Beilstein J Org Chem. 2014 Jun 05;10:1299-307. doi: 10.3762/bjoc.10.131. eCollection 2014.

Substitution effect and effect of axle's flexibility at (pseudo-)rotaxanes.

Beilstein journal of organic chemistry

Friedrich Malberg, Jan Gerit Brandenburg, Werner Reckien, Oldamur Hollóczki, Stefan Grimme, Barbara Kirchner

PMID: 24991282 PMCID: PMC4077404 DOI: 10.3762/bjoc.10.131

Abstract

This study investigates the effect of substitution with different functional groups and of molecular flexibility by changing within the axle from a single C-C bond to a double C=C bond. Therefore, we present static quantum chemical calculations at the dispersion-corrected density functional level (DFT-D3) for several Leigh-type rotaxanes. The calculated crystal structure is in close agreement with the experimental X-ray data. Compared to a stiffer axle, a more flexible one results in a stronger binding by 1-3 kcal/mol. Alterations of the binding energy in the range of 5 kcal/mol could be achieved by substitution with different functional groups. The hydrogen bond geometry between the isophtalic unit and the carbonyl oxygen atoms of the axle exhibited distances in the range of 2.1 to 2.4 Å for six contact points, which shows that not solely but to a large amount the circumstances in the investigated rotaxanes are governed by hydrogen bonding. Moreover, the complex with the more flexible axle is usually more unsymmetrical than the one with the stiff axle. The opposite is observed for the experimentally investigated axle with the four phenyl stoppers. Furthermore, we considered an implicit continuum solvation model and found that the complex binding is weakened by approximately 10 kcal/mol, and hydrogen bonds are slightly shortened (by up to 0.2 Å).

Keywords: dispersion interaction; hydrogen bond; supramolecular chemistry; template; theoretical chemistry

References

1. J Chem Phys. 2011 Feb 28;134(8):084107 - PubMed
2. Chem Commun (Camb). 2012 Feb 18;48(15):2083-5 - PubMed
3. Top Curr Chem. 2014;345:1-23 - PubMed
4. Chemistry. 2004 Oct 4;10(19):4777-89 - PubMed
5. J Org Chem. 2008 Nov 21;73(22):8772-9 - PubMed
6. J Am Chem Soc. 2002 May 29;124(21):6206-15 - PubMed
7. Angew Chem Int Ed Engl. 2008;47(42):8036-9 - PubMed
8. J Am Chem Soc. 2012 Jan 25;134(3):1860-8 - PubMed
9. J Am Chem Soc. 2010 Jan 20;132(2):484-94 - PubMed
10. Chemistry. 2013 Apr 26;19(18):5566-77 - PubMed
11. J Phys Chem B. 2008 May 1;112(17):5268-71 - PubMed
12. Angew Chem Int Ed Engl. 2007;46(1-2):72-191 - PubMed
13. Org Lett. 2011 Sep 16;13(18):4838-41 - PubMed
14. Angew Chem Int Ed Engl. 2013 Jul 15;52(29):7437-41 - PubMed
15. J Phys Chem A. 2006 Oct 26;110(42):11862-9 - PubMed
16. J Chem Phys. 2010 Apr 21;132(15):154104 - PubMed
17. Phys Chem Chem Phys. 2012 Feb 14;14(6):1865-75 - PubMed
18. Angew Chem Int Ed Engl. 2003 May 25;42(20):2296-300 - PubMed
19. J Comput Chem. 2011 May;32(7):1456-65 - PubMed
20. Chemistry. 2012 Aug 6;18(32):9955-64 - PubMed
21. J Mol Model. 2008 Oct;14(10):879-86 - PubMed
22. Angew Chem Int Ed Engl. 2000 Jan;39(2):350-353 - PubMed
23. J Am Chem Soc. 1991 Jun;113(13):5131-5133 - PubMed
24. Chemistry. 2008;14(4):1216-27 - PubMed
25. Chem Commun (Camb). 2011 Jun 7;47(21):6012-4 - PubMed
26. Angew Chem Int Ed Engl. 2008;47(17):3174-9 - PubMed
27. J Phys Chem A. 2010 Nov 4;114(43):11814-24 - PubMed
28. J Phys Chem A. 2006 Nov 30;110(47):12963-70 - PubMed
29. Phys Rev A Gen Phys. 1988 Sep 15;38(6):3098-3100 - PubMed
30. J Chem Phys. 2006 May 7;124(17):174506 - PubMed
31. Phys Rev B Condens Matter. 1994 Dec 15;50(24):17953-17979 - PubMed
32. Org Biomol Chem. 2005 Aug 7;3(15):2691-700 - PubMed
33. Org Biomol Chem. 2012 Aug 14;10(30):5954-64 - PubMed
34. Phys Rev Lett. 1996 Oct 28;77(18):3865-3868 - PubMed
35. Science. 2013 Jan 11;339(6116):189-93 - PubMed
36. Phys Chem Chem Phys. 2011 Apr 14;13(14):6670-88 - PubMed
37. Phys Chem Chem Phys. 2013 Oct 14;15(38):16031-42 - PubMed
38. J Am Chem Soc. 2004 Oct 27;126(42):13562-3 - PubMed

Publication Types

• Journal Article