supplementary materials
1,3-Bis(1H-benzimidazol-2-yl)-2-oxapropane
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.
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)
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).
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).
1,3-Bis(1
H-benzimidazol-2-yl)-2-oxapropane
top
Crystal data top
| C16H14N4O | F(000) = 584 |
| Mr = 278.31 | Dx = 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 | Rint = 0.045 |
| φ and ω scans | θmax = 27.5°, θmin = 3.5° |
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995) | h = −10→10 |
| Tmin = 0.983, Tmax = 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(Fo2) + (0.0566P)2 + 0.3224P]
where P = (Fo2 + 2Fc2)/3 |
| S = 1.08 | (Δ/σ)max < 0.001 |
| 1525 reflections | Δρmax = 0.22 e Å−3 |
| 108 parameters | Δρmin = −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 |
| Mr = 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 | 1189 reflections with I > 2σ(I) |
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995) | Rint = 0.045 |
| Tmin = 0.983, Tmax = 0.992 | θmax = 27.5° |
| 11836 measured reflections | Standard reflections: 0 |
| 1525 independent reflections | |
Refinement top
| R[F2 > 2σ(F2)] = 0.043 | H atoms treated by a mixture of independent and constrained refinement |
| wR(F2) = 0.112 | Δρmax = 0.22 e Å−3 |
| S = 1.08 | Δρmin = −0.20 e Å−3 |
| 1525 reflections | Absolute structure: ? |
| 108 parameters | Flack parameter: ? |
| 0 restraints | Rogers parameter: ? |
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 | Uiso*/Ueq | 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, °) 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*—H8*A | 0.9600 |
| C3—C4 | 1.402 (2) | C8*—H8*B | 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—C8*i | 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*—H8*A | 111.9 |
| C6—C5—H5A | 121.7 | C7—C8*—H8*A | 111.5 |
| N2—C6—C5 | 132.03 (12) | O1i—C8*—H8*A | 154.1 |
| N2—C6—C1 | 105.38 (11) | O1—C8*—H8*B | 107.5 |
| C5—C6—C1 | 122.58 (13) | C7—C8*—H8*B | 107.6 |
| N1—C7—N2 | 113.54 (12) | H8B—C8*—H8*B | 115.5 |
| N1—C7—C8* | 123.3 (5) | H8*A—C8*—H8*B | 107.3 |
| N2—C7—C8* | 122.5 (5) | | |
| Symmetry codes: (i) −x+2, −y+1, −z+1. |
Hydrogen-bond geometry (Å, °) 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 codes: (ii) −x+3/2, y+1/2, z. |
Table 1
Hydrogen-bond geometry (Å, °) 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 codes: (i) −x+3/2, y+1/2, z. |
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.
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.
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.
Min, K. S. & Suh, M. P. (2000). J. Am. Chem. Soc. 122, 6834-6840.
Tarazon Navarro, A. & McKee, V. (2003). Acta Cryst. E59, o1199-1201.
Rigaku/MSC (2004). RAPID-AUTO. Rigaku/MSC, The Woodlands, Texas, USA.
Roderick, W. R., Nordeen, C. W., Von Esch, A. M. & Appell, R. N. J. (1972). J. Med. Chem. 15, 655–658.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.
![[Figure 1]](./lh2795fig1thm.gif)
![[Figure 2]](./lh2795fig2thm.gif)
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).