3-[(1H-Benzimidazol-2-yl)sulfanyl­methyl]benzonitrile

Lin, J.R.; He, J.; Qian, Y.; Zhao, H.

doi:10.1107/S1600536809018546

organic compounds

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Volume 65| Part 6| June 2009| Page o1358

doi:10.1107/S1600536809018546

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3-[(1H-Benzimidazol-2-yl)sulfanylmethyl]benzonitrile

Jin Rui Lin,^a Jia He,^a Yang Qian ^a and Hong Zhao ^a ^*

^aOrdered Matter Science Research Center, College of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: zhaohong@seu.edu.cn

(Received 4 May 2009; accepted 16 May 2009; online 23 May 2009)

In the title compound, C₁₅H₁₁N₃S, the dihedral angle between the benzimidazole ring system and the benzene ring is 51.8 (2)°. The crystal structure exhibits intermolecular N—H⋯N hydrogen bonds which lead to the formation of C(4) chains along the [001] direction.

Related literature

For pharmacological activities of benzimidazole and its derivatives, see: Negwer & Scharnow (2001 ). For graph-set notation, see: Bernstein et al. (1995 ).

Experimental

Crystal data

C₁₅H₁₁N₃S
M_r = 265.33
Monoclinic, P 2₁ /c
a = 15.384 (4) Å
b = 9.280 (4) Å
c = 9.887 (4) Å
β = 101.63 (3)°
V = 1382.5 (8) Å³
Z = 4
Mo Kα radiation
μ = 0.22 mm⁻¹
T = 292 K
0.35 × 0.30 × 0.25 mm

Data collection

Rigaku SCXmini diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.927, T_max = 0.947
12254 measured reflections
2711 independent reflections
1926 reflections with I > 2σ(I)
R_int = 0.052

Refinement

R[F² > 2σ(F²)] = 0.070
wR(F²) = 0.184
S = 1.13
2711 reflections
172 parameters
H-atom parameters constrained
Δρ_max = 0.23 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯N1ⁱ	0.86	1.98	2.838 (3)	174
Symmetry code: (i) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809018546/bx2210sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809018546/bx2210Isup2.hkl

checkCIF report

Comment top

It is well known that Benzimidazole and its derivatives have received much attention due to their versatile pharmacological activities (Negwer & Scharnow, 2001). To further investigate the influence of the bridging ligand on the formation of supramolecular complexes, we designed and prepared a Benzimidazole-containing ligand, and used the ligand to generate some coordination polymers with interesting topologies. Here, we reported the crystal structure of the title compound. The molecular structure of the title compound, C₁₅H₁₁N₃S, and the atomic labeling scheme are shown in Fig. 1. In this Structure, the nine-membered benzimidazole ring system C1/N1/C2/C3/C4/C5/C6/C7/N2 is essentially planar. The phenyl ring C9/C10–C14 is connected to the benzimidazole ring system by the SCH₂ group. The bond lengths and angles have normal values, the dihedral angle between the benzimidazole ring system and the phenyl substituent is 51.77 (22)°, and the molecules are linked by intermolecular N—H···N hydrogen bonds which leads to the formation chains C(4) along the [001] direction (Bernstein et al., 1995).

Related literature top

For pharmacological activities of benzimidazole and its derivatives, see: Negwer & Scharnow (2001). For graph-set notation, see: Bernstein et al. (1995).

Experimental top

3-(bromomethyl)benzonitrile (11 mmol) was added to 2-mercaptobenzimidazole (10 mmol) in dry ethanol (25 ml). The mixture was refluxed for 24 h. The reaction mixture was diluted with ethyl acetate (100 ml), and the resulting solid was collected and dissolved in 20 ml of water. 40 ml of a solution of sodium hydrogen carbonate (35 g in 100 ml of water) was added. A white powder was isolated by filtration and dried to give the title compound. Colourless crystals of the title compound suitble for X-ray diffraction were from a solution of 50 mg in 20 ml methanol after 7 d.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound, showing the atomic numbering scheme. The displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. Packing diagram of the title compound, showing the structure along the a axis.

3-[(1H-Benzimidazol-2-yl)sulfanylmethyl]benzonitrile top

Crystal data top

C₁₅H₁₁N₃S	F(000) = 552
M_r = 265.33	D_x = 1.275 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2386 reflections
a = 15.384 (4) Å	θ = 2.6–27.5°
b = 9.280 (4) Å	µ = 0.22 mm⁻¹
c = 9.887 (4) Å	T = 292 K
β = 101.63 (3)°	Prism, colourless
V = 1382.5 (8) Å³	0.35 × 0.30 × 0.25 mm
Z = 4

Data collection top

Rigaku SCXmini diffractometer	2711 independent reflections
Radiation source: fine-focus sealed tube	1926 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.052
Detector resolution: 13.6612 pixels mm^-1	θ_max = 26.0°, θ_min = 2.6°
ω scans	h = −18→18
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −11→11
T_min = 0.927, T_max = 0.947	l = −12→12
12254 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.070	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.184	H-atom parameters constrained
S = 1.13	w = 1/[σ²(F_o²) + (0.0802P)² + 0.4001P] where P = (F_o² + 2F_c²)/3
2711 reflections	(Δ/σ)_max < 0.001
172 parameters	Δρ_max = 0.23 e Å⁻³
0 restraints	Δρ_min = −0.16 e Å⁻³

Crystal data top

C₁₅H₁₁N₃S	V = 1382.5 (8) Å³
M_r = 265.33	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 15.384 (4) Å	µ = 0.22 mm⁻¹
b = 9.280 (4) Å	T = 292 K
c = 9.887 (4) Å	0.35 × 0.30 × 0.25 mm
β = 101.63 (3)°

Data collection top

Rigaku SCXmini diffractometer	2711 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1926 reflections with I > 2σ(I)
T_min = 0.927, T_max = 0.947	R_int = 0.052
12254 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.070	0 restraints
wR(F²) = 0.184	H-atom parameters constrained
S = 1.13	Δρ_max = 0.23 e Å⁻³
2711 reflections	Δρ_min = −0.16 e Å⁻³
172 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.3269 (2)	0.2203 (3)	0.2414 (3)	0.0566 (8)
C2	0.3718 (2)	0.4296 (3)	0.3180 (3)	0.0541 (8)
C3	0.3983 (3)	0.5528 (3)	0.3966 (3)	0.0666 (9)
H3	0.3940	0.5575	0.4890	0.080*
C4	0.4308 (3)	0.6672 (3)	0.3330 (3)	0.0710 (10)
H4	0.4484	0.7505	0.3834	0.085*
C5	0.4379 (3)	0.6608 (3)	0.1944 (3)	0.0684 (9)
H5	0.4602	0.7398	0.1546	0.082*
C6	0.4125 (2)	0.5406 (3)	0.1158 (3)	0.0639 (9)
H6	0.4175	0.5362	0.0237	0.077*
C7	0.3791 (2)	0.4256 (3)	0.1795 (3)	0.0517 (7)
C8	0.2071 (3)	0.0318 (4)	0.3261 (4)	0.0835 (11)
H8A	0.2330	0.0408	0.4236	0.100*
H8B	0.1646	0.1092	0.3001	0.100*
C9	0.1622 (3)	−0.1128 (4)	0.2964 (4)	0.0772 (10)
C10	0.1924 (3)	−0.2344 (5)	0.3728 (5)	0.0999 (14)
H10	0.2388	−0.2259	0.4489	0.120*
C11	0.1549 (4)	−0.3684 (5)	0.3378 (6)	0.1166 (17)
H11	0.1762	−0.4493	0.3897	0.140*
C12	0.0852 (4)	−0.3812 (5)	0.2247 (6)	0.1106 (16)
H12	0.0605	−0.4711	0.1993	0.133*
C13	0.0527 (3)	−0.2595 (4)	0.1495 (5)	0.0899 (12)
C14	0.0911 (3)	−0.1256 (4)	0.1844 (4)	0.0814 (11)
H14	0.0694	−0.0446	0.1332	0.098*
C15	−0.0208 (4)	−0.2675 (6)	0.0345 (6)	0.1185 (18)
N1	0.33875 (19)	0.2979 (3)	0.3553 (2)	0.0602 (7)
N2	0.34898 (18)	0.2904 (2)	0.1329 (2)	0.0572 (7)
H2A	0.3450	0.2572	0.0507	0.069*
N3	−0.0786 (4)	−0.2759 (6)	−0.0567 (6)	0.161 (2)
S1	0.29335 (7)	0.03901 (9)	0.22331 (9)	0.0739 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.090 (2)	0.0474 (16)	0.0342 (14)	−0.0029 (15)	0.0174 (15)	0.0013 (12)
C2	0.087 (2)	0.0441 (14)	0.0328 (14)	0.0006 (14)	0.0159 (14)	0.0015 (11)
C3	0.109 (3)	0.0535 (17)	0.0404 (16)	−0.0015 (17)	0.0226 (17)	−0.0079 (13)
C4	0.112 (3)	0.0462 (17)	0.0565 (19)	−0.0052 (18)	0.0212 (19)	−0.0082 (14)
C5	0.103 (3)	0.0458 (16)	0.0602 (19)	−0.0037 (17)	0.0247 (19)	0.0059 (15)
C6	0.101 (3)	0.0558 (18)	0.0389 (15)	−0.0017 (17)	0.0245 (16)	0.0057 (13)
C7	0.083 (2)	0.0421 (14)	0.0311 (13)	0.0052 (14)	0.0148 (13)	0.0009 (11)
C8	0.108 (3)	0.081 (3)	0.067 (2)	−0.022 (2)	0.031 (2)	−0.0129 (19)
C9	0.095 (3)	0.068 (2)	0.073 (2)	−0.016 (2)	0.027 (2)	0.0022 (19)
C10	0.104 (3)	0.094 (3)	0.100 (3)	−0.017 (3)	0.018 (3)	0.016 (3)
C11	0.119 (4)	0.081 (3)	0.146 (5)	−0.016 (3)	0.017 (4)	0.031 (3)
C12	0.123 (4)	0.065 (3)	0.149 (5)	−0.023 (3)	0.040 (4)	0.002 (3)
C13	0.101 (3)	0.074 (3)	0.095 (3)	−0.024 (2)	0.021 (3)	−0.008 (2)
C14	0.096 (3)	0.066 (2)	0.083 (3)	−0.010 (2)	0.023 (2)	−0.0007 (19)
C15	0.139 (5)	0.100 (4)	0.112 (4)	−0.041 (3)	0.018 (4)	−0.014 (3)
N1	0.104 (2)	0.0477 (13)	0.0330 (12)	−0.0047 (13)	0.0241 (13)	−0.0015 (10)
N2	0.0971 (19)	0.0497 (13)	0.0276 (11)	−0.0005 (13)	0.0189 (12)	−0.0020 (10)
N3	0.159 (5)	0.158 (5)	0.149 (5)	−0.053 (4)	−0.010 (4)	−0.015 (4)
S1	0.1199 (8)	0.0501 (5)	0.0600 (6)	−0.0158 (5)	0.0378 (5)	−0.0082 (4)

Geometric parameters (Å, º) top

C1—N1	1.319 (3)	C8—S1	1.829 (4)
C1—N2	1.355 (3)	C8—H8A	0.9700
C1—S1	1.758 (3)	C8—H8B	0.9700
C2—C3	1.396 (4)	C9—C10	1.385 (6)
C2—C7	1.397 (4)	C9—C14	1.396 (6)
C2—N1	1.401 (4)	C10—C11	1.386 (6)
C3—C4	1.379 (4)	C10—H10	0.9300
C3—H3	0.9300	C11—C12	1.390 (7)
C4—C5	1.398 (4)	C11—H11	0.9300
C4—H4	0.9300	C12—C13	1.389 (6)
C5—C6	1.370 (4)	C12—H12	0.9300
C5—H5	0.9300	C13—C14	1.389 (5)
C6—C7	1.390 (4)	C13—C15	1.435 (8)
C6—H6	0.9300	C14—H14	0.9300
C7—N2	1.384 (4)	C15—N3	1.135 (7)
C8—C9	1.510 (5)	N2—H2A	0.8600

N1—C1—N2	113.6 (3)	H8A—C8—H8B	108.7
N1—C1—S1	126.6 (2)	C10—C9—C14	119.1 (4)
N2—C1—S1	119.6 (2)	C10—C9—C8	121.8 (4)
C3—C2—C7	119.7 (3)	C14—C9—C8	119.0 (4)
C3—C2—N1	130.4 (3)	C9—C10—C11	121.2 (5)
C7—C2—N1	109.9 (2)	C9—C10—H10	119.4
C4—C3—C2	118.0 (3)	C11—C10—H10	119.4
C4—C3—H3	121.0	C10—C11—C12	119.5 (5)
C2—C3—H3	121.0	C10—C11—H11	120.2
C3—C4—C5	121.4 (3)	C12—C11—H11	120.2
C3—C4—H4	119.3	C13—C12—C11	119.8 (4)
C5—C4—H4	119.3	C13—C12—H12	120.1
C6—C5—C4	121.4 (3)	C11—C12—H12	120.1
C6—C5—H5	119.3	C12—C13—C14	120.4 (4)
C4—C5—H5	119.3	C12—C13—C15	121.6 (4)
C5—C6—C7	117.2 (3)	C14—C13—C15	118.0 (4)
C5—C6—H6	121.4	C13—C14—C9	119.9 (4)
C7—C6—H6	121.4	C13—C14—H14	120.0
N2—C7—C6	132.4 (3)	C9—C14—H14	120.0
N2—C7—C2	105.3 (2)	N3—C15—C13	179.0 (7)
C6—C7—C2	122.3 (3)	C1—N1—C2	104.3 (2)
C9—C8—S1	106.2 (3)	C1—N2—C7	107.0 (2)
C9—C8—H8A	110.5	C1—N2—H2A	126.5
S1—C8—H8A	110.5	C7—N2—H2A	126.5
C9—C8—H8B	110.5	C1—S1—C8	102.13 (15)
S1—C8—H8B	110.5

C7—C2—C3—C4	0.0 (5)	C11—C12—C13—C15	−178.2 (5)
N1—C2—C3—C4	178.4 (3)	C12—C13—C14—C9	−0.6 (7)
C2—C3—C4—C5	−0.4 (6)	C15—C13—C14—C9	179.4 (4)
C3—C4—C5—C6	0.2 (6)	C10—C9—C14—C13	−1.1 (6)
C4—C5—C6—C7	0.3 (5)	C8—C9—C14—C13	175.6 (4)
C5—C6—C7—N2	−179.1 (3)	C12—C13—C15—N3	−23 (38)
C5—C6—C7—C2	−0.6 (5)	C14—C13—C15—N3	157 (37)
C3—C2—C7—N2	179.3 (3)	N2—C1—N1—C2	−0.4 (4)
N1—C2—C7—N2	0.6 (4)	S1—C1—N1—C2	175.5 (3)
C3—C2—C7—C6	0.5 (5)	C3—C2—N1—C1	−178.6 (4)
N1—C2—C7—C6	−178.2 (3)	C7—C2—N1—C1	−0.2 (4)
S1—C8—C9—C10	88.9 (4)	N1—C1—N2—C7	0.8 (4)
S1—C8—C9—C14	−87.8 (4)	S1—C1—N2—C7	−175.4 (2)
C14—C9—C10—C11	1.6 (7)	C6—C7—N2—C1	177.8 (4)
C8—C9—C10—C11	−175.0 (4)	C2—C7—N2—C1	−0.8 (3)
C9—C10—C11—C12	−0.4 (8)	N1—C1—S1—C8	41.3 (4)
C10—C11—C12—C13	−1.3 (8)	N2—C1—S1—C8	−143.1 (3)
C11—C12—C13—C14	1.9 (8)	C9—C8—S1—C1	170.0 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.86	1.98	2.838 (3)	174

Symmetry code: (i) x, −y+1/2, z−1/2.

Experimental details

Crystal data
Chemical formula	C₁₅H₁₁N₃S
M_r	265.33
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	292
a, b, c (Å)	15.384 (4), 9.280 (4), 9.887 (4)
β (°)	101.63 (3)
V (Å³)	1382.5 (8)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.22
Crystal size (mm)	0.35 × 0.30 × 0.25

Data collection
Diffractometer	Rigaku SCXmini diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.927, 0.947
No. of measured, independent and observed [I > 2σ(I)] reflections	12254, 2711, 1926
R_int	0.052
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.070, 0.184, 1.13
No. of reflections	2711
No. of parameters	172
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.16

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2A···N1ⁱ	0.86	1.98	2.838 (3)	173.8

Symmetry code: (i) x, −y+1/2, z−1/2.

Acknowledgements

This work was supported by financial support from Southeast University for Young Researchers (grant No. 4007041027).

References

Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Negwer, M. & Scharnow, H. G. (2001). Organic Chemical Drugs and Their Synonyms, 8th extensively enlarged ed. Weinheim: Wiley–VCH Verlag GmbH. Google Scholar
Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar