Decomposition of energy and free energy changes by following the flow of work along reaction path

Journal of Chemical Physics

Volumn 131, Issue 14, 2009, Pages

  Haas, Kevin ^a   Chu, Jhih Wei ^a  

^a University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATED PROCESS; ALANINE DIPEPTIDES; AMIDE HYDROGENS; BIOCATALYTIC PROCESS; CARBONYL OXYGEN; DECOMPOSITION ANALYSIS; ENERGETIC COSTS; ENERGY DECOMPOSITION; EXPLICIT WATER; FREE ENERGY CHANGE; FREE ENERGY LANDSCAPE; FREE-ENERGY DIFFERENCE; HYDROGEN BONDINGS; IN-VACUUM; MECHANICAL ANALYSIS; MECHANICAL WORK; MINIMUM ENERGY PATHS; MINIMUM FREE ENERGIES; MOLECULAR ENGINEERING; REACTION PATHS; STRONG STABILIZATION; STRUCTURAL REARRANGEMENT; TEST CASE; TETRAHEDRAL INTERMEDIATES; TRANSESTERIFICATION REACTION; TWO-STATE; WATER MOLECULE;

AMIDES; ATOMS; DECOMPOSITION; ELECTRON ENERGY LEVELS; ELECTRON TRANSITIONS; FUNCTIONAL GROUPS; HYDROGEN; HYDROGEN BONDS; ISOMERIZATION; ISOMERS; OXYGEN; POTENTIAL ENERGY; REACTION KINETICS; WATER ANALYSIS;

FREE ENERGY;

EID: 70350464003     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3243080     Document Type: Article

References (38)

1. S. Glasstone, K. J. Laidler, and H. Eyring, The Theory of Rate Processes (McGraw-Hill, New York, 1941); J. I. Steinfeld, J. S. Francisco, and W. L. Hase, Chemical Kinetics and Dynamics (Prentice Hall, New York, 1999).
2. R. Elber and M. Karplus, Chem. Phys. Lett. 0009-2614 139, 375 (1987) 10.1016/0009-2614(87)80576-6; H. Woodcock, M. Hodoscek, P. Sherwood, Y. Lee, H. Schaefer, and B. Brooks, Theor. Chem. Acc. 1432-881X 109, 140 (2003) 10.1007/s00214-002-0421-3; J. -W. Chu, B. Trout, and B. Brooks, J. Chem. Phys. 0021-9606 119, 12708 (2003). 10.1063/1.1627754
3. H. Jónsson, G. Mills, and K. W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by, B. J. Berne, G. Ciccoti, and, D. F. Coker, (World Scientific, Singapore, 1998), p. 185.
4. P. Bolhuis, D. Chandler, C. Dellago, and P. Geissler, Annu. Rev. Phys. Chem. 0066-426X 53, 291 (2002) 10.1146/annurev.physchem.53.082301.113146; C. Dellago, P. Bolhuis, F. Csajka, and D. Chandler, J. Chem. Phys. 0021-9606 108, 1964 (1998). 10.1063/1.475562
5. C. Dellago and P. G. Bolhuis, Top. Curr. Chem. 0071-7894 268, 291 (2007). 10.1007/128-085
6. W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 0163-1829 66, 052301 (2002). 10.1103/PhysRevB.66.052301
7. L. Maragliano, A. Fischer, E. Vanden-Eijnden, and G. Ciccotti, J. Chem. Phys. 0021-9606 125, 024106 (2006). 10.1063/1.2212942 (Pubitemid 44088333)
8. W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 1089-5647 109, 6688 (2005). 10.1021/jp0455430 (Pubitemid 40552536)
9. M. Sprik and G. Ciccotti, J. Chem. Phys. 0021-9606 109, 7737 (1998). 10.1063/1.477419 (Pubitemid 128678344)
10. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford University Press, New York, 1987).
11. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 99, 12562 (2002). 10.1073/pnas.202427399
12. L. Zheng, M. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 105, 20227 (2008). 10.1073/pnas.0810631106
13. R. Radhakrishnan and T. Schlick, J. Chem. Phys. 0021-9606 121, 2436 (2004). 10.1063/1.1766014
14. U. Singh, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 85, 4280 (1988) 10.1073/pnas.85.12.4280; U. Singh and S. Benkovic, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 85, 9519 (1988) 10.1073/pnas.85.24.9519; L. Dang, K. Merz, and P. Kollman, J. Am. Chem. Soc. 0002-7863 111, 8505 (1989) 10.1021/ja00204a027; J. Gao, K. Kuczera, B. Tidor, and M. Karplus, Science 0036-8075 244, 1069 (1989) 10.1126/science.2727695; C. Brooks and S. Fleischman, J. Am. Chem. Soc. 0002-7863 112, 3307 (1990) 10.1021/ja00165a008; F. Lee, Z. Chu, and A. Warshel, J. Comput. Chem. 0192-8651 14, 161 (1993) 10.1002/jcc.540140205; A. Mark and W. Vangunsteren, J. Mol. Biol. 0022-2836 240, 167 (1994). 10.1006/jmbi.1994.1430
15. S. Y. Noskov and C. Lim, Biophys. J. 0006-3495 81, 737 (2001) 10.1016/S0006-3495(01)75738-4; H. Gohlke, C. Kiel, and D. A. Case, J. Mol. Biol. 0022-2836 330, 891 (2003) 10.1016/S0022-2836(03)00610-7; V. Zoete, M. Meuwly, and M. Karplus, Proteins 0887-3585 61, 79 (2005) 10.1002/prot.20528; Y. Deng and B. Roux, J. Phys. Chem. B 1089-5647 113, 2234 (2009) 10.1021/jp807701h; J. L. Gao and X. F. Xia, Science 0036-8075 258, 631 (1992) 10.1126/science.1411573; M. Strajbl, Y. Y. Sham, J. Villa, Z. T. Chu, and A. Warshel, J. Phys. Chem. B 1089-5647 104, 4578 (2000) 10.1021/jp0003095; T. Ishida, J. Chem. Phys. 0021-9606 129, 125105 (2008) 10.1063/1.2977458; M. Garcia-Viloca, D. G. Truhlar, and J. L. Gao, J. Mol. Biol. 0022-2836 327, 549 (2003) 10.1016/S0022-2836(03) 00123-2; C. Curutchet, C. J. Cramer, D. G. Truhlar, M. F. Ruiz-Lopez, D. Rinaldi, M. Orozco, and F. J. Luque, J. Comput. Chem. 0192-8651 24, 284 (2003). 10.1002/jcc.10143
16. R. Z. Khaliullin, E. A. Cobar, R. C. Lochan, A. T. Bell, and M. Head-Gordon, J. Phys. Chem. A 1089-5639 111, 8753 (2007). 10.1021/jp073685z (Pubitemid 47497589)
17. M. P. Mitoraj, A. Michalak, and T. Ziegler, J. Chem. Theory Comput. 1549-9618 5, 962 (2009). 10.1021/ct800503d
18. R. Olender and R. Elber, J. Mol. Struct.: THEOCHEM 0166-1280 398, 63 (1997) 10.1016/S0166-1280(97)00038-9; E. Vanden-Eijnden and M. Heymann, J. Chem. Phys. 0021-9606 128, 061103 (2008). 10.1063/1.2833040
19. M. Chen and W. Yang, J. Comput. Chem. 0192-8651 30, 1649 (2009). 10.1002/jcc.21311
20. P. A. Rejto, E. Bindewald, and D. Chandler, Nature (London) 0028-0836 375, 129 (1995). 10.1038/375129a0
21. W. E and E. Vanden-Eijnden, J. Stat. Phys. 0022-4715 123, 503 (2006) 10.1007/s10955-005-9003-9; E. Vanden-Eijnden, Lect. Notes Phys. 0075-8450 703, 439 (2006).
22. C. Jarzynski, Phys. Rev. Lett. 0031-9007 78, 2690 (1997) 10.1103/PhysRevLett.78.2690; C. Jarzynski, Phys. Rev. E 1063-651X 56, 5018 (1997) 10.1103/PhysRevE.56.5018; G. E. Crooks, Phys. Rev. E 1063-651X 60, 2721 (1999). 10.1103/PhysRevE.60.2721
23. J. B. Brokaw, K. R. Haas, and J. -W. Chu, J. Chem. Theory Comput. 1549-9618 5, 2050 (2009). 10.1021/ct9001398
24. Weinan E., W. Q. Ren, and E. Vanden-Eijnden, Chem. Phys. Lett. 0009-2614 413, 242 (2005). 10.1016/j.cplett.2005.07.084 (Pubitemid 41252399)
25. G. Hummer and I. G. Kevrekidis, J. Chem. Phys. 0021-9606 118, 10762 (2003) 10.1063/1.1574777; R. R. Coifman, I. G. Kevrekidis, S. Lafon, M. Maggioni, and B. Nadler, Multiscale Model. Simul. 1540-3459 7, 842 (2008) 10.1137/070696325; A. C. Pan and B. Roux, J. Chem. Phys. 0021-9606 129, 064107 (2008) 10.1063/1.2959573; A. K. Faradjian and R. Elber, J. Chem. Phys. 0021-9606 120, 10880 (2004) 10.1063/1.1738640; A. Ma and A. R. Dinner, J. Phys. Chem. B 1089-5647 109, 6769 (2005) 10.1021/jp045546c; B. Peters and B. L. Trout, J. Chem. Phys. 0021-9606 125, 054108 (2006). 10.1063/1.2234477
26. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 98, 3658 (2001) 10.1073/pnas.071034098; E. N. Zimanyi and R. J. Silbey, J. Chem. Phys. 0021-9606 130, 171102 (2009). 10.1063/1.3132747
27. W. Kabsch, Acta Crystallogr., Sect. A: Cryst. Phys., Diffr., Theor. Gen. Crystallogr. 0567-7394 32, 922 (1976). 10.1107/S0567739476001873
28. G. Henkelman and H. Jónsson, J. Chem. Phys. 0021-9606 113, 9978 (2000). 10.1063/1.1323224 (Pubitemid 32076892)
29. A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B 1089-5647 102, 3586 (1998). 10.1021/jp973084f
30. A. D. Mackerell, M. Feig, and C. L. Brooks, J. Comput. Chem. 0192-8651 25, 1400 (2004). 10.1002/jcc.20065
31. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 0192-8651 4, 187 (1983). 10.1002/jcc.540040211
32. W. Ren, E. Vanden-Eijnden, P. Maragakis, and W. N. E, J. Chem. Phys. 0021-9606 123, 134109 (2005). 10.1063/1.2013256 (Pubitemid 41435113)
33. M. Feig, J. Chem. Theory Comput. 1549-9618 3, 1734 (2007). 10.1021/ct7000705
34. D. Darnoko and M. Cheryan, J. Am. Oil Chem. Soc. 0003-021X 77, 1263 (2000). 10.1007/s11746-000-0198-y
35. D. Voet and J. G. Voet, Biochemistry, 3rd ed. (Wiley, Hoboken, NJ, 2004).
36. R. K. Eppler, R. S. Komor, J. Huynh, J. S. Dordick, J. A. Reimer, and D. S. Clark, Proc. Natl. Acad. Sci. U.S.A. 0027-8424 103, 5706 (2006). 10.1073/pnas.0601113103
37. H. L. Woodcock, M. Hodoscek, A. T. B. Gilbert, P. M. W. Gill, H. F. Schaefer, and B. R. Brooks, J. Comput. Chem. 0192-8651 28, 1485 (2007). 10.1002/jcc.20587 (Pubitemid 46853788)
38. G. K. Schenter, G. Mills, and H. Jónsson, J. Chem. Phys. 0021-9606 101, 8964 (1994). 10.1063/1.468447