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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): o1495.
Published online 2010 May 29. doi:  10.1107/S1600536810019367
PMCID: PMC2979569

4-(1H-Benzimidazol-2-ylmeth­yl)-2H-1,4-benzothia­zin-3(4H)-one

Abstract

In the title compound, C16H13N3OS, the thio­morpholine ring exists in a screw boat conformation. The angle between the benzimidazole ring system and the benzene ring fused to the thia­zine ring is 67.22 (6)°. In the crystal, mol­ecules form infinite chains along the a axis via inter­molecular N—H(...)N inter­actions. C—H(...)π inter­actions also contribute to the stability of the crystal structure.

Related literature

For the biological activity of mol­ecules containing 1H-benzimidazole, see: Sridhar & Ramesh (2001 [triangle]); Guven et al. (2007 [triangle]); Nofal et al. (2002 [triangle]); Pedini et al. (1994 [triangle]). For a related structure, see: Fun et al. (2009 [triangle]). For ring puckering parameters, see: Cremer & Pople (1975 [triangle]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 [triangle]).

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Object name is e-66-o1495-scheme1.jpg

Experimental

Crystal data

  • C16H13N3OS
  • M r = 295.35
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1495-efi1.jpg
  • a = 9.4498 (8) Å
  • b = 17.0223 (16) Å
  • c = 17.4454 (16) Å
  • V = 2806.2 (4) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.23 mm−1
  • T = 100 K
  • 0.50 × 0.20 × 0.13 mm

Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.893, T max = 0.969
  • 16727 measured reflections
  • 4075 independent reflections
  • 3185 reflections with I > 2σ(I)
  • R int = 0.040

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.119
  • S = 1.03
  • 4075 reflections
  • 194 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.44 e Å−3
  • Δρmin = −0.26 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810019367/wn2387sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810019367/wn2387Isup2.hkl

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

Acknowledgments

FHK and MMR thank Universiti Sains Malaysia for the Research University Golden Goose grant (No. 1001/PFIZIK/811012).

supplementary crystallographic information

Comment

A number of molecules containing the 1H-benzimidazole nucleus exhibit a broad spectrum of biological activity, including anti-inflammatory (Sridhar et al., 2001), antifungal (Guven et al., 2007), antibacterial (Nofal et al., 2002) and anthelmintic (Pedini et al., 1994) properties. With these results in mind, we have paid particular attention to the preparation of derivatives of 1H-benzimidazole and we report here the crystal structure of the title compound, a 1H-benzimidazole derivative containing 2H-1,4-benzothiazin-3(4H)-one.

The bond lengths and angles are within normal ranges. The thiomorpholine ring (C1, C6-C8, N3, S1) adopts a screw boat confirmation with puckering parameters (Cremer & Pople, 1975) being Q = 0.6563 (13) Å; θ = 66.76 (12)° and [var phi] = 334.16 (14)°. The angle between the benzimidazole ring system and the benzene ring fused to the thiazine ring is 67.22 (6)°.

The intermolecular interaction N1—H1N1···N2 links the molecules to form infinite chains along the a-axis. The crystal structure is further stabilized by C—H···π interactions involving the C1-C6 (Cg1) and C11-C16 (Cg2) benzene rings (Table 1).

Experimental

A mixture of 2-(3-oxo-2,3-dihydro-4H-1,4-benzothiazin-4-yl)acetic acid (3.3 mmol) (Fun et al., 2009) and o-phenylenediamine (2.2 mmol) was heated at 140 °C under solvent-free conditions for 3 h and completion of the reaction was checked by TLC. The reaction mixture was cooled to room temperature and the solid product was washed with a saturated solution of sodium bicarbonate to yield 4-(1H-benzimidazol-2-ylmethyl)-2H-1,4-benzothiazin-3(4H)-one as a red solid. Single crystals suitable for X-ray analysis were obtained by crystallization from absolute ethanol under slow evaporation (M.p. 493 K).

Refinement

The H atom attached to N1 was located in a difference map and refined isotropically; N1—H1N1 = 0.86 (2) Å. The carbon-bound H atoms were positioned geometrically [C—H = 0.93 or 0.97 Å] and were refined using a riding model, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure, showing 50% probability displacement ellipsoids and the atom-numbering scheme. Hydrogen atoms are shown as spheres of arbitrary radius.
Fig. 2.
The crystal structure, showing infinite chains along the a-axis. Dashed lines indicate hydrogen bonds. H atoms not involved in the hydrogen bond interactions have been omitted for clarity.

Crystal data

C16H13N3OSF(000) = 1232
Mr = 295.35Dx = 1.398 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 4703 reflections
a = 9.4498 (8) Åθ = 2.4–31.6°
b = 17.0223 (16) ŵ = 0.23 mm1
c = 17.4454 (16) ÅT = 100 K
V = 2806.2 (4) Å3Block, red
Z = 80.50 × 0.20 × 0.13 mm

Data collection

Bruker APEXII DUO CCD area-detector diffractometer4075 independent reflections
Radiation source: fine-focus sealed tube3185 reflections with I > 2σ(I)
graphiteRint = 0.040
[var phi] and ω scansθmax = 30.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −13→13
Tmin = 0.893, Tmax = 0.969k = −23→23
16727 measured reflectionsl = −24→21

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.03w = 1/[σ2(Fo2) + (0.0605P)2 + 1.2202P] where P = (Fo2 + 2Fc2)/3
4075 reflections(Δ/σ)max = 0.001
194 parametersΔρmax = 0.44 e Å3
0 restraintsΔρmin = −0.25 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
S10.69098 (4)0.04490 (2)0.49857 (2)0.02567 (12)
O10.90053 (12)−0.12536 (7)0.41611 (7)0.0283 (2)
N11.05774 (11)−0.12424 (7)0.21967 (7)0.0169 (2)
N20.82471 (11)−0.10176 (7)0.21708 (7)0.0166 (2)
N30.84628 (12)−0.01064 (7)0.35843 (7)0.0180 (2)
C10.75457 (14)0.05425 (8)0.34596 (8)0.0177 (3)
C20.74342 (15)0.08809 (8)0.27346 (8)0.0210 (3)
H2A0.79350.06680.23250.025*
C30.65796 (16)0.15354 (9)0.26189 (9)0.0251 (3)
H3A0.65300.17640.21350.030*
C40.58032 (16)0.18488 (9)0.32169 (10)0.0275 (3)
H4A0.52320.22860.31370.033*
C50.58816 (16)0.15078 (9)0.39359 (10)0.0256 (3)
H5A0.53460.17110.43370.031*
C60.67593 (15)0.08616 (8)0.40635 (8)0.0206 (3)
C70.70051 (17)−0.05535 (9)0.46596 (9)0.0261 (3)
H7A0.7100−0.09000.50980.031*
H7B0.6134−0.06880.43960.031*
C80.82425 (15)−0.06773 (8)0.41241 (8)0.0209 (3)
C90.96991 (14)−0.02207 (8)0.30913 (8)0.0191 (3)
H9A1.0499−0.03740.34060.023*
H9B0.99330.02740.28470.023*
C100.94729 (13)−0.08304 (8)0.24863 (8)0.0159 (2)
C111.00375 (13)−0.17492 (8)0.16502 (8)0.0165 (3)
C121.06703 (15)−0.23109 (9)0.11796 (8)0.0213 (3)
H12A1.1636−0.24150.12010.026*
C130.97847 (17)−0.27045 (9)0.06787 (9)0.0245 (3)
H13A1.0162−0.30860.03560.029*
C140.83220 (16)−0.25414 (9)0.06449 (9)0.0234 (3)
H14A0.7765−0.28090.02910.028*
C150.76917 (15)−0.19954 (8)0.11228 (8)0.0198 (3)
H15A0.6724−0.18980.11050.024*
C160.85770 (13)−0.15965 (8)0.16350 (8)0.0158 (2)
H1N11.143 (2)−0.1173 (12)0.2353 (12)0.033 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0341 (2)0.02221 (19)0.02070 (19)−0.00054 (14)0.00590 (14)−0.00461 (13)
O10.0333 (6)0.0235 (5)0.0283 (6)0.0070 (4)0.0003 (5)0.0023 (4)
N10.0100 (5)0.0214 (6)0.0192 (5)−0.0003 (4)−0.0003 (4)−0.0010 (4)
N20.0117 (5)0.0174 (5)0.0208 (6)−0.0010 (4)0.0004 (4)−0.0003 (4)
N30.0166 (5)0.0180 (5)0.0194 (6)0.0007 (4)0.0020 (4)−0.0006 (4)
C10.0157 (6)0.0154 (6)0.0221 (6)−0.0018 (4)0.0004 (5)−0.0017 (5)
C20.0220 (6)0.0180 (6)0.0230 (7)−0.0014 (5)0.0003 (5)−0.0005 (5)
C30.0282 (7)0.0192 (7)0.0279 (8)−0.0014 (5)−0.0046 (6)0.0018 (6)
C40.0238 (7)0.0185 (6)0.0402 (9)0.0032 (5)−0.0036 (6)−0.0013 (6)
C50.0220 (7)0.0214 (7)0.0334 (8)0.0014 (5)0.0045 (6)−0.0069 (6)
C60.0201 (6)0.0187 (6)0.0230 (7)−0.0025 (5)0.0021 (5)−0.0039 (5)
C70.0349 (8)0.0197 (7)0.0236 (7)−0.0006 (6)0.0088 (6)−0.0004 (6)
C80.0247 (7)0.0187 (6)0.0192 (7)−0.0005 (5)−0.0001 (5)−0.0014 (5)
C90.0133 (5)0.0209 (6)0.0232 (7)−0.0019 (5)0.0004 (5)−0.0036 (5)
C100.0116 (5)0.0173 (6)0.0188 (6)−0.0007 (4)0.0018 (5)0.0013 (5)
C110.0138 (5)0.0191 (6)0.0167 (6)−0.0002 (4)0.0006 (5)0.0011 (5)
C120.0182 (6)0.0245 (7)0.0211 (7)0.0030 (5)0.0035 (5)−0.0009 (5)
C130.0293 (7)0.0238 (7)0.0204 (7)0.0013 (6)0.0038 (6)−0.0042 (5)
C140.0256 (7)0.0241 (7)0.0204 (7)−0.0036 (5)−0.0026 (5)−0.0012 (5)
C150.0171 (6)0.0214 (6)0.0211 (7)−0.0029 (5)−0.0027 (5)0.0019 (5)
C160.0134 (5)0.0171 (6)0.0168 (6)−0.0011 (4)0.0003 (5)0.0030 (5)

Geometric parameters (Å, °)

S1—C61.7611 (16)C5—C61.396 (2)
S1—C71.8011 (16)C5—H5A0.9300
O1—C81.2191 (18)C7—C81.511 (2)
N1—C101.3552 (16)C7—H7A0.9700
N1—C111.3831 (17)C7—H7B0.9700
N1—H1N10.86 (2)C9—C101.4955 (19)
N2—C101.3214 (16)C9—H9A0.9700
N2—C161.3936 (17)C9—H9B0.9700
N3—C81.3692 (19)C11—C121.3950 (19)
N3—C11.4207 (17)C11—C161.4046 (18)
N3—C91.4637 (17)C12—C131.383 (2)
C1—C21.394 (2)C12—H12A0.9300
C1—C61.3990 (19)C13—C141.411 (2)
C2—C31.391 (2)C13—H13A0.9300
C2—H2A0.9300C14—C151.383 (2)
C3—C41.382 (2)C14—H14A0.9300
C3—H3A0.9300C15—C161.3998 (19)
C4—C51.384 (2)C15—H15A0.9300
C4—H4A0.9300
C6—S1—C795.35 (7)H7A—C7—H7B108.0
C10—N1—C11107.20 (11)O1—C8—N3121.18 (13)
C10—N1—H1N1122.3 (14)O1—C8—C7122.47 (14)
C11—N1—H1N1130.5 (14)N3—C8—C7116.35 (12)
C10—N2—C16104.70 (11)N3—C9—C10113.14 (11)
C8—N3—C1124.36 (12)N3—C9—H9A109.0
C8—N3—C9115.55 (12)C10—C9—H9A109.0
C1—N3—C9120.02 (11)N3—C9—H9B109.0
C2—C1—C6118.86 (13)C10—C9—H9B109.0
C2—C1—N3120.42 (12)H9A—C9—H9B107.8
C6—C1—N3120.71 (13)N2—C10—N1113.27 (12)
C3—C2—C1120.45 (14)N2—C10—C9125.91 (12)
C3—C2—H2A119.8N1—C10—C9120.81 (11)
C1—C2—H2A119.8N1—C11—C12132.45 (12)
C4—C3—C2120.52 (15)N1—C11—C16105.08 (11)
C4—C3—H3A119.7C12—C11—C16122.47 (13)
C2—C3—H3A119.7C13—C12—C11116.39 (13)
C3—C4—C5119.58 (14)C13—C12—H12A121.8
C3—C4—H4A120.2C11—C12—H12A121.8
C5—C4—H4A120.2C12—C13—C14121.59 (13)
C4—C5—C6120.46 (14)C12—C13—H13A119.2
C4—C5—H5A119.8C14—C13—H13A119.2
C6—C5—H5A119.8C15—C14—C13121.92 (14)
C5—C6—C1120.11 (14)C15—C14—H14A119.0
C5—C6—S1120.53 (11)C13—C14—H14A119.0
C1—C6—S1119.35 (11)C14—C15—C16116.96 (13)
C8—C7—S1111.46 (10)C14—C15—H15A121.5
C8—C7—H7A109.3C16—C15—H15A121.5
S1—C7—H7A109.3N2—C16—C15129.61 (12)
C8—C7—H7B109.3N2—C16—C11109.75 (11)
S1—C7—H7B109.3C15—C16—C11120.64 (13)
C8—N3—C1—C2−150.61 (14)C8—N3—C9—C1076.17 (15)
C9—N3—C1—C225.96 (19)C1—N3—C9—C10−100.69 (14)
C8—N3—C1—C630.5 (2)C16—N2—C10—N10.06 (15)
C9—N3—C1—C6−152.88 (13)C16—N2—C10—C9178.82 (13)
C6—C1—C2—C31.4 (2)C11—N1—C10—N2−0.62 (16)
N3—C1—C2—C3−177.44 (13)C11—N1—C10—C9−179.45 (12)
C1—C2—C3—C4−1.5 (2)N3—C9—C10—N228.7 (2)
C2—C3—C4—C50.1 (2)N3—C9—C10—N1−152.62 (12)
C3—C4—C5—C61.3 (2)C10—N1—C11—C12−179.20 (15)
C4—C5—C6—C1−1.4 (2)C10—N1—C11—C160.88 (14)
C4—C5—C6—S1177.68 (12)N1—C11—C12—C13−178.56 (14)
C2—C1—C6—C50.0 (2)C16—C11—C12—C131.3 (2)
N3—C1—C6—C5178.85 (13)C11—C12—C13—C140.3 (2)
C2—C1—C6—S1−179.06 (10)C12—C13—C14—C15−1.7 (2)
N3—C1—C6—S1−0.20 (18)C13—C14—C15—C161.3 (2)
C7—S1—C6—C5142.33 (13)C10—N2—C16—C15−178.42 (14)
C7—S1—C6—C1−38.62 (13)C10—N2—C16—C110.52 (15)
C6—S1—C7—C858.75 (12)C14—C15—C16—N2179.23 (13)
C1—N3—C8—O1173.88 (13)C14—C15—C16—C110.4 (2)
C9—N3—C8—O1−2.8 (2)N1—C11—C16—N2−0.88 (15)
C1—N3—C8—C7−5.6 (2)C12—C11—C16—N2179.20 (12)
C9—N3—C8—C7177.65 (12)N1—C11—C16—C15178.18 (12)
S1—C7—C8—O1137.50 (14)C12—C11—C16—C15−1.8 (2)
S1—C7—C8—N3−42.98 (17)

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the C1–C6 and C11–C16 rings, respectively.
D—H···AD—HH···AD···AD—H···A
N1—H1N1···N2i0.859 (19)1.926 (19)2.7800 (15)173 (2)
C12—H12A···Cg1ii0.932.973.6736 (16)134
C3—H3A···Cg2iii0.932.613.4750 (17)155

Symmetry codes: (i) x+1/2, y, −z+1/2; (ii) x+5/2, −y−1/2, −z; (iii) x+1, −y−1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: WN2387).

References

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