The title compound, C
12H
7N
2O
2+·Br
− is, to our knowledge, the first reported example of a simple salt of cationic mono-
N-protonated 1,10-phenanthroline-5,6-dione. All of the atoms lie on a crystallographic mirror plane and the cation is therefore totally planar. As a consequence, the compound has a well defined layer structure in which N—H
Br, C—H
Br and C—H
O contacts within the layers interconnect the ionic species.
Supporting information
CCDC reference: 204720
Key indicators
- Single-crystal X-ray study
- T = 120 K
- Mean (C-C) = 0.004 Å
- R factor = 0.029
- wR factor = 0.077
- Data-to-parameter ratio = 13.4
checkCIF results
No syntax errors found
ADDSYM reports no extra symmetry
Alert Level B:
ABSTM_02 Alert B The ratio of expected to reported Tmax/Tmin(RR) is > 1.50
Tmin and Tmax reported: 0.248 0.283
Tmin and Tmax expected: 0.342 0.743
RR = 1.903
Please check that your absorption correction is appropriate.
| Author response: ......
The multi-scan process for correction for absorption, such as that provided
SORTAV and used here, does the best it can and is usually effective.
Sometimes, as here, the values of Tmin and Tmax predicted by the software
differ significantly from those calculated on the basis of the dimensions of
the sample crystal. It is likely that the crystal dimensions, reproduced
in good faith below, are the main contributors to the problem reported.
|
Alert Level C:
PLAT_369 Alert C Long C(sp2)-C(sp2) Bond C(5) - C(6) = 1.54 Ang.
General Notes
ABSTM_02 When printed, the submitted absorption T values will be replaced
by the scaled T values. Since the ratio of scaled T's is
identical to the ratio of reported T values, the scaling does
not imply a change to the absorption corrections used in the
study.
Ratio of Tmax expected/reported 2.623
Tmax scaled 0.743 Tmin scaled 0.651
0 Alert Level A = Potentially serious problem
1 Alert Level B = Potential problem
1 Alert Level C = Please check
The crystals of (I) were obtained as the result of the attempted recrystallization from moist, i.e. not specifically anhydrous, ethanol of the product obtained by reaction, over an extended period in ethanol solution, of dimethyltin dibromide and 1,10-phenanthroline-5,6-dione. The adventitious water has clearly brought about protonation of the intrinsically extremely basic dione ligand to provide the cation, and a degree of hydrolysis of the tin compound to provide the bromide counter-anion.
All H atoms were placed in calculated positions, with C—H and N—H distances of 0.95 and 0.88 Å, respectively, and were refined with a riding model, with Uiso values equal to 1.2Ueq of the non-H atom to which they are attached.
Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 1990).
5,6-Dioxo-1,10-phenanthrolin-1-ium bromide
top
Crystal data top
C12H7N2O2+·Br− | Dx = 1.752 Mg m−3 |
Mr = 291.11 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, Pnma | Cell parameters from 10916 reflections |
a = 14.2379 (3) Å | θ = 2.9–27.5° |
b = 6.2978 (1) Å | µ = 3.71 mm−1 |
c = 12.3110 (3) Å | T = 120 K |
V = 1103.90 (4) Å3 | Block, orange |
Z = 4 | 0.30 × 0.28 × 0.08 mm |
F(000) = 576 | |
Data collection top
Enraf-Nonius KappaCCD area-detector diffractometer | 1376 independent reflections |
Radiation source: Enraf Nonius FR591 rotating anode | 1259 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.052 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.3° |
ϕ and ω scans | h = −18→18 |
Absorption correction: multi-scan (SORTAV; Blessing, 1995, 1997) | k = −8→8 |
Tmin = 0.248, Tmax = 0.283 | l = −15→15 |
15272 measured reflections | |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.029 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.077 | H-atom parameters constrained |
S = 1.11 | w = 1/[σ2(Fo2) + (0.0421P)2 + 0.8806P] where P = (Fo2 + 2Fc2)/3 |
1376 reflections | (Δ/σ)max < 0.001 |
103 parameters | Δρmax = 0.69 e Å−3 |
0 restraints | Δρmin = −0.59 e Å−3 |
Crystal data top
C12H7N2O2+·Br− | V = 1103.90 (4) Å3 |
Mr = 291.11 | Z = 4 |
Orthorhombic, Pnma | Mo Kα radiation |
a = 14.2379 (3) Å | µ = 3.71 mm−1 |
b = 6.2978 (1) Å | T = 120 K |
c = 12.3110 (3) Å | 0.30 × 0.28 × 0.08 mm |
Data collection top
Enraf-Nonius KappaCCD area-detector diffractometer | 1376 independent reflections |
Absorption correction: multi-scan (SORTAV; Blessing, 1995, 1997) | 1259 reflections with I > 2σ(I) |
Tmin = 0.248, Tmax = 0.283 | Rint = 0.052 |
15272 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.029 | 0 restraints |
wR(F2) = 0.077 | H-atom parameters constrained |
S = 1.11 | Δρmax = 0.69 e Å−3 |
1376 reflections | Δρmin = −0.59 e Å−3 |
103 parameters | |
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 | x | y | z | Uiso*/Ueq | |
Br1 | 0.28493 (2) | 0.2500 | 0.51188 (2) | 0.02273 (13) | |
O1 | 0.33230 (16) | 0.2500 | −0.12867 (18) | 0.0322 (5) | |
O2 | 0.35374 (17) | 0.2500 | 0.09181 (19) | 0.0397 (6) | |
N1 | 0.00332 (17) | 0.2500 | −0.0857 (2) | 0.0201 (5) | |
H1N | −0.0445 | 0.2500 | −0.0404 | 0.024* | |
N2 | 0.02030 (18) | 0.2500 | 0.1310 (2) | 0.0229 (5) | |
C1 | −0.0144 (2) | 0.2500 | −0.1923 (2) | 0.0250 (6) | |
H1 | −0.0775 | 0.2500 | −0.2175 | 0.030* | |
C2 | 0.0585 (2) | 0.2500 | −0.2656 (2) | 0.0272 (7) | |
H2 | 0.0465 | 0.2500 | −0.3415 | 0.033* | |
C3 | 0.1499 (2) | 0.2500 | −0.2268 (2) | 0.0246 (6) | |
H3 | 0.2012 | 0.2500 | −0.2761 | 0.030* | |
C4 | 0.1664 (2) | 0.2500 | −0.1149 (2) | 0.0208 (6) | |
C5 | 0.2640 (2) | 0.2500 | −0.0705 (2) | 0.0236 (6) | |
C6 | 0.2757 (2) | 0.2500 | 0.0540 (3) | 0.0258 (7) | |
C7 | 0.1897 (2) | 0.2500 | 0.1221 (2) | 0.0215 (6) | |
C8 | 0.1952 (2) | 0.2500 | 0.2350 (2) | 0.0256 (7) | |
H8 | 0.2545 | 0.2500 | 0.2704 | 0.031* | |
C9 | 0.1131 (2) | 0.2500 | 0.2946 (2) | 0.0276 (7) | |
H9 | 0.1150 | 0.2500 | 0.3718 | 0.033* | |
C10 | 0.0275 (2) | 0.2500 | 0.2400 (2) | 0.0263 (7) | |
H10 | −0.0286 | 0.2500 | 0.2817 | 0.032* | |
C11 | 0.1004 (2) | 0.2500 | 0.0749 (2) | 0.0189 (6) | |
C12 | 0.0906 (2) | 0.2500 | −0.0442 (2) | 0.0191 (5) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Br1 | 0.0238 (2) | 0.0269 (2) | 0.01745 (18) | 0.000 | −0.00096 (10) | 0.000 |
O1 | 0.0252 (12) | 0.0466 (14) | 0.0247 (11) | 0.000 | 0.0065 (9) | 0.000 |
O2 | 0.0241 (12) | 0.0686 (18) | 0.0263 (12) | 0.000 | −0.0046 (10) | 0.000 |
N1 | 0.0218 (12) | 0.0208 (12) | 0.0176 (11) | 0.000 | 0.0003 (9) | 0.000 |
N2 | 0.0264 (13) | 0.0248 (13) | 0.0175 (12) | 0.000 | 0.0040 (10) | 0.000 |
C1 | 0.0295 (16) | 0.0244 (15) | 0.0210 (14) | 0.000 | −0.0081 (12) | 0.000 |
C2 | 0.0385 (19) | 0.0288 (16) | 0.0143 (13) | 0.000 | −0.0057 (12) | 0.000 |
C3 | 0.0316 (16) | 0.0257 (15) | 0.0165 (14) | 0.000 | 0.0025 (12) | 0.000 |
C4 | 0.0232 (15) | 0.0223 (14) | 0.0169 (13) | 0.000 | 0.0003 (11) | 0.000 |
C5 | 0.0240 (15) | 0.0286 (15) | 0.0184 (14) | 0.000 | 0.0023 (11) | 0.000 |
C6 | 0.0222 (15) | 0.0345 (17) | 0.0208 (15) | 0.000 | −0.0013 (11) | 0.000 |
C7 | 0.0256 (14) | 0.0228 (14) | 0.0160 (13) | 0.000 | −0.0007 (11) | 0.000 |
C8 | 0.0304 (17) | 0.0276 (16) | 0.0187 (15) | 0.000 | −0.0042 (11) | 0.000 |
C9 | 0.0413 (18) | 0.0279 (15) | 0.0136 (13) | 0.000 | 0.0001 (12) | 0.000 |
C10 | 0.0350 (18) | 0.0264 (15) | 0.0174 (14) | 0.000 | 0.0075 (12) | 0.000 |
C11 | 0.0238 (14) | 0.0179 (13) | 0.0151 (12) | 0.000 | 0.0005 (10) | 0.000 |
C12 | 0.0229 (14) | 0.0179 (13) | 0.0165 (12) | 0.000 | −0.0022 (11) | 0.000 |
Geometric parameters (Å, º) top
O1—C5 | 1.208 (4) | C4—C12 | 1.386 (4) |
O2—C6 | 1.205 (4) | C4—C5 | 1.493 (4) |
N1—C1 | 1.337 (4) | C5—C6 | 1.542 (4) |
N1—C12 | 1.344 (4) | C6—C7 | 1.485 (4) |
N1—H1N | 0.8800 | C7—C8 | 1.392 (4) |
N2—C11 | 1.334 (4) | C7—C11 | 1.397 (4) |
N2—C10 | 1.345 (4) | C8—C9 | 1.381 (5) |
C1—C2 | 1.376 (5) | C8—H8 | 0.9500 |
C1—H1 | 0.9500 | C9—C10 | 1.392 (5) |
C2—C3 | 1.386 (5) | C9—H9 | 0.9500 |
C2—H2 | 0.9500 | C10—H10 | 0.9500 |
C3—C4 | 1.397 (4) | C11—C12 | 1.473 (4) |
C3—H3 | 0.9500 | | |
| | | |
C1—N1—C12 | 123.2 (3) | O2—C6—C5 | 119.0 (3) |
C1—N1—H1N | 118.4 | C7—C6—C5 | 118.2 (2) |
C12—N1—H1N | 118.4 | C8—C7—C11 | 117.9 (3) |
C11—N2—C10 | 116.8 (3) | C8—C7—C6 | 121.1 (3) |
N1—C1—C2 | 120.1 (3) | C11—C7—C6 | 121.0 (3) |
N1—C1—H1 | 120.0 | C9—C8—C7 | 118.8 (3) |
C2—C1—H1 | 120.0 | C9—C8—H8 | 120.6 |
C1—C2—C3 | 118.9 (3) | C7—C8—H8 | 120.6 |
C1—C2—H2 | 120.6 | C8—C9—C10 | 119.0 (3) |
C3—C2—H2 | 120.6 | C8—C9—H9 | 120.5 |
C2—C3—C4 | 119.8 (3) | C10—C9—H9 | 120.5 |
C2—C3—H3 | 120.1 | N2—C10—C9 | 123.3 (3) |
C4—C3—H3 | 120.1 | N2—C10—H10 | 118.3 |
C12—C4—C3 | 119.2 (3) | C9—C10—H10 | 118.3 |
C12—C4—C5 | 119.6 (3) | N2—C11—C7 | 124.2 (3) |
C3—C4—C5 | 121.1 (3) | N2—C11—C12 | 115.8 (2) |
O1—C5—C4 | 122.2 (3) | C7—C11—C12 | 120.0 (3) |
O1—C5—C6 | 120.1 (3) | N1—C12—C4 | 118.8 (3) |
C4—C5—C6 | 117.7 (2) | N1—C12—C11 | 117.8 (2) |
O2—C6—C7 | 122.8 (3) | C4—C12—C11 | 123.5 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···Br1i | 0.88 | 2.45 | 3.239 (2) | 149 |
C1—H1···O1ii | 0.95 | 2.29 | 3.102 (4) | 143 |
C3—H3···Br1iii | 0.95 | 2.87 | 3.748 (3) | 154 |
C10—H10···O2i | 0.95 | 2.29 | 3.227 (4) | 170 |
C8—H8···Br1 | 0.95 | 3.00 | 3.640 (3) | 126 |
C9—H9···Br1 | 0.95 | 2.97 | 3.625 (3) | 127 |
Symmetry codes: (i) x−1/2, −y+1/2, −z+1/2; (ii) x−1/2, −y+1/2, −z−1/2; (iii) x, y, z−1. |
Experimental details
Crystal data |
Chemical formula | C12H7N2O2+·Br− |
Mr | 291.11 |
Crystal system, space group | Orthorhombic, Pnma |
Temperature (K) | 120 |
a, b, c (Å) | 14.2379 (3), 6.2978 (1), 12.3110 (3) |
V (Å3) | 1103.90 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 3.71 |
Crystal size (mm) | 0.30 × 0.28 × 0.08 |
|
Data collection |
Diffractometer | Enraf-Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SORTAV; Blessing, 1995, 1997) |
Tmin, Tmax | 0.248, 0.283 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 15272, 1376, 1259 |
Rint | 0.052 |
(sin θ/λ)max (Å−1) | 0.649 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.029, 0.077, 1.11 |
No. of reflections | 1376 |
No. of parameters | 103 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.69, −0.59 |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···Br1i | 0.88 | 2.45 | 3.239 (2) | 149 |
C1—H1···O1ii | 0.95 | 2.29 | 3.102 (4) | 143 |
C3—H3···Br1iii | 0.95 | 2.87 | 3.748 (3) | 154 |
C10—H10···O2i | 0.95 | 2.29 | 3.227 (4) | 170 |
C8—H8···Br1 | 0.95 | 3.00 | 3.640 (3) | 126 |
C9—H9···Br1 | 0.95 | 2.97 | 3.625 (3) | 127 |
Symmetry codes: (i) x−1/2, −y+1/2, −z+1/2; (ii) x−1/2, −y+1/2, −z−1/2; (iii) x, y, z−1. |
Bond distances and angles (Å, °) in the Hpdon cation of (I) and molecular pdon top | Hpdona | pdonb | |
| | Molecule 1 | Molecule 2 |
C12—N1 | 1.344 (4) | 1.343 (3) | 1.339 (3) |
N1—C1 | 1.337 (4) | 1.336 (3) | 1.336 (3) |
C1—C2 | 1.376 (5) | 1.379 (4) | 1.369 (4) |
C2—C3 | 1.386 (5) | 1.370 (4) | 1.371 (4) |
C3—C4 | 1.397 (4) | 1.391 (4) | 1.385 (4) |
C4—C5 | 1.493 (4) | 1.476 (4) | 1.477 (4) |
C4—C12 | 1.386 (4) | 1.395 (4) | 1.402 (3) |
C5—C6 | 1.542 (4) | 1.529 (4) | 1.539 (4) |
C5—O1 | 1.208 (4) | 1.214 (3) | 1.207 (3) |
C6—C7 | 1.485 (4) | 1.476 (4) | 1.469 (4) |
C6—O2 | 1.205 (4) | 1.208 (3) | 1.209 (3) |
C7—C8 | 1.392 (4) | 1.391 (4) | 1.389 (4) |
C7—C11 | 1.397 (4) | 1.401 (3) | 1.393 (4) |
C8—C9 | 1.381 (5) | 1.371 (4) | 1.365 (4) |
C9—C10 | 1.392 (5) | 1.369 (4) | 1.376 (4) |
C10—N2 | 1.345 (4) | 1.339 (3) | 1.338 (3) |
N2—C11 | 1.334 (4) | 1.339 (3) | 1.343 (3) |
C11—C12 | 1.473 (4) | 1.489 (4) | 1.494 (3) |
C12—N1—C1c | 123.2 (3) | 116.7 (2) | 116.7 (2) |
N1—C1—C2c | 120.1 (3) | 125.0 (2) | 125.2 (3) |
C1—C2—C3 | 118.9 (3) | 118.0 (3) | 117.9 (3) |
C2—C3—C4 | 119.8 (3) | 118.8 (3) | 119.3 (2) |
C3—C4—C5 | 121.1 (3) | 123.1 (3) | 120.2 (2) |
C3—C4—C12 | 119.2 (3) | 119.2 (2) | 118.6 (2) |
C5—C4—C12 | 119.6 (3) | 120.8 (2) | 121.2 (2) |
C4—C5—C6 | 117.7 (2) | 118.1 (2) | 117.9 (2) |
C4—C5—O1 | 122.2 (3) | 123.1 (3) | 123.0 (2) |
C6—C5—O1 | 120.1 (3) | 118.8 (2) | 119.1 (2) |
C5—C6—C7 | 118.2 (2) | 118.2 (2) | 117.9 (2) |
C5—C6—O2 | 119.0 (3) | 119.5 (2) | 118.9 (2) |
C7—C6—O2 | 122.8 (3) | 122.3 (2) | 123.3 (3) |
C6—C7—C8 | 121.1 (3) | 120.0 (2) | 119.4 (2) |
C6—C7—C11 | 121.0 (3) | 121.0 (2) | 121.8 (2) |
C8—C7—C11 | 117.9 (3) | 119.0 (2) | 118.9 (2) |
C7—C8—C9 | 118.8 (3) | 118.6 (2) | 119.3 (3) |
C8—C9—C10 | 119.0 (3) | 118.5 (3) | 118.3 (3) |
C9—C10—N2 | 123.3 (3) | 124.7 (3) | 124.2 (2) |
C10—N2—C11 | 116.8 (3) | 117.0 (2) | 117.3 (2) |
N2—C11—C12 | 115.8 (2) | 117.4 (2) | 117.3 (2) |
N2—C11—C7 | 124.2 (3) | 122.1 (2) | 122.1 (2) |
C12—C11—C7 | 120.0 (3) | 120.6 (2) | 120.6 (2) |
C11—C12—N1 | 117.8 (2) | 116.6 (2) | 117.0 (2) |
C11—C12—C4 | 123.5 (3) | 121.2 (2) | 120.6 (2) |
N1—C12—C4c | 118.8 (3) | 122.2 (2) | 122.4 (2) |
O1—C5—C6—O2 | 0 | 3.4 (4) | -0.6 (4) |
Notes: (q) atom designations as for Hpdon in Fig. 1; (b) values obtained with PLATON (Spek, 1990) from CSD CIF data (MEJWED; Calderazzo et al., 1999); (c) entries showing particularly marked differences between Hpdon and pdon. |
A search of the current issue (Version 24) of the Cambridge Structural Database (Allen, 2002) reveals 144 structures containing the well known 1,10-phenanthroline (C12H8N2, phen) moiety and a further 50 containing the related mono-N-protonated species (C12H9N2+, Hphen). In contrast, only three entries other than that corresponding to the ligand itself (MEJWED; Calderazzo et al., 1999) are found for complexes containing the related 1,10-phenanthroline-5,6-dione (C12H6N2O2, pdon), and none at all for the corresponding N-protonated cation (C12H7N2O2+, Hpdon). This is the basis for the claimed novelty of the structure of the compound, (I), described here, which is simply the Hpdon cation with a bromide counter-anion, i.e (Hpdon)Br, (I).
The asymmetric unit and atom-labelling scheme for (I) are shown in Fig. 1. A l l of the atoms lie on a crystallographic mirror plane. As a consequence, the cation, Hpdon, is completely planar. The comparatively high Ueq values of O1 and O2, ~1.5Ueq of the other non-H atoms of the cation, suggests that the crystallographically induced planarity introduces a degree of simplification into the structural model because the planarity completely precludes displacement of O1 and O2 from the plane of the cation which might relieve any strain caused by intramolecular steric effects. However, the O1—C5—C6—O2 torsion angles of 3.4 (4) and −0.6 (4)° for the unconstrained unprotonated pdon molecules in Table 1 suggest that the displacement is likely to be small and the consequent degree of simplification negligible.
The remaining bond lengths and angles in Table 1 show that protonation to form the cation has no significant effect upon the bond lengths and that the only significant differences in the geometries of Hpdon and pdon are the angles at protonated atom N1 and the adjacent atoms C1 and C12. Comparison of the molecular geometries of the analogous 1,10-phenanthroline species, phen (OPENAN; Nishigaki et al., 1978) and (Hphen)Cl (CUZDIK; Hensen et al., 2000), shows precisely the same effect, which is therefore presumed to be likely to occur in other N-aryl heterocyclic systems.
Because all of the atoms lie on crystallographic mirror planes of the space group Pnma, the constituent ions of (I) are found in well defined layers parallel to (010) (Fig. 2), b/2 [3.14890 (5) Å] apart. As shown in Fig. 2 and Table 2, a variety of N—H···Br, C—H···O and C—H···Br contacts occur within each layer. There are, however, no similar interlayer contacts. The layers, stacked in the direction of b, are related one to the next by the operation of crystallographic centres of symmetry (Fig. 3), in such a way that the cations overlap Br in adjacent layers but not, to any significant extent, one another. That is, there is no π–π interaction between the layers, presumably because the interlayer separation (see above) is too small to accommodate it. Also discernible in Fig. 3 are channels parallel to b, centred on row vectors 1/2,y,0 and 0,y,1/2, which, being unoccupied, account for the void space of 46.7 Å3 per cell, ~4.2%, noted in the checkCIF report.