Activation energy for a model ferrous-ferric half reaction from transition path sampling

Journal of Chemical Physics

Volumn 136, Issue 3, 2012, Pages

  Drechsel Grau, Christof ^a,b   Sprik, Michiel ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENTROPIES; ACTIVATION FREE ENERGY; ACTIVATION PARAMETER; DIABATIC; FERROUS ION; HALF REACTIONS; LINEAR RESPONSE; MARCUS MODELS; MARCUS THEORY; MODEL SYSTEM; MOLECULAR SIMULATIONS; REACTION COORDINATES; STATISTICAL UNCERTAINTY; TEMPERATURE DEPENDENCE; THERMODYNAMIC INTEGRATION; TRANSITION PATH SAMPLING;

COMPUTER SIMULATION; ENTROPY; FREE ENERGY; IRON; SAMPLING;

ACTIVATION ENERGY;

EID: 84856436089     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3677195     Document Type: Article

References (75)

1. P. W. Atkins and J. de Paula, Atkins Physical Chemistry, 9th ed. (Oxford University Press, Oxford, 2009).
2. R. M. Levy and E. Gallicchio, Annu. Rev. Phys. Chem. 49, 531 (1998). 10.1146/annurev.physchem.49.1.531
3. C. Dellago and P. G. Bolhuis, Mol. Simul. 30, 795 (2004). 10.1080/08927020412331294869 (Pubitemid 40026281)
4. M. Grnwald and C. Dellago, J. Chem. Phys. 131, 164116 (2009). 10.1063/1.3253700
5. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002). 10.1146/annurev.physchem.53.082301.113146 (Pubitemid 35336255)
6. C. Dellago, P. G. Bolhuis, and P. Geissler, Adv. Chem. Phys. 123, 1 (2002). 10.1002/0471231509
7. C. Dellago, P. G. Bolhuis, and P. L. Geissler, Transition path sampling methods., in Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology-Vol. 1, Lecture Notes in Physics Vol. 703, edited by, M. Ferrario, G. Ciccotti, and, K. Binder, (Springer, Berlin, 2006), pp. 349-391.
8. P. Kollman, Chem. Rev. 93, 2395 (1993). 10.1021/cr00023a004
9. N. Lu, D. A. Kofke, and T. B. Woolf, J. Phys. Chem. B 107, 5598 (2003). 10.1021/jp027627j
10. R. A. Kuharski, J. S. Bader, D. Chandler, M. Sprik, M. L. Klein, and R. W. Impey, J. Chem. Phys. 89, 3248 (1988). 10.1063/1.454929
11. K. Ando, J. Chem. Phys. 106, 116 (1997). 10.1063/1.473037
12. K. Ando, J. Chem. Phys. 114, 9470 (2001). 10.1063/1.1369128 (Pubitemid 32535615)
13. R. B. Yelle and T. Ichiye, J. Phys. Chem. B 101, 4127 (1997). 10.1021/jp970081u
14. R. Ayala and M. Sprik, J. Phys. Chem. B 112, 257 (2008). 10.1021/jp0748516 (Pubitemid 351184598)
15. R. A. Marcus, J. Chem. Phys. 24, 966 (1956). 10.1063/1.1742723
16. R. A. Marcus, J. Chem. Phys. 24, 979 (1956). 10.1063/1.1742724
17. R. A. Marcus, Discuss. Faraday Soc. 29, 21 (1960). 10.1039/df9602900021
18. R. A. Marcus, J. Chem. Phys. 43, 679 (1965). 10.1063/1.1696792
19. R. A. Marcus, Rev. Mod. Phys. 65, 599 (1993). 10.1103/RevModPhys.65.599
20. J. Kstner and W. Thiel, J. Chem. Phys. 123, 144104 (2005). 10.1063/1.2052648 (Pubitemid 41476700)
21. G. King and A. Warshel, J. Chem. Phys. 93, 8682 (1990). 10.1063/1.459255
22. A. A. Milischuk, D. V. Matyushov, and M. D. Newton, Chem. Phys. 324, 172 (2006). 10.1016/j.chemphys.2005.11.037
23. P. K. Ghorai and D. V. Matyushov, J. Phys. Chem. A 110, 8857 (2006). 10.1021/jp056261i (Pubitemid 44187388)
24. J. Blumberger and M. Sprik, Theor. Chem. Acc. 115, 113 (2006). 10.1007/s00214-005-0058-0 (Pubitemid 43346554)
25. J. Blumberger, I. Tavernelli, M. L. Klein, and M. Sprik, J. Chem. Phys. 124, 064507 (2006). 10.1063/1.2162881 (Pubitemid 43248033)
26. F. Costanzo, M. Sulpizi, R. G. DellaValle, and M. Sprik, J. Chem. Phys. 134, 244508 (2011). 10.1063/1.3597603
27. A. Warshel, J. Phys. Chem. 86, 2218 (1982). 10.1021/j100209a016
28. J.-K. Hwang and A. Warshel, J. Am. Chem. Soc. 109, 715 (1987). 10.1021/ja00237a013
29. E. A. Carter and J. T. Hynes, J. Phys. Chem. 93, 2184 (1989). 10.1021/j100343a002
30. M. Tachiya, J. Phys. Chem. 93, 7050 (1989). 10.1021/j100357a005
31. H.-X. Zhou and A. Szabo, J. Chem. Phys. 103, 3481 (1995). 10.1063/1.470232
32. C. Hartnig and M. T.M. Koper, J. Chem. Phys. 115, 8540 (2001). 10.1063/1.1408295 (Pubitemid 33084393)
33. J. G. Kirkwood, J. Chem. Phys. 3, 300 (1935). 10.1063/1.1749657
34. D. V. Matyushov and G. A. Voth, J. Chem. Phys. 113, 5413 (2000). 10.1063/1.1289886
35. T. Simonson, Proc. Natl. Acad. Sci. U.S.A. 99, 6544 (2002). 10.1073/pnas.082657099 (Pubitemid 34526169)
36. B. S. Brunschwig and N. Sutin, Coord. Chem. Rev. 187, 233 (1999). 10.1016/S0010-8545(98)00255-0
37. G. M. Torrie and J. P. Valleau, Chem. Phys. Lett. 28, 578 (1974). 10.1016/0009-2614(74)80109-0
38. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977). 10.1016/0021-9991(77)90121-8
39. J. Kstner and W. Thiel, J. Chem. Phys. 124, 234106 (2006). 10.1063/1.2206775 (Pubitemid 43938886)
40. A. Nitzan, Chemical Dynamics in Condensed Phases: Relaxation, Transfer, and Reactions in Condensed Molecular Systems (Oxford University Press, Oxford, 2006).
41. W. H. Miller, Acc. Chem. Res. 9, 306 (1976). 10.1021/ar50104a005
42. D. Chandler, J. Chem. Phys. 68, 2959 (1978). 10.1063/1.436049
43. H. J. C. Berendsen, J. P. Postma, W. F. van Gunsteren, and J. Hermans, Interaction models for water in relation to protein hydration., in Intermolecular Forces, edited by, B. Pullman, (Reidel, Dordrecht, 1981), pp. 331-342.
44. J. Blumberger and M. Sprik, J. Phys. Chem. B 109, 6793 (2005). 10.1021/jp0455879 (Pubitemid 40538448)
45. A. Warshel and R. M. Weiss, J. Am. Chem. Soc. 102, 6218 (1980). 10.1021/ja00540a008
46. D. A. Zichi, G. Ciccotti, J. T. Hynes, and M. Ferrario, J. Phys. Chem. 93, 6261 (1989). 10.1021/j100354a001
47. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed. (Academic, San Diego, 2002).
48. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1989).
49. Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. 124, 024503 (2006). 10.1063/1.2136877 (Pubitemid 43100215)
50. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998). 10.1063/1.475562
51. W. Smith, T. R. Forester, and I. T. Todorov, The DL-POLY-2 user manual version 2.18, STFC Daresbury Laboratory, Daresbury, Warrington WA4 4AD, Cheshire, UK.
52. L. Verlet, Phys. Rev. 159, 98 (1967). 10.1103/PhysRev.159.98
53. W. C. Swope, H. C. Andersen, P. H. Berens, and K. R. Wilson, J. Chem. Phys. 76, 637 (1982). 10.1063/1.442716
54. H. C. Andersen, J. Comput. Phys. 52, 24 (1983). 10.1016/0021-9991(83) 90014-1
55. S. Nos, Mol. Phys. 52, 255 (1984). 10.1080/00268978400101201
56. S. Nos, J. Chem. Phys. 81, 511 (1984). 10.1063/1.447334
57. W. G. Hoover, Phys. Rev. A 31, 1695 (1985). 10.1103/PhysRevA.31.1695
58. C. L. Brooks III, J. Phys. Chem. 90, 6680 (1986). 10.1021/j100283a017
59. C. Peter, C. Oostenbrink, A. van Dorp, and W. F. van Gunsteren, J. Chem. Phys. 120, 2652 (2004). 10.1063/1.1636153
60. W. F. van Gunsteren, X. Daura, and A. E. Mark, Helv. Chim. Acta 85, 3113 (2002). 10.1002/1522-2675(200210)85:10%3c3113::AID-HLCA3113%3e3.0.CO;2-0
61. P. L. Geissler and D. Chandler, J. Chem. Phys. 113, 9759 (2000). 10.1063/1.1290136 (Pubitemid 32085157)
62. G. Hummer, L. R. Pratt, and A. E. Garca, J. Phys. Chem. 100, 1206 (1996). 10.1021/jp951011v
63. P. H. Hnenberger and J. A. McCammon, J. Chem. Phys. 110, 1856 (1999). 10.1063/1.477873
64. C. Peter, W. F. van Gunsteren, and P. H. Hnenberger, J. Chem. Phys. 119, 12205 (2003). 10.1063/1.1624054
65. H. Flyvbjerg and H. G. Petersen, J. Chem. Phys. 91, 461 (1989). 10.1063/1.457480
66. A. A. Clifford, Multivariate Error Analysis: A Handbook of Error Propagation and Calculation in Many-Parameter Systems (Applied Science, London, 1973).
67. H. B. Mann, Econometrica 13, 245 (1945). 10.2307/1907187
68. S. K. Schiferl and D. C. Wallace, J. Chem. Phys. 83, 5203 (1985). 10.1063/1.449733
69. J. von Neumann, Ann. Math. Stat. 12, 367 (1941). 10.1214/aoms/1177731677
70. J. von Neumann, R. H. Kent, H. R. Bellinson, and B. I. Hart, Ann. Math. Stat. 12, 153 (1941). 10.1214/aoms/1177731746
71. F. E. Croxton and D. J. Cowden, Applied General Statistics, 2nd ed. (Pitman, London, 1963).
72. E. S. Pearson, Biometrika 22, 239 (1930). 10.1093/biomet/22.1-2.239
73. C. Dellago, P. G. Bolhuis, and D. Chandler, J. Chem. Phys. 110, 6617 (1999). 10.1063/1.478569
74. M. Tachiya, J. Phys. Chem. 97, 5911 (1993). 10.1021/j100124a023
75. D. P. Fernndez, Y. Mulev, A. R.H. Goodwin, and J. M. H. Levelt Sengers, J. Phys. Chem. Ref. Data 24, 33 (1995). 10.1063/1.555977