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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): o290.
Published online 2007 December 18. doi:  10.1107/S1600536807066172
PMCID: PMC2915341

5,6-Dioxo-1,10-phenanthrolin-1-ium nitrate

Abstract

In the title salt, C12H7N2O2 +·NO3 , the monoprotonated cation is connected to the nitrate anion by a hydrogen bond. Weak C—H(...)O hydrogen bonds hold the planar cations together in a layer structure.

Related literature

For related literature, see Fujihara et al. (2004 [triangle]); Larsson & Ohström (2004 [triangle]). For the bromide salt, see: Bomfim et al. (2003 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o290-scheme1.jpg

Experimental

Crystal data

  • C12H7N2O2 +·NO3
  • M r = 273.21
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o290-efi1.jpg
  • a = 14.4860 (19) Å
  • b = 12.5177 (13) Å
  • c = 13.4535 (16) Å
  • β = 101.720 (12)°
  • V = 2388.7 (5) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.12 mm−1
  • T = 290 (2) K
  • 0.30 × 0.10 × 0.08 mm

Data collection

  • Oxford Diffraction Xcalibur 3 CCD diffractometer
  • Absorption correction: numerical (X-RED; Stoe & Cie, 1997 [triangle]) T min = 0.960, T max = 0.989
  • 7311 measured reflections
  • 2095 independent reflections
  • 635 reflections with I > 2σ(I)
  • R int = 0.068

Refinement

  • R[F 2 > 2σ(F 2)] = 0.038
  • wR(F 2) = 0.060
  • S = 0.83
  • 2095 reflections
  • 182 parameters
  • H-atom parameters constrained
  • Δρmax = 0.31 e Å−3
  • Δρmin = −0.14 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2003 [triangle]); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2003 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 [triangle]); molecular graphics: DIAMOND (Brandenburg, 2001 [triangle]); software used to prepare material for publication: PLATON (Spek, 2003 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536807066172/ng2405sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807066172/ng2405Isup2.hkl

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

Acknowledgments

This work was supported by grants from the University of Tehran and the Swedish Research Council. The authors are grateful to Professor Magnus Sandström for his support.

supplementary crystallographic information

Comment

From a survey of the Cambridge Structural Database [version 5.28, updated Jan. 2007], we found two complexes containing O-protonated pdon (Fujihara, et al., 2004; Larsson, & Ohström, 2004). However, up to now, only one molecule is reported for the N-protonated pdon (C12H7N2O2+, Hpdon) with bromide ions as counter ion (Bomfim et al., 2003).

The molecular structure and atom-labeling scheme for (I) are shown in Fig. 1. There is a relatively strong hydrogen bond between the nitrate ion and to the protonated nitrogen atom in Hpdon (N1—H1···O5, 2.703 (4) Å). Weak C–H···O hydrogen bonds hold the approximately planar cations together in a layer structure (Fig. 2). The packing of the layers is similar to that in the bromide salt of Hpdon (Bomfim et al., 2003) without specific directional interactions between the layers. Ring A (C1–C5/N1), B (C6–C10/N2) and C (C1/C2/C12/C11/C7/C6) in the cation (C12H7N2O2+, Hpdon) is approximately planar. The interplanar angle between the least-square planes defined by ring A and two other rings, B and C, are 1.69 (5)° and 1.17 (5)°, respectively. While, rings B and C are almost planar, 0.52 (5)°. However, the C—N—C angle is affected by protonation and causes to increase from 116.6 (3)° to 122.7 (3)° in the rings B and A, respectively. Similar effect has also been shown in the previously reported Hpdon bromide by increasing from 116.8 (3)° to 123.2 (3)° for the corresponding values. The comparison of the torsion angle, O1—C12—C11—O2, 2.5 (6)°, in (I) with the molecular pdon indicates that the N-protonation in (I) doesn't significantly affect on dione groups.

Experimental

The title compound was obtained during the reaction of thorium nitrate, Th(NO3)4.5H2O (Merck, 99%), and 1,10-phenanthroline-5,6-dione (Aldrich, 97%) in ethanolic solution. Pale-yellow crystals of Hpdon were taken from the obtained greenish precipitates. The presence of water in the ethanolic solution and the high basicity of dione ligand can be the reason for the protonation, providing the C12H7N2O2+, Hpdon cation. Thin fragile layer crystals were obtained by recrystallization from acetonitrile.

Refinement

All H atoms were geometrically positioned and constrained to ride on their parent atoms, with Uiso(H) = 1.2 times Ueq(C,N).

Figures

Fig. 1.
Molecular structure of (I), with 50% probability displacement ellipsoids. H atoms are shown as circles of arbitrary radii.
Fig. 2.
Packing view for (I), showing the hydrogen bonds as dashed lines.

Crystal data

C12H7N2O2+·NO3F000 = 1120
Mr = 273.21Dx = 1.519 Mg m3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 7311 reflections
a = 14.4860 (19) Åθ = 3.5–25.0º
b = 12.5177 (13) ŵ = 0.12 mm1
c = 13.4535 (16) ÅT = 290 (2) K
β = 101.720 (12)ºNeedle, pale-yellow
V = 2388.7 (5) Å30.30 × 0.10 × 0.08 mm
Z = 8

Data collection

Oxford Diffraction Xcalibur 3 CCD diffractometer2095 independent reflections
Radiation source: fine-focus sealed tube635 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.068
Detector resolution: 12 pixels mm-1θmax = 25.0º
T = 290(2) Kθmin = 3.8º
ω–scans at different [var phi]h = −17→17
Absorption correction: numerical(X-RED; Stoe & Cie, 1997)k = −14→14
Tmin = 0.960, Tmax = 0.989l = −10→15
7311 measured reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.038  w = 1/[σ2(Fo2) + (0.01P)2] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.060(Δ/σ)max < 0.001
S = 0.83Δρmax = 0.31 e Å3
2095 reflectionsΔρmin = −0.14 e Å3
182 parametersExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.00072 (4)
Secondary atom site location: difference Fourier map

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
O10.85417 (17)−0.13522 (19)0.12439 (18)0.0673 (8)
O20.85003 (19)0.08376 (19)0.1238 (2)0.0834 (10)
O30.30299 (14)0.0377 (2)0.07097 (16)0.0649 (7)
O40.22236 (15)−0.03456 (19)0.17219 (15)0.0613 (6)
O50.34903 (16)−0.11186 (18)0.14632 (16)0.0622 (7)
N10.52797 (19)−0.1426 (2)0.12265 (18)0.0439 (9)
H10.4776−0.10630.12300.053*
N20.5205 (2)0.0692 (2)0.1274 (2)0.0488 (9)
N30.29121 (19)−0.0361 (3)0.1292 (2)0.0476 (8)
C10.6089 (3)−0.0896 (3)0.1224 (2)0.0370 (9)
C20.6903 (3)−0.1473 (3)0.1211 (2)0.0374 (10)
C30.6870 (3)−0.2573 (3)0.1201 (2)0.0528 (11)
H30.7411−0.29690.11910.063*
C40.6018 (3)−0.3086 (3)0.1207 (2)0.0550 (11)
H40.5986−0.38280.11980.066*
C50.5228 (3)−0.2490 (3)0.1224 (2)0.0502 (11)
H50.4657−0.28260.12350.060*
C60.6062 (3)0.0275 (3)0.1258 (2)0.0380 (9)
C70.6867 (3)0.0879 (3)0.1278 (2)0.0421 (10)
C80.6798 (3)0.1978 (3)0.1312 (2)0.0534 (13)
H80.73200.24110.13190.064*
C90.5922 (3)0.2415 (3)0.1336 (2)0.0589 (12)
H90.58520.31510.13690.071*
C100.5151 (3)0.1749 (3)0.1308 (3)0.0589 (13)
H100.45680.20580.13140.071*
C110.7780 (3)0.0351 (4)0.1244 (2)0.0526 (10)
C120.7807 (3)−0.0894 (3)0.1227 (2)0.0469 (11)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0405 (19)0.064 (2)0.102 (2)0.0165 (15)0.0270 (16)0.0046 (15)
O20.051 (2)0.062 (2)0.146 (2)−0.0150 (16)0.0412 (18)−0.0002 (17)
O30.0736 (19)0.0573 (18)0.0696 (16)0.0079 (15)0.0282 (13)0.0205 (15)
O40.0508 (18)0.0664 (15)0.0730 (16)0.0081 (16)0.0276 (13)0.0048 (14)
O50.0453 (17)0.0477 (18)0.0977 (18)0.0163 (14)0.0242 (14)0.0116 (15)
N10.036 (2)0.038 (2)0.0605 (19)0.0038 (18)0.0143 (17)0.0013 (19)
N20.054 (2)0.035 (2)0.0620 (19)0.0086 (17)0.0214 (18)−0.0027 (17)
N30.041 (2)0.051 (2)0.053 (2)−0.005 (2)0.0144 (17)−0.001 (2)
C10.034 (3)0.038 (3)0.041 (2)−0.007 (2)0.012 (2)−0.003 (2)
C20.037 (3)0.033 (3)0.044 (2)0.008 (2)0.011 (2)0.006 (2)
C30.056 (3)0.043 (3)0.065 (3)0.009 (3)0.023 (2)0.002 (2)
C40.067 (4)0.034 (3)0.066 (3)0.001 (3)0.020 (2)0.004 (2)
C50.050 (3)0.035 (3)0.068 (3)−0.007 (2)0.017 (2)0.000 (2)
C60.037 (3)0.035 (3)0.042 (2)−0.001 (3)0.0093 (19)−0.010 (3)
C70.038 (3)0.036 (3)0.053 (2)0.002 (2)0.011 (2)0.002 (2)
C80.060 (4)0.030 (3)0.070 (3)−0.005 (2)0.012 (2)0.003 (2)
C90.073 (4)0.037 (3)0.065 (3)0.015 (3)0.010 (3)−0.001 (2)
C100.058 (4)0.045 (3)0.075 (3)0.005 (2)0.016 (3)−0.003 (2)
C110.052 (3)0.051 (3)0.059 (2)−0.002 (3)0.021 (2)0.001 (3)
C120.050 (3)0.048 (3)0.046 (2)0.000 (3)0.018 (2)−0.002 (2)

Geometric parameters (Å, °)

O1—C121.206 (4)C3—C41.392 (4)
O2—C111.210 (3)C3—H30.9300
O3—N31.244 (3)C4—C51.371 (4)
O4—N31.251 (3)C4—H40.9300
O5—N31.256 (3)C5—H50.9300
N1—C51.335 (4)C6—C71.385 (4)
N1—C11.347 (4)C7—C81.381 (4)
N1—H10.8600C7—C111.488 (4)
N2—C101.326 (4)C8—C91.387 (4)
N2—C61.350 (4)C8—H80.9300
C1—C21.387 (4)C9—C101.389 (4)
C1—C61.467 (4)C9—H90.9300
C2—C31.377 (4)C10—H100.9300
C2—C121.492 (4)C11—C121.559 (4)
C5—N1—C1122.7 (3)N2—C6—C7124.1 (4)
C5—N1—H1118.7N2—C6—C1114.7 (4)
C1—N1—H1118.7C7—C6—C1121.2 (4)
C10—N2—C6116.6 (3)C8—C7—C6118.5 (4)
O3—N3—O4120.3 (3)C8—C7—C11120.9 (4)
O3—N3—O5120.3 (3)C6—C7—C11120.5 (4)
O4—N3—O5119.4 (3)C7—C8—C9117.8 (4)
N1—C1—C2119.1 (4)C7—C8—H8121.1
N1—C1—C6117.6 (4)C9—C8—H8121.1
C2—C1—C6123.3 (4)C8—C9—C10119.8 (4)
C3—C2—C1119.5 (4)C8—C9—H9120.1
C3—C2—C12121.0 (4)C10—C9—H9120.1
C1—C2—C12119.5 (4)N2—C10—C9123.1 (4)
C2—C3—C4119.4 (4)N2—C10—H10118.4
C2—C3—H3120.3C9—C10—H10118.4
C4—C3—H3120.3O2—C11—C7123.4 (5)
C5—C4—C3119.6 (4)O2—C11—C12118.6 (4)
C5—C4—H4120.2C7—C11—C12118.0 (4)
C3—C4—H4120.2O1—C12—C2122.5 (4)
N1—C5—C4119.8 (4)O1—C12—C11120.0 (4)
N1—C5—H5120.1C2—C12—C11117.5 (4)
C4—C5—H5120.1
C5—N1—C1—C20.5 (5)N2—C6—C7—C11−179.1 (3)
C5—N1—C1—C6−178.2 (3)C1—C6—C7—C111.2 (5)
N1—C1—C2—C30.0 (5)C6—C7—C8—C90.7 (5)
C6—C1—C2—C3178.6 (3)C11—C7—C8—C9179.5 (3)
N1—C1—C2—C12−178.9 (3)C7—C8—C9—C10−1.0 (5)
C6—C1—C2—C12−0.3 (5)C6—N2—C10—C9−0.5 (5)
C1—C2—C3—C4−0.1 (5)C8—C9—C10—N21.0 (6)
C12—C2—C3—C4178.7 (3)C8—C7—C11—O2−0.4 (5)
C2—C3—C4—C5−0.2 (5)C6—C7—C11—O2178.4 (3)
C1—N1—C5—C4−0.8 (5)C8—C7—C11—C12178.9 (3)
C3—C4—C5—N10.6 (6)C6—C7—C11—C12−2.3 (5)
C10—N2—C6—C70.2 (5)C3—C2—C12—O1−0.9 (5)
C10—N2—C6—C1179.8 (3)C1—C2—C12—O1178.0 (4)
N1—C1—C6—N2−0.9 (5)C3—C2—C12—C11−179.6 (3)
C2—C1—C6—N2−179.5 (3)C1—C2—C12—C11−0.8 (4)
N1—C1—C6—C7178.7 (3)O2—C11—C12—O12.5 (6)
C2—C1—C6—C70.1 (5)C7—C11—C12—O1−176.8 (3)
N2—C6—C7—C8−0.3 (5)O2—C11—C12—C2−178.6 (3)
C1—C6—C7—C8−179.9 (3)C7—C11—C12—C22.1 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O50.861.952.703 (4)145
C8—H8···O5i0.932.483.396 (4)167
C9—H9···O4i0.932.713.359 (5)128
C4—H4···O4ii0.932.613.323 (4)134
C3—H3···O3ii0.932.403.209 (4)146
C10—H10···O1iii0.932.473.318 (5)151
C5—H5···O2iv0.932.373.266 (5)162

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2405).

References

  • Bomfim, J. A. S., Filgueiras, C. A. L., Howie, R. A. & Wardell, J. L. (2003). Acta Cryst. E59, o244–o246.
  • Brandenburg, K. (2001). DIAMOND Version 2.1e. Crystal Impact GbR, Bonn, Germany.
  • Fujihara, T., Wada, T. & Tanaka, K. (2004). Dalton Trans. pp. 645–652. [PubMed]
  • Larsson, K. & Ohström, L. (2004). Inorg. Chim. Acta, 357, 657–664.
  • Oxford Diffraction (2003). CrysAlis CCD and CrysAlis RED Versions 1.171.29.2. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.
  • Sheldrick, G. M. (1997). SHELXS97 and SHELXL97 University of Göttingen, Germany.
  • Spek, A. L. (2003). J. Appl. Cryst.36, 7–13.
  • Stoe & Cie (1997). X-RED Version 1.09. Stoe & Cie GmbH, Darmstadt, Germany.

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