Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807030036/gk2089sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807030036/gk2089Isup2.hkl |
CCDC reference: 655023
Key indicators
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C)= 0.003 Å
- R factor = 0.030
- wR factor = 0.083
- Data-to-parameter ratio = 10.2
checkCIF/PLATON results
No syntax errors found No errors found in this datablock
For previously reported polymorphs of the title compound, see: Takusagawa et al. (1974), Shi et al. (2006). For applications of pyrazine-2-carboxylic acid, see: Wieser et al. (1997), Shul'pin & Suss-Fink (1995).
Commercially available 2-pyrazinic acid (CAS: 98–97-5) was recrystallized from saturated water solution.
The C bonded hydrogen atoms were placed in calculated positions after four cycles of anisotropic refinement and were refined as riding on adjacent carbon atom with Uiso(H) = 1.2Ueq(C). The O bonded H atom was found in a difference Fourier synthesis after four cycles of anisotropic refinement and was refined as riding on adjacent O atom with Uiso(H) = 1.5Ueq(O).
The pyrazine-2-carboxylic acid is a one of the most common substances used for synthesis of pyrazine derivatives, which are important due to their bacteriostatic activity (Shi et al., 2006), antituberculous activity (Wieser et al., 1997) and selective oxidizing properties toward alkanes, benzene and alcohols (Shul'pin & Suss-Fink, 1995).
The title compound was reported in two polymorphic forms: orthorhombic, space group Pna21, (Ia) (Takusagawa et al., 1974), and monoclinic, space group P21, (Ib) (Shi et al., 2006). The structure of the polymorph (Ia) was determined by photographic methods and, based on solution derived from a sharpened Patterson map, the Pna21 space group was chosen as the correct one. However closer inspection of the atomic coordinates shows that the entire molecule is located on a mirror plane perpendicular to the z axis.
We have redetermined the crystal structure of the polymorph (Ia) in the Pnma space group at 150 K. Our results show that for the earlier reported crystal structure the choice of non-centrosymmetric space group was incorrect.
In (Ia) all atoms lie on a symmetry plane. The molecules are connected via O1—H1O···N2 hydrogen bonds (Table 1) into a zigzag chain extending along the [100] direction and further through C—H···O interactions (Table 1) into a sheet parallel to the (010) plane. This sheet is nearly identical to that observed in the polymorph (Ib). The main structural difference between the two polymorphs is in stacking of the adjacent sheets: in (Ib) they are related by a translation along the a axis (3.7249 (14) Å) whereas in (Ia) they are related by a 21 screw axis parallel to b. In the first case the sheet packing leads to face-to-face stacking interactions of the aromatic rings whereas in (Ia) no stacking interactions are observed as the closest distance between the ring centroids is 5.1427 (10) Å.
For previously reported polymorphs of the title compound, see: Takusagawa et al. (1974), Shi et al. (2006). For applications of pyrazine-2-carboxylic acid, see: Wieser et al. (1997), Shul'pin & Suss-Fink (1995).
Data collection: CrysAlis CCD (UNILIC & Kuma, 2000); cell refinement: CrysAlis RED (UNILIC & Kuma, 2000); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP in SHELXTL/PC (Sheldrick, 1990) and ORTEP-3 (Version 1.062; Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 1990).
C5H4N2O2 | F(000) = 256 |
Mr = 124.10 | Dx = 1.570 Mg m−3 |
Orthorhombic, Pnma | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2n | Cell parameters from 984 reflections |
a = 11.3261 (18) Å | θ = 3–20° |
b = 6.3180 (12) Å | µ = 0.13 mm−1 |
c = 7.3389 (11) Å | T = 150 K |
V = 525.16 (15) Å3 | Prism, colourless |
Z = 4 | 0.20 × 0.08 × 0.05 mm |
Kuma KM-4-CCD diffractometer | 561 independent reflections |
Radiation source: fine-focus sealed tube | 399 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.028 |
Detector resolution: 1048576 pixels mm-1 | θmax = 26.0°, θmin = 3.3° |
ω scans | h = −13→12 |
Absorption correction: numerical (X-RED; Stoe & Cie, 1999) | k = −7→6 |
Tmin = 0.990, Tmax = 0.999 | l = −9→9 |
3291 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: structure-invariant direct methods |
R[F2 > 2σ(F2)] = 0.030 | Hydrogen site location: mixed |
wR(F2) = 0.083 | H-atom parameters constrained |
S = 0.96 | w = 1/[σ2(Fo2) + (0.0564P)2] where P = (Fo2 + 2Fc2)/3 |
561 reflections | (Δ/σ)max = 0.003 |
55 parameters | Δρmax = 0.12 e Å−3 |
0 restraints | Δρmin = −0.30 e Å−3 |
C5H4N2O2 | V = 525.16 (15) Å3 |
Mr = 124.10 | Z = 4 |
Orthorhombic, Pnma | Mo Kα radiation |
a = 11.3261 (18) Å | µ = 0.13 mm−1 |
b = 6.3180 (12) Å | T = 150 K |
c = 7.3389 (11) Å | 0.20 × 0.08 × 0.05 mm |
Kuma KM-4-CCD diffractometer | 561 independent reflections |
Absorption correction: numerical (X-RED; Stoe & Cie, 1999) | 399 reflections with I > 2σ(I) |
Tmin = 0.990, Tmax = 0.999 | Rint = 0.028 |
3291 measured reflections |
R[F2 > 2σ(F2)] = 0.030 | 0 restraints |
wR(F2) = 0.083 | H-atom parameters constrained |
S = 0.96 | Δρmax = 0.12 e Å−3 |
561 reflections | Δρmin = −0.30 e Å−3 |
55 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 | ||
O2 | −0.13159 (11) | 0.2500 | 0.57951 (18) | 0.0269 (4) | |
O1 | −0.00947 (12) | 0.2500 | 0.82097 (18) | 0.0286 (4) | |
H1O | −0.0764 | 0.2500 | 0.8797 | 0.043* | |
N1 | 0.05965 (14) | 0.2500 | 0.3485 (2) | 0.0239 (4) | |
N2 | 0.28508 (14) | 0.2500 | 0.5024 (2) | 0.0249 (4) | |
C1 | 0.07595 (16) | 0.2500 | 0.5291 (3) | 0.0209 (5) | |
C2 | 0.18758 (17) | 0.2500 | 0.6053 (3) | 0.0227 (5) | |
H2 | 0.1951 | 0.2500 | 0.7315 | 0.027* | |
C3 | 0.26968 (18) | 0.2500 | 0.3227 (3) | 0.0247 (5) | |
H3 | 0.3353 | 0.2500 | 0.2465 | 0.030* | |
C4 | 0.15758 (17) | 0.2500 | 0.2468 (3) | 0.0254 (5) | |
H4 | 0.1502 | 0.2500 | 0.1206 | 0.031* | |
C5 | −0.03326 (18) | 0.2500 | 0.6448 (3) | 0.0223 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O2 | 0.0166 (8) | 0.0410 (9) | 0.0232 (8) | 0.000 | −0.0006 (6) | 0.000 |
O1 | 0.0170 (7) | 0.0515 (9) | 0.0174 (8) | 0.000 | 0.0006 (6) | 0.000 |
N1 | 0.0215 (10) | 0.0315 (9) | 0.0185 (9) | 0.000 | −0.0003 (6) | 0.000 |
N2 | 0.0190 (9) | 0.0377 (10) | 0.0181 (9) | 0.000 | 0.0019 (7) | 0.000 |
C1 | 0.0192 (10) | 0.0254 (10) | 0.0181 (10) | 0.000 | 0.0000 (8) | 0.000 |
C2 | 0.0192 (10) | 0.0333 (11) | 0.0156 (10) | 0.000 | −0.0003 (8) | 0.000 |
C3 | 0.0206 (10) | 0.0340 (11) | 0.0194 (11) | 0.000 | 0.0033 (8) | 0.000 |
C4 | 0.0254 (12) | 0.0341 (11) | 0.0168 (10) | 0.000 | 0.0008 (8) | 0.000 |
C5 | 0.0200 (10) | 0.0272 (11) | 0.0196 (10) | 0.000 | −0.0006 (8) | 0.000 |
O2—C5 | 1.212 (2) | C1—C2 | 1.382 (3) |
O1—C5 | 1.321 (2) | C1—C5 | 1.500 (3) |
O1—H1O | 0.8718 | C2—H2 | 0.9300 |
N1—C4 | 1.337 (3) | C3—C4 | 1.386 (3) |
N1—C1 | 1.338 (2) | C3—H3 | 0.9300 |
N2—C3 | 1.330 (3) | C4—H4 | 0.9300 |
N2—C2 | 1.338 (2) | ||
C5—O1—H1O | 107.9 | N2—C3—C4 | 121.22 (19) |
C4—N1—C1 | 116.02 (16) | N2—C3—H3 | 119.4 |
C3—N2—C2 | 116.84 (17) | C4—C3—H3 | 119.4 |
N1—C1—C2 | 121.79 (17) | N1—C4—C3 | 122.36 (19) |
N1—C1—C5 | 116.53 (17) | N1—C4—H4 | 118.8 |
C2—C1—C5 | 121.68 (18) | C3—C4—H4 | 118.8 |
N2—C2—C1 | 121.77 (18) | O2—C5—O1 | 125.05 (19) |
N2—C2—H2 | 119.1 | O2—C5—C1 | 122.27 (17) |
C1—C2—H2 | 119.1 | O1—C5—C1 | 112.69 (17) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O···N2i | 0.87 | 1.79 | 2.664 (2) | 179 |
C2—H2···O1 | 0.93 | 2.41 | 2.736 (2) | 101 |
C2—H2···O2ii | 0.93 | 2.40 | 3.089 (2) | 131 |
C3—H3···O2iii | 0.93 | 2.42 | 3.156 (2) | 136 |
Symmetry codes: (i) x−1/2, y, −z+3/2; (ii) x+1/2, y, −z+3/2; (iii) x+1/2, y, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C5H4N2O2 |
Mr | 124.10 |
Crystal system, space group | Orthorhombic, Pnma |
Temperature (K) | 150 |
a, b, c (Å) | 11.3261 (18), 6.3180 (12), 7.3389 (11) |
V (Å3) | 525.16 (15) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.20 × 0.08 × 0.05 |
Data collection | |
Diffractometer | Kuma KM-4-CCD |
Absorption correction | Numerical (X-RED; Stoe & Cie, 1999) |
Tmin, Tmax | 0.990, 0.999 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3291, 561, 399 |
Rint | 0.028 |
(sin θ/λ)max (Å−1) | 0.616 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.030, 0.083, 0.96 |
No. of reflections | 561 |
No. of parameters | 55 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.12, −0.30 |
Computer programs: CrysAlis CCD (UNILIC & Kuma, 2000), CrysAlis RED (UNILIC & Kuma, 2000), CrysAlis RED, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), XP in SHELXTL/PC (Sheldrick, 1990) and ORTEP-3 (Version 1.062; Farrugia, 1997), SHELXL97 and PLATON (Spek, 1990).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O···N2i | 0.87 | 1.79 | 2.664 (2) | 179.2 |
C2—H2···O1 | 0.93 | 2.41 | 2.736 (2) | 100.6 |
C2—H2···O2ii | 0.93 | 2.40 | 3.089 (2) | 130.5 |
C3—H3···O2iii | 0.93 | 2.42 | 3.156 (2) | 135.8 |
Symmetry codes: (i) x−1/2, y, −z+3/2; (ii) x+1/2, y, −z+3/2; (iii) x+1/2, y, −z+1/2. |
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The pyrazine-2-carboxylic acid is a one of the most common substances used for synthesis of pyrazine derivatives, which are important due to their bacteriostatic activity (Shi et al., 2006), antituberculous activity (Wieser et al., 1997) and selective oxidizing properties toward alkanes, benzene and alcohols (Shul'pin & Suss-Fink, 1995).
The title compound was reported in two polymorphic forms: orthorhombic, space group Pna21, (Ia) (Takusagawa et al., 1974), and monoclinic, space group P21, (Ib) (Shi et al., 2006). The structure of the polymorph (Ia) was determined by photographic methods and, based on solution derived from a sharpened Patterson map, the Pna21 space group was chosen as the correct one. However closer inspection of the atomic coordinates shows that the entire molecule is located on a mirror plane perpendicular to the z axis.
We have redetermined the crystal structure of the polymorph (Ia) in the Pnma space group at 150 K. Our results show that for the earlier reported crystal structure the choice of non-centrosymmetric space group was incorrect.
In (Ia) all atoms lie on a symmetry plane. The molecules are connected via O1—H1O···N2 hydrogen bonds (Table 1) into a zigzag chain extending along the [100] direction and further through C—H···O interactions (Table 1) into a sheet parallel to the (010) plane. This sheet is nearly identical to that observed in the polymorph (Ib). The main structural difference between the two polymorphs is in stacking of the adjacent sheets: in (Ib) they are related by a translation along the a axis (3.7249 (14) Å) whereas in (Ia) they are related by a 21 screw axis parallel to b. In the first case the sheet packing leads to face-to-face stacking interactions of the aromatic rings whereas in (Ia) no stacking interactions are observed as the closest distance between the ring centroids is 5.1427 (10) Å.