3-(3-Methoxy­phen­yl)-5-[(5-methyl-1,3,4-thia­diazol-2-yl)sulfanylmeth­yl]-1,2,4-oxadiazole

The title compound, C₁₃H₁₂N₄O₂S₂, was synthesized via condensation of 5-chloro­methyl-3-(3-methoxy­phen­yl)-1,2,4-oxadiazole with (5-methyl-1,3,4-thia­diazol-2-yl)methane­thiol. The benzene and oxadiazole rings are coplanar due to the extended aromatic system. The angle between this plane and the thia­diazole ring is 77.8 (3)°.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.046
• wR factor = 0.128
• Data-to-parameter ratio = 14.7

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)       3000 Deg.
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
   2 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   3 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 thioether 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). This compound crystallizes in the triclinic system, space group P1. There are three rings in the molecule. The benzene and oxadiazole ring are of course coplanar due to the extended aromatic system. The angle between the before mentioned plane and the thiadiazole moiety is 102.2 (3)°. There is no classic hydrogen bond in the crystal structure. The molecular structure of (I) is shown in Fig. 1. Bond lengths and angles are given in Table 1.

Related literature

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

S2. Experimental

(5-Methyl-[1,3,4]thiadiazol-2-yl)methanethiol (20 mmol) was dissolved in ethanol (70 ml) and water (70 mmol). Sodium acetate (20 mmol) was added to this mixture. Then 5-chlormethyl-3-(3-(methoxy)phenyl)-[1,2,4]oxadiazole (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 obstained by crystallization from a mixture of ethyl acetate (8 ml) and light petrolum (bp. 333–363 K) (6 ml). Crystals of (I) suitable for X-ray diffraction were obstained by slow evaporation of an ethanolic solution. ¹H NMR (CDCl₃, δ, p.p.m.): 7.21–7.22 (m, 1H), 7.03–7.04 (m, 1H), 6.95–6.97 (m, 1H), 6.75–6.76 (m, 1H), 4.18–4.19 (s, 2H), 3.72–3.73 (s, 3H), 2.32–2.33 (s, 3H).

S3. Refinement

All H atoms bonded to the C atoms were placed geometrically at distances of 0.93–0.96 Å and included in the refinement using a 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. Molecular structure of (I), showing displacement ellipsoids at the 30% probability level.

3-(3-Methoxyphenyl)-5-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfanylmethyl]- 1,2,4-oxadiazole

Crystal data

C13H12N4O2S2	Z = 2
Mr = 320.39	F(000) = 332
Triclinic, P1	Dx = 1.490 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.139 (1) Å	Cell parameters from 25 reflections
b = 9.890 (2) Å	θ = 9–13°
c = 12.658 (3) Å	µ = 0.38 mm^−1
α = 72.45 (3)°	T = 293 K
β = 85.91 (3)°	Block, colourless
γ = 77.12 (3)°	0.30 × 0.10 × 0.10 mm
V = 714.3 (3) Å^3

Data collection

Nonius CAD-4 diffractometer	2063 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.042
Graphite monochromator	θmax = 26.0°, θmin = 1.7°
ω/2θ scans	h = −7→7
Absorption correction: ψ scan (North et al., 1968)	k = −11→12
Tmin = 0.894, Tmax = 0.963	l = 0→15
3078 measured reflections	3 standard reflections every 200 reflections
2802 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)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.128	H-atom parameters constrained
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0486P)^2 + 0.4476P] where P = (Fo^2 + 2Fc^2)/3
2802 reflections	(Δ/σ)max = 0.002
191 parameters	Δρmax = 0.19 e Å^−3
0 restraints	Δρmin = −0.28 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	0.10119 (14)	0.96648 (9)	0.81705 (7)	0.0591 (3)
O1	−0.0772 (3)	0.5239 (2)	0.82199 (18)	0.0542 (5)
N1	−0.1954 (4)	0.8596 (3)	0.9446 (2)	0.0597 (7)
C1	−0.3048 (6)	1.1241 (4)	0.8789 (3)	0.0724 (10)
H1B	−0.4264	1.1101	0.9302	0.109*
H1C	−0.3623	1.1662	0.8049	0.109*
H1D	−0.2248	1.1878	0.8960	0.109*
S2	0.37028 (13)	0.66652 (9)	0.84080 (7)	0.0526 (2)
O2	0.3255 (4)	0.1410 (3)	0.4522 (2)	0.0658 (6)
N2	−0.0301 (4)	0.7422 (3)	0.9376 (2)	0.0572 (7)
C2	−0.1523 (5)	0.9826 (3)	0.8873 (2)	0.0512 (7)
N3	0.1928 (4)	0.3948 (2)	0.74697 (19)	0.0436 (6)
C3	0.1342 (5)	0.7819 (3)	0.8740 (2)	0.0455 (7)
N4	−0.1791 (4)	0.4826 (3)	0.7427 (2)	0.0542 (6)
C4	0.2916 (5)	0.4923 (3)	0.8934 (2)	0.0451 (7)
H4B	0.4258	0.4161	0.9054	0.054*
H4C	0.2177	0.4863	0.9646	0.054*
C5	0.1416 (4)	0.4666 (3)	0.8184 (2)	0.0431 (7)
C6	−0.0109 (4)	0.4076 (3)	0.7011 (2)	0.0395 (6)
C7	−0.0365 (4)	0.3450 (3)	0.6138 (2)	0.0413 (6)
C8	−0.2466 (5)	0.3615 (3)	0.5687 (3)	0.0530 (8)
H8A	−0.3742	0.4107	0.5963	0.064*
C9	−0.2626 (5)	0.3047 (4)	0.4837 (3)	0.0578 (8)
H9A	−0.4018	0.3172	0.4533	0.069*
C10	−0.0764 (5)	0.2296 (3)	0.4427 (3)	0.0508 (7)
H10A	−0.0903	0.1914	0.3854	0.061*
C11	0.1300 (5)	0.2115 (3)	0.4868 (2)	0.0463 (7)
C12	0.1486 (5)	0.2702 (3)	0.5724 (2)	0.0440 (7)
H12A	0.2884	0.2584	0.6019	0.053*
C13	0.3205 (6)	0.0859 (4)	0.3617 (3)	0.0632 (9)
H13A	0.4692	0.0399	0.3462	0.095*
H13B	0.2624	0.1640	0.2977	0.095*
H13C	0.2266	0.0163	0.3798	0.095*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0622 (5)	0.0439 (4)	0.0664 (5)	−0.0132 (4)	0.0141 (4)	−0.0110 (4)
O1	0.0392 (11)	0.0621 (13)	0.0624 (13)	0.0001 (10)	0.0046 (10)	−0.0288 (11)
N1	0.0627 (17)	0.0475 (15)	0.0632 (17)	−0.0066 (13)	0.0197 (14)	−0.0159 (13)
C1	0.079 (2)	0.052 (2)	0.073 (2)	0.0034 (18)	0.0129 (19)	−0.0144 (18)
S2	0.0426 (4)	0.0518 (5)	0.0632 (5)	−0.0071 (3)	0.0029 (3)	−0.0195 (4)
O2	0.0509 (13)	0.0825 (16)	0.0708 (15)	0.0001 (12)	−0.0045 (11)	−0.0421 (13)
N2	0.0592 (16)	0.0441 (14)	0.0604 (16)	−0.0060 (12)	0.0170 (13)	−0.0114 (12)
C2	0.0551 (18)	0.0469 (17)	0.0480 (17)	−0.0052 (14)	0.0051 (14)	−0.0137 (14)
N3	0.0405 (13)	0.0424 (13)	0.0441 (13)	−0.0010 (10)	−0.0007 (10)	−0.0125 (11)
C3	0.0503 (17)	0.0431 (15)	0.0437 (16)	−0.0086 (13)	−0.0007 (13)	−0.0143 (13)
N4	0.0429 (14)	0.0585 (16)	0.0656 (17)	−0.0059 (12)	−0.0008 (12)	−0.0281 (13)
C4	0.0441 (16)	0.0431 (15)	0.0453 (16)	0.0005 (12)	−0.0021 (13)	−0.0153 (13)
C5	0.0396 (15)	0.0364 (14)	0.0450 (16)	−0.0030 (12)	0.0012 (12)	−0.0039 (12)
C6	0.0341 (14)	0.0359 (14)	0.0427 (15)	−0.0057 (11)	0.0032 (11)	−0.0049 (12)
C7	0.0392 (15)	0.0378 (14)	0.0404 (15)	−0.0071 (11)	0.0021 (12)	−0.0032 (12)
C8	0.0361 (15)	0.0587 (19)	0.062 (2)	−0.0088 (14)	0.0015 (14)	−0.0154 (16)
C9	0.0414 (17)	0.072 (2)	0.062 (2)	−0.0154 (15)	−0.0060 (15)	−0.0185 (17)
C10	0.0559 (19)	0.0518 (17)	0.0480 (17)	−0.0179 (15)	−0.0039 (14)	−0.0139 (14)
C11	0.0437 (16)	0.0451 (16)	0.0478 (16)	−0.0082 (13)	−0.0006 (13)	−0.0110 (13)
C12	0.0397 (15)	0.0446 (15)	0.0467 (16)	−0.0101 (12)	−0.0039 (12)	−0.0103 (13)
C13	0.072 (2)	0.067 (2)	0.0543 (19)	−0.0092 (18)	0.0069 (17)	−0.0286 (17)

Geometric parameters (Å, º)

S1—C3	1.719 (3)	C4—C5	1.480 (4)
S1—C2	1.737 (3)	C4—H4B	0.9700
O1—C5	1.340 (3)	C4—H4C	0.9700
O1—N4	1.420 (3)	C6—C7	1.453 (4)
N1—C2	1.288 (4)	C7—C12	1.373 (4)
N1—N2	1.382 (3)	C7—C8	1.403 (4)
C1—C2	1.479 (4)	C8—C9	1.374 (4)
C1—H1B	0.9600	C8—H8A	0.9300
C1—H1C	0.9600	C9—C10	1.377 (4)
C1—H1D	0.9600	C9—H9A	0.9300
S2—C3	1.745 (3)	C10—C11	1.374 (4)
S2—C4	1.811 (3)	C10—H10A	0.9300
O2—C11	1.362 (3)	C11—C12	1.397 (4)
O2—C13	1.413 (4)	C12—H12A	0.9300
N2—C3	1.299 (4)	C13—H13A	0.9600
N3—C5	1.291 (3)	C13—H13B	0.9600
N3—C6	1.381 (3)	C13—H13C	0.9600
N4—C6	1.308 (3)
C3—S1—C2	87.03 (15)	O1—C5—C4	118.0 (3)
C5—O1—N4	106.0 (2)	N4—C6—N3	113.8 (2)
C2—N1—N2	113.3 (3)	N4—C6—C7	122.9 (2)
C2—C1—H1B	109.5	N3—C6—C7	123.3 (2)
C2—C1—H1C	109.5	C12—C7—C8	118.9 (3)
H1B—C1—H1C	109.5	C12—C7—C6	119.6 (3)
C2—C1—H1D	109.5	C8—C7—C6	121.4 (3)
H1B—C1—H1D	109.5	C9—C8—C7	119.6 (3)
H1C—C1—H1D	109.5	C9—C8—H8A	120.2
C3—S2—C4	101.41 (14)	C7—C8—H8A	120.2
C11—O2—C13	118.5 (2)	C8—C9—C10	121.3 (3)
C3—N2—N1	112.0 (2)	C8—C9—H9A	119.4
N1—C2—C1	123.9 (3)	C10—C9—H9A	119.4
N1—C2—S1	113.4 (2)	C11—C10—C9	119.7 (3)
C1—C2—S1	122.7 (2)	C11—C10—H10A	120.1
C5—N3—C6	103.2 (2)	C9—C10—H10A	120.1
N2—C3—S1	114.2 (2)	O2—C11—C10	124.9 (3)
N2—C3—S2	126.1 (2)	O2—C11—C12	115.6 (3)
S1—C3—S2	119.65 (17)	C10—C11—C12	119.5 (3)
C6—N4—O1	103.5 (2)	C7—C12—C11	121.0 (3)
C5—C4—S2	113.3 (2)	C7—C12—H12A	119.5
C5—C4—H4B	108.9	C11—C12—H12A	119.5
S2—C4—H4B	108.9	O2—C13—H13A	109.5
C5—C4—H4C	108.9	O2—C13—H13B	109.5
S2—C4—H4C	108.9	H13A—C13—H13B	109.5
H4B—C4—H4C	107.7	O2—C13—H13C	109.5
N3—C5—O1	113.5 (3)	H13A—C13—H13C	109.5
N3—C5—C4	128.4 (2)	H13B—C13—H13C	109.5
C2—N1—N2—C3	−0.1 (4)	O1—N4—C6—C7	−178.8 (2)
N2—N1—C2—C1	178.5 (3)	C5—N3—C6—N4	−0.4 (3)
N2—N1—C2—S1	0.1 (4)	C5—N3—C6—C7	179.0 (2)
C3—S1—C2—N1	−0.1 (3)	N4—C6—C7—C12	178.6 (3)
C3—S1—C2—C1	−178.5 (3)	N3—C6—C7—C12	−0.8 (4)
N1—N2—C3—S1	0.0 (3)	N4—C6—C7—C8	−0.1 (4)
N1—N2—C3—S2	−178.1 (2)	N3—C6—C7—C8	−179.5 (3)
C2—S1—C3—N2	0.1 (2)	C12—C7—C8—C9	−0.9 (4)
C2—S1—C3—S2	178.2 (2)	C6—C7—C8—C9	177.8 (3)
C4—S2—C3—N2	10.8 (3)	C7—C8—C9—C10	1.0 (5)
C4—S2—C3—S1	−167.13 (17)	C8—C9—C10—C11	−0.4 (5)
C5—O1—N4—C6	−0.5 (3)	C13—O2—C11—C10	2.3 (4)
C3—S2—C4—C5	79.9 (2)	C13—O2—C11—C12	−176.6 (3)
C6—N3—C5—O1	0.0 (3)	C9—C10—C11—O2	−179.2 (3)
C6—N3—C5—C4	−179.7 (3)	C9—C10—C11—C12	−0.3 (4)
N4—O1—C5—N3	0.3 (3)	C8—C7—C12—C11	0.2 (4)
N4—O1—C5—C4	−179.9 (2)	C6—C7—C12—C11	−178.5 (2)
S2—C4—C5—N3	97.6 (3)	O2—C11—C12—C7	179.4 (2)
S2—C4—C5—O1	−82.1 (3)	C10—C11—C12—C7	0.4 (4)
O1—N4—C6—N3	0.6 (3)