Oxygen and nitrogen in competitive situations: Which is the hydrogen-bond acceptor?

Chemistry - A European Journal

Volumn 2, Issue 12, 1996, Pages 1509-1513

  Bohm H J ^a,b,c   Klebe, G ^a   Brode, S ^a   Hesse, U ^a  

^a BASF SE   (Germany)

^b F HOFFMANN LA ROCHE LTD   (Switzerland)

^c PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

Ab initio calculations; Binding studies; Crystal packing; Drug design; Hydrogen bonds

Indexed keywords

AB INITIO CALCULATIONS; BINDING CHARACTERISTICS; BINDING STUDIES; CRYSTAL PACKINGS; DRUG DESIGN; INTERACTION ENERGIES; OXYGEN AND NITROGENS; OXYGEN CONTAINING GROUPS;

CALCULATIONS; FUNCTIONAL GROUPS; HYDROGEN BONDS; MOLECULAR OXYGEN; MOLECULES; NITROGEN;

ATOMS;

EID: 0011639217     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.19960021206     Document Type: Article

References (31)

1. P. Kollman, J. Am. Chem. Soc. 1977, 99, 4875-4893.
2. P. A. Kollman, L. C. Allen, J. Am. Chem. Soc. 1971, 93, 4991-5000.
3. M. C. Etter, S. M. Reutzel, J. Am. Chem. Soc. 1991, 113, 2586-2598.
4. M. C. Etter, D. A. Adsmond, J. Chem. Soc. Chem. Commun. 1990, 589-591.
5. For a review see G. Klebe in Structure Correlation (Eds.: H. B. Bürgi, J. D. Dunitz), VCH, Weinheim, 1994, p. 543-603.
6. P. Murray-Rust, J. P. Glusker, J. Am. Chem. Soc. 1984, 106, 1018-1025.
7. G. Klebe, J. Mol. Biol. 1994, 237, 212-235.
8. A. Schäfer, H. Horn, R. Ahlrichs, J. Chem. Phys. 1992, 97, 2571-2577.
9. S. Huzinaga, J. Chem. Phys. 1965, 42, 1293-1302.
10. L. A. Curtiss, D. J. Frurip, M. Blander, J. Chem. Phys. 1979, 71, 2703-2711.
11. J. G. C. M. van Duijneveldt-van de Riijdt, F. B. van Duijneveldt, J. Chem. Phys. 1992, 97, 6649-6662.
12. F. H. Allen, O. Kennard, Acc. Chem. Res. 1983, 16, 146-153.
13. G. A. Jeffrey, W. Saenger, Hydrogen bonding in Biological Structures, Springer, Berlin, 1991.
14. Independently from us, Robin Taylor at the Cambridge Crystallographic Data Centre made the same observation that furans and isoxazoles are rarely involved in hydrogen bonds (personal communication).
15. H. J. Böhm, G. Klebe, Angew. Chem. 1996, 108, 2750-2778;
16. Angew. Chem. Int. Ed. Engl. 1996, 35, 2588-2614.
17. S. Cabani, P. Gianni, V. Mollica, L. Lepori, J. Solut. Chem. 1981, 10, 563-595.
18. R. Kikumoto, Y. Tamao, K. Ohkubo, T. Tezuka, S. Tonomura, S. Okamoto, Y. Funahara, A. Hijikata, J. Med. Chem. 1980, 23, 830-836.
19. D. A. Matthews, J. T. Bolin, J. M. Burridge, D. J. Filman, K. W. Volz, B. T. Kaufmann, C. R. Bedell, J. N. Champness, D. K. Stammers, J. Kraut, J. Biol. Chem. 1985, 260, 381-391.
20. J. Badger, I. Minor, M. J. Kremer, M. A. Oliveira, T. J. Smith, J. P. Griffith, D. M. A. Guerin, S. Krishnaswamy, M. Luo, M. G. Rossmann, M. A. McKinlay, G. D. Diana, F. J. Dutko, M. Fancher, R. R. Rueckert, B. A. Heinz, Proc. Natl. Acad. Sci. USA, 1988, 85, 3304-3308.
21. J. M. Schulman, M. L. Sabio, R. L. Disch, J. Med. Chem. 1983, 26, 817-823.
22. M. Clark, R. D. Cramer III, N. v. Opdenbosch, J. Comput. Chem. 1989, 10, 982-1012.
23. P. Dauber-Osguthorpe, V. A. Roberts, D. J. Osguthorpe, J. Wolff, M. Genest, A. T. Hagler, Proteins 1988, 4, 31-42.
24. CHARMM force field, as implemented in the program QUANTA, distributed by Molecular Simulations, Burlington, Ma (USA).
25. W. L. Jorgensen, J. Tirado-Rives, J. Am. Chem. Soc. 1988, 110, 1657-1666.
26. S. J. Weiner, P. A. Kollman, D. T. Nguygen, D. A. Case, J. Comput. Chem. 1986, 7, 230-252.
27. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, P. Weiner, J. Am. Chem. Soc. 1984, 106, 765-784.
28. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, P. A. Kollman, J. Am. Chem. Soc. 1995, 117, 5179-5197.
29. R. Dixon, P. A. Kollman, unpublished results.
30. Y. K. Kang, G. Nemethy, H. A. Scheraga, J. Phys. Chem. 1987, 91, 4105-4109 and 4109-4117.
31. To avoid any bias from the differences in van der Waals radii of oxygen and nitrogen, the 73 "planar" examples were split into O···HO (46 examples, mean 2.94(10) Å) and N···HO (27 examples, 3.07(11) Å), and the 13 "twisted" cases were separated into O···HO (4 examples, 3.05 (11) Å) and N···HO (9 examples, 2.88 (13) Å). However, evidence for a lengthening of the hydrogen bond was still not detected.