A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods

Journal of Computational Chemistry

Volumn 24, Issue 8, 2003, Pages 990-996

  Alfonso, Dominic R ^a,b   Jordan, Kenneth D ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b NATIONAL ENERGY TECHNOLOGY LABORATORY   (United States)

Author keywords

Driver program; Minimum energy path; Nudged elastic band; Reaction pathway exploration; Transition state structure

Indexed keywords

ALGORITHMS; DESORPTION; ELECTRONIC STRUCTURE; ISOMERIZATION; OPTIMIZATION; RATE CONSTANTS; THERMODYNAMICS;

MINIMUM ENERGY PATHS;

POTENTIAL ENERGY;

EID: 0038369141     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10233     Document Type: Article

References (70)

1. Eyring, H. J Chem Phys 1935, 3, 107.
2. Wigner, E. Trans Faraday Soc 1938, 34, 29.
3. Vineyard, G. H. J Phys Chem Solids 1957, 3, 121
4. Keck, J. C. Adv Chem 1967, 13, 85.
5. Bell, S.; Crighton J. S. J Chem Phys 1984, 80, 2464.
6. Schlegel, H. B. Adv Chem Phys 1987, 67, 249.
7. Head, J. D.; Zerner M. C. Adv Quantum Chem 1989, 20, 239.
8. McKee, M. L.; Page, M. Rev Comp Chem 1993, 4, 35.
9. Henkelman, G.; Jönsson, H. J Chem Phys 1999, 111, 7010.
10. Halgren, T. A.; Lipscomb, W. N. Chem Phys Lett 1977, 49, 225.
11. Peng, C.; Schlegel, H. B. Isr J Chem 1994, 33, 449.
12. Crippen, G. M.; Scheraga, H. A. Arch Biochem Biophys 1971, 144, 462.
13. Ionova, I. V.; Carter, E. A. J Chem Phys 1993, 98, 6377; Ionova, I. V.; Carter E. A. J Chem Phys 1995, 102, 1251.
14. Ionova, I. V.; Carter, E. A. J Chem Phys 1993, 98, 6377; Ionova, I. V.; Carter E. A. J Chem Phys 1995, 102, 1251.
15. Ayala, P. Y.; Schlegel, H. B. J Chem Phys 1997, 107, 375.
16. Hilderbrandt, R. L. Comput Chem 1977, 1, 179.
17. Cerjan, C. J.; Miller, W. H. J Chem Phys 1981, 75, 2800.
18. Simons, J.; Jørgensen, P.; Taylor, H.; Ozment, J. J Phys Chem 1983, 87, 2745.
19. Nichols, J.; Taylor, H.; Schmidt, P.; Simons, J. J Chem Phys 1990, 92, 340.
20. Wales, D. J. J Chem Phys 1989, 91, 7002.
21. Munro, L. J.; Wales, D. J. Phys Rev B 1999, 59, 3969; Kumeda, Y.; Wales, D. J.; Munro, L. J. Chem Phys Lett 2001, 341, 185.
22. Munro, L. J.; Wales, D. J. Phys Rev B 1999, 59, 3969; Kumeda, Y.; Wales, D. J.; Munro, L. J. Chem Phys Lett 2001, 341, 185.
23. Jönsson, H.; Mills, G.; Jacobsen, K. W. In Classical and Quantum Dynamics in Condensed Phase Simulations; Berne, B. J.; Ciccotti, G.; Coker, D. F., Eds.; World Scientific: Singapore, 1995.
24. Mills, G.; Jönsson, H. Phys Rev Lett 1994, 72, 1124.
25. Mills, G.; Jönsson, H.; Schenter, G. K. Surf Sci 1995, 324, 305.
26. Eiber, R.; Karplus, M. Chem Phys Lett 1987, 139, 375; Czerminski, R.; Eiber, R. Int J Quantum Chem 1990, 24, 167; Choi, C.; Eiber, R. J Chem Phys 1991, 94, 751.
27. Eiber, R.; Karplus, M. Chem Phys Lett 1987, 139, 375; Czerminski, R.; Eiber, R. Int J Quantum Chem 1990, 24, 167; Choi, C.; Eiber, R. J Chem Phys 1991, 94, 751.
28. Eiber, R.; Karplus, M. Chem Phys Lett 1987, 139, 375; Czerminski, R.; Eiber, R. Int J Quantum Chem 1990, 24, 167; Choi, C.; Eiber, R. J Chem Phys 1991, 94, 751.
29. See, for example, Windl, W.; Bunea, M. M.; Stumpf, R. Phys Rev Lett 1999, 83, 4345; Stumpf, R.; Liu, C. L.; Tracy, C. Phys Rev B 1999, 59, 16047; Uberuaga, B. P.; Levskovar, M.; Smith, A. P. Phys Rev Lett 2000, 84, 2441; Shen, T. C.; Steckel, J. A.; Jordan, K. D. Surf Sci 2000, 446, 211; Henkelman, G.; Jönsson, H. Phys Rev Lett 2001, 86, 664; Logadottir, A.; Rod, T. H.; Nørskov, J. K.; Hammer, B.; Dahl, S.; Jacobsen, C. J. M. J Catal 2001, 197, 229.
30. See, for example, Windl, W.; Bunea, M. M.; Stumpf, R. Phys Rev Lett 1999, 83, 4345; Stumpf, R.; Liu, C. L.; Tracy, C. Phys Rev B 1999, 59, 16047; Uberuaga, B. P.; Levskovar, M.; Smith, A. P. Phys Rev Lett 2000, 84, 2441; Shen, T. C.; Steckel, J. A.; Jordan, K. D. Surf Sci 2000, 446, 211; Henkelman, G.; Jönsson, H. Phys Rev Lett 2001, 86, 664; Logadottir, A.; Rod, T. H.; Nørskov, J. K.; Hammer, B.; Dahl, S.; Jacobsen, C. J. M. J Catal 2001, 197, 229.
31. See, for example, Windl, W.; Bunea, M. M.; Stumpf, R. Phys Rev Lett 1999, 83, 4345; Stumpf, R.; Liu, C. L.; Tracy, C. Phys Rev B 1999, 59, 16047; Uberuaga, B. P.; Levskovar, M.; Smith, A. P. Phys Rev Lett 2000, 84, 2441; Shen, T. C.; Steckel, J. A.; Jordan, K. D. Surf Sci 2000, 446, 211; Henkelman, G.; Jönsson, H. Phys Rev Lett 2001, 86, 664; Logadottir, A.; Rod, T. H.; Nørskov, J. K.; Hammer, B.; Dahl, S.; Jacobsen, C. J. M. J Catal 2001, 197, 229.
32. See, for example, Windl, W.; Bunea, M. M.; Stumpf, R. Phys Rev Lett 1999, 83, 4345; Stumpf, R.; Liu, C. L.; Tracy, C. Phys Rev B 1999, 59, 16047; Uberuaga, B. P.; Levskovar, M.; Smith, A. P. Phys Rev Lett 2000, 84, 2441; Shen, T. C.; Steckel, J. A.; Jordan, K. D. Surf Sci 2000, 446, 211; Henkelman, G.; Jönsson, H. Phys Rev Lett 2001, 86, 664; Logadottir, A.; Rod, T. H.; Nørskov, J. K.; Hammer, B.; Dahl, S.; Jacobsen, C. J. M. J Catal 2001, 197, 229.
33. See, for example, Windl, W.; Bunea, M. M.; Stumpf, R. Phys Rev Lett 1999, 83, 4345; Stumpf, R.; Liu, C. L.; Tracy, C. Phys Rev B 1999, 59, 16047; Uberuaga, B. P.; Levskovar, M.; Smith, A. P. Phys Rev Lett 2000, 84, 2441; Shen, T. C.; Steckel, J. A.; Jordan, K. D. Surf Sci 2000, 446, 211; Henkelman, G.; Jönsson, H. Phys Rev Lett 2001, 86, 664; Logadottir, A.; Rod, T. H.; Nørskov, J. K.; Hammer, B.; Dahl, S.; Jacobsen, C. J. M. J Catal 2001, 197, 229.
34. See, for example, Windl, W.; Bunea, M. M.; Stumpf, R. Phys Rev Lett 1999, 83, 4345; Stumpf, R.; Liu, C. L.; Tracy, C. Phys Rev B 1999, 59, 16047; Uberuaga, B. P.; Levskovar, M.; Smith, A. P. Phys Rev Lett 2000, 84, 2441; Shen, T. C.; Steckel, J. A.; Jordan, K. D. Surf Sci 2000, 446, 211; Henkelman, G.; Jönsson, H. Phys Rev Lett 2001, 86, 664; Logadottir, A.; Rod, T. H.; Nørskov, J. K.; Hammer, B.; Dahl, S.; Jacobsen, C. J. M. J Catal 2001, 197, 229.
35. Villarba, M.; Jönsson, H. Surf Sci 1994, 317, 15; Villarba, M.; Jönsson, H. Surf Sci 1995, 324, 35; Sørensen, M. R.; Jacobsen, K. W.; Jönsson, H. Phys Rev Lett 1996, 77, 5067.
36. Villarba, M.; Jönsson, H. Surf Sci 1994, 317, 15; Villarba, M.; Jönsson, H. Surf Sci 1995, 324, 35; Sørensen, M. R.; Jacobsen, K. W.; Jönsson, H. Phys Rev Lett 1996, 77, 5067.
37. Villarba, M.; Jönsson, H. Surf Sci 1994, 317, 15; Villarba, M.; Jönsson, H. Surf Sci 1995, 324, 35; Sørensen, M. R.; Jacobsen, K. W.; Jönsson, H. Phys Rev Lett 1996, 77, 5067.
38. Frisch, M. J., et al. Gaussian 98; Gaussian Inc.: Pittsburgh, PA, 1998.
39. Gillilan, R. E.; Wilson, K. R. J Chem Phys 1992, 97, 1757.
40. Henkelman, G.; Jönsson, H. J Chem Phys 2000, 113, 9901.
41. Vanderbilt, D.; Louie, S. G. Phys Rev B, 1984, 30, 6118.
42. See, for example, Alfonso, D. R.; Jaffe, J. E.; Hess, A. C. Hess; Gutowski, M. Surf Sci 2000, 466, 111; Alfonso, D. R.; Snyder, J. A.; Jaffe, J. E.; Hess, A. C.; Gutowski, M. Phys Rev B 2000, 62, 8318; Alfonso, D. R.; Snyder, J. A.; Jaffe, J. E., Hess, A. C.; Gutowski, M. Surf Sci 2000, 453, 130.
43. See, for example, Alfonso, D. R.; Jaffe, J. E.; Hess, A. C. Hess; Gutowski, M. Surf Sci 2000, 466, 111; Alfonso, D. R.; Snyder, J. A.; Jaffe, J. E.; Hess, A. C.; Gutowski, M. Phys Rev B 2000, 62, 8318; Alfonso, D. R.; Snyder, J. A.; Jaffe, J. E., Hess, A. C.; Gutowski, M. Surf Sci 2000, 453, 130.
44. See, for example, Alfonso, D. R.; Jaffe, J. E.; Hess, A. C. Hess; Gutowski, M. Surf Sci 2000, 466, 111; Alfonso, D. R.; Snyder, J. A.; Jaffe, J. E.; Hess, A. C.; Gutowski, M. Phys Rev B 2000, 62, 8318; Alfonso, D. R.; Snyder, J. A.; Jaffe, J. E., Hess, A. C.; Gutowski, M. Surf Sci 2000, 453, 130.
45. Alfonso, D. R.; Jordan, K. D. J Chem Phys 2002, 116, 3612.
46. Johnson, D. D. Phys Rev B 1988, 38, 12807.
47. Kresse, G.; Furtmüller, J. Phys Rev B 1996, 54, 11169.
48. Bockstedte, M.; Kley, A.; Neugebauer, J.; Scheffler, M. Comp Phys Commun 2000, 107, 187.
49. Andersen, H. C. J Chem Phys 1980, 72, 2384.
50. Mousseau, N.; Barkema, G. T. Phys Rev E 1998, 57, 2419; Mousseau, N. (private communication).
51. Mousseau, N.; Barkema, G. T. Phys Rev E 1998, 57, 2419; Mousseau, N. (private communication).
52. Hehre, W. J.; Radom, L.; Schleyer, P. V. R.; Pople, J. A. Ab Initio Molecular Orbital Theory; John Wiley and Sons: New York.
53. Hariharan, P. C.; Pople, J. A. Theor Chim Acta 1973, 28, 213; Francl, M.; Pietro, W. J.; Hehre, W. J.; Binkley, J. S.; Gordon, M. S; DeFrees, D. J.; Pople, J. A. J Chem Phys 1980, 77, 3654.
54. Hariharan, P. C.; Pople, J. A. Theor Chim Acta 1973, 28, 213; Francl, M.; Pietro, W. J.; Hehre, W. J.; Binkley, J. S.; Gordon, M. S; DeFrees, D. J.; Pople, J. A. J Chem Phys 1980, 77, 3654.
55. Wales, D. J. In Computational Molecular Spectroscopy; Jensen, P.; Bunker, P. R., Eds.; John Wiley and Sons: Chichester, 2000.
56. Frisch, M. J.; Pople, J. A.; Binkley, J. S. J Chem Phys 1984, 80, 3265.
57. Steckel, J. A.; Phung, T.; Jordan, K. D.; Nachtigall, P. J Phys Chem 2001, 105, 4031.
58. The Becke3LYP functional combines Becke's 1993 exchange functional (Becke, A. D. J Chem Phys 1993, 98, 5648) and the correlation functional of Lee, Yang, and Parr (Lee, C.; Yang, W.; Parr, R.G. Phys Rev B 1988, 37, 785) with weighting factors from Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J Phys Chem 1994, 98, 11623.
59. The Becke3LYP functional combines Becke's 1993 exchange functional (Becke, A. D. J Chem Phys 1993, 98, 5648) and the correlation functional of Lee, Yang, and Parr (Lee, C.; Yang, W.; Parr, R.G. Phys Rev B 1988, 37, 785) with weighting factors from Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J Phys Chem 1994, 98, 11623.
60. The Becke3LYP functional combines Becke's 1993 exchange functional (Becke, A. D. J Chem Phys 1993, 98, 5648) and the correlation functional of Lee, Yang, and Parr (Lee, C.; Yang, W.; Parr, R.G. Phys Rev B 1988, 37, 785) with weighting factors from Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J Phys Chem 1994, 98, 11623.
61. McLean, A. D.; Chandler, G. S. J Chem Phys 1980, 72, 5639; Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. J Chem Phys 1980, 72, 650.
62. McLean, A. D.; Chandler, G. S. J Chem Phys 1980, 72, 5639; Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. J Chem Phys 1980, 72, 650.
63. Hehre, W. J.; Ditchfield, R.; Pople, J. A. J Chem Phys 1972, 56, 2257; Gordon, M. S. Chem Phys Lett 1980, 76, 163.
64. Hehre, W. J.; Ditchfield, R.; Pople, J. A. J Chem Phys 1972, 56, 2257; Gordon, M. S. Chem Phys Lett 1980, 76, 163.
65. Binkley, J. S.; Pople, J. A.; Hehre, W. J. J Am Chem Soc 1980, 102, 939; Gordon, M. S.; Binkley, J. S.; Pople, J. A.; Pietro, W. J.; Hehre, W. J. J Am Chem Soc 1982, 104, 2797; Dobbs, K. D.; Hehre, W. J. J Comput Chem 1987, 8, 880.
66. Binkley, J. S.; Pople, J. A.; Hehre, W. J. J Am Chem Soc 1980, 102, 939; Gordon, M. S.; Binkley, J. S.; Pople, J. A.; Pietro, W. J.; Hehre, W. J. J Am Chem Soc 1982, 104, 2797; Dobbs, K. D.; Hehre, W. J. J Comput Chem 1987, 8, 880.
67. Binkley, J. S.; Pople, J. A.; Hehre, W. J. J Am Chem Soc 1980, 102, 939; Gordon, M. S.; Binkley, J. S.; Pople, J. A.; Pietro, W. J.; Hehre, W. J. J Am Chem Soc 1982, 104, 2797; Dobbs, K. D.; Hehre, W. J. J Comput Chem 1987, 8, 880.
68. Vittadini, A.; Selloni, A. Chem Phys Lett 1995, 235, 334.
69. Gonzalez, C.; Schlegel, H. B. J Chem Phys 1989, 90, 2154; Gonzalez, C.; Schlegel, H. B. J Phys Chem 1990, 94, 5523.
70. Gonzalez, C.; Schlegel, H. B. J Chem Phys 1989, 90, 2154; Gonzalez, C.; Schlegel, H. B. J Phys Chem 1990, 94, 5523.