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Acta Crystallogr Sect E Struct Rep Online. 2008 August 1; 64(Pt 8): o1489.
Published online 2008 July 16. doi:  10.1107/S160053680802093X
PMCID: PMC2962096

3a,11b-Dihydr­oxy-2-oxo-2,3,3a,11b-tetra­hydro-1H-imidazo[4,5-f][1,10]phenanthrolin-7-ium chloride

Abstract

In the crystal structure of the title compound, C13H11N4O3 +·Cl, the dihedral angle between the two pyridine rings is 9.72 (9) Å. Ions are linked via N—H(...)Cl, O—H(...)Cl and O—H(...)O hydrogen bonds, forming a three-dimensional framework.

Related literature

For general background, see: Zhao et al. (2004 [triangle]); Zheng et al. (2005 [triangle]).

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Object name is e-64-o1489-scheme1.jpg

Experimental

Crystal data

  • C13H11N4O3 +·Cl
  • M r = 306.71
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1489-efi1.jpg
  • a = 7.9420 (13) Å
  • b = 20.352 (3) Å
  • c = 8.2972 (14) Å
  • β = 106.620 (5)°
  • V = 1285.1 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.31 mm−1
  • T = 293 (2) K
  • 0.31 × 0.22 × 0.19 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.909, T max = 0.943
  • 13480 measured reflections
  • 2261 independent reflections
  • 2094 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.103
  • S = 1.05
  • 2261 reflections
  • 190 parameters
  • H-atom parameters constrained
  • Δρmax = 0.48 e Å−3
  • Δρmin = −0.52 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680802093X/at2573sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053680802093X/at2573Isup2.hkl

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

Acknowledgments

We acknowledge the support of the National Natural Science Foundation of China (No. 20662003) and the Foundation of the Governor of Guizhou Province, China.

supplementary crystallographic information

Comment

Recent year, we used different alkyl-substituted glycolurils as the building blocks to synthesize the partially alkyl substituted cucurbit[n]urils (Zhao et al., 2004; Zheng et al., 2005). In this work, we further report the crystal structure of a phenanthroline-substituted semi-glycoluril.

In the title compound (I), (Fig. 1), consists of organic cations, Cl- anions. The dihedral angle between two pyridine rings is 9.72 (9) Å. Molecules are linked via N—H···Cl, O—H···Cl and O—H···O hydrogen bonds forming a three-dimensional framework. (Table 1).

Experimental

1,10-Phenanthroline-5,6-dione (3.00 g,14.29 mmol) and carbamide (15.00 g, 250 mmol) were dissolved in acetic acid glacial (120 mL) and hydrochloric acid (5 mL) at room temperature. There was a lot of deposit after the mixture were stirred 5 h. Filtrate, solid was washed by ethanol, drying, gained white powder 2.46 g [yield: 63%].

Refinement

H atoms were placed in calculated positions with C—H = 0.93, N—H = 0.86 and O—H = 0.82 Å and refined as riding, with Uiso(H) = 1.2-1.5Ueq.

Figures

Fig. 1.
The molecular structure of (I) showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C13H11N4O3+·ClF000 = 632
Mr = 306.71Dx = 1.585 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2261 reflections
a = 7.9420 (13) Åθ = 2.0–25.0º
b = 20.352 (3) ŵ = 0.31 mm1
c = 8.2972 (14) ÅT = 293 (2) K
β = 106.620 (5)ºPrism, colourless
V = 1285.1 (4) Å30.31 × 0.22 × 0.19 mm
Z = 4

Data collection

Bruker APEXII CCD area-detector diffractometer2261 independent reflections
Radiation source: fine-focus sealed tube2094 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.022
T = 293(2) Kθmax = 25.0º
[var phi] and ω scansθmin = 2.0º
Absorption correction: multi-scan(SADABS; Bruker, 2005)h = −8→9
Tmin = 0.909, Tmax = 0.943k = −24→24
13480 measured reflectionsl = −9→8

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.037H-atom parameters constrained
wR(F2) = 0.103  w = 1/[σ2(Fo2) + (0.0589P)2 + 0.7326P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
2261 reflectionsΔρmax = 0.48 e Å3
190 parametersΔρmin = −0.51 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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
C1−0.0113 (3)0.58542 (11)0.2547 (3)0.0409 (5)
H1−0.08910.56580.16160.049*
C2−0.0166 (3)0.65219 (11)0.2779 (3)0.0446 (5)
H2−0.09820.67810.20150.054*
C30.1010 (2)0.68003 (10)0.4159 (3)0.0376 (5)
H30.09600.72490.43520.045*
C40.2275 (2)0.64158 (9)0.5271 (2)0.0280 (4)
C50.3591 (2)0.67304 (8)0.6779 (2)0.0288 (4)
C60.6083 (2)0.70941 (8)0.6106 (2)0.0286 (4)
C70.5217 (2)0.62729 (8)0.7653 (2)0.0265 (4)
C80.4878 (2)0.55393 (8)0.7408 (2)0.0250 (4)
C90.6001 (2)0.50849 (9)0.8421 (2)0.0311 (4)
H90.69630.52260.92820.037*
C100.5678 (2)0.44209 (9)0.8141 (2)0.0325 (4)
H100.64230.41110.88050.039*
C110.4231 (3)0.42256 (9)0.6860 (2)0.0327 (4)
H110.40090.37780.66930.039*
C120.3479 (2)0.52914 (8)0.6134 (2)0.0258 (4)
C130.2261 (2)0.57459 (8)0.5007 (2)0.0261 (4)
N10.10578 (19)0.54886 (8)0.36612 (19)0.0314 (4)
H1A0.10460.50700.35160.038*
N20.3139 (2)0.46487 (7)0.58529 (19)0.0315 (4)
N30.44790 (19)0.72802 (7)0.6258 (2)0.0337 (4)
H3A0.40540.76710.60710.040*
N40.64752 (19)0.64940 (7)0.68046 (18)0.0284 (3)
H40.73730.62680.67520.034*
O10.70045 (17)0.74179 (6)0.54285 (17)0.0374 (3)
O20.26989 (17)0.69570 (7)0.79061 (17)0.0389 (3)
H2A0.22160.66470.82240.058*
O30.58135 (18)0.63742 (6)0.93855 (15)0.0355 (3)
H3B0.60130.67660.95770.053*
Cl10.03122 (6)0.58193 (2)0.83116 (6)0.03931 (18)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0294 (10)0.0529 (13)0.0332 (10)−0.0040 (9)−0.0026 (8)0.0010 (9)
C20.0330 (10)0.0466 (12)0.0450 (12)0.0029 (9)−0.0037 (9)0.0121 (10)
C30.0304 (10)0.0314 (10)0.0473 (12)0.0010 (8)0.0053 (8)0.0062 (8)
C40.0242 (9)0.0289 (9)0.0305 (9)−0.0007 (7)0.0073 (7)0.0014 (7)
C50.0289 (9)0.0228 (8)0.0336 (10)−0.0010 (7)0.0071 (7)−0.0031 (7)
C60.0302 (9)0.0226 (8)0.0285 (9)−0.0043 (7)0.0014 (7)−0.0017 (7)
C70.0274 (9)0.0252 (9)0.0239 (8)−0.0032 (7)0.0028 (7)−0.0008 (7)
C80.0270 (8)0.0242 (9)0.0239 (8)−0.0019 (7)0.0074 (7)0.0005 (6)
C90.0308 (9)0.0313 (9)0.0282 (9)−0.0021 (7)0.0037 (7)0.0017 (7)
C100.0357 (10)0.0285 (9)0.0331 (10)0.0041 (8)0.0099 (8)0.0067 (8)
C110.0402 (10)0.0225 (9)0.0369 (10)−0.0016 (7)0.0133 (8)0.0001 (7)
C120.0266 (8)0.0247 (8)0.0270 (9)−0.0017 (7)0.0092 (7)−0.0021 (7)
C130.0230 (8)0.0296 (9)0.0255 (9)−0.0025 (7)0.0065 (7)−0.0014 (7)
N10.0281 (8)0.0325 (8)0.0305 (8)−0.0031 (6)0.0031 (6)−0.0043 (6)
N20.0337 (8)0.0258 (8)0.0328 (8)−0.0031 (6)0.0061 (6)−0.0036 (6)
N30.0296 (8)0.0197 (7)0.0488 (10)0.0004 (6)0.0065 (7)0.0035 (7)
N40.0258 (7)0.0233 (7)0.0348 (8)0.0006 (6)0.0064 (6)0.0037 (6)
O10.0358 (7)0.0304 (7)0.0443 (8)−0.0045 (6)0.0088 (6)0.0097 (6)
O20.0381 (7)0.0349 (7)0.0468 (8)−0.0022 (6)0.0172 (6)−0.0118 (6)
O30.0482 (8)0.0293 (7)0.0239 (7)−0.0074 (6)0.0021 (6)−0.0027 (5)
Cl10.0309 (3)0.0414 (3)0.0425 (3)−0.00238 (18)0.0053 (2)−0.0005 (2)

Geometric parameters (Å, °)

C1—N11.335 (3)C7—C81.520 (2)
C1—C21.375 (3)C8—C91.388 (2)
C1—H10.9300C8—C121.391 (2)
C2—C31.376 (3)C9—C101.383 (3)
C2—H20.9300C9—H90.9300
C3—C41.394 (3)C10—C111.382 (3)
C3—H30.9300C10—H100.9300
C4—C131.380 (2)C11—N21.333 (2)
C4—C51.523 (2)C11—H110.9300
C5—O21.403 (2)C12—N21.342 (2)
C5—N31.453 (2)C12—C131.466 (2)
C5—C71.589 (2)C13—N11.350 (2)
C6—O11.233 (2)N1—H1A0.8600
C6—N41.350 (2)N3—H3A0.8600
C6—N31.369 (2)N4—H40.8600
C7—O31.394 (2)O2—H2A0.8200
C7—N41.449 (2)O3—H3B0.8200
N1—C1—C2119.82 (18)C12—C8—C7122.01 (15)
N1—C1—H1120.1C10—C9—C8119.56 (17)
C2—C1—H1120.1C10—C9—H9120.2
C1—C2—C3118.87 (19)C8—C9—H9120.2
C1—C2—H2120.6C11—C10—C9118.93 (17)
C3—C2—H2120.6C11—C10—H10120.5
C2—C3—C4120.59 (19)C9—C10—H10120.5
C2—C3—H3119.7N2—C11—C10123.04 (16)
C4—C3—H3119.7N2—C11—H11118.5
C13—C4—C3118.54 (17)C10—C11—H11118.5
C13—C4—C5121.21 (16)N2—C12—C8124.23 (16)
C3—C4—C5120.21 (16)N2—C12—C13116.16 (15)
O2—C5—N3109.01 (14)C8—C12—C13119.61 (15)
O2—C5—C4109.09 (14)N1—C13—C4119.09 (16)
N3—C5—C4110.92 (15)N1—C13—C12117.68 (15)
O2—C5—C7112.82 (15)C4—C13—C12123.23 (16)
N3—C5—C7100.76 (13)C1—N1—C13122.99 (17)
C4—C5—C7113.94 (14)C1—N1—H1A118.5
O1—C6—N4125.80 (17)C13—N1—H1A118.5
O1—C6—N3125.70 (16)C11—N2—C12117.26 (16)
N4—C6—N3108.49 (15)C6—N3—C5110.99 (14)
O3—C7—N4112.13 (14)C6—N3—H3A124.5
O3—C7—C8106.15 (13)C5—N3—H3A124.5
N4—C7—C8111.12 (14)C6—N4—C7112.54 (15)
O3—C7—C5112.10 (14)C6—N4—H4123.7
N4—C7—C5100.35 (13)C7—N4—H4123.7
C8—C7—C5115.14 (14)C5—O2—H2A109.5
C9—C8—C12116.98 (16)C7—O3—H3B109.5
C9—C8—C7120.98 (15)
N1—C1—C2—C30.5 (3)C9—C8—C12—N21.3 (3)
C1—C2—C3—C42.3 (3)C7—C8—C12—N2179.10 (16)
C2—C3—C4—C13−3.4 (3)C9—C8—C12—C13−179.17 (16)
C2—C3—C4—C5178.93 (18)C7—C8—C12—C13−1.4 (2)
C13—C4—C5—O2−110.16 (18)C3—C4—C13—N11.7 (3)
C3—C4—C5—O267.4 (2)C5—C4—C13—N1179.35 (15)
C13—C4—C5—N3129.75 (17)C3—C4—C13—C12−177.36 (17)
C3—C4—C5—N3−52.7 (2)C5—C4—C13—C120.3 (3)
C13—C4—C5—C716.9 (2)N2—C12—C13—N1−8.7 (2)
C3—C4—C5—C7−165.51 (16)C8—C12—C13—N1171.79 (15)
O2—C5—C7—O3−21.6 (2)N2—C12—C13—C4170.44 (16)
N3—C5—C7—O394.51 (16)C8—C12—C13—C4−9.1 (3)
C4—C5—C7—O3−146.68 (15)C2—C1—N1—C13−2.3 (3)
O2—C5—C7—N4−140.73 (14)C4—C13—N1—C11.1 (3)
N3—C5—C7—N4−24.66 (16)C12—C13—N1—C1−179.75 (17)
C4—C5—C7—N494.16 (16)C10—C11—N2—C12−0.7 (3)
O2—C5—C7—C899.91 (17)C8—C12—N2—C11−0.6 (3)
N3—C5—C7—C8−144.01 (14)C13—C12—N2—C11179.89 (16)
C4—C5—C7—C8−25.2 (2)O1—C6—N3—C5167.40 (17)
O3—C7—C8—C9−39.1 (2)N4—C6—N3—C5−12.0 (2)
N4—C7—C8—C983.02 (19)O2—C5—N3—C6142.10 (15)
C5—C7—C8—C9−163.78 (16)C4—C5—N3—C6−97.76 (17)
O3—C7—C8—C12143.18 (16)C7—C5—N3—C623.22 (18)
N4—C7—C8—C12−94.67 (19)O1—C6—N4—C7173.90 (17)
C5—C7—C8—C1218.5 (2)N3—C6—N4—C7−6.7 (2)
C12—C8—C9—C10−0.8 (3)O3—C7—N4—C6−98.97 (17)
C7—C8—C9—C10−178.56 (16)C8—C7—N4—C6142.41 (15)
C8—C9—C10—C11−0.4 (3)C5—C7—N4—C620.17 (17)
C9—C10—C11—N21.2 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···Cl1i0.862.413.1512 (17)145
N3—H3A···O2ii0.862.653.146 (2)118
N4—H4···Cl1iii0.862.503.2490 (16)147
O2—H2A···Cl10.822.283.0712 (15)163
O3—H3B···O1iv0.821.892.6867 (18)165

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2573).

References

  • Bruker, (2005). APEX2, SAINT and SADABS Bruker AXS, Inc., Madison, Wisconsin, USA.
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Zhao, Y. J., Xue, S. F., Zhu, Q. J., Tao, Z., Zhang, J. X., Wei, Z. B., Long, L. S., Hu, M. L., Xiao, H. P. & Day, A. I. (2004). Chin. Sci. Bull.49, 1111–1116.
  • Zheng, L. M., Zhu, J. N., Zhang, Y. Q., Tao, Z., Xue, S. F., Zhu, Q. J., Wei, Z. B. & Long, L. S. (2005). Chin. J. Inorg. Chem.21, 1583–1588.

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