Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807027730/at2322sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807027730/at2322Isup2.hkl |
CCDC reference: 654944
A pure sample of the compound was obtained from Strides Arco Labs, Mangalore, India and crystallized from DMF (m.p. 528–530 K).
All H atoms except the methyl's were located in difference Fourier map and refined freely. The H atoms of methyl were positioned at their positions [C—H = 0.96 Å, Uiso(H) = 1.5Ueq(C)] and allowed to ride and to rotate as well.
Benzimidazole derivatives are inhibitors of cyclin-dependent kinase and useful for inhibiting cell proliferation, in for the treatment of cancer and bis-benzimidazoles have potent activity against a number of microorganisms including those that lead to AIDS-related infections. These compounds bind to DNA in AT-rich sequences. Recently, benzimidazole derived drugs have received much attention owing to the fact that benzimidazole residue is a constituent of vitamin B12 which supports their potential use as therapeutics. The derivatives are also well known antioxidants used in the manufacture of rubber and anticorrosive agents for mild steel. In view of the importance of the title compound, (I), C8H8N2OS, a crystal structure is reported (Fig. 1).
Compund (I) displays two moderate intermolecular hydrogen bond (Table 1) involving atoms O, S and N. In (I), the molecules are linked through an N—H···O and an N—H···S intramolecular hydrogen bonds and these hydrogen bonds generate edge-fussed centrosymmetric [R22(8) R44(20)R22(8)] ring motifs (Fig.2) (Etter, 1990) linked also by π···π interactions.
The intermolecular π···π interactions combine to stabilize the extended structure (Fig. 2). These π···π interactions occur between the C2—C7 rings of the molecules at (x, y, z) and (1 - x, 1 - y, 1 - z), with a centroid-to-centroid distance of 3.658 (1) Å and a plane-to-plane separation of 3.321 Å.
For related structures, see: Ravikumar et al. (1995); Elerman & Kabak (1997); Swamy & Ravikumar (2005); Jian et al. (2006); Navarrete-Vázquez et al. (2006). For related literature, see: Bell et al. (1993); Skalitzky et al. (2003); Lalezari et al. (2002); Singh & Dash (1988); Sakemi et al. (2002); Wang (2001); Etter (1990). [With the exception of Etter, none of these references is actually cited in the Comment section of the CIF. Can they be removed from the Reference list, or do you wish to add citations to the Comment? If the latter, please email the whole revised Comment section of the CIF, in CIF format.]
Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).
C8H8N2OS | Z = 2 |
Mr = 180.22 | F(000) = 188 |
Triclinic, P1 | Dx = 1.521 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.4922 (8) Å | Cell parameters from 8166 reflections |
b = 7.6532 (8) Å | θ = 3.1–28.8° |
c = 8.8403 (9) Å | µ = 0.36 mm−1 |
α = 90.316 (8)° | T = 296 K |
β = 114.148 (8)° | Prism, colourless |
γ = 118.516 (7)° | 0.56 × 0.42 × 0.27 mm |
V = 393.47 (9) Å3 |
Stoe IPDS II diffractometer | 1545 independent reflections |
Radiation source: sealed X-ray tube, 12 x 0.4 mm long-fine focus | 1445 reflections with I > 2σ(I) |
Plane graphite monochromator | Rint = 0.084 |
Detector resolution: 6.67 pixels mm-1 | θmax = 26.0°, θmin = 3.1° |
ω scans | h = −9→9 |
Absorption correction: integration (X-RED32; Stoe & Cie, 2002) | k = −9→9 |
Tmin = 0.829, Tmax = 0.935 | l = −10→10 |
8166 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.039 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.106 | w = 1/[σ2(Fo2) + (0.0648P)2 + 0.0705P] where P = (Fo2 + 2Fc2)/3 |
S = 1.08 | (Δ/σ)max < 0.001 |
1545 reflections | Δρmax = 0.33 e Å−3 |
131 parameters | Δρmin = −0.38 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.081 (14) |
C8H8N2OS | γ = 118.516 (7)° |
Mr = 180.22 | V = 393.47 (9) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.4922 (8) Å | Mo Kα radiation |
b = 7.6532 (8) Å | µ = 0.36 mm−1 |
c = 8.8403 (9) Å | T = 296 K |
α = 90.316 (8)° | 0.56 × 0.42 × 0.27 mm |
β = 114.148 (8)° |
Stoe IPDS II diffractometer | 1545 independent reflections |
Absorption correction: integration (X-RED32; Stoe & Cie, 2002) | 1445 reflections with I > 2σ(I) |
Tmin = 0.829, Tmax = 0.935 | Rint = 0.084 |
8166 measured reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.106 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.08 | Δρmax = 0.33 e Å−3 |
1545 reflections | Δρmin = −0.38 e Å−3 |
131 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.8686 (3) | 1.0602 (3) | 0.7350 (2) | 0.0330 (4) | |
C2 | 0.8064 (3) | 0.7699 (2) | 0.6012 (2) | 0.0296 (4) | |
C3 | 0.7925 (3) | 0.5877 (2) | 0.5602 (2) | 0.0319 (4) | |
C4 | 0.6897 (3) | 0.4987 (2) | 0.3873 (2) | 0.0317 (4) | |
C5 | 0.6006 (3) | 0.5849 (3) | 0.2616 (2) | 0.0374 (4) | |
C6 | 0.6166 (3) | 0.7675 (3) | 0.3053 (2) | 0.0383 (4) | |
C7 | 0.7245 (3) | 0.8611 (3) | 0.4768 (2) | 0.0314 (4) | |
C8 | 0.6164 (4) | 0.2430 (3) | 0.1758 (3) | 0.0476 (5) | |
H8A | 0.4554 | 0.1883 | 0.1039 | 0.071* | |
H8B | 0.6494 | 0.1371 | 0.1699 | 0.071* | |
H8C | 0.7041 | 0.3540 | 0.1374 | 0.071* | |
N1 | 0.8937 (2) | 0.8967 (2) | 0.75761 (19) | 0.0330 (3) | |
N2 | 0.7669 (3) | 1.0393 (2) | 0.56429 (19) | 0.0346 (3) | |
O1 | 0.6761 (2) | 0.3167 (2) | 0.34818 (17) | 0.0419 (3) | |
S1 | 0.94575 (8) | 1.25049 (7) | 0.88771 (6) | 0.0405 (2) | |
H1 | 0.943 (4) | 0.875 (3) | 0.858 (3) | 0.043 (6)* | |
H2 | 0.742 (4) | 1.131 (4) | 0.519 (3) | 0.045 (6)* | |
H3 | 0.848 (4) | 0.520 (3) | 0.643 (3) | 0.041 (5)* | |
H5 | 0.518 (4) | 0.516 (4) | 0.137 (3) | 0.050 (6)* | |
H6 | 0.551 (4) | 0.831 (3) | 0.219 (3) | 0.041 (5)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0352 (8) | 0.0329 (8) | 0.0326 (9) | 0.0182 (7) | 0.0169 (7) | 0.0127 (7) |
C2 | 0.0306 (7) | 0.0308 (8) | 0.0283 (8) | 0.0157 (6) | 0.0150 (6) | 0.0114 (6) |
C3 | 0.0352 (8) | 0.0313 (8) | 0.0319 (9) | 0.0191 (7) | 0.0160 (7) | 0.0129 (7) |
C4 | 0.0351 (8) | 0.0286 (8) | 0.0353 (9) | 0.0168 (6) | 0.0196 (7) | 0.0114 (7) |
C5 | 0.0456 (9) | 0.0390 (9) | 0.0286 (9) | 0.0233 (8) | 0.0170 (7) | 0.0110 (7) |
C6 | 0.0480 (9) | 0.0415 (9) | 0.0311 (9) | 0.0280 (8) | 0.0176 (8) | 0.0168 (7) |
C7 | 0.0351 (8) | 0.0316 (8) | 0.0323 (8) | 0.0192 (6) | 0.0177 (7) | 0.0128 (7) |
C8 | 0.0669 (12) | 0.0356 (10) | 0.0411 (10) | 0.0250 (9) | 0.0285 (10) | 0.0086 (8) |
N1 | 0.0399 (7) | 0.0325 (7) | 0.0272 (7) | 0.0205 (6) | 0.0144 (6) | 0.0113 (6) |
N2 | 0.0445 (8) | 0.0327 (7) | 0.0319 (8) | 0.0239 (6) | 0.0180 (6) | 0.0134 (6) |
O1 | 0.0605 (8) | 0.0363 (7) | 0.0368 (7) | 0.0296 (6) | 0.0244 (6) | 0.0137 (6) |
S1 | 0.0559 (3) | 0.0359 (3) | 0.0343 (3) | 0.0271 (2) | 0.0215 (2) | 0.0113 (2) |
C1—N2 | 1.350 (2) | C5—H5 | 1.00 (3) |
C1—N1 | 1.356 (2) | C6—C7 | 1.378 (3) |
C1—S1 | 1.6775 (18) | C6—H6 | 0.99 (2) |
C2—C3 | 1.382 (2) | C7—N2 | 1.390 (2) |
C2—N1 | 1.386 (2) | C8—O1 | 1.426 (2) |
C2—C7 | 1.392 (2) | C8—H8A | 0.9600 |
C3—C4 | 1.385 (2) | C8—H8B | 0.9600 |
C3—H3 | 0.97 (2) | C8—H8C | 0.9600 |
C4—O1 | 1.379 (2) | N1—H1 | 0.86 (3) |
C4—C5 | 1.392 (2) | N2—H2 | 0.87 (3) |
C5—C6 | 1.383 (3) | ||
N2—C1—N1 | 106.42 (15) | C5—C6—H6 | 122.9 (13) |
N2—C1—S1 | 126.47 (14) | C6—C7—N2 | 132.91 (16) |
N1—C1—S1 | 127.11 (14) | C6—C7—C2 | 120.72 (16) |
C3—C2—N1 | 131.56 (15) | N2—C7—C2 | 106.30 (15) |
C3—C2—C7 | 122.33 (16) | O1—C8—H8A | 109.5 |
N1—C2—C7 | 106.11 (14) | O1—C8—H8B | 109.5 |
C2—C3—C4 | 116.21 (15) | H8A—C8—H8B | 109.5 |
C2—C3—H3 | 124.8 (13) | O1—C8—H8C | 109.5 |
C4—C3—H3 | 119.0 (13) | H8A—C8—H8C | 109.5 |
O1—C4—C3 | 115.58 (15) | H8B—C8—H8C | 109.5 |
O1—C4—C5 | 122.35 (16) | C1—N1—C2 | 110.65 (14) |
C3—C4—C5 | 122.04 (16) | C1—N1—H1 | 120.8 (15) |
C6—C5—C4 | 120.86 (16) | C2—N1—H1 | 128.1 (15) |
C6—C5—H5 | 117.2 (14) | C1—N2—C7 | 110.51 (15) |
C4—C5—H5 | 121.9 (15) | C1—N2—H2 | 123.3 (17) |
C7—C6—C5 | 117.78 (16) | C7—N2—H2 | 126.0 (17) |
C7—C6—H6 | 119.3 (13) | C4—O1—C8 | 117.01 (15) |
N1—C2—C3—C4 | 179.05 (15) | N1—C2—C7—N2 | 0.19 (16) |
C7—C2—C3—C4 | −0.7 (2) | N2—C1—N1—C2 | −0.44 (18) |
C2—C3—C4—O1 | −179.72 (13) | S1—C1—N1—C2 | 179.04 (12) |
C2—C3—C4—C5 | −1.4 (2) | C3—C2—N1—C1 | −179.58 (16) |
O1—C4—C5—C6 | 179.81 (16) | C7—C2—N1—C1 | 0.16 (17) |
C3—C4—C5—C6 | 1.6 (3) | N1—C1—N2—C7 | 0.56 (19) |
C4—C5—C6—C7 | 0.3 (3) | S1—C1—N2—C7 | −178.92 (12) |
C5—C6—C7—N2 | −178.88 (17) | C6—C7—N2—C1 | 176.43 (18) |
C5—C6—C7—C2 | −2.3 (3) | C2—C7—N2—C1 | −0.47 (18) |
C3—C2—C7—C6 | 2.6 (2) | C3—C4—O1—C8 | −167.30 (16) |
N1—C2—C7—C6 | −177.18 (15) | C5—C4—O1—C8 | 14.4 (2) |
C3—C2—C7—N2 | 179.95 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···S1i | 0.86 (3) | 2.43 (3) | 3.2853 (16) | 169 (2) |
N2—H2···O1ii | 0.87 (3) | 2.15 (3) | 2.997 (2) | 165 (2) |
Symmetry codes: (i) −x+2, −y+2, −z+2; (ii) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C8H8N2OS |
Mr | 180.22 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 296 |
a, b, c (Å) | 7.4922 (8), 7.6532 (8), 8.8403 (9) |
α, β, γ (°) | 90.316 (8), 114.148 (8), 118.516 (7) |
V (Å3) | 393.47 (9) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.36 |
Crystal size (mm) | 0.56 × 0.42 × 0.27 |
Data collection | |
Diffractometer | Stoe IPDS II |
Absorption correction | Integration (X-RED32; Stoe & Cie, 2002) |
Tmin, Tmax | 0.829, 0.935 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8166, 1545, 1445 |
Rint | 0.084 |
(sin θ/λ)max (Å−1) | 0.617 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.106, 1.08 |
No. of reflections | 1545 |
No. of parameters | 131 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.33, −0.38 |
Computer programs: X-AREA (Stoe & Cie, 2002), X-AREA, X-RED32 (Stoe & Cie, 2002), SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···S1i | 0.86 (3) | 2.43 (3) | 3.2853 (16) | 169 (2) |
N2—H2···O1ii | 0.87 (3) | 2.15 (3) | 2.997 (2) | 165 (2) |
Symmetry codes: (i) −x+2, −y+2, −z+2; (ii) x, y+1, z. |
Benzimidazole derivatives are inhibitors of cyclin-dependent kinase and useful for inhibiting cell proliferation, in for the treatment of cancer and bis-benzimidazoles have potent activity against a number of microorganisms including those that lead to AIDS-related infections. These compounds bind to DNA in AT-rich sequences. Recently, benzimidazole derived drugs have received much attention owing to the fact that benzimidazole residue is a constituent of vitamin B12 which supports their potential use as therapeutics. The derivatives are also well known antioxidants used in the manufacture of rubber and anticorrosive agents for mild steel. In view of the importance of the title compound, (I), C8H8N2OS, a crystal structure is reported (Fig. 1).
Compund (I) displays two moderate intermolecular hydrogen bond (Table 1) involving atoms O, S and N. In (I), the molecules are linked through an N—H···O and an N—H···S intramolecular hydrogen bonds and these hydrogen bonds generate edge-fussed centrosymmetric [R22(8) R44(20)R22(8)] ring motifs (Fig.2) (Etter, 1990) linked also by π···π interactions.
The intermolecular π···π interactions combine to stabilize the extended structure (Fig. 2). These π···π interactions occur between the C2—C7 rings of the molecules at (x, y, z) and (1 - x, 1 - y, 1 - z), with a centroid-to-centroid distance of 3.658 (1) Å and a plane-to-plane separation of 3.321 Å.