Can the MaxFlux algorithm describe bifurcating paths? A comparison with analytic and Transition Path Sampling results

Theoretical Chemistry Accounts

Volumn 118, Issue 4, 2007, Pages 769-775

  Jiménez, Aurora ^a   Crehuet, Ramon ^a  

^a DEPARTMENT OF ENVIRONMENTAL CHEMISTRY   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 35348830579     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-007-0290-x     Document Type: Article

References (39)

1. Carpenter BK (1998). Dynamic behaviour of organic reactive intermediates. Angew Che Int Ed 37: 3340
2. Bartsch RA, Chae YM, Ham S and Birney DM (2001). Experimental and theoretical studies on the thermal decomposition of heterocyclic nitrosamines. J Am Chem Soc 123(31): 7479
3. Zhou C and Birney DM (2002). Sequential transition states and the valley-ridge inflection point in the formation of semibullvalene. Org Lett 4(19): 3279
4. Carpenter BK (2005). Nonstatistical dynamics in thermal reactions of polyatomic molecules. Annu Rev Phys Chem 56: 57
5. Lasorne B, Dive G and Desouter-Lecompte M (2005). Wave packets in a bifurcating region of an energy landscape: Diels-Alder dimerisation of cyclopentadiene. J Chem Phys 122: 184304
6. Doubleday C, Suhrada CP and Houk KN (2006). Dynamics of the degenerate rearrangement of bicyclo[3.1.0]hex-2-ene. J Am Chem Soc 128: 90
7. Ussing BR, Hang C and Singleton DA (2006). Dynamic effects on the periselectivity, rate, isotope effects, and mechanism of cycloadditions of ketenes with cyclopentadiene. J Am Chem Soc 128: 7594
8. Olender R, Elber R (1997) Yet another look at the steepest descent path. J Mol Struct THEOCHEM 398-399:63
9. Vanden-Eijnden E (2006) Transition path theory. In: Ferrario M, Ciccotti G, Binder K (eds). Computer simulations in condensed matter: from materials to chemical biology, vol. 1 1st edn. Lecture Notes in Physics vol 703. Springer, Berlin
10. González-Lafont A, Moreno M and Lluch JM (2004). Variational transition state theory as a tool to determine kinetic selectivity in reactions involving a valley-ridge inflection point. J Am Chem Soc 126(40): 13089
11. Valtazanos P and Ruedenberg K (1986). Bifurcations and transition states. Theor Chim Acta 69: 281
12. Quapp W, Hirsch M and Heidrich D (2004). An approach to reaction path branching using valley-ridge inflection points of potential energy surfaces. Theor Chem Acc 112: 40
13. Hirsch M and Quapp W (2004). Reaction pathways and convexity of the potential energy surface: application of Newton trajectories. J Math Chem 36: 307
14. Aguilar-Mogas A, Crehuet R, Giménez X, Bofill JM (2007) Applications of analytic and geometry concepts of the theory of calculus of variations to the intrinsic reaction coordinate model. (submitted to Mol Phys)
15. Bakken V, Danovich D, Shaik S and Schlegel HB (2001). A single transition state serves two mechanisms: an ab initio classical trajectory study of the electron transfer and substitution mechanisms in reactions of ketyl radical anions with alkyl halides. J Am Chem Soc 123: 130
16. Berkowitz M, Morgan JD, McCammon JD and Northrup SH (1983). Diffusion-controlled reactions: A variational formula for the optimum reaction coordinate. J Chem Phys 79(11): 5563
17. Huo S and Straub JE (1997). The MaxFlux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body systems at a finite temperature. J Chem Phys 107(13): 5000
18. Crehuet R and Field MJ (2003). A temperature-dependent nudged-elastic-band algorithm. J Chem Phys 118: 9563
19. Jónsson H, Mills G and Jacobsen KW (1998). Nudged elastic band method for finding minimum energy paths of transitions. In: Berne, BJ, Ciccotti, G, and Coker, DF (eds) Classical and quantum dynamics in condensed phase simulations, pp 385-404. World Scientific, Singapore
20. Field MJ, Albe M, Bret C, Proust-de Martin F and Thomas A (2000). The library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials. J Comput Chem 21(12): 1088
21. Elber R and Shalloway D (2000). Temperature dependent reaction coordinates. J Chem Phys 112(13): 5539
22. Soskin SM (2006). Most probable transition path in an overdamped system for a finite transition time. Phys Lett A 353: 281
23. Apostolakis J, Ferrara P and Caflisch A (1999). Calculation of conformational transitions and barriers in solvated systems: application to the alanine dipeptide in water. J Chem Phys 110(4): 2099
24. Bolhuis PG, Dellago C and Chandler D (2000). Reaction coordinates of biomolecular isomerization. Proc Nat Acad Sci 97(11): 5877
25. Ren W, Vanden-Eijnden E, Maragakis P and E W (2005). Transition pathways in complex systems: application of the finite-temperature string method to the alanine dipeptide. J Chem Phys 123: 134109
26. Maragliano L, Fischer A, Vanden-Eijnden E and Ciccotti G (2006). String method in collective variables: minimum free energy paths and isocommittor surfaces. J Chem Phys 125: 024106
27. Still WC, Tempczyk A, Hawley RC and Hendrickson T (1990). Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112: 6127
28. Qiu D, Shenkin PS, Hollinger FP and Still WC (1997). The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J Phys Chem A 101: 3005
29. Jorgensen WL, Maxwell DS and Tirado-Rives J (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118: 11225
30. Dellago C, Bolhuis PG and Geissler PL (2002). Transition path sampling. Adv Chem Phys 123: 1
31. Crehuet R, Field MJ (2006) A transition path sampling study of the reaction catalyzed by the enzyme chorismate mutase. J Phys Chem B (in press). doi:10.1021/jp067629u
32. Gershinsky G and Berne BJ (1999). The dependence of the rate constant for isomerisation on the competition between intramolecular vibrational relaxation and energy transfer to the bath: a stochastic model. J Chem Phys 110: 1053
33. Nummela JA and Carpenter BK (2002). Nonstatistical dynamics in deep potential wells: a quasiclassical trajectory study of methyl loss from the acetone radical cation. J Am Chem Soc 124(29): 8512
34. Crehuet R and Bofill JM (2005). The reaction path intrinsic reaction coordinate method and the Hamilton-Jacobi theory. J Chem Phys 122: 234105
35. Quapp W (2001) Comment on the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states (by J. M. Anglada, E. Besalú, J. M. Bofill, and R. Crehuet, J Comput Chem 2001, 22, 4, 387-406).
36. J Comput Chem 22(5):537
37. E W, Ren W and Vanden-Eijnden E (2005). Finite temperature string method for the study of rare events. J Phys Chem B 109: 6688
38. Miller WH, Handy NC and Adams JE (1980). Reaction path hamiltonian for polyatomic molecules. J Chem Phys 72(1): 99
39. González J, Giménez X and Bofill JM (2001). On the reaction path hamiltonian for polyatomic molecules. J Phys Chem A 105(20): 5022