2-Chloro-5-{[5-(4-pyrid­yl)-1,3,4-oxa­diazol-2-yl]sulfanylmeth­yl}pyridine

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.

Key indicators

• Single-crystal X-ray study
• T = 297 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.042
• wR factor = 0.131
• Data-to-parameter ratio = 14.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT154_ALERT_1_C The su's on the Cell Angles are Equal  (x 10000)        100 Deg.
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

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.

Related literature

For the biological and pharmaceutical activity of oxadiazols, see Reddy & Reddy (1987); Hui et al. (2000). Many derivatives of oxadiazols have been prepared by Lin et al. (2002). For related literature, see: Allen et al. (1987).

S2. Experimental

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).

S3. Refinement

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 U_iso(H) = 1.2–1.5U_eq(carrier atom).

Computing details

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).

Figures

	Fig. 1. The structure of (I). showing 50% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 2. Crystal Packing diagram of (I). Hydrogen bonds are shown as dashed lines.

2-Chloro-5-{[5-(4-pyridyl)-1,3,4-oxadiazol-2-yl]sulfanylmethyl}pyridine

Crystal data

C13H9ClN4OS	Z = 2
Mr = 304.75	F(000) = 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 = 2.7–28.2°
c = 14.0994 (11) Å	µ = 0.45 mm^−1
α = 85.520 (1)°	T = 297 K
β = 77.793 (1)°	Block, colourless
γ = 68.637 (1)°	0.30 × 0.20 × 0.20 mm
V = 655.70 (9) Å^3

Data collection

Bruker SMART CCD area-detector diffractometer	2544 independent reflections
Radiation source: fine-focus sealed tube	2108 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.047
φ and ω scans	θmax = 26.0°, θmin = 1.5°
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

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.042	H-atom parameters constrained
wR(F^2) = 0.131	w = 1/[σ^2(Fo^2) + (0.0696P)^2 + 0.0355P] where P = (Fo^2 + 2Fc^2)/3
S = 1.13	(Δ/σ)max < 0.001
2544 reflections	Δρmax = 0.27 e Å^−3
182 parameters	Δρmin = −0.25 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.069 (8)

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	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)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

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)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C2—H2···N4^i	0.93	2.61	3.515 (3)	164
C13—H13···N3^ii	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.