1,3-Bis(1H-benzimidazol-2-yl)-2-oxapropane

Chen, Y.; Guo, J.; Yun, R.; Wu, H.

doi:10.1107/S1600536809011507

organic compounds

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ISSN: 2056-9890

Volume 65| Part 5| May 2009| Page o948

doi:10.1107/S1600536809011507

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1,3-Bis(1H-benzimidazol-2-yl)-2-oxapropane

Ying Chen,^a Jixi Guo,^b Ruirui Yun ^a and Huilu Wu ^a ^*

^aSchool of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou 730070, People's Republic of China, and ^bInstitute of Applied Chemistry, Xinjiang University, Urumqi 830046, Xinjiang, People's Republic of China
^*Correspondence e-mail: wuhuilu@163.com

(Received 21 March 2009; accepted 28 March 2009; online 2 April 2009)

The title molecule, C₁₆H₁₄N₄O, lies on a crystallographic inversion center. The –CH₂– groups and the O atom are disordered over two sites with equal occupancy, the disorder of the O atom being symmetry imposed. In the crystal structure, molecules are linked into a two-dimensional network parallel to (001) via intermolecular N—H⋯N hydrogen bonds.

Related literature

For the applications of bis(2-benzimidazolyl)alkanes, see: Cai et al. (2003 ); Min & Suh (2000 ); Roderick et al. (1972 ). For the isostructural amine analog, see: Tarazon Navarro & McKee (2003 ).

Experimental

Crystal data

C₁₆H₁₄N₄O
M_r = 278.31
Orthorhombic, P b c a
a = 8.2143 (4) Å
b = 9.6296 (3) Å
c = 16.8088 (7) Å
V = 1329.58 (9) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 153 K
0.19 × 0.13 × 0.09 mm

Data collection

Rigaku R-AXIS Spider diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.983, T_max = 0.992
11836 measured reflections
1525 independent reflections
1189 reflections with I > 2σ(I)
R_int = 0.045

Refinement

R[F² > 2σ(F²)] = 0.043
wR(F²) = 0.112
S = 1.08
1525 reflections
108 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2N⋯N1ⁱ	0.953 (19)	1.951 (19)	2.8803 (16)	164.2 (15)
Symmetry code: (i) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z]$ .

Data collection: RAPID-AUTO (Rigaku/MSC, 2004 ); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; 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 global, I. DOI: 10.1107/S1600536809011507/lh2795sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809011507/lh2795Isup2.hkl

checkCIF report

Comment top

Interest in bis(2-benzimidazolyl)alkanes and their derivatives are widespread and has originated from their wide-ranging anti-viral activity and their importance in selective ion-exchange resins (Cai et al., 2003; Min et al., 2000; Roderick et al., 1972). The molecular structure of the title compound is shown in Fig. 1 and is isostructural with the amine analog (Tarazon Navarro & McKee, 2003). In the crystal structure, molecules are linked into a two-dimensional network parallel to the (001) plane via intermolecular N-H···N hydrogen bonds (Fig. 2).

Related literature top

For the applications of bis(2-benzimidazolyl)alkanes, see: Cai et al. (2003); Min et al. (2000); Roderick et al. (1972). For the isostructural amine analog, see: Tarazon Navarro & McKee (2003).

Experimental top

21.44 g (160 mmol) of diglycolic acid was combined with 34.56 g (320 mmol) of o-phenylenediamine in 350 ml of 5 N HCl. The solution was refluxed for 24 h. The resulting solution was neutralized with NH₄OH. The white precipitate was collected, washed with MeOH and absolute Et₂O, and dried in vacuo. The dried precipitate was dissolved in DMF to a green solution and through the ether diffusion exhalation crystal after three days at room temperature. The colorless crystals suitable for X-ray diffraction studies were obtained after four weeks. Yield, 29.36 g (66%). (found: C, 68.78; H, 5.09; N,20.51 Calcd. for C16H14N4O: C, 69.05; H, 5.07; N, 20.13)

Computing details top

Data collection: RAPID-AUTO (Rigaku/MSC, 2004); cell refinement: RAPID-AUTO (Rigaku/MSC, 2004); data reduction: RAPID-AUTO (Rigaku/MSC, 2004); 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 with displacement ellipsoids shown at the 30% probability level. Open bonds indicate the disorder component. Symmetry code (A): -x+2, -y+1, -z+1.
	Fig. 2. Part of the crystal structure of the title compound with hydrogen bonds shown as dashed lines. Only H atoms involed in hydrogen bonds are shown. The disorder is not shown.

1,3-Bis(1H-benzimidazol-2-yl)-2-oxapropane top

Crystal data top

C₁₆H₁₄N₄O	F(000) = 584
M_r = 278.31	D_x = 1.390 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1231 reflections
a = 8.2143 (4) Å	θ = 3.5–25.5°
b = 9.6296 (3) Å	µ = 0.09 mm⁻¹
c = 16.8088 (7) Å	T = 153 K
V = 1329.58 (9) Å³	Prism, colourless
Z = 4	0.19 × 0.13 × 0.09 mm

Data collection top

Rigaku R-AXIS Spider diffractometer	1525 independent reflections
Radiation source: fine-focus sealed tube	1189 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.045
ϕ and ω scans	θ_max = 27.5°, θ_min = 3.5°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −10→10
T_min = 0.983, T_max = 0.992	k = −12→11
11836 measured reflections	l = −20→21

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.043	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.112	w = 1/[σ²(F_o²) + (0.0566P)² + 0.3224P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max < 0.001
1525 reflections	Δρ_max = 0.22 e Å⁻³
108 parameters	Δρ_min = −0.20 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.015 (3)

Crystal data top

C₁₆H₁₄N₄O	V = 1329.58 (9) Å³
M_r = 278.31	Z = 4
Orthorhombic, Pbca	Mo Kα radiation
a = 8.2143 (4) Å	µ = 0.09 mm⁻¹
b = 9.6296 (3) Å	T = 153 K
c = 16.8088 (7) Å	0.19 × 0.13 × 0.09 mm

Data collection top

Rigaku R-AXIS Spider diffractometer	1525 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1189 reflections with I > 2σ(I)
T_min = 0.983, T_max = 0.992	R_int = 0.045
11836 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	0 restraints
wR(F²) = 0.112	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	Δρ_max = 0.22 e Å⁻³
1525 reflections	Δρ_min = −0.20 e Å⁻³
108 parameters

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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	Occ. (<1)
O1	0.9632 (3)	0.5599 (2)	0.53873 (12)	0.0332 (5)	0.50
N1	0.64853 (14)	0.36549 (11)	0.43694 (6)	0.0256 (3)
N2	0.71007 (14)	0.59185 (11)	0.43361 (7)	0.0254 (3)
H2N	0.770 (2)	0.675 (2)	0.4419 (10)	0.049 (5)*
C1	0.54372 (16)	0.43254 (13)	0.38456 (8)	0.0245 (3)
C2	0.41904 (18)	0.37997 (14)	0.33731 (9)	0.0329 (4)
H2A	0.3907	0.2844	0.3391	0.039*
C3	0.3378 (2)	0.47100 (16)	0.28783 (10)	0.0391 (4)
H3A	0.2525	0.4372	0.2549	0.047*
C4	0.3787 (2)	0.61227 (16)	0.28509 (9)	0.0366 (4)
H4A	0.3217	0.6717	0.2496	0.044*
C5	0.49977 (17)	0.66712 (14)	0.33267 (8)	0.0303 (3)
H5A	0.5257	0.7633	0.3319	0.036*
C6	0.58166 (16)	0.57462 (13)	0.38169 (7)	0.0237 (3)
C7	0.74397 (17)	0.46457 (12)	0.46425 (8)	0.0254 (3)
C8	0.8957 (12)	0.4403 (12)	0.5122 (5)	0.0319 (12)	0.50
H8A	0.8872	0.3484	0.5339	0.038*	0.50
H8B	0.9052	0.5059	0.5549	0.038*	0.50
C8*	0.8603 (12)	0.4441 (12)	0.5307 (5)	0.0319 (12)	0.50
H8*A	0.8049	0.4226	0.5795	0.038*	0.50
H8*B	0.9273	0.3657	0.5177	0.038*	0.50

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0271 (11)	0.0310 (10)	0.0415 (11)	−0.0002 (8)	−0.0057 (9)	−0.0077 (8)
N1	0.0253 (6)	0.0221 (6)	0.0293 (6)	0.0006 (4)	0.0002 (5)	0.0014 (4)
N2	0.0249 (6)	0.0218 (6)	0.0297 (6)	−0.0011 (5)	−0.0015 (5)	0.0011 (4)
C1	0.0220 (7)	0.0231 (7)	0.0283 (7)	0.0009 (5)	0.0033 (5)	0.0007 (5)
C2	0.0314 (8)	0.0266 (7)	0.0406 (8)	−0.0031 (6)	−0.0052 (6)	−0.0021 (6)
C3	0.0342 (9)	0.0363 (8)	0.0469 (9)	−0.0002 (6)	−0.0148 (7)	−0.0009 (6)
C4	0.0346 (8)	0.0344 (8)	0.0407 (8)	0.0067 (6)	−0.0091 (7)	0.0039 (6)
C5	0.0312 (8)	0.0225 (7)	0.0372 (7)	0.0037 (5)	−0.0002 (6)	0.0016 (5)
C6	0.0208 (7)	0.0230 (6)	0.0273 (6)	0.0008 (5)	0.0010 (5)	−0.0009 (5)
C7	0.0262 (7)	0.0221 (7)	0.0279 (6)	0.0010 (5)	−0.0001 (5)	0.0012 (5)
C8	0.029 (4)	0.0320 (9)	0.034 (4)	−0.001 (2)	−0.004 (2)	0.002 (2)
C8*	0.029 (4)	0.0320 (9)	0.034 (4)	−0.001 (2)	−0.004 (2)	0.002 (2)

Geometric parameters (Å, º) top

O1—C8*	1.405 (12)	C4—C5	1.381 (2)
O1—C8ⁱ	1.441 (7)	C4—H4A	0.9500
N1—C7	1.3175 (17)	C5—C6	1.3874 (18)
N1—C1	1.3904 (17)	C5—H5A	0.9500
N2—C7	1.3583 (16)	C7—C8*	1.483 (12)
N2—C6	1.3790 (17)	C7—C8	1.502 (12)
N2—H2N	0.953 (19)	C8—O1ⁱ	1.441 (7)
C1—C2	1.3914 (19)	C8—H8A	0.9600
C1—C6	1.4041 (19)	C8—H8B	0.9600
C2—C3	1.380 (2)	C8*—O1ⁱ	1.862 (7)
C2—H2A	0.9500	C8—H8A	0.9600
C3—C4	1.402 (2)	C8—H8B	0.9600
C3—H3A	0.9500

C8—O1—C8ⁱ	97.6 (5)	N1—C7—C8	124.6 (5)
C8*—O1—C8ⁱ	115.2 (7)	N2—C7—C8	120.9 (5)
C8—O1—C8*ⁱ	95.4 (5)	O1—C8—C7	112.6 (8)
C8—O1—C8ⁱ	113.1 (3)	O1ⁱ—C8—C7	110.5 (6)
C8ⁱ—O1—H8B	136.0	O1—C8—H8A	133.4
C8*ⁱ—O1—H8B	134.6	O1ⁱ—C8—H8A	106.5
C7—N1—C1	104.64 (10)	C7—C8—H8A	106.7
C7—N2—C6	106.76 (11)	O1ⁱ—C8—H8B	112.3
C7—N2—H2N	126.8 (11)	C7—C8—H8B	111.5
C6—N2—H2N	126.2 (11)	H8A—C8—H8B	109.1
N1—C1—C2	130.41 (12)	O1—C8—H8*A	93.2
N1—C1—C6	109.68 (12)	O1ⁱ—C8—H8*A	158.6
C2—C1—C6	119.88 (12)	C7—C8—H8*A	90.6
C3—C2—C1	117.95 (13)	H8A—C8—H8*A	62.0
C3—C2—H2A	121.0	H8B—C8—H8*A	60.4
C1—C2—H2A	121.0	O1—C8—H8*B	128.0
C2—C3—C4	121.35 (14)	O1ⁱ—C8—H8*B	78.4
C2—C3—H3A	119.3	C7—C8—H8*B	119.4
C4—C3—H3A	119.3	H8B—C8—H8*B	119.7
C5—C4—C3	121.63 (14)	O1—C8*—C7	110.8 (7)
C5—C4—H4A	119.2	O1—C8*—H8A	128.6
C3—C4—H4A	119.2	C7—C8*—H8A	108.8
C4—C5—C6	116.58 (13)	H8A—C8*—H8B	125.3
C4—C5—H5A	121.7	O1—C8—H8A	111.9
C6—C5—H5A	121.7	C7—C8—H8A	111.5
N2—C6—C5	132.03 (12)	O1ⁱ—C8—H8A	154.1
N2—C6—C1	105.38 (11)	O1—C8—H8B	107.5
C5—C6—C1	122.58 (13)	C7—C8—H8B	107.6
N1—C7—N2	113.54 (12)	H8B—C8—H8B	115.5
N1—C7—C8*	123.3 (5)	H8A—C8—H8*B	107.3
N2—C7—C8*	122.5 (5)

Symmetry code: (i) −x+2, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···N1ⁱⁱ	0.953 (19)	1.951 (19)	2.8803 (16)	164.2 (15)

Symmetry code: (ii) −x+3/2, y+1/2, z.

Experimental details

Crystal data
Chemical formula	C₁₆H₁₄N₄O
M_r	278.31
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	153
a, b, c (Å)	8.2143 (4), 9.6296 (3), 16.8088 (7)
V (Å³)	1329.58 (9)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.19 × 0.13 × 0.09

Data collection
Diffractometer	Rigaku R-AXIS Spider diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.983, 0.992
No. of measured, independent and observed [I > 2σ(I)] reflections	11836, 1525, 1189
R_int	0.045
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.112, 1.08
No. of reflections	1525
No. of parameters	108
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.20

Computer programs: RAPID-AUTO (Rigaku/MSC, 2004), 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—H2N···N1ⁱ	0.953 (19)	1.951 (19)	2.8803 (16)	164.2 (15)

Symmetry code: (i) −x+3/2, y+1/2, z.

Acknowledgements

The authors acknowledge the financial support and a grant from the Qing Lan Talent Engineering Funds of Lanzhou Jiaotong University. A grant from the Middle-Young Age Science Foundation of Gansu Province (grant No. 3YS061-A25–023,24) is also acknowledged.

References

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