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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1360.
Published online 2009 May 23. doi:  10.1107/S1600536809018558
PMCID: PMC2969558

2-(2-Pyrrolidinio)-1H-benzimidazol-3-ium dinitrate

Abstract

In the title compound, C11H15N3 2+·2NO3 , one of the imidazole N atoms and the N atom of the pyrrolidine ring are protonated. The pyrrolidine ring adopts an envelope conformation, with the C atom carrying the benzoimidazolium substituent as the flap atom. In the crystal structure, cations and anions are linked through N—H(...)O hydrogen bonds, forming chains that run parallel to the c axis.

Related literature

For background to the applications of proline derivatives, see: Fu et al. (2007 [triangle]); Aminabhavi et al. (1986 [triangle]). For the structures of metal complexes with ligands similar to the title compound, 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-o1360-scheme1.jpg

Experimental

Crystal data

  • C11H15N3 2+·2NO3
  • M r = 313.28
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1360-efi1.jpg
  • a = 22.078 (2) Å
  • b = 11.154 (1) Å
  • c = 14.670 (1) Å
  • β = 127.18 (1)°
  • V = 2878.3 (4) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 298 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
  • 14543 measured reflections
  • 3276 independent reflections
  • 2195 reflections with I > 2σ(I)
  • R int = 0.048

Refinement

  • R[F 2 > 2σ(F 2)] = 0.059
  • wR(F 2) = 0.144
  • S = 1.09
  • 3276 reflections
  • 199 parameters
  • H-atom parameters constrained
  • Δρmax = 0.31 e Å−3
  • Δρmin = −0.19 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: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809018558/sj2610sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018558/sj2610Isup2.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

Heterocyclic amine derivatives have found wide range of applications in material science and display ferroelectric, fluorescence and dielectric behaviors. There has also been an increased interest in the preparation of coordination compounds from these heterocyclic ligands (Aminabhavi et al., 1986; Dai & Fu, 2008a,b; Fu & Ye, 2007; Fu et al., 2007). We report here the crystal structure of the title compound, (I), 2-(pyrrolidinium-2-yl)-1H-benzo[d] imidazol-3-ium dinitrate.

In the title compound, (C11H15N3)2+.2(NO3)-, the N4 atom of the imidazole and the N5 atom of pyrrolidine ring are protonated. The pyrrolidine ring adopts an envelope conformation with the C8 atom carrying the benzoimidazolium substituent as the flap atom. In the crystal structure, cations and anions are linked through N—H···O hydrogen bonds forming chains that run parallel to the c axis. (Fig. 2, Table 1).

Experimental

The homochiral ligand S-2-(pyrrolidin-2-yl)-1H-benzo[d]imidazole 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). S-2-(pyrrolidin-2-yl)-1H-benzo[d]imidazole (3 mmol) was dissolved in distilled water (20 ml) and nitric acid (1 ml). The solution was evaporated in air affording colorless block-like crystals of (I) suitable for X-ray analysis.

Refinement

All H atoms attached to C and N 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 (N5), 0.86 Å (N3, N4) with Uiso(H) = 1.2Ueq(C,N).

Figures

Fig. 1.
A view of the title compound with the atomic numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
Partial packing view of the title compound showing the formation of a chain parallel to the c axis. All H atoms not involved in hydrogen bonding (dashed lines) were omitted for clarity.

Crystal data

C11H15N32+·2NO3F(000) = 1312
Mr = 313.28Dx = 1.446 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 3275 reflections
a = 22.078 (2) Åθ = 3.2–27.5°
b = 11.154 (1) ŵ = 0.12 mm1
c = 14.670 (1) ÅT = 298 K
β = 127.18 (1)°Block, colourless
V = 2878.3 (4) Å30.35 × 0.30 × 0.15 mm
Z = 8

Data collection

Rigaku Mercury2 diffractometer3276 independent reflections
Radiation source: fine-focus sealed tube2195 reflections with I > 2σ(I)
graphiteRint = 0.048
Detector resolution: 13.6612 pixels mm-1θmax = 27.5°, θmin = 3.2°
ω scansh = −28→28
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)k = −14→14
Tmin = 0.959, Tmax = 0.982l = −18→19
14543 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)] = 0.059Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.144H-atom parameters constrained
S = 1.09w = 1/[σ2(Fo2) + (0.0493P)2 + 2.1933P] where P = (Fo2 + 2Fc2)/3
3276 reflections(Δ/σ)max < 0.001
199 parametersΔρmax = 0.31 e Å3
0 restraintsΔρmin = −0.19 e Å3

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*/Ueq
N30.66938 (10)0.39290 (15)0.56483 (15)0.0433 (4)
H3A0.69660.32900.59370.052*
N40.63804 (11)0.58040 (17)0.53606 (17)0.0513 (5)
H4A0.64140.65720.54280.062*
N50.83307 (9)0.45350 (16)0.71441 (14)0.0429 (4)
H5A0.81630.41190.65060.052*
H5B0.84250.40160.76860.052*
C10.57133 (13)0.5163 (2)0.4595 (2)0.0500 (6)
C20.49697 (15)0.5521 (3)0.3784 (3)0.0709 (8)
H20.48320.63250.36640.085*
C30.44437 (16)0.4628 (3)0.3162 (3)0.0778 (9)
H30.39390.48340.25990.093*
C40.46486 (16)0.3430 (3)0.3353 (2)0.0725 (8)
H40.42730.28560.29200.087*
C50.53812 (15)0.3057 (2)0.4155 (2)0.0593 (7)
H50.55130.22500.42760.071*
C60.59181 (12)0.3961 (2)0.47789 (19)0.0448 (5)
C70.69499 (12)0.50468 (19)0.59632 (18)0.0418 (5)
C80.77457 (13)0.54335 (19)0.6904 (2)0.0465 (6)
H80.77850.55300.76020.056*
C90.80026 (15)0.6590 (2)0.6698 (2)0.0616 (7)
H9A0.77990.72810.68310.074*
H9B0.78520.66260.59260.074*
C100.88635 (15)0.6521 (2)0.7577 (2)0.0617 (7)
H10A0.91120.70440.73670.074*
H10B0.90220.67450.83310.074*
C110.90467 (14)0.5220 (2)0.7552 (2)0.0556 (6)
H11A0.94710.49530.83080.067*
H11B0.91740.51070.70300.067*
O10.64618 (11)0.82051 (14)0.60914 (14)0.0612 (5)
O20.58007 (14)0.83408 (18)0.42662 (16)0.0852 (7)
O30.59348 (11)0.98868 (15)0.52487 (15)0.0672 (5)
N10.60605 (11)0.88315 (18)0.51830 (16)0.0492 (5)
O40.74570 (10)0.68205 (14)0.85048 (13)0.0533 (4)
O50.81397 (9)0.66960 (14)1.03479 (13)0.0513 (4)
O60.74016 (11)0.52300 (15)0.93113 (17)0.0698 (5)
N20.76639 (11)0.62317 (16)0.93912 (16)0.0447 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N30.0448 (10)0.0328 (9)0.0462 (10)0.0007 (8)0.0243 (9)−0.0039 (8)
N40.0516 (12)0.0344 (10)0.0625 (13)0.0033 (9)0.0316 (11)−0.0006 (9)
N50.0440 (10)0.0434 (10)0.0335 (9)−0.0035 (8)0.0193 (8)−0.0069 (8)
C10.0441 (13)0.0517 (14)0.0519 (14)0.0021 (11)0.0278 (12)0.0013 (11)
C20.0538 (17)0.0731 (19)0.0754 (19)0.0149 (14)0.0336 (15)0.0152 (15)
C30.0405 (15)0.110 (3)0.0671 (19)0.0017 (17)0.0243 (14)0.0035 (18)
C40.0516 (17)0.092 (2)0.0664 (18)−0.0206 (16)0.0319 (15)−0.0162 (17)
C50.0569 (16)0.0599 (16)0.0629 (16)−0.0148 (13)0.0371 (14)−0.0149 (13)
C60.0439 (13)0.0464 (13)0.0459 (13)−0.0027 (10)0.0280 (11)−0.0055 (10)
C70.0455 (13)0.0349 (11)0.0445 (12)−0.0014 (9)0.0270 (11)−0.0066 (9)
C80.0518 (13)0.0391 (12)0.0487 (13)−0.0036 (10)0.0304 (12)−0.0098 (10)
C90.0662 (17)0.0392 (13)0.0772 (18)−0.0109 (12)0.0421 (15)−0.0112 (13)
C100.0657 (16)0.0575 (16)0.0641 (16)−0.0226 (13)0.0404 (14)−0.0202 (13)
C110.0496 (14)0.0642 (16)0.0529 (14)−0.0100 (12)0.0310 (12)−0.0077 (12)
O10.0807 (12)0.0462 (10)0.0502 (10)0.0166 (9)0.0361 (10)0.0115 (8)
O20.1258 (19)0.0759 (14)0.0539 (12)−0.0102 (13)0.0543 (13)−0.0108 (10)
O30.0808 (13)0.0431 (10)0.0649 (12)0.0163 (9)0.0373 (10)0.0099 (8)
N10.0563 (12)0.0456 (12)0.0463 (11)0.0003 (9)0.0313 (10)0.0037 (9)
O40.0766 (12)0.0444 (9)0.0399 (9)0.0054 (8)0.0357 (9)0.0043 (7)
O50.0596 (10)0.0485 (9)0.0389 (9)−0.0026 (8)0.0261 (8)0.0033 (7)
O60.0716 (12)0.0441 (10)0.0778 (13)−0.0113 (9)0.0367 (11)0.0063 (9)
N20.0514 (11)0.0372 (10)0.0485 (11)0.0065 (9)0.0318 (10)0.0053 (9)

Geometric parameters (Å, °)

N3—C71.331 (3)C5—H50.9300
N3—C61.386 (3)C7—C81.499 (3)
N3—H3A0.8600C8—C91.511 (3)
N4—C71.316 (3)C8—H80.9800
N4—C11.393 (3)C9—C101.523 (4)
N4—H4A0.8600C9—H9A0.9700
N5—C81.499 (3)C9—H9B0.9700
N5—C111.516 (3)C10—C111.514 (4)
N5—H5A0.9000C10—H10A0.9700
N5—H5B0.9000C10—H10B0.9700
C1—C21.382 (4)C11—H11A0.9700
C1—C61.388 (3)C11—H11B0.9700
C2—C31.375 (4)O1—N11.274 (2)
C2—H20.9300O2—N11.227 (2)
C3—C41.384 (4)O3—N11.226 (2)
C3—H30.9300O4—N21.270 (2)
C4—C51.369 (4)O5—N21.249 (2)
C4—H40.9300O6—N21.231 (2)
C5—C61.396 (3)
C7—N3—C6108.93 (18)N3—C7—C8127.21 (19)
C7—N3—H3A125.5N5—C8—C7112.84 (17)
C6—N3—H3A125.5N5—C8—C9104.12 (19)
C7—N4—C1109.12 (19)C7—C8—C9115.8 (2)
C7—N4—H4A125.4N5—C8—H8107.9
C1—N4—H4A125.4C7—C8—H8107.9
C8—N5—C11107.51 (17)C9—C8—H8107.9
C8—N5—H5A110.2C8—C9—C10102.4 (2)
C11—N5—H5A110.2C8—C9—H9A111.3
C8—N5—H5B110.2C10—C9—H9A111.3
C11—N5—H5B110.2C8—C9—H9B111.3
H5A—N5—H5B108.5C10—C9—H9B111.3
C2—C1—C6121.6 (2)H9A—C9—H9B109.2
C2—C1—N4132.3 (2)C11—C10—C9104.05 (19)
C6—C1—N4106.1 (2)C11—C10—H10A110.9
C3—C2—C1116.8 (3)C9—C10—H10A110.9
C3—C2—H2121.6C11—C10—H10B110.9
C1—C2—H2121.6C9—C10—H10B110.9
C2—C3—C4121.5 (3)H10A—C10—H10B109.0
C2—C3—H3119.2C10—C11—N5105.2 (2)
C4—C3—H3119.2C10—C11—H11A110.7
C5—C4—C3122.7 (3)N5—C11—H11A110.7
C5—C4—H4118.7C10—C11—H11B110.7
C3—C4—H4118.7N5—C11—H11B110.7
C4—C5—C6116.0 (3)H11A—C11—H11B108.8
C4—C5—H5122.0O3—N1—O2122.4 (2)
C6—C5—H5122.0O3—N1—O1119.45 (19)
N3—C6—C1106.27 (19)O2—N1—O1118.1 (2)
N3—C6—C5132.2 (2)O6—N2—O5120.74 (19)
C1—C6—C5121.5 (2)O6—N2—O4120.96 (19)
N4—C7—N3109.58 (19)O5—N2—O4118.29 (18)
N4—C7—C8123.10 (19)
C7—N4—C1—C2−180.0 (3)C1—N4—C7—N3−0.9 (3)
C7—N4—C1—C60.2 (3)C1—N4—C7—C8−177.2 (2)
C6—C1—C2—C3−0.4 (4)C6—N3—C7—N41.2 (3)
N4—C1—C2—C3179.8 (3)C6—N3—C7—C8177.4 (2)
C1—C2—C3—C41.0 (4)C11—N5—C8—C7149.12 (19)
C2—C3—C4—C5−0.9 (5)C11—N5—C8—C922.8 (2)
C3—C4—C5—C60.1 (4)N4—C7—C8—N5−157.4 (2)
C7—N3—C6—C1−1.0 (2)N3—C7—C8—N526.9 (3)
C7—N3—C6—C5−180.0 (2)N4—C7—C8—C9−37.6 (3)
C2—C1—C6—N3−179.4 (2)N3—C7—C8—C9146.7 (2)
N4—C1—C6—N30.5 (2)N5—C8—C9—C10−38.4 (2)
C2—C1—C6—C5−0.3 (4)C7—C8—C9—C10−162.8 (2)
N4—C1—C6—C5179.6 (2)C8—C9—C10—C1139.8 (3)
C4—C5—C6—N3179.2 (2)C9—C10—C11—N5−25.8 (3)
C4—C5—C6—C10.4 (4)C8—N5—C11—C102.0 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3A···O4i0.861.932.788 (2)177
N3—H3A···O5i0.862.503.020 (2)120
N5—H5B···O1i0.901.892.771 (2)167
N5—H5B···O3i0.902.643.149 (2)117
N5—H5A···O5ii0.901.902.768 (2)162
N4—H4A···O10.862.042.850 (2)157
N4—H4A···O20.862.423.121 (3)139

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SJ2610).

References

  • Aminabhavi, T. M., Biradar, N. S. & Patil, S. B. (1986). Inorg. Chim. Acta, 125, 125–128.
  • Dai, W. & Fu, D.-W. (2008a). Acta Cryst. E64, m1016. [PMC free article] [PubMed]
  • Dai, W. & Fu, D.-W. (2008b). Acta Cryst. E64, m1017. [PMC free article] [PubMed]
  • 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.
  • Rigaku (2005). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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