organic compounds
5,6-Dioxo-1,10-phenanthrolin-1-ium nitrate
aSchool of Chemistry, University College of Science, University of Tehran, Tehran, Iran
*Correspondence e-mail: aabbasi@khayam.ut.ac.ir
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); Larsson & Ohström (2004). For the bromide salt, see: Bomfim et al. (2003).
Experimental
Crystal data
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Refinement
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Data collection: CrysAlis CCD (Oxford Diffraction, 2003); cell CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Brandenburg, 2001); software used to prepare material for publication: PLATON (Spek, 2003).
Supporting information
https://doi.org/10.1107/S1600536807066172/ng2405sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807066172/ng2405Isup2.hkl
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.
All H atoms were geometrically positioned and constrained to ride on their parent atoms, with Uiso(H) = 1.2 times Ueq(C,N).
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.
For related literature, see Fujihara et al. (2004); Larsson & Ohström (2004). For the bromide salt, see: Bomfim et al. (2003).
Data collection: CrysAlis CCD (Oxford Diffraction, 2003); cell
CrysAlis CCD (Oxford Diffraction, 2003); data reduction: CrysAlis RED (Oxford Diffraction, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: DIAMOND (Brandenburg, 2001); software used to prepare material for publication: PLATON (Spek, 2003).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. |
C12H7N2O2+·NO3− | F(000) = 1120 |
Mr = 273.21 | Dx = 1.519 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 7311 reflections |
a = 14.4860 (19) Å | θ = 3.5–25.0° |
b = 12.5177 (13) Å | µ = 0.12 mm−1 |
c = 13.4535 (16) Å | T = 290 K |
β = 101.720 (12)° | Needle, pale-yellow |
V = 2388.7 (5) Å3 | 0.30 × 0.10 × 0.08 mm |
Z = 8 |
Oxford Diffraction Xcalibur 3 CCD diffractometer | 2095 independent reflections |
Radiation source: fine-focus sealed tube | 635 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.068 |
Detector resolution: 12 pixels mm-1 | θmax = 25.0°, θmin = 3.8° |
ω–scans at different φ | h = −17→17 |
Absorption correction: numerical (X-RED; Stoe & Cie, 1997) | k = −14→14 |
Tmin = 0.960, Tmax = 0.989 | l = −10→15 |
7311 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.038 | H-atom parameters constrained |
wR(F2) = 0.060 | w = 1/[σ2(Fo2) + (0.01P)2] where P = (Fo2 + 2Fc2)/3 |
S = 0.83 | (Δ/σ)max < 0.001 |
2095 reflections | Δρmax = 0.31 e Å−3 |
182 parameters | Δρmin = −0.14 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.00072 (4) |
C12H7N2O2+·NO3− | V = 2388.7 (5) Å3 |
Mr = 273.21 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 14.4860 (19) Å | µ = 0.12 mm−1 |
b = 12.5177 (13) Å | T = 290 K |
c = 13.4535 (16) Å | 0.30 × 0.10 × 0.08 mm |
β = 101.720 (12)° |
Oxford Diffraction Xcalibur 3 CCD diffractometer | 2095 independent reflections |
Absorption correction: numerical (X-RED; Stoe & Cie, 1997) | 635 reflections with I > 2σ(I) |
Tmin = 0.960, Tmax = 0.989 | Rint = 0.068 |
7311 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.060 | H-atom parameters constrained |
S = 0.83 | Δρmax = 0.31 e Å−3 |
2095 reflections | Δρmin = −0.14 e Å−3 |
182 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.85417 (17) | −0.13522 (19) | 0.12439 (18) | 0.0673 (8) | |
O2 | 0.85003 (19) | 0.08376 (19) | 0.1238 (2) | 0.0834 (10) | |
O3 | 0.30299 (14) | 0.0377 (2) | 0.07097 (16) | 0.0649 (7) | |
O4 | 0.22236 (15) | −0.03456 (19) | 0.17219 (15) | 0.0613 (6) | |
O5 | 0.34903 (16) | −0.11186 (18) | 0.14632 (16) | 0.0622 (7) | |
N1 | 0.52797 (19) | −0.1426 (2) | 0.12265 (18) | 0.0439 (9) | |
H1 | 0.4776 | −0.1063 | 0.1230 | 0.053* | |
N2 | 0.5205 (2) | 0.0692 (2) | 0.1274 (2) | 0.0488 (9) | |
N3 | 0.29121 (19) | −0.0361 (3) | 0.1292 (2) | 0.0476 (8) | |
C1 | 0.6089 (3) | −0.0896 (3) | 0.1224 (2) | 0.0370 (9) | |
C2 | 0.6903 (3) | −0.1473 (3) | 0.1211 (2) | 0.0374 (10) | |
C3 | 0.6870 (3) | −0.2573 (3) | 0.1201 (2) | 0.0528 (11) | |
H3 | 0.7411 | −0.2969 | 0.1191 | 0.063* | |
C4 | 0.6018 (3) | −0.3086 (3) | 0.1207 (2) | 0.0550 (11) | |
H4 | 0.5986 | −0.3828 | 0.1198 | 0.066* | |
C5 | 0.5228 (3) | −0.2490 (3) | 0.1224 (2) | 0.0502 (11) | |
H5 | 0.4657 | −0.2826 | 0.1235 | 0.060* | |
C6 | 0.6062 (3) | 0.0275 (3) | 0.1258 (2) | 0.0380 (9) | |
C7 | 0.6867 (3) | 0.0879 (3) | 0.1278 (2) | 0.0421 (10) | |
C8 | 0.6798 (3) | 0.1978 (3) | 0.1312 (2) | 0.0534 (13) | |
H8 | 0.7320 | 0.2411 | 0.1319 | 0.064* | |
C9 | 0.5922 (3) | 0.2415 (3) | 0.1336 (2) | 0.0589 (12) | |
H9 | 0.5852 | 0.3151 | 0.1369 | 0.071* | |
C10 | 0.5151 (3) | 0.1749 (3) | 0.1308 (3) | 0.0589 (13) | |
H10 | 0.4568 | 0.2058 | 0.1314 | 0.071* | |
C11 | 0.7780 (3) | 0.0351 (4) | 0.1244 (2) | 0.0526 (10) | |
C12 | 0.7807 (3) | −0.0894 (3) | 0.1227 (2) | 0.0469 (11) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0405 (19) | 0.064 (2) | 0.102 (2) | 0.0165 (15) | 0.0270 (16) | 0.0046 (15) |
O2 | 0.051 (2) | 0.062 (2) | 0.146 (2) | −0.0150 (16) | 0.0412 (18) | −0.0002 (17) |
O3 | 0.0736 (19) | 0.0573 (18) | 0.0696 (16) | 0.0079 (15) | 0.0282 (13) | 0.0205 (15) |
O4 | 0.0508 (18) | 0.0664 (15) | 0.0730 (16) | 0.0081 (16) | 0.0276 (13) | 0.0048 (14) |
O5 | 0.0453 (17) | 0.0477 (18) | 0.0977 (18) | 0.0163 (14) | 0.0242 (14) | 0.0116 (15) |
N1 | 0.036 (2) | 0.038 (2) | 0.0605 (19) | 0.0038 (18) | 0.0143 (17) | 0.0013 (19) |
N2 | 0.054 (2) | 0.035 (2) | 0.0620 (19) | 0.0086 (17) | 0.0214 (18) | −0.0027 (17) |
N3 | 0.041 (2) | 0.051 (2) | 0.053 (2) | −0.005 (2) | 0.0144 (17) | −0.001 (2) |
C1 | 0.034 (3) | 0.038 (3) | 0.041 (2) | −0.007 (2) | 0.012 (2) | −0.003 (2) |
C2 | 0.037 (3) | 0.033 (3) | 0.044 (2) | 0.008 (2) | 0.011 (2) | 0.006 (2) |
C3 | 0.056 (3) | 0.043 (3) | 0.065 (3) | 0.009 (3) | 0.023 (2) | 0.002 (2) |
C4 | 0.067 (4) | 0.034 (3) | 0.066 (3) | 0.001 (3) | 0.020 (2) | 0.004 (2) |
C5 | 0.050 (3) | 0.035 (3) | 0.068 (3) | −0.007 (2) | 0.017 (2) | 0.000 (2) |
C6 | 0.037 (3) | 0.035 (3) | 0.042 (2) | −0.001 (3) | 0.0093 (19) | −0.010 (3) |
C7 | 0.038 (3) | 0.036 (3) | 0.053 (2) | 0.002 (2) | 0.011 (2) | 0.002 (2) |
C8 | 0.060 (4) | 0.030 (3) | 0.070 (3) | −0.005 (2) | 0.012 (2) | 0.003 (2) |
C9 | 0.073 (4) | 0.037 (3) | 0.065 (3) | 0.015 (3) | 0.010 (3) | −0.001 (2) |
C10 | 0.058 (4) | 0.045 (3) | 0.075 (3) | 0.005 (2) | 0.016 (3) | −0.003 (2) |
C11 | 0.052 (3) | 0.051 (3) | 0.059 (2) | −0.002 (3) | 0.021 (2) | 0.001 (3) |
C12 | 0.050 (3) | 0.048 (3) | 0.046 (2) | 0.000 (3) | 0.018 (2) | −0.002 (2) |
O1—C12 | 1.206 (4) | C3—C4 | 1.392 (4) |
O2—C11 | 1.210 (3) | C3—H3 | 0.9300 |
O3—N3 | 1.244 (3) | C4—C5 | 1.371 (4) |
O4—N3 | 1.251 (3) | C4—H4 | 0.9300 |
O5—N3 | 1.256 (3) | C5—H5 | 0.9300 |
N1—C5 | 1.335 (4) | C6—C7 | 1.385 (4) |
N1—C1 | 1.347 (4) | C7—C8 | 1.381 (4) |
N1—H1 | 0.8600 | C7—C11 | 1.488 (4) |
N2—C10 | 1.326 (4) | C8—C9 | 1.387 (4) |
N2—C6 | 1.350 (4) | C8—H8 | 0.9300 |
C1—C2 | 1.387 (4) | C9—C10 | 1.389 (4) |
C1—C6 | 1.467 (4) | C9—H9 | 0.9300 |
C2—C3 | 1.377 (4) | C10—H10 | 0.9300 |
C2—C12 | 1.492 (4) | C11—C12 | 1.559 (4) |
C5—N1—C1 | 122.7 (3) | N2—C6—C7 | 124.1 (4) |
C5—N1—H1 | 118.7 | N2—C6—C1 | 114.7 (4) |
C1—N1—H1 | 118.7 | C7—C6—C1 | 121.2 (4) |
C10—N2—C6 | 116.6 (3) | C8—C7—C6 | 118.5 (4) |
O3—N3—O4 | 120.3 (3) | C8—C7—C11 | 120.9 (4) |
O3—N3—O5 | 120.3 (3) | C6—C7—C11 | 120.5 (4) |
O4—N3—O5 | 119.4 (3) | C7—C8—C9 | 117.8 (4) |
N1—C1—C2 | 119.1 (4) | C7—C8—H8 | 121.1 |
N1—C1—C6 | 117.6 (4) | C9—C8—H8 | 121.1 |
C2—C1—C6 | 123.3 (4) | C8—C9—C10 | 119.8 (4) |
C3—C2—C1 | 119.5 (4) | C8—C9—H9 | 120.1 |
C3—C2—C12 | 121.0 (4) | C10—C9—H9 | 120.1 |
C1—C2—C12 | 119.5 (4) | N2—C10—C9 | 123.1 (4) |
C2—C3—C4 | 119.4 (4) | N2—C10—H10 | 118.4 |
C2—C3—H3 | 120.3 | C9—C10—H10 | 118.4 |
C4—C3—H3 | 120.3 | O2—C11—C7 | 123.4 (5) |
C5—C4—C3 | 119.6 (4) | O2—C11—C12 | 118.6 (4) |
C5—C4—H4 | 120.2 | C7—C11—C12 | 118.0 (4) |
C3—C4—H4 | 120.2 | O1—C12—C2 | 122.5 (4) |
N1—C5—C4 | 119.8 (4) | O1—C12—C11 | 120.0 (4) |
N1—C5—H5 | 120.1 | C2—C12—C11 | 117.5 (4) |
C4—C5—H5 | 120.1 | ||
C5—N1—C1—C2 | 0.5 (5) | N2—C6—C7—C11 | −179.1 (3) |
C5—N1—C1—C6 | −178.2 (3) | C1—C6—C7—C11 | 1.2 (5) |
N1—C1—C2—C3 | 0.0 (5) | C6—C7—C8—C9 | 0.7 (5) |
C6—C1—C2—C3 | 178.6 (3) | C11—C7—C8—C9 | 179.5 (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—N2 | 1.0 (6) |
C12—C2—C3—C4 | 178.7 (3) | C8—C7—C11—O2 | −0.4 (5) |
C2—C3—C4—C5 | −0.2 (5) | C6—C7—C11—O2 | 178.4 (3) |
C1—N1—C5—C4 | −0.8 (5) | C8—C7—C11—C12 | 178.9 (3) |
C3—C4—C5—N1 | 0.6 (6) | C6—C7—C11—C12 | −2.3 (5) |
C10—N2—C6—C7 | 0.2 (5) | C3—C2—C12—O1 | −0.9 (5) |
C10—N2—C6—C1 | 179.8 (3) | C1—C2—C12—O1 | 178.0 (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—C7 | 178.7 (3) | O2—C11—C12—O1 | 2.5 (6) |
C2—C1—C6—C7 | 0.1 (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—C2 | 2.1 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O5 | 0.86 | 1.95 | 2.703 (4) | 145 |
C8—H8···O5i | 0.93 | 2.48 | 3.396 (4) | 167 |
C9—H9···O4i | 0.93 | 2.71 | 3.359 (5) | 128 |
C4—H4···O4ii | 0.93 | 2.61 | 3.323 (4) | 134 |
C3—H3···O3ii | 0.93 | 2.40 | 3.209 (4) | 146 |
C10—H10···O1iii | 0.93 | 2.47 | 3.318 (5) | 151 |
C5—H5···O2iv | 0.93 | 2.37 | 3.266 (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. |
Experimental details
Crystal data | |
Chemical formula | C12H7N2O2+·NO3− |
Mr | 273.21 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 290 |
a, b, c (Å) | 14.4860 (19), 12.5177 (13), 13.4535 (16) |
β (°) | 101.720 (12) |
V (Å3) | 2388.7 (5) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.30 × 0.10 × 0.08 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur 3 CCD |
Absorption correction | Numerical (X-RED; Stoe & Cie, 1997) |
Tmin, Tmax | 0.960, 0.989 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7311, 2095, 635 |
Rint | 0.068 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.038, 0.060, 0.83 |
No. of reflections | 2095 |
No. of parameters | 182 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.31, −0.14 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2003), CrysAlis RED (Oxford Diffraction, 2003), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), DIAMOND (Brandenburg, 2001), PLATON (Spek, 2003).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O5 | 0.86 | 1.95 | 2.703 (4) | 145.1 |
C8—H8···O5i | 0.93 | 2.48 | 3.396 (4) | 167.0 |
C9—H9···O4i | 0.93 | 2.71 | 3.359 (5) | 127.9 |
C4—H4···O4ii | 0.93 | 2.61 | 3.323 (4) | 133.9 |
C3—H3···O3ii | 0.93 | 2.40 | 3.209 (4) | 145.8 |
C10—H10···O1iii | 0.93 | 2.47 | 3.318 (5) | 150.9 |
C5—H5···O2iv | 0.93 | 2.37 | 3.266 (5) | 162.0 |
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. |
Acknowledgements
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.
References
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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.