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

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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

(Received 25 September 2012; accepted 12 November 2012; online 24 November 2012)

The title hydrated salt, C18H18N42+·2Cl·2H2O, sits about an inversion centre, such that the asymmetric unit contains one half-mol­ecule. In the crystal, hydrogen bonds occur between the water mol­ecules and chloride anions, and there is ππ 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[Harrell, C. C., Kohli, P., Siwy, Z. & Martin, C. R. (2004). J. Am. Chem. Soc. 126, 15646-15647.]). For a related structure, see: Sun et al. (2010[Sun, T., Li, K., Lai, Y., Chen, R. & Wu, H. (2010). Acta Cryst. E66, m1058.]).

[Scheme 1]

Experimental

Crystal data
  • C18H18N42+·2Cl·2H2O

  • Mr = 397.30

  • Monoclinic, P 21 /c

  • a = 8.1080 (12) Å

  • b = 9.0857 (14) Å

  • c = 12.9188 (19) Å

  • β = 94.426 (2)°

  • V = 948.8 (2) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.36 mm−1

  • T = 296 K

  • 0.38 × 0.28 × 0.17 mm

Data collection
  • Bruker SMART APEXII CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2002[Bruker (2002). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.876, Tmax = 0.943

  • 4604 measured reflections

  • 1681 independent reflections

  • 1371 reflections with I > 2σ(I)

  • Rint = 0.021

Refinement
  • R[F2 > 2σ(F2)] = 0.038

  • wR(F2) = 0.114

  • S = 1.07

  • 1681 reflections

  • 127 parameters

  • 2 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.16 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
O1—H1C⋯Cl1i 0.83 2.33 3.1558 (19) 170
O1—H1D⋯Cl1ii 0.83 2.37 3.190 (2) 170
Symmetry codes: (i) x, y, z-1; (ii) -x+1, -y, -z+1.

Data collection: APEX2 (Bruker, 2002[Bruker (2002). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2002[Bruker (2002). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; 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

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.

Related literature top

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 top

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 column chromatography (10% hexane/ethyl acetate) to give green needle-like crystals of the title compound.

Refinement top

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.

Computing details top

Data collection: APEX2 (Bruker, 2002); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. A view of the molecular structure of title compound. Displacement ellipsoids are drawn at the 35% probability level. Unlabelled atoms are related by inversion (1-x, -y, 1-z) to their labelled counterparts.
[Figure 2] Fig. 2. A three dimensional stacking diagram of (1) viewed down the b axis.
10,20-Dimethyl-3,10,13,20- tetraazapentacyclo[11.7.0.03,11.04,9.014,19]icosa- 1(20),4(9),5,7,10,14,16,18-octaene-10,20-diium top
Crystal data top
C18H18N42+·2Cl·2H2OF(000) = 416
Mr = 397.30Dx = 1.391 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1814 reflections
a = 8.1080 (12) Åθ = 2.5–26.8°
b = 9.0857 (14) ŵ = 0.36 mm1
c = 12.9188 (19) ÅT = 296 K
β = 94.426 (2)°Block, white
V = 948.8 (2) Å30.38 × 0.28 × 0.17 mm
Z = 2
Data collection top
Bruker SMART APEXII CCD
diffractometer
1681 independent reflections
Radiation source: fine-focus sealed tube1371 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
ϕ and ω scansθmax = 25.1°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Bruker, 2002)
h = 99
Tmin = 0.876, Tmax = 0.943k = 1010
4604 measured reflectionsl = 1015
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.114H 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 parametersΔρmax = 0.16 e Å3
2 restraintsΔρmin = 0.20 e Å3
Crystal data top
C18H18N42+·2Cl·2H2OV = 948.8 (2) Å3
Mr = 397.30Z = 2
Monoclinic, P21/cMo Kα radiation
a = 8.1080 (12) ŵ = 0.36 mm1
b = 9.0857 (14) ÅT = 296 K
c = 12.9188 (19) Å0.38 × 0.28 × 0.17 mm
β = 94.426 (2)°
Data collection top
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 = 0.943Rint = 0.021
4604 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0382 restraints
wR(F2) = 0.114H atoms treated by a mixture of independent and constrained refinement
S = 1.07Δρmax = 0.16 e Å3
1681 reflectionsΔρmin = 0.20 e Å3
127 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.49232 (8)0.17546 (7)0.85285 (4)0.0755 (3)
N10.35268 (18)0.00311 (15)0.44209 (10)0.0454 (4)
N20.2397 (2)0.17478 (16)0.53127 (12)0.0521 (4)
O10.7107 (3)0.0906 (2)0.05725 (17)0.0961 (6)
C10.4743 (2)0.0970 (2)0.40528 (14)0.0532 (5)
H1A0.50020.06870.33600.064*
H1B0.43010.19620.40210.064*
C20.3745 (2)0.09265 (19)0.52381 (13)0.0462 (4)
C30.2198 (3)0.2890 (2)0.60909 (19)0.0701 (6)
H3A0.29120.26820.67010.105*
H3B0.10690.29080.62680.105*
H3C0.24820.38300.58150.105*
C40.1255 (2)0.1382 (2)0.44954 (16)0.0557 (5)
C50.0348 (3)0.1869 (3)0.4213 (2)0.0725 (7)
H50.08540.25900.45900.087*
C60.1142 (3)0.1222 (3)0.3345 (2)0.0825 (8)
H60.22160.15150.31360.099*
C70.0399 (3)0.0149 (3)0.2772 (2)0.0805 (7)
H70.09810.02470.21880.097*
C80.1178 (3)0.0338 (2)0.30476 (16)0.0642 (6)
H80.16820.10560.26670.077*
C90.1975 (2)0.0297 (2)0.39233 (14)0.0509 (5)
H1C0.653 (3)0.101 (3)0.0016 (12)0.081 (8)*
H1D0.667 (4)0.021 (2)0.087 (2)0.105 (11)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0922 (5)0.0875 (5)0.0477 (3)0.0113 (3)0.0113 (3)0.0030 (2)
N10.0513 (9)0.0469 (8)0.0380 (8)0.0018 (6)0.0036 (6)0.0004 (6)
N20.0584 (10)0.0490 (9)0.0508 (9)0.0069 (7)0.0152 (7)0.0038 (6)
O10.0995 (15)0.1007 (15)0.0839 (14)0.0151 (12)0.0199 (11)0.0121 (12)
C10.0599 (12)0.0587 (11)0.0414 (9)0.0051 (9)0.0068 (8)0.0074 (8)
C20.0525 (11)0.0475 (10)0.0396 (9)0.0030 (8)0.0103 (8)0.0028 (7)
C30.0826 (15)0.0569 (12)0.0742 (14)0.0093 (10)0.0278 (12)0.0077 (10)
C40.0539 (11)0.0548 (10)0.0593 (12)0.0024 (9)0.0102 (9)0.0165 (9)
C50.0604 (13)0.0688 (14)0.0901 (17)0.0111 (10)0.0171 (12)0.0306 (12)
C60.0567 (14)0.0892 (17)0.0993 (19)0.0038 (12)0.0093 (13)0.0444 (16)
C70.0726 (16)0.0880 (17)0.0773 (16)0.0122 (13)0.0181 (13)0.0283 (14)
C80.0688 (13)0.0683 (13)0.0538 (12)0.0082 (10)0.0063 (10)0.0120 (10)
C90.0504 (11)0.0549 (10)0.0472 (10)0.0026 (8)0.0023 (8)0.0117 (8)
Geometric parameters (Å, º) top
N1—C21.334 (2)C3—H3B0.9600
N1—C91.389 (2)C3—H3C0.9600
N1—C11.448 (2)C4—C91.388 (3)
N2—C21.333 (2)C4—C51.394 (3)
N2—C41.390 (3)C5—C61.382 (4)
N2—C31.462 (3)C5—H50.9300
O1—H1C0.830 (10)C6—C71.389 (4)
O1—H1D0.827 (10)C6—H60.9300
C1—C2i1.473 (3)C7—C81.374 (3)
C1—H1A0.9700C7—H70.9300
C1—H1B0.9700C8—C91.385 (3)
C2—C1i1.473 (3)C8—H80.9300
C3—H3A0.9600
C2—N1—C9108.69 (15)H3A—C3—H3C109.5
C2—N1—C1126.20 (15)H3B—C3—H3C109.5
C9—N1—C1124.93 (15)C9—C4—N2106.96 (16)
C2—N2—C4108.25 (15)C9—C4—C5120.5 (2)
C2—N2—C3125.56 (18)N2—C4—C5132.5 (2)
C4—N2—C3126.12 (17)C6—C5—C4116.4 (2)
H1C—O1—H1D104 (3)C6—C5—H5121.8
N1—C1—C2i109.51 (14)C4—C5—H5121.8
N1—C1—H1A109.8C5—C6—C7122.5 (2)
C2i—C1—H1A109.8C5—C6—H6118.7
N1—C1—H1B109.8C7—C6—H6118.7
C2i—C1—H1B109.8C8—C7—C6121.4 (2)
H1A—C1—H1B108.2C8—C7—H7119.3
N2—C2—N1109.82 (16)C6—C7—H7119.3
N2—C2—C1i125.99 (16)C7—C8—C9116.3 (2)
N1—C2—C1i124.19 (15)C7—C8—H8121.8
N2—C3—H3A109.5C9—C8—H8121.8
N2—C3—H3B109.5C8—C9—C4122.85 (19)
H3A—C3—H3B109.5C8—C9—N1130.88 (19)
N2—C3—H3C109.5C4—C9—N1106.27 (16)
C2—N1—C1—C2i3.6 (3)N2—C4—C5—C6178.57 (19)
C9—N1—C1—C2i178.11 (15)C4—C5—C6—C70.4 (3)
C4—N2—C2—N10.86 (19)C5—C6—C7—C80.6 (4)
C3—N2—C2—N1177.88 (17)C6—C7—C8—C90.0 (3)
C4—N2—C2—C1i179.73 (17)C7—C8—C9—C40.8 (3)
C3—N2—C2—C1i2.7 (3)C7—C8—C9—N1178.01 (18)
C9—N1—C2—N21.22 (19)N2—C4—C9—C8179.65 (17)
C1—N1—C2—N2176.48 (16)C5—C4—C9—C81.1 (3)
C9—N1—C2—C1i179.35 (16)N2—C4—C9—N10.56 (19)
C1—N1—C2—C1i4.1 (3)C5—C4—C9—N1177.98 (17)
C2—N2—C4—C90.16 (19)C2—N1—C9—C8179.92 (19)
C3—N2—C4—C9177.16 (17)C1—N1—C9—C84.6 (3)
C2—N2—C4—C5178.5 (2)C2—N1—C9—C41.08 (19)
C3—N2—C4—C54.5 (3)C1—N1—C9—C4176.42 (16)
C9—C4—C5—C60.5 (3)
Symmetry code: (i) x+1, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1C···Cl1ii0.832.333.1558 (19)170
O1—H1D···Cl1i0.832.373.190 (2)170
Symmetry codes: (i) x+1, y, z+1; (ii) x, y, z1.

Experimental details

Crystal data
Chemical formulaC18H18N42+·2Cl·2H2O
Mr397.30
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)8.1080 (12), 9.0857 (14), 12.9188 (19)
β (°) 94.426 (2)
V3)948.8 (2)
Z2
Radiation typeMo Kα
µ (mm1)0.36
Crystal size (mm)0.38 × 0.28 × 0.17
Data collection
DiffractometerBruker SMART APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2002)
Tmin, Tmax0.876, 0.943
No. of measured, independent and
observed [I > 2σ(I)] reflections
4604, 1681, 1371
Rint0.021
(sin θ/λ)max1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.114, 1.07
No. of reflections1681
No. of parameters127
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.16, 0.20

Computer programs: APEX2 (Bruker, 2002), SAINT (Bruker, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1C···Cl1i0.832.333.1558 (19)169.6
O1—H1D···Cl1ii0.832.373.190 (2)170.2
Symmetry codes: (i) x, y, z1; (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

First citationBruker (2002). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationHarrell, C. C., Kohli, P., Siwy, Z. & Martin, C. R. (2004). J. Am. Chem. Soc. 126, 15646–15647.  Web of Science CrossRef PubMed CAS
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationSun, T., Li, K., Lai, Y., Chen, R. & Wu, H. (2010). Acta Cryst. E66, m1058.  Web of Science CSD CrossRef IUCr Journals

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

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