Abstract
The title molecule, C12H6Cl2N2, is almost planar (the r.m.s. deviation of C atoms is 0.04 Å). The C—N and C—C distances indicate delocalization of the π-electrons in the aromatic fused-ring system.
Related literature
For the synthesis, see: Yamada et al. (1990 ▶). The compound is used for the synthesis of other phenanthroline-like heterocycles; see: Hamilton et al. (2004 ▶); Ohira et al. (2005 ▶); Zong & Thummel (2004 ▶, 2005 ▶).
Experimental
Crystal data
C12H6Cl2N2
M r = 249.09
Orthorhombic,
a = 19.4035 (3) Å
b = 4.4330 (1) Å
c = 11.7695 (2) Å
V = 1012.36 (3) Å3
Z = 4
Mo Kα radiation
μ = 0.61 mm−1
T = 100 K
0.36 × 0.18 × 0.02 mm
Data collection
Bruker SMART APEX diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.811, T max = 0.988
8646 measured reflections
2315 independent reflections
2248 reflections with I > 2σ(I)
R int = 0.022
Refinement
R[F 2 > 2σ(F 2)] = 0.022
wR(F 2) = 0.061
S = 1.02
2315 reflections
145 parameters
1 restraint
H-atom parameters constrained
Δρmax = 0.27 e Å−3
Δρmin = −0.16 e Å−3
Absolute structure: Flack (1983 ▶), 1097 Friedel pairs
Flack parameter: −0.01 (4)
Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: X-SEED (Barbour, 2001 ▶); software used to prepare material for publication: publCIF (Westrip, 2009 ▶).
Supplementary Material
Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809011180/tk2404sup1.cif
Structure factors: contains datablocks I. DOI: 10.1107/S1600536809011180/tk2404Isup2.hkl
Additional supplementary materials: crystallographic information; 3D view; checkCIF report
Acknowledgments
We thank the Organization for the Prohibition of Chemical Weapons and the University of Malaya for supporting this study.
supplementary crystallographic information
Experimental
A mixture of 6,7-dihydro-3H-[1,4]diazepino[1,2,3,4-lmn][1,10]phenanthroline-3,9(5H)-dione (1.7 g, 6.7 mmol) and phosphorus pentachloride (3 g, 14.4 mmol) was reacted in thionyl chloride (20 ml, 170 mmol) for 16 h at room temperature. The thionyl chloride was removed under reduced pressure and the residue was suspended in cold ammonium hydroxide. A light-tan precipitate was formed which was dissolved in hot benzene; crystals were obtained upon recrystallization from benzene (1.1 g 65%)
Refinement
Carbon-bound H-atoms were placed in calculated positions (C—H 0.95 Å) and were included in the refinement in the riding model approximation, with U(H) set to 1.2Ueq(C).
Figures
Fig. 1.
Thermal ellipsoid plot (Barbour, 2001) plot of C12H6Cl2N2 at the 70% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.
Crystal data
| C12H6Cl2N2 | F(000) = 504 |
| Mr = 249.09 | Dx = 1.634 Mg m−3 |
| Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
| Hall symbol: P 2c -2n | Cell parameters from 5870 reflections |
| a = 19.4035 (3) Å | θ = 2.7–28.3° |
| b = 4.4330 (1) Å | µ = 0.61 mm−1 |
| c = 11.7695 (2) Å | T = 100 K |
| V = 1012.36 (3) Å3 | Plate, colourless |
| Z = 4 | 0.36 × 0.18 × 0.02 mm |
Data collection
| Bruker SMART APEX diffractometer | 2315 independent reflections |
| Radiation source: fine-focus sealed tube | 2248 reflections with I > 2σ(I) |
| graphite | Rint = 0.022 |
| ω scans | θmax = 27.5°, θmin = 2.1° |
| Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −25→25 |
| Tmin = 0.811, Tmax = 0.988 | k = −5→5 |
| 8646 measured reflections | l = −15→15 |
Refinement
| 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)] = 0.022 | H-atom parameters constrained |
| wR(F2) = 0.061 | w = 1/[σ2(Fo2) + (0.0436P)2 + 0.147P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.02 | (Δ/σ)max = 0.001 |
| 2315 reflections | Δρmax = 0.27 e Å−3 |
| 145 parameters | Δρmin = −0.16 e Å−3 |
| 1 restraint | Absolute structure: Flack (1983), 1097 Friedel pairs |
| Primary atom site location: structure-invariant direct methods | Flack parameter: −0.01 (4) |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | ||
| Cl1 | 0.027691 (18) | 0.55270 (8) | 0.25010 (3) | 0.01876 (10) | |
| Cl2 | 0.35805 (2) | 0.89704 (8) | 0.45699 (4) | 0.02052 (10) | |
| N1 | 0.11803 (7) | 0.4349 (3) | 0.40752 (11) | 0.0151 (3) | |
| N2 | 0.24727 (7) | 0.5756 (3) | 0.48930 (11) | 0.0153 (3) | |
| C1 | 0.05604 (8) | 0.3672 (3) | 0.37354 (12) | 0.0158 (3) | |
| C2 | 0.01038 (8) | 0.1645 (4) | 0.42492 (13) | 0.0183 (3) | |
| H2 | −0.0341 | 0.1269 | 0.3945 | 0.022* | |
| C3 | 0.03326 (8) | 0.0226 (4) | 0.52172 (14) | 0.0184 (3) | |
| H3 | 0.0046 | −0.1192 | 0.5595 | 0.022* | |
| C4 | 0.09941 (8) | 0.0884 (3) | 0.56464 (14) | 0.0159 (3) | |
| C5 | 0.14049 (8) | 0.2979 (4) | 0.50487 (12) | 0.0150 (3) | |
| C6 | 0.12494 (9) | −0.0487 (3) | 0.66693 (14) | 0.0178 (3) | |
| H6 | 0.0980 | −0.1968 | 0.7048 | 0.021* | |
| C7 | 0.18689 (8) | 0.0307 (4) | 0.70984 (13) | 0.0176 (3) | |
| H7 | 0.2025 | −0.0587 | 0.7785 | 0.021* | |
| C8 | 0.22933 (8) | 0.2478 (3) | 0.65313 (13) | 0.0158 (3) | |
| C9 | 0.20767 (8) | 0.3756 (3) | 0.54864 (13) | 0.0150 (3) | |
| C10 | 0.29315 (8) | 0.3417 (4) | 0.69870 (14) | 0.0189 (3) | |
| H10 | 0.3088 | 0.2647 | 0.7695 | 0.023* | |
| C11 | 0.33217 (9) | 0.5458 (4) | 0.63927 (14) | 0.0195 (3) | |
| H11 | 0.3752 | 0.6152 | 0.6676 | 0.023* | |
| C12 | 0.30611 (7) | 0.6483 (3) | 0.53484 (13) | 0.0164 (3) |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Cl1 | 0.01835 (17) | 0.02130 (17) | 0.01663 (17) | 0.00087 (13) | −0.00441 (14) | −0.00032 (15) |
| Cl2 | 0.01900 (17) | 0.02184 (16) | 0.02072 (17) | −0.00573 (14) | 0.00151 (15) | −0.00218 (15) |
| N1 | 0.0165 (6) | 0.0163 (6) | 0.0124 (6) | 0.0010 (5) | 0.0008 (5) | −0.0019 (5) |
| N2 | 0.0154 (6) | 0.0158 (6) | 0.0146 (6) | 0.0001 (5) | 0.0000 (5) | −0.0014 (4) |
| C1 | 0.0173 (7) | 0.0174 (7) | 0.0126 (7) | 0.0046 (6) | −0.0004 (6) | −0.0028 (5) |
| C2 | 0.0154 (7) | 0.0197 (7) | 0.0199 (8) | 0.0007 (6) | −0.0002 (6) | −0.0062 (6) |
| C3 | 0.0183 (8) | 0.0186 (7) | 0.0182 (8) | −0.0024 (6) | 0.0051 (6) | −0.0023 (6) |
| C4 | 0.0192 (7) | 0.0150 (7) | 0.0136 (7) | 0.0014 (5) | 0.0028 (6) | −0.0030 (5) |
| C5 | 0.0158 (7) | 0.0170 (7) | 0.0121 (6) | 0.0017 (5) | 0.0013 (5) | −0.0018 (6) |
| C6 | 0.0220 (8) | 0.0167 (7) | 0.0146 (7) | 0.0000 (6) | 0.0060 (7) | 0.0008 (6) |
| C7 | 0.0231 (8) | 0.0177 (7) | 0.0122 (6) | 0.0047 (6) | 0.0017 (6) | 0.0004 (6) |
| C8 | 0.0181 (7) | 0.0161 (7) | 0.0132 (7) | 0.0036 (6) | 0.0001 (6) | −0.0022 (5) |
| C9 | 0.0178 (7) | 0.0143 (6) | 0.0130 (7) | 0.0015 (5) | 0.0014 (6) | −0.0027 (6) |
| C10 | 0.0212 (8) | 0.0212 (8) | 0.0145 (7) | 0.0056 (6) | −0.0033 (6) | −0.0020 (6) |
| C11 | 0.0174 (8) | 0.0223 (8) | 0.0187 (8) | 0.0003 (6) | −0.0041 (6) | −0.0052 (6) |
| C12 | 0.0156 (7) | 0.0170 (7) | 0.0166 (7) | −0.0003 (6) | 0.0022 (6) | −0.0030 (6) |
Geometric parameters (Å, °)
| Cl1—C1 | 1.758 (2) | C4—C6 | 1.437 (2) |
| Cl2—C12 | 1.752 (2) | C5—C9 | 1.443 (2) |
| N1—C1 | 1.303 (2) | C6—C7 | 1.350 (2) |
| N1—C5 | 1.368 (2) | C6—H6 | 0.9500 |
| N2—C12 | 1.302 (2) | C7—C8 | 1.432 (2) |
| N2—C9 | 1.365 (2) | C7—H7 | 0.9500 |
| C1—C2 | 1.399 (2) | C8—C10 | 1.412 (2) |
| C2—C3 | 1.375 (2) | C8—C9 | 1.418 (2) |
| C2—H2 | 0.9500 | C10—C11 | 1.372 (2) |
| C3—C4 | 1.410 (2) | C10—H10 | 0.9500 |
| C3—H3 | 0.9500 | C11—C12 | 1.405 (2) |
| C4—C5 | 1.412 (2) | C11—H11 | 0.9500 |
| C1—N1—C5 | 116.68 (13) | C4—C6—H6 | 119.7 |
| C12—N2—C9 | 116.36 (14) | C6—C7—C8 | 120.86 (14) |
| N1—C1—C2 | 126.86 (14) | C6—C7—H7 | 119.6 |
| N1—C1—Cl1 | 115.78 (12) | C8—C7—H7 | 119.6 |
| C2—C1—Cl1 | 117.36 (12) | C10—C8—C9 | 118.15 (14) |
| C3—C2—C1 | 116.59 (14) | C10—C8—C7 | 121.70 (14) |
| C3—C2—H2 | 121.7 | C9—C8—C7 | 120.16 (14) |
| C1—C2—H2 | 121.7 | N2—C9—C8 | 122.43 (14) |
| C2—C3—C4 | 119.74 (15) | N2—C9—C5 | 118.74 (14) |
| C2—C3—H3 | 120.1 | C8—C9—C5 | 118.81 (14) |
| C4—C3—H3 | 120.1 | C11—C10—C8 | 118.99 (15) |
| C3—C4—C5 | 118.14 (15) | C11—C10—H10 | 120.5 |
| C3—C4—C6 | 121.77 (15) | C8—C10—H10 | 120.5 |
| C5—C4—C6 | 120.08 (14) | C10—C11—C12 | 117.45 (15) |
| N1—C5—C4 | 121.97 (14) | C10—C11—H11 | 121.3 |
| N1—C5—C9 | 118.72 (14) | C12—C11—H11 | 121.3 |
| C4—C5—C9 | 119.29 (14) | N2—C12—C11 | 126.57 (15) |
| C7—C6—C4 | 120.66 (15) | N2—C12—Cl2 | 116.43 (12) |
| C7—C6—H6 | 119.7 | C11—C12—Cl2 | 117.00 (12) |
| C5—N1—C1—C2 | −1.3 (2) | C12—N2—C9—C8 | −1.2 (2) |
| C5—N1—C1—Cl1 | 178.60 (10) | C12—N2—C9—C5 | 177.09 (13) |
| N1—C1—C2—C3 | 0.2 (2) | C10—C8—C9—N2 | 2.5 (2) |
| Cl1—C1—C2—C3 | −179.66 (12) | C7—C8—C9—N2 | −177.70 (13) |
| C1—C2—C3—C4 | 0.8 (2) | C10—C8—C9—C5 | −175.77 (13) |
| C2—C3—C4—C5 | −0.8 (2) | C7—C8—C9—C5 | 4.0 (2) |
| C2—C3—C4—C6 | 178.52 (14) | N1—C5—C9—N2 | −2.1 (2) |
| C1—N1—C5—C4 | 1.3 (2) | C4—C5—C9—N2 | 179.17 (13) |
| C1—N1—C5—C9 | −177.33 (14) | N1—C5—C9—C8 | 176.22 (13) |
| C3—C4—C5—N1 | −0.4 (2) | C4—C5—C9—C8 | −2.5 (2) |
| C6—C4—C5—N1 | −179.63 (14) | C9—C8—C10—C11 | −1.5 (2) |
| C3—C4—C5—C9 | 178.30 (14) | C7—C8—C10—C11 | 178.68 (15) |
| C6—C4—C5—C9 | −1.0 (2) | C8—C10—C11—C12 | −0.5 (2) |
| C3—C4—C6—C7 | −176.22 (15) | C9—N2—C12—C11 | −1.1 (2) |
| C5—C4—C6—C7 | 3.0 (2) | C9—N2—C12—Cl2 | 178.34 (10) |
| C4—C6—C7—C8 | −1.5 (2) | C10—C11—C12—N2 | 2.0 (2) |
| C6—C7—C8—C10 | 177.72 (15) | C10—C11—C12—Cl2 | −177.45 (12) |
| C6—C7—C8—C9 | −2.1 (2) |
Footnotes
Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2404).
References
- Barbour, L. J. (2001). J. Supramol. Chem.1, 189–191.
- Bruker (2008). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
- Flack, H. D. (1983). Acta Cryst. A39, 876–881.
- Hamilton, C. W., Laitar, D. S. & Sadighi, J. P. (2004). Chem. Commun. pp. 1628–1629. [DOI] [PubMed]
- Ohira, J., Hirabayashi, M., Nakayama, N. & Ogawa, S. (2005). Nippon Kagakkai Yokoshu, 85, p. 942. (Abstract.)
- Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
- Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
- Westrip, S. P. (2009). publCIF In preparation.
- Yamada, M., Nakamura, Y., Kuroda, S. & Shimao, I. (1990). Bull. Chem. Soc. Jpn, 63, 2710–2712.
- Zong, F. & Thummel, R. P. (2004). J. Am. Chem. Soc.126, 10800–10801. [DOI] [PubMed]
- Zong, F. & Thummel, R. P. (2005). Inorg. Chem.44, 5984–4986. [DOI] [PubMed]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809011180/tk2404sup1.cif
Structure factors: contains datablocks I. DOI: 10.1107/S1600536809011180/tk2404Isup2.hkl
Additional supplementary materials: crystallographic information; 3D view; checkCIF report