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Acta Crystallogr Sect E Struct Rep Online. 2008 July 1; 64(Pt 7): m942–m943.
Published online 2008 June 19. doi:  10.1107/S1600536808018011
PMCID: PMC2961898

Dichloridobis[2-(2-chloro­ethyl)-1,2,3,4-tetra­hydro­pyrazino[1,2-a]benzimidazole-κN]cobalt(II)

Abstract

In the title compound, [CoCl2(C12H14ClN3)2], the central CoII ion lies on a twofold rotation axis and adopts a distorted tetra­hedral coordination geometry defined by two N atoms from two 2-(2-chloro­ethyl)-1,2,3,4-tetra­hydro­pyrazino[1,2-a]benzimidazole ligands and two chloride anions. The Cl atom located in the side chain of the ligand is involved in inter­molecular C—H(...)Cl hydrogen bonding, which links neutral complex units into a one-dimensional right-handed helical chain running along a crystallographic 41 axis. Such hydrogen-bonded helical chains are connected to each other to form a homochiral three-dimensional supra­molecular network. One C atom of the 2-chloro­ethyl chain is disordered over two positions, with site-occupancy factors of 0.52 and 0.48.

Related literature

For related literature, see: Balamurugan et al. (2004 [triangle]); Matrick & Day (1961 [triangle]); Parker et al. (2004 [triangle]); Sundberg et al. (1977 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0m942-scheme1.jpg

Experimental

Crystal data

  • [CoCl2(C12H14ClN3)2]
  • M r = 601.25
  • Tetragonal, An external file that holds a picture, illustration, etc.
Object name is e-64-0m942-efi4.jpg
  • a = 9.5706 (8) Å
  • c = 29.911 (4) Å
  • V = 2739.7 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 1.04 mm−1
  • T = 293 (2) K
  • 0.32 × 0.21 × 0.18 mm

Data collection

  • Bruker SMART APEX CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2000 [triangle]) T min = 0.763, T max = 0.829
  • 14573 measured reflections
  • 2703 independent reflections
  • 2219 reflections with I > 2σ(I)
  • R int = 0.061

Refinement

  • R[F 2 > 2σ(F 2)] = 0.055
  • wR(F 2) = 0.131
  • S = 1.01
  • 2703 reflections
  • 169 parameters
  • 2 restraints
  • H-atom parameters constrained
  • Δρmax = 0.54 e Å−3
  • Δρmin = −0.80 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1274 Friedel pairs
  • Flack parameter: 0.07 (5)

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT (Bruker, 2000 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: DIAMOND (Brandenburg, 1998 [triangle]) and ORTEP-3 (Farrugia, 1997 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Selected geometric parameters (Å, °)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808018011/om2235sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808018011/om2235Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This project was supported by the Nature Science Foundation of China (grant No. 20475026).

supplementary crystallographic information

Comment

Nitrogen mustards that contain a reactive N,N-bis-(2-chloroethyl)amine group are widely used as alkylating agents in cancer chemotherapy. However, these nitrogen mustards exhibit high chemical reactivity and usually show no selectivity of DNA alkylation. Recently, it has been proved that complexation of macrocyclic nitrogen mustards with metals may be an effective strategy in the design of hypoxia-selective antitumor prodrugs (Parker et al., 2004). As part of our work, some metal complexes of a monofunctional mustard, 2-(2-chloroethyl)-l,2,3,4-tetrahydropyrazino[1,2-a]benzimidazole (L), were prepared in order to evaluate their antitumor and antimalarial activities. Here, we report the crystal structure of a novel Co(II) mustard complex.

As depicted in Fig. 1, the complete complex molecule is generated by a twofold symmetry operation, with the CoII ion located on the rotation axis. The distorted tetrahedral coordination sphere around the CoII center consists of two benzimidazole N atoms from two L ligands and two chloride anions. The Co—N distance of 2.026 (4) Å and Co—Cl length of 2.2423 (13) Å (Table 1) are comparable to those reported in the literature (Sundberg et al., 1977).

In the crystal packing, intermolecular C—H···Cl hydrogen bonding play a key role. Fig. 2 illustrates that adjacent neutral complex units are connected by C1—H1A···Cl1 interactions into a one-dimensional right-handed helical architecture running along a crystallographic 41 screw axis in the c direction. Five complex fragments form a helix turn with a long pitch of 29.911 (4) Å. The shortest intrachain Co—Co distance is 10.072 Å. Further C—H···Cl hydrogen bond linkages (Table 2) extend such one-dimensional helical chains into a homochiral three-dimensional hydrogen-bonded network (Balamurugan et al., 2004).

Experimental

The ligand 2-(2-chloroethyl)-l,2,3,4-tetrahydropyrazino[1,2-a]benzimidazole was synthesized according to a literature method (Matrick & Day, 1961).

The title compound was prepared by adding a methanol solution (10 ml) of CoCl2.6H2O (1 mmol) into a methanol solution (10 ml) of 2-(2-chloroethyl)-l,2,3,4-tetrahydropyrazino[1,2-a]benzimidazole (2 mmol). The resulting mixture was refluxed for two hours and filtered after cooling to room temperature. Blue single crystals of the title compound suitable for X-ray diffraction analysis were obtained by slow diffusion of diethyl ether into the filtrate. Elemental analysis found: C 47.80; H 4.60; N 14.03%; calculated for C24H28Cl4CoN6: C 47.94; H 4.69; N 13.98%.

Refinement

The 2-chloroethyl chain attached to N atom displays rotational disorder and its C12 atom was split into two positions (C12A and C12B) with site-occupancy factors of 0.52 and 0.48. A l l H atoms were placed in calculated positions and refined using a riding model, with C—H = 0.93 - 0.97 Å and with Uiso(H) = 1.2 Ueq(C).

Figures

Fig. 1.
The molecular structure with atom labels and 30% probability displacement ellipsoids for non-H atoms. Both disordered components of the 2-chloroethyl chain are shown. [Symmetry code: (i) y, x, -z]
Fig. 2.
Fragment of a one-dimensional right-handed helical chain with the intermolecular C—H···Cl hydrogen bond indicated by dashed line. For clarity only the major disordered component is shown. [Symmetry code: (ii) 3/2 - x, -1/2 ...

Crystal data

[CoCl2(C12H14ClN3)2]Z = 4
Mr = 601.25F000 = 1236
Tetragonal, P41212Dx = 1.458 Mg m3
Hall symbol: P 4abw 2nwMo Kα radiation λ = 0.71073 Å
a = 9.5706 (8) ÅCell parameters from 835 reflections
b = 9.5706 (8) Åθ = 2.5–16.9º
c = 29.911 (4) ŵ = 1.04 mm1
α = 90ºT = 293 (2) K
β = 90ºPrism, blue
γ = 90º0.32 × 0.21 × 0.18 mm
V = 2739.7 (5) Å3

Data collection

Bruker SMART APEX CCD area-detector diffractometer2703 independent reflections
Radiation source: sealed tube2219 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.061
T = 293(2) Kθmax = 26.0º
[var phi] and ω scansθmin = 2.2º
Absorption correction: multi-scan(SADABS; Bruker, 2000)h = −11→7
Tmin = 0.763, Tmax = 0.829k = −11→11
14573 measured reflectionsl = −36→35

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.055  w = 1/[σ2(Fo2) + (0.0877P)2 + 1.82P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.131(Δ/σ)max < 0.001
S = 1.01Δρmax = 0.54 e Å3
2703 reflectionsΔρmin = −0.80 e Å3
169 parametersExtinction correction: none
2 restraintsAbsolute structure: Flack (1983), 1274 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.07 (5)
Secondary atom site location: difference Fourier map

Special details

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)

xyzUiso*/UeqOcc. (<1)
Co10.99857 (7)0.99857 (7)0.00000.0305 (2)
C10.7722 (5)0.8869 (5)0.07778 (15)0.0312 (10)
H1A0.78250.79090.06790.037*
H1B0.86350.92110.08660.037*
C20.7177 (5)0.9724 (5)0.04111 (16)0.0327 (11)
C30.6905 (5)1.0950 (5)−0.01903 (17)0.0336 (11)
C40.7080 (5)1.1677 (5)−0.05859 (18)0.0332 (11)
H40.79451.1750−0.07260.040*
C50.5873 (5)1.2300 (5)−0.07639 (16)0.0339 (11)
H50.59401.2775−0.10340.041*
C60.4595 (6)1.2234 (5)−0.05550 (17)0.0368 (12)
H60.38261.2693−0.06750.044*
C70.4469 (5)1.1478 (5)−0.01639 (16)0.0317 (11)
H70.36041.1398−0.00240.038*
C80.5617 (5)1.0847 (5)0.00170 (18)0.0335 (11)
C90.4822 (5)0.9696 (5)0.07306 (16)0.0325 (11)
H9A0.39640.93990.05870.039*
H9B0.46121.04960.09180.039*
C100.5382 (5)0.8555 (5)0.10051 (16)0.0354 (12)
H10A0.47800.83970.12610.042*
H10B0.54180.77010.08310.042*
C110.7325 (6)0.8092 (5)0.15130 (16)0.0348 (11)
H11A0.77240.72470.13870.042*0.520 (13)
H11B0.65580.78160.17060.042*0.520 (13)
H11C0.83350.81740.15150.042*0.480 (13)
H11D0.70950.71200.14580.042*0.480 (13)
C12A0.8428 (10)0.8809 (9)0.1796 (3)0.033 (3)0.520 (13)
H12A0.91320.92120.16010.039*0.520 (13)
H12B0.88830.81210.19840.039*0.520 (13)
C12B0.6908 (11)0.8567 (10)0.1978 (3)0.034 (3)0.480 (13)
H12C0.71540.78450.21920.040*0.480 (13)
H12D0.59030.86910.19880.040*0.480 (13)
N10.6779 (4)0.8924 (5)0.11560 (13)0.0345 (9)
N20.7894 (4)1.0231 (4)0.00683 (13)0.0341 (9)
N30.5833 (4)1.0082 (5)0.03979 (13)0.0359 (9)
Cl10.77153 (12)1.01254 (13)0.21326 (4)0.0341 (3)
Cl21.10525 (13)1.08043 (13)0.06139 (4)0.0345 (3)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Co10.0302 (3)0.0302 (3)0.0311 (4)−0.0010 (4)0.0031 (3)−0.0031 (3)
C10.033 (3)0.030 (2)0.030 (2)−0.004 (2)−0.003 (2)0.001 (2)
C20.036 (3)0.032 (3)0.031 (2)0.003 (2)0.012 (2)0.005 (2)
C30.035 (3)0.028 (3)0.038 (3)0.000 (2)−0.009 (2)−0.007 (2)
C40.029 (3)0.032 (3)0.039 (3)0.001 (2)−0.005 (2)0.007 (2)
C50.036 (3)0.028 (3)0.037 (3)−0.006 (2)−0.002 (2)0.017 (2)
C60.038 (3)0.032 (3)0.040 (3)0.005 (2)−0.002 (2)−0.003 (2)
C70.032 (3)0.032 (3)0.031 (2)0.005 (2)0.000 (2)−0.0074 (19)
C80.031 (3)0.035 (3)0.035 (2)0.005 (2)−0.009 (2)−0.007 (2)
C90.031 (3)0.035 (3)0.031 (2)−0.005 (2)0.002 (2)0.0002 (19)
C100.036 (3)0.041 (3)0.029 (2)0.001 (2)0.003 (2)0.016 (2)
C110.040 (3)0.036 (3)0.029 (3)0.002 (2)−0.002 (2)−0.003 (2)
C12A0.036 (5)0.031 (5)0.031 (5)0.000 (4)−0.002 (4)0.007 (4)
C12B0.032 (6)0.032 (6)0.036 (6)0.001 (4)−0.003 (4)0.002 (4)
N10.039 (2)0.035 (2)0.030 (2)0.0055 (19)0.0004 (18)0.0035 (18)
N20.035 (2)0.037 (2)0.0303 (19)0.0010 (18)−0.0003 (17)−0.0028 (17)
N30.036 (2)0.035 (2)0.037 (2)−0.0003 (19)0.0060 (18)0.005 (2)
Cl10.0330 (6)0.0355 (6)0.0339 (6)−0.0082 (5)−0.0012 (5)−0.0007 (5)
Cl20.0367 (7)0.0333 (7)0.0336 (6)−0.0011 (5)−0.0071 (5)−0.0038 (5)

Geometric parameters (Å, °)

Co1—N2i2.026 (4)C9—N31.436 (6)
Co1—N22.026 (4)C9—C101.468 (6)
Co1—Cl22.2423 (13)C9—H9A0.9700
Co1—Cl2i2.2423 (13)C9—H9B0.9700
C1—N11.448 (6)C10—N11.454 (7)
C1—C21.465 (6)C10—H10A0.9700
C1—H1A0.9700C10—H10B0.9700
C1—H1B0.9700C11—N11.431 (6)
C2—N21.325 (6)C11—C12A1.517 (10)
C2—N31.332 (6)C11—C12B1.517 (10)
C3—C41.383 (7)C11—H11A0.9700
C3—C81.383 (7)C11—H11B0.9700
C3—N21.403 (6)C11—H11C0.9700
C4—C51.405 (7)C11—H11D0.9700
C4—H40.9300C12A—Cl11.752 (9)
C5—C61.374 (7)C12A—H11C1.0395
C5—H50.9300C12A—H12A0.9700
C6—C71.381 (7)C12A—H12B0.9700
C6—H60.9300C12B—Cl11.742 (9)
C7—C81.366 (7)C12B—H12C0.9700
C7—H70.9300C12B—H12D0.9700
C8—N31.370 (7)
N2i—Co1—N2103.8 (2)N1—C10—C9109.2 (4)
N2i—Co1—Cl2112.03 (12)N1—C10—H10A109.8
N2—Co1—Cl2109.08 (12)C9—C10—H10A109.8
N2i—Co1—Cl2i109.08 (12)N1—C10—H10B109.8
N2—Co1—Cl2i112.03 (12)C9—C10—H10B109.8
Cl2—Co1—Cl2i110.64 (7)H10A—C10—H10B108.3
N1—C1—C2110.0 (4)N1—C11—C12A114.8 (5)
N1—C1—H1A109.7N1—C11—C12B114.9 (5)
C2—C1—H1A109.7N1—C11—H11A108.6
N1—C1—H1B109.7C12A—C11—H11A108.6
C2—C1—H1B109.7N1—C11—H11B108.6
H1A—C1—H1B108.2C12A—C11—H11B108.6
N2—C2—N3112.5 (4)H11A—C11—H11B107.6
N2—C2—C1126.8 (5)N1—C11—H11C109.0
N3—C2—C1120.6 (4)C12B—C11—H11C103.4
C4—C3—C8121.8 (5)N1—C11—H11D109.0
C4—C3—N2129.6 (5)C12B—C11—H11D112.5
C8—C3—N2108.6 (4)H11C—C11—H11D107.8
C3—C4—C5116.0 (5)C11—C12A—Cl1112.0 (6)
C3—C4—H4122.0C11—C12A—H12A109.2
C5—C4—H4122.0Cl1—C12A—H12A109.2
C6—C5—C4122.7 (4)C11—C12A—H12B109.2
C6—C5—H5118.7Cl1—C12A—H12B109.2
C4—C5—H5118.7H12A—C12A—H12B107.9
C5—C6—C7119.2 (5)C11—C12B—Cl1112.5 (6)
C5—C6—H6120.4C11—C12B—H12C109.1
C7—C6—H6120.4Cl1—C12B—H12C109.1
C8—C7—C6119.8 (5)C11—C12B—H12D109.1
C8—C7—H7120.1Cl1—C12B—H12D109.1
C6—C7—H7120.1H12C—C12B—H12D107.8
C7—C8—N3133.4 (5)C11—N1—C1109.6 (4)
C7—C8—C3120.5 (5)C11—N1—C10115.6 (4)
N3—C8—C3106.1 (4)C1—N1—C10108.8 (4)
N3—C9—C10109.4 (4)C2—N2—C3104.9 (4)
N3—C9—H9A109.8C2—N2—Co1123.2 (3)
C10—C9—H9A109.8C3—N2—Co1131.9 (3)
N3—C9—H9B109.8C2—N3—C8107.9 (4)
C10—C9—H9B109.8C2—N3—C9124.4 (4)
H9A—C9—H9B108.2C8—N3—C9127.7 (4)

Symmetry codes: (i) y, x, −z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C1—H1A···Cl1ii0.972.873.812 (5)164
C5—H5···Cl2iii0.932.793.709 (5)171

Symmetry codes: (ii) −x+3/2, y−1/2, −z+1/4; (iii) y−1/2, −x+5/2, z−1/4.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: OM2235).

References

  • Balamurugan, V., Hundal, M. S. & Mukherjee, R. (2004). Chem. Eur. J.10, 1683–1690. [PubMed]
  • Brandenburg, K. (1998). DIAMOND University of Bonn, Germany.
  • Bruker (2000). SMART, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Matrick, H. & Day, A. R. (1961). J. Org. Chem.26, 1511–1514.
  • Parker, L. L., Lacy, S. M., Farrugia, L. J., Evans, C., Robins, D. J., O’Hare, C. C., Hartley, J. A., Jaffar, M. & Stratford, I. J. (2004). J. Med. Chem.47, 5683–5689. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Sundberg, R. J., Yilmaz, I. & Mente, D. C. (1977). Inorg. Chem.16, 1470–1476.

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