2-(Hy­droxy­meth­yl)pyridin-3-ol

He, X.-J.; Qiu, J.-K.; Jia, Y.-C.; Wang, D.-C.; Ou-Yang, P.-K.

doi:10.1107/S1600536812002759

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 68| Part 3| March 2012| Page o722

doi:10.1107/S1600536812002759

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2-(Hydroxymethyl)pyridin-3-ol

Xue-Jun He,^a Jiang-Kai Qiu,^a Yu-Chi Jia,^a De-Cai Wang ^a ^* and Ping-Kai Ou-Yang ^a

^aState Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing University of Technology, Nanjing 210009, People's Republic of China
^*Correspondence e-mail: dc_wang@hotmail.com

(Received 31 December 2011; accepted 22 January 2012; online 17 February 2012)

In the crystal structure of the title compound, C₆H₇NO₂, the molecules are are linked by intermolecular O—H⋯N and O—H⋯O hydrogen bonds; π–π stacking is observed between parallel pyridine rings of adjacent molecules [centroid-to-centroid distance = 3.7649 (12) Å].

Related literature

For the synthesis of the title compound, see: Dabak (2002 ).

Experimental

Crystal data

C₆H₇NO₂
M_r = 125.13
Monoclinic, P 2₁ /n
a = 7.0430 (14) Å
b = 7.1280 (14) Å
c = 12.264 (3) Å
β = 100.30 (3)°
V = 605.8 (2) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 293 K
0.30 × 0.20 × 0.10 mm

Data collection

Enraf–Nonius CAD-4 diffractometer
Absorption correction: ψ scan (XCAD4; Harms & Wocadlo, 1995 ) T_min = 0.969, T_max = 0.990
2263 measured reflections
1089 independent reflections
932 reflections with I > 2σ(I)
R_int = 0.028
3 standard reflections every 200 reflections intensity decay: 1%

Refinement

R[F² > 2σ(F²)] = 0.036
wR(F²) = 0.136
S = 0.99
1089 reflections
85 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.15 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1A⋯O2ⁱ	0.82	1.85	2.6502 (17)	166
O2—H2A⋯Nⁱⁱ	0.82	1.92	2.7216 (17)	167
Symmetry codes: (i) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) -x+1, -y, -z.

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994 ); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812002759/xu5437sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812002759/xu5437Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812002759/xu5437Isup3.cml

checkCIF report

Comment top

The title compound is an important organic intermediate for the synthesis of 2-pyrimidine-oxy-N-aryl benzyl amine derivatives, an important compound for new pesticides. In the process of synthesis, we obtained the crystal of the intermediate and we report its crystal structure.

As illustrated in Fig. 1, the hydroxyl oxygen O1 and the hydroxymethyl carbon C6 are approximately coplanar with the pyridine ring (C1—C5/N) with the maximum deviation of -0.0227 Å. The crystal structure is stabilized by intermolecular N—H···O and O—H···O hydrogen bonds (Table 1), and is further stabilized by π–π stacking between pyridine rings [centroid–centroid distance = 3.7649 (12) Å]

Related literature top

For the synthesis of the title compound, see: Dabak (2002).

Experimental top

The synthesis is according to the literature (Dabak, 2002). The formaldehyde solution (12.6 ml, 0.156 mol) and sodium hydroxide (6.3 g, 0.158 mol) was added to a solution of 3-hydroxypyridine (15.0 g, 0.156 mol) in water (63 ml). The reaction mixture was heated at 373 K for 12 h and then allowed to cool to ambient temperature. Acetic acid (9.47 ml, 0.156 mol) was added and water was removed in vacuo and the solid obtained was stirred with acetone (200 ml). The extract was purified by silica gel column chromatography and the colourless crystals were obtained in a yield of 20.3%.

Computing details top

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS (Enraf–Nonius, 1994); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. The structure of the title compound, showing the atomic numbering scheme. Non-H atoms are shown with 30% probability displacement ellipsoids.

2-(Hydroxymethyl)pyridin-3-ol top

Crystal data top

C₆H₇NO₂	F(000) = 264
M_r = 125.13	D_x = 1.372 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 25 reflections
a = 7.0430 (14) Å	θ = 9–13°
b = 7.1280 (14) Å	µ = 0.10 mm⁻¹
c = 12.264 (3) Å	T = 293 K
β = 100.30 (3)°	Block, colourless
V = 605.8 (2) Å³	0.30 × 0.20 × 0.10 mm
Z = 4

Data collection top

Enraf–Nonius CAD-4 diffractometer	932 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.028
Graphite monochromator	θ_max = 25.2°, θ_min = 3.1°
ω/2θ scans	h = 0→8
Absorption correction: ψ scan (XCAD4; Harms & Wocadlo, 1995)	k = −8→8
T_min = 0.969, T_max = 0.990	l = −14→14
2263 measured reflections	3 standard reflections every 200 reflections
1089 independent reflections	intensity decay: 1%

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)] = 0.036	H-atom parameters constrained
wR(F²) = 0.136	w = 1/[σ²(F_o²) + (0.1P)² + 0.069P] where P = (F_o² + 2F_c²)/3
S = 0.99	(Δ/σ)_max < 0.001
1089 reflections	Δρ_max = 0.18 e Å⁻³
85 parameters	Δρ_min = −0.15 e Å⁻³
0 restraints	Extinction correction: SHELXTL (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.67 (5)

Crystal data top

C₆H₇NO₂	V = 605.8 (2) Å³
M_r = 125.13	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 7.0430 (14) Å	µ = 0.10 mm⁻¹
b = 7.1280 (14) Å	T = 293 K
c = 12.264 (3) Å	0.30 × 0.20 × 0.10 mm
β = 100.30 (3)°

Data collection top

Enraf–Nonius CAD-4 diffractometer	932 reflections with I > 2σ(I)
Absorption correction: ψ scan (XCAD4; Harms & Wocadlo, 1995)	R_int = 0.028
T_min = 0.969, T_max = 0.990	3 standard reflections every 200 reflections
2263 measured reflections	intensity decay: 1%
1089 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.036	0 restraints
wR(F²) = 0.136	H-atom parameters constrained
S = 0.99	Δρ_max = 0.18 e Å⁻³
1089 reflections	Δρ_min = −0.15 e Å⁻³
85 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.

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 > σ(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
N	0.59730 (19)	0.28061 (17)	0.05259 (10)	0.0374 (4)
O1	0.21831 (16)	0.3738 (2)	0.20521 (9)	0.0531 (5)
H1A	0.2217	0.4225	0.2661	0.080*
C1	0.7372 (2)	0.3911 (2)	0.10511 (13)	0.0418 (5)
H1B	0.8548	0.3932	0.0807	0.050*
O2	0.27768 (19)	−0.02901 (16)	0.08581 (9)	0.0504 (5)
H2A	0.3277	−0.1099	0.0527	0.076*
C2	0.7152 (2)	0.5019 (2)	0.19373 (13)	0.0436 (5)
H2B	0.8160	0.5772	0.2284	0.052*
C3	0.5409 (2)	0.4995 (2)	0.23031 (13)	0.0410 (5)
H3A	0.5223	0.5731	0.2901	0.049*
C4	0.3939 (2)	0.3855 (2)	0.17644 (12)	0.0358 (5)
C5	0.4270 (2)	0.2764 (2)	0.08702 (11)	0.0340 (5)
C6	0.2761 (2)	0.1456 (2)	0.02825 (13)	0.0421 (5)
H6A	0.1500	0.2034	0.0225	0.050*
H6B	0.2994	0.1228	−0.0462	0.050*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N	0.0432 (8)	0.0343 (7)	0.0360 (7)	0.0046 (5)	0.0108 (5)	0.0008 (5)
O1	0.0435 (8)	0.0704 (9)	0.0487 (8)	−0.0087 (6)	0.0176 (5)	−0.0177 (6)
C1	0.0383 (9)	0.0407 (9)	0.0478 (10)	0.0024 (7)	0.0115 (7)	0.0030 (7)
O2	0.0729 (9)	0.0392 (7)	0.0462 (7)	−0.0084 (6)	0.0299 (6)	−0.0068 (5)
C2	0.0415 (9)	0.0399 (9)	0.0471 (10)	−0.0041 (7)	0.0020 (7)	−0.0038 (6)
C3	0.0462 (9)	0.0392 (8)	0.0377 (9)	0.0008 (7)	0.0076 (7)	−0.0074 (6)
C4	0.0381 (9)	0.0362 (8)	0.0336 (8)	0.0030 (6)	0.0078 (6)	0.0003 (6)
C5	0.0416 (9)	0.0318 (8)	0.0284 (8)	0.0033 (6)	0.0053 (6)	0.0034 (5)
C6	0.0472 (10)	0.0421 (9)	0.0371 (8)	−0.0027 (7)	0.0078 (7)	−0.0049 (6)

Geometric parameters (Å, º) top

N—C1	1.334 (2)	C2—C3	1.381 (2)
N—C5	1.3412 (19)	C2—H2B	0.9300
O1—C4	1.3478 (19)	C3—C4	1.387 (2)
O1—H1A	0.8200	C3—H3A	0.9300
C1—C2	1.375 (2)	C4—C5	1.397 (2)
C1—H1B	0.9300	C5—C6	1.499 (2)
O2—C6	1.430 (2)	C6—H6A	0.9700
O2—H2A	0.8200	C6—H6B	0.9700

C1—N—C5	119.08 (12)	O1—C4—C3	123.57 (14)
C4—O1—H1A	109.5	O1—C4—C5	117.43 (13)
N—C1—C2	122.91 (15)	C3—C4—C5	118.99 (15)
N—C1—H1B	118.5	N—C5—C4	121.25 (13)
C2—C1—H1B	118.5	N—C5—C6	117.37 (12)
C6—O2—H2A	109.5	C4—C5—C6	121.35 (14)
C1—C2—C3	118.82 (15)	O2—C6—C5	111.22 (13)
C1—C2—H2B	120.6	O2—C6—H6A	109.4
C3—C2—H2B	120.6	C5—C6—H6A	109.4
C2—C3—C4	118.94 (14)	O2—C6—H6B	109.4
C2—C3—H3A	120.5	C5—C6—H6B	109.4
C4—C3—H3A	120.5	H6A—C6—H6B	108.0

C5—N—C1—C2	0.0 (2)	O1—C4—C5—N	179.61 (13)
N—C1—C2—C3	−0.1 (2)	C3—C4—C5—N	−0.1 (2)
C1—C2—C3—C4	0.0 (2)	O1—C4—C5—C6	−2.4 (2)
C2—C3—C4—O1	−179.62 (15)	C3—C4—C5—C6	177.80 (13)
C2—C3—C4—C5	0.1 (2)	N—C5—C6—O2	95.53 (15)
C1—N—C5—C4	0.1 (2)	C4—C5—C6—O2	−82.49 (17)
C1—N—C5—C6	−177.96 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O2ⁱ	0.82	1.85	2.6502 (17)	166
O2—H2A···Nⁱⁱ	0.82	1.92	2.7216 (17)	167

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

Experimental details

Crystal data
Chemical formula	C₆H₇NO₂
M_r	125.13
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	7.0430 (14), 7.1280 (14), 12.264 (3)
β (°)	100.30 (3)
V (Å³)	605.8 (2)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.30 × 0.20 × 0.10

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	ψ scan (XCAD4; Harms & Wocadlo, 1995)
T_min, T_max	0.969, 0.990
No. of measured, independent and observed [I > 2σ(I)] reflections	2263, 1089, 932
R_int	0.028
(sin θ/λ)_max (Å⁻¹)	0.599

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.036, 0.136, 0.99
No. of reflections	1089
No. of parameters	85
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.15

Computer programs: CAD-4 EXPRESS (Enraf–Nonius, 1994), XCAD4 (Harms & Wocadlo, 1995), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1A···O2ⁱ	0.82	1.85	2.6502 (17)	166
O2—H2A···Nⁱⁱ	0.82	1.92	2.7216 (17)	167

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

Acknowledgements

This work was supported by the Center of Testing and Analysis, Nanjing University, China.

References

Dabak, K. (2002). Turk. J. Chem. 26, 955–963. CAS Google Scholar
Enraf–Nonius (1994). CAD-4 EXPRESS. Enraf–Nonius, Delft, The Netherlands. Google Scholar
Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar