organic compounds
N-(2-Chloroethyl)pyrazine-2-carboxamide
aFundaçao Oswaldo Cruz, Instituto de Tecnologia em Fármacos - Farmanguinhos, R. Sizenando Nabuco 100, Manguinhos, 21041-250, Rio de Janeiro, RJ, Brazil, bCHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY, Scotland, cCentro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Casa Amarela, Campus de Manguinhos, Av. Brasil 4365, 21040-900, Rio de Janeiro, RJ, Brazil, and dDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
*Correspondence e-mail: Edward.Tiekink@gmail.com
In the title molecule, C7H8ClN3O, the pyrazine and amide groups are almost co-planar [N—C—C—N torsion angle = −2.4 (2) °], a conformation stabilized by an intramolecular N—H⋯N hydrogen bond. The chloroethyl group lies out of the plane [N—C—C—Cl = −65.06 (17) °]. In the crystal, the presence of N—H⋯N hydrogen bonds leads to the formation of a C(6) supramolecular chain along the b axis. The carbonyl-O atom accepts two C—H⋯O interactions. These, plus Cl⋯Cl short contacts [3.3653 (6) Å], consolidate the packing of the chains in the crystal.
Related literature
For the antimycobacterial activity of pyrazinamide, see: Chaisson et al. (2002); Gordin et al. (2000); de Souza (2006). For structural studies on pyrazinamide derivatives; see: Wardell et al. (2008); Baddeley et al. (2009); Howie et al. (2010a,b,c,d).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Hooft, 1998); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).
Supporting information
https://doi.org/10.1107/S1600536810041656/hb5682sup1.cif
contains datablocks general, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810041656/hb5682Isup2.hkl
The title compound was prepared by refluxing a mixture of thionyl chloride (1 ml) and N-(2-chloroethyl)pyrazine-2-carboxamide (0.2 g), obtained from methyl 2-pyrazinecarboxylate, ethanolamine and triethylamine. After 6 h, the excess thionyl chloride was removed under reduced pressure, the residue extracted into ethyl acetate (20 ml) and washed with saturated sodium bicarbonate solution (60 ml). The organic phase was dried over Na2SO4 and concentrated under reduced pressure to afford title compound, yield: 70%; m. pt.: 384–386 K. The crystals used in the
were grown from EtOH solution.1H NMR (200 MHz, DMSO-d6) δ: 9.19 (1H, s, H3), 9.12 (1H, s, NH), 8.88 (1H, s, H6), 8.74 (1H, s, H5), 3.76–3.63 (4H, m, CH2CH2Cl). 13C NMR (50 MHz, DMSO-d6) δ: 153.8, 138.4, 135.2, 134.3, 134.1, 33.6, 31.6 p.p.m.. MS/ESI: [M—H]: 184.
The C-bound H atoms were geometrically placed (C–H = 0.95–0.99 Å) and refined as riding with Uiso(H) = 1.2Ueq(C). The N-bound H atom was located from a difference map and refined with the distance restraint N–H = 0.88±0.01 Å, and with Uiso(H) = 1.2Ueq(N).
Pyrazinamide has well known anti-mycobacterial activity and is the one of the most important drugs used in tuberculosis treatment (Chaisson et al., 2002; Gordin et al., 2000; de Souza, 2006). In continuation of our studies on pyrazinamide derivatives (Wardell et al., 2008; Baddeley et al., 2009; Howie et al., 2010a, 2010b, 2010c, 2010d), we report the structure of title compound, (I).
The pyrazine and amide groups are co-planar as seen in the value of the N1—C1—C2—N2 torsion angle of -2.4 (2) °, a conformation stabilized by an intramolecular N1—H···N2 hydrogen bond, Table 1. The ethyl group lies out of the plane through the rest of the molecule as seen in the N1—C6—C7—Cl1 torsion angle of -65.06 (17) °. The carbonyl-O1 lies to the opposite side of the molecule occupied by the amide and chlorido atoms.
In the crystal packing, the most prominent interactions are hydrogen bonding interactions of the type N—H···N, Table 1, which lead to a supramolecular chain along the screw axis, Fig. 2. The chains are connected into the 3-D structure by C—H···O interactions, involving the bifurcated carbonyl-O atom interacting with two methylene-H atoms, Table 1, and Cl···Cl contacts [Cl1···Cl1i = 3.3653 (6) Å for i: 1 - x, 1 - y, 1 - z], Fig. 3.
For the antimycobacterial activity of pyrazinamide, see: Chaisson et al. (2002); Gordin et al. (2000); de Souza (2006). For structural studies on pyrazinamide derivatives; see: Wardell et al. (2008); Baddeley et al. (2009); Howie et al. (2010a,b,c,d).
Data collection: COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010).Fig. 1. The molecular structure of (I) showing displacement ellipsoids at the 50% probability level. | |
Fig. 2. Supramolecular chain in (I) aligned along the b axis. The N—H···N hydrogen bonds are shown as blue dashed lines. | |
Fig. 3. A view in projection down the a axis of the crystal packing in (I). The N—H···N hydrogen bonds, and C—H···O and Cl···Cl contacts are shown as blue, orange and green dashed lines, respectively. |
C7H8ClN3O | F(000) = 384 |
Mr = 185.61 | Dx = 1.491 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 25954 reflections |
a = 4.4639 (2) Å | θ = 2.9–27.5° |
b = 10.6865 (6) Å | µ = 0.41 mm−1 |
c = 17.3583 (9) Å | T = 120 K |
β = 93.028 (3)° | Prism, colourless |
V = 826.89 (7) Å3 | 0.28 × 0.18 × 0.03 mm |
Z = 4 |
Nonius KappaCCD diffractometer | 1867 independent reflections |
Radiation source: Enraf Nonius FR591 rotating anode | 1628 reflections with I > 2σ(I) |
10 cm confocal mirrors monochromator | Rint = 0.044 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.0° |
φ and ω scans | h = −5→5 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2007) | k = −13→13 |
Tmin = 0.631, Tmax = 0.746 | l = −22→22 |
16245 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.110 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.15 | w = 1/[σ2(Fo2) + (0.0577P)2 + 0.3276P] where P = (Fo2 + 2Fc2)/3 |
1867 reflections | (Δ/σ)max < 0.001 |
112 parameters | Δρmax = 0.23 e Å−3 |
1 restraint | Δρmin = −0.37 e Å−3 |
C7H8ClN3O | V = 826.89 (7) Å3 |
Mr = 185.61 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 4.4639 (2) Å | µ = 0.41 mm−1 |
b = 10.6865 (6) Å | T = 120 K |
c = 17.3583 (9) Å | 0.28 × 0.18 × 0.03 mm |
β = 93.028 (3)° |
Nonius KappaCCD diffractometer | 1867 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2007) | 1628 reflections with I > 2σ(I) |
Tmin = 0.631, Tmax = 0.746 | Rint = 0.044 |
16245 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | 1 restraint |
wR(F2) = 0.110 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.15 | Δρmax = 0.23 e Å−3 |
1867 reflections | Δρmin = −0.37 e Å−3 |
112 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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 | ||
Cl1 | 0.65306 (10) | 0.64380 (4) | 0.49830 (2) | 0.02780 (17) | |
O1 | 0.7056 (3) | 1.04630 (12) | 0.60138 (7) | 0.0247 (3) | |
N1 | 0.8112 (3) | 0.84349 (13) | 0.63161 (8) | 0.0195 (3) | |
H1n | 0.785 (5) | 0.7824 (15) | 0.6637 (10) | 0.028* | |
N2 | 0.4415 (3) | 0.85341 (14) | 0.75082 (8) | 0.0222 (3) | |
N3 | 0.1647 (4) | 1.07915 (15) | 0.78848 (9) | 0.0275 (4) | |
C1 | 0.6754 (4) | 0.95343 (16) | 0.64249 (9) | 0.0182 (3) | |
C2 | 0.4763 (4) | 0.95775 (15) | 0.70976 (9) | 0.0180 (3) | |
C3 | 0.2635 (4) | 0.86226 (18) | 0.80989 (10) | 0.0249 (4) | |
H3 | 0.2273 | 0.7897 | 0.8396 | 0.030* | |
C4 | 0.1292 (4) | 0.97467 (19) | 0.82923 (10) | 0.0264 (4) | |
H4 | 0.0087 | 0.9772 | 0.8727 | 0.032* | |
C5 | 0.3352 (4) | 1.06922 (17) | 0.72769 (10) | 0.0229 (4) | |
H5 | 0.3607 | 1.1403 | 0.6959 | 0.028* | |
C6 | 1.0072 (4) | 0.82477 (17) | 0.56832 (9) | 0.0212 (4) | |
H6A | 1.1499 | 0.7565 | 0.5821 | 0.025* | |
H6B | 1.1252 | 0.9020 | 0.5613 | 0.025* | |
C7 | 0.8395 (4) | 0.79260 (17) | 0.49280 (10) | 0.0232 (4) | |
H7A | 0.9823 | 0.7900 | 0.4511 | 0.028* | |
H7B | 0.6894 | 0.8586 | 0.4799 | 0.028* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0327 (3) | 0.0252 (3) | 0.0255 (3) | −0.00579 (17) | 0.00184 (18) | −0.00416 (17) |
O1 | 0.0294 (7) | 0.0222 (7) | 0.0229 (6) | −0.0018 (5) | 0.0045 (5) | 0.0058 (5) |
N1 | 0.0221 (7) | 0.0200 (8) | 0.0164 (7) | −0.0010 (6) | 0.0025 (5) | 0.0017 (5) |
N2 | 0.0248 (8) | 0.0230 (8) | 0.0190 (7) | −0.0010 (6) | 0.0023 (6) | 0.0019 (6) |
N3 | 0.0312 (8) | 0.0271 (9) | 0.0245 (8) | −0.0003 (6) | 0.0048 (6) | −0.0055 (6) |
C1 | 0.0173 (7) | 0.0210 (8) | 0.0163 (7) | −0.0040 (6) | −0.0011 (6) | −0.0017 (6) |
C2 | 0.0190 (8) | 0.0194 (8) | 0.0152 (7) | −0.0036 (6) | −0.0014 (6) | −0.0013 (6) |
C3 | 0.0293 (9) | 0.0279 (10) | 0.0179 (8) | −0.0026 (7) | 0.0042 (7) | 0.0026 (7) |
C4 | 0.0282 (9) | 0.0333 (10) | 0.0181 (8) | −0.0029 (8) | 0.0047 (7) | −0.0031 (7) |
C5 | 0.0272 (9) | 0.0211 (9) | 0.0206 (8) | −0.0024 (7) | 0.0028 (7) | −0.0015 (7) |
C6 | 0.0189 (8) | 0.0253 (9) | 0.0199 (8) | −0.0018 (7) | 0.0046 (6) | −0.0006 (7) |
C7 | 0.0273 (9) | 0.0237 (9) | 0.0190 (8) | −0.0025 (7) | 0.0044 (7) | 0.0011 (7) |
Cl1—C7 | 1.7997 (19) | C2—C5 | 1.390 (2) |
O1—C1 | 1.234 (2) | C3—C4 | 1.391 (3) |
N1—C1 | 1.340 (2) | C3—H3 | 0.9500 |
N1—C6 | 1.454 (2) | C4—H4 | 0.9500 |
N1—H1n | 0.870 (10) | C5—H5 | 0.9500 |
N2—C3 | 1.334 (2) | C6—C7 | 1.514 (2) |
N2—C2 | 1.337 (2) | C6—H6A | 0.9900 |
N3—C4 | 1.336 (3) | C6—H6B | 0.9900 |
N3—C5 | 1.338 (2) | C7—H7A | 0.9900 |
C1—C2 | 1.505 (2) | C7—H7B | 0.9900 |
C1—N1—C6 | 121.46 (14) | C3—C4—H4 | 119.0 |
C1—N1—H1N | 119.4 (14) | N3—C5—C2 | 121.86 (17) |
C6—N1—H1N | 119.1 (14) | N3—C5—H5 | 119.1 |
C3—N2—C2 | 116.20 (15) | C2—C5—H5 | 119.1 |
C4—N3—C5 | 116.09 (16) | N1—C6—C7 | 113.30 (14) |
O1—C1—N1 | 124.03 (15) | N1—C6—H6A | 108.9 |
O1—C1—C2 | 120.73 (15) | C7—C6—H6A | 108.9 |
N1—C1—C2 | 115.24 (14) | N1—C6—H6B | 108.9 |
N2—C2—C5 | 121.91 (15) | C7—C6—H6B | 108.9 |
N2—C2—C1 | 118.55 (15) | H6A—C6—H6B | 107.7 |
C5—C2—C1 | 119.53 (15) | C6—C7—Cl1 | 111.32 (12) |
N2—C3—C4 | 121.91 (17) | C6—C7—H7A | 109.4 |
N2—C3—H3 | 119.0 | Cl1—C7—H7A | 109.4 |
C4—C3—H3 | 119.0 | C6—C7—H7B | 109.4 |
N3—C4—C3 | 121.95 (16) | Cl1—C7—H7B | 109.4 |
N3—C4—H4 | 119.0 | H7A—C7—H7B | 108.0 |
C6—N1—C1—O1 | −0.6 (2) | C2—N2—C3—C4 | −2.0 (3) |
C6—N1—C1—C2 | 179.20 (13) | C5—N3—C4—C3 | 0.4 (3) |
C3—N2—C2—C5 | 0.1 (2) | N2—C3—C4—N3 | 1.8 (3) |
C3—N2—C2—C1 | 179.85 (15) | C4—N3—C5—C2 | −2.3 (3) |
O1—C1—C2—N2 | 177.44 (15) | N2—C2—C5—N3 | 2.2 (3) |
N1—C1—C2—N2 | −2.4 (2) | C1—C2—C5—N3 | −177.58 (15) |
O1—C1—C2—C5 | −2.8 (2) | C1—N1—C6—C7 | −83.3 (2) |
N1—C1—C2—C5 | 177.37 (15) | N1—C6—C7—Cl1 | −65.06 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1n···N2 | 0.87 (2) | 2.34 (2) | 2.7162 (19) | 107 (1) |
N1—H1n···N3i | 0.87 (2) | 2.33 (2) | 3.146 (2) | 156 (2) |
C5—H5···N2ii | 0.95 | 2.60 | 3.212 (2) | 123 |
C7—H7A···O1iii | 0.99 | 2.44 | 3.180 (2) | 131 |
C7—H7B···O1iv | 0.99 | 2.42 | 3.337 (2) | 153 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x+1, y+1/2, −z+3/2; (iii) −x+2, −y+2, −z+1; (iv) −x+1, −y+2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C7H8ClN3O |
Mr | 185.61 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 120 |
a, b, c (Å) | 4.4639 (2), 10.6865 (6), 17.3583 (9) |
β (°) | 93.028 (3) |
V (Å3) | 826.89 (7) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.41 |
Crystal size (mm) | 0.28 × 0.18 × 0.03 |
Data collection | |
Diffractometer | Nonius KappaCCD |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2007) |
Tmin, Tmax | 0.631, 0.746 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16245, 1867, 1628 |
Rint | 0.044 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.110, 1.15 |
No. of reflections | 1867 |
No. of parameters | 112 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.23, −0.37 |
Computer programs: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and DIAMOND (Brandenburg, 2006), publCIF (Westrip, 2010).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1n···N2 | 0.870 (17) | 2.34 (2) | 2.7162 (19) | 106.6 (14) |
N1—H1n···N3i | 0.870 (17) | 2.332 (16) | 3.146 (2) | 155.9 (17) |
C5—H5···N2ii | 0.95 | 2.60 | 3.212 (2) | 123 |
C7—H7A···O1iii | 0.99 | 2.44 | 3.180 (2) | 131 |
C7—H7B···O1iv | 0.99 | 2.42 | 3.337 (2) | 153 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x+1, y+1/2, −z+3/2; (iii) −x+2, −y+2, −z+1; (iv) −x+1, −y+2, −z+1. |
Footnotes
‡Additional correspondence author, e-mail: j.wardell@abdn.ac.uk.
Acknowledgements
The use of the EPSRC X-ray crystallographic service at the University of Southampton, England, and the valuable assistance of the staff there is gratefully acknowledged. JLW acknowledges support from CAPES (Brazil).
References
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Pyrazinamide has well known anti-mycobacterial activity and is the one of the most important drugs used in tuberculosis treatment (Chaisson et al., 2002; Gordin et al., 2000; de Souza, 2006). In continuation of our studies on pyrazinamide derivatives (Wardell et al., 2008; Baddeley et al., 2009; Howie et al., 2010a, 2010b, 2010c, 2010d), we report the structure of title compound, (I).
The pyrazine and amide groups are co-planar as seen in the value of the N1—C1—C2—N2 torsion angle of -2.4 (2) °, a conformation stabilized by an intramolecular N1—H···N2 hydrogen bond, Table 1. The ethyl group lies out of the plane through the rest of the molecule as seen in the N1—C6—C7—Cl1 torsion angle of -65.06 (17) °. The carbonyl-O1 lies to the opposite side of the molecule occupied by the amide and chlorido atoms.
In the crystal packing, the most prominent interactions are hydrogen bonding interactions of the type N—H···N, Table 1, which lead to a supramolecular chain along the screw axis, Fig. 2. The chains are connected into the 3-D structure by C—H···O interactions, involving the bifurcated carbonyl-O atom interacting with two methylene-H atoms, Table 1, and Cl···Cl contacts [Cl1···Cl1i = 3.3653 (6) Å for i: 1 - x, 1 - y, 1 - z], Fig. 3.