| Literature DB >> 21578333 |
Jing Miao1, Maomao Jia, Xianlin Liu, Wei Xiong, Zilu Chen.
Abstract
In the structure of the title compound, C(8)H(7)N(5)O, the pyridine ring and the imidazole ring are nearly coplanar, making a dihedral angle of 2.97 (15)°. An intra-molecular N-H⋯O hydrogen bond occurs. In the crystal mol-ecules are connected by inter-molecular hydrogen bonds and π-π stacking inter-actions between neighboring imidazole rings [centroid-centroid distance = 3.5842 (5) Å and off-set angle = 21.77°], leading to the formation of a two-dimensional supra-molecular sheet.Entities:
Year: 2009 PMID: 21578333 PMCID: PMC2970976 DOI: 10.1107/S1600536809041269
Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN: 1600-5368
| C8H7N5O | |
| Monoclinic, | Mo |
| Hall symbol: -P 2yn | Cell parameters from 1623 reflections |
| θ = 3.0–28.0° | |
| µ = 0.11 mm−1 | |
| β = 90.700 (3)° | Block, colorless |
| 0.26 × 0.24 × 0.18 mm | |
| Bruker APEXII CCD area-detector diffractometer | 1443 independent reflections |
| Radiation source: fine-focus sealed tube | 961 reflections with |
| graphite | |
| φ and ω scans | θmax = 25.0°, θmin = 2.3° |
| Absorption correction: multi-scan ( | |
| 3938 measured reflections |
| Refinement on | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| H-atom parameters constrained | |
| (Δ/σ)max < 0.001 | |
| 1443 reflections | Δρmax = 0.17 e Å−3 |
| 128 parameters | Δρmin = −0.16 e Å−3 |
| 0 restraints | Extinction correction: |
| Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.024 (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 |
| N1 | 0.6956 (2) | 0.7443 (3) | 0.35815 (9) | 0.0470 (5) | |
| N2 | 0.77449 (17) | 0.4023 (3) | 0.46730 (8) | 0.0410 (5) | |
| H21 | 0.8406 | 0.5181 | 0.4539 | 0.061* | |
| C5 | 0.5911 (2) | 0.5707 (4) | 0.37611 (10) | 0.0389 (5) | |
| C6 | 0.6318 (2) | 0.3877 (4) | 0.43697 (10) | 0.0391 (5) | |
| N4 | 0.74724 (18) | 0.0445 (3) | 0.54961 (8) | 0.0438 (5) | |
| H41 | 0.6579 | −0.0130 | 0.5370 | 0.066* | |
| N5 | 0.83128 (19) | −0.0771 (3) | 0.60411 (9) | 0.0481 (5) | |
| N3 | 0.96153 (18) | 0.2595 (3) | 0.55752 (9) | 0.0454 (5) | |
| C3 | 0.4141 (3) | 0.7178 (5) | 0.28387 (12) | 0.0529 (7) | |
| H3 | 0.3198 | 0.7083 | 0.2589 | 0.063* | |
| C4 | 0.4492 (2) | 0.5512 (4) | 0.34098 (11) | 0.0478 (6) | |
| H4 | 0.3789 | 0.4286 | 0.3555 | 0.057* | |
| C1 | 0.6574 (3) | 0.9042 (4) | 0.30331 (12) | 0.0547 (6) | |
| H1 | 0.7281 | 1.0284 | 0.2905 | 0.066* | |
| C7 | 0.8255 (2) | 0.2395 (4) | 0.52329 (11) | 0.0380 (5) | |
| C2 | 0.5196 (3) | 0.8965 (5) | 0.26449 (12) | 0.0534 (7) | |
| H2 | 0.4990 | 1.0104 | 0.2260 | 0.064* | |
| C8 | 0.9568 (2) | 0.0599 (4) | 0.60561 (11) | 0.0490 (6) | |
| H8 | 1.0385 | 0.0229 | 0.6379 | 0.059* | |
| O1 | 0.53795 (16) | 0.2298 (3) | 0.45747 (8) | 0.0520 (5) |
| N1 | 0.0448 (11) | 0.0521 (13) | 0.0439 (10) | −0.0024 (9) | −0.0056 (8) | 0.0052 (10) |
| N2 | 0.0348 (10) | 0.0466 (12) | 0.0414 (10) | −0.0067 (8) | −0.0051 (8) | 0.0074 (9) |
| C5 | 0.0382 (12) | 0.0424 (13) | 0.0360 (11) | 0.0004 (10) | −0.0015 (9) | −0.0021 (10) |
| C6 | 0.0346 (11) | 0.0436 (14) | 0.0390 (12) | −0.0060 (10) | −0.0031 (9) | −0.0033 (10) |
| N4 | 0.0371 (10) | 0.0510 (13) | 0.0431 (10) | −0.0086 (9) | −0.0042 (8) | 0.0068 (9) |
| N5 | 0.0419 (10) | 0.0541 (13) | 0.0481 (10) | −0.0055 (10) | −0.0077 (8) | 0.0132 (9) |
| N3 | 0.0391 (10) | 0.0500 (12) | 0.0469 (10) | −0.0077 (9) | −0.0092 (8) | 0.0089 (9) |
| C3 | 0.0490 (14) | 0.0611 (18) | 0.0482 (13) | 0.0082 (12) | −0.0150 (11) | −0.0033 (12) |
| C4 | 0.0438 (13) | 0.0529 (15) | 0.0465 (13) | −0.0028 (11) | −0.0065 (10) | −0.0015 (11) |
| C1 | 0.0580 (15) | 0.0517 (16) | 0.0542 (14) | −0.0055 (12) | −0.0027 (11) | 0.0127 (12) |
| C7 | 0.0320 (11) | 0.0441 (14) | 0.0379 (11) | −0.0058 (10) | −0.0014 (9) | −0.0008 (10) |
| C2 | 0.0620 (16) | 0.0542 (17) | 0.0439 (12) | 0.0088 (13) | −0.0074 (11) | 0.0059 (12) |
| C8 | 0.0438 (13) | 0.0582 (16) | 0.0447 (13) | −0.0034 (12) | −0.0128 (10) | 0.0109 (12) |
| O1 | 0.0390 (9) | 0.0594 (11) | 0.0574 (10) | −0.0141 (8) | −0.0100 (7) | 0.0117 (8) |
| N1—C5 | 1.333 (2) | N5—C8 | 1.309 (3) |
| N1—C1 | 1.333 (3) | N3—C7 | 1.329 (2) |
| N2—C6 | 1.349 (2) | N3—C8 | 1.362 (2) |
| N2—C7 | 1.388 (2) | C3—C2 | 1.364 (3) |
| N2—H21 | 0.8751 | C3—C4 | 1.379 (3) |
| C5—C4 | 1.381 (3) | C3—H3 | 0.9300 |
| C5—C6 | 1.495 (3) | C4—H4 | 0.9300 |
| C6—O1 | 1.226 (2) | C1—C2 | 1.377 (3) |
| N4—C7 | 1.324 (2) | C1—H1 | 0.9300 |
| N4—N5 | 1.371 (2) | C2—H2 | 0.9300 |
| N4—H41 | 0.8612 | C8—H8 | 0.9300 |
| C5—N1—C1 | 116.71 (19) | C4—C3—H3 | 120.4 |
| C6—N2—C7 | 122.55 (17) | C3—C4—C5 | 118.5 (2) |
| C6—N2—H21 | 122.2 | C3—C4—H4 | 120.7 |
| C7—N2—H21 | 115.2 | C5—C4—H4 | 120.7 |
| N1—C5—C4 | 123.29 (19) | N1—C1—C2 | 124.0 (2) |
| N1—C5—C6 | 117.68 (18) | N1—C1—H1 | 118.0 |
| C4—C5—C6 | 119.02 (19) | C2—C1—H1 | 118.0 |
| O1—C6—N2 | 122.01 (19) | N4—C7—N3 | 110.85 (18) |
| O1—C6—C5 | 120.34 (18) | N4—C7—N2 | 125.30 (17) |
| N2—C6—C5 | 117.65 (18) | N3—C7—N2 | 123.85 (18) |
| C7—N4—N5 | 110.26 (16) | C3—C2—C1 | 118.4 (2) |
| C7—N4—H41 | 130.3 | C3—C2—H2 | 120.8 |
| N5—N4—H41 | 119.4 | C1—C2—H2 | 120.8 |
| C8—N5—N4 | 101.06 (17) | N5—C8—N3 | 116.56 (18) |
| C7—N3—C8 | 101.28 (17) | N5—C8—H8 | 121.7 |
| C2—C3—C4 | 119.1 (2) | N3—C8—H8 | 121.7 |
| C2—C3—H3 | 120.4 | ||
| C1—N1—C5—C4 | 0.0 (3) | C5—N1—C1—C2 | −1.0 (3) |
| C1—N1—C5—C6 | 179.44 (19) | N5—N4—C7—N3 | −0.1 (2) |
| C7—N2—C6—O1 | 0.4 (3) | N5—N4—C7—N2 | 179.57 (17) |
| C7—N2—C6—C5 | −178.98 (17) | C8—N3—C7—N4 | 0.3 (2) |
| N1—C5—C6—O1 | 177.46 (18) | C8—N3—C7—N2 | −179.40 (19) |
| C4—C5—C6—O1 | −3.1 (3) | C6—N2—C7—N4 | 4.8 (3) |
| N1—C5—C6—N2 | −3.1 (3) | C6—N2—C7—N3 | −175.51 (19) |
| C4—C5—C6—N2 | 176.30 (17) | C4—C3—C2—C1 | −0.4 (3) |
| C7—N4—N5—C8 | −0.1 (2) | N1—C1—C2—C3 | 1.2 (4) |
| C2—C3—C4—C5 | −0.5 (3) | N4—N5—C8—N3 | 0.3 (2) |
| N1—C5—C4—C3 | 0.7 (3) | C7—N3—C8—N5 | −0.4 (2) |
| C6—C5—C4—C3 | −178.68 (19) |
| H··· | ||||
| N2—H21···N3i | 0.88 | 2.09 | 2.946 (2) | 164 |
| N4—H41···O1ii | 0.86 | 2.06 | 2.873 (2) | 158 |
| N4—H41···O1 | 0.86 | 2.17 | 2.629 (2) | 113 |
Hydrogen-bond geometry (Å, °)
| H⋯ | ||||
|---|---|---|---|---|
| N2—H21⋯N3i | 0.88 | 2.09 | 2.946 (2) | 164 |
| N4—H41⋯O1ii | 0.86 | 2.06 | 2.873 (2) | 158 |
| N4—H41⋯O1 | 0.86 | 2.17 | 2.629 (2) | 113 |
Symmetry codes: (i) ; (ii) .