Acta Cryst. (2007). E63, o3721 [ doi:10.1107/S1600536807036148 ]
In the title compound, C13H9ClN4OS, the mean plane of the oxadiazole ring makes a dihedral angle of 6.34 (13)° with the mean plane of the pyridine ring. The dihedral angle between the chloropyridine ring and the oxadiazole ring is 74.43 (12)°, and the dihedral angle between the chloropyridine ring and the pyridine ring is 69.78 (11)°. The crystal packing is stabilized by inter- and intramolecular C-H
N hydrogen bonds.
5-Pyridin-4-yl-1,3,4-oxadiazole-2-thiol (0.72 g, 4 mmol) was added to a solution of 1.2% sodium hydroxide at room temperature while stirring. The mixture of 2-Chloro-5-chloromethyl-pyridine (0.72 g, 4.4 mmol) in methanol (4 ml) was added dropwise while the 5-Pyridin-4-yl-1,3,4-oxadiazole-2-thiol was dissolved. The mixture was then stirred at room temperature for 6 h. The white solid was filtered and recrystallized from dimethylformamide-water mixture to give the title compound (yield 54%). Colourless crystals of (I) suitable for X-ray structure analysis were grown from the mixture of dichloromethane and n-hexane (v/v, 1:8).
All H atoms were placed in calculated positions, with C—H distances in the range 0.93–0.97 Å, and included in the final cycles of refinement using a riding-model approximation, with Uiso(H) = 1.2–1.5Ueq(carrier atom).
Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXTL (Bruker, 1997).
![[Figure 1]](./bx2092fig1thm.gif)
| Fig. 1. The structure of (I). showing 50% probability displacement ellipsoids and the atom-numbering scheme. |
![[Figure 2]](./bx2092fig2thm.gif)
| Fig. 2. Crystal Packing diagram of (I). Hydrogen bonds are shown as dashed lines. |
| C13H9ClN4OS | Z = 2 |
| Mr = 304.75 | F000 = 312 |
| Triclinic, P1 | Dx = 1.544 Mg m−3 |
| Hall symbol: -p 1 | Mo Kα radiation λ = 0.71073 Å |
| a = 6.2729 (5) Å | Cell parameters from 2330 reflections |
| b = 8.1448 (6) Å | θ = 2.7–28.2º |
| c = 14.0994 (11) Å | µ = 0.45 mm−1 |
| α = 85.520 (1)º | T = 297 (2) K |
| β = 77.793 (1)º | Block, colourless |
| γ = 68.637 (1)º | 0.30 × 0.20 × 0.20 mm |
| V = 655.70 (9) Å3 |
| Bruker SMART CCD area-detector diffractometer | 2544 independent reflections |
| Radiation source: fine-focus sealed tube | 2108 reflections with I > 2σ(I) |
| Monochromator: graphite | Rint = 0.047 |
| T = 297(2) K | θmax = 26.0º |
| φ and ω scans | θmin = 1.5º |
| Absorption correction: multi-scan (SADABS; Bruker, 2000) | h = −7→7 |
| Tmin = 0.877, Tmax = 0.915 | k = −6→10 |
| 4655 measured reflections | l = −16→17 |
| Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
| Least-squares matrix: full | H-atom parameters constrained |
| R[F2 > 2σ(F2)] = 0.042 | w = 1/[σ2(Fo2) + (0.0696P)2 + 0.0355P] where P = (Fo2 + 2Fc2)/3 |
| wR(F2) = 0.131 | (Δ/σ)max < 0.001 |
| S = 1.13 | Δρmax = 0.27 e Å−3 |
| 2544 reflections | Δρmin = −0.25 e Å−3 |
| 182 parameters | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
| Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.069 (8) |
| Secondary atom site location: difference Fourier map |
| C13H9ClN4OS | γ = 68.637 (1)º |
| Mr = 304.75 | V = 655.70 (9) Å3 |
| Triclinic, P1 | Z = 2 |
| a = 6.2729 (5) Å | Mo Kα |
| b = 8.1448 (6) Å | µ = 0.45 mm−1 |
| c = 14.0994 (11) Å | T = 297 (2) K |
| α = 85.520 (1)º | 0.30 × 0.20 × 0.20 mm |
| β = 77.793 (1)º |
| Bruker SMART CCD area-detector diffractometer | 2544 independent reflections |
| Absorption correction: multi-scan (SADABS; Bruker, 2000) | 2108 reflections with I > 2σ(I) |
| Tmin = 0.877, Tmax = 0.915 | Rint = 0.047 |
| 4655 measured reflections |
| R[F2 > 2σ(F2)] = 0.042 | 182 parameters |
| wR(F2) = 0.131 | H-atom parameters constrained |
| S = 1.13 | Δρmax = 0.27 e Å−3 |
| 2544 reflections | Δρmin = −0.25 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 > 2sigma(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 | ||
| C1 | 0.6614 (4) | 0.2322 (3) | 0.49086 (15) | 0.0395 (5) | |
| C2 | 0.8922 (4) | 0.2144 (3) | 0.47658 (17) | 0.0436 (5) | |
| H2 | 1.0002 | 0.1538 | 0.4234 | 0.052* | |
| C3 | 0.9574 (4) | 0.2900 (3) | 0.54425 (17) | 0.0435 (5) | |
| H3 | 1.1120 | 0.2809 | 0.5376 | 0.052* | |
| C4 | 0.7901 (4) | 0.3801 (3) | 0.62265 (15) | 0.0381 (5) | |
| C5 | 0.5648 (4) | 0.3872 (3) | 0.62834 (15) | 0.0413 (5) | |
| H5 | 0.4522 | 0.4472 | 0.6806 | 0.050* | |
| C6 | 0.8574 (4) | 0.4667 (3) | 0.69576 (17) | 0.0462 (6) | |
| H6A | 0.7238 | 0.5685 | 0.7225 | 0.055* | |
| H6B | 0.9804 | 0.5086 | 0.6630 | 0.055* | |
| C7 | 0.6924 (4) | 0.3411 (3) | 0.86759 (16) | 0.0403 (5) | |
| C8 | 0.4622 (4) | 0.2839 (3) | 0.98761 (15) | 0.0396 (5) | |
| C9 | 0.3821 (4) | 0.1990 (3) | 1.07587 (15) | 0.0390 (5) | |
| C10 | 0.5377 (4) | 0.0739 (3) | 1.12639 (17) | 0.0432 (5) | |
| H10 | 0.6981 | 0.0388 | 1.1039 | 0.052* | |
| C11 | 0.4464 (4) | 0.0041 (3) | 1.21055 (17) | 0.0498 (6) | |
| H11 | 0.5506 | −0.0794 | 1.2438 | 0.060* | |
| C12 | 0.0730 (5) | 0.1666 (4) | 1.19713 (19) | 0.0543 (7) | |
| H12 | −0.0866 | 0.1978 | 1.2208 | 0.065* | |
| C13 | 0.1458 (4) | 0.2445 (3) | 1.11242 (18) | 0.0484 (6) | |
| H13 | 0.0374 | 0.3265 | 1.0803 | 0.058* | |
| Cl1 | 0.57259 (11) | 0.14110 (9) | 0.40489 (4) | 0.0542 (2) | |
| N1 | 0.4965 (3) | 0.3144 (3) | 0.56436 (13) | 0.0423 (5) | |
| N2 | 0.4872 (3) | 0.4496 (3) | 0.86157 (13) | 0.0464 (5) | |
| N3 | 0.3340 (3) | 0.4109 (3) | 0.94122 (14) | 0.0448 (5) | |
| N4 | 0.2198 (4) | 0.0483 (3) | 1.24723 (15) | 0.0528 (5) | |
| O1 | 0.6933 (3) | 0.23080 (19) | 0.94565 (10) | 0.0410 (4) | |
| S1 | 0.95815 (10) | 0.32163 (9) | 0.79527 (4) | 0.0493 (2) |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| C1 | 0.0466 (13) | 0.0414 (12) | 0.0346 (11) | −0.0197 (10) | −0.0112 (9) | 0.0048 (9) |
| C2 | 0.0417 (12) | 0.0459 (13) | 0.0398 (12) | −0.0155 (10) | −0.0014 (9) | 0.0006 (10) |
| C3 | 0.0320 (11) | 0.0519 (14) | 0.0465 (13) | −0.0169 (10) | −0.0052 (9) | 0.0042 (10) |
| C4 | 0.0408 (12) | 0.0415 (12) | 0.0377 (11) | −0.0209 (10) | −0.0115 (9) | 0.0084 (9) |
| C5 | 0.0371 (12) | 0.0518 (14) | 0.0350 (11) | −0.0178 (10) | −0.0037 (9) | −0.0008 (10) |
| C6 | 0.0481 (14) | 0.0538 (15) | 0.0465 (13) | −0.0282 (12) | −0.0147 (10) | 0.0070 (11) |
| C7 | 0.0468 (13) | 0.0399 (12) | 0.0362 (11) | −0.0138 (10) | −0.0145 (9) | −0.0022 (9) |
| C8 | 0.0436 (12) | 0.0373 (12) | 0.0374 (12) | −0.0111 (10) | −0.0108 (9) | −0.0068 (9) |
| C9 | 0.0432 (12) | 0.0385 (12) | 0.0364 (11) | −0.0131 (9) | −0.0104 (9) | −0.0068 (9) |
| C10 | 0.0390 (12) | 0.0475 (13) | 0.0416 (12) | −0.0116 (10) | −0.0096 (9) | −0.0047 (10) |
| C11 | 0.0596 (15) | 0.0462 (14) | 0.0418 (13) | −0.0143 (12) | −0.0149 (11) | 0.0011 (10) |
| C12 | 0.0505 (15) | 0.0587 (16) | 0.0504 (15) | −0.0190 (12) | −0.0013 (11) | −0.0070 (12) |
| C13 | 0.0478 (14) | 0.0460 (14) | 0.0498 (14) | −0.0114 (11) | −0.0144 (11) | −0.0034 (11) |
| Cl1 | 0.0654 (4) | 0.0628 (4) | 0.0448 (4) | −0.0320 (3) | −0.0145 (3) | −0.0048 (3) |
| N1 | 0.0397 (10) | 0.0537 (12) | 0.0382 (10) | −0.0224 (9) | −0.0078 (8) | 0.0007 (9) |
| N2 | 0.0459 (11) | 0.0469 (11) | 0.0412 (11) | −0.0091 (9) | −0.0120 (9) | 0.0015 (9) |
| N3 | 0.0388 (10) | 0.0503 (12) | 0.0392 (10) | −0.0081 (9) | −0.0082 (8) | −0.0013 (9) |
| N4 | 0.0583 (13) | 0.0546 (13) | 0.0471 (12) | −0.0232 (11) | −0.0069 (10) | −0.0040 (10) |
| O1 | 0.0416 (9) | 0.0421 (9) | 0.0377 (8) | −0.0112 (7) | −0.0114 (6) | 0.0007 (7) |
| S1 | 0.0399 (4) | 0.0629 (4) | 0.0474 (4) | −0.0184 (3) | −0.0153 (3) | 0.0045 (3) |
| C1—N1 | 1.320 (3) | C7—S1 | 1.720 (2) |
| C1—C2 | 1.374 (3) | C8—N3 | 1.286 (3) |
| C1—Cl1 | 1.748 (2) | C8—O1 | 1.364 (3) |
| C2—C3 | 1.377 (3) | C8—C9 | 1.461 (3) |
| C2—H2 | 0.9300 | C9—C13 | 1.381 (3) |
| C3—C4 | 1.392 (3) | C9—C10 | 1.398 (3) |
| C3—H3 | 0.9300 | C10—C11 | 1.380 (3) |
| C4—C5 | 1.378 (3) | C10—H10 | 0.9300 |
| C4—C6 | 1.501 (3) | C11—N4 | 1.328 (3) |
| C5—N1 | 1.335 (3) | C11—H11 | 0.9300 |
| C5—H5 | 0.9300 | C12—N4 | 1.341 (3) |
| C6—S1 | 1.826 (2) | C12—C13 | 1.378 (4) |
| C6—H6A | 0.9700 | C12—H12 | 0.9300 |
| C6—H6B | 0.9700 | C13—H13 | 0.9300 |
| C7—N2 | 1.285 (3) | N2—N3 | 1.412 (3) |
| C7—O1 | 1.365 (3) | ||
| N1—C1—C2 | 125.6 (2) | N3—C8—O1 | 112.8 (2) |
| N1—C1—Cl1 | 116.04 (17) | N3—C8—C9 | 126.5 (2) |
| C2—C1—Cl1 | 118.31 (18) | O1—C8—C9 | 120.72 (17) |
| C1—C2—C3 | 117.3 (2) | C13—C9—C10 | 118.2 (2) |
| C1—C2—H2 | 121.3 | C13—C9—C8 | 119.7 (2) |
| C3—C2—H2 | 121.3 | C10—C9—C8 | 122.1 (2) |
| C2—C3—C4 | 119.5 (2) | C11—C10—C9 | 118.1 (2) |
| C2—C3—H3 | 120.3 | C11—C10—H10 | 120.9 |
| C4—C3—H3 | 120.3 | C9—C10—H10 | 120.9 |
| C5—C4—C3 | 117.2 (2) | N4—C11—C10 | 124.3 (2) |
| C5—C4—C6 | 122.8 (2) | N4—C11—H11 | 117.8 |
| C3—C4—C6 | 120.1 (2) | C10—C11—H11 | 117.8 |
| N1—C5—C4 | 124.8 (2) | N4—C12—C13 | 123.5 (2) |
| N1—C5—H5 | 117.6 | N4—C12—H12 | 118.2 |
| C4—C5—H5 | 117.6 | C13—C12—H12 | 118.2 |
| C4—C6—S1 | 113.78 (16) | C12—C13—C9 | 119.0 (2) |
| C4—C6—H6A | 108.8 | C12—C13—H13 | 120.5 |
| S1—C6—H6A | 108.8 | C9—C13—H13 | 120.5 |
| C4—C6—H6B | 108.8 | C1—N1—C5 | 115.59 (19) |
| S1—C6—H6B | 108.8 | C7—N2—N3 | 105.74 (18) |
| H6A—C6—H6B | 107.7 | C8—N3—N2 | 106.27 (17) |
| N2—C7—O1 | 113.2 (2) | C11—N4—C12 | 116.8 (2) |
| N2—C7—S1 | 129.65 (19) | C8—O1—C7 | 102.04 (16) |
| O1—C7—S1 | 117.16 (15) | C7—S1—C6 | 99.33 (11) |
| N1—C1—C2—C3 | −0.6 (3) | C8—C9—C13—C12 | −178.3 (2) |
| Cl1—C1—C2—C3 | 178.82 (16) | C2—C1—N1—C5 | 1.0 (3) |
| C1—C2—C3—C4 | −0.2 (3) | Cl1—C1—N1—C5 | −178.40 (16) |
| C2—C3—C4—C5 | 0.5 (3) | C4—C5—N1—C1 | −0.7 (3) |
| C2—C3—C4—C6 | −178.6 (2) | O1—C7—N2—N3 | −0.4 (3) |
| C3—C4—C5—N1 | −0.1 (3) | S1—C7—N2—N3 | −178.04 (18) |
| C6—C4—C5—N1 | 179.0 (2) | O1—C8—N3—N2 | −0.4 (2) |
| C5—C4—C6—S1 | 92.6 (2) | C9—C8—N3—N2 | 179.6 (2) |
| C3—C4—C6—S1 | −88.4 (2) | C7—N2—N3—C8 | 0.5 (2) |
| N3—C8—C9—C13 | 5.5 (4) | C10—C11—N4—C12 | 1.1 (4) |
| O1—C8—C9—C13 | −174.5 (2) | C13—C12—N4—C11 | −1.2 (4) |
| N3—C8—C9—C10 | −173.4 (2) | N3—C8—O1—C7 | 0.2 (2) |
| O1—C8—C9—C10 | 6.6 (3) | C9—C8—O1—C7 | −179.87 (19) |
| C13—C9—C10—C11 | −0.7 (3) | N2—C7—O1—C8 | 0.2 (2) |
| C8—C9—C10—C11 | 178.3 (2) | S1—C7—O1—C8 | 178.12 (15) |
| C9—C10—C11—N4 | −0.2 (4) | N2—C7—S1—C6 | −11.0 (2) |
| N4—C12—C13—C9 | 0.4 (4) | O1—C7—S1—C6 | 171.46 (17) |
| C10—C9—C13—C12 | 0.6 (4) | C4—C6—S1—C7 | −82.18 (19) |
| D—H···A | D—H | H···A | D···A | D—H···A |
| C2—H2···N4i | 0.93 | 2.61 | 3.515 (3) | 164 |
| C13—H13···N3ii | 0.93 | 2.58 | 3.462 (3) | 158 |
| C5—H5···N2 | 0.93 | 2.61 | 3.273 (3) | 129 |
| C6—H6A···N2 | 0.97 | 2.55 | 2.961 (3) | 106 |
| Symmetry codes: (i) x+1, y, z−1; (ii) −x, −y+1, −z+2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| C2—H2···N4i | 0.93 | 2.61 | 3.515 (3) | 164 |
| C13—H13···N3ii | 0.93 | 2.58 | 3.462 (3) | 158 |
| C5—H5···N2 | 0.93 | 2.61 | 3.273 (3) | 129 |
| C6—H6A···N2 | 0.97 | 2.55 | 2.961 (3) | 106 |
| Symmetry codes: (i) x+1, y, z−1; (ii) −x, −y+1, −z+2. |
The authors gratefully acknowledge financial support of this work by the National Basic Research Programme of China (grant No. 2003CB114400) and the National Natural Science Foundation of China (grant No. 20372023).
Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
Bruker (1997). SHELXTL. Version 5.10. Bruker AXS Inc., Madison, Wisconsin, USA.
Bruker (2000). SMART (Version 5.059), SAINT (Version 6.01) and SADABS (Version 6.10). Bruker AXS Inc., Madison, Wisconsin, USA.
Hui, X. P., Chu, C. H., Zhang, Z. Y., Wang, Q. & Zhang, Q. (2000). Indian J. Chem. Sect. B, 41, 2176–2179.
Lin, N.-H., Dong, L., Bunnelle, W. H., Anderson, D. J. & Meyer, M. D. (2002). Bioorg. Med. Chem. Lett. 12, 3321–3324.
Reddy, P. S. N. & Reddy, P. P. (1987). Indian J. Chem. Sect. B, 26, 890–891.
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Göttingen, Germany.
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13.
1,3,4,-oxadiazole derivatives are important compounds with versatile industrial and medical applications (Reddy & Reddy, 1987; Hui et al., 2000; Lin et al., 2002). We report here the molecular structure of (I). In the title compound, all bond lengths and angles are within normal ranges (Allen et al., 1987) and the molecules are stabilized by intra and intermolecular hydrogen bonds (Table 1). The crystal packing also shows two weak intramolecular π— π stacking interactions.