3-(1H-Benzimidazol-2-ylsulfan­yl)propan-1-ol

Mol­ecules of the title compound, C₁₀H₁₂N₂OS, are inter­connected by N—H...O hydrogen bonds of moderate strength into infinite chains. There are also intra­molecular O—H...N bonds of moderate length. Weaker inter­actions are represented by C—H...N bonds as well as by π–π inter­actions between the imidazole and benzene rings [distance between centroids = 3.6865 (8) Å].

Key indicators

• Single-crystal X-ray study
• T = 294 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.038
• wR factor = 0.105
• Data-to-parameter ratio = 21.5

checkCIF/PLATON results

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Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.98

   0 ALERT level A = In general: serious problem
   0 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
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S1. Comment

Benzimidazole derivatives are important pharmaceutical intermediates. They are used in the design of antihelmintic (Dubey et al., 1985) and antiviral pharmaceutics (Garuti et al., 2000). Therefore we have decided to study this class of compounds. The title compound has been synthesized and its structure has been determined in order to study influence of new substituents on the biological activity of the new benzimidazole derivative.

In the title molecule the benzimidazole unit C1/N2/C3/C4/C5/C6/C7/C8/N9 is essentially planar, with a mean deviation of 0.0087 Å. The structure packing exhibits intra and intermolecular hydrogen bonds - see also Tab. 1 and Fig. 2.

Related literature

For related literature see: Dubey et al., 1985; Garuti et al., 2000. For refinement weighting scheme, see: Prince (1982); Watkin (1994).

S2. Experimental

2 ml of triethylamine (19.98 mmol) and 3-chloropropan-1-ol (1.7 ml, 19.98 mmol) was added to 2-mercatobenzimidazole (1 g, 6.66 mmol) in dry ethanol (20 ml). The mixture was refluxed for 24 h. The solvent was evaporated in vacuum. The residue was purified by column chromatography on a silica gel (Elution: ethyl acetate/dichloromethane (1:9, v/v)) and the title compound was yielded as a yellow powder (1.12 g, 81%) with a melting point 395 K. The compound was dissolved in ethanol and pentane and after 72 h prismatic crystals were obtained. ¹H NMR(DMSO, 300 MHz) δ (p.p.m.):1.832–1.919 (m, 2H, CH₂S), 3.321–3.429 (m, 2H, CH2), 3.526 (m, 2H, CH₂O), 4.774 (s, 1H, OH), 7.078–7.440 (m, 4H, C₆H₄), 12.556 (s, 1H, NH). ¹³C NMR (DMSO, 300 MHz) δ (p.p.m.):28.18 (CH₂S), 32.62 (CH₂), 59.09 (CH₂O), 110.60, 116.85, 121.38, 135.44, 143.42 (C4, C5, C6, C7, C8, C9), 150.50 (C═N).

S3. Refinement

All the H atoms were discernable in a difference Fourier map. The C—H distances were contrained to 0.95 and 0.98 Å for aryl and methylene H atoms, respectively, while U_iso(H) = 1.2U_eq(C). The positional parameters as well as the U_iso of the H atoms H9 and H14, i.e. the H atoms involved in the N—H···O and O—H···N hydrogen bonds, respectively, were refined freely.

Computing details

Data collection: COLLECT (Nonius, 1997); 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 for Windows (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures

	Fig. 1. A view of the title molecule with the atom labelling scheme. The displacement ellipsoids are drawn at the 30% probability level. The H atoms are shown as spheres of arbitary radius.
	Fig. 2. A motif of the N—H···O hydrogen bonds forming the chains in the title structure.

3-(1H-Benzimidazol-2-ylsulfanyl)propan-1-ol

Crystal data

C10H12N2OS	F(000) = 440
Mr = 208.28	Dx = 1.351 Mg m^−3
Monoclinic, P21/c	Melting point: 395 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 7.1472 (3) Å	Cell parameters from 14014 reflections
b = 11.5574 (6) Å	θ = 2–30°
c = 12.5284 (6) Å	µ = 0.28 mm^−1
β = 98.343 (4)°	T = 294 K
V = 1023.93 (8) Å^3	Prism, yellow
Z = 4	0.40 × 0.35 × 0.25 mm

Data collection

Nonius KappaCCD diffractometer	2469 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.028
Graphite monochromator	θmax = 30.0°, θmin = 2.4°
φ scans	h = −10→10
14014 measured reflections	k = −16→16
2905 independent reflections	l = −17→17

Refinement

Refinement on F^2	40 constraints
Least-squares matrix: full	Primary atom site location: structure-invariant direct methods
R[F^2 > 2σ(F^2)] = 0.039	Hydrogen site location: difference Fourier map
wR(F^2) = 0.105	H atoms treated by a mixture of independent and constrained refinement
S = 0.96	Method, part 1, Chebychev polynomial, (Watkin, 1994, Prince, 1982) [weight] = 1.0/[A0*T0(x) + A1*T1(x) ··· + An-1]*Tn-1(x)] where Ai are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] * [1-(deltaF/6*sigmaF)^2]^2 Ai are: 401. 643. 404. 180. 52.0
2897 reflections	(Δ/σ)max = 0.001
135 parameters	Δρmax = 0.24 e Å^−3
0 restraints	Δρmin = −0.29 e Å^−3

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

	x	y	z	Uiso*/Ueq
C1	0.20606 (16)	0.48268 (12)	0.70598 (10)	0.0398
N2	0.33956 (14)	0.46390 (10)	0.64550 (9)	0.0405
C3	0.25166 (16)	0.39740 (11)	0.55977 (10)	0.0367
C4	0.32332 (19)	0.35508 (12)	0.46994 (11)	0.0437
C5	0.2028 (2)	0.29163 (13)	0.39578 (11)	0.0500
C6	0.0160 (2)	0.27040 (13)	0.41022 (12)	0.0524
C7	−0.05715 (19)	0.31195 (12)	0.49875 (12)	0.0490
C8	0.06357 (16)	0.37607 (11)	0.57329 (10)	0.0382
N9	0.03898 (15)	0.43166 (10)	0.66774 (9)	0.0419
S10	0.22683 (5)	0.56461 (4)	0.82388 (3)	0.0543
C11	0.4478 (2)	0.64012 (12)	0.81673 (12)	0.0497
C12	0.6209 (2)	0.58824 (14)	0.88430 (12)	0.0519
C13	0.6655 (2)	0.46502 (14)	0.85854 (12)	0.0506
O14	0.70311 (14)	0.44920 (10)	0.75131 (9)	0.0511
H9	−0.063 (3)	0.4384 (16)	0.6965 (16)	0.061 (5)*
H14	0.602 (3)	0.4573 (17)	0.7080 (18)	0.067 (6)*
H7	−0.1845	0.2974	0.5083	0.0582*
H6	−0.0628	0.2262	0.3578	0.0621*
H5	0.2482	0.2619	0.3337	0.0604*
H4	0.4506	0.3693	0.4600	0.0533*
H111	0.4340	0.7200	0.8407	0.0592*
H112	0.4698	0.6400	0.7413	0.0592*
H121	0.6009	0.5917	0.9600	0.0613*
H122	0.7308	0.6355	0.8743	0.0613*
H131	0.7770	0.4400	0.9081	0.0607*
H132	0.5569	0.4168	0.8691	0.0607*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0318 (5)	0.0495 (7)	0.0390 (6)	0.0036 (5)	0.0086 (4)	0.0026 (5)
N2	0.0303 (4)	0.0541 (6)	0.0381 (5)	−0.0015 (4)	0.0078 (4)	−0.0024 (4)
C3	0.0320 (5)	0.0405 (6)	0.0378 (5)	0.0001 (4)	0.0061 (4)	0.0041 (4)
C4	0.0423 (6)	0.0493 (7)	0.0414 (6)	0.0001 (5)	0.0117 (5)	0.0020 (5)
C5	0.0627 (8)	0.0481 (7)	0.0401 (6)	−0.0025 (6)	0.0098 (6)	−0.0008 (5)
C6	0.0601 (8)	0.0460 (7)	0.0487 (7)	−0.0118 (6)	−0.0004 (6)	0.0013 (6)
C7	0.0394 (6)	0.0490 (7)	0.0569 (8)	−0.0090 (5)	0.0018 (5)	0.0076 (6)
C8	0.0331 (5)	0.0405 (6)	0.0413 (6)	0.0001 (4)	0.0068 (4)	0.0072 (5)
N9	0.0292 (5)	0.0530 (6)	0.0452 (6)	0.0016 (4)	0.0114 (4)	0.0040 (5)
S10	0.0455 (2)	0.0749 (3)	0.04444 (19)	0.00492 (16)	0.01321 (14)	−0.01196 (16)
C11	0.0562 (8)	0.0419 (6)	0.0508 (7)	0.0025 (6)	0.0069 (6)	−0.0057 (5)
C12	0.0499 (7)	0.0588 (8)	0.0460 (7)	−0.0021 (6)	0.0037 (6)	−0.0097 (6)
C13	0.0486 (7)	0.0607 (8)	0.0433 (7)	0.0115 (6)	0.0093 (5)	0.0015 (6)
O14	0.0320 (4)	0.0762 (7)	0.0464 (5)	0.0055 (4)	0.0097 (4)	−0.0085 (5)

Geometric parameters (Å, º)

C1—N2	1.3197 (15)	C8—N9	1.3800 (17)
C1—N9	1.3554 (16)	N9—H9	0.86 (2)
C1—S10	1.7427 (14)	S10—C11	1.8182 (16)
N2—C3	1.3939 (16)	C11—C12	1.517 (2)
C3—C4	1.3912 (17)	C11—H111	0.980
C3—C8	1.4009 (16)	C11—H112	0.980
C4—C5	1.382 (2)	C12—C13	1.505 (2)
C4—H4	0.950	C12—H121	0.980
C5—C6	1.395 (2)	C12—H122	0.980
C5—H5	0.950	C13—O14	1.4195 (17)
C6—C7	1.379 (2)	C13—H131	0.980
C6—H6	0.950	C13—H132	0.980
C7—C8	1.3899 (19)	O14—H14	0.84 (2)
C7—H7	0.950
N2—C1—N9	113.50 (12)	C8—N9—H9	128.4 (13)
N2—C1—S10	126.61 (10)	C1—N9—H9	124.6 (13)
N9—C1—S10	119.89 (9)	C1—S10—C11	100.77 (6)
C1—N2—C3	104.51 (10)	S10—C11—C12	115.24 (11)
N2—C3—C4	129.75 (11)	S10—C11—H111	108.1
N2—C3—C8	109.70 (11)	C12—C11—H111	108.2
C4—C3—C8	120.55 (12)	S10—C11—H112	108.0
C3—C4—C5	117.63 (12)	C12—C11—H112	107.8
C3—C4—H4	121.2	H111—C11—H112	109.5
C5—C4—H4	121.2	C11—C12—C13	115.82 (12)
C4—C5—C6	121.39 (13)	C11—C12—H121	107.6
C4—C5—H5	119.3	C13—C12—H121	108.1
C6—C5—H5	119.3	C11—C12—H122	108.2
C5—C6—C7	121.64 (13)	C13—C12—H122	107.5
C5—C6—H6	119.2	H121—C12—H122	109.5
C7—C6—H6	119.2	C12—C13—O14	113.58 (13)
C6—C7—C8	117.08 (12)	C12—C13—H131	108.8
C6—C7—H7	121.5	O14—C13—H131	108.3
C8—C7—H7	121.5	C12—C13—H132	108.2
C3—C8—C7	121.71 (12)	O14—C13—H132	108.5
C3—C8—N9	105.40 (11)	H131—C13—H132	109.5
C7—C8—N9	132.88 (12)	C13—O14—H14	109.5 (14)
C8—N9—C1	106.88 (10)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O14—H14···N2	0.84 (2)	1.93 (2)	2.746 (2)	163 (2)
N9—H9···O14^i	0.86 (2)	1.90 (2)	2.762 (2)	176 (2)
C11—H112···N2	0.98	2.47	2.978 (2)	112

Symmetry code: (i) x−1, y, z.