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Acta Cryst. (2008). E64, o1489    [ doi:10.1107/S160053680802093X ]

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

Y. Huang, M.-H. Chen, Y.-Q. Zhang, S.-F. Xue and Z. Tao

Abstract top

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.

Comment top

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).

Related literature top

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

Experimental top

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 top

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.

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.
3a,11b-Dihydroxy-2-oxo-2,3,3a,11b-tetrahydro-1H- imidazo[4,5-f][1,10]phenanthrolin-7-ium chloride top
Crystal data top
C13H11N4O3+·Cl–F000 = 632
Mr = 306.71Dx = 1.585 Mg m−3
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 mm−1
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 top
Bruker APEXII CCD area-detector
diffractometer		2261 independent reflections
Radiation source: fine-focus sealed tube2094 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.022
T = 293(2) Kθmax = 25.0º
φ 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 top
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 Å−3
190 parametersΔρmin = −0.51 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
C13H11N4O3+·Cl–V = 1285.1 (4) Å3
Mr = 306.71Z = 4
Monoclinic, P21/cMo Kα
a = 7.9420 (13) ŵ = 0.31 mm−1
b = 20.352 (3) ÅT = 293 (2) K
c = 8.2972 (14) Å0.31 × 0.22 × 0.19 mm
β = 106.620 (5)º
Data collection top
Bruker APEXII CCD area-detector
diffractometer		2261 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2005)		2094 reflections with I > 2σ(I)
Tmin = 0.909, Tmax = 0.943Rint = 0.022
13480 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.037190 parameters
wR(F2) = 0.103H-atom parameters constrained
S = 1.05Δρmax = 0.48 e Å−3
2261 reflectionsΔρmin = −0.51 e Å−3
Special details top

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) top
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) top
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, °) top
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, °) top
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.
Table 1
Hydrogen-bond geometry (Å, °) top
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.
references
References top

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.

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.