5-Meth­oxy-1H-benzo[d]imidazole-2(3H)-thione

The title compound, C₈H₈N₂OS, is stabilized by inter­molecular N—H...O and N—H...S hydrogen bonds and by π–π inter­actions. The hydrogen bonds generate a two-dimensional network with edge-fused centrosymmetric [R₂²(8)R₄⁴(20)R₂²(8)] motifs, and these networks are connected by the π–π inter­actions. These π–π interactions occur between the homoaromatic rings of the molecules at () and (); the centroid–centroid distance is 3.658 (1) Å and the plane–plane separation is 3.321 Å. The mol­ecule is approximately planar, with a dihedral angle of 1.58 (13)° between the two rings.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C)= 0.003 Å
• R factor = 0.039
• wR factor = 0.106
• Data-to-parameter ratio = 11.8

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S1. Comment

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.

Related literature

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.]

S2. Experimental

A pure sample of the compound was obtained from Strides Arco Labs, Mangalore, India and crystallized from DMF (m.p. 528–530 K).

S3. Refinement

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, U_iso(H) = 1.5U_eq(C)] and allowed to ride and to rotate as well.

Computing details

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).

Figures

	Fig. 1. A view of (I) showing the atomic numbering scheme with displacement ellipsoids drawn at the 30% probability level.
	Fig. 2. Part of the crystal structure of (I). For the sake of clarity, H atoms not involved in the hydrogen bonding motifs shown have been omitted; hydrogen bonds are drawn as dashed lines. [Symmetry codes: (i) 2 - x, 2 - y, 2 - z; (ii) x, 1 - y, z; (iii) x, 1 + y, z].

5-Methoxy-1H-benzo[d]imidazole-2(3H)-thione

Crystal data

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) Å^3

Data collection

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

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.106	w = 1/[σ^2(Fo^2) + (0.0648P)^2 + 0.0705P] where P = (Fo^2 + 2Fc^2)/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+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.081 (14)

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
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)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

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)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···S1^i	0.86 (3)	2.43 (3)	3.2853 (16)	169 (2)
N2—H2···O1^ii	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.