Computational studies on pseudorotaxanes by molecular dynamics and free energy perturbation simulations

Journal of Organic Chemistry

Volumn 68, Issue 4, 2003, Pages 1539-1547

  Grabuleda, Xavi ^a   Ivanov, Petko ^a,b   Jaime, Carlos ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b INSTITUTE OF ORGANIC CHEMISTRY   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; FREE ENERGY; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; SOLVENTS;

SOLVENT MODELS;

PHENOLS;

ACETONITRILE; BENZIDINE DERIVATIVE; CHLORIDE; PHENOL DERIVATIVE; PSEUDOROTAXANE; ROTAXANE; SOLVENT; UNCLASSIFIED DRUG; WATER;

ARTICLE; CHEMICAL STRUCTURE; COMPUTER SIMULATION; ENERGY; GAS; MOLECULAR DYNAMICS; MOLECULAR MODEL;

EID: 0037458987     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo0265636     Document Type: Article

References (58)

1. Bissell, R. A.; Córdova, E.; Kaifer, A. E.; Stoddart, J. F. Nature 1994, 369, 133-137.
2. (a) Ballardini, R.; Balzani, V.; Gandolfi, M. T.; Prodi, L.; Venturi, M.; Philp, D.; Ricketts, H. G.; Stoddart, J. F. Angew. Chem., Int. Ed. Engl. 1993, 32, 1301-1303.
3. (b) Benniston, A. C.; Harriman, A. Angew. Chem., Int. Ed. Engl. 1993, 32, 1459-1461.
4. (c) Balzani, V.; Credi, A.; Raymo, F. M.; Stoddart, J. F. Angew. Chem., Int. Ed. 2000, 39, 3348-3391 and references therein.
5. (d) Ballardini, R.; Balzani, V.; Credi, A.; Gandolfi, M. T.; Ventura, M. Acc. Chem. Res. 2001, 34, 445-455.
6. (e) Schalley, C. A.; Beizai, K.; Vögtle, F. Acc. Chem. Res. 2001, 34, 465-476.
7. Amabilino, D. B.; Ashton, P. R.; Bêlchradskxc, M.; Raymo, F. M.; Stoddart, J. F. J. Chem. Soc., Chem. Commun. 1995, 751-754.
8. (a) Asakawa, M.; Iqbal, S.; Stoddart, J. F.; Tinker, N. D. Angew. Chem., Int. Ed. Engl. 1996, 35, 976-978.
9. (b) Ballardini, R.; Balzani, V.; Credi, A.; Gandolfi, M. T.; Langford, S. J.; Menzer, S.; Prodi, L.; Stoddart, J. F.; Venturi, M.; Williams, D. J. Angew. Chem., Int. Ed. Engl. 1996, 35, 978-981.
10. Credi, A.; Balzani, V.; Langford, S. J.; Stoddart, J. F. J. Am. Chem. Soc. 1997, 119, 2679-2681.
11. Asakawa, M.; Ashton, P. R.; Balzani, V.; Credi, A.; Mattersteig, G.; Matthews, O. A.; Montalti, M.; Spencer, N.; Stoddart, J. F.; Venturi, M. Chem. Eur. J. 1997, 3, 1992-1996.
12. (a) Ashton, P. R.; Ballardini, R.; Balzani, V.; Constable, E. C.; Credi, A.; Kocian, O.; Langford, S. J.; Preece, J. A.; Prodi, L.; Schofield, E. R.; Spencer, N.; Stoddart, J. F.; Wenger, S. Chem. Eur. J. 1998, 4, 2413-2422.
13. (b) Ballardini, R.; Balzani, V.; Clemente-León, M.; Credi, A.; Gandolfi, M. T.; Ishow, E.; Perkins, J.; Stoddart, J. F.; Tseng, H.R.; Wenger, S. J. Am. Chem. Soc. 2002, 124, 12786-12795.
14. Asakawa, M.; Brancato, G.; Fanti, M.; Leigh, D. A.; Shimizu, T.; Slavin, A. M. Z.; Wong, J. K. Y.; Zerbetto, F.; Zhang, S. J. Am. Chem. Soc. 2002, 124, 2939-2950.
15. (a) Balzani, V.; Gómez-López, M.; Stoddart, J. F. Acc. Chem. Res. 1998, 31, 405-414.
16. (b) Shipway, A. N.; Willner, I. Acc. Chem. Res. 2001, 34, 421-432.
17. Laitenberger, P.; Claessens, C. G.; Kuipers, F. M.; Raymo, F. M.; Palmer, R. E.; Stoddart, J. F. Chem. Phys. Lett. 1997, 279, 209-214.
18. Chia, S.; Cao, J.; Stoddart, J. F.; Zink, J. I. Angew. Chem., Int. Ed. 2001, 40, 2447-2451.
19. Luo, Y.; Collier, C. P.; Jeppesen, J. O.; Nielsen, K. A.; Delonno, E.; Ho, G.; Perkins, J.; Tseng, H.-R.; Yamamoto, T.; Stoddart, J. F.; Heath, J. R. ChemPhysChem 2002, 3, 519-525.
20. (a) Ahuja, R. C.; Caruso, P.-L.; Möbius, D.; Wildburg, G.; Ringsdorf, H.; Philp, D.; Preece, J. A.; Stoddart, J. F. Langmuir 1993, 9, 1534-1544.
21. (b) Pease, A. R.; Jeppesen, J. O.; Stoddart, J. F.; Luo, Y.; Collier, C. P.; Heath, J. R. Acc. Chem. Res. 2001, 34, 433-444.
22. Collier, C. P.; Jeppesen, J. O.; Luo, Y.; Perkins, J.; Wong, E. W.; Heath, J. R.; Stoddart, J. F. J. Am. Chem. Soc. 2001, 123, 12632-12641.
23. Collier, C. P.; Wong, E. W.; Bêlohradskxc, M.; Raymo, F. M.; Stoddart, J. F.; Kuekes, P. J.; Williams, R. S.; Heath, J. R. Science 1999, 285, 391-394.
24. See the special issue on nanoscale materials, guest editor J. R. Heath in Acc. Chem. Res. 1999, 32, all pages.
25. (a) Ball, P. Nature 2000, 406, 118-120.
26. (b) Pease, A. R.; Stoddart, J. F. Struct. Bonding (Berlin) 2001, 99, 189-236.
27. As examples, see: (a) Amabilino, D. B.; Asakawa, M.; Ashton, P. R.; Ballardini, R.; Balzani, V.; Belohradsky, M.; Credi, A.; Higuchi, M.; Raymo, F. M.; Shimizu, T.; Stoddart, J. F.; Venturi, M.; Yase, K. New. J. Chem. 1998, 22, 959-972.
28. (b) Ashton, P. R.; Boyd, S. E.; Menzer, S.; Pasini, D.; Raymo, F. M.; Spencer, N.; Stoddart, J. F.; White, A. J. P.; Williams, D. J.; Wyatt, P. G. Chem. Eur. J. 1998, 4, 299-310.
29. (a) Mayer, B.; Klein, C. T.; Topchieva, I. N.; Kohler, G. J. Comput. Aid. Mol. Design 1999, 13, 373-383.
30. (b) Pozuelo, J.; Mendicuti, F.; Saiz, E. Polymer 2001, 43, 523-531.
31. (c) Pozuelo, J.; Mendicuti, F.; Mattice, W. L. Polym. J. 1998, 30, 479-484.
32. (d) Pozuelo, J.; Mendicuti, F.; Mattice, W. L. Macromolecules 1997, 30, 3685-3690.
33. (e) Horsky, J. Macromol. Theory Simul. 2000, 9, 759-771.
34. Raymo, F. M.; Houk, K. N.; Stoddart, J. F. J. Org. Chem. 1998, 63, 6523-6528.
35. Zhang, K.-C.; Liu, L.; Mu, T.-W.; Guo, Q.-X. Chem. Phys. Lett. 2001, 333, 195-198.
36. Kaminski, G. A.; Jorgensen, W. L. J. Chem. Soc., Perkin Trans. 2 1999, 2365-2375.
37. Castro, R.; Davidov, P. D.; Kumar, K. A.; Marchand, A. P.; Evanseck, J. D.; Kaifer, A. E. J. Phys. Org. Chem. 1997, 10, 369-382.
38. Lipton, M. A. Tetrahedron Lett. 1996, 37, 287-290.
39. Raymo, F. M.; Bartberger, M. D.; Houk, K. N.; Stoddart, J. F. J. Am. Chem. Soc. 2001, 123, 9264-9267.
40. Grabuleda, X.; Jaime, C. J. Org. Chem. 1998, 63, 9635-9643.
41. Grabuleda, X.; Jaime, C.; Kollman, P. A. J. Comput. Chem. 2000, 21, 901-908.
42. Córdova, E.; Bissell, R. A.; Spencer, N.; Ashton, P. R.; Stoddart, J. F.; Kaifer, A. E. J. Org. Chem. 1993, 58, 6550-6552.
43. Kollman, P. A. Chem. Rev. 1993, 93, 2395-2417.
44. Miller, J. L.; Kollman, P. A. J. Phys. Chem. 1996, 100, 8587-8594.
45. Meng, E. C.; Caldwell, J. W.; Kollman, P. A. J. Phys. Chem. 1996, 100, 2367-2371.
46. Pearlman, D. A.; Connely, P. R. J. Mol. Biol. 1995, 148, 696-717.
47. Mezei, M.; Beveridge, D. L. Ann. N. Y. Acad. Sci. 1986, 482, 1-23.
48. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M. Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R. J.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 5; University of California-San Francisco, San Francisco, 1997.
49. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
50. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
51. Grabuleda, X., Ph.D. Thesis, Universitat Autònoma de Barcelona, Barcelona, 2000.
52. Pearlman, D. A.; Kollman, P. A. J. Chem. Phys. 1989, 91, 7831-7839.
53. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman; J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez; C.; Pople, J. A. Gaussian 94 (revision A.1); Gaussian, Inc.: Pittsburgh, PA, 1995.
54. Geometry was optimized with the HF/6-31G* basis set, and the molecular electrostatic potential was computed using the keywords iop-(6/33) = 2 and Pop = mk (Besler, B. H.; Merz, K. M.; Kollman, P. A. J. Comput. Chem. 1990, 11, 431-439).
55. Comparison of our computed charges with those contained in the parmf94 force field of AMBER shows similar values for the different functional groups studied, e.g., the charges for adenine present values -0.912 for N and 0.417 for its hydrogens. Analogously, the charge for the hydroxylic oxygen of tyrosine is -0.558 and that for its hydrogen is 0.399.
56. (a) Allwood, B. L.; Spencer, N.; Shahriari-Zavareh, H.; Stoddart, J. F.; Williams, D. J. J. Chem. Soc., Chem. Commun. 1987, 1061-1064.
57. (b) Sttodart, J. F. Pure Appl. Chem. 1988, 60, 467-472.
58. Ivanov, P. M. J. Mol. Struct. 1997, 415, 179.