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Studying the hydrogen atom position in the strong-short intermolecular hydrogen bond of pure and 5-substituted 9-hydroxyphenalenones by invariom refinement and ONIOM cluster computations

Irina Gruber , Lisa Bensch , Thomas J. J. Müller ORCID logo , Christoph Janiak ORCID logo and Birger Dittrich ORCID logo EMAIL logo

Abstract

The solid-state structures of three H-bonded enol forms of 5-substituted 9-hydroxyphenalenones were investigated to accurately determine the H atom positions of the intramolecular hydrogen bond. For this purpose, single-crystal X-ray diffraction (SC-XRD) data were evaluated by invariom-model refinement. In addition, QM/MM computations of central molecules in their crystal environment show that results of an earlier standard independent atom model refinement, which pointed to the presence of a resonance-assisted hydrogen bond in unsubstituted 9-hydroxyphenalone, are misleading: in all our three and the earlier solid-state structures the lowest energy form is that of an asymmetric hydrogen bond (CS form). Apparent differences of results from SC-XRD and other analytical methods are explained.


Corresponding author: Birger Dittrich, Institut für Anorganische Chemie und Strukturchemie II, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany, E-mail:

Funding source: DFG

Award Identifier / Grant number: DI 921/6-1

Acknowledgments

We thank the DFG, project DI 921/6-1, for financial support.

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: B.D. acknowledges funding from the Deutsche Forschungsgemeinschaft DFG, project DI 921/6-1.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

References

1. Jeffrey, G. A. An Introduction to Hydrogen Bonding; Oxford University Press: New York, NY, 1997.Search in Google Scholar

2. Desiraju, G. R., Steiner, T. The Weak Hydrogen Bond in Structural Chemistry and Biology; Oxford University Press: New York, NY, 1999.Search in Google Scholar

3. Grabowski, S. J. Hydrogen Bonding – New Insights; Ed.; Springer: Dordrecht, Netherlands, 2006.10.1007/978-1-4020-4853-1Search in Google Scholar

4 Scheiner, S., Ed. Molecular Interactions: From van der Waals to Strongly Bound Complexes; Wiley: Chichester, UK, 1997.Search in Google Scholar

5. Garcia-Viloca, M., González-Lafont, A., Lluch, J. M. J. Am. Chem. Soc. 1997, 119, 1081–1086; doi: https://doi.org/10.1021/ja962662n.Search in Google Scholar

6. Garcia-Viloca, M., Gelabert, R., González-Lafont, A., Moreno, M., Lluch, J. M. J. Phys. Chem. A 1997, 101, 8727–8733; doi: https://doi.org/10.1021/jp972335h.Search in Google Scholar

7. Perrin, C. L., Nielson, J. B. Annu. Rev. Phys. Chem. 1997, 48, 511–544; doi: https://doi.org/10.1146/annurev.physchem.48.1.511.Search in Google Scholar

8. Mochida, T., Izuoka, A., Sugawara, T., Moritomo, Y., Tokura, Y. J. Am. Chem. Soc. 1994, 101, 7971–7974; doi: https://doi.org/10.1063/1.468224.Search in Google Scholar

9. Malaspinna, L. A., Edwards, A. J., Woińska, M., Jayatilaka, D., Turner, M. J., Price, J. R., Herbst-Irmer, R., Sugimoto, K., Nishibori, E., Grabowsky, S. Cryst. Grow. Des. 2017, 17, 3812–3825; doi: https://doi.org/10.1021/acs.cgd.7b00390.Search in Google Scholar

10. Hibbert, F., Emsley, J. J. Adv. Phys. Org. Chem. 1990, 26, 255–379; doi: https://doi.org/10.1016/S0065-3160(08)60047-7.Search in Google Scholar

11. Emsley, J. Struct. Bond. 1984, 57, 147–191; doi: https://doi.org/10.1007/BFb0111456.Search in Google Scholar

12. Gilli, G., Bellucci, F., Ferretti, V., Bertolasi, V. J. Am. Chem. Soc. 1989, 111, 1023−1028; doi: https://doi.org/10.1021/ja00185a035.Search in Google Scholar

13. Bertolasi, V., Gilli, P., Ferretti, V., Gilli, G. Chem. Eur. J. 1996, 2, 925–934; doi: https://doi.org/10.1002/chem.19960020806.Search in Google Scholar

14. Mahmudov, K. T., Pombeiro, A. J. L. Chem. Eur. J. 2016, 22, 16356−16398; doi: https://doi.org/10.1002/chem.201601766.Search in Google Scholar PubMed

15. Brown, R. S., Tse, A., Nakashima, T., Haddon, R. C. J. Am. Chem. Soc. 1979, 101, 3157–3162; doi: https://doi.org/10.1021/ja00506a003.Search in Google Scholar

16. Demura, Y., Kawato, T., Kanatomi, H., Murase, I. Bull. Chem. Soc. Jpn. 1975, 48, 2820–2824; doi: https://doi.org/10.1246/bcsj.48.2820.Search in Google Scholar

17. Svensson, C., Abrahams, S. C., Bernstein, J. L., Haddon, R. C., J. Am. Chem. Soc. 1979, 101, 5759–5764; doi: https://doi.org/10.1021/ja00513a048.Search in Google Scholar

18. Svensson, C., Abrahams, S. C. Acta Crystallogr. 1986, B42, 280–286; doi: https://doi.org/10.1107/S0108768186098221.Search in Google Scholar

19. Jackman, L. M., Trewella, J. C., Haddon, R. C. J. Am. Chem. Soc. 1980, 102, 2519–2525; doi: https://doi.org/10.1021/ja00528a001.Search in Google Scholar

20. Rossetti, R., Haddon, R. C., Brus, L. E. J. Am. Chem. Soc. 1980, 102, 6913–6916; doi: https://doi.org/10.1021/ja00543a002.Search in Google Scholar

21. Hameka, H., de la Vega, J. R. J. Am. Chem. Soc. 1984, 106, 7703–7705; doi: https://doi.org/10.1021/ja00337a009.Search in Google Scholar

22. Gilli, P., Bertolasi, V., Ferretti, V., Gilli, G. J. Am. Chem. Soc. 1994, 116, 909–915; doi: https://doi.org/10.1021/ja00082a011.Search in Google Scholar

23. Gilli, G., Gilli, P. The Nature of Hydrogen Bond; Oxford University Press: New York, NY, 2009.10.1093/acprof:oso/9780199558964.001.0001Search in Google Scholar

24. Kovács, A., Izvekov, V., Zauer, K., Ohta, K. J. Phys. Chem. A 2001, 105, 5000–5009; doi: https://doi.org/10.1021/jp0045033.Search in Google Scholar

25. Pal, S. K., Itkis, M. E., Reed, R. W., Oakley, R. T., Cordes, A. W., Tham, F. S., Siegrist, T., Haddon, R. C. J. Am. Chem. Soc. 2004, 126, 1478–1484; doi: https://doi.org/10.1021/ja037864f.Search in Google Scholar PubMed

26. Pariyar, A., Vijaykumar, G., Bhunia, M., Dey, S. K., Singh, S. K., Kurungot, S., Mandal, S. K. J. Am. Chem. Soc. 2015, 137, 5955–5960; doi: https://doi.org/10.1021/jacs.5b00272.Search in Google Scholar PubMed

27. Das, A., Scherer, T. M., Mondal, P., Mobin, S. M., Kaim, W., Lahiri, G. K. Chem. Eur. J. 2012, 18, 14434–14443; doi: https://doi.org/10.1002/chem.201201785.Search in Google Scholar PubMed

28. Dey, S. K., Honecker, A., Mitra, P., Mandal, S. K., Mukherjee, A. Eur. J. Inorg. Chem. 2012, 35, 5814–5824; doi: https://doi.org/10.1002/ejic.201200800.Search in Google Scholar

29. Mochida, T., Torigoe, R., Koinuma, T., Asano, C., Satou, T., Koike, K., Nikaido, T. Eur. J. Inorg. Chem. 2006, 3, 558–565; doi: https://doi.org/10.1002/ejic.200500778.Search in Google Scholar

30. Gu, Y.-J., Yan, B. Inorg. Chim. Acta 2013, 408, 96–102; doi: https://doi.org/10.1016/j.ica.2013.09.008.Search in Google Scholar

31. Koelsch, C. F., Anthes, J. A. J. Org. Chem. 1941, 6, 558–565; doi: https://doi.org/10.1021/jo01204a009.Search in Google Scholar

32. Das, A., Ghosh, T. K., Dutta Chowdhury, A., Mobin, S. M., Lahiri, G. K. Polyhedron 2013, 52, 1130–1137; doi: https://doi.org/10.1016/j.poly.2012.06.057.Search in Google Scholar

33. Mandal, S. K., Samanta, S., Itkis, M. E., Jensen, D. W., Reed, R. W., Oakley, R. T., Tham, F. S., Donnadieu, B., Haddon, R. C. J. Am. Chem. Soc. 2006, 128, 1982–1994; doi: https://doi.org/10.1021/ja0560276.Search in Google Scholar PubMed

34. He, G., Hou, Y., Sui, D., Wan, X., Long, G., Yun, P., Yu, A., Zhang, M., Chen, Y. Tetrahedron 2013, 69, 6890–6896; doi: https://doi.org/10.1016/j.tet.2013.05.111.Search in Google Scholar

35. Bensch, L., Gruber, I., Janiak, C., Müller, T. J. J. Chem. Eur. J. 2017, 23, 10551–10558; doi: https://doi.org/10.1002/chem.201700553.Search in Google Scholar PubMed

36. Engdahl, C., Gogoll, A., Edlund, U., Magn. Reson. Chem. 1991, 29, 54–62; doi: https://doi.org/10.1002/mrc.1260290112.Search in Google Scholar

37. Ozeki, H., Takahashi, M., Okuyama, K., Kimura, K. J. Chem. Phys. 1993, 99, 56–66; doi: https://doi.org/10.1063/1.465783.Search in Google Scholar

38. Kunze, K. L., de la Vega, J. R. J. Am. Chem. Soc. 1984, 106, 6528–6533; doi: https://doi.org/10.1021/ja00334a012.Search in Google Scholar

39. Svensson, C., Abrahams, S. C. J. Appl. Crystallogr. 1984, 17, 459–463; doi: https://doi.org/10.1107/S0021889884011936.Search in Google Scholar

40. Dittrich, B., Koritsanszky, T., Luger, P. Angew. Chem. Int. Ed. 2004, 43, 2718–2721; doi: https://doi.org/10.1002/anie.200353596.Search in Google Scholar PubMed

41. Dittrich, B., Lübben, J., Mebs, S., Wagner, A., Luger, P., Flaig, R. Chem. Eur. J. 2017, 23, 4605–4614; doi: https://doi.org/10.1002/chem.201604705.Search in Google Scholar PubMed PubMed Central

42. Dittrich, B., Hübschle, C. B., Pröpper, K., Dietrich, F., Stolper, T., Holstein, J. J. Acta Crystallogr. 2013, B69, 91–104; doi: https://doi.org/10.1107/S2052519213002285.Search in Google Scholar PubMed

43. Stewart, R. F. Acta Crystallogr. 1976, A32, 565–574; doi: https://doi.org/10.1107/S056773947600123X.Search in Google Scholar

44. Hansen, N., Coppens, P. Acta Crystallogr. 1978, A34, 909–921; doi: https://doi.org/10.1107/S0567739478001886.Search in Google Scholar

45. Bensch, L., Ebeling, R., Arasu, N. P., Schulze Lammers, B., Mayer, B., Müller, T. J. J., Vázquez, H. S., Karthäuser. submitted for publication.Search in Google Scholar

46. Kabsch, W. Acta Crystallogr. 2010, D66, 125–132; doi: https://doi.org/10.1107/S0907444909047337.Search in Google Scholar PubMed PubMed Central

47. Sheldrick, G. M. Acta Crystallogr. 2015, C71, 3–8; doi: https://doi.org/10.1107/S2053273314026370.Search in Google Scholar PubMed PubMed Central

48. Krause, L., Herbst-Irmer, R., Sheldrick, G. M., Stalke, D. J. Appl. Crystallogr. 2015, 48, 3–10; doi: https://doi.org/10.1107/S1600576714022985.Search in Google Scholar PubMed PubMed Central

49. Parsons, S., Flack, H. D., Wagner, T. Acta Crystallogr. 2013, B69, 249–259; doi: https://doi.org/10.1107/S2052519213010014.Search in Google Scholar PubMed PubMed Central

50. Volkov, A., Macchi, P., Farrugia, L. J., Gatti, C., Mallinson, P., Richter, T., Koritsánszky, T. XD2006. University at Buffalo USA, University of Milan, Italy, University of CNRIST Mand Middle Tennessee State University, NY Glasgow, UK Milan, Italy TN, USA, 2006.Search in Google Scholar

51. Weininger, D. J. Chem. Inf. Comp. Sci. 1988, 28, 31–36; doi: https://doi.org/10.1021/ci00057a005.Search in Google Scholar

52. Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., Zheng, G., Sonnenberg, J. L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J. A.Jr., Peralta, J. E., Ogliaro, F., Bearpark, M., Heyd, J. J., Brothers, E., Kudin, K. N., Staroverov, V. N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J. C., Iyengar, S. S., Tomasi, J., Cossi, M., Rega, N., Millam, J. M., Klene, M., Knox, J. E., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Martin, R. L., Morokuma, K., Zakrzewski, V. G., Voth, G. A., Salvador, P., Dannenberg, J. J., Dapprich, S., Daniels, A. D., Farkas, Ö., Foresman, J. B., Ortiz, J. V., Cioslowski, J., Fox, D. J., Frisch, M. J., GAUSSIAN 09(Revision D.01). Gaussian, Inc.: Wallingford CT, 2013.Search in Google Scholar

53. Jayatilaka, D., Grimwood, D. J. Tonto: A fortran based object-oriented system for quantum chemistry and crystallography. In Computational Science – ICCS 2003. ICCS 2003. Lecture Notes in Computer Science, vol 2660; Sloot P. M. A., Abramson D., Bogdanov A. V., Gorbachev Y. E., Dongarra J. J., Zomaya A. Y., Eds. Springer: Berlin, Heidelberg, 2003; pp. 142–151.Search in Google Scholar

54. Hübschle, C. B., Dittrich, B. J. Appl. Crystallogr. 2011, 44, 238–240; doi: https://doi.org/10.1107/S0021889810042482.Search in Google Scholar PubMed PubMed Central

55. Dittrich, B., Hübschle, C. B., Luger, P., Spackman, M. A. Acta Crystallogr. 2006, D62, 1325–1335; doi: https://doi.org/10.1107/S090744490602899X.Search in Google Scholar PubMed

56. Hübschle, C. B., Dittrich, B. J. Appl. Crystallogr. 2011, 44, 238–240; doi: https://doi.org/10.1107/S0021889810042482.Search in Google Scholar

57. Svensson, M., Humbel, S., Froese, R. D. J., Matsubara, T., Sieber, S., Morokuma, K. J. Phys. Chem. 1996, 100, 19357–19363; doi: https://doi.org/10.1021/jp962071j.Search in Google Scholar

58. Dittrich, B., Pfitzenreuter, S., Hübschle, C. B. Acta Crystallogr. A 2012, 68, 110–116; doi: https://doi.org/10.1107/S0108767311037974.Search in Google Scholar PubMed

59. Besler, B. H., Merz, K. M.Jr., Kollman, P. A. J. Comput. Chem 1990, 11, 431–439; doi: https://doi.org/10.1002/jcc.540110404.Search in Google Scholar

60. Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., Skid, W. M., Bernstein, E. R. J. Am. Chem. Soc. 1992, 114, 10024–10039; doi: https://doi.org/10.1021/ja00051a040.Search in Google Scholar

61. Bannwarth, C., Ehlert, S., Grimme, S. J. Chem. Theory Comput. 2019, 15, 1652–1671; doi: https://doi.org/10.1021/acs.jctc.8b01176.Search in Google Scholar PubMed


Supplementary Material

The online version of this article offers supplementary material (https://doi.org/10.1515/zkri-2020-0022).


Received: 2020-03-02
Accepted: 2020-05-04
Published Online: 2020-06-03
Published in Print: 2020-07-28

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