organic compounds
5,12-Dimethylpyrazino[1,2-a:4,5-a′]dibenzimidazole-5,12-diium dichloride dihydrate
aResearch Institute of Shaanxi Yanchang Petroleum (Group) Co. Ltd, Ke Ji No. 2 Road 75, Xi'an 710075, Shaanxi, People's Republic of China, bDepartment of Pharmacology, School of Pharmacy, Forth Military Medical University, Chang-le West Road 17, Xi'an 710032, Shaanxi, People's Republic of China, and cCollege of Chemistry & Chemical Engineering, Xianyang Normal University, Xianyang 712000, Shaanxi, People's Republic of China
*Correspondence e-mail: eota@163.com
The title hydrated salt, C18H18N42+·2Cl−·2H2O, sits about an inversion centre, such that the contains one half-molecule. In the crystal, hydrogen bonds occur between the water molecules and chloride anions, and there is π–π stacking of the benzene and imidazole rings of inversion-related pairs of molecules, with a centroid–centroid distance of 3.704 (17) Å.
Related literature
For descriptions of clinical applications of the benzimidazole ring system, see: Harrell et al. (2004). For a related structure, see: Sun et al. (2010).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2002); cell SAINT (Bruker, 2002); data reduction: SAINT; 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
10.1107/S1600536812046594/pk2446sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812046594/pk2446Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812046594/pk2446Isup3.cml
N-methylbenzene-1,2-diamine (2.5 mol), 2-chloroacetic acid (3 mmol), polyphosphoric acid (10 ml) and silica gel (1 g) were mixed and introduced in an open Erlenmeyer flask. The reaction mixture was irradiated in a domestic microwave oven for 3 min. After cooling to room temperature, methanol was added (20 ml) and the reaction mixture filtered. The filtrate was evaporated to dryness and subjected to
(10% hexane/ethyl acetate) to give green needle-like crystals of the title compound.All H atoms attached to C atoms were generated in idealized positions and constrained to ride on their parent atoms, with C—H = 0.96 Å (methyl) and 0.93 Å (aromatic) with Uiso(H) = 1.2Ueq(C, aromatic) and Uiso(H) = 1.5Ueq(C, methyl). H atoms of water molecules were located in a difference Fourier map and refined with 1,2 and 1,3 distance restraints of 0.85 (2) Å and 1.39 (2) Å.
Data collection: APEX2 (Bruker, 2002); cell
SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); 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).C18H18N42+·2Cl−·2H2O | F(000) = 416 |
Mr = 397.30 | Dx = 1.391 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1814 reflections |
a = 8.1080 (12) Å | θ = 2.5–26.8° |
b = 9.0857 (14) Å | µ = 0.36 mm−1 |
c = 12.9188 (19) Å | T = 296 K |
β = 94.426 (2)° | Block, white |
V = 948.8 (2) Å3 | 0.38 × 0.28 × 0.17 mm |
Z = 2 |
Bruker SMART APEXII CCD diffractometer | 1681 independent reflections |
Radiation source: fine-focus sealed tube | 1371 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.021 |
ϕ and ω scans | θmax = 25.1°, θmin = 2.5° |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | h = −9→9 |
Tmin = 0.876, Tmax = 0.943 | k = −10→10 |
4604 measured reflections | l = −10→15 |
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)] = 0.038 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.114 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0587P)2 + 0.1961P] where P = (Fo2 + 2Fc2)/3 |
1681 reflections | (Δ/σ)max < 0.001 |
127 parameters | Δρmax = 0.16 e Å−3 |
2 restraints | Δρmin = −0.20 e Å−3 |
C18H18N42+·2Cl−·2H2O | V = 948.8 (2) Å3 |
Mr = 397.30 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.1080 (12) Å | µ = 0.36 mm−1 |
b = 9.0857 (14) Å | T = 296 K |
c = 12.9188 (19) Å | 0.38 × 0.28 × 0.17 mm |
β = 94.426 (2)° |
Bruker SMART APEXII CCD diffractometer | 1681 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | 1371 reflections with I > 2σ(I) |
Tmin = 0.876, Tmax = 0.943 | Rint = 0.021 |
4604 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 2 restraints |
wR(F2) = 0.114 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.07 | Δρmax = 0.16 e Å−3 |
1681 reflections | Δρmin = −0.20 e Å−3 |
127 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.49232 (8) | 0.17546 (7) | 0.85285 (4) | 0.0755 (3) | |
N1 | 0.35268 (18) | 0.00311 (15) | 0.44209 (10) | 0.0454 (4) | |
N2 | 0.2397 (2) | 0.17478 (16) | 0.53127 (12) | 0.0521 (4) | |
O1 | 0.7107 (3) | 0.0906 (2) | 0.05725 (17) | 0.0961 (6) | |
C1 | 0.4743 (2) | −0.0970 (2) | 0.40528 (14) | 0.0532 (5) | |
H1A | 0.5002 | −0.0687 | 0.3360 | 0.064* | |
H1B | 0.4301 | −0.1962 | 0.4021 | 0.064* | |
C2 | 0.3745 (2) | 0.09265 (19) | 0.52381 (13) | 0.0462 (4) | |
C3 | 0.2198 (3) | 0.2890 (2) | 0.60909 (19) | 0.0701 (6) | |
H3A | 0.2912 | 0.2682 | 0.6701 | 0.105* | |
H3B | 0.1069 | 0.2908 | 0.6268 | 0.105* | |
H3C | 0.2482 | 0.3830 | 0.5815 | 0.105* | |
C4 | 0.1255 (2) | 0.1382 (2) | 0.44954 (16) | 0.0557 (5) | |
C5 | −0.0348 (3) | 0.1869 (3) | 0.4213 (2) | 0.0725 (7) | |
H5 | −0.0854 | 0.2590 | 0.4590 | 0.087* | |
C6 | −0.1142 (3) | 0.1222 (3) | 0.3345 (2) | 0.0825 (8) | |
H6 | −0.2216 | 0.1515 | 0.3136 | 0.099* | |
C7 | −0.0399 (3) | 0.0149 (3) | 0.2772 (2) | 0.0805 (7) | |
H7 | −0.0981 | −0.0247 | 0.2188 | 0.097* | |
C8 | 0.1178 (3) | −0.0338 (2) | 0.30476 (16) | 0.0642 (6) | |
H8 | 0.1682 | −0.1056 | 0.2667 | 0.077* | |
C9 | 0.1975 (2) | 0.0297 (2) | 0.39233 (14) | 0.0509 (5) | |
H1C | 0.653 (3) | 0.101 (3) | 0.0016 (12) | 0.081 (8)* | |
H1D | 0.667 (4) | 0.021 (2) | 0.087 (2) | 0.105 (11)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0922 (5) | 0.0875 (5) | 0.0477 (3) | 0.0113 (3) | 0.0113 (3) | −0.0030 (2) |
N1 | 0.0513 (9) | 0.0469 (8) | 0.0380 (8) | 0.0018 (6) | 0.0036 (6) | 0.0004 (6) |
N2 | 0.0584 (10) | 0.0490 (9) | 0.0508 (9) | 0.0069 (7) | 0.0152 (7) | 0.0038 (6) |
O1 | 0.0995 (15) | 0.1007 (15) | 0.0839 (14) | −0.0151 (12) | −0.0199 (11) | 0.0121 (12) |
C1 | 0.0599 (12) | 0.0587 (11) | 0.0414 (9) | 0.0051 (9) | 0.0068 (8) | −0.0074 (8) |
C2 | 0.0525 (11) | 0.0475 (10) | 0.0396 (9) | 0.0030 (8) | 0.0103 (8) | 0.0028 (7) |
C3 | 0.0826 (15) | 0.0569 (12) | 0.0742 (14) | 0.0093 (10) | 0.0278 (12) | −0.0077 (10) |
C4 | 0.0539 (11) | 0.0548 (10) | 0.0593 (12) | 0.0024 (9) | 0.0102 (9) | 0.0165 (9) |
C5 | 0.0604 (13) | 0.0688 (14) | 0.0901 (17) | 0.0111 (10) | 0.0171 (12) | 0.0306 (12) |
C6 | 0.0567 (14) | 0.0892 (17) | 0.0993 (19) | −0.0038 (12) | −0.0093 (13) | 0.0444 (16) |
C7 | 0.0726 (16) | 0.0880 (17) | 0.0773 (16) | −0.0122 (13) | −0.0181 (13) | 0.0283 (14) |
C8 | 0.0688 (13) | 0.0683 (13) | 0.0538 (12) | −0.0082 (10) | −0.0063 (10) | 0.0120 (10) |
C9 | 0.0504 (11) | 0.0549 (10) | 0.0472 (10) | −0.0026 (8) | 0.0023 (8) | 0.0117 (8) |
N1—C2 | 1.334 (2) | C3—H3B | 0.9600 |
N1—C9 | 1.389 (2) | C3—H3C | 0.9600 |
N1—C1 | 1.448 (2) | C4—C9 | 1.388 (3) |
N2—C2 | 1.333 (2) | C4—C5 | 1.394 (3) |
N2—C4 | 1.390 (3) | C5—C6 | 1.382 (4) |
N2—C3 | 1.462 (3) | C5—H5 | 0.9300 |
O1—H1C | 0.830 (10) | C6—C7 | 1.389 (4) |
O1—H1D | 0.827 (10) | C6—H6 | 0.9300 |
C1—C2i | 1.473 (3) | C7—C8 | 1.374 (3) |
C1—H1A | 0.9700 | C7—H7 | 0.9300 |
C1—H1B | 0.9700 | C8—C9 | 1.385 (3) |
C2—C1i | 1.473 (3) | C8—H8 | 0.9300 |
C3—H3A | 0.9600 | ||
C2—N1—C9 | 108.69 (15) | H3A—C3—H3C | 109.5 |
C2—N1—C1 | 126.20 (15) | H3B—C3—H3C | 109.5 |
C9—N1—C1 | 124.93 (15) | C9—C4—N2 | 106.96 (16) |
C2—N2—C4 | 108.25 (15) | C9—C4—C5 | 120.5 (2) |
C2—N2—C3 | 125.56 (18) | N2—C4—C5 | 132.5 (2) |
C4—N2—C3 | 126.12 (17) | C6—C5—C4 | 116.4 (2) |
H1C—O1—H1D | 104 (3) | C6—C5—H5 | 121.8 |
N1—C1—C2i | 109.51 (14) | C4—C5—H5 | 121.8 |
N1—C1—H1A | 109.8 | C5—C6—C7 | 122.5 (2) |
C2i—C1—H1A | 109.8 | C5—C6—H6 | 118.7 |
N1—C1—H1B | 109.8 | C7—C6—H6 | 118.7 |
C2i—C1—H1B | 109.8 | C8—C7—C6 | 121.4 (2) |
H1A—C1—H1B | 108.2 | C8—C7—H7 | 119.3 |
N2—C2—N1 | 109.82 (16) | C6—C7—H7 | 119.3 |
N2—C2—C1i | 125.99 (16) | C7—C8—C9 | 116.3 (2) |
N1—C2—C1i | 124.19 (15) | C7—C8—H8 | 121.8 |
N2—C3—H3A | 109.5 | C9—C8—H8 | 121.8 |
N2—C3—H3B | 109.5 | C8—C9—C4 | 122.85 (19) |
H3A—C3—H3B | 109.5 | C8—C9—N1 | 130.88 (19) |
N2—C3—H3C | 109.5 | C4—C9—N1 | 106.27 (16) |
C2—N1—C1—C2i | 3.6 (3) | N2—C4—C5—C6 | −178.57 (19) |
C9—N1—C1—C2i | 178.11 (15) | C4—C5—C6—C7 | −0.4 (3) |
C4—N2—C2—N1 | −0.86 (19) | C5—C6—C7—C8 | 0.6 (4) |
C3—N2—C2—N1 | −177.88 (17) | C6—C7—C8—C9 | 0.0 (3) |
C4—N2—C2—C1i | 179.73 (17) | C7—C8—C9—C4 | −0.8 (3) |
C3—N2—C2—C1i | 2.7 (3) | C7—C8—C9—N1 | 178.01 (18) |
C9—N1—C2—N2 | 1.22 (19) | N2—C4—C9—C8 | 179.65 (17) |
C1—N1—C2—N2 | 176.48 (16) | C5—C4—C9—C8 | 1.1 (3) |
C9—N1—C2—C1i | −179.35 (16) | N2—C4—C9—N1 | 0.56 (19) |
C1—N1—C2—C1i | −4.1 (3) | C5—C4—C9—N1 | −177.98 (17) |
C2—N2—C4—C9 | 0.16 (19) | C2—N1—C9—C8 | 179.92 (19) |
C3—N2—C4—C9 | 177.16 (17) | C1—N1—C9—C8 | 4.6 (3) |
C2—N2—C4—C5 | 178.5 (2) | C2—N1—C9—C4 | −1.08 (19) |
C3—N2—C4—C5 | −4.5 (3) | C1—N1—C9—C4 | −176.42 (16) |
C9—C4—C5—C6 | −0.5 (3) |
Symmetry code: (i) −x+1, −y, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1C···Cl1ii | 0.83 | 2.33 | 3.1558 (19) | 170 |
O1—H1D···Cl1i | 0.83 | 2.37 | 3.190 (2) | 170 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, y, z−1. |
Experimental details
Crystal data | |
Chemical formula | C18H18N42+·2Cl−·2H2O |
Mr | 397.30 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 296 |
a, b, c (Å) | 8.1080 (12), 9.0857 (14), 12.9188 (19) |
β (°) | 94.426 (2) |
V (Å3) | 948.8 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.36 |
Crystal size (mm) | 0.38 × 0.28 × 0.17 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2002) |
Tmin, Tmax | 0.876, 0.943 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4604, 1681, 1371 |
Rint | 0.021 |
(sin θ/λ)max (Å−1) | 0.597 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.114, 1.07 |
No. of reflections | 1681 |
No. of parameters | 127 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.16, −0.20 |
Computer programs: APEX2 (Bruker, 2002), SAINT (Bruker, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1C···Cl1i | 0.83 | 2.33 | 3.1558 (19) | 169.6 |
O1—H1D···Cl1ii | 0.83 | 2.37 | 3.190 (2) | 170.2 |
Symmetry codes: (i) x, y, z−1; (ii) −x+1, −y, −z+1. |
Acknowledgements
The work was supported by 2009ZX09103–111, the China Postdoctoral Science Foundation (No. 2009041446), the Special Research Fund of the Education Department of Shaanxi Province (12 J K0631) and the Special Research Fund of Xianyang Normal University (11XSYK204). We thank the Instrumental Analysis Center of Northwest University for the data collection.
References
Bruker (2002). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Harrell, C. C., Kohli, P., Siwy, Z. & Martin, C. R. (2004). J. Am. Chem. Soc. 126, 15646–15647. Web of Science CrossRef PubMed CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sun, T., Li, K., Lai, Y., Chen, R. & Wu, H. (2010). Acta Cryst. E66, m1058. Web of Science CSD CrossRef IUCr Journals Google Scholar
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Bis-benzimidazoles are DNA-minor grove binding agents that possess anti-tumor activity. The benzimidazole ring system is present in clinically approved antihistamines, antivirals, anthelmintics, and antiulcer medications (Harrell et al., 2004). In addition to their biological activity, there are numerous other studies, including coordination and corrosion inhibitor abilities of benzimidazoles. Bis-benzimidazoles are also strong chelating agents (Sun et al., 2010). Some of these derivatives are used as photographic materials and dyes. As part of our ongoing investigation of benzimidazole derivatives, the title compound was synthesized and its crystal structure is reported herein.