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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): o2032.
Published online 2009 July 29. doi:  10.1107/S1600536809028451
PMCID: PMC2977472

(S)-2-(1-Hydroxy­ethyl)benzimid­azolium dihydrogen phosphate

Abstract

The asymmetric unit of the title compound, C9H11N2O+·H2PO4 , is built up from a 2-(1-hydroxy­ethyl)benz­imid­a­zol­ium cation and a dihydrogen phosphate anion which are connected by an N—H(...)O hydrogen bond. The cation is roughly planar, the dihedral angle between the rings being only 1.4 (2)°. The S configuration is deduced from the synthetic pathway and supported by the refinement of the Flack parameter. Inter­molecular O—H(...)O and N—H(...)O hydrogen bonds build up a three-dimensionnal network.

Related literature

For the biological and pharmaceutical activity of imidazole and benzimidazole derivatives, see: Rodembusch et al. (2004 [triangle]); Gong et al. (2005 [triangle]); Chen (2005 [triangle]); Belmar et al. (1999 [triangle]). For the synthesis and crystal structure of (±)-1-(1H-benzimidazol-2-yl)ethanol, see: Xia & Xu (2008 [triangle]).

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Object name is e-65-o2032-scheme1.jpg

Experimental

Crystal data

  • C9H11N2O+·H2PO4
  • M r = 260.18
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2032-efi1.jpg
  • a = 4.5869 (13) Å
  • b = 15.749 (5) Å
  • c = 15.876 (5) Å
  • V = 1146.8 (6) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.25 mm−1
  • T = 293 K
  • 0.20 × 0.20 × 0.20 mm

Data collection

  • Rigaku SCXmini diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 [triangle]) T min = 0.951, T max = 0.953
  • 11500 measured reflections
  • 2565 independent reflections
  • 1749 reflections with I > 2σ(I)
  • R int = 0.125

Refinement

  • R[F 2 > 2σ(F 2)] = 0.052
  • wR(F 2) = 0.118
  • S = 0.82
  • 2565 reflections
  • 159 parameters
  • H-atom parameters constrained
  • Δρmax = 0.39 e Å−3
  • Δρmin = −0.37 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 1030 Friedel pairs
  • Flack parameter: 0.16 (17)

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/S1600536809028451/dn2468sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809028451/dn2468Isup2.hkl

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

Acknowledgments

The author gratefully acknowledges financial support by the start-up fund of Southeast University.

supplementary crystallographic information

Comment

The benzimidazoles, benzothiazoles, and benzoxazoles can be utilized as not only a wide variety of biologically active and medicinally significant compounds but also as advanced materials including non-linear optics (NLO), organic light-emitting diodes (OLED), and liquid crystals (Rodembusch et al., 2004; Gong et al., 2005; Chen, 2005; Belmar et al., 1999).

The title compound is built up from a dihydrogen phosphate anion and a (1H-benzimidazol-2-yl)ethanolium cation which are connected by a N-H···O hydrogen bond (Fig. 1).The S absolute configuration is deduced from the synthetic pathway and supported by the refinement of the Flack parameter (Flack, 1983). The phenyl ring and imidazole ring are roughly planar, making a dihedral angle of only1.4°. All bond lengths and angels are normal.

The molecules are connected via O—H···O and N—H···O hydrogen bonds making a three dimensionnal network (Table 1, Fig. 2).

Experimental

A solution of phosphoric acid (1 mmol) in water was added to a methanol solution of L-(-)-1-(1H-Benzimidazol-2-yl)ethanol (1 mmol), and then the mixture was stirred for half an hour at room temperature. The mixture was then filtered and the filtrate was evaporated at room temperature for a period of one month.Crystals suitable for X-ray diffraction analysis were obtained then. L-(-)-1-(1H-Benzimidazol-2-yl)ethanol was synthesized by the reaction of Benzene-1, 2-diamine and Ethyl L-(-)-lactate(R. Xia, et al., 2008).

Refinement

All H atoms attached to C and O atom were fixed geometrically and treated as riding with C—H = 0.93–0.98 Å, O—H = 0.82 Å and with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(C, O) for methyl and hydroxyl.

The su on the Flack parameter is rather high, however the value of the parameter agrees with the S configuration. Moreover, inverting the configuration leads to the value 0.88 close to 1.

Figures

Fig. 1.
Molecular structure of the title compound with the atom labeling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are represented as small spheres of arbitrary radii. H bond is shown as dashed line.
Fig. 2.
Packing diagram of the title compound viewed along the a axis. Intermolecular O—H···O hydrogen bonds and N—H···O hydrogen bonds are shown as dashed lines. H atoms not involved in hydrogen ...

Crystal data

C9H11N2O+·H2PO4F(000) = 544
Mr = 260.18Dx = 1.507 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 3144 reflections
a = 4.5869 (13) Åθ = 2.6–27.4°
b = 15.749 (5) ŵ = 0.25 mm1
c = 15.876 (5) ÅT = 293 K
V = 1146.8 (6) Å3Block, pale yellow
Z = 40.20 × 0.20 × 0.20 mm

Data collection

Rigaku SCXmini diffractometer2565 independent reflections
Radiation source: fine-focus sealed tube1749 reflections with I > 2σ(I)
graphiteRint = 0.125
Detector resolution: 13.6612 pixels mm-1θmax = 27.3°, θmin = 2.6°
ω scansh = −5→5
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)k = −20→20
Tmin = 0.951, Tmax = 0.953l = −20→20
11500 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.052H-atom parameters constrained
wR(F2) = 0.118w = 1/[σ2(Fo2) + (0.0314P)2] where P = (Fo2 + 2Fc2)/3
S = 0.82(Δ/σ)max < 0.001
2565 reflectionsΔρmax = 0.39 e Å3
159 parametersΔρmin = −0.37 e Å3
0 restraintsAbsolute structure: Flack (1983), 1030 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.16 (17)

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 > 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
P10.8027 (2)0.34270 (6)0.42082 (6)0.0274 (2)
O50.8944 (6)0.34283 (14)0.51179 (14)0.0379 (7)
O41.0419 (5)0.36640 (16)0.35969 (15)0.0389 (7)
O30.5477 (6)0.40686 (15)0.4094 (2)0.0470 (8)
H30.39680.38090.39920.070*
O20.6959 (7)0.25204 (15)0.39269 (13)0.0415 (7)
H20.57760.23390.42700.062*
N20.8351 (7)0.44478 (17)0.21853 (17)0.0336 (7)
H2A0.91800.42660.26360.040*
N10.7140 (7)0.52823 (18)0.11523 (16)0.0369 (8)
H10.70600.57220.08320.044*
C81.0565 (9)0.5932 (2)0.2193 (2)0.0385 (9)
H81.22330.60300.18200.046*
O10.8750 (6)0.66679 (16)0.21909 (17)0.0514 (8)
H1A0.93670.70100.18440.077*
C10.5597 (9)0.4529 (2)0.1022 (2)0.0336 (9)
C50.5154 (9)0.3179 (2)0.1774 (2)0.0421 (10)
H50.56430.28220.22190.051*
C20.3599 (10)0.4283 (3)0.0413 (2)0.0449 (11)
H2B0.30660.4640−0.00270.054*
C60.6383 (9)0.3991 (2)0.1692 (2)0.0322 (9)
C70.8737 (8)0.5219 (2)0.1839 (2)0.0329 (9)
C40.3198 (10)0.2939 (2)0.1167 (2)0.0478 (11)
H40.23450.24040.12000.057*
C91.1665 (13)0.5756 (2)0.3069 (3)0.0635 (14)
H9A1.27560.62370.32670.095*
H9B1.29000.52640.30600.095*
H9C1.00430.56560.34370.095*
C30.2448 (10)0.3478 (3)0.0497 (2)0.0523 (12)
H3A0.11270.32850.00960.063*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
P10.0291 (5)0.0195 (4)0.0336 (4)−0.0002 (4)−0.0001 (4)0.0016 (4)
O50.0578 (18)0.0220 (12)0.0341 (13)0.0091 (14)0.0013 (13)−0.0032 (10)
O40.0261 (14)0.0505 (17)0.0400 (15)−0.0040 (13)−0.0005 (12)0.0139 (12)
O30.0274 (15)0.0281 (14)0.085 (2)0.0010 (13)−0.0108 (17)−0.0035 (14)
O20.065 (2)0.0229 (13)0.0362 (14)−0.0107 (15)0.0061 (14)−0.0083 (10)
N20.043 (2)0.0280 (16)0.0300 (15)0.0026 (15)−0.0003 (16)0.0105 (12)
N10.053 (2)0.0261 (16)0.0315 (15)0.0063 (17)0.0011 (16)0.0088 (12)
C80.038 (2)0.0279 (19)0.050 (2)−0.0014 (19)0.004 (2)0.0047 (17)
O10.067 (2)0.0256 (15)0.0619 (19)0.0066 (16)0.0083 (17)0.0083 (12)
C10.040 (2)0.030 (2)0.030 (2)0.0079 (19)0.0019 (18)0.0006 (14)
C50.054 (3)0.027 (2)0.045 (2)0.003 (2)0.003 (2)0.0048 (16)
C20.057 (3)0.048 (2)0.030 (2)0.012 (2)−0.003 (2)0.0021 (17)
C60.036 (2)0.0259 (18)0.035 (2)0.0062 (17)0.0018 (17)0.0025 (14)
C70.039 (2)0.0258 (18)0.0341 (19)0.0044 (17)0.0068 (17)0.0041 (14)
C40.059 (3)0.032 (2)0.053 (3)−0.008 (2)0.001 (2)−0.0043 (17)
C90.082 (4)0.037 (2)0.071 (3)−0.010 (3)−0.033 (3)0.007 (2)
C30.057 (3)0.050 (3)0.050 (2)−0.004 (3)−0.012 (2)−0.012 (2)

Geometric parameters (Å, °)

P1—O51.504 (2)C8—H80.9800
P1—O41.512 (3)O1—H1A0.8200
P1—O31.556 (3)C1—C21.388 (5)
P1—O21.574 (2)C1—C61.406 (4)
O3—H30.8200C5—C41.370 (5)
O2—H20.8200C5—C61.404 (5)
N2—C71.345 (4)C5—H50.9300
N2—C61.395 (4)C2—C31.380 (5)
N2—H2A0.8600C2—H2B0.9300
N1—C71.317 (4)C4—C31.403 (5)
N1—C11.397 (4)C4—H40.9300
N1—H10.8600C9—H9A0.9600
C8—O11.427 (4)C9—H9B0.9600
C8—C91.505 (5)C9—H9C0.9600
C8—C71.510 (5)C3—H3A0.9300
O5—P1—O4114.40 (15)C4—C5—C6116.7 (4)
O5—P1—O3108.76 (16)C4—C5—H5121.7
O4—P1—O3108.07 (15)C6—C5—H5121.7
O5—P1—O2111.14 (13)C3—C2—C1116.2 (3)
O4—P1—O2105.53 (15)C3—C2—H2B121.9
O3—P1—O2108.77 (16)C1—C2—H2B121.9
P1—O3—H3109.5N2—C6—C5132.6 (3)
P1—O2—H2109.5N2—C6—C1106.3 (3)
C7—N2—C6108.7 (3)C5—C6—C1121.1 (4)
C7—N2—H2A125.6N1—C7—N2109.5 (3)
C6—N2—H2A125.6N1—C7—C8124.1 (3)
C7—N1—C1109.9 (3)N2—C7—C8126.3 (3)
C7—N1—H1125.1C5—C4—C3121.8 (4)
C1—N1—H1125.1C5—C4—H4119.1
O1—C8—C9110.3 (3)C3—C4—H4119.1
O1—C8—C7106.2 (3)C8—C9—H9A109.5
C9—C8—C7113.2 (3)C8—C9—H9B109.5
O1—C8—H8109.0H9A—C9—H9B109.5
C9—C8—H8109.0C8—C9—H9C109.5
C7—C8—H8109.0H9A—C9—H9C109.5
C8—O1—H1A109.5H9B—C9—H9C109.5
C2—C1—N1132.5 (3)C2—C3—C4122.3 (4)
C2—C1—C6121.8 (4)C2—C3—H3A118.8
N1—C1—C6105.7 (3)C4—C3—H3A118.8

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O3—H3···O4i0.821.762.532 (4)156
O2—H2···O5ii0.821.762.539 (3)157
N2—H2A···O40.861.882.729 (4)167
N1—H1···O5iii0.861.812.659 (4)167
O1—H1A···O2iv0.822.232.971 (4)150

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: DN2468).

References

  • Belmar, J., Para, M., Zuniga, C., Perez, C. & Munoz, C. (1999). Liq. Cryst.26, 389–396.
  • Chen, T.-R. (2005). J. Mol. Struct 737, 35–41.
  • Flack, H. D. (1983). Acta Cryst. A39, 876–881.
  • Gong, J. R., Wan, L.-J., Lei, S.-B., Bai, C.-L., Zhang, X.-H. & Lee, S.-T. (2005). J. Phys. Chem. B, 109, 1675–1682. [PubMed]
  • Rigaku (2005). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Rodembusch, F. S., Buckup, T., Segala, M., Tavares, L., Correia, R. R. B. & Stefani, V. (2004). Chem. Phys 305, 115–121.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Xia, R. & Xu, H.-J. (2008). Acta Cryst. E64, o1223. [PMC free article] [PubMed]

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