Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water

Journal of Chemical Physics

Volumn 123, Issue 11, 2005, Pages

  Elmer, Sidney P ^a   Park, Sanghyun ^a   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METHANOL; OLIGOMERS; PROBABILITY; SOLVENTS;

ALL-ATOM MODELS; METHANOL SOLUTIONS; SOLVENT QUALITY;

MARKOV PROCESSES;

EID: 25444493142     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2001648     Document Type: Article

References (35)

1. E. Drexler and R. Smalley, Chem. Eng. News 81, 37 (2003).
2. S. Elmer and V. Pande, J. Phys. Chem. B 105, 482 (2001).
3. S. P. Elmer and V. S. Pande, J. Chem. Phys. 121, 12760 (2004).
4. S. P. Elmer and V. S. Pande, J. Chem. Phys. 122, 124908 (2005).
5. J. Nelson, J. Saven, J. Moore, and P. Wolynes, Science 277, 1793 (1997).
6. R. Prince, J. Saven, P. Wolynes, and J. Moore, J. Am. Chem. Soc. 121, 3114 (1999).
7. O. Lee and J. Saven, J. Phys. Chem. B 108, 11988 (2004).
8. W. Y. Yang, R. B. Prince, J. Sabelko, J. S. Moore, and M. Gruebele, J. Am. Chem. Soc. 122, 3248 (2000).
9. R. Prince, S. Barnes, and J. Moore, J. Am. Chem. Soc. 122, 2758 (2000).
10. M. S. Gin and J. S. Moore, Org. Lett. 2, 135 (2000).
11. M. J. Mio, R. B. Prince, J. S. Moore, C. Kuebel, and D. C. Martin, J. Am. Chem. Soc. 122, 6134 (2000).
12. R. B. Prince, L. Brunsveld, E. W. Meijer, and J. S. Moore, Angew. Chem., Int. Ed. 39, 228 (2000).
13. A. Tanatani, M. J. Mio, and J. S. Moore, J. Am. Chem. Soc. 123, 1792 (2001).
14. K. Oh, K. S. Jeong, and J. S. Moore, Nature (London) 414, 889 (2001).
15. A. Tanatani, T. S. Hughes, and J. S. Moore, Angew. Chem., Int. Ed. 41, 325 (2001).
16. D. H. Zhao and J. S. Moore, J. Am. Chem. Soc. 124, 9996 (2002).
17. D. J. Hill, M. J. Mio, R. B. Prince, T. S. Hughes, and J. S. Moore, Chem. Rev. (Washington, D.C.) 101, 3893 (2001).
18. D. Hill and J. Moore, Proc. Natl. Acad. Sci. U.S.A. 99, 5053 (2002).
19. L. Brunsveld, E. W. Meijer, R. B. Prince, and J. S. Moore, J. Am. Chem. Soc. 123, 7978 (2001).
20. M. T. Stone and J. S. Moore, Org. Lett. 6, 469 (2004).
21. J. S. Moore, Acc. Chem. Res. 30, 402 (1997).
22. E. J. Sorin, B. J. Nakatani, Y. M. Rhee, G. Jayachandran, V. Vishal, and V. S. Pande, J. Mol. Biol. 337, 789 (2004).
23. S. Elmer, S. Park, and V. Pande, J. Chem. Phys. 123, 114903 (2005).
24. K. Okuyama, T. Hasegawa, M. Ito, and N. Mikami, J. Phys. Chem. 88, 1711 (1984).
25. CRC Handbook of Chemistry and Physics (CRC, Cleveland, Ohio, 1977), p. v.
26. N. G. V. Kampen, Stochastic Processes in Physics and Chemistry, rev. and enl. ed. (North-Holland, Amsterdam, 1992).
27. I. Oppenheim, K. E. Shuler, and G. H. Weiss, Stochastic Processes in Chemical Physics: The Master Equation (MIT, Cambridge, Mass., 1977).
28. W. C. Swope, J. W. Pitera, and F. Suits, J. Phys. Chem. B 108, 6571 (2004).
29. W. C. Swope, J. W. Pitera, F. Suits, J. Phys. Chem. B 108, 6582 (2004).
30. N. Singhal, C. D. Snow, and V. S. Pande, J. Chem. Phys. 121, 415 (2004).
31. P. Deuflhard, W. Huisinga, A. Fischer, and C. Schutte, Linear Algebr. Appl. 315, 39 (2000).
32. M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande, J. Chem. Phys. 119, 5740 (2003).
33. M. R. Shirts and V. S. Pande, J. Chem. Phys. 122, 134508 (2005).
34. A. Ë. Grosberg and A. R. Khokhlov, Statistical Physics of Macromolecules (AIP, New York, 1994).
35. A. R. Fersht, Proc. Natl. Acad. Sci. U.S.A. 99, 14122 (2002).