2-{[3-(4-Chloro­phen­yl)-1,2,4-oxadiazol-5-yl]methyl­sulfan­yl}-5-methyl-1,3,4-thia­diazole

The title compound, C₁₂H₉ClN₄OS₂, was synthesized via condensation of 5-chloro­methyl-3-(4-chloro­phen­yl)-1,2,4-oxadiazole with 5-mercapto-2-methyl-1,3,4-thia­diazole. The benzene and oxadiazole rings are coplanar due to the extended aromatic system. The angle between this plane and the thia­diazole ring is 82.2 (3)°.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.007 Å
• R factor = 0.057
• wR factor = 0.159
• Data-to-parameter ratio = 15.0

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          7

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
   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

1,2,4-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 a thiadiazole sulfanylether group present in the molecule, (I). This compound crystallizes in the monoclinic system, space group P2₁/c. 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 measures to 82.2 (3)°. There is no classic hydrogen bond in the molecular structure. The molecular structure of (I) is shown in Fig. 1. The 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-Mercapto-2-methyl-1,3,4-thiadiazole (20 mmol) was dissolved in ethanol (70 ml) and water (70 mmol). Sodium acetate (20 mmol) was added to this mixture. Then 3-[4-(chloro)phenyl]-5-chloromethyl-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 recrystallization from a mixture of ethyl acetate (8 ml) and light petrolum (bp. 333–363 K) (4 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.): 7.45–7.47(m, 2H), 7.35–7.36 (m, 2H), 4.17–4.18 (s, 2H), 2.35–2.36 (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. A view of the molecular structure of (I), showing displacement ellipsoids at the 30% probability level.

2-{[3-(4-Chlorophenyl)-1,2,4-oxadiazol-5-yl]methylsulfanyl}-5-methyl- 1,3,4-thiadiazole

Crystal data

C12H9ClN4OS2	F(000) = 664
Mr = 324.80	Dx = 1.544 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 25 reflections
a = 5.857 (1) Å	θ = 9–13°
b = 27.104 (5) Å	µ = 0.57 mm^−1
c = 9.026 (2) Å	T = 293 K
β = 102.85 (3)°	Block, colourless
V = 1397.0 (5) Å^3	0.40 × 0.20 × 0.10 mm
Z = 4

Data collection

Enraf–Nonius CAD-4 diffractometer	1783 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.043
Graphite monochromator	θmax = 26.0°, θmin = 1.5°
ω/2θ scans	h = −7→7
Absorption correction: ψ scan (North et al., 1968)	k = 0→33
Tmin = 0.804, Tmax = 0.945	l = 0→11
2999 measured reflections	3 standard reflections every 200 reflections
2733 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)] = 0.057	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.159	H-atom parameters constrained
S = 1.05	w = 1/[σ^2(Fo^2) + (0.06P)^2 + 1.5P] where P = (Fo^2 + 2Fc^2)/3
2733 reflections	(Δ/σ)max < 0.001
182 parameters	Δρmax = 0.31 e Å^−3
0 restraints	Δρmin = −0.36 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
Cl	1.1111 (2)	−0.13088 (5)	1.04622 (16)	0.0869 (5)
O	0.5610 (6)	0.09306 (13)	0.4953 (4)	0.0756 (10)
S1	0.6416 (2)	0.25547 (5)	0.78126 (12)	0.0620 (4)
N1	0.7360 (6)	0.23958 (14)	0.5242 (4)	0.0604 (10)
C1	0.9769 (8)	0.30697 (17)	0.6594 (5)	0.0669 (12)
H1B	1.0282	0.3101	0.5660	0.100*
H1C	1.1078	0.2985	0.7400	0.100*
H1D	0.9114	0.3377	0.6826	0.100*
S2	0.2753 (2)	0.17581 (4)	0.71433 (13)	0.0600 (3)
N2	0.5640 (6)	0.20583 (15)	0.5361 (4)	0.0634 (10)
C2	0.7962 (7)	0.26766 (16)	0.6434 (4)	0.0546 (10)
C3	0.4946 (7)	0.21095 (16)	0.6626 (4)	0.0529 (10)
N3	0.4483 (6)	0.05758 (13)	0.6854 (4)	0.0558 (9)
N4	0.7201 (7)	0.05395 (15)	0.5459 (5)	0.0727 (11)
C4	0.2231 (8)	0.13062 (17)	0.5637 (5)	0.0622 (11)
H4B	0.0729	0.1149	0.5593	0.075*
H4C	0.2159	0.1471	0.4673	0.075*
C5	0.4090 (8)	0.09241 (16)	0.5865 (5)	0.0568 (11)
C6	0.6443 (7)	0.03463 (16)	0.6587 (4)	0.0552 (11)
C7	0.7599 (7)	−0.00683 (16)	0.7487 (4)	0.0528 (10)
C8	0.9555 (8)	−0.02945 (18)	0.7194 (5)	0.0658 (12)
H8A	1.0164	−0.0187	0.6383	0.079*
C9	1.0614 (8)	−0.06754 (19)	0.8081 (6)	0.0719 (13)
H9A	1.1929	−0.0827	0.7865	0.086*
C10	0.9735 (8)	−0.08369 (17)	0.9301 (5)	0.0625 (11)
C11	0.7767 (8)	−0.06139 (18)	0.9601 (5)	0.0683 (13)
H11A	0.7159	−0.0720	1.0414	0.082*
C12	0.6719 (8)	−0.02366 (18)	0.8695 (5)	0.0638 (12)
H12A	0.5385	−0.0090	0.8895	0.077*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl	0.0857 (9)	0.0915 (10)	0.0884 (10)	0.0198 (7)	0.0295 (7)	0.0077 (8)
O	0.091 (2)	0.081 (2)	0.067 (2)	−0.0018 (19)	0.0442 (18)	0.0078 (18)
S1	0.0772 (7)	0.0716 (8)	0.0434 (6)	−0.0138 (6)	0.0266 (5)	−0.0068 (5)
N1	0.066 (2)	0.077 (3)	0.0416 (19)	−0.0086 (19)	0.0185 (17)	0.0008 (18)
C1	0.081 (3)	0.070 (3)	0.054 (3)	−0.012 (2)	0.025 (2)	0.007 (2)
S2	0.0631 (7)	0.0634 (7)	0.0582 (7)	−0.0014 (5)	0.0238 (5)	0.0031 (5)
N2	0.075 (2)	0.077 (3)	0.0411 (19)	−0.010 (2)	0.0197 (17)	−0.0036 (18)
C2	0.060 (2)	0.066 (3)	0.039 (2)	−0.004 (2)	0.0143 (18)	0.008 (2)
C3	0.062 (2)	0.057 (3)	0.041 (2)	0.0049 (19)	0.0156 (18)	0.0045 (19)
N3	0.061 (2)	0.062 (2)	0.050 (2)	−0.0076 (17)	0.0250 (16)	−0.0032 (18)
N4	0.087 (3)	0.072 (3)	0.074 (3)	−0.007 (2)	0.050 (2)	−0.004 (2)
C4	0.057 (2)	0.067 (3)	0.062 (3)	−0.010 (2)	0.011 (2)	0.007 (2)
C5	0.066 (3)	0.062 (3)	0.047 (2)	−0.015 (2)	0.024 (2)	−0.006 (2)
C6	0.069 (3)	0.060 (3)	0.047 (2)	−0.011 (2)	0.036 (2)	−0.015 (2)
C7	0.060 (2)	0.057 (3)	0.049 (2)	−0.0140 (19)	0.0288 (19)	−0.0159 (19)
C8	0.070 (3)	0.073 (3)	0.069 (3)	−0.009 (2)	0.046 (2)	−0.011 (3)
C9	0.064 (3)	0.081 (3)	0.082 (3)	−0.001 (3)	0.043 (3)	−0.015 (3)
C10	0.062 (3)	0.070 (3)	0.060 (3)	−0.002 (2)	0.023 (2)	−0.008 (2)
C11	0.076 (3)	0.078 (3)	0.062 (3)	0.003 (3)	0.040 (2)	0.000 (3)
C12	0.073 (3)	0.073 (3)	0.059 (3)	0.008 (2)	0.044 (2)	−0.002 (2)

Geometric parameters (Å, º)

Cl—C10	1.735 (5)	N4—C6	1.307 (5)
O—C5	1.341 (5)	C4—C5	1.483 (6)
O—N4	1.418 (5)	C4—H4B	0.9700
S1—C3	1.713 (4)	C4—H4C	0.9700
S1—C2	1.726 (4)	C6—C7	1.461 (6)
N1—C2	1.301 (5)	C7—C8	1.376 (6)
N1—N2	1.382 (5)	C7—C12	1.383 (5)
C1—C2	1.486 (6)	C8—C9	1.368 (7)
C1—H1B	0.9600	C8—H8A	0.9300
C1—H1C	0.9600	C9—C10	1.386 (6)
C1—H1D	0.9600	C9—H9A	0.9300
S2—C3	1.744 (4)	C10—C11	1.380 (6)
S2—C4	1.805 (5)	C11—C12	1.367 (6)
N2—C3	1.302 (5)	C11—H11A	0.9300
N3—C5	1.284 (5)	C12—H12A	0.9300
N3—C6	1.373 (5)
C5—O—N4	105.7 (3)	N3—C5—O	113.3 (4)
C3—S1—C2	87.5 (2)	N3—C5—C4	128.5 (4)
C2—N1—N2	113.0 (3)	O—C5—C4	118.2 (4)
C2—C1—H1B	109.5	N4—C6—N3	113.4 (4)
C2—C1—H1C	109.5	N4—C6—C7	123.0 (4)
H1B—C1—H1C	109.5	N3—C6—C7	123.6 (3)
C2—C1—H1D	109.5	C8—C7—C12	118.5 (4)
H1B—C1—H1D	109.5	C8—C7—C6	122.6 (4)
H1C—C1—H1D	109.5	C12—C7—C6	118.9 (4)
C3—S2—C4	100.4 (2)	C9—C8—C7	120.8 (4)
C3—N2—N1	111.9 (4)	C9—C8—H8A	119.6
N1—C2—C1	123.8 (4)	C7—C8—H8A	119.6
N1—C2—S1	113.3 (3)	C8—C9—C10	120.2 (4)
C1—C2—S1	122.9 (3)	C8—C9—H9A	119.9
N2—C3—S1	114.3 (3)	C10—C9—H9A	119.9
N2—C3—S2	124.7 (3)	C11—C10—C9	119.4 (5)
S1—C3—S2	121.0 (2)	C11—C10—Cl	120.0 (4)
C5—N3—C6	103.8 (3)	C9—C10—Cl	120.5 (4)
C6—N4—O	103.8 (3)	C12—C11—C10	119.6 (4)
C5—C4—S2	111.9 (3)	C12—C11—H11A	120.2
C5—C4—H4B	109.2	C10—C11—H11A	120.2
S2—C4—H4B	109.2	C11—C12—C7	121.5 (4)
C5—C4—H4C	109.2	C11—C12—H12A	119.3
S2—C4—H4C	109.2	C7—C12—H12A	119.3
H4B—C4—H4C	107.9
C2—N1—N2—C3	2.3 (5)	O—N4—C6—N3	0.4 (5)
N2—N1—C2—C1	−179.9 (4)	O—N4—C6—C7	−178.7 (4)
N2—N1—C2—S1	−0.9 (5)	C5—N3—C6—N4	−1.2 (5)
C3—S1—C2—N1	−0.5 (3)	C5—N3—C6—C7	177.9 (4)
C3—S1—C2—C1	178.6 (4)	N4—C6—C7—C8	−1.4 (7)
N1—N2—C3—S1	−2.7 (5)	N3—C6—C7—C8	179.6 (4)
N1—N2—C3—S2	178.4 (3)	N4—C6—C7—C12	177.7 (4)
C2—S1—C3—N2	1.8 (4)	N3—C6—C7—C12	−1.4 (6)
C2—S1—C3—S2	−179.2 (3)	C12—C7—C8—C9	−0.3 (7)
C4—S2—C3—N2	7.5 (4)	C6—C7—C8—C9	178.7 (4)
C4—S2—C3—S1	−171.4 (3)	C7—C8—C9—C10	−0.5 (7)
C5—O—N4—C6	0.5 (4)	C8—C9—C10—C11	0.8 (7)
C3—S2—C4—C5	76.7 (3)	C8—C9—C10—Cl	−178.3 (4)
C6—N3—C5—O	1.6 (5)	C9—C10—C11—C12	−0.2 (7)
C6—N3—C5—C4	−178.0 (4)	Cl—C10—C11—C12	178.9 (4)
N4—O—C5—N3	−1.3 (5)	C10—C11—C12—C7	−0.6 (7)
N4—O—C5—C4	178.2 (4)	C8—C7—C12—C11	0.9 (7)
S2—C4—C5—N3	71.5 (5)	C6—C7—C12—C11	−178.1 (4)
S2—C4—C5—O	−108.0 (4)