1-Methyl-2,3-dihydro-1H-benzimidazole-2-selone

Abstract

The title compound C₈H₈N₂Se, is the product of the reaction of 2-chloro-1-methyl­benzimidazole with sodium hydro­selenide. The mol­ecule is almost planar (r.m.s. deviation = 0.041 Å) owing to the presence of the long chain of conjugated bonds (Se=C—NMe—C=C—C=C—C=C—NH). The C=Se bond length [1.838 (2) Å] corresponds well to those found in the close analogs and indicates its pronounced double-bond character. In the crystal, mol­ecules form helicoidal chains along the b axis by means of N—H⋯Se hydrogen bonds.

Related literature  

For selones as potential anti­thyroid drugs, see: Taurog et al. (1994 ▶); Roy & Mugesh (2005 ▶, 2006 ▶); Roy et al. (2007 ▶, 2011 ▶). For related compounds, see: Guziec & Guziec (1994 ▶); Husebye et al. (1997 ▶); Aydin et al. (1999 ▶); Akkurt et al. (2004 ▶, 2011 ▶); Landry et al. (2006 ▶); Nakanishi et al. (2008 ▶); Mammadova et al. (2011 ▶). For hypervalent adducts of selones with dihalogens and inter­halogens, see: Aragoni et al. (2001 ▶); Boyle & Godfrey (2001 ▶); Roy et al. (2011 ▶).

Experimental  

Crystal data  

• C₈H₈N₂Se

• M _r = 211.12

• Monoclinic,

• a = 9.9434 (13) Å

• b = 5.8472 (8) Å

• c = 13.6387 (18) Å

• β = 95.360 (2)°

• V = 789.50 (18) ų

• Z = 4

• Mo Kα radiation

• μ = 4.69 mm⁻¹

• T = 100 K

• 0.24 × 0.20 × 0.20 mm

Data collection  

• Bruker APEXII CCD diffractometer

• Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ▶) T _min = 0.399, T _max = 0.454

• 9470 measured reflections

• 2304 independent reflections

• 1941 reflections with I > 2σ(I)

• R _int = 0.030

Refinement  

• R[F ² > 2σ(F ²)] = 0.027

• wR(F ²) = 0.068

• S = 1.00

• 2304 reflections

• 101 parameters

• H-atom parameters constrained

• Δρ_max = 1.10 e Å⁻³

• Δρ_min = −0.28 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT-Plus (Bruker, 2001 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536812013700/rk2347Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3N⋯Se1i	0.91	2.58	3.471 (2)	168

Symmetry code: (i) .

supplementary crystallographic information

Comment

In the last years, the selone derivatives have attracted considerable attention owing to their antithyroid properties (Taurog et al., 1994; Roy & Mugesh, 2005, 2006; Roy et al., 2007, 2011) as well as selone-selenol tautomerism (Guziec & Guziec, 1994; Husebye et al., 1997; Landry et al., 2006; Mammadova et al., 2011). Moreover, they are used as substrates in the preparation of hypervalent adducts in reactions with dihalogens and interhalogens (Aydin et al., 1999; Aragoni et al., 2001; Boyle & Godfrey, 2001; Akkurt et al., 2004, 2011; Roy et al., 2011).

The title compound - 1-methyl-2,3-dihydro-1H-benzimidazole-2-selone, I was obtained by a reaction of 2-chloro-1-methylbenzimidazole with sodium hydroselenide (Fig. 1). The molecule of I is almost planar (r.m.s. deviation = 0.041Å) owing to the presence of the long chain of conjugated bonds (Se═C—NMe—C═C—C═C—C═C—NH) (Fig. 2). The length of the C═Se bond (1.838 (2)Å) corresponds well to those found in the closer analogs of I - 1,3-dimethylbenzimidazole-2-selone (1.825 (7)Å) (Aydin et al., 1999), 1-ethyl-3-(2-phenylethyl)benzimidazole-2-selone (1.829 (3)Å) (Akkurt et al., 2004) and 1,3-bis(3-phenylpropyl)-1H-1,3-benzimidazole-2(3H)-selone (1.828 (2)Å) (Akkurt et al., 2011) indicating its pronounced double character.

In the crystal, molecules form helicoidal chains along the b axis by means of intermolecular N—H···Seⁱ hydrogen bonds (Fig. 3, Table 1). Symmetry code: (i) -x+1/2, y+1/2, -z+3/2.

Experimental

A solution of NaBH₄ (3.83 g, 100.0 mmol) in water (25 ml) was added to a suspension of selenium (3.77 g, 47.7 mmol) in water (30 ml) with stirring at room temperature under argon. After 15 min, a solution of 2-chloro-1-methylbenzimidazole (6.60 g, 39.6 mmol) in C₂H₅OH (25 ml) was added. The resulting mixture was refluxed for 5 h. At the end of the reaction the solvents were evaporated in vacuo, and formed precipitate was extracted with CH₂Cl₂. Then the extract was dried over MgSO₄. Further crystallization from CH₂Cl₂ gives the selone I as colourless crystals. Yield is 7.81 g (93%). M.p. = 470-471 K. IR(KBr), ν/cm^-1: 3095, 1618, 1438, 1382, 11330, 1223, 1091, 746, 709. ¹H NMR (DMSO-d₆, 600 MHz, 303 K): δ = 3.63 (s, 3H, Me), 7.15 (t, 1H, H6, J = 7.1), 7.19 (t, 1H, H5, J = 7.1), 7.37 (d, 1H, H4, J = 7.1), 7.43 (d, 1H, H7, J = 7.1), 13.25 (s, 1H, H3). Anal. Calc. for C₈H₈N₂Se: C, 45.53; H, 3.82; N, 13.27. Found: C, 45.43; H, 2.78; N, 13.19.

Refinement

The hydrogen atom of the amino group was localized in the difference-Fourier map and included in the refinement with fixed positional and isotropic displacement parameters [U_iso(H) = 1.2U_eq(N)]. The other hydrogen atoms were placed in calculated positions with C—H = 0.95–0.98Å and refined in the riding model with fixed isotropic displacement parameters [U_iso(H) = 1.5U_eq(C) for the methyl group and 1.2U_eq(C) for the other groups].

Figures

Fig. 1.

Reaction of 2-chloro-1-methylbenzimidazole with sodium hydroselenide.

Fig. 2.

Molecular structure of I with the atom numbering scheme. Displacement ellipsoids are shown at the 50% probability level. H atoms are presented as a small spheres of arbitrary radius.

Fig. 3.

The helicoidal chains of I along the b axis. Dashed lines indicate the intermolecular N–H···Se hydrogen bonds.

Crystal data

C8H8N2Se	F(000) = 416
Mr = 211.12	Dx = 1.776 Mg m−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 3916 reflections
a = 9.9434 (13) Å	θ = 2.4–32.5°
b = 5.8472 (8) Å	µ = 4.69 mm−1
c = 13.6387 (18) Å	T = 100 K
β = 95.360 (2)°	Prism, yellow
V = 789.50 (18) Å3	0.24 × 0.20 × 0.20 mm
Z = 4

Data collection

Bruker APEXII CCD diffractometer	2304 independent reflections
Radiation source: fine-focus sealed tube	1941 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.030
φ– and ω–scans	θmax = 30.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −13→13
Tmin = 0.399, Tmax = 0.454	k = −8→8
9470 measured reflections	l = −19→19

Refinement

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)] = 0.027	Hydrogen site location: difference Fourier map
wR(F2) = 0.068	H-atom parameters constrained
S = 1.00	w = 1/[σ2(Fo2) + (0.0345P)2 + 0.745P] where P = (Fo2 + 2Fc2)/3
2304 reflections	(Δ/σ)max = 0.001
101 parameters	Δρmax = 1.10 e Å−3
0 restraints	Δρmin = −0.28 e Å−3

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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
Se1	0.26128 (2)	1.12016 (4)	0.878637 (16)	0.02213 (7)
N1	0.47551 (17)	0.8571 (3)	0.80856 (13)	0.0200 (3)
C2	0.3951 (2)	1.0457 (4)	0.79997 (16)	0.0203 (4)
N3	0.43002 (18)	1.1660 (3)	0.72130 (13)	0.0209 (3)
H3N	0.3892	1.2987	0.7005	0.025*
C3A	0.5294 (2)	1.0505 (4)	0.67611 (16)	0.0206 (4)
C4	0.5950 (2)	1.0978 (4)	0.59324 (16)	0.0224 (4)
H4	0.5785	1.2350	0.5568	0.027*
C5	0.6860 (2)	0.9352 (4)	0.56600 (17)	0.0242 (4)
H5	0.7320	0.9611	0.5090	0.029*
C6	0.7122 (2)	0.7339 (4)	0.62006 (16)	0.0240 (4)
H6	0.7745	0.6260	0.5986	0.029*
C7	0.6488 (2)	0.6890 (4)	0.70443 (16)	0.0220 (4)
H7	0.6674	0.5539	0.7419	0.026*
C7A	0.5571 (2)	0.8506 (3)	0.73148 (15)	0.0200 (4)
C8	0.4688 (2)	0.6817 (4)	0.88271 (17)	0.0255 (4)
H8A	0.4578	0.7533	0.9464	0.038*
H8B	0.5524	0.5919	0.8876	0.038*
H8C	0.3918	0.5810	0.8644	0.038*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Se1	0.02158 (11)	0.02058 (11)	0.02486 (11)	−0.00119 (8)	0.00548 (7)	−0.00250 (8)
N1	0.0202 (8)	0.0177 (8)	0.0225 (8)	−0.0010 (6)	0.0030 (6)	0.0026 (6)
C2	0.0191 (9)	0.0196 (9)	0.0219 (9)	−0.0018 (7)	0.0011 (7)	−0.0011 (7)
N3	0.0219 (8)	0.0174 (8)	0.0236 (8)	0.0020 (6)	0.0037 (6)	0.0018 (6)
C3A	0.0195 (9)	0.0184 (9)	0.0236 (10)	−0.0006 (7)	0.0007 (7)	0.0000 (7)
C4	0.0227 (9)	0.0221 (10)	0.0222 (9)	−0.0013 (8)	0.0017 (7)	0.0027 (8)
C5	0.0231 (10)	0.0272 (11)	0.0227 (10)	−0.0019 (8)	0.0037 (8)	−0.0019 (8)
C6	0.0204 (10)	0.0242 (10)	0.0274 (11)	0.0021 (8)	0.0029 (8)	−0.0023 (8)
C7	0.0200 (9)	0.0192 (9)	0.0263 (10)	0.0007 (7)	0.0005 (8)	−0.0008 (8)
C7A	0.0184 (9)	0.0199 (9)	0.0216 (9)	−0.0015 (7)	0.0009 (7)	−0.0005 (7)
C8	0.0258 (10)	0.0237 (10)	0.0275 (11)	0.0005 (8)	0.0058 (8)	0.0063 (8)

Geometric parameters (Å, º)

Se1—C2	1.838 (2)	C4—H4	0.9500
N1—C2	1.361 (3)	C5—C6	1.400 (3)
N1—C7A	1.387 (3)	C5—H5	0.9500
N1—C8	1.446 (3)	C6—C7	1.388 (3)
C2—N3	1.355 (3)	C6—H6	0.9500
N3—C3A	1.388 (3)	C7—C7A	1.387 (3)
N3—H3N	0.9090	C7—H7	0.9500
C3A—C4	1.385 (3)	C8—H8A	0.9800
C3A—C7A	1.405 (3)	C8—H8B	0.9800
C4—C5	1.387 (3)	C8—H8C	0.9800
C2—N1—C7A	109.74 (17)	C6—C5—H5	119.0
C2—N1—C8	124.74 (18)	C7—C6—C5	121.3 (2)
C7A—N1—C8	125.35 (18)	C7—C6—H6	119.4
N3—C2—N1	107.24 (18)	C5—C6—H6	119.4
N3—C2—Se1	126.35 (16)	C7A—C7—C6	116.9 (2)
N1—C2—Se1	126.40 (16)	C7A—C7—H7	121.5
C2—N3—C3A	110.20 (18)	C6—C7—H7	121.5
C2—N3—H3N	123.4	C7—C7A—N1	131.8 (2)
C3A—N3—H3N	126.3	C7—C7A—C3A	121.6 (2)
C4—C3A—N3	132.4 (2)	N1—C7A—C3A	106.60 (18)
C4—C3A—C7A	121.4 (2)	N1—C8—H8A	109.5
N3—C3A—C7A	106.12 (18)	N1—C8—H8B	109.5
C3A—C4—C5	116.8 (2)	H8A—C8—H8B	109.5
C3A—C4—H4	121.6	N1—C8—H8C	109.5
C5—C4—H4	121.6	H8A—C8—H8C	109.5
C4—C5—C6	121.9 (2)	H8B—C8—H8C	109.5
C4—C5—H5	119.0
C7A—N1—C2—N3	−3.4 (2)	C5—C6—C7—C7A	1.1 (3)
C8—N1—C2—N3	−178.94 (19)	C6—C7—C7A—N1	178.4 (2)
C7A—N1—C2—Se1	175.35 (15)	C6—C7—C7A—C3A	0.0 (3)
C8—N1—C2—Se1	−0.2 (3)	C2—N1—C7A—C7	−175.6 (2)
N1—C2—N3—C3A	2.5 (2)	C8—N1—C7A—C7	−0.1 (4)
Se1—C2—N3—C3A	−176.20 (15)	C2—N1—C7A—C3A	2.9 (2)
C2—N3—C3A—C4	178.0 (2)	C8—N1—C7A—C3A	178.45 (19)
C2—N3—C3A—C7A	−0.7 (2)	C4—C3A—C7A—C7	−1.5 (3)
N3—C3A—C4—C5	−176.7 (2)	N3—C3A—C7A—C7	177.40 (19)
C7A—C3A—C4—C5	1.9 (3)	C4—C3A—C7A—N1	179.74 (19)
C3A—C4—C5—C6	−0.8 (3)	N3—C3A—C7A—N1	−1.3 (2)
C4—C5—C6—C7	−0.7 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···Se1i	0.91	2.58	3.471 (2)	168

Symmetry code: (i) −x+1/2, y+1/2, −z+3/2.