organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

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[Cai, Y. P., Chen, C. L., Zhang, L., Shi, J. L., Xu, A. W., Su, C. Y. & Kang, B. S. (2003). Inorg. Chim. Acta, 342, 107-113.]); Min & Suh (2000[Min, K. S. & Suh, M. P. (2000). J. Am. Chem. Soc. 122, 6834-6840.]); Roderick et al. (1972[Roderick, W. R., Nordeen, C. W., Von Esch, A. M. & Appell, R. N. J. (1972). J. Med. Chem. 15, 655-658.]). For the isostructural amine analog, see: Tarazon Navarro & McKee (2003[Tarazon Navarro, A. & McKee, V. (2003). Acta Cryst. E59, o1199-o1201.]).

[Scheme 1]

Experimental

Crystal data
  • C16H14N4O

  • Mr = 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.983, Tmax = 0.992

  • 11836 measured reflections

  • 1525 independent reflections

  • 1189 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.22 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Rigaku/MSC (2004). RAPID-AUTO. Rigaku/MSC, The Woodlands, Texas, USA.]); cell refinement: RAPID-AUTO; data reduction: RAPID-AUTO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


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)

Refinement top

H atoms were included in calclulated positions and refined in a riding-model approximation with C—H distances ranging from 0.95 to 0.96Å and Uiso(H) = 1.2 Ueq(C). The H atom bonded to N2 was refined independently with an isotropic displacement parameter. The -CH2 groups and the O atom are disordered over two sites with equall occupancy, the disorder of the O atom being symmetry imposed. The anisotropic displacement parameters of C8 and C8* were constrained to be equall using the EADP instruction in SHELXL (Sheldrick, 2008).

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
[Figure 1] 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.
[Figure 2] 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
C16H14N4OF(000) = 584
Mr = 278.31Dx = 1.390 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 1231 reflections
a = 8.2143 (4) Åθ = 3.5–25.5°
b = 9.6296 (3) ŵ = 0.09 mm1
c = 16.8088 (7) ÅT = 153 K
V = 1329.58 (9) Å3Prism, colourless
Z = 40.19 × 0.13 × 0.09 mm
Data collection top
Rigaku R-AXIS Spider
diffractometer
1525 independent reflections
Radiation source: fine-focus sealed tube1189 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.045
ϕ and ω scansθmax = 27.5°, θmin = 3.5°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 1010
Tmin = 0.983, Tmax = 0.992k = 1211
11836 measured reflectionsl = 2021
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.043H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.112 w = 1/[σ2(Fo2) + (0.0566P)2 + 0.3224P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
1525 reflectionsΔρmax = 0.22 e Å3
108 parametersΔρmin = 0.20 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.015 (3)
Crystal data top
C16H14N4OV = 1329.58 (9) Å3
Mr = 278.31Z = 4
Orthorhombic, PbcaMo Kα radiation
a = 8.2143 (4) ŵ = 0.09 mm1
b = 9.6296 (3) ÅT = 153 K
c = 16.8088 (7) Å0.19 × 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)
Tmin = 0.983, Tmax = 0.992Rint = 0.045
11836 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0430 restraints
wR(F2) = 0.112H atoms treated by a mixture of independent and constrained refinement
S = 1.08Δρmax = 0.22 e Å3
1525 reflectionsΔρmin = 0.20 e Å3
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
xyzUiso*/UeqOcc. (<1)
O10.9632 (3)0.5599 (2)0.53873 (12)0.0332 (5)0.50
N10.64853 (14)0.36549 (11)0.43694 (6)0.0256 (3)
N20.71007 (14)0.59185 (11)0.43361 (7)0.0254 (3)
H2N0.770 (2)0.675 (2)0.4419 (10)0.049 (5)*
C10.54372 (16)0.43254 (13)0.38456 (8)0.0245 (3)
C20.41904 (18)0.37997 (14)0.33731 (9)0.0329 (4)
H2A0.39070.28440.33910.039*
C30.3378 (2)0.47100 (16)0.28783 (10)0.0391 (4)
H3A0.25250.43720.25490.047*
C40.3787 (2)0.61227 (16)0.28509 (9)0.0366 (4)
H4A0.32170.67170.24960.044*
C50.49977 (17)0.66712 (14)0.33267 (8)0.0303 (3)
H5A0.52570.76330.33190.036*
C60.58166 (16)0.57462 (13)0.38169 (7)0.0237 (3)
C70.74397 (17)0.46457 (12)0.46425 (8)0.0254 (3)
C80.8957 (12)0.4403 (12)0.5122 (5)0.0319 (12)0.50
H8A0.88720.34840.53390.038*0.50
H8B0.90520.50590.55490.038*0.50
C8*0.8603 (12)0.4441 (12)0.5307 (5)0.0319 (12)0.50
H8*A0.80490.42260.57950.038*0.50
H8*B0.92730.36570.51770.038*0.50
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0271 (11)0.0310 (10)0.0415 (11)0.0002 (8)0.0057 (9)0.0077 (8)
N10.0253 (6)0.0221 (6)0.0293 (6)0.0006 (4)0.0002 (5)0.0014 (4)
N20.0249 (6)0.0218 (6)0.0297 (6)0.0011 (5)0.0015 (5)0.0011 (4)
C10.0220 (7)0.0231 (7)0.0283 (7)0.0009 (5)0.0033 (5)0.0007 (5)
C20.0314 (8)0.0266 (7)0.0406 (8)0.0031 (6)0.0052 (6)0.0021 (6)
C30.0342 (9)0.0363 (8)0.0469 (9)0.0002 (6)0.0148 (7)0.0009 (6)
C40.0346 (8)0.0344 (8)0.0407 (8)0.0067 (6)0.0091 (7)0.0039 (6)
C50.0312 (8)0.0225 (7)0.0372 (7)0.0037 (5)0.0002 (6)0.0016 (5)
C60.0208 (7)0.0230 (6)0.0273 (6)0.0008 (5)0.0010 (5)0.0009 (5)
C70.0262 (7)0.0221 (7)0.0279 (6)0.0010 (5)0.0001 (5)0.0012 (5)
C80.029 (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—C51.381 (2)
O1—C8i1.441 (7)C4—H4A0.9500
N1—C71.3175 (17)C5—C61.3874 (18)
N1—C11.3904 (17)C5—H5A0.9500
N2—C71.3583 (16)C7—C8*1.483 (12)
N2—C61.3790 (17)C7—C81.502 (12)
N2—H2N0.953 (19)C8—O1i1.441 (7)
C1—C21.3914 (19)C8—H8A0.9600
C1—C61.4041 (19)C8—H8B0.9600
C2—C31.380 (2)C8*—O1i1.862 (7)
C2—H2A0.9500C8*—H8*A0.9600
C3—C41.402 (2)C8*—H8*B0.9600
C3—H3A0.9500
C8—O1—C8i97.6 (5)N1—C7—C8124.6 (5)
C8*—O1—C8i115.2 (7)N2—C7—C8120.9 (5)
C8—O1—C8*i95.4 (5)O1—C8—C7112.6 (8)
C8*—O1—C8*i113.1 (3)O1i—C8—C7110.5 (6)
C8i—O1—H8B136.0O1—C8—H8A133.4
C8*i—O1—H8B134.6O1i—C8—H8A106.5
C7—N1—C1104.64 (10)C7—C8—H8A106.7
C7—N2—C6106.76 (11)O1i—C8—H8B112.3
C7—N2—H2N126.8 (11)C7—C8—H8B111.5
C6—N2—H2N126.2 (11)H8A—C8—H8B109.1
N1—C1—C2130.41 (12)O1—C8—H8*A93.2
N1—C1—C6109.68 (12)O1i—C8—H8*A158.6
C2—C1—C6119.88 (12)C7—C8—H8*A90.6
C3—C2—C1117.95 (13)H8A—C8—H8*A62.0
C3—C2—H2A121.0H8B—C8—H8*A60.4
C1—C2—H2A121.0O1—C8—H8*B128.0
C2—C3—C4121.35 (14)O1i—C8—H8*B78.4
C2—C3—H3A119.3C7—C8—H8*B119.4
C4—C3—H3A119.3H8B—C8—H8*B119.7
C5—C4—C3121.63 (14)O1—C8*—C7110.8 (7)
C5—C4—H4A119.2O1—C8*—H8A128.6
C3—C4—H4A119.2C7—C8*—H8A108.8
C4—C5—C6116.58 (13)H8A—C8*—H8B125.3
C4—C5—H5A121.7O1—C8*—H8*A111.9
C6—C5—H5A121.7C7—C8*—H8*A111.5
N2—C6—C5132.03 (12)O1i—C8*—H8*A154.1
N2—C6—C1105.38 (11)O1—C8*—H8*B107.5
C5—C6—C1122.58 (13)C7—C8*—H8*B107.6
N1—C7—N2113.54 (12)H8B—C8*—H8*B115.5
N1—C7—C8*123.3 (5)H8*A—C8*—H8*B107.3
N2—C7—C8*122.5 (5)
Symmetry code: (i) x+2, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···N1ii0.953 (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 formulaC16H14N4O
Mr278.31
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)153
a, b, c (Å)8.2143 (4), 9.6296 (3), 16.8088 (7)
V3)1329.58 (9)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.19 × 0.13 × 0.09
Data collection
DiffractometerRigaku R-AXIS Spider
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.983, 0.992
No. of measured, independent and
observed [I > 2σ(I)] reflections
11836, 1525, 1189
Rint0.045
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.112, 1.08
No. of reflections1525
No. of parameters108
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N2—H2N···N1i0.953 (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

First citationCai, Y. P., Chen, C. L., Zhang, L., Shi, J. L., Xu, A. W., Su, C. Y. & Kang, B. S. (2003). Inorg. Chim. Acta, 342, 107–113.  Web of Science CSD CrossRef CAS Google Scholar
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationMin, K. S. & Suh, M. P. (2000). J. Am. Chem. Soc. 122, 6834-6840.  Web of Science CSD CrossRef CAS Google Scholar
First citationTarazon Navarro, A. & McKee, V. (2003). Acta Cryst. E59, o1199–o1201.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationRigaku/MSC (2004). RAPID-AUTO. Rigaku/MSC, The Woodlands, Texas, USA.  Google Scholar
First citationRoderick, W. R., Nordeen, C. W., Von Esch, A. M. & Appell, R. N. J. (1972). J. Med. Chem. 15, 655–658.  CrossRef CAS PubMed Web of Science Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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