027 (11)	0.0529 (5)
H6A	0.2458	0.9661	0.0388	0.063*
H6B	0.3512	0.9272	−0.026	0.063*
C7	0.4057 (2)	0.78510 (17)	0.05647 (9)	0.0382 (4)
C8	0.3819 (2)	0.63422 (19)	0.05958 (10)	0.0481 (4)
H8	0.2873	0.5885	0.0327	0.058*
C9	0.5017 (2)	0.5534 (2)	0.10339 (10)	0.0544 (5)
H9	0.4889	0.4517	0.1065	0.065*
C10	0.6403 (2)	0.62335 (19)	0.14246 (9)	0.0497 (4)
H10	0.7221	0.5703	0.1724	0.06*
C11	0.6554 (2)	0.77450 (18)	0.13620 (8)	0.0424 (4)
N12	0.53963 (18)	0.85448 (15)	0.09409 (7)	0.0402 (3)
C13	0.8035 (3)	0.8643 (2)	0.17501 (11)	0.0619 (5)
H13A	0.8628	0.9211	0.1408	0.074*
H13B	0.7503	0.9334	0.2059	0.074*
N14	0.9367 (2)	0.77839 (17)	0.21661 (8)	0.0504 (4)
N15	0.9129 (2)	0.7377 (2)	0.28293 (8)	0.0620 (5)
C16	1.0538 (3)	0.6541 (3)	0.30142 (12)	0.0687 (6)
H16	1.0754	0.61	0.3455	0.082*
C17	1.1637 (3)	0.6396 (3)	0.24904 (14)	0.0860 (8)
H17	1.2698	0.5859	0.25	0.103*
C18	1.0849 (3)	0.7199 (3)	0.19552 (12)	0.0785 (7)
H18	1.1269	0.7323	0.1514	0.094*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0469 (8)	0.0497 (9)	0.0545 (9)	−0.0040 (7)	0.0074 (7)	0.0014 (7)
C2	0.0445 (10)	0.0549 (11)	0.0728 (13)	−0.0086 (9)	0.0029 (9)	−0.0026 (10)
C3	0.0622 (13)	0.0643 (13)	0.0615 (13)	−0.0056 (10)	−0.0110 (10)	−0.0094 (10)
C4	0.0613 (12)	0.0639 (12)	0.0458 (10)	0.0064 (10)	0.0063 (9)	0.0065 (9)
N5	0.0406 (7)	0.0410 (8)	0.0486 (8)	−0.0031 (6)	−0.0016 (6)	0.0103 (6)
C6	0.0475 (10)	0.0387 (9)	0.0696 (12)	−0.0087 (8)	−0.0093 (9)	0.0157 (8)
C7	0.0357 (8)	0.0361 (8)	0.0435 (9)	−0.0018 (6)	0.0068 (7)	0.0050 (7)
C8	0.0437 (9)	0.0375 (9)	0.0616 (11)	−0.0065 (7)	−0.0034 (8)	0.0042 (8)
C9	0.0583 (11)	0.0314 (8)	0.0721 (13)	−0.0021 (8)	−0.0015 (9)	0.0070 (8)
C10	0.0550 (11)	0.0414 (9)	0.0512 (10)	0.0062 (8)	−0.0033 (8)	0.0083 (8)
C11	0.0476 (9)	0.0409 (9)	0.0385 (8)	0.0012 (7)	0.0025 (7)	0.0003 (7)
N12	0.0441 (8)	0.0340 (7)	0.0419 (7)	−0.0017 (6)	0.0015 (6)	0.0032 (6)
C13	0.0706 (13)	0.0468 (11)	0.0633 (12)	−0.0017 (9)	−0.0204 (10)	−0.0002 (9)
N14	0.0540 (9)	0.0551 (9)	0.0396 (8)	−0.0044 (7)	−0.0075 (7)	0.0015 (7)
N15	0.0639 (10)	0.0806 (12)	0.0411 (9)	−0.0067 (9)	0.0033 (8)	0.0023 (8)
C16	0.0755 (14)	0.0739 (14)	0.0521 (12)	−0.0096 (12)	−0.0173 (11)	0.0148 (11)
C17	0.0613 (14)	0.115 (2)	0.0787 (17)	0.0220 (14)	−0.0098 (13)	0.0017 (15)
C18	0.0617 (13)	0.121 (2)	0.0539 (13)	0.0083 (14)	0.0119 (11)	0.0059 (13)

Geometric parameters (Å, º) top

N1—C2	1.317 (2)	C9—H9	0.93
N1—N5	1.345 (2)	C10—C11	1.383 (2)
C2—C3	1.372 (3)	C10—H10	0.93
C2—H2	0.93	C11—N12	1.336 (2)
C3—C4	1.358 (3)	C11—C13	1.511 (2)
C3—H3	0.93	C13—N14	1.441 (2)
C4—N5	1.340 (2)	C13—H13A	0.97
C4—H4	0.93	C13—H13B	0.97
N5—C6	1.442 (2)	N14—C18	1.326 (3)
C6—C7	1.511 (2)	N14—N15	1.343 (2)
C6—H6A	0.97	N15—C16	1.319 (3)
C6—H6B	0.97	C16—C17	1.357 (3)
C7—N12	1.332 (2)	C16—H16	0.93
C7—C8	1.383 (2)	C17—C18	1.342 (3)
C8—C9	1.376 (2)	C17—H17	0.93
C8—H8	0.93	C18—H18	0.93
C9—C10	1.372 (2)

C2—N1—N5	104.28 (15)	C8—C9—H9	120.1
N1—C2—C3	112.10 (18)	C9—C10—C11	118.44 (16)
N1—C2—H2	123.9	C9—C10—H10	120.8
C3—C2—H2	123.9	C11—C10—H10	120.8
C4—C3—C2	105.09 (18)	N12—C11—C10	122.49 (16)
C4—C3—H3	127.5	N12—C11—C13	113.78 (15)
C2—C3—H3	127.5	C10—C11—C13	123.73 (16)
N5—C4—C3	106.77 (18)	C7—N12—C11	118.43 (14)
N5—C4—H4	126.6	N14—C13—C11	114.41 (16)
C3—C4—H4	126.6	N14—C13—H13A	108.7
C4—N5—N1	111.76 (15)	C11—C13—H13A	108.7
C4—N5—C6	128.93 (17)	N14—C13—H13B	108.7
N1—N5—C6	119.07 (15)	C11—C13—H13B	108.7
N5—C6—C7	113.96 (14)	H13A—C13—H13B	107.6
N5—C6—H6A	108.8	C18—N14—N15	111.34 (17)
C7—C6—H6A	108.8	C18—N14—C13	127.23 (18)
N5—C6—H6B	108.8	N15—N14—C13	121.22 (17)
C7—C6—H6B	108.8	C16—N15—N14	103.57 (17)
H6A—C6—H6B	107.7	N15—C16—C17	112.7 (2)
N12—C7—C8	122.57 (15)	N15—C16—H16	123.7
N12—C7—C6	114.16 (14)	C17—C16—H16	123.7
C8—C7—C6	123.27 (15)	C18—C17—C16	104.5 (2)
C9—C8—C7	118.33 (16)	C18—C17—H17	127.7
C9—C8—H8	120.8	C16—C17—H17	127.7
C7—C8—H8	120.8	N14—C18—C17	107.9 (2)
C10—C9—C8	119.73 (16)	N14—C18—H18	126
C10—C9—H9	120.1	C17—C18—H18	126

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4···N15ⁱ	0.93	2.62	3.550 (3)	178
C6—H6B···N12ⁱⁱ	0.97	2.54	3.430 (2)	152

Symmetry codes: (i) x−1/2, −y+3/2, z−1/2; (ii) −x+1, −y+2, −z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C4—H4···N15ⁱ	0.93	2.62	3.550 (3)	178
C6—H6B···N12ⁱⁱ	0.97	2.54	3.430 (2)	152

Symmetry codes: (i) x−1/2, −y+3/2, z−1/2; (ii) −x+1, −y+2, −z.

Acknowledgements

This work was supported by the research fund of Chungnam National University.

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