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Acta Crystallogr Sect E Struct Rep Online. 2010 December 1; 66(Pt 12): o3137.
Published online 2010 November 13. doi:  10.1107/S1600536810045897
PMCID: PMC3011576

3-[2-(1H-Benzimidazol-2-ylsulfan­yl)eth­yl]-1,3-oxazolidin-2-one

Abstract

In the title compound, C12H13N3O2S, the oxazolidin ring displays an envelope conformation. The dihedral angle between the benzimidazole ring and the 1,3-oxazolidin-2-one mean plane is 69.85 (13)°. In the crystal, mol­ecules are linked by inter­molecular N—H(...)N hydrogen bonds, forming a chain parallel to the b axis.

Related literature

For the structures of oxazolidin-2-one linked to dioxoindolin, quinoxaline, benzodiazepin-2(3H)-one and indolo[2,3-b]quinoxalin, see: Al Subari et al. (2010a [triangle],b [triangle]); Ahoya et al. (2010 [triangle]); Ballo et al. (2010 [triangle]). For puckering parameters, see: Cremer & Pople (1975 [triangle]).

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Object name is e-66-o3137-scheme1.jpg

Experimental

Crystal data

  • C12H13N3O2S
  • M r = 263.31
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o3137-efi3.jpg
  • a = 8.258 (1) Å
  • b = 10.074 (1) Å
  • c = 29.201 (3) Å
  • V = 2429.3 (5) Å3
  • Z = 8
  • Cu Kα radiation
  • μ = 2.37 mm−1
  • T = 296 K
  • 0.25 × 0.10 × 0.05 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer
  • Absorption correction: ψ scan (North et al., 1968 [triangle]) T min = 0.589, T max = 0.891
  • 2065 measured reflections
  • 2065 independent reflections
  • 1580 reflections with I > 2σ(I)
  • 2 standard reflections every 90 min intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.048
  • wR(F 2) = 0.138
  • S = 1.04
  • 2065 reflections
  • 164 parameters
  • H-atom parameters constrained
  • Δρmax = 0.50 e Å−3
  • Δρmin = −0.26 e Å−3

Data collection: CAD-4 Software (Enraf–Nonius, 1989 [triangle]); cell refinement: CAD-4 Software; data reduction: CAD-4 Software; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEPIII (Burnett & Johnson, 1996 [triangle]), ORTEP-3 for Windows (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2010 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810045897/dn2620sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810045897/dn2620Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

The synthesis of new oxindole derivatives having an oxazolindin-2-one unit has been detailed in recent reports (Al Subari et al., 2010a,b; Ahoya et al., 2010; Ballo et al.,2010).

In the new oxazolidin-2-one, C12H13N3O2S, the dihedral angle between the 1H-benzimidazole ring and the 1,3-oxazolidin-2-one mean plane is: 69.85 (13)° (Fig.1). The oxazolidin ring is not planar but display envelope conformation on C14 with puckering parameters Q(2) = 0.258 (3) Å and [var phi](2) = 63.3 (7) ° (Cremer & Pople, 1975).

In the crystal structure, the molecules are linked by intermolecular N—H···N hydrogen bonds forming a chain parallel to the b axis (Table 1, Fig. 2).

Experimental

To the solution of benzimidazole-2-thione (1,35 g, 9 mmoles) and dichloroethyl amine hydrochloride (2,41 g, 13.5 mmoles) in dimethylformamide (80 ml) were added potassium carbonate (4,14 g, 30 mmoles) and tetra-n-butylammonium bromide (0,10 g, 0,3 mmoles). The resulting mixture was refluxed for 4 h. After filtering the solvent was removed and the residue was purified by column chromatography on silica gel (Hexane/AcOEt: 60/40) to afford the title compound.

Yield = 55%

F = 230–232 °C (ethanol-water).

RMN 1H (d p.p.m.): 3.57: SCH2 (2H, t, J = 6.25 Hz); 3,36: NCH2 (4H, m); 4.23: OCH2 (4H, t, J = 6,25 Hz); 7.30–7.70: CH (benzénique)(8H, m); 11.57: NH (1H, s)

Mass Spectre IE: M+ (m/z=263).

Refinement

All H atoms were fixed geometrically and treated as riding with C—H = 0.97 Å (methyne) and 0.93Å (aromatic) with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
Molecular view of the title compound showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii.
Fig. 2.
Partial packing view showing the chain formed by N-H···N hydrogen bondings. H atoms not involved in hydrogen bonds have been omitted for clarity. [Symmetry code: (i) -x+1/2, y+1/2, z ]

Crystal data

C12H13N3O2SF(000) = 1104
Mr = 263.31Dx = 1.440 Mg m3
Orthorhombic, PbcaCu Kα radiation, λ = 1.54180 Å
Hall symbol: -P 2ac 2abCell parameters from 25 reflections
a = 8.258 (1) Åθ = 25–35°
b = 10.074 (1) ŵ = 2.37 mm1
c = 29.201 (3) ÅT = 296 K
V = 2429.3 (5) Å3Plate, colourless
Z = 80.25 × 0.10 × 0.05 mm

Data collection

Enraf–Nonius CAD-4 diffractometer1580 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.0000
graphiteθmax = 64.9°, θmin = 3.0°
ω–2θ scansh = 0→9
Absorption correction: ψ scan (North et al., 1968)k = 0→11
Tmin = 0.589, Tmax = 0.891l = 0→34
2065 measured reflections2 standard reflections every 90 min
2065 independent reflections intensity decay: none

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.138w = 1/[σ2(Fo2) + (0.0753P)2 + 1.285P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
2065 reflectionsΔρmax = 0.50 e Å3
164 parametersΔρmin = −0.26 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0023 (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 (Å2)

xyzUiso*/Ueq
C10.4252 (3)0.6613 (3)0.32287 (8)0.0308 (6)
C20.5563 (4)0.7150 (3)0.29974 (10)0.0418 (7)
H20.57650.80580.29960.050*
C30.6553 (4)0.6266 (3)0.27685 (11)0.0491 (8)
H30.74510.65890.26120.059*
C40.6247 (4)0.4910 (3)0.27658 (10)0.0452 (8)
H40.69300.43490.26020.054*
C50.4960 (4)0.4382 (3)0.29994 (10)0.0387 (7)
H50.47720.34710.30000.046*
C60.3939 (3)0.5243 (3)0.32364 (8)0.0300 (6)
N70.2541 (3)0.4990 (2)0.34878 (7)0.0331 (5)
C80.2044 (3)0.6179 (3)0.36218 (9)0.0323 (6)
N90.3018 (3)0.7182 (2)0.34785 (7)0.0341 (5)
H90.28900.80140.35330.041*
S100.03324 (10)0.65185 (8)0.39498 (3)0.0466 (3)
C11−0.0806 (4)0.5004 (3)0.38524 (11)0.0461 (8)
H11A−0.07860.47860.35290.055*
H11B−0.03060.42790.40190.055*
C12−0.2545 (4)0.5167 (4)0.40086 (11)0.0515 (8)
H12A−0.30710.58240.38170.062*
H12B−0.31090.43310.39670.062*
N13−0.2688 (3)0.5569 (3)0.44810 (8)0.0421 (6)
C14−0.2251 (4)0.4720 (4)0.48622 (11)0.0524 (9)
H14A−0.11010.45270.48660.063*
H14B−0.28570.38950.48590.063*
C15−0.2743 (4)0.5603 (4)0.52586 (12)0.0624 (10)
H15A−0.31620.50790.55110.075*
H15B−0.18320.61240.53660.075*
O16−0.3993 (3)0.6452 (2)0.50692 (8)0.0568 (6)
C17−0.3857 (4)0.6431 (3)0.46087 (11)0.0465 (8)
O18−0.4713 (3)0.7117 (3)0.43673 (9)0.0683 (8)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0367 (14)0.0282 (15)0.0275 (12)0.0002 (11)−0.0008 (11)0.0017 (10)
C20.0495 (18)0.0290 (15)0.0469 (17)−0.0053 (13)0.0046 (14)0.0035 (12)
C30.0486 (18)0.0473 (18)0.0513 (18)−0.0047 (16)0.0098 (15)0.0036 (15)
C40.0474 (17)0.0447 (18)0.0436 (17)0.0103 (15)0.0090 (13)−0.0055 (13)
C50.0432 (16)0.0254 (14)0.0474 (16)0.0052 (13)0.0044 (13)−0.0010 (12)
C60.0351 (14)0.0218 (13)0.0330 (13)0.0008 (11)−0.0046 (11)0.0008 (10)
N70.0381 (12)0.0221 (12)0.0391 (12)0.0007 (9)0.0051 (10)0.0001 (9)
C80.0376 (15)0.0227 (13)0.0365 (14)0.0019 (11)0.0012 (11)−0.0006 (11)
N90.0406 (13)0.0176 (11)0.0441 (13)−0.0002 (10)0.0036 (10)−0.0018 (9)
S100.0457 (5)0.0336 (4)0.0604 (5)−0.0002 (3)0.0160 (3)−0.0094 (3)
C110.0460 (17)0.0395 (18)0.0527 (18)−0.0037 (14)0.0117 (15)−0.0059 (13)
C120.0413 (16)0.061 (2)0.0521 (18)−0.0089 (16)0.0026 (15)−0.0091 (16)
N130.0346 (13)0.0480 (15)0.0437 (13)0.0020 (12)0.0031 (11)0.0000 (11)
C140.0382 (17)0.059 (2)0.060 (2)0.0090 (16)0.0014 (15)0.0143 (17)
C150.047 (2)0.088 (3)0.053 (2)−0.003 (2)−0.0054 (15)0.0077 (19)
O160.0518 (14)0.0638 (17)0.0549 (13)0.0065 (12)0.0019 (11)−0.0115 (11)
C170.0414 (17)0.0403 (17)0.0578 (19)−0.0041 (15)0.0020 (15)−0.0040 (15)
O180.0727 (17)0.0523 (16)0.0798 (18)0.0179 (14)−0.0127 (14)0.0047 (13)

Geometric parameters (Å, °)

S10—C81.741 (3)C4—C51.370 (4)
S10—C111.815 (3)C5—C61.394 (4)
O16—C151.450 (4)C11—C121.516 (5)
O16—C171.350 (4)C14—C151.515 (5)
O18—C171.214 (4)C2—H20.9298
N7—C61.392 (3)C3—H30.9299
N7—C81.325 (4)C4—H40.9308
N9—C11.378 (3)C5—H50.9308
N9—C81.358 (4)C11—H11A0.9697
N13—C121.443 (4)C11—H11B0.9698
N13—C141.449 (4)C12—H12A0.9694
N13—C171.351 (4)C12—H12B0.9700
N9—H90.8597C14—H14A0.9694
C1—C21.386 (4)C14—H14B0.9702
C1—C61.404 (4)C15—H15A0.9704
C2—C31.381 (4)C15—H15B0.9694
C3—C41.389 (4)
C8—S10—C1199.74 (15)C1—C2—H2121.75
C15—O16—C17108.2 (2)C3—C2—H2121.73
C6—N7—C8104.3 (2)C2—C3—H3118.96
C1—N9—C8107.0 (2)C4—C3—H3119.10
C12—N13—C14123.3 (3)C3—C4—H4119.32
C12—N13—C17120.2 (3)C5—C4—H4119.35
C14—N13—C17110.2 (2)C4—C5—H5120.87
C8—N9—H9126.57C6—C5—H5120.79
C1—N9—H9126.47S10—C11—H11A109.53
N9—C1—C6105.3 (2)S10—C11—H11B109.51
N9—C1—C2132.3 (3)C12—C11—H11A109.50
C2—C1—C6122.4 (3)C12—C11—H11B109.51
C1—C2—C3116.5 (3)H11A—C11—H11B108.10
C2—C3—C4121.9 (3)N13—C12—H12A108.88
C3—C4—C5121.3 (3)N13—C12—H12B108.92
C4—C5—C6118.3 (3)C11—C12—H12A108.95
N7—C6—C5130.5 (3)C11—C12—H12B108.85
C1—C6—C5119.5 (2)H12A—C12—H12B107.78
N7—C6—C1109.9 (2)N13—C14—H14A111.78
N7—C8—N9113.5 (2)N13—C14—H14B111.70
S10—C8—N7126.3 (2)C15—C14—H14A111.82
S10—C8—N9120.3 (2)C15—C14—H14B111.83
S10—C11—C12110.6 (2)H14A—C14—H14B109.49
N13—C12—C11113.3 (3)O16—C15—H15A110.90
N13—C14—C15100.0 (3)O16—C15—H15B110.88
O16—C15—C14104.2 (3)C14—C15—H15A110.88
O18—C17—N13128.4 (3)C14—C15—H15B110.91
O16—C17—O18121.4 (3)H15A—C15—H15B109.00
O16—C17—N13110.2 (3)
C11—S10—C8—N7−20.2 (3)C14—N13—C17—O1614.2 (4)
C11—S10—C8—N9159.9 (2)C14—N13—C12—C11−68.2 (4)
C8—S10—C11—C12−166.3 (2)C12—N13—C17—O16167.1 (3)
C15—O16—C17—O18−176.2 (3)C12—N13—C17—O18−12.7 (5)
C15—O16—C17—N134.0 (3)N9—C1—C6—N7−0.1 (3)
C17—O16—C15—C14−19.3 (3)N9—C1—C2—C3−178.2 (3)
C6—N7—C8—S10179.8 (2)N9—C1—C6—C5178.2 (2)
C8—N7—C6—C10.3 (3)C6—C1—C2—C30.5 (4)
C6—N7—C8—N9−0.3 (3)C2—C1—C6—N7−179.2 (2)
C8—N7—C6—C5−177.8 (3)C2—C1—C6—C5−0.9 (4)
C1—N9—C8—N70.3 (3)C1—C2—C3—C40.6 (5)
C1—N9—C8—S10−179.83 (18)C2—C3—C4—C5−1.4 (5)
C8—N9—C1—C6−0.1 (3)C3—C4—C5—C61.0 (5)
C8—N9—C1—C2178.9 (3)C4—C5—C6—C10.1 (4)
C12—N13—C14—C15−176.6 (3)C4—C5—C6—N7178.0 (3)
C14—N13—C17—O18−165.6 (3)S10—C11—C12—N13−55.8 (4)
C17—N13—C12—C11142.6 (3)N13—C14—C15—O1625.6 (3)
C17—N13—C14—C15−24.7 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N9—H9···N7i0.862.032.866 (3)165

Symmetry codes: (i) −x+1/2, y+1/2, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2620).

References

  • Ahoya, C. A., Bouhfid, R., Daouda, B., Essassi, E. M. & El Ammari, L. (2010). Acta Cryst. E66, o1050. [PMC free article] [PubMed]
  • Al Subari, A., Bouhfid, R., Zouihri, H., Essassi, E. M. & Ng, S. W. (2010a). Acta Cryst. E66, o2461. [PMC free article] [PubMed]
  • Al Subari, A., Bouhfid, R., Zouihri, H., Essassi, E. M. & Ng, S. W. (2010b). Acta Cryst. E66, o454. [PMC free article] [PubMed]
  • Ballo, D., Ahabchane, N. H., Zouihri, H., Essassi, E. M. & Ng, S. W. (2010). Acta Cryst. E66, o2080. [PMC free article] [PubMed]
  • Burnett, M. N. & Johnson, C. K. (1996). ORTEPIII Report ORNL-6895. Oak Ridge National Laboratory, Tennessee, USA.
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  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
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