2-Methyl-5-{3-[4-(methyl­sulfon­yl)­phenyl]-1,2,4-oxadiazol-5-ylmethyl­sulfan­yl}-1,3,4-thia­diazole

The title compound, C₁₃H₁₂N₄O₃S₃, was synthesized via condensation of 1,2,4-oxadiazole chloro­methane with 1,3,4-thia­diazo­lethiol. There are three rings in the molecule. The benzene and oxadiazole rings are coplanar due to the extended aromatic system. The angle between this plane and the thiadiazole plane is 82.2°.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.051
• wR factor = 0.138
• Data-to-parameter ratio = 14.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT322_ALERT_2_C Check Hybridisation of  S1     in Main Residue .          ?

Alert level G
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K

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

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 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

1,2,4-Oxadiazoles represent an important class of five-membered heterocycles. Some derivatives of 1,2,4-oxadiazoles have anti-inflammatory (Nicolaides et al., 1998) and antipicornaviral (Romero, 2001) properties. We are focusing our synthetic and structural studies on new oxindole derivatives. The sulfurether compounds exhibited considerably strong inhibiting activity to Staphylococcus aureus (Talar & Dejai, 1996). We report here the structure of its close analogue with thiadiazole sulfanylether group, (I). The benzene and oxadiazole rings are almost coplanar, howvever, the thiadiazole ring deviates from this plane. There are no classic hydrogen bonds in the molecular structure. The molecular structure of (I) is shown in Fig. 1.

Related literature

For related literature, see: Nicolaides et al. (1998); Romero (2001); Talar & Dejai (1996).

S2. Experimental

5-Mercapto-2-methyl-1,3,4-thiadiazole (20 mmol) was dissolve in ethanol (70 ml) and water (70 mmol). Sodium acetate (20 mmol) was added to this mixture. Then 3-[4-(Methylsulfonyl)phenyl]-5-chloromethyl-1,2,4-oxadiazol (40 mmol) was added. The resulting mixture was refluxed for 8 h. After cooling and filtrating, crude compound (I) was gained. Pure compound (I) was obtained by crystallizing from a mixture of ethyl acetate (8 ml) and petrolum ether (4 ml). Crystals of (I) suitable for X-ray diffraction were obtained by slow evaporation of an ethanol solution. ¹H NMR (CDCl₃, δ, p.p.m.): 7.95–7.99 (m, 2H), 7.75–7.76 (m, 2H), 4.17–4.18 (s, 2H), 2.85–2.86 (s,3H), 2.35–2.36 (s,3H).

S3. Refinement

All H atoms bonded to the C atoms were placed geometrically at the distances of 0.93–0.96 Å and included in the refinement in riding motion approximation with U_iso(H) = 1.2 or 1.5U_eq of the carrier atom.

Computing details

Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell refinement: CAD-4 Software (Enraf–Nonius, 1989); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Siemens, 1996); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures

Fig. 1. A view of the molecular structure of (I), showing displacement ellipsoids at the 30% probability level.

2-Methyl-5-{3-[4-(methylsulfonyl)phenyl]-1,2,4-oxadiazol-5-ylmethylsulfanyl}- 1,3,4-thiadiazole

Crystal data

C13H12N4O3S3	F(000) = 760
Mr = 368.45	Dx = 1.585 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 25 reflections
a = 12.365 (3) Å	θ = 10–13°
b = 15.956 (3) Å	µ = 0.50 mm^−1
c = 8.2400 (16) Å	T = 293 K
β = 108.26 (3)°	Block, colourless
V = 1543.9 (6) Å^3	0.40 × 0.30 × 0.20 mm
Z = 4

Data collection

Enraf–Nonius CAD-4 diffractometer	2349 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.032
Graphite monochromator	θmax = 26.0°, θmin = 1.7°
ω/2θ scans	h = −15→14
Absorption correction: ψ scan (North et al., 1968)	k = 0→19
Tmin = 0.825, Tmax = 0.907	l = 0→10
3239 measured reflections	3 standard reflections every 200 reflections
3019 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.051	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.138	H-atom parameters constrained
S = 1.07	w = 1/[σ^2(Fo^2) + (0.08P)^2 + 0.5P] where P = (Fo^2 + 2Fc^2)/3
3019 reflections	(Δ/σ)max < 0.001
208 parameters	Δρmax = 0.37 e Å^−3
0 restraints	Δρmin = −0.57 e Å^−3

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
S1	0.72521 (7)	0.34658 (5)	0.36586 (11)	0.0417 (2)
O1	0.4584 (2)	0.04592 (14)	0.1689 (3)	0.0481 (6)
N1	0.7921 (2)	0.19730 (17)	0.4507 (4)	0.0441 (7)
C1	0.9215 (3)	0.3017 (2)	0.6335 (5)	0.0467 (8)
H1B	0.9637	0.2532	0.6874	0.070*
H1C	0.8978	0.3329	0.7159	0.070*
H1D	0.9690	0.3363	0.5886	0.070*
S2	0.52374 (7)	0.27954 (6)	0.09389 (12)	0.0481 (3)
O2	0.1594 (2)	0.01484 (14)	0.9643 (3)	0.0488 (6)
N2	0.6927 (2)	0.18906 (16)	0.3141 (4)	0.0450 (7)
C2	0.8194 (3)	0.27461 (18)	0.4915 (4)	0.0372 (7)
S3	0.10797 (6)	0.07761 (4)	0.83848 (10)	0.0334 (2)
O3	0.1006 (2)	0.16209 (13)	0.8943 (3)	0.0482 (6)
N3	0.3686 (2)	0.15372 (15)	0.2358 (3)	0.0376 (6)
C3	0.6486 (3)	0.26122 (18)	0.2582 (4)	0.0363 (7)
N4	0.4067 (2)	0.01607 (16)	0.2870 (4)	0.0433 (6)
C4	0.4766 (3)	0.1743 (2)	0.0265 (4)	0.0487 (9)
H4B	0.4181	0.1771	−0.0840	0.058*
H4C	0.5401	0.1430	0.0120	0.058*
C5	0.4305 (3)	0.1279 (2)	0.1470 (4)	0.0399 (7)
C6	0.3552 (2)	0.08168 (17)	0.3201 (4)	0.0338 (6)
C7	0.2925 (2)	0.07993 (17)	0.4449 (4)	0.0340 (7)
C8	0.2290 (3)	0.14939 (19)	0.4627 (4)	0.0426 (8)
H8A	0.2247	0.1960	0.3933	0.051*
C9	0.1727 (3)	0.14945 (18)	0.5821 (4)	0.0394 (7)
H9A	0.1297	0.1956	0.5938	0.047*
C10	0.1810 (2)	0.07929 (17)	0.6852 (4)	0.0323 (6)
C11	0.2437 (3)	0.00997 (18)	0.6702 (4)	0.0374 (7)
H11A	0.2484	−0.0363	0.7407	0.045*
C13	−0.0297 (3)	0.0440 (2)	0.7251 (4)	0.0442 (8)
H13A	−0.0750	0.0415	0.8008	0.066*
H13B	−0.0262	−0.0106	0.6782	0.066*
H13C	−0.0636	0.0827	0.6342	0.066*
C12	0.2993 (2)	0.01041 (18)	0.5485 (4)	0.0376 (7)
H12A	0.3414	−0.0361	0.5361	0.045*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0426 (4)	0.0254 (4)	0.0617 (5)	0.0052 (3)	0.0227 (4)	0.0095 (3)
O1	0.0512 (14)	0.0434 (13)	0.0611 (15)	−0.0006 (11)	0.0341 (12)	−0.0035 (11)
N1	0.0510 (16)	0.0318 (14)	0.0530 (16)	0.0119 (12)	0.0215 (14)	0.0076 (12)
C1	0.0410 (18)	0.0450 (19)	0.056 (2)	0.0067 (15)	0.0188 (15)	0.0063 (16)
S2	0.0403 (5)	0.0470 (5)	0.0606 (5)	0.0017 (4)	0.0208 (4)	0.0177 (4)
O2	0.0559 (14)	0.0431 (13)	0.0513 (13)	0.0099 (11)	0.0222 (11)	0.0146 (11)
N2	0.0509 (16)	0.0290 (13)	0.0609 (17)	0.0083 (12)	0.0258 (14)	0.0082 (13)
C2	0.0400 (16)	0.0305 (16)	0.0501 (18)	0.0080 (13)	0.0273 (14)	0.0082 (13)
S3	0.0354 (4)	0.0268 (4)	0.0415 (4)	0.0008 (3)	0.0172 (3)	0.0019 (3)
O3	0.0613 (15)	0.0302 (12)	0.0605 (14)	0.0002 (10)	0.0296 (12)	−0.0083 (10)
N3	0.0371 (14)	0.0346 (13)	0.0462 (15)	−0.0045 (11)	0.0205 (12)	0.0019 (11)
C3	0.0412 (16)	0.0275 (14)	0.0499 (18)	0.0026 (12)	0.0284 (14)	0.0057 (13)
N4	0.0460 (15)	0.0361 (14)	0.0564 (17)	−0.0041 (12)	0.0281 (13)	−0.0012 (12)
C4	0.048 (2)	0.058 (2)	0.0481 (19)	−0.0096 (17)	0.0268 (16)	−0.0005 (16)
C5	0.0350 (16)	0.0419 (18)	0.0459 (18)	−0.0076 (13)	0.0170 (14)	−0.0034 (14)
C6	0.0282 (14)	0.0314 (15)	0.0444 (16)	−0.0058 (12)	0.0153 (12)	−0.0019 (12)
C7	0.0269 (14)	0.0271 (15)	0.0519 (18)	−0.0045 (11)	0.0180 (13)	0.0013 (13)
C8	0.0475 (18)	0.0276 (15)	0.062 (2)	0.0043 (13)	0.0304 (16)	0.0120 (14)
C9	0.0408 (17)	0.0253 (14)	0.0605 (19)	0.0077 (13)	0.0280 (15)	0.0090 (14)
C10	0.0285 (14)	0.0266 (14)	0.0460 (16)	−0.0008 (11)	0.0178 (12)	0.0010 (12)
C11	0.0375 (15)	0.0229 (14)	0.0564 (19)	0.0032 (12)	0.0214 (14)	0.0085 (13)
C13	0.0377 (17)	0.0413 (18)	0.057 (2)	−0.0043 (14)	0.0192 (15)	−0.0019 (15)
C12	0.0354 (15)	0.0270 (15)	0.0555 (19)	0.0032 (12)	0.0215 (14)	0.0035 (13)

Geometric parameters (Å, º)

S1—C2	1.729 (3)	N4—C6	1.298 (4)
S1—C3	1.736 (3)	C4—C5	1.488 (4)
O1—C5	1.350 (4)	C4—H4B	0.9700
O1—N4	1.405 (3)	C4—H4C	0.9700
N1—C2	1.295 (4)	C6—C7	1.468 (4)
N1—N2	1.389 (4)	C7—C12	1.386 (4)
C1—C2	1.492 (5)	C7—C8	1.393 (4)
C1—H1B	0.9600	C8—C9	1.372 (4)
C1—H1C	0.9600	C8—H8A	0.9300
C1—H1D	0.9600	C9—C10	1.389 (4)
S2—C3	1.730 (3)	C9—H9A	0.9300
S2—C4	1.807 (4)	C10—C11	1.378 (4)
O2—S3	1.439 (2)	C11—C12	1.383 (4)
N2—C3	1.295 (4)	C11—H11A	0.9300
S3—O3	1.436 (2)	C13—H13A	0.9600
S3—C13	1.750 (3)	C13—H13B	0.9600
S3—C10	1.768 (3)	C13—H13C	0.9600
N3—C5	1.281 (4)	C12—H12A	0.9300
N3—C6	1.380 (4)
C2—S1—C3	86.69 (15)	N3—C5—O1	114.1 (3)
C5—O1—N4	105.6 (2)	N3—C5—C4	130.0 (3)
C2—N1—N2	113.1 (3)	O1—C5—C4	115.9 (3)
C2—C1—H1B	109.5	N4—C6—N3	114.9 (3)
C2—C1—H1C	109.5	N4—C6—C7	122.2 (3)
H1B—C1—H1C	109.5	N3—C6—C7	122.8 (2)
C2—C1—H1D	109.5	C12—C7—C8	119.9 (3)
H1B—C1—H1D	109.5	C12—C7—C6	120.2 (3)
H1C—C1—H1D	109.5	C8—C7—C6	119.8 (3)
C3—S2—C4	101.93 (16)	C9—C8—C7	120.4 (3)
C3—N2—N1	111.8 (3)	C9—C8—H8A	119.8
N1—C2—C1	124.5 (3)	C7—C8—H8A	119.8
N1—C2—S1	113.9 (3)	C8—C9—C10	118.7 (3)
C1—C2—S1	121.6 (2)	C8—C9—H9A	120.6
O3—S3—O2	118.73 (15)	C10—C9—H9A	120.6
O3—S3—C13	108.04 (16)	C11—C10—C9	121.9 (3)
O2—S3—C13	107.96 (16)	C11—C10—S3	118.6 (2)
O3—S3—C10	108.20 (14)	C9—C10—S3	119.5 (2)
O2—S3—C10	108.40 (13)	C10—C11—C12	118.9 (3)
C13—S3—C10	104.63 (15)	C10—C11—H11A	120.6
C5—N3—C6	102.0 (3)	C12—C11—H11A	120.6
N2—C3—S2	127.0 (3)	S3—C13—H13A	109.5
N2—C3—S1	114.5 (3)	S3—C13—H13B	109.5
S2—C3—S1	118.54 (17)	H13A—C13—H13B	109.5
C6—N4—O1	103.4 (2)	S3—C13—H13C	109.5
C5—C4—S2	114.3 (2)	H13A—C13—H13C	109.5
C5—C4—H4B	108.7	H13B—C13—H13C	109.5
S2—C4—H4B	108.7	C11—C12—C7	120.2 (3)
C5—C4—H4C	108.7	C11—C12—H12A	119.9
S2—C4—H4C	108.7	C7—C12—H12A	119.9
H4B—C4—H4C	107.6
C2—N1—N2—C3	−0.3 (4)	C5—N3—C6—C7	177.7 (3)
N2—N1—C2—C1	179.7 (3)	N4—C6—C7—C12	8.7 (4)
N2—N1—C2—S1	0.0 (3)	N3—C6—C7—C12	−168.0 (3)
C3—S1—C2—N1	0.3 (2)	N4—C6—C7—C8	−173.3 (3)
C3—S1—C2—C1	−179.5 (3)	N3—C6—C7—C8	10.0 (4)
N1—N2—C3—S2	−178.4 (2)	C12—C7—C8—C9	−0.1 (5)
N1—N2—C3—S1	0.6 (3)	C6—C7—C8—C9	−178.2 (3)
C4—S2—C3—N2	−0.4 (3)	C7—C8—C9—C10	0.4 (5)
C4—S2—C3—S1	−179.38 (17)	C8—C9—C10—C11	−0.2 (5)
C2—S1—C3—N2	−0.5 (2)	C8—C9—C10—S3	−179.4 (3)
C2—S1—C3—S2	178.59 (19)	O3—S3—C10—C11	150.6 (2)
C5—O1—N4—C6	0.3 (3)	O2—S3—C10—C11	20.6 (3)
C3—S2—C4—C5	73.2 (3)	C13—S3—C10—C11	−94.4 (3)
C6—N3—C5—O1	−0.6 (4)	O3—S3—C10—C9	−30.3 (3)
C6—N3—C5—C4	−179.9 (3)	O2—S3—C10—C9	−160.3 (2)
N4—O1—C5—N3	0.2 (4)	C13—S3—C10—C9	84.7 (3)
N4—O1—C5—C4	179.7 (3)	C9—C10—C11—C12	−0.2 (5)
S2—C4—C5—N3	38.5 (5)	S3—C10—C11—C12	178.9 (2)
S2—C4—C5—O1	−140.8 (3)	C10—C11—C12—C7	0.5 (5)
O1—N4—C6—N3	−0.6 (4)	C8—C7—C12—C11	−0.4 (5)
O1—N4—C6—C7	−177.6 (3)	C6—C7—C12—C11	177.7 (3)
C5—N3—C6—N4	0.8 (4)