2-Benzyl­sulfanyl-1H-benzimidazole

In the mol­ecule of the title compound, C₁₄H₁₂N₂S, the benzimidazole ring system and the phenyl ring form a dihedral angle of 81.36 (7)°. The crystal structure exhibits inter­molecular C—H...N and N—H...N hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 294 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.038
• wR factor = 0.069
• Data-to-parameter ratio = 14.2

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT029_ALERT_3_B _diffrn_measured_fraction_theta_full Low .......       0.95

Alert level C
PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low ....       0.94

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Benzimidazole derivatives are important pharmaceutical intermediates because of their therapeutic properties in modern drug discovery (Tebbe et al., 1997). For example, omeprazole, which contains benzimidazole and pyridine, is the best selling anti-ulcer drug nowadays (Carlsson et al., 2002). Benzimidazole derivatives generally exhibit versatile pharmacological activities, such as antibacterial, antifungal, antihelmintic, anti-allergic, antineoplastic, local analgesic, antihistaminic, vasodilative, hypotensive and spasmolytic activities (Easmon et al., 2001; Güneş & Coşar, 1992; Küçükbay et al., 2004). In order to have a better knowledge of their structure, we have embarked on a study of this class of compounds. The molecular structure of the title compound, C₁₄H₁₂N₂S (I), and the atomic labeling scheme are shown in Fig.1. In this structure, the nine-membered benzimidazole ring system C1/N2/C3/C4/C5/C6/N7/C8/C9 is essentially planar, the maximum deviation from planarity being 0.022 (1) Å for atom N2. The phenyl ring C12/C13—C17 is connected to the benzimidazole ring system by the SCH₂ group. The classical intermolecular N—H···N hydrogen bond, which leads to the formation of infinite molecular chains along the [001] direction, and the weak C—H···N hydrogen bond consolidate the structure (Fig.2).

Related literature

For related literature see: Carlsson et al. (2002); Easmon et al. (2001); Güneş & Coşar (1992); Küçükbay et al. (2004); Tebbe et al. (1997). For the refinement weighting scheme, see: Watkin (1994); Prince (1982).

S2. Experimental

Benzyl chloride (0.84 ml, 7.3 mmol) was added to 2-mercaptobenzimidazole (1 g, 6.7 mmol) in dry ethanol (15 ml). The mixture was refluxed for 7 h. The reaction mixture was diluted with ethyl acetate, and the resulting solid was collected and dissolved in 15 ml of water. 30 ml of a solution of sodium hydrogen carbonate (30 g in 100 ml of water) was then added. A white powder was isolated by filtration and dried to give (I) as colorless crystals (1.4 g, 88%), mp: 397 K. ¹H NMR (CD₃COCD₃, 300 MHz, p.pm.) δ: 4.09 (s, 2H, CH₂); 7.19–7.35 (2 m, 9H, H aromatic); 12.5 (1H, NH). ¹³C NMR (CD₃COCD₃, 300 MHz, p.pm.) δ: 34.3 (CH2); 116.5–127.9 (C₆H₅ and C₆H₄); 168.3 (C═N).

S3. Refinement

The H atom bonded to N7 was located in a difference Fourier map; the positional parameters and U_iso were refined freely. Other H atoms were placed at calculated positions, with C—H = 0.93 Å (aromatic) or 0.96 Å (methylene) and refined using a riding model with U_iso(H) constrained to be 1.2U_eq(C).

Computing details

Data collection: COLLECT (Nonius, 2001); cell refinement: DENZO/SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO/SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures

	Fig. 1. The molecular structure of (I) showing the atomic labeling scheme, with displacement ellipsoids drawn at the 50% probability level. H atoms are shown as spheres of arbitrary radius.
	Fig. 2. Crystal packing of compound (I) viewed down the b axis, showing the hydrogen bond C—H···N and the hydrogen-bonded chains N—H···N along the c axis. Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonds have been omitted for clarity.

2-Benzylsulfanyl-1H-benzimidazole

Crystal data

C14H12N2S	F(000) = 504
Mr = 240.33	Dx = 1.323 Mg m^−3
Monoclinic, P21/c	Melting point: 397 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 12.373 (7) Å	Cell parameters from 8533 reflections
b = 9.807 (5) Å	θ = 1.7–26.1°
c = 9.942 (3) Å	µ = 0.25 mm^−1
β = 91.084 (3)°	T = 294 K
V = 1206.2 (10) Å^3	Block, colorless
Z = 4	0.40 × 0.20 × 0.15 mm

Data collection

Nonius KappaCCD diffractometer	1988 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.035
Graphite monochromator	θmax = 26.1°, θmin = 1.7°
ϕ scans	h = −15→15
8533 measured reflections	k = −12→12
2236 independent reflections	l = −11→11

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.069	H atoms treated by a mixture of independent and constrained refinement
S = 0.93	w = [1-(Fo-Fc)^2/36σ^2(F)]^2/[168T0(x) + 239T1(x) + 121T2(x) + 25.6T3(x)] where Ti are Chebychev polynomials and x = Fc/Fmax (Prince, 1982; Watkin, 1994)
2229 reflections	(Δ/σ)max = 0.000223
157 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.24 e Å^−3
44 constraints

Special details

Refinement. The reflections 1 0 0; 2 0 0; 1 1 0; 2 1 0;-1 1 1; 0 1 1; 1 1 1 have been measured with too low intensities. It might be caused by some systematical error, probably by shielding by a beam stop of these diffractions. They were not used in the refinement.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
H3	0.8977	0.5371	0.9572	0.0468*
H4	0.9477	0.7303	0.8390	0.0562*
H5	0.9362	0.7373	0.6089	0.0552*
H6	0.8783	0.5489	0.4847	0.0480*
H7	0.8127 (14)	0.2722 (19)	0.528 (2)	0.048 (5)*
H13	0.5879	0.2781	0.4779	0.0600*
H14	0.4254	0.3911	0.5037	0.0756*
H15	0.2973	0.3051	0.6440	0.0744*
H16	0.3322	0.1087	0.7641	0.0696*
H17	0.4954	−0.0036	0.7410	0.0564*
C1	0.79925 (12)	0.23145 (15)	0.72299 (15)	0.0308
N2	0.82205 (10)	0.29955 (13)	0.83423 (13)	0.0320
C3	0.89447 (13)	0.53917 (17)	0.86371 (17)	0.0393
C4	0.92308 (14)	0.65360 (18)	0.79260 (19)	0.0460
C5	0.91706 (14)	0.65750 (18)	0.65297 (19)	0.0462
C6	0.88252 (13)	0.54683 (17)	0.57815 (18)	0.0397
N7	0.81656 (11)	0.30395 (13)	0.60891 (13)	0.0324
C8	0.85906 (11)	0.42602 (15)	0.78982 (15)	0.0299
C9	0.85465 (11)	0.43068 (15)	0.64996 (15)	0.0293
S10	0.75958 (4)	0.06141 (4)	0.72740 (5)	0.0435
C11	0.66222 (13)	0.04929 (18)	0.58752 (18)	0.0412
C12	0.55881 (13)	0.12579 (16)	0.60721 (17)	0.0370
C13	0.53667 (16)	0.24409 (19)	0.5364 (2)	0.0504
C14	0.43910 (19)	0.3110 (2)	0.5511 (2)	0.0628
C15	0.36300 (18)	0.2602 (2)	0.6351 (2)	0.0618
C16	0.38381 (16)	0.1429 (2)	0.7063 (2)	0.0583
C17	0.48110 (15)	0.0758 (2)	0.69275 (19)	0.0475
H111	0.6957	0.0843	0.5083	0.0492*
H112	0.6449	−0.0453	0.5745	0.0492*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0341 (8)	0.0334 (8)	0.0248 (8)	0.0003 (6)	−0.0003 (6)	0.0008 (6)
N2	0.0372 (7)	0.0359 (7)	0.0229 (7)	−0.0006 (5)	0.0000 (5)	−0.0001 (5)
C3	0.0426 (9)	0.0458 (10)	0.0293 (9)	−0.0035 (7)	−0.0026 (7)	−0.0077 (7)
C4	0.0458 (10)	0.0411 (9)	0.0511 (12)	−0.0106 (8)	−0.0007 (8)	−0.0103 (8)
C5	0.0509 (10)	0.0391 (9)	0.0488 (12)	−0.0115 (8)	0.0031 (8)	0.0049 (8)
C6	0.0467 (9)	0.0434 (9)	0.0292 (9)	−0.0037 (7)	0.0037 (7)	0.0052 (7)
N7	0.0419 (7)	0.0353 (7)	0.0199 (7)	−0.0033 (6)	0.0009 (5)	−0.0033 (5)
C8	0.0307 (7)	0.0349 (8)	0.0241 (8)	0.0005 (6)	0.0005 (6)	−0.0016 (6)
C9	0.0297 (7)	0.0328 (8)	0.0256 (8)	−0.0003 (6)	0.0022 (6)	−0.0023 (6)
S10	0.0553 (3)	0.0336 (2)	0.0411 (3)	−0.00599 (19)	−0.00933 (19)	0.00478 (17)
C11	0.0471 (9)	0.0412 (9)	0.0354 (10)	−0.0087 (7)	−0.0012 (7)	−0.0084 (7)
C12	0.0448 (9)	0.0369 (9)	0.0291 (9)	−0.0079 (7)	−0.0029 (7)	−0.0058 (6)
C13	0.0613 (12)	0.0435 (10)	0.0462 (12)	−0.0089 (9)	−0.0016 (9)	0.0029 (8)
C14	0.0740 (14)	0.0419 (11)	0.0716 (16)	0.0053 (10)	−0.0178 (12)	−0.0045 (10)
C15	0.0572 (12)	0.0585 (13)	0.0692 (16)	0.0094 (10)	−0.0123 (11)	−0.0262 (11)
C16	0.0469 (11)	0.0806 (15)	0.0476 (13)	−0.0095 (10)	0.0048 (9)	−0.0138 (10)
C17	0.0496 (10)	0.0544 (11)	0.0383 (11)	−0.0070 (8)	−0.0014 (8)	0.0034 (8)

Geometric parameters (Å, º)

H3—C3	0.930	C4—C5	1.389 (3)
H4—C4	0.930	C5—C6	1.379 (2)
H5—C5	0.930	C6—C9	1.391 (2)
H6—C6	0.930	N7—C9	1.388 (2)
H7—N7	0.87 (2)	C8—C9	1.391 (2)
H13—C13	0.930	S10—C11	1.8264 (18)
H14—C14	0.930	C11—C12	1.499 (2)
H15—C15	0.930	C11—H111	0.960
H16—C16	0.930	C11—H112	0.960
H17—C17	0.930	C12—C13	1.382 (2)
C1—N2	1.3179 (19)	C12—C17	1.385 (2)
C1—N7	1.359 (2)	C13—C14	1.384 (3)
C1—S10	1.7391 (17)	C14—C15	1.365 (3)
N2—C8	1.397 (2)	C15—C16	1.372 (3)
C3—C4	1.376 (3)	C16—C17	1.381 (3)
C3—C8	1.397 (2)
N2—C1—N7	113.62 (14)	C1—S10—C11	103.04 (8)
N2—C1—S10	121.39 (12)	S10—C11—C12	114.85 (12)
N7—C1—S10	124.86 (12)	S10—C11—H111	108.2
C1—N2—C8	104.54 (13)	C12—C11—H111	108.1
H3—C3—C4	121.6	S10—C11—H112	107.9
H3—C3—C8	121.0	C12—C11—H112	108.2
C4—C3—C8	117.32 (17)	H111—C11—H112	109.5
H4—C4—C3	119.3	C11—C12—C13	121.00 (16)
H4—C4—C5	118.9	C11—C12—C17	120.48 (16)
C3—C4—C5	121.75 (16)	C13—C12—C17	118.46 (17)
C4—C5—H5	119.0	C12—C13—H13	119.2
C4—C5—C6	121.84 (16)	C12—C13—C14	120.60 (19)
H5—C5—C6	119.2	H13—C13—C14	120.2
H6—C6—C5	122.2	C13—C14—H14	119.9
H6—C6—C9	121.4	C13—C14—C15	120.3 (2)
C5—C6—C9	116.41 (17)	H14—C14—C15	119.8
C1—N7—H7	125.7 (13)	H15—C15—C14	120.0
C1—N7—C9	106.32 (13)	H15—C15—C16	120.3
H7—N7—C9	127.5 (13)	C14—C15—C16	119.8 (2)
N2—C8—C3	129.85 (15)	H16—C16—C15	119.8
N2—C8—C9	109.77 (13)	H16—C16—C17	119.9
C3—C8—C9	120.37 (15)	C15—C16—C17	120.3 (2)
C8—C9—C6	122.30 (15)	C12—C17—C16	120.51 (19)
C8—C9—N7	105.74 (13)	C12—C17—H17	119.0
C6—C9—N7	131.94 (15)	C16—C17—H17	120.4

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N7—H7···N2^i	0.87 (2)	2.05 (2)	2.915 (1)	173.50 (17)
C11—H111···N2^i	0.96	2.62	3.555 (3)	166

Symmetry code: (i) x, −y+1/2, z−1/2.