2-Methyl-5-[3-(4-nitro­phen­yl)-1,2,4-oxadiazol-5-ylmethyl­enesulfan­yl]-1,3,4-thia­diazole

The title compound, C₁₂H₉N₅O₃S₂, was synthesized via condensation of 1,2,4-oxadiazole chloro­methane with 1,3,4-thia­diazo­lethiol. The benzene and oxadiazole rings are almost coplanar, making a twist angle of only 4.6 (3)°, but the thia­diazole ring deviates from the mol­ecular plane, making a dihedral angle of 87.9 (3)° with the oxadiazole ring.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.064
• wR factor = 0.212
• Data-to-parameter ratio = 13.6

checkCIF/PLATON results

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Alert level C
PLAT230_ALERT_2_C Hirshfeld Test Diff for    C6     -   C7      ..       5.55 su
PLAT322_ALERT_2_C Check Hybridisation of  S1     in Main Residue .          ?
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          6
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety         C1

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
   4 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
   2 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
   1 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). This compound crystallizes in the monoclinic system,space group C2/c. There are three rings in the molecule. The benzene and oxadiazole rings are nearly coplanar, but the thiadiazole ring deviates from the molecular plane. 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 (30 mmol) was dissolve in ethanol (70 ml) and water (70 mmol). Sodium acetate (30 mmol) was added to this mixture. Then 3-[4-(nitro)phenyl]-5-chloromethyl-1,2,4-oxadiazol (50 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 crystallizing from a mixture of ethyl acetate (6 ml) and petrolum ether (6 ml). Crystals of (I) suitable for X-ray diffraction were obstained by slow evaporation of an ethanol solution. ¹H NMR (CDCl₃, δ, p.p.m.): 8.25–8.29 (m, 2H), 7.72–7.75 (m, 2H), 4.81–4.82 (s, 2H), 2.36–2.38 (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-nitrophenyl)-1,2,4-oxadiazol-5-ylmethylenesulfanyl]-1,3,4- thiadiazole

Crystal data

C12H9N5O3S2	F(000) = 1376
Mr = 335.36	Dx = 1.600 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 25 reflections
a = 35.939 (7) Å	θ = 9–13°
b = 5.6540 (11) Å	µ = 0.40 mm^−1
c = 13.714 (3) Å	T = 293 K
β = 92.55 (3)°	Block, colourless
V = 2783.9 (10) Å^3	0.40 × 0.30 × 0.20 mm
Z = 8

Data collection

Enraf–Nonius CAD-4 diffractometer	1965 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.033
Graphite monochromator	θmax = 26.0°, θmin = 1.1°
ω/2θ scans	h = −44→44
Absorption correction: ψ scan (North et al., 1968)	k = 0→6
Tmin = 0.855, Tmax = 0.924	l = 0→16
2772 measured reflections	3 standard reflections every 200 reflections
2727 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)] = 0.064	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.212	H-atom parameters constrained
S = 1.10	w = 1/[σ^2(Fo^2) + (0.1P)^2 + 1P] where P = (Fo^2 + 2Fc^2)/3
2727 reflections	(Δ/σ)max < 0.001
200 parameters	Δρmax = 0.30 e Å^−3
0 restraints	Δρmin = −0.31 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	0.48917 (3)	0.5272 (2)	0.62377 (9)	0.0525 (4)
S2	0.56945 (4)	0.6940 (2)	0.64667 (10)	0.0565 (4)
O1	0.61049 (9)	0.4474 (6)	0.4886 (2)	0.0542 (9)
O2	0.75292 (12)	−0.7027 (8)	0.3772 (3)	0.0766 (12)
O3	0.72006 (12)	−0.6820 (7)	0.2417 (3)	0.0709 (11)
N1	0.51318 (12)	0.1027 (8)	0.6228 (3)	0.0598 (11)
N2	0.54470 (11)	0.2462 (8)	0.6310 (3)	0.0554 (10)
N3	0.64182 (10)	0.1824 (7)	0.5757 (3)	0.0465 (9)
N4	0.62608 (11)	0.2924 (7)	0.4218 (3)	0.0516 (10)
N5	0.72802 (12)	−0.6150 (8)	0.3256 (3)	0.0541 (10)
C1	0.44496 (15)	0.1124 (11)	0.6123 (4)	0.0652 (14)
H1B	0.4420	0.0103	0.6673	0.098*
H1C	0.4425	0.0218	0.5532	0.098*
H1D	0.4262	0.2334	0.6115	0.098*
C2	0.48254 (14)	0.2238 (9)	0.6198 (3)	0.0522 (12)
C3	0.53603 (13)	0.4704 (8)	0.6337 (3)	0.0465 (11)
C4	0.61043 (14)	0.5081 (10)	0.6631 (4)	0.0594 (13)
H4B	0.6314	0.6079	0.6830	0.071*
H4C	0.6064	0.3991	0.7162	0.071*
C5	0.62069 (12)	0.3713 (8)	0.5783 (3)	0.0447 (10)
C6	0.64432 (12)	0.1382 (8)	0.4777 (3)	0.0447 (10)
C7	0.66602 (11)	−0.0549 (7)	0.4390 (3)	0.0401 (9)
C8	0.68800 (12)	−0.2013 (8)	0.5007 (3)	0.0462 (11)
H8A	0.6887	−0.1742	0.5677	0.055*
C9	0.70838 (12)	−0.3833 (9)	0.4645 (3)	0.0488 (11)
H9A	0.7227	−0.4804	0.5060	0.059*
C10	0.70704 (12)	−0.4188 (8)	0.3649 (3)	0.0445 (10)
C11	0.68665 (13)	−0.2755 (8)	0.3014 (3)	0.0482 (11)
H11A	0.6870	−0.3000	0.2344	0.058*
C12	0.66587 (12)	−0.0965 (9)	0.3382 (3)	0.0481 (11)
H12A	0.6515	−0.0015	0.2959	0.058*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0564 (7)	0.0482 (7)	0.0516 (7)	0.0156 (6)	−0.0111 (5)	−0.0032 (5)
S2	0.0608 (8)	0.0420 (7)	0.0656 (8)	0.0118 (6)	−0.0108 (6)	−0.0096 (6)
O1	0.0568 (19)	0.0386 (18)	0.065 (2)	0.0108 (15)	−0.0173 (16)	0.0030 (16)
O2	0.082 (3)	0.070 (3)	0.078 (3)	0.031 (2)	0.000 (2)	0.006 (2)
O3	0.091 (3)	0.055 (2)	0.066 (2)	0.003 (2)	−0.002 (2)	−0.0173 (19)
N1	0.058 (3)	0.044 (2)	0.077 (3)	0.009 (2)	−0.005 (2)	0.007 (2)
N2	0.048 (2)	0.047 (2)	0.070 (3)	0.0111 (19)	−0.0053 (19)	0.006 (2)
N3	0.045 (2)	0.046 (2)	0.047 (2)	0.0083 (17)	−0.0105 (16)	−0.0058 (17)
N4	0.055 (2)	0.044 (2)	0.055 (2)	0.0066 (19)	−0.0124 (17)	0.0054 (19)
N5	0.055 (2)	0.043 (2)	0.064 (3)	0.0014 (19)	0.001 (2)	−0.003 (2)
C1	0.061 (3)	0.061 (3)	0.073 (3)	0.006 (3)	−0.010 (3)	0.014 (3)
C2	0.055 (3)	0.054 (3)	0.046 (2)	0.016 (2)	−0.010 (2)	0.003 (2)
C3	0.051 (3)	0.048 (3)	0.040 (2)	0.011 (2)	−0.0060 (18)	−0.002 (2)
C4	0.052 (3)	0.056 (3)	0.068 (3)	0.014 (2)	−0.017 (2)	−0.018 (3)
C5	0.041 (2)	0.041 (2)	0.051 (2)	−0.003 (2)	−0.0118 (18)	−0.002 (2)
C6	0.045 (2)	0.039 (2)	0.049 (2)	−0.012 (2)	−0.0130 (18)	0.0035 (19)
C7	0.039 (2)	0.035 (2)	0.045 (2)	−0.0041 (18)	−0.0117 (17)	−0.0029 (18)
C8	0.050 (2)	0.049 (3)	0.038 (2)	−0.007 (2)	−0.0134 (18)	0.008 (2)
C9	0.045 (2)	0.045 (3)	0.055 (3)	0.003 (2)	−0.017 (2)	0.007 (2)
C10	0.041 (2)	0.039 (2)	0.053 (2)	−0.0056 (19)	−0.0114 (18)	0.002 (2)
C11	0.053 (3)	0.045 (3)	0.046 (2)	−0.003 (2)	−0.011 (2)	0.001 (2)
C12	0.047 (2)	0.054 (3)	0.042 (2)	0.003 (2)	−0.0132 (18)	0.010 (2)

Geometric parameters (Å, º)

S1—C3	1.714 (5)	C1—H1C	0.9600
S1—C2	1.732 (6)	C1—H1D	0.9600
S2—C3	1.747 (5)	C4—C5	1.457 (7)
S2—C4	1.815 (5)	C4—H4B	0.9700
O1—C5	1.340 (5)	C4—H4C	0.9700
O1—N4	1.402 (5)	C6—C7	1.456 (6)
O2—N5	1.221 (5)	C7—C8	1.402 (6)
O3—N5	1.232 (5)	C7—C12	1.402 (6)
N1—C2	1.296 (6)	C8—C9	1.369 (7)
N1—N2	1.394 (6)	C8—H8A	0.9300
N2—C3	1.307 (6)	C9—C10	1.380 (6)
N3—C5	1.312 (6)	C9—H9A	0.9300
N3—C6	1.374 (6)	C10—C11	1.376 (6)
N4—C6	1.316 (6)	C11—C12	1.367 (7)
N5—C10	1.458 (6)	C11—H11A	0.9300
C1—C2	1.490 (7)	C12—H12A	0.9300
C1—H1B	0.9600
C3—S1—C2	87.2 (2)	S2—C4—H4C	108.2
C3—S2—C4	98.3 (2)	H4B—C4—H4C	107.4
C5—O1—N4	107.4 (3)	N3—C5—O1	111.8 (4)
C2—N1—N2	112.4 (4)	N3—C5—C4	128.4 (4)
C3—N2—N1	111.9 (4)	O1—C5—C4	119.6 (4)
C5—N3—C6	103.8 (4)	N4—C6—N3	113.4 (4)
C6—N4—O1	103.7 (4)	N4—C6—C7	123.1 (4)
O2—N5—O3	123.3 (4)	N3—C6—C7	123.5 (4)
O2—N5—C10	118.2 (4)	C8—C7—C12	118.3 (4)
O3—N5—C10	118.4 (4)	C8—C7—C6	121.3 (4)
C2—C1—H1B	109.5	C12—C7—C6	120.4 (4)
C2—C1—H1C	109.5	C9—C8—C7	121.4 (4)
H1B—C1—H1C	109.5	C9—C8—H8A	119.3
C2—C1—H1D	109.5	C7—C8—H8A	119.3
H1B—C1—H1D	109.5	C8—C9—C10	118.2 (4)
H1C—C1—H1D	109.5	C8—C9—H9A	120.9
N1—C2—C1	123.0 (5)	C10—C9—H9A	120.9
N1—C2—S1	114.0 (4)	C11—C10—C9	122.3 (4)
C1—C2—S1	123.0 (4)	C11—C10—N5	118.9 (4)
N2—C3—S1	114.5 (4)	C9—C10—N5	118.7 (4)
N2—C3—S2	122.8 (4)	C12—C11—C10	119.1 (4)
S1—C3—S2	122.8 (3)	C12—C11—H11A	120.4
C5—C4—S2	116.2 (4)	C10—C11—H11A	120.4
C5—C4—H4B	108.2	C11—C12—C7	120.6 (4)
S2—C4—H4B	108.2	C11—C12—H12A	119.7
C5—C4—H4C	108.2	C7—C12—H12A	119.7
C2—N1—N2—C3	0.0 (6)	C5—N3—C6—N4	0.7 (5)
C5—O1—N4—C6	−0.2 (4)	C5—N3—C6—C7	178.6 (4)
N2—N1—C2—C1	−179.3 (4)	N4—C6—C7—C8	173.6 (4)
N2—N1—C2—S1	1.5 (6)	N3—C6—C7—C8	−4.1 (7)
C3—S1—C2—N1	−1.9 (4)	N4—C6—C7—C12	−5.3 (7)
C3—S1—C2—C1	178.9 (4)	N3—C6—C7—C12	176.9 (4)
N1—N2—C3—S1	−1.5 (5)	C12—C7—C8—C9	−1.1 (7)
N1—N2—C3—S2	178.4 (3)	C6—C7—C8—C9	179.9 (4)
C2—S1—C3—N2	1.9 (4)	C7—C8—C9—C10	0.5 (7)
C2—S1—C3—S2	−178.0 (3)	C8—C9—C10—C11	1.3 (7)
C4—S2—C3—N2	−4.6 (5)	C8—C9—C10—N5	−178.8 (4)
C4—S2—C3—S1	175.3 (3)	O2—N5—C10—C11	161.8 (4)
C3—S2—C4—C5	68.1 (5)	O3—N5—C10—C11	−17.3 (6)
C6—N3—C5—O1	−0.8 (5)	O2—N5—C10—C9	−18.1 (7)
C6—N3—C5—C4	−175.6 (5)	O3—N5—C10—C9	162.8 (4)
N4—O1—C5—N3	0.7 (5)	C9—C10—C11—C12	−2.4 (7)
N4—O1—C5—C4	176.0 (4)	N5—C10—C11—C12	177.7 (4)
S2—C4—C5—N3	−160.2 (4)	C10—C11—C12—C7	1.7 (7)
S2—C4—C5—O1	25.4 (6)	C8—C7—C12—C11	0.0 (7)
O1—N4—C6—N3	−0.3 (5)	C6—C7—C12—C11	179.0 (4)
O1—N4—C6—C7	−178.2 (4)