Fluoroolefins as peptide mimetics. 2. A computational study of the conformational ramifications of peptide bond replacement

Journal of Physical Chemistry A

Volumn 114, Issue 2, 2010, Pages 1123-1133

  McKinney, Brian E ^a   Urban, Joseph J ^a  

^a UNITED STATES NAVAL ACADEMY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE DIPEPTIDES; AQUEOUS PHASE; C-TERMINAL PEPTIDES; COMPUTATIONAL STUDIES; CONFORMATIONAL ENERGIES; CONFORMATIONAL PREFERENCES; FOLDED CONFORMATION; INTRAMOLECULAR HYDROGEN BOND; INTRAMOLECULAR HYDROGEN BONDING; MODEL COMPOUND; MONTE CARLO; N-TERMINALS; PEPTIDE BONDS; PEPTIDE MIMETICS; PEPTIDOMIMETICS; THREE SYSTEMS;

ADA (PROGRAMMING LANGUAGE); BIOMIMETICS; FEEDBACK AMPLIFIERS; NANOSTRUCTURED MATERIALS; OLEFINS; PEPTIDES; PIPELINE PROCESSING SYSTEMS;

HYDROGEN BONDS;

ALANYLALANINE; ALKENE; BIOMIMETIC MATERIAL; DIPEPTIDE; FLUORINATED HYDROCARBON; PEPTIDE;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GAS; MONTE CARLO METHOD; QUANTUM THEORY; THERMODYNAMICS;

ALGORITHMS; ALKENES; BIOMIMETIC MATERIALS; DIPEPTIDES; GASES; HYDROCARBONS, FLUORINATED; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; MONTE CARLO METHOD; PEPTIDES; QUANTUM THEORY; THERMODYNAMICS;

EID: 75249094301     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9094535     Document Type: Article

References (50)

1. Lin, J.; Toscano, P. J.; Welch, J. T. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 14020.
2. Ng, P.-S.; Bergstrom Donald, E. Nano Lett. 2005, 5, 107.
3. Wipf, P.; Henninger, T. C.; Geib, S. J. J. Org. Chem. 1998, 63, 6088.
4. Arnt, L.; Rennie, J. R.; Linser, S.; Willumeit, R.; Tew, G. N. J. Phys. Chem. B 2006, 110, 3527.
5. Van der Veken, P.; Senten, K.; Kertesz, I.; De Meester, I.; Lambeir, A.-M.; Maes, M.-B.; Scharpe, S.; Haemers, A.; Augustyns, K. J. Med. Chem. 2005, 48, 1768.
6. Niida, A.; Tomita, K.; Mizumoto, M.; Tanigaki, H.; Terada, T.; Oishi, S.; Otaka, A.; Inui, K.-I.; Fujii, N. Org. Lett. 2006, 8, 613.
7. Vasbinder, M. M.; Jarvo, E. R.; Miller, S. J. Angew. Chem., Int. Ed. 2001, 40, 2824.
8. Vasbinder, M. M.; Miller, S. J. J. Org. Chem. 2002, 67, 6240.
9. Bartlett, P. A.; Otake, A. J. Org. Chem. 1995, 60, 3107.
10. Boros, L. G.; Corte, B. D.; Gimi, R. H.; Welch, J. T.; Wu, Y.; Handschumacher, R. E. Tetrahedron Lett. 1994, 35, 6033.
11. Cieplak, P.; Kollman, P. A.; Radomski, J. P. ACS Symp. Ser. 1996, 639, 143.
12. Cox, D. G.; Gurusamy, N.; Burton, D. J. J. Am. Chem. Soc. 1985, 107, 2811.
13. Okada, M.; Nakamura, Y.; Saito, A.; Sato, A.; Horikawa, H.; Taguchi, T. Tetrahedron Lett. 2002, 43, 5845.
14. Otaka, A.; Watanabe, H.; Yukimasa, A.; Oishi, S.; Tamamura, H.; Fujii, N. Tetrahedron Lett. 2001, 42, 5443.
15. Urban, J. J.; Tillman, B. G.; Cronin, W. A. J. Phys. Chem. A 2006, 110, 11120.
16. Wang, Z. X.; Duan, Y. J. Comput. Chem. 2004, 25, 1699.
17. Mehta, M. A.; Fry, E. A.; Eddy, M. T.; Dedeo, M. T.; Anagnost, A. E.; Long, J. R. J. Phys. Chem. B 2004, 108, 2777.
18. Takekiyo, T.; Imai, T.; Kato, M.; Taniguchi, Y. Biopolymers 2004, 73, 283.
19. Chang, G.; Guida, W. C.; Still, W. C. J. Am. Chem. Soc. 1989, 111, 4379.
20. Saunders, M.; Houk, K. N.; Wu, Y.-D.; Still, W. C.; Lipton, M.; Chang, G.; Guida, W. C. J. Am. Chem. Soc. 1990, 112, 1419.
21. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440.
22. Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
23. Halgren, T. A. J. Comput. Chem. 1996, 17, 520.
24. Halgren, T. A. J. Comput. Chem. 1996, 17, 553.
25. Halgren, T. A. J. Comput. Chem. 1996, 17, 615.
26. Halgren, T. A.; Nachbar, R. J. Comput. Chem. 1996, 17, 587.
27. Hasel, W.; F., H. T.; Still, W. C. Tetrahedron Comput. Method 1988, 1, 103.
28. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian03, revision E.01; Gaussian, Inc: Wallingford, CT, 2004.
29. Møller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618.
30. Becke, A. D. Phys. Rev. A: At., Mol, Opt. Phys. 1988, 38, 3098.
31. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1988, B37, 785.
32. Cances, E.; Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 107, 3032.
33. Cossi, M.; Barone, V.; Mennucci, B.; Tomasi, J. Chem. Phys. Lett. 1998, 286, 253.
34. Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 106, 5151.
35. Cossi, M.; Scalmani, G.; Rega, N.; Barone, V. J. Chem. Phys. 2002, 117, 43.
36. Kaminsky, J.; Jensen, F. J. Chem. Theory Comput. 2007, 3, 1774.
37. IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules (1969). Biochemistry, 1970, 9, 3471.
38. Voet, D.; Voet, J. G. Biochemistry; John Wiley and Sons: Hoboken, NJ, 2004.
39. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157.
40. Antony, J.; Grimme, S. Phys. Chem. Chem. Phys. 2006, 8, 5287.
41. Schreiner, P. R. Angew. Chem., Int. Ed. 2007, 46, 4217.
42. Gnanakaran, S.; Hochstrasser, R. M. J. Am. Chem. Soc. 2001, 123, 12886.
43. Lee, M.-E.; Lee, S. Y.; Joo, S.-W.; Cho, K.-H. J. Phys. Chem. B 2009, 113, 6894.
44. Madison, V.; Kopple, K. D. J. Am. Chem. Soc. 1980, 102, 4855.
45. Han, W.-G.; Jalkanen, K. J.; Elstner, M.; Suhai, S. J. Phys. Chem. B 1998, 102, 2587.
46. Subtelny, A. O.; Hartman, M. C. T.; Szostak, J. W. J. Am. Chem. Soc. 2008, 130, 6131.
47. Shah, N. H.; Butterfoss, G. L.; Nguyen, K.; Yoo, B.; Bonneau, R.; Rabenstein, D. L.; Kirshenbaum, K. J. Am. Chem. Soc. 2008, 130, 16622.
48. Alkorta, I.; Rozas, I.; Elguero, J. J. Fluorine Chem. 2000, 101, 233.
49. Dunitz, J. D.; Taylor, R. Chems-Eur. J. 1997, 3, 89.
50. Howard, J. A. K.; Hoy, V. J.; O'Hagan, D.; Smith, G. T. Tetrahedron 1996, 52, 12613.