2-Methyl­sulfanyl-1-(morpholin-4-yl­meth­yl)-1H-benzimidazole

Abou, A.; Bany, G.E.; Kakou-Yao, R.; Seikou, T.; Ebby, N.D.

doi:10.1107/S1600536807047344

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2-Methylsulfanyl-1-(morpholin-4-ylmethyl)-1H-benzimidazole

A. Abou, G. E. Bany, R. Kakou-Yao, T. Seikou and N. D. Ebby

In the title compound, C₁₃H₁₇N₃OS, the morpholine ring has a chair conformation. The crystal structure exhibits intermolecular C—H

O and C—H

N interactions to form a consolidated array.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807047344/tk2195sup1.cif Contains datablocks I, global
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807047344/tk2195Isup2.hkl Contains datablock I

CCDC reference: 667281

checkCIF report

Key indicators

Single-crystal X-ray study
T = 294 K
Mean (C-C) = 0.002 Å
R factor = 0.043
wR factor = 0.096
Data-to-parameter ratio = 23.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.98
PLAT480_ALERT_4_C Long H...A H-Bond Reported H7     ..  O14     ..       2.62 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H4     ..  N3      ..       2.64 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H102   ..  N3      ..       2.66 Ang.

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 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
   1 ALERT type 3 Indicator that the structure quality may be low
   3 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

Comment top

Benzimidazole derivatives are important pharmaceutical intermediates. For example, they are used in the design of anti-helmintic (Dubey et al., 1985) and anti-viral (Garuti et al., 2000) pharmaceutics. In order to have a better knowledge of their structure, we have embarked on a study this class of compounds. In the title compound, C₁₃H₁₇N₃OS (I), the benzimidazole ring N1/C2/N3/C4—C9 is essentially planar and is connected to the morpholine ring, N11/C12/C13/O14/C15/C16, by the methylene-C10 atom. The morpholine ring has a chair conformation as judged from the puckering parameters: Q_T = 0.571 Å, θ = 179.4° and φ = 184.6° (Cremer & Pople, 1975) with the C10 atom in an equatorial position. The structure is consolidated by weak intermolecular interactions (Table 1).

Related literature top

For related literature, see: Dubey et al. (1985); Garuti et al. (2000); Cremer & Pople (1975); Katritzky et al. (1997).

Experimental top

Morpholine (0.6 ml, 6.09 mmol) and formaldehyde (0.5 ml, 18.27 mmol) were added to 2-methylthiobenzimidazole (1 g, 6.09 mmol) in dry ethanol (20 ml). The mixture was refluxed for 3 h, the solvent removed under vacuum, the residue diluted with water, and extracted with dichloromethane. The organic phase was dried (MgSO₄), filtered, and concentrated in vacuo. The residue was purified by chromatography (elution with ethyl acetate) to give (I) as colorless crystals (1.1 g, 69%): m. p. 352 K. ¹H NMR (DMSO, 300 MHz, p.p.m.) δ 2.50 (t, 4H, 2CH₂N), 2.67 (s, 3H, CH₃), 3.51 (t, 4H, 2CH₂O), 4.76 (s, 2H, CH₂, NCH₂N), 7.06–7.54 (m, 4H, C₆H₄). ¹³C NMR (DMSO, 300 MHz, p.p.m.) δ 14.47 (CH₃), 50.50 (CH₂NCH₂), 65.08 (NCH₂N), 65.89 (2 CH₂O), 110.15, 117.44, 120.99, 121.54, 134.02, 142.87 (C4—C9), 153.35 (C═N).

Structure description top

For related literature, see: Dubey et al. (1985); Garuti et al. (2000); Cremer & Pople (1975); Katritzky et al. (1997).

Computing details top

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 for Windows (Farrugia, 1997); software used to prepare material for publication: CRYSTALS (Betteridge et al., 2003).

Figures top

Fig. 1. The molecular structure of (I) showing the atomic labeling scheme with displacement ellipsoids drawn at the 30% probability level. H atoms are shown as spheres of arbitary radius.

2-Methylsulfanyl-1-(morpholin-4-ylmethyl)-1H-benzimidazole top

Crystal data top

C₁₃H₁₇N₃OS	Z = 2
M_r = 263.36	F(000) = 280
Triclinic, P1	D_x = 1.300 Mg m⁻³
Hall symbol: -P 1	Melting point: 352 K
a = 6.2461 (2) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.7949 (2) Å	Cell parameters from 3812 reflections
c = 11.6966 (5) Å	θ = 4–30°
α = 75.475 (1)°	µ = 0.23 mm⁻¹
β = 84.808 (1)°	T = 294 K
γ = 76.251 (2)°	Prism, colorless
V = 672.51 (4) Å³	0.40 × 0.30 × 0.30 mm

Data collection top

Nonius KappaCCD diffractometer	R_int = 0.026
Graphite monochromator	θ_max = 30.0°, θ_min = 1.8°
φ scans	h = −8→8
12818 measured reflections	k = −12→13
3812 independent reflections	l = −16→16
3284 reflections with I > 2σ(I)

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.043	H-atom parameters constrained
wR(F²) = 0.096	Method, part 1, Chebychev polynomial, [Watkin, D. (1994). Acta Cryst. A50, 411–437. Prince, E. (1982). Mathematical Techniques in Crystallography and Materials Science. New York: Springer-Verlag.] [weight] = 1.0/[A₀T₀(x) + A₁T₁(x) ··· + A_n-1]T_n-1(x)] where A_i are the Chebychev coefficients listed below and x = F /Fmax Method = Robust Weighting (Prince, 1982) W = [weight] [1-(deltaF/6*sigmaF)²]² A_i are: 488. 738. 431. 172. 33.5
S = 0.92	(Δ/σ)_max < 0.001
3817 reflections	Δρ_max = 0.23 e Å⁻³
163 parameters	Δρ_min = −0.25 e Å⁻³
0 restraints

Crystal data top

C₁₃H₁₇N₃OS	γ = 76.251 (2)°
M_r = 263.36	V = 672.51 (4) Å³
Triclinic, P1	Z = 2
a = 6.2461 (2) Å	Mo Kα radiation
b = 9.7949 (2) Å	µ = 0.23 mm⁻¹
c = 11.6966 (5) Å	T = 294 K
α = 75.475 (1)°	0.40 × 0.30 × 0.30 mm
β = 84.808 (1)°

Data collection top

Nonius KappaCCD diffractometer	3284 reflections with I > 2σ(I)
12818 measured reflections	R_int = 0.026
3812 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	0 restraints
wR(F²) = 0.096	H-atom parameters constrained
S = 0.92	Δρ_max = 0.23 e Å⁻³
3817 reflections	Δρ_min = −0.25 e Å⁻³
163 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
H4	0.0870	−0.1337	0.4686	0.0597*
H5	0.2946	−0.3677	0.4625	0.0673*
H6	0.6429	−0.4009	0.3691	0.0660*
H7	0.8112	−0.2040	0.2879	0.0591*
H101	0.9009	0.0258	0.2412	0.0582*
H102	0.8445	0.1724	0.2873	0.0590*
H121	1.1010	0.1571	0.0820	0.0683*
H122	1.0136	0.3003	0.1296	0.0674*
H131	1.1036	0.3597	−0.0774	0.0902*
H132	0.8395	0.4284	−0.0455	0.0896*
H151	0.5774	0.3214	−0.0837	0.0965*
H152	0.6497	0.1739	−0.1392	0.0961*
H161	0.5522	0.1153	0.0655	0.0701*
H162	0.8054	0.0401	0.0394	0.0708*
H181	0.1456	0.3821	0.4361	0.0934*
H182	0.1018	0.5284	0.3327	0.0928*
H183	0.0064	0.3947	0.3217	0.0930*
N1	0.58426 (17)	0.08468 (11)	0.29036 (9)	0.0419
C2	0.3987 (2)	0.17950 (13)	0.31895 (11)	0.0409
N3	0.24286 (17)	0.11681 (11)	0.37395 (10)	0.0434
C4	0.2341 (2)	−0.14769 (15)	0.43270 (12)	0.0498
C5	0.3558 (3)	−0.28335 (16)	0.42638 (14)	0.0572
C6	0.5646 (3)	−0.30343 (16)	0.37240 (14)	0.0576
C7	0.6637 (2)	−0.18902 (15)	0.32349 (13)	0.0499
C8	0.5408 (2)	−0.05237 (13)	0.33039 (10)	0.0399
C9	0.3294 (2)	−0.03035 (13)	0.38288 (10)	0.0400
C10	0.7913 (2)	0.11818 (16)	0.23991 (12)	0.0488
N11	0.76733 (17)	0.20686 (12)	0.12018 (9)	0.0427
C12	0.9767 (2)	0.24619 (18)	0.07720 (13)	0.0550
C13	0.9562 (3)	0.3378 (2)	−0.04718 (15)	0.0732
O14	0.8918 (2)	0.26370 (17)	−0.12346 (10)	0.0819
C15	0.6858 (3)	0.2283 (3)	−0.08343 (15)	0.0769
C16	0.6983 (3)	0.13381 (18)	0.04037 (13)	0.0556
S17	0.38074 (7)	0.36544 (4)	0.27562 (4)	0.0558
C18	0.1258 (3)	0.42494 (17)	0.35116 (16)	0.0639

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0372 (5)	0.0433 (5)	0.0423 (5)	−0.0112 (4)	−0.0017 (4)	−0.0026 (4)
C2	0.0416 (6)	0.0404 (6)	0.0394 (6)	−0.0092 (5)	−0.0060 (5)	−0.0053 (5)
N3	0.0404 (5)	0.0425 (5)	0.0457 (6)	−0.0097 (4)	−0.0006 (4)	−0.0073 (4)
C4	0.0508 (7)	0.0506 (7)	0.0472 (7)	−0.0193 (6)	0.0000 (5)	−0.0029 (5)
C5	0.0712 (9)	0.0439 (7)	0.0551 (8)	−0.0213 (7)	−0.0070 (7)	0.0004 (6)
C6	0.0679 (9)	0.0407 (7)	0.0585 (8)	−0.0043 (6)	−0.0095 (7)	−0.0061 (6)
C7	0.0469 (7)	0.0476 (7)	0.0496 (7)	−0.0029 (5)	−0.0037 (5)	−0.0077 (5)
C8	0.0400 (6)	0.0414 (6)	0.0359 (5)	−0.0095 (5)	−0.0054 (4)	−0.0028 (4)
C9	0.0402 (6)	0.0417 (6)	0.0365 (5)	−0.0102 (5)	−0.0038 (4)	−0.0042 (4)
C10	0.0376 (6)	0.0604 (8)	0.0453 (7)	−0.0167 (6)	−0.0063 (5)	0.0003 (6)
N11	0.0387 (5)	0.0477 (6)	0.0412 (5)	−0.0144 (4)	−0.0016 (4)	−0.0054 (4)
C12	0.0493 (7)	0.0644 (9)	0.0542 (8)	−0.0273 (7)	0.0019 (6)	−0.0070 (6)
C13	0.0788 (11)	0.0854 (12)	0.0571 (9)	−0.0430 (10)	0.0057 (8)	0.0004 (8)
O14	0.0874 (9)	0.1174 (11)	0.0467 (6)	−0.0465 (8)	0.0116 (6)	−0.0125 (7)
C15	0.0796 (12)	0.1112 (15)	0.0468 (8)	−0.0419 (11)	−0.0058 (8)	−0.0105 (9)
C16	0.0552 (8)	0.0686 (9)	0.0499 (7)	−0.0265 (7)	−0.0015 (6)	−0.0146 (7)
S17	0.0609 (2)	0.04020 (18)	0.0633 (2)	−0.01433 (15)	−0.00462 (17)	−0.00330 (14)
C18	0.0739 (10)	0.0477 (8)	0.0681 (10)	−0.0049 (7)	−0.0021 (8)	−0.0182 (7)

Geometric parameters (Å, º) top

H4—C4	0.969	N1—C10	1.4473 (15)
H5—C5	0.976	C2—N3	1.3083 (16)
H6—C6	0.972	C2—S17	1.7426 (13)
H7—C7	0.970	N3—C9	1.3947 (16)
H101—C10	0.994	C4—C5	1.381 (2)
H102—C10	0.982	C4—C9	1.3934 (17)
H121—C12	1.014	C5—C6	1.389 (2)
H122—C12	0.977	C6—C7	1.382 (2)
H131—C13	1.008	C7—C8	1.3935 (18)
H132—C13	1.009	C8—C9	1.3969 (17)
H151—C15	0.998	C10—N11	1.4506 (16)
H152—C15	1.009	N11—C12	1.4612 (16)
H161—C16	0.977	N11—C16	1.4573 (18)
H162—C16	1.001	C12—C13	1.504 (2)
H181—C18	0.983	C13—O14	1.419 (2)
H182—C18	0.959	O14—C15	1.420 (2)
H183—C18	0.982	C15—C16	1.508 (2)
N1—C2	1.3753 (16)	S17—C18	1.7943 (17)
N1—C8	1.3891 (15)

C2—N1—C8	106.01 (10)	C12—N11—C16	109.85 (11)
C2—N1—C10	127.25 (11)	H121—C12—N11	111.3
C8—N1—C10	126.47 (11)	H121—C12—H122	106.5
N1—C2—N3	113.89 (11)	N11—C12—H122	107.8
N1—C2—S17	120.33 (9)	H121—C12—C13	110.9
N3—C2—S17	125.69 (10)	N11—C12—C13	110.13 (13)
C2—N3—C9	104.42 (10)	H122—C12—C13	110.1
H4—C4—C5	121.8	C12—C13—H132	107.4
H4—C4—C9	120.9	C12—C13—H131	109.4
C5—C4—C9	117.30 (13)	H132—C13—H131	112.1
H5—C5—C4	119.0	C12—C13—O14	110.91 (14)
H5—C5—C6	119.1	H132—C13—O14	109.3
C4—C5—C6	121.91 (13)	H131—C13—O14	107.7
H6—C6—C5	118.9	C13—O14—C15	109.89 (14)
H6—C6—C7	119.2	H152—C15—H151	113.6
C5—C6—C7	121.89 (14)	H152—C15—O14	106.7
H7—C7—C6	121.5	H151—C15—O14	106.8
H7—C7—C8	122.4	H152—C15—C16	109.4
C6—C7—C8	116.07 (13)	H151—C15—C16	109.1
C7—C8—N1	132.06 (12)	O14—C15—C16	111.21 (14)
C7—C8—C9	122.65 (12)	C15—C16—N11	109.90 (13)
N1—C8—C9	105.28 (10)	C15—C16—H162	108.5
C8—C9—N3	110.40 (10)	N11—C16—H162	110.9
C8—C9—C4	120.17 (12)	C15—C16—H161	108.5
N3—C9—C4	129.42 (12)	N11—C16—H161	109.6
N1—C10—H101	108.4	H162—C16—H161	109.4
N1—C10—H102	109.7	C2—S17—C18	98.85 (7)
H101—C10—H102	109.1	S17—C18—H181	107.5
N1—C10—N11	111.62 (10)	S17—C18—H183	109.7
H101—C10—N11	110.4	H181—C18—H183	111.4
H102—C10—N11	107.6	S17—C18—H182	105.0
C10—N11—C12	109.15 (10)	H181—C18—H182	112.1
C10—N11—C16	112.30 (11)	H183—C18—H182	110.9

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7···O14ⁱ	0.97	2.62	3.526 (2)	155
C4—H4···N3ⁱⁱ	0.97	2.64	3.574 (2)	162
C10—H102···N3ⁱⁱⁱ	0.98	2.66	3.344 (2)	127

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

Experimental details

Crystal data
Chemical formula	C₁₃H₁₇N₃OS
M_r	263.36
Crystal system, space group	Triclinic, P1
Temperature (K)	294
a, b, c (Å)	6.2461 (2), 9.7949 (2), 11.6966 (5)
α, β, γ (°)	75.475 (1), 84.808 (1), 76.251 (2)
V (Å³)	672.51 (4)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.23
Crystal size (mm)	0.40 × 0.30 × 0.30

Data collection
Diffractometer	Nonius KappaCCD
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	12818, 3812, 3284
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.703

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.096, 0.92
No. of reflections	3817
No. of parameters	163
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.25

Computer programs: COLLECT (Nonius, 2001), DENZO/SCALEPACK (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), CRYSTALS (Betteridge et al., 2003), ORTEP-3 for Windows (Farrugia, 1997).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7···O14ⁱ	0.97	2.62	3.526 (2)	155
C4—H4···N3ⁱⁱ	0.97	2.64	3.574 (2)	162
C10—H102···N3ⁱⁱⁱ	0.98	2.66	3.344 (2)	127

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

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