Abstract
C5H10N2O, monoclinic, Ia (no. 9), a = 4.7212(4) Å, b = 11.1424(8) Å, c = 12.8211(9) Å, β = 94.349(3)°, V = 672.52(9) Å3, Z = 4, Rgt(F) = 0.0280, wRref(F2) = 0.0821, T = 200 K.
The molecular structure is shown in the Figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.
Data collection and handling.
| Crystal: | Colourless block |
| Size: | 0.55 × 0.42 × 0.22 mm |
| Wavelength: | Mo Kα radiation (0.71073 Å) |
| μ: | 0.08 mm−1 |
| Diffractometer, scan mode: | Bruker APEX-II, φ and ω |
| θmax, completeness: | 28.3°, 99% |
| N(hkl)measured, N(hkl)unique, Rint: | 3023, 1582, 0.010 |
| Criterion for Iobs, N(hkl)gt: | Iobs > 2 σ(Iobs), 1557 |
| N(param)refined: | 88 |
| Programs: | Bruker [1], [, 2], SHELX [3], WinGX/ORTEP [4], Mercury [5], PLATON [6] |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).
| Atom | x | y | z | Uiso*/Ueq |
|---|---|---|---|---|
| N1 | 0.5153 (2) | 0.71437 (11) | 0.51093 (10) | 0.0380 (3) |
| N2 | 0.5133 (2) | 0.81707 (12) | 0.65708 (10) | 0.0393 (3) |
| H2A | 0.472 (5) | 0.839 (2) | 0.717 (2) | 0.059 (7)* |
| C1 | 0.4111 (3) | 0.71980 (12) | 0.60389 (11) | 0.0360 (3) |
| C2 | 0.6901 (3) | 0.87642 (13) | 0.59414 (13) | 0.0422 (3) |
| H2 | 0.792360 | 0.948236 | 0.610629 | 0.051* |
| C3 | 0.6908 (3) | 0.81291 (14) | 0.50409 (11) | 0.0381 (3) |
| C4 | 0.2098 (4) | 0.63294 (15) | 0.64498 (14) | 0.0482 (4) |
| H4A | 0.056739 | 0.676547 | 0.676052 | 0.072* |
| H4B | 0.310313 | 0.582509 | 0.698370 | 0.072* |
| H4C | 0.129063 | 0.582293 | 0.587710 | 0.072* |
| C5 | 0.8447 (4) | 0.8372 (2) | 0.40854 (15) | 0.0543 (4) |
| H5A | 0.706676 | 0.851559 | 0.348855 | 0.081* |
| H5B | 0.962909 | 0.767831 | 0.393875 | 0.081* |
| H5C | 0.965501 | 0.908214 | 0.420304 | 0.081* |
| O1 | 0.4029 (2) | 0.56654 (9) | 0.34354 (8) | 0.0373 (3) |
| H1A | 0.246 (6) | 0.530 (2) | 0.3499 (19) | 0.051 (6)* |
| H1B | 0.421 (6) | 0.611 (2) | 0.400 (2) | 0.062 (7)* |
Source of material
The compound was obtained commercially (Aldrich). Crystals suitable for the diffraction study were taken directly from the provided product.
Experimental details
Carbon-bound H atoms were placed in calculated positions (C–H 0.95 Å for aromatic carbon atoms) and were included in the refinement in the riding model approximation, with U(H) set to 1.2Ueq(C).
The H atoms of the methyl groups were allowed to rotate with a fixed angle around the C–C bond to best fit the experimental electron density (HFIX 137 in the SHELX program suite [3]), with U(H) set to 1.5Ueq(C).
The H atoms of the water molecule as well as the nitrogen-bound H atom were located on a difference Fourier map and refined freely.
Given the space group is non-centrosymmetric, the structure was formally refined as an inversion twin with a volume ratio of 73.4:26.6.
Due to the absence of a strong anomalous scatterer, the Flack parameter is meaningless. Thus, the item was removed from the CIF.
Comment
Synthesis and analysis are the two major aspects of historic and contemporary chemistry. For a large variety of reactions well-established standard synthesis procedures are apparent that form the basis of vast sections of practical laboratory courses during undergraduate student training. Against this backdrop it then seems improbable that one specific synthesis reaction (whose nature is known and understood) would then – all of a sudden – yield surprising results contradicting experience. The latter is a particularly suspicious development if the unexpected results coincide with a change in reagent supply as the historic example of the Simmons–Smith reaction has shown when success or failure during the early years of this reaction being applied could be attributed to the catalytic effects of silver present in one of the starting materials [7], [8], [9], [10], [11]. In our case, coordination reactions involving 2,4-dimethylimidazole as a ligand started providing unexpected results indicative of partial hydrolysis reactions. As the onset of the changed behaviour coincided with an older batch of the reagent being used in our laboratories, the nature of the compound was checked by means of a diffraction study. Structural information about the title compound acting as a cation is apparent in the literature [12], [, 13].
The structure solution shows a surprising picture. Apart from the expected dimethylated heterocycle one molecule of water is present in the asymmetric unit. C–N bond lengths of 1.3250(17) and 1.382(2) Å for the imine-type nitrogen atom and 1.3501(19) and 1.374(2) Å for the amine-type nitrogen atom are in good agreement with values found for other imidazole derivatives whose metrical parameters have been deposited with the Cambridge Structural Database [14]. The molecule is essentially planar with the largest deviation found for the least-squares plane as defined by the non-hydrogen atoms of the heterocycle measured at 0.340(8) Å for the intracyclic carbon atom bearing one of the methyl groups and bonding to only one of the two pnicogen atoms.
In the crystal, classical hydrogen bonds of the O–H⃛O and O–H⃛N type are observed next to N–H⃛O ones. The water molecules form a cooperative chain of hydrogen bonds with one of its protons while the second proton uses the imine-type nitrogen atom as acceptor. In terms of graph-set analysis [15], [, 16], the descriptor for these bonds is
The results of this study strengthen the notion that even simple, solid organic compounds that enjoy a – supposedly! – infinite shelf-live and are impervious to decomposition can undergo chemical alterations over prolonged storage.
Funding source: National Research Foundation
Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.
Researchfunding: National Research Foundation.
Conflict of interest statement: The authors declare no conflicts of interest regarding this article.
References
1. Bruker. APEX2; Bruker AXS Inc.: Madison, Wisconsin, USA, 2012.Search in Google Scholar
2. Bruker. SADABS; Bruker AXS Inc.: Madison, Wisconsin, USA, 2008.Search in Google Scholar
3. Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. 2008, A64, 112–122. https://doi.org/10.1107/s0108767307043930.Search in Google Scholar
4. Farrugia, L. J. WinGX and ORTEP for Windows: an update. J. Appl. Crystallogr. 2012, 45, 849–854. https://doi.org/10.1107/s0021889812029111.Search in Google Scholar
5. Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J., Wood, P. A. Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures. J. Appl. Crystallogr. 2008, 41, 466–470. https://doi.org/10.1107/s0021889807067908.Search in Google Scholar
6. Spek, A. L. Structure validation in chemical crystallography. Acta Crystallogr. 2009, D65, 148–155. https://doi.org/10.1107/s090744490804362x.Search in Google Scholar
7. Simmons, H. E.Jr., Smith, R. D. A new synthesis of cyclopropanes from olefins. J. Am. Chem. Soc. 1958, 80, 5323–5324. https://doi.org/10.1021/ja01552a080.Search in Google Scholar
8. Simmons, H. E., Smith, R. D. A new synthesis of cyclopropanes. J. Am. Chem. Soc. 1959, 81, 4256–4264. https://doi.org/10.1021/ja01525a036.Search in Google Scholar
9. Denis, J. M., Girard, J. M., Conia, J. M. Improved Simmons–Smith reactions. Synthesis 1972, 10, 549–551. https://doi.org/10.1055/s-1972-21919.Search in Google Scholar
10. Charette, A. B., Beauchemin, A. Simmons-Smith cyclopropanation reaction. Org. React. 2004, 58, 1–415. https://doi.org/10.1002/0471264180.or058.01.Search in Google Scholar
11. Lévesque, E., Goudreau, S. R., Charette, A. B. Improved zinc-catalyzed Simmons–Smith reaction: access to various 1,2,3-trisubstituted cyclopropanes. Org. Lett. 2014, 16, 1490–1493. https://doi.org/10.1021/ol500267w.Search in Google Scholar
12. Wang, L., Hu, Y., Xu, W., Pang, Y., Liu, F., Yang, Y. Investigation of hydrogen bonding patterns in a series of multi-component molecular solids formed by tetrabromoterephthalic acid with selected N-heterocycles. RSC Adv. 2014, 4, 56816–56830. https://doi.org/10.1039/c4ra08452g.Search in Google Scholar
13. Boeer, A. B., Collison, D., Muryn, C. A., Timco, G. A., Tuna, F., Winpenny, R. E. P. Linkage isomerism and spin frustration in heterometallic rings: synthesis, structural characterization, and magnetic and EPR spectroscopic studies of Cr7Ni, Cr6Ni2, and Cr7Ni2 rings templated about imidazolium cations. Chem. Eur. J. 2009, 15, 13150–13160. https://doi.org/10.1002/chem.200901938.Search in Google Scholar
14. Allen, F. H. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr. 2002, B58, 380–388. https://doi.org/10.1107/s0108768102003890.Search in Google Scholar
15. Bernstein, J., Davis, R. E., Shimoni, L., Chang, N.-L. Patterns in hydrogen bonding: functionality and graph set analysis in crystals. Angew. Chem. Int. Ed. Engl. 1995, 34, 1555–1573. https://doi.org/10.1002/anie.199515551.Search in Google Scholar
16. Etter, M. C., MacDonald, J. C., Bernstein, J. Graph-set analysis of hydrogen-bond patterns in organic crystals. Acta Crystallogr. 1990, B46, 256–262. https://doi.org/10.1107/s0108768189012929.Search in Google Scholar
© 2020 Eric C. Hosten and Richard Betz, published by De Gruyter, Berlin/Boston
This work is licensed under the Creative Commons Attribution 4.0 International License.
