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

Peukert, M.; Seichter, W.; Weber, E.

doi:10.1107/S1600536814004450

organic compounds

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Volume 70| Part 4| April 2014| Pages o426-o427

doi:10.1107/S1600536814004450

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

Max Peukert,^a Wilhelm Seichter ^a and Edwin Weber ^a ^*

^aInstitut für Organische Chemie, TU Bergakademie Freiberg, Leipziger Strasse 29, D-09596 Freiberg/Sachsen, Germany
^*Correspondence e-mail: edwin.weber@chemie.tu-freiberg.de

(Received 22 January 2014; accepted 26 February 2014; online 12 March 2014)

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.

CCDC reference: 988898

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, P b c m
a = 8.6775 (7) Å
b = 12.4069 (10) Å
c = 6.1995 (5) Å
V = 667.44 (9) Å³
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[F² > 2σ(F²)] = 0.049
wR(F²) = 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

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) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

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.

Supporting information

CCDC reference: 988898

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S1600536814004450/zp2011sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536814004450/zp2011Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536814004450/zp2011Isup3.cml

checkCIF report

Comment top

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.

Related literature top

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 top

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.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT-NT (Bruker, 2008); data reduction: SAINT-NT (Bruker, 2008); 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 (Sheldrick, 2008).

Figures top

	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.

2-Methyl-4-nitropyridine N-oxide top

Crystal data top

C₆H₆N₂O₃	F(000) = 320
M_r = 154.13	D_x = 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 top

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

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)] = 0.049	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.147	w = 1/[σ²(F_o²) + (0.0871P)² + 0.2298P] where P = (F_o² + 2F_c²)/3
S = 1.10	(Δ/σ)_max < 0.001
1100 reflections	Δρ_max = 0.36 e Å⁻³
74 parameters	Δρ_min = −0.34 e Å⁻³
Primary atom site location: structure-invariant direct methods

Crystal data top

C₆H₆N₂O₃	V = 667.44 (9) Å³
M_r = 154.13	Z = 4
Orthorhombic, Pbcm	Mo Kα radiation
a = 8.6775 (7) Å	µ = 0.13 mm⁻¹
b = 12.4069 (10) Å	T = 153 K
c = 6.1995 (5) Å	0.57 × 0.30 × 0.23 mm

Data collection top

Bruker APEXII CCD area-detector diffractometer	1100 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2008)	973 reflections with I > 2σ(I)
T_min = 0.932, T_max = 0.972	R_int = 0.028
19832 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.049	74 parameters
wR(F²) = 0.147	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.36 e Å⁻³
1100 reflections	Δρ_min = −0.34 e Å⁻³

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. 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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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) top

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) top

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.

Hydrogen-bond geometry (Å, º) top

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.

Acknowledgements

The authors thank the German Research Foundation within the priority programme Porous Metal-Organic Frameworks (SPP 1362, MOFs).

References

Ashimori, A., Ono, T., Uchida, T., Ohtaki, Y., Fukaja, C., Watanabe, M. & Yokoyama, K. (1990). Chem. Pharm. Bull. 38, 2446–2458. CrossRef CAS PubMed Google Scholar
Bruker (2008). APEX2, SAINT-NT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond In Structural Chemistry and Biology, ch. 2. Oxford University Press. Google Scholar
Elemans, J. A. A. W., Lei, S. & De Feyter, S. (2009). Angew. Chem. Int. Ed. 48, 7298–7332. Web of Science CrossRef CAS Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Fontenas, C., Bejan, E., Ait Haddou, H. & Balavoine, G. G. A. (1995). Synth. Commun. 25, 629–633. CrossRef CAS Web of Science Google Scholar
Katritzky, A. R. & Lagowski, J. M. (1971). In Chemistry of the Heterocyclic N-Oxides. New York: Academic Press. Google Scholar
Kilenyi, S. N. (2001). In Encyclopedia of Reagents for Organic Synthesis, edited by L. A. Paquette. New York: Wiley. Google Scholar
Li, S., Liu, S. & Wu, W. (1987). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24. Google Scholar
Mosher, H. S., Turner, L. & Carlsmith, A. (1963). Org. Synth., Coll. Vol. 4, 828–830. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Weber, E. & Vögtle, F. (1976). Chem. Ber. 109, 1803–1831. CrossRef CAS Web of Science Google Scholar
Winter, S., Seichter, W. & Weber, E. (2004). J. Coord. Chem. 57, 991–1014. Web of Science CSD CrossRef Google Scholar