organic compounds
Redetermination of 2-methyl-4-nitropyridine N-oxide
aInstitut für Organische Chemie, TU Bergakademie Freiberg, Leipziger Strasse 29, D-09596 Freiberg/Sachsen, Germany
*Correspondence e-mail: edwin.weber@chemie.tu-freiberg.de
An improved 6H6N2O3, is reported. The structure, previously solved [Li et al. (1987). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24] in the orthorhombic Pca21 and refined to R = 0.067, has been solved in the orthorhombic 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 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 consolidate the stacking of the layers.
of the title compound, CCCDC 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 see: Li et al. (1987). For non-classical hydrogen bonds, see: Desiraju & Steiner (1999).
Experimental
Crystal data
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Data collection: APEX2 (Bruker, 2008); cell 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
10.1107/S1600536814004450/zp2011sup1.cif
contains datablocks I, New_Global_Publ_Block. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814004450/zp2011Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814004450/zp2011Isup3.cml
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.
Aromatic H atoms were positioned geometrically and allowed to ride on their parent atoms, with C—H = 0.95 Å and Uiso = 1.2 Ueq(C).
Data collection: APEX2 (Bruker, 2008); cell
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).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 |
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 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 |
C6H6N2O3 | V = 667.44 (9) Å3 |
Mr = 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 |
Bruker APEXII CCD area-detector diffractometer | 1100 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 973 reflections with I > 2σ(I) |
Tmin = 0.932, Tmax = 0.972 | Rint = 0.028 |
19832 measured reflections |
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 | Δρmax = 0.36 e Å−3 |
1100 reflections | Δρmin = −0.34 e Å−3 |
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. |
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)* |
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 |
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 |
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. |
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
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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···ON-oxide 2.29 Å, 169 °) and nitro groups (C—H···Onitro 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.