A doubly nudged elastic band method for finding transition states

Journal of Chemical Physics

Volumn 120, Issue 5, 2004, Pages 2082-2094

  Trygubenko, Semen A ^a   Wales, David J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; IMAGE ANALYSIS; INTERPOLATION; ISOMERS; ITERATIVE METHODS; OPTIMIZATION; POTENTIAL ENERGY; VECTORS;

EUCLIDEAN SEPARATION; ITERATION DENSITIES; TRANSITION STATES;

PHASE TRANSITIONS;

EID: 1442282189     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1636455     Document Type: Article

References (105)

1. H. Eyring, Chem. Rev. (Washington, D.C.) 17, 65 (1935).
2. M. G. Evans and M. Polanyi, Trans. Faraday Soc. 31, 875 (1935).
3. K. J. Laidler, Chemical Kinetics (Harper & Row, New York, 1987).
4. J. N. Murrell and K. J. Laidler, Trans. Faraday Soc. 64, 371 (1968).
5. D. J. Wales, Energy Landscapes: Applications to Clusters, Biomolecules and Glasses (Cambridge University Press, Cambridge, 2003).
6. P. Pulay, G. Fogorasi, F. Pang, and J. E. Boggs, J. Am. Chem. Soc. 101, 2550 (1979).
7. G. Fogorasi, X. Zhou, P. W. Taylor, and P. Pulay, J. Am. Chem. Soc. 114, 8191 (1992).
8. P. Pulay and G. Fogorasi, J. Chem. Phys. 96, 2856 (1996).
9. J. Baker, A. Kessi, and B. Delley, J. Chem. Phys. 105, 192 (1996).
10. C. Peng, P. Y. Ayala, H. B. Schlegel, and M. J. Frisch, J. Comput. Chem. 17, 49 (1996).
11. J. Baker, D. Kinghorn, and P. Pulay, J. Chem. Phys. 110, 4986 (1999).
12. S. R. Billeter, A. J. Turner, and W. Thiel, Phys. Chem. Chem. Phys. 2, 2177 (2000).
13. B. Paizs, J. Baker, S. Suhai, and P. Pulay, J. Chem. Phys. 113, 6566 (2000).
14. V. Bakken and T. Helgaker, J. Chem. Phys. 117, 9160 (2002).
15. G. M. Crippen and H. A. Scheraga, Arch. Biochem. Biophys. 144, 462 (1971).
16. J. W. McIver and A. Komornicki, J. Am. Chem. Soc. 94, 2625 (1972).
17. J. Pancíř, Collect. Czech. Chem. Commun. 40, 1112 (1974).
18. R. L. Hilderbrandt, Comput. Chem. (Oxford) 1, 179 (1977).
19. C. J. Cerjan and W. H. Miller, J. Chem. Phys. 75, 2800 (1981).
20. J. Simons, P. Jørgenson, H. Taylor, and J. Ozment, J. Phys. Chem. 87, 2745 (1983).
21. D. O'Neal, H. Taylor, and J. Simons, J. Phys. Chem. 88, 1510 (1984).
22. S. Bell and J. S. Crighton, J. Chem. Phys. 80, 2464 (1984).
23. A. Banerjee, N. Adams, J. Simons, and R. Shepard, J. Phys. Chem. 89, 52 (1985).
24. J. Baker, J. Comput. Chem. 7, 385 (1986).
25. D. T. Nguyen and D. A. Case, J. Phys. Chem. 89, 4020 (1985).
26. J. Baker, J. Comput. Chem. 8, 563 (1987).
27. M. C. Smith, Int. J. Quantum Chem. 37, 773 (1990).
28. J. Nichols, H. Taylor, P. Schmidt, and J. Simons, J. Chem. Phys. 92, 340 (1990).
29. J. Baker and W. H. Hehre. Int. J. Quantum Chem. 12, 606 (1991).
30. J. Baker, J. Comput. Chem. 13, 240 (1992).
31. C. J. Tsai and K. D. Jordan, J. Phys. Chem. 97, 11227 (1993).
32. D. J. Wales, J. Chem. Soc. Faraday Trans. 89, 1305 (1993).
33. S. F. Chekmarev, Chem. Phys. Lett. 227, 354 (1994).
34. D. J. Wales, J. Chem. Phys. 101, 3750 (1994).
35. D. J. Wales and J. Uppenbrink, Phys. Rev. B 50, 12342 (1994).
36. J.-Q. Sun and K. Ruedenberg, J. Chem. Phys. 101, 2157 (1994).
37. J.-Q. Sun and K. Ruedenberg, J. Chem. Phys. 101, 2168 (1994).
38. F. Jensen, J. Chem. Phys. 102, 6706 (1995).
39. J. M. Bofill and M. Comajuan, J. Comput. Chem. 16, 1326 (1995).
40. Q. Zhao and J. B. Nicholas, J. Chem. Phys. 104, 767 (1996).
41. W. Quapp, Chem, Phys. Lett. 253, 286 (1996).
42. J. Baker and F. Chan, J. Comput. Chem. 17, 888 (1996).
43. T. R. Walsh and D. J. Wales, J. Chem. Soc., Faraday Trans. 92, 2505 (1996).
44. P. Y. Ayala and H. B. Schlegel, J. Chem. Phys. 107, 375 (1997).
45. L. J. Munro and D. J. Wales, Faraday Discuss. 106, 409 (1997).
46. A. Ulitsky and D. Shalloway, J. Chem. Phys. 106, 10099 (1997).
47. B. Paizs, G. Fogarasi, and P. Pulay, J. Chem. Phys. 109, 6571 (1998).
48. O. Farkas and H. B. Schlegel, J. Chem. Phys. 109, 7100 (1998).
49. N. Mousseau and G. T. Barkema, Phys. Rev. E 57, 2419 (1998).
50. H. Goto, Chem. Phys. Lett. 292, 254 (1998).
51. W. Quapp, M. Hirsch, O. Imig, and D. Heidrich, J. Comput. Chem. 19, 1087 (1998).
52. O. Farkas and H. B. Schlegel, J. Chem. Phys. 111, 10806 (1999).
53. L. J. Munro and D. J. Wales, Phys. Rev. B 59, 3969 (1999).
54. D. J. Wales, J. P. K. Doye, M. A. Miller, P. N. Mortenson, and T. R. Walsh, Adv. Chem. Phys. 115, 1 (2000).
55. Y. Kumeda, L. J. Munro, and D. J. Wales, Chem. Phys. Lett. 341, 185 (2001).
56. L. R. Pratt, J. Chem. Phys. 85, 5045 (1986).
57. R. Elber and M. Karplus, Chem. Phys. Lett. 139, 375 (1987).
58. R. S. Berry, H. L. Davis, and T. L. Beck, Chem. Phys. Lett. 147, 13 (1988).
59. R. Czerminski and R. Elber, J. Chem. Phys. 92, 5580 (1990).
60. S. Fischer and M. Karplus, Chem. Phys. Lett. 194, 252 (1992).
61. L. L. Stachó and M. I. Bán, Theor. Chim. Acta 83, 433 (1992).
62. I. V. Ionova and E. A. Carter, J. Chem. Phys. 98, 6377 (1993).
63. L. L. Stachó and M. I. Bán, Theor. Chim. Acta 84, 535 (1993).
64. G. Dömötör, M. I. Bán, and L. L. Stachó, J. Comput. Chem. 14, 1491 (1993).
65. C. Peng and H. B. Schlegel, Isr. J. Chem. 33, 449 (1993).
66. A. Matro, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 101, 10458 (1994).
67. O. S. Smart, Chem. Phys. Lett. 222, 503 (1994).
68. M. I. Bán, G. Dömötör, and L. L. Stachó, J. Mol. Struct.: THEOCHEM 311, 29 (1994).
69. G. Mills and H. Jónsson, Phys. Rev. Lett. 72, 1124 (1994).
70. I. V. Ionova and E. A. Carter, J. Chem. Phys. 103, 5437 (1995).
71. H. Jónsson, G. Mills, and W. Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by B. J. Berne, G. Ciccotti, and D. F. Coker (World Scientific, Singapore, 1998), p. 385.
72. L. L. Stachó, G. Dömötör, and M. I. Bán, Chem. Phys. Lett. 311, 328 (1999).
73. R. Elber and M. Karplus, Chem. Phys. Lett. 311, 335 (1999).
74. G. Henkelman and H. Jónsson, J. Chem. Phys. 111, 7010 (1999).
75. G. Henkelman, B. P. Uberuaga, and H. Jonsson, J. Chem. Phys. 113, 9901 (2000).
76. G. Henkelman and H. Jónsson, J. Chem. Phys. 113, 9978 (2000).
77. G. Henkelman and H. Jónsson, J. Chem. Phys. 115, 9657 (2001).
78. R. A. Miron and K. A. Fichthorn, J. Chem. Phys. 115, 8742 (2001).
79. P. Maragakis, S. A. Andreev, Y. Brumer, D. R. Reichman, and E. Kaxiras, J. Chem. Phys. 117, 4651 (2002).
80. D. J. Wales and T. R. Walsh, J. Chem. Phys. 105, 6957 (1996).
81. D. J. Wales, Mol. Phys. 100, 3285 (2002).
82. D. A. Evans and D. J. Wales, J. Chem. Phys. 119, 9947 (2003).
83. H. B. Schlegel, J. Comput. Chem. 24, 1514 (2003).
84. G. Henkelman, G. Johannesson, and H. Jónsson, in Progress in Theoretical Chemistry and Physics, edited by S. D. Schwartz (Kluwer Academic, Dordrecht, 2000), p. 269.
85. T. A. Halgren and W. N. Lipscomb, Chem. Phys. Lett. 49, 225 (1977).
86. M. J. S. Dewar, E. F. Healy, and J. J. P. Stewart, J. Chem. Soc., Faraday Trans. 280, 227 (1984).
87. C. Cardenas-Lailhacar and M. C. Zerner, Int. J. Quantum Chem. 55, 429 (1995).
88. D. A. Liotard, Int. J. Quantum Chem. 44, 723 (1992).
89. C. Choi and R. Elber, J. Chem. Phys. 94, 751 (1991).
90. F. Jensen, Introduction to Computational Chemistry (Wiley, New York, 1999).
91. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1989).
92. R. Crehuet and M. J. Field, J. Chem. Phys. 118, 9563 (2003).
93. D. C. Liu and J. Nocedal, Math. Program. 45, 503 (1989).
94. J. Nocedal, Math. Comput. 35. 773 (1980).
95. J. Nocedal, Software for Large-scale Unconstrained Optimization (Northwestern University Press, Evanston, 2000) 〈http://www.ece.northwestern.edu/~nocedal/lbfgs.html〉
96. K. Müller and L. D. Brown, Theor. Chim. Acta 53, 75 (1979).
97. D. R. Alfonso and K. D. Jordan, J. Comput. Chem. 24, 990 (2003).
98. D. R. Alfonso, Driver for Performing Minimum Energy Path Optimizations Using the Nudged Elastic Band Algorithm (2002). 〈http://www.pitt.edu/~alfonso/NEB/neb.html〉
99. D. J. Wales. OPTIM: A Program for Optimizing Geometries and Calculating Reaction Pathways (University of Cambridge Press, Cambridge, U.K., 2003) 〈http://www-wales.ch.cam.ac.uk/software.html〉
100. Y. M. Rhee, J. Chem. Phys. 113, 6021 (2000).
101. R. E. Leone and P. v. R. Schleyer, Angew. Chem., Int. Ed. Engl. 9, 860 (1970).
102. J. P. K. Doye, M. A. Miller, and D. J. Wales, J. Chem. Phys. 111, 8417 (1999).
103. M. A. Miller, J. P. K. Doye, and D. J. Wales, Phys. Rev. E 60, 3701 (1999).
104. J. P. Neirotti, F. Calvo, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 112, 10340 (2000).
105. F. Calvo, J. P. Neirotti, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 112, 10350 (2000).