supplementary materials


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Acta Cryst. (2013). E69, o727    [ doi:10.1107/S1600536813008805 ]

3-(4-Methylphenyl)-4-[(thiosemicarbazono)methyl]-1,2,3-oxadiazol-3-ium-5-olate 1,4-dioxane hemisolvate

M. Abdul Rahiman, G. N. Ravikumar, W.-S. Loh and I. A. Razak

Abstract top

The asymmetric unit of the title compound, C11H11N5O2S·0.5C4H8O2, contains one 3-(p-tolyl)sydnone 4-thiosemicarbazone molecule and a half molecule of 1,4-dioxane, which lies abount an inversion centre. The sydnone ring is almost planar, with a maximum deviation of 0.002 (1) Å, and forms a dihedral angle of 46.31 (5)° with the benzene ring. In the crystal, the two components are linked into a tape along [01-1] by N-H...O and N-H...S hydrogen bonds. The crystal structure is further stabilized by C-H...O and C-H...[pi] interactions, forming a three-dimensional network.

Comment top

Sydnones are mesoionic heterocyclic aromatic compounds. The study of sydnones still remains a field of interest because of their electronic structures and also because of the varied types of biological activities displayed by some of them (Rai et al., 2008). Recently sydnone derivatives were found to exhibit promising antimicrobial (Jyothi et al., 2008), anti-inflammatory (Nithinchandra et al., 2012) and CNS depressant properties (Kalluraya et al., 2001). Since their discovery, sydnones have shown diverse biological activities and it is thought that the meso-ionic nature of the sydnone ring promotes significant interactions with biological systems.

The asymmetric unit of the title compound, Fig. 1, contains one 3-(p-tolyl)-sydnone-4-thiosemicarbazone molecule and half of a 1,4-dioxane molecule. The sydnone ring (N1/N2/O1/C7/C8) is almost planar with maximum deviation of 0.002 (1) Å at O1 and it forms dihedral angle of 46.31 (5)° with the benzene ring (C1–C6).The complete 1–4 dioxane molecule is generated by crystallograhic inversion symmetry [symmetry code = -x, -y, -z + 2]. Bond lengths and angles are almost comparable with the related structure (Fun et al., 2011).

In the crystal structure, Fig. 2, the molecules are linked into three dimensional network by intermolecular N4—H1N4···O3, N5—H1N5···S1, C5—H5A···O2, C9—H9A···O3 and C12—H12B···O2 hydrogen bonds (Table 1). The crystal structure was further stabilized by C—H···π interactions (Table 1), involving the centroid of the benzene ring (Cg1).

Related literature top

For the biological acitivity of sydnones, see: Rai et al. (2008); Jyothi et al. (2008); Nithinchandra et al. (2012); Kalluraya et al. (2001). For a related structure, see: Fun et al. (2011). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).

Experimental top

To a mixture of 4-formyl-3-(p-tolyl)sydnone (0.01 mol) and thiosemicarbazide (0.01 mol) in ethanol, a catalytic amount of concentrated H2SO4 was added. The solution was stirred at room temperature for 23 h. The solid product that separated out was filtered and dried. The recrystallization of the sample was done using an ethanol-dioxane (1:1 v/v) mixture. The slow evaporation of the ethanol-dioxane mixture of the compound resulted in crystals suitable for X-ray analysis.

Refinement top

N-bound H atoms were located in a difference Fourier map and were refined freely [N—H = 0.868 (17) to 0.872 (18) Å]. The remaining H atoms were located geometrically and were refined using a riding model with Uiso(H) = 1.2 or 1.5Ueq(C) (C—H = 0.95 to 0.99 Å). A rotating group model was applied to the methyl group. In the final refinement, two outliners (-3 6 14 and 1 8 14) were omitted.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed along the b axis. H atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity.
3-(4-Methylphenyl)-4-[(thiosemicarbazono)methyl]-1,2,3-oxadiazol-3-ium-5-olate 1,4-dioxane hemisolvate top
Crystal data top
C11H11N5O2S·0.5C4H8O2Z = 2
Mr = 321.36F(000) = 336
Triclinic, P1Dx = 1.432 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.7463 (1) ÅCell parameters from 9931 reflections
b = 9.3776 (1) Åθ = 2.2–32.7°
c = 10.4449 (2) ŵ = 0.24 mm1
α = 79.689 (1)°T = 100 K
β = 87.168 (1)°Block, yellow
γ = 87.461 (1)°0.35 × 0.29 × 0.24 mm
V = 745.09 (2) Å3
Data collection top
Bruker APEXII CCD area-detector
diffractometer
5407 independent reflections
Radiation source: fine-focus sealed tube4782 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
φ and ω scansθmax = 32.7°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 1111
Tmin = 0.921, Tmax = 0.944k = 1414
19865 measured reflectionsl = 1515
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.090H atoms treated by a mixture of independent and constrained refinement
S = 1.08 w = 1/[σ2(Fo2) + (0.0369P)2 + 0.310P]
where P = (Fo2 + 2Fc2)/3
5407 reflections(Δ/σ)max = 0.002
212 parametersΔρmax = 0.43 e Å3
0 restraintsΔρmin = 0.24 e Å3
Crystal data top
C11H11N5O2S·0.5C4H8O2γ = 87.461 (1)°
Mr = 321.36V = 745.09 (2) Å3
Triclinic, P1Z = 2
a = 7.7463 (1) ÅMo Kα radiation
b = 9.3776 (1) ŵ = 0.24 mm1
c = 10.4449 (2) ÅT = 100 K
α = 79.689 (1)°0.35 × 0.29 × 0.24 mm
β = 87.168 (1)°
Data collection top
Bruker APEXII CCD area-detector
diffractometer
5407 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
4782 reflections with I > 2σ(I)
Tmin = 0.921, Tmax = 0.944Rint = 0.021
19865 measured reflectionsθmax = 32.7°
Refinement top
R[F2 > 2σ(F2)] = 0.035H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.090Δρmax = 0.43 e Å3
S = 1.08Δρmin = 0.24 e Å3
5407 reflectionsAbsolute structure: ?
212 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.

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 (Å2) top
xyzUiso*/Ueq
S11.09153 (3)0.32862 (3)0.33706 (2)0.01659 (6)
O10.47671 (10)0.67385 (8)0.20795 (7)0.01898 (15)
O20.57636 (11)0.75787 (8)0.00058 (8)0.02035 (15)
N10.59090 (11)0.46077 (9)0.24338 (8)0.01427 (15)
N20.48951 (12)0.54926 (10)0.29962 (9)0.01841 (17)
N30.79973 (11)0.49150 (9)0.07807 (8)0.01443 (15)
N40.91376 (11)0.40423 (9)0.13781 (8)0.01460 (15)
N50.90336 (13)0.57238 (10)0.32586 (9)0.01962 (17)
C10.68059 (14)0.31717 (11)0.44782 (10)0.01739 (18)
H1A0.68550.40400.48230.021*
C20.72069 (14)0.18334 (11)0.52322 (10)0.01834 (18)
H2A0.75120.17870.61090.022*
C30.71703 (13)0.05535 (11)0.47262 (10)0.01713 (18)
C40.66732 (14)0.06363 (11)0.34462 (10)0.01855 (18)
H4A0.66330.02280.30950.022*
C50.62369 (14)0.19592 (11)0.26773 (10)0.01751 (18)
H5A0.58830.20080.18120.021*
C60.63314 (13)0.32100 (10)0.32082 (9)0.01490 (17)
C70.57264 (13)0.65882 (11)0.09278 (10)0.01562 (17)
C80.64729 (12)0.51563 (10)0.11978 (9)0.01360 (16)
C90.76555 (12)0.44016 (10)0.04353 (9)0.01363 (16)
H9A0.81970.35120.08270.016*
C100.96088 (12)0.44310 (10)0.26539 (9)0.01415 (16)
C110.76728 (15)0.08866 (12)0.55341 (11)0.0222 (2)
H11A0.69670.16430.53130.033*
H11B0.74800.08380.64600.033*
H11C0.88980.11170.53560.033*
O30.07175 (11)0.12953 (8)1.03347 (8)0.02138 (16)
C120.07792 (15)0.05932 (12)1.09562 (11)0.0217 (2)
H12A0.04190.00771.17590.026*
H12B0.15170.13281.12030.026*
C130.17918 (15)0.02410 (13)0.99557 (12)0.0237 (2)
H13A0.28150.07370.95180.028*
H13B0.22030.04361.07390.028*
H1N40.947 (2)0.3189 (18)0.0967 (16)0.028 (4)*
H1N50.919 (2)0.5963 (19)0.4101 (18)0.036 (4)*
H2N50.826 (2)0.6209 (18)0.2864 (16)0.030 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.02010 (12)0.01732 (11)0.01242 (10)0.00041 (8)0.00249 (8)0.00394 (8)
O10.0199 (3)0.0181 (3)0.0193 (3)0.0032 (3)0.0007 (3)0.0054 (3)
O20.0241 (4)0.0157 (3)0.0206 (4)0.0000 (3)0.0040 (3)0.0009 (3)
N10.0148 (3)0.0160 (3)0.0123 (3)0.0012 (3)0.0019 (3)0.0038 (3)
N20.0190 (4)0.0195 (4)0.0168 (4)0.0016 (3)0.0036 (3)0.0054 (3)
N30.0155 (3)0.0152 (3)0.0129 (3)0.0005 (3)0.0013 (3)0.0036 (3)
N40.0182 (4)0.0145 (3)0.0107 (3)0.0008 (3)0.0022 (3)0.0021 (3)
N50.0247 (4)0.0181 (4)0.0139 (4)0.0032 (3)0.0046 (3)0.0006 (3)
C10.0214 (4)0.0179 (4)0.0133 (4)0.0031 (4)0.0020 (3)0.0042 (3)
C20.0215 (5)0.0214 (4)0.0123 (4)0.0021 (4)0.0009 (3)0.0031 (3)
C30.0170 (4)0.0184 (4)0.0149 (4)0.0002 (3)0.0018 (3)0.0007 (3)
C40.0240 (5)0.0168 (4)0.0153 (4)0.0014 (4)0.0013 (3)0.0042 (3)
C50.0224 (5)0.0180 (4)0.0125 (4)0.0027 (4)0.0012 (3)0.0037 (3)
C60.0166 (4)0.0155 (4)0.0121 (4)0.0018 (3)0.0025 (3)0.0015 (3)
C70.0158 (4)0.0161 (4)0.0160 (4)0.0012 (3)0.0012 (3)0.0056 (3)
C80.0149 (4)0.0138 (4)0.0120 (4)0.0007 (3)0.0013 (3)0.0026 (3)
C90.0148 (4)0.0139 (4)0.0124 (4)0.0012 (3)0.0007 (3)0.0032 (3)
C100.0149 (4)0.0155 (4)0.0122 (4)0.0027 (3)0.0012 (3)0.0026 (3)
C110.0242 (5)0.0199 (5)0.0206 (5)0.0029 (4)0.0003 (4)0.0004 (4)
O30.0263 (4)0.0143 (3)0.0233 (4)0.0020 (3)0.0021 (3)0.0041 (3)
C120.0271 (5)0.0205 (5)0.0178 (5)0.0019 (4)0.0015 (4)0.0036 (4)
C130.0207 (5)0.0227 (5)0.0281 (5)0.0016 (4)0.0007 (4)0.0060 (4)
Geometric parameters (Å, º) top
S1—C101.6893 (10)C3—C111.5051 (14)
O1—N21.3749 (12)C4—C51.3897 (14)
O1—C71.4079 (12)C4—H4A0.9500
O2—C71.2126 (12)C5—C61.3903 (14)
N1—N21.3122 (11)C5—H5A0.9500
N1—C81.3597 (12)C7—C81.4244 (13)
N1—C61.4449 (13)C8—C91.4306 (13)
N3—C91.2939 (12)C9—H9A0.9500
N3—N41.3797 (11)C11—H11A0.9800
N4—C101.3534 (12)C11—H11B0.9800
N4—H1N40.871 (16)C11—H11C0.9800
N5—C101.3316 (13)O3—C121.4329 (14)
N5—H1N50.872 (18)O3—C131.4395 (14)
N5—H2N50.868 (17)C12—C13i1.5076 (16)
C1—C61.3878 (14)C12—H12A0.9900
C1—C21.3884 (14)C12—H12B0.9900
C1—H1A0.9500C13—C12i1.5076 (16)
C2—C31.3972 (14)C13—H13A0.9900
C2—H2A0.9500C13—H13B0.9900
C3—C41.3974 (14)
N2—O1—C7111.07 (7)O2—C7—C8135.35 (10)
N2—N1—C8114.90 (8)O1—C7—C8104.14 (8)
N2—N1—C6116.69 (8)N1—C8—C7105.26 (8)
C8—N1—C6128.37 (8)N1—C8—C9123.94 (9)
N1—N2—O1104.63 (7)C7—C8—C9130.70 (9)
C9—N3—N4113.44 (8)N3—C9—C8120.84 (9)
C10—N4—N3120.28 (8)N3—C9—H9A119.6
C10—N4—H1N4118.9 (11)C8—C9—H9A119.6
N3—N4—H1N4120.4 (11)N5—C10—N4117.10 (9)
C10—N5—H1N5119.6 (12)N5—C10—S1124.08 (7)
C10—N5—H2N5119.2 (11)N4—C10—S1118.81 (7)
H1N5—N5—H2N5118.8 (15)C3—C11—H11A109.5
C6—C1—C2118.34 (9)C3—C11—H11B109.5
C6—C1—H1A120.8H11A—C11—H11B109.5
C2—C1—H1A120.8C3—C11—H11C109.5
C1—C2—C3121.26 (9)H11A—C11—H11C109.5
C1—C2—H2A119.4H11B—C11—H11C109.5
C3—C2—H2A119.4C12—O3—C13110.28 (8)
C2—C3—C4118.66 (9)O3—C12—C13i109.89 (9)
C2—C3—C11120.90 (9)O3—C12—H12A109.7
C4—C3—C11120.44 (9)C13i—C12—H12A109.7
C5—C4—C3121.25 (9)O3—C12—H12B109.7
C5—C4—H4A119.4C13i—C12—H12B109.7
C3—C4—H4A119.4H12A—C12—H12B108.2
C4—C5—C6118.22 (9)O3—C13—C12i109.94 (9)
C4—C5—H5A120.9O3—C13—H13A109.7
C6—C5—H5A120.9C12i—C13—H13A109.7
C1—C6—C5122.23 (9)O3—C13—H13B109.7
C1—C6—N1117.89 (9)C12i—C13—H13B109.7
C5—C6—N1119.87 (9)H13A—C13—H13B108.2
O2—C7—O1120.50 (9)
C8—N1—N2—O10.38 (11)N2—O1—C7—O2179.80 (9)
C6—N1—N2—O1177.55 (8)N2—O1—C7—C80.36 (10)
C7—O1—N2—N10.46 (10)N2—N1—C8—C70.17 (11)
C9—N3—N4—C10179.48 (9)C6—N1—C8—C7177.48 (9)
C6—C1—C2—C31.24 (16)N2—N1—C8—C9176.73 (9)
C1—C2—C3—C41.73 (16)C6—N1—C8—C90.92 (16)
C1—C2—C3—C11177.64 (10)O2—C7—C8—N1179.92 (12)
C2—C3—C4—C50.61 (16)O1—C7—C8—N10.12 (10)
C11—C3—C4—C5178.75 (10)O2—C7—C8—C93.7 (2)
C3—C4—C5—C60.93 (16)O1—C7—C8—C9176.11 (10)
C2—C1—C6—C50.39 (15)N4—N3—C9—C8178.91 (8)
C2—C1—C6—N1179.72 (9)N1—C8—C9—N3172.48 (9)
C4—C5—C6—C11.46 (15)C7—C8—C9—N311.90 (16)
C4—C5—C6—N1179.22 (9)N3—N4—C10—N55.06 (14)
N2—N1—C6—C145.36 (13)N3—N4—C10—S1176.46 (7)
C8—N1—C6—C1132.25 (11)C13—O3—C12—C13i58.64 (12)
N2—N1—C6—C5133.99 (10)C12—O3—C13—C12i58.67 (12)
C8—N1—C6—C548.40 (14)
Symmetry code: (i) x, y, z+2.
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C1–C6 benzene ring.
D—H···AD—HH···AD···AD—H···A
N4—H1N4···O3ii0.872 (17)2.040 (17)2.8624 (12)156.8 (14)
N5—H1N5···S1iii0.872 (18)2.613 (18)3.4754 (9)170.2 (14)
C5—H5A···O2iv0.952.313.2215 (13)162
C9—H9A···O3ii0.952.343.1394 (12)141
C12—H12B···O2v0.992.563.2626 (14)128
C11—H11A···Cg1vi0.982.943.5736 (12)123
Symmetry codes: (ii) x+1, y, z1; (iii) x+2, y+1, z1; (iv) x+1, y+1, z; (v) x+1, y+1, z+1; (vi) x+1, y, z+1.
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C1–C6 benzene ring.
D—H···AD—HH···AD···AD—H···A
N4—H1N4···O3i0.872 (17)2.040 (17)2.8624 (12)156.8 (14)
N5—H1N5···S1ii0.872 (18)2.613 (18)3.4754 (9)170.2 (14)
C5—H5A···O2iii0.952.313.2215 (13)162
C9—H9A···O3i0.952.343.1394 (12)141
C12—H12B···O2iv0.992.563.2626 (14)128
C11—H11A···Cg1v0.982.943.5736 (12)123
Symmetry codes: (i) x+1, y, z1; (ii) x+2, y+1, z1; (iii) x+1, y+1, z; (iv) x+1, y+1, z+1; (v) x+1, y, z+1.
Acknowledgements top

The authors thank Universiti Sains Malaysia (USM) for the Research University Grant (1001/PFIZIK/811160). WSL also thanks the Malaysian Government and USM for the award of the post of Research Officer under the Research University Grant (1001/PFIZIK/811160).

references
References top

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