Redetermination of 2-methyl-4-nitro­pyridine N-oxide

Abstract

An improved crystal structure of the title compound, C₆H₆N₂O₃, is reported. The structure, previously solved [Li et al. (1987 ▶). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24] in the ortho­rhom­bic space group Pca2₁ and refined to R = 0.067, has been solved in the ortho­rhom­bic space group Pbcm with data of enhanced quality, giving an improved structure (R = 0.0485). The mol­ecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of mol­ecular sheets extending parallel to the ab plane and connected via C—H⋯O contacts involving ring H atoms and O atoms of the N-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers.

Related literature  

For the synthesis and preparative aspects of pyridine-N-oxides, see: Fontenas et al. (1995 ▶); Katritzky & Lagowski (1971 ▶); Kilenyi (2001 ▶); Mosher et al. (1963 ▶). For the preparation of the title compound, see: Ashimori et al. (1990 ▶) and for potential applications, see: Elemans et al. (2009 ▶); Weber & Vögtle (1976 ▶); Winter et al. (2004 ▶). For the previous report of its crystal structure, see: Li et al. (1987 ▶). For non-classical hydrogen bonds, see: Desiraju & Steiner (1999 ▶).

Experimental  

Crystal data  

• C₆H₆N₂O₃

• M _r = 154.13

• Orthorhombic,

• a = 8.6775 (7) Å

• b = 12.4069 (10) Å

• c = 6.1995 (5) Å

• V = 667.44 (9) ų

• Z = 4

• Mo Kα radiation

• μ = 0.13 mm⁻¹

• T = 153 K

• 0.57 × 0.30 × 0.23 mm

Data collection  

• Bruker APEXII CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T _min = 0.932, T _max = 0.972

• 19832 measured reflections

• 1100 independent reflections

• 973 reflections with I > 2σ(I)

• R _int = 0.028

Refinement  

• R[F ² > 2σ(F ²)] = 0.049

• wR(F ²) = 0.147

• S = 1.10

• 1100 reflections

• 74 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.36 e Å⁻³

• Δρ_min = −0.34 e Å⁻³

Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT-NT (Bruker, 2008 ▶); data reduction: SAINT-NT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▶); software used to prepare material for publication: SHELXL97.

Supplementary Material

CCDC reference: 988898

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

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C2—H2A⋯O1i	0.95	2.29	3.225 (2)	169
C5—H5⋯O2ii	0.95	2.36	3.301 (2)	173

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

1. Comment

Pyridine N-oxides are readily formed by oxidation of corresponding pyridines (Kilenyi, 2001; Mosher et al., 1963). In contrast to the simple pyridines they facilitate an electrophilic substitution reaction in the ring position-4, hence being important intermediates in the synthesis of pyridine derivatives featuring a complex substitution pattern (Katritzky & Lagowski, 1971). Moreover, when 2-methylpyridine N-oxides are treated with trifluoroacetic anhydride, the Boekelheide reaction occurs to give 2-(hydroxymethyl)pyridines (Fontenas et al., 1995) which are of relevance to make available chelating (Winter et al., 2004), macrocyclic (Weber & Vögtle, 1976) and linker-type (Elemans et al., 2009) ligands. In the course of a respective synthesis of the latter kind, the title compound was prepared and its structure redetermined. The previous crystal structure of the compound (reported in 1987 by Li et al.) has been solved in the orthorhombic space group Pca2₁ and refined to an R-value of 6.7%. The repeated analysis of the crystal structure with data of enhanced quality yields a crystal structure of space group Pbcm with nearly identical cell dimensions. The centrosymmetry of the crystal structure is sustained by the statistical analysis of E-values. The molecule is located on the crystallographic symmetry plane and thus adopts perfect planarity (Fig. 1). According to this, two-dimensional supramolecular aggregates extending parallel to the crystallographic ab-plane and with the molecules connected via C—H···O hydrogen bonding (Desiraju & Steiner, 1999) that involves ring H atoms and both O atoms of the N-oxide (C—H···O_N-oxide 2.29 Å, 169 °) and nitro groups (C—H···O_nitro 2.36 Å, 173 °) represent the basic entities of the crystal structure (Fig. 2). As no other type of intermolecular interactions are observed, the crystal structure is stabilized by van der Waals forces in direction of the stacking axes of the molecular sheets.

2. Experimental

The title compound was synthesized via nitration of 2-methylpyridine N-oxide following a described procedure (Ashimori et al., 1990). Crystallization from toluene/chloroform (1/1) yielded yellow needles which were used for X-ray single-crystal structure analysis.

3. Refinement

Aromatic H atoms were positioned geometrically and allowed to ride on their parent atoms, with C—H = 0.95 Å and U_iso = 1.2 U_eq(C).

Figures

Fig. 1.

Perspective view of the molecular structure of the title compound including the atom numbering. Anisotropic displacement parameters for non-hydrogen atoms are drawn at a 50% probability level.

Fig. 2.

Packing diagram of the title compound viewed down the c-axis. Hydrogen bonds are displayed as broken lines.

Crystal data

C6H6N2O3	F(000) = 320
Mr = 154.13	Dx = 1.534 Mg m−3
Orthorhombic, Pbcm	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2c 2b	Cell parameters from 6590 reflections
a = 8.6775 (7) Å	θ = 2.4–35.0°
b = 12.4069 (10) Å	µ = 0.13 mm−1
c = 6.1995 (5) Å	T = 153 K
V = 667.44 (9) Å3	Column, yellow
Z = 4	0.57 × 0.30 × 0.23 mm

Data collection

Bruker APEXII CCD area-detector diffractometer	1100 independent reflections
Radiation source: fine-focus sealed tube	973 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.028
phi and ω scans	θmax = 30.4°, θmin = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −12→12
Tmin = 0.932, Tmax = 0.972	k = −17→17
19832 measured reflections	l = −8→8

Refinement

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)] = 0.049	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.147	w = 1/[σ2(Fo2) + (0.0871P)2 + 0.2298P] where P = (Fo2 + 2Fc2)/3
S = 1.10	(Δ/σ)max < 0.001
1100 reflections	Δρmax = 0.36 e Å−3
74 parameters	Δρmin = −0.34 e Å−3
Primary atom site location: structure-invariant direct methods

Special details

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. The C—H bonds of the methyl group were restrained to a target value of 0.89 (1) Å.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.52895 (16)	0.30510 (10)	0.2500	0.0309 (3)
O2	1.05609 (15)	−0.02519 (12)	0.2500	0.0355 (4)
O3	0.85937 (17)	−0.13544 (11)	0.2500	0.0441 (4)
N1	0.61843 (17)	0.22205 (10)	0.2500	0.0223 (3)
N2	0.91523 (17)	−0.04406 (12)	0.2500	0.0276 (3)
C1	0.55535 (18)	0.12002 (13)	0.2500	0.0216 (3)
C2	0.65356 (17)	0.03153 (12)	0.2500	0.0203 (3)
H2A	0.6128	−0.0395	0.2500	0.024*
C3	0.81182 (18)	0.04811 (12)	0.2500	0.0214 (3)
C4	0.87504 (19)	0.15129 (13)	0.2500	0.0249 (3)
H4	0.9834	0.1621	0.2500	0.030*
C5	0.77482 (19)	0.23649 (13)	0.2500	0.0247 (3)
H5	0.8150	0.3077	0.2500	0.030*
C6	0.38480 (19)	0.11425 (16)	0.2500	0.0283 (4)
H6A	0.3468 (19)	0.1469 (13)	0.133 (2)	0.040 (5)*
H6B	0.358 (3)	0.0444 (9)	0.2500	0.035 (6)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0389 (7)	0.0217 (6)	0.0322 (7)	0.0136 (5)	0.000	0.000
O2	0.0209 (6)	0.0365 (7)	0.0492 (8)	0.0072 (5)	0.000	0.000
O3	0.0376 (8)	0.0197 (6)	0.0750 (12)	0.0050 (5)	0.000	0.000
N1	0.0277 (7)	0.0182 (6)	0.0210 (6)	0.0033 (5)	0.000	0.000
N2	0.0254 (6)	0.0243 (7)	0.0329 (7)	0.0049 (5)	0.000	0.000
C1	0.0232 (6)	0.0210 (7)	0.0206 (7)	0.0009 (5)	0.000	0.000
C2	0.0211 (7)	0.0170 (6)	0.0228 (7)	−0.0018 (5)	0.000	0.000
C3	0.0214 (7)	0.0182 (6)	0.0247 (7)	0.0023 (5)	0.000	0.000
C4	0.0272 (7)	0.0215 (7)	0.0259 (7)	−0.0047 (6)	0.000	0.000
C5	0.0286 (7)	0.0211 (7)	0.0244 (7)	−0.0050 (6)	0.000	0.000
C6	0.0202 (7)	0.0350 (9)	0.0296 (8)	0.0013 (6)	0.000	0.000

Geometric parameters (Å, º)

O1—N1	1.2902 (17)	C2—C3	1.389 (2)
O2—N2	1.244 (2)	C2—H2A	0.9500
O3—N2	1.233 (2)	C3—C4	1.393 (2)
N1—C5	1.369 (2)	C4—C5	1.369 (2)
N1—C1	1.379 (2)	C4—H4	0.9500
N2—C3	1.454 (2)	C5—H5	0.9500
C1—C2	1.390 (2)	C6—H6A	0.892 (9)
C1—C6	1.482 (2)	C6—H6B	0.898 (10)
O1—N1—C5	119.48 (14)	C2—C3—C4	121.72 (14)
O1—N1—C1	119.61 (14)	C2—C3—N2	119.61 (14)
C5—N1—C1	120.91 (13)	C4—C3—N2	118.68 (14)
O3—N2—O2	123.99 (15)	C5—C4—C3	117.36 (15)
O3—N2—C3	118.73 (14)	C5—C4—H4	121.3
O2—N2—C3	117.28 (14)	C3—C4—H4	121.3
N1—C1—C2	118.79 (14)	N1—C5—C4	121.92 (14)
N1—C1—C6	116.16 (14)	N1—C5—H5	119.0
C2—C1—C6	125.05 (15)	C4—C5—H5	119.0
C3—C2—C1	119.30 (14)	C1—C6—H6A	110.3 (11)
C3—C2—H2A	120.3	C1—C6—H6B	108.0 (16)
C1—C2—H2A	120.3	H6A—C6—H6B	109.9 (14)
O1—N1—C1—C2	180.0	O2—N2—C3—C2	180.0
C5—N1—C1—C2	0.0	O3—N2—C3—C4	180.0
O1—N1—C1—C6	0.0	O2—N2—C3—C4	0.0
C5—N1—C1—C6	180.0	C2—C3—C4—C5	0.0
N1—C1—C2—C3	0.0	N2—C3—C4—C5	180.0
C6—C1—C2—C3	180.0	O1—N1—C5—C4	180.0
C1—C2—C3—C4	0.0	C1—N1—C5—C4	0.0
C1—C2—C3—N2	180.0	C3—C4—C5—N1	0.0
O3—N2—C3—C2	0.0

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2A···O1i	0.95	2.29	3.225 (2)	169
C5—H5···O2ii	0.95	2.36	3.301 (2)	173

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