organic compounds
N-(2-Nitrooxyethyl)picolinamide
aInstituto de Química – UFU, Uberlândia, MG, Brazil, and bDepartamento de Química – UFMG, Belo Horizonte, MG, Brazil
*Correspondence e-mail: silvana@ufu.br
In the title molecule, C8H9N3O4, the amide group is involved in the formation of an intramolecular N—H⋯N hydrogen bond. In the crystal, molecules related by translation along the a axis are linked into chains via weak intermolecular C—H⋯O interactions.
Related literature
For related structures, see: Eremenko et al. (1996); Fedorov et al. (2001). For further synthetic details, see: Samejima (1960); Jiao et al. (1990).
Experimental
Crystal data
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Data collection
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Refinement
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Data collection: COLLECT (Nonius, 2000); cell DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK; 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, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
Supporting information
https://doi.org/10.1107/S1600536811039572/cv5154sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811039572/cv5154Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S1600536811039572/cv5154Isup3.cml
The title product was synthesized by heating ethylnicotinate with an excess 2-ethanolamine to give N-(2-hydroxyethyl)picolinamide in 92% yield (Samejima, 1960). The nitration of N-(2-hydroxyethyl)picolinamide (0.10 mmol) was held by mixing it with fuming nitric acid (1.00 mmol) at -5°C and stirred for 2 h.
The reaction mixture was poured into water and ice, and the pH was adjusted to 6.0 adding (CaCO3). The white solid obtained was filtered at reduced pressure and recrystallized in ethanol, forming the N-(2-nitrooxyethyl)picolinamide in 63% yield (Jiao et al., 1990). MP: 61.2–63.0°C. 1H-NMR (200 MHz, CDCl3): 3.85 (2H, q, J = 5.6 Hz), 4.67 (2H, t, J = 5.2 Hz),7.42–7.48 (1H, m), 7.83–7.90 (1H, m), 8.19 (1H, d, J = 7.9 Hz), 8.39 (1H, br s), 8.56 (1H, d, J = 4.4 Hz). 13C-NMR (200 MHz, CDCl3): 36.7, 71.7, 122.2, 126.4, 137.4, 148.1, 149.11, 164.7.
H atoms were geometrically positioned (C—H 0.93-0.97 Å, N—H 0.86 Å) and refined as riding, with Uiso(H) = 1.2 Ueq of the parent atom. In the absence of significant anomalous scatterers in the molecule, attempts to confirm the
by of the in the presence of 871 sets of Friedel equivalents led to an inconclusive value of -0.2 (13). Therefore, the Friedel pairs were merged before the final refinement.The title compound (I) can be considered as a potential nitric oxide donating drug. Herewith we present its crystal structure.
The molecule of (I) adopts a folded conformation and contains a planar pyridine cycle (NC5H4) bearing a CO group attached to the α-carbon atom (Fig. 1). The dihedral angle between the pyridine ring and the O1/C6/N2 plane is 11.3 (2)°. This angle is smaller than that in the nicorandyl [22.8 (2)°] (Eremenko et al., 1996).The dihedral angle between the mean planes O1/C6/N2/C7 and C8/O2/N3/O3/O4 is 44.74 (7)°. The C═O and CH2–ONO2 bonds are oriented trans to the pyridine nitrogen atom. In the nicorandyl compound these groups were found in the cis position (Eremenko et al., 1996). Another structural isomer (Fedorov et al., 2001), [N-(2-nitrooxyethyl)isonicotinamide], displays a different and crystallizes in the same centrosymmetric P21/c as nicorandil.
The
of (I) is stabilized through weak non-classical intermolecular H-bonds of the type C—H···O in [100] direction, involving the carbon atom of the nitrooxyethyl group and the oxygen atom of carbonylamide. Moreover, were observed one intramolecular interactions of the type N—H···N (Table 1). On the other hand, the compound nicorandil has only one intermolecular interaction of the type N—H···O. The results for compound (I) and its structural isomers show that the position of the ligand in pyridine ring affects the conformation of the molecule and the interactions present in the crystal packing.For related structures, see: Eremenko et al. (1996); Fedorov et al. (2001). For further synthetic details, see: Samejima (1960); Jiao et al. (1990).
Data collection: COLLECT (Nonius, 2000); cell
DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); 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, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).Fig. 1. The molecular structure of (I) showing the atom labeling. Displacement ellipsoids are drawn at the 30% probability level. |
C8H9N3O4 | Dx = 1.475 Mg m−3 |
Mr = 211.18 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 2165 reflections |
a = 5.5075 (2) Å | θ = 2.9–27.5° |
b = 13.6114 (5) Å | µ = 0.12 mm−1 |
c = 12.6822 (4) Å | T = 295 K |
V = 950.72 (6) Å3 | Prism, colourless |
Z = 4 | 0.49 × 0.21 × 0.19 mm |
F(000) = 440 |
Nonius KappaCCD diffractometer | 1039 reflections with I > 2σ(I) |
Radiation source: Enraf–Nonius | Rint = 0.020 |
Graphite monochromator | θmax = 27.5°, θmin = 3.2° |
Detector resolution: 9 pixels mm-1 | h = −7→7 |
CCD rotation images, thick slices scans | k = −16→17 |
4037 measured reflections | l = −15→15 |
1265 independent reflections |
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)] = 0.038 | H-atom parameters constrained |
wR(F2) = 0.108 | w = 1/[σ2(Fo2) + (0.0654P)2 + 0.0645P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max < 0.001 |
1265 reflections | Δρmax = 0.23 e Å−3 |
137 parameters | Δρmin = −0.15 e Å−3 |
0 restraints | Extinction correction: SHELXL |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.124 (13) |
C8H9N3O4 | V = 950.72 (6) Å3 |
Mr = 211.18 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 5.5075 (2) Å | µ = 0.12 mm−1 |
b = 13.6114 (5) Å | T = 295 K |
c = 12.6822 (4) Å | 0.49 × 0.21 × 0.19 mm |
Nonius KappaCCD diffractometer | 1039 reflections with I > 2σ(I) |
4037 measured reflections | Rint = 0.020 |
1265 independent reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.108 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.23 e Å−3 |
1265 reflections | Δρmin = −0.15 e Å−3 |
137 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | −0.1820 (3) | 0.49141 (13) | 0.05722 (14) | 0.0662 (5) | |
O2 | 0.2098 (3) | 0.55263 (11) | −0.11459 (12) | 0.0528 (4) | |
O3 | −0.0499 (4) | 0.67762 (12) | −0.11167 (15) | 0.0705 (5) | |
O4 | −0.1235 (4) | 0.54631 (16) | −0.20249 (14) | 0.0797 (6) | |
N1 | 0.1892 (3) | 0.31135 (13) | 0.17680 (14) | 0.0509 (5) | |
N2 | 0.2136 (4) | 0.49676 (13) | 0.10379 (15) | 0.0532 (5) | |
H | 0.3331 | 0.4648 | 0.1308 | 0.064* | |
N3 | −0.0061 (4) | 0.59684 (13) | −0.14445 (15) | 0.0532 (5) | |
C1 | −0.0042 (4) | 0.34497 (13) | 0.12528 (15) | 0.0430 (5) | |
C2 | 0.1867 (5) | 0.21623 (15) | 0.20374 (19) | 0.0570 (6) | |
H2 | 0.3191 | 0.1914 | 0.2407 | 0.068* | |
C3 | −0.0002 (5) | 0.15319 (15) | 0.17994 (18) | 0.0565 (6) | |
H3 | 0.0066 | 0.0875 | 0.1998 | 0.068* | |
C4 | −0.1974 (5) | 0.18928 (16) | 0.12612 (19) | 0.0561 (6) | |
H4 | −0.3265 | 0.1484 | 0.1086 | 0.067* | |
C5 | −0.2003 (4) | 0.28722 (15) | 0.09855 (18) | 0.0516 (5) | |
H5 | −0.332 | 0.3138 | 0.0626 | 0.062* | |
C6 | −0.0002 (4) | 0.45146 (14) | 0.09262 (15) | 0.0459 (5) | |
C7 | 0.2509 (5) | 0.59775 (15) | 0.07192 (18) | 0.0592 (6) | |
H7A | 0.3618 | 0.629 | 0.1209 | 0.071* | |
H7B | 0.0973 | 0.6325 | 0.0754 | 0.071* | |
C8 | 0.3520 (5) | 0.60631 (17) | −0.03806 (19) | 0.0595 (6) | |
H8A | 0.3569 | 0.6751 | −0.0581 | 0.071* | |
H8B | 0.5171 | 0.5816 | −0.0387 | 0.071* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0545 (10) | 0.0624 (10) | 0.0817 (12) | 0.0089 (8) | −0.0073 (9) | 0.0174 (9) |
O2 | 0.0556 (9) | 0.0472 (7) | 0.0555 (8) | 0.0094 (7) | 0.0037 (7) | 0.0021 (6) |
O3 | 0.0751 (12) | 0.0563 (9) | 0.0800 (12) | 0.0189 (9) | 0.0063 (10) | 0.0087 (9) |
O4 | 0.0799 (13) | 0.0921 (13) | 0.0672 (11) | −0.0228 (11) | −0.0137 (10) | 0.0037 (10) |
N1 | 0.0505 (10) | 0.0471 (9) | 0.0550 (10) | −0.0004 (8) | −0.0099 (9) | 0.0039 (8) |
N2 | 0.0585 (12) | 0.0429 (8) | 0.0581 (11) | −0.0035 (8) | −0.0129 (9) | 0.0069 (8) |
N3 | 0.0538 (11) | 0.0526 (10) | 0.0533 (11) | 0.0014 (9) | 0.0050 (9) | 0.0093 (8) |
C1 | 0.0447 (11) | 0.0457 (10) | 0.0385 (10) | 0.0022 (9) | 0.0016 (9) | −0.0010 (7) |
C2 | 0.0584 (13) | 0.0492 (11) | 0.0633 (14) | 0.0021 (10) | −0.0085 (12) | 0.0074 (10) |
C3 | 0.0685 (15) | 0.0433 (10) | 0.0577 (13) | −0.0026 (11) | 0.0050 (12) | 0.0021 (9) |
C4 | 0.0574 (13) | 0.0521 (12) | 0.0588 (12) | −0.0105 (11) | 0.0019 (11) | −0.0068 (10) |
C5 | 0.0455 (11) | 0.0559 (12) | 0.0534 (12) | −0.0002 (9) | −0.0029 (10) | −0.0011 (9) |
C6 | 0.0491 (12) | 0.0459 (9) | 0.0428 (10) | 0.0022 (9) | −0.0026 (9) | 0.0003 (8) |
C7 | 0.0773 (17) | 0.0433 (10) | 0.0570 (13) | −0.0099 (11) | −0.0131 (12) | 0.0011 (9) |
C8 | 0.0519 (13) | 0.0536 (12) | 0.0728 (16) | −0.0090 (10) | −0.0059 (12) | 0.0097 (11) |
O1—C6 | 1.225 (3) | C2—C3 | 1.374 (3) |
O2—N3 | 1.385 (3) | C2—H2 | 0.93 |
O2—C8 | 1.445 (3) | C3—C4 | 1.374 (4) |
O3—N3 | 1.200 (2) | C3—H3 | 0.93 |
O4—N3 | 1.197 (3) | C4—C5 | 1.378 (3) |
N1—C1 | 1.330 (3) | C4—H4 | 0.93 |
N1—C2 | 1.339 (3) | C5—H5 | 0.93 |
N2—C6 | 1.337 (3) | C7—C8 | 1.506 (3) |
N2—C7 | 1.447 (3) | C7—H7A | 0.97 |
N2—H | 0.86 | C7—H7B | 0.97 |
C1—C5 | 1.378 (3) | C8—H8A | 0.97 |
C1—C6 | 1.508 (3) | C8—H8B | 0.97 |
N3—O2—C8 | 115.41 (16) | C5—C4—H4 | 120.6 |
C1—N1—C2 | 116.73 (19) | C4—C5—C1 | 118.7 (2) |
C6—N2—C7 | 122.2 (2) | C4—C5—H5 | 120.7 |
C6—N2—H | 118.9 | C1—C5—H5 | 120.7 |
C7—N2—H | 118.9 | O1—C6—N2 | 123.66 (18) |
O4—N3—O3 | 129.1 (2) | O1—C6—C1 | 121.03 (18) |
O4—N3—O2 | 112.47 (19) | N2—C6—C1 | 115.30 (18) |
O3—N3—O2 | 118.4 (2) | N2—C7—C8 | 112.60 (19) |
N1—C1—C5 | 123.50 (19) | N2—C7—H7A | 109.1 |
N1—C1—C6 | 116.99 (18) | C8—C7—H7A | 109.1 |
C5—C1—C6 | 119.49 (19) | N2—C7—H7B | 109.1 |
N1—C2—C3 | 123.7 (2) | C8—C7—H7B | 109.1 |
N1—C2—H2 | 118.1 | H7A—C7—H7B | 107.8 |
C3—C2—H2 | 118.1 | O2—C8—C7 | 112.49 (19) |
C4—C3—C2 | 118.6 (2) | O2—C8—H8A | 109.1 |
C4—C3—H3 | 120.7 | C7—C8—H8A | 109.1 |
C2—C3—H3 | 120.7 | O2—C8—H8B | 109.1 |
C3—C4—C5 | 118.8 (2) | C7—C8—H8B | 109.1 |
C3—C4—H4 | 120.6 | H8A—C8—H8B | 107.8 |
C8—O2—N3—O4 | −175.41 (19) | C7—N2—C6—O1 | −1.7 (3) |
C8—O2—N3—O3 | 5.3 (3) | C7—N2—C6—C1 | 177.33 (19) |
C2—N1—C1—C5 | −0.5 (3) | N1—C1—C6—O1 | −170.5 (2) |
C2—N1—C1—C6 | −178.70 (19) | C5—C1—C6—O1 | 11.2 (3) |
C1—N1—C2—C3 | 0.9 (3) | N1—C1—C6—N2 | 10.4 (3) |
N1—C2—C3—C4 | −0.5 (4) | C5—C1—C6—N2 | −167.8 (2) |
C2—C3—C4—C5 | −0.3 (3) | C6—N2—C7—C8 | −94.3 (3) |
C3—C4—C5—C1 | 0.6 (3) | N3—O2—C8—C7 | 76.5 (2) |
N1—C1—C5—C4 | −0.2 (3) | N2—C7—C8—O2 | 52.7 (3) |
C6—C1—C5—C4 | 177.95 (19) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H···N1 | 0.86 | 2.31 | 2.692 (3) | 107 |
C8—H8B···O1i | 0.97 | 2.39 | 3.239 (3) | 145 |
Symmetry code: (i) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C8H9N3O4 |
Mr | 211.18 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 295 |
a, b, c (Å) | 5.5075 (2), 13.6114 (5), 12.6822 (4) |
V (Å3) | 950.72 (6) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.49 × 0.21 × 0.19 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4037, 1265, 1039 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.108, 1.07 |
No. of reflections | 1265 |
No. of parameters | 137 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.23, −0.15 |
Computer programs: COLLECT (Nonius, 2000), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H···N1 | 0.86 | 2.31 | 2.692 (3) | 107.2 |
C8—H8B···O1i | 0.97 | 2.39 | 3.239 (3) | 145.4 |
Symmetry code: (i) x+1, y, z. |
Acknowledgements
The authors thank Professor Dr Javier Ellena of the IFSC, USP, Brazil, for the X-ray data collection. This work was supported financially by FAPEMIG and CNPq.
References
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The title compound (I) can be considered as a potential nitric oxide donating drug. Herewith we present its crystal structure.
The molecule of (I) adopts a folded conformation and contains a planar pyridine cycle (NC5H4) bearing a CO group attached to the α-carbon atom (Fig. 1). The dihedral angle between the pyridine ring and the O1/C6/N2 plane is 11.3 (2)°. This angle is smaller than that in the nicorandyl [22.8 (2)°] (Eremenko et al., 1996).The dihedral angle between the mean planes O1/C6/N2/C7 and C8/O2/N3/O3/O4 is 44.74 (7)°. The C═O and CH2–ONO2 bonds are oriented trans to the pyridine nitrogen atom. In the nicorandyl compound these groups were found in the cis position (Eremenko et al., 1996). Another structural isomer (Fedorov et al., 2001), [N-(2-nitrooxyethyl)isonicotinamide], displays a different molecular conformation and crystallizes in the same centrosymmetric space group P21/c as nicorandil.
The crystal structure of (I) is stabilized through weak non-classical intermolecular H-bonds of the type C—H···O in [100] direction, involving the carbon atom of the nitrooxyethyl group and the oxygen atom of carbonylamide. Moreover, were observed one intramolecular interactions of the type N—H···N (Table 1). On the other hand, the compound nicorandil has only one intermolecular interaction of the type N—H···O. The results for compound (I) and its structural isomers show that the position of the ligand in pyridine ring affects the conformation of the molecule and the interactions present in the crystal packing.