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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1392.
Published online 2009 May 23. doi:  10.1107/S1600536809019084
PMCID: PMC2969638

(S)-2-(2-Pyrrolidinio)-1H-benzimidazol-3-ium dichloride monohydrate

Abstract

In the title compound, C11H15N3 2+·2Cl·H2O, one N atom of the imidazole ring and the N atom of the pyrrolidine ring are protonated. The crystal structure is stabilized by aromatic π–π inter­actions between the benzene rings of neighbouring benzimidazole systems [centroid–centroid duistance = 3.712 (2) Å]. The crystal structure is further stabilized by inter­molecular N—H(...)Cl, O—H(...)Cl and N—H(...)O hydrogen bonds.

Related literature

For proline derivatives, see: Fu et al. (2007 [triangle]); Aminabhavi et al. (1986 [triangle]). For related structures, see: Dai & Fu (2008a [triangle],b [triangle]); Fu & Ye (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1392-scheme1.jpg

Experimental

Crystal data

  • C11H15N3 2+·2Cl·H2O
  • M r = 278.18
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1392-efi1.jpg
  • a = 7.493 (2) Å
  • b = 9.739 (2) Å
  • c = 9.937 (2) Å
  • α = 99.23 (3)°
  • β = 95.73 (3)°
  • γ = 106.27 (3)°
  • V = 679.0 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.47 mm−1
  • T = 293 K
  • 0.35 × 0.30 × 0.15 mm

Data collection

  • Rigaku Mercury2 diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 [triangle]) T min = 0.959, T max = 0.982 (expected range = 0.911–0.932)
  • 7119 measured reflections
  • 3108 independent reflections
  • 2310 reflections with I > 2σ(I)
  • R int = 0.037

Refinement

  • R[F 2 > 2σ(F 2)] = 0.050
  • wR(F 2) = 0.120
  • S = 1.08
  • 3108 reflections
  • 162 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.28 e Å−3
  • Δρmin = −0.24 e Å−3

Data collection: CrystalClear (Rigaku, 2005 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and DIAMOND (Brandenburg, 1998 [triangle]); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809019084/lx2100sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809019084/lx2100Isup2.hkl

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

Acknowledgments

This work was supported by a start-up grant from Southeast University to Professor Ren-Gen Xiong.

supplementary crystallographic information

Comment

Amino acid derivatives provide wide applications in the field of material science, such as ferroelectric, fluorescence and dielectric behaviors. Also,there have been much attention in the preparation of amino acid coordination compound. (Aminabhavi et al., 1986; Dai & Fu 2008a,b; Fu & Ye 2007; Fu, et al. 2007). Here we report the crystal structure of the title compound, (S)-2-(pyrrolidinium-2-yl)-1H-benzimidazol-3-ium dichloride monohydrate (Fig. 1).

The crystal packing (Fig. 2) is stabilized by aromatic π–π interactions between the benzene rings of the neighbouring benzimidazole systems. The Cg···Cgi distance is 3.712 (2) Å (Cg is the centroide of the C1—C6 benzene ring, symmetry code as in Fig. 2). The molecular packing is further stabilized by intermolecular N—H···Cl, O—H···Cl and N—H···O hydrogen bonds (Fig. 2 and Table 1; symmetry code as in Fig. 2).

Experimental

The homochiral ligand (S)-2-(pyrrolidin-2-yl)-1H-benzimidazole was synthesized by reaction of S-pyrrolidine-2-carboxylic acid and benzene-1,2-diamine according to the procedure described in the literature(Aminabhavi, et al.(1986)). Then (S)-2-(pyrrolidin-2-yl)-1H-benzimidazole (3 mmol) was dissolved in the solution of distilled water (20 ml) and hydrochloric acid (1 ml) and evaporated in the air affording colorless block crystals of this compound suitable for X-ray analysis.

Refinement

All H atoms attached to C, N and O atoms were fixed geometrically and treated as riding with C—H = 0.93 Å (aromatic), 0.97 Å (methylene) or 0.98 Å (methine) and N—H = 0.90 Å (N3), 0.86 Å (N1, N2) and O—H = 0.85 Å with Uiso(H) = 1.2Ueq(C,N) and Uiso(H) = 1.5Ueq(O). The distances of O1W—H were restrained to 0.85 (1) Å using command DFIX.

Figures

Fig. 1.
A view of the title compound with the atomic numbering scheme. Displacement ellipsoids were drawn at the 30% probability level.
Fig. 2.
The π–π, N—H···Cl, O—H···Cl and N—H···O interactions (dotted line) in the title compound. Cg denotes the ring centroid of the C1-C6 ...

Crystal data

C11H15N32+·2Cl·H2OZ = 2
Mr = 278.18F(000) = 292
Triclinic, P1Dx = 1.361 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.493 (2) ÅCell parameters from 3108 reflections
b = 9.739 (2) Åθ = 3.1–27.5°
c = 9.937 (2) ŵ = 0.47 mm1
α = 99.23 (3)°T = 293 K
β = 95.73 (3)°Block, colorless
γ = 106.27 (3)°0.35 × 0.30 × 0.15 mm
V = 679.0 (3) Å3

Data collection

Rigaku Mercury2 diffractometer3108 independent reflections
Radiation source: fine-focus sealed tube2310 reflections with I > 2σ(I)
graphiteRint = 0.037
Detector resolution: 13.6612 pixels mm-1θmax = 27.5°, θmin = 3.1°
CCD profile fitting scansh = −9→9
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)k = −12→12
Tmin = 0.959, Tmax = 0.982l = −12→12
7119 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050Hydrogen site location: difference Fourier map
wR(F2) = 0.120H atoms treated by a mixture of independent and constrained refinement
S = 1.08w = 1/[σ2(Fo2) + (0.0354P)2 + 0.3615P] where P = (Fo2 + 2Fc2)/3
3108 reflections(Δ/σ)max < 0.001
162 parametersΔρmax = 0.28 e Å3
2 restraintsΔρmin = −0.24 e Å3

Special details

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)

xyzUiso*/Ueq
Cl10.81735 (10)0.00616 (8)0.30163 (7)0.0600 (2)
Cl20.79242 (9)0.58762 (8)0.97152 (7)0.0597 (2)
N10.2136 (3)0.5855 (2)0.31035 (18)0.0390 (4)
H10.20580.54450.22570.047*
N20.2230 (3)0.7465 (2)0.48963 (18)0.0414 (5)
H2A0.22240.82690.54000.050*
N30.1820 (3)0.7775 (2)0.11964 (19)0.0425 (5)
H3A0.08230.70240.07590.051*
H3B0.28750.75180.11230.051*
C10.2450 (3)0.6267 (3)0.5381 (2)0.0405 (5)
C20.2697 (4)0.5979 (3)0.6704 (3)0.0573 (7)
H20.27380.66660.74830.069*
C30.2877 (4)0.4640 (4)0.6804 (3)0.0662 (8)
H30.30580.44190.76740.079*
C40.2798 (4)0.3597 (3)0.5650 (3)0.0628 (8)
H40.29190.26970.57660.075*
C50.2546 (4)0.3866 (3)0.4338 (3)0.0537 (6)
H50.24810.31690.35620.064*
C60.2394 (3)0.5228 (2)0.4234 (2)0.0379 (5)
C70.2029 (3)0.7186 (2)0.3528 (2)0.0364 (5)
C80.1637 (3)0.8211 (3)0.2668 (2)0.0409 (5)
H80.03410.82250.27090.049*
C90.2916 (4)0.9767 (3)0.3080 (3)0.0529 (6)
H9A0.41850.97930.34260.063*
H9B0.24541.03270.37860.063*
C100.2868 (6)1.0359 (3)0.1762 (3)0.0755 (9)
H10A0.21911.10770.18220.091*
H10B0.41371.08220.16090.091*
C110.1905 (5)0.9111 (3)0.0618 (3)0.0666 (8)
H11A0.26060.9135−0.01520.080*
H11B0.06480.91340.03020.080*
O1W0.5254 (3)0.7671 (3)0.0856 (3)0.0863 (8)
H1A0.613 (4)0.832 (3)0.142 (3)0.117 (16)*
H1B0.572 (5)0.707 (3)0.043 (3)0.102 (13)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0704 (5)0.0589 (4)0.0530 (4)0.0339 (4)0.0092 (3)−0.0076 (3)
Cl20.0536 (4)0.0722 (5)0.0447 (4)0.0234 (3)0.0033 (3)−0.0186 (3)
N10.0487 (11)0.0378 (10)0.0303 (9)0.0166 (9)0.0067 (8)−0.0010 (7)
N20.0501 (11)0.0408 (11)0.0331 (10)0.0182 (9)0.0101 (8)−0.0037 (8)
N30.0439 (11)0.0448 (11)0.0382 (10)0.0161 (9)0.0007 (8)0.0050 (8)
C10.0378 (12)0.0459 (13)0.0378 (12)0.0124 (10)0.0106 (9)0.0056 (10)
C20.0588 (16)0.0740 (19)0.0380 (13)0.0176 (14)0.0137 (12)0.0085 (13)
C30.0662 (19)0.086 (2)0.0546 (17)0.0220 (17)0.0159 (14)0.0355 (16)
C40.0642 (18)0.0557 (17)0.077 (2)0.0197 (14)0.0146 (15)0.0316 (15)
C50.0593 (16)0.0436 (14)0.0600 (17)0.0172 (12)0.0119 (13)0.0104 (12)
C60.0380 (12)0.0374 (12)0.0381 (12)0.0111 (10)0.0082 (9)0.0052 (9)
C70.0357 (11)0.0376 (12)0.0350 (11)0.0123 (9)0.0076 (9)0.0010 (9)
C80.0392 (12)0.0445 (13)0.0420 (13)0.0197 (10)0.0086 (10)0.0031 (10)
C90.0599 (16)0.0413 (14)0.0550 (16)0.0156 (12)0.0086 (13)0.0021 (11)
C100.110 (3)0.0456 (16)0.069 (2)0.0160 (17)0.0164 (18)0.0150 (14)
C110.092 (2)0.0606 (18)0.0564 (18)0.0338 (17)0.0045 (16)0.0239 (14)
O1W0.0539 (13)0.0682 (15)0.125 (2)0.0221 (12)0.0145 (14)−0.0227 (14)

Geometric parameters (Å, °)

N1—C71.324 (3)C4—H40.9300
N1—C61.384 (3)C5—C61.381 (3)
N1—H10.8600C5—H50.9300
N2—C71.327 (3)C7—C81.484 (3)
N2—C11.376 (3)C8—C91.514 (3)
N2—H2A0.8600C8—H80.9800
N3—C81.487 (3)C9—C101.514 (4)
N3—C111.492 (3)C9—H9A0.9700
N3—H3A0.9000C9—H9B0.9700
N3—H3B0.9000C10—C111.481 (4)
C1—C61.386 (3)C10—H10A0.9700
C1—C21.393 (3)C10—H10B0.9700
C2—C31.366 (4)C11—H11A0.9700
C2—H20.9300C11—H11B0.9700
C3—C41.389 (4)O1W—H1A0.85 (3)
C3—H30.9300O1W—H1B0.84 (3)
C4—C51.375 (4)
C7—N1—C6109.38 (18)N1—C6—C1105.90 (19)
C7—N1—H1125.3N1—C7—N2108.91 (19)
C6—N1—H1125.3N1—C7—C8127.69 (19)
C7—N2—C1109.25 (18)N2—C7—C8123.30 (19)
C7—N2—H2A125.4C7—C8—N3112.88 (18)
C1—N2—H2A125.4C7—C8—C9115.7 (2)
C8—N3—C11104.06 (19)N3—C8—C9103.78 (19)
C8—N3—H3A110.9C7—C8—H8108.1
C11—N3—H3A110.9N3—C8—H8108.1
C8—N3—H3B110.9C9—C8—H8108.1
C11—N3—H3B110.9C8—C9—C10104.4 (2)
H3A—N3—H3B109.0C8—C9—H9A110.9
N2—C1—C6106.55 (19)C10—C9—H9A110.9
N2—C1—C2132.8 (2)C8—C9—H9B110.9
C6—C1—C2120.7 (2)C10—C9—H9B110.9
C3—C2—C1116.9 (3)H9A—C9—H9B108.9
C3—C2—H2121.6C11—C10—C9107.4 (2)
C1—C2—H2121.6C11—C10—H10A110.2
C2—C3—C4122.2 (3)C9—C10—H10A110.2
C2—C3—H3118.9C11—C10—H10B110.2
C4—C3—H3118.9C9—C10—H10B110.2
C5—C4—C3121.5 (3)H10A—C10—H10B108.5
C5—C4—H4119.3C10—C11—N3105.7 (2)
C3—C4—H4119.3C10—C11—H11A110.6
C4—C5—C6116.5 (3)N3—C11—H11A110.6
C4—C5—H5121.8C10—C11—H11B110.6
C6—C5—H5121.8N3—C11—H11B110.6
C5—C6—N1131.8 (2)H11A—C11—H11B108.7
C5—C6—C1122.3 (2)H1A—O1W—H1B109 (4)
C7—N2—C1—C60.6 (2)C6—N1—C7—N20.8 (2)
C7—N2—C1—C2−179.6 (3)C6—N1—C7—C8−175.7 (2)
N2—C1—C2—C3−179.8 (3)C1—N2—C7—N1−0.9 (3)
C6—C1—C2—C30.0 (4)C1—N2—C7—C8175.8 (2)
C1—C2—C3—C4−0.7 (4)N1—C7—C8—N3−14.5 (3)
C2—C3—C4—C50.4 (5)N2—C7—C8—N3169.4 (2)
C3—C4—C5—C60.6 (4)N1—C7—C8—C9−133.8 (2)
C4—C5—C6—N1−180.0 (2)N2—C7—C8—C950.1 (3)
C4—C5—C6—C1−1.3 (4)C11—N3—C8—C7−164.9 (2)
C7—N1—C6—C5178.4 (3)C11—N3—C8—C9−38.9 (2)
C7—N1—C6—C1−0.4 (2)C7—C8—C9—C10154.4 (2)
N2—C1—C6—C5−179.1 (2)N3—C8—C9—C1030.1 (3)
C2—C1—C6—C51.1 (4)C8—C9—C10—C11−10.2 (3)
N2—C1—C6—N1−0.1 (2)C9—C10—C11—N3−13.5 (4)
C2—C1—C6—N1−180.0 (2)C8—N3—C11—C1032.6 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···Cl2i0.862.173.018 (2)169
N2—H2A···Cl1i0.862.183.021 (2)166
N3—H3A···Cl2ii0.902.203.058 (2)158
N3—H3B···O1W0.901.802.656 (3)159
O1W—H1A···Cl1iii0.85 (3)2.22 (3)3.069 (3)174 (4)
O1W—H1B···Cl2iv0.84 (3)2.37 (4)3.181 (2)161 (4)

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x−1, y, z−1; (iii) x, y+1, z; (iv) x, y, z−1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LX2100).

References

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  • Dai, W. & Fu, D.-W. (2008b). Acta Cryst. E64, m1017. [PMC free article] [PubMed]
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Fu, D.-W., Song, Y.-M., Wang, G.-X., Ye, Q. & Xiong, R.-G. (2007). J. Am. Chem. Soc 129, 5346–5347. [PubMed]
  • Fu, D.-W. & Ye, H.-Y. (2007). Acta Cryst. E63, m2453.
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