Topologically invariant reaction coordinates for simulating multistate chemical reactions

Journal of Physical Chemistry B

Volumn 116, Issue 51, 2012, Pages 14876-14885

  Mones, Letif ^a   Csányi, Gábor ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REACTIONS; FREE ENERGY;

ACTIVATION BARRIERS; ATOMIC COORDINATE; COLLECTIVE VARIABLES; COMPLEX ENVIRONMENTS; ENERGY DIFFERENCES; ENERGY PROFILE; FORCE FIELDS; MULTI-STATE; POTENTIAL OF MEAN FORCE; REACTION COORDINATES; SIDE REACTIONS; TRANSITION STATE ENSEMBLES;

TOPOLOGY;

EID: 84871666792     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp307648s     Document Type: Article

References (35)

1. Kastner, J.; Thiel, W. J. Chem. Phys. 2005, 123, 144104
2. Isralewitz, B.; Gao, M.; Schulten, K. Curr. Opin. Struct. Biol. 2001, 11, 224-230
3. Carter, E.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Chem. Phys. Lett. 1989, 156, 472-477
4. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562-12566
5. Darve, E.; Pohorille, A. J. Chem. Phys. 2001, 115, 9169-9183
6. Metzner, P.; Schutte, C.; Vanden-Eijnden, E. J. Chem. Phys. 2006, 125, 084110
7. Vanden-Eijnden, E.; Venturoli, M.; Ciccotti, G.; Elber, R. J. Chem. Phys. 2008, 129, 174102
8. Vanden-Eijnden, E. In Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology; Ferrario, M.; Ciccotti, G.; Binder, K., Eds.; Springer-Verlag: Berlin Heidelberg, 2006; Vol. 1, pp 453-493.
9. E, W.; Vanden-Eijnden, E. Annu. Rev. Phys. Chem. 2010, 61, 391-420
10. Geissler, P. L.; Dellago, C.; Chandler, D. J. Phys. Chem. B 1999, 103, 3706-3710
11. Mones, L.; Kulhánek, P.; Simon, I.; Laio, A.; Fuxreiter, M. J. Phys. Chem. B 2009, 113, 7867-7873
12. Rosta, E.; Woodcock, H. L.; Brooks, B. R.; Hummer, G. J. Comput. Chem. 2009, 30, 1634-1641
13. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. J. Chem. Phys. 1998, 108, 1964-1977
14. E, W.; Ren, W.; Vanden-Eijnden, E. J. Phys. Chem. B 2005, 109, 6688-6693
15. Marcus, R. A. Annu. Rev. Phys. Chem. 1964, 15, 155-196
16. Marcus, R. A. J. Chem. Phys. 1965, 43, 679-701
17. Warshel, A.; Weiss, R. M. J. Am. Chem. Soc. 1980, 102, 6218-6226
18. Warshel, A. J. Phys. Chem. 1982, 86, 2218-2224
19. Sprik, M. Faraday Discuss. 1998, 110, 437-445
20. Vuilleumier, R.; Borgis, D. J. Mol. Struct. 1997, 436-437, 555-565
21. Schmitt, U. W.; Voth, G. A. J. Phys. Chem. B 1998, 102, 5547-5551
22. C̆uma, M.; Schmitt, U. W.; Voth, G. A. J. Phys. Chem. A 2001, 105, 2814-2823
23. Swanson, J. M. J.; Maupin, C. M.; Chen, H.; Petersen, M. K.; Xu, J.; Wu, Y.; Voth, G. A. J. Phys. Chem. B 2007, 111, 4300-4314
24. Case, D. A.; Darden, T. A.; Cheatham, III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; AMBER 9; University of California: San Francisco, CA, 2006.
25. Kulhánek, P.; Fuxreiter, M.; Koča, J.; Mones, L.; Střelcová, Z.; Petřek, M. PMFLib: A Toolkit for Free Energy Calculations. https://lcc.ncbr.muni.cz/whitezone/development/pmflib.
26. Repasky, M. P.; Chandrasekhar, J.; Jorgensen, W. L. J. Comput. Chem. 2002, 23, 1601-1622
27. Luz, Z.; Meiboom, S. J. Am. Chem. Soc. 1964, 86, 4768-4769
28. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. J. Phys. Chem. B 1998, 102, 3586-3616
29. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089-10092
30. Adelman, S. A.; Doll, J. D. J. Chem. Phys. 1976, 64, 2375-2388
31. Lelievre, T.; Rousset, M.; Stoltz, G. J. Chem. Phys. 2007, 126, 134111
32. Torrie, G.; Valleau, J. J. Comput. Phys. 1977, 23, 187-199
33. Berg, B. A.; Harris, R. C. Comput. Phys. Commun. 2008, 179, 443-448
34. Lim, T.-C. J. Math. Chem. 2003, 33, 279-285
35. Lelièvre, T.; Rousset, M.; Stoltz, G. Nonlinearity 2008, 21, 1155