Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

Journal of Chemical Physics

Volumn 142, Issue 13, 2015, Pages

  Wales, D J ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION THEORY; DYNAMICS; MOLECULAR PHYSICS; POTENTIAL ENERGY SURFACES;

CLUSTER MORPHOLOGY; COMPUTATIONAL ASPECTS; CONFIGURATION SPACE; POTENTIAL ENERGY LANDSCAPES; POTENTIAL OF MEAN FORCE; REACTION COORDINATES; STRUCTURAL ORDER PARAMETER; STRUCTURE PREDICTION;

POTENTIAL ENERGY;

EID: 84926483311     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4916307     Document Type: Article

References (175)

1. D. J. Wales, Energy Landscapes (Cambridge University Press, Cambridge, 2003).
2. R. H. Swendsen and J.-S. Wang, Phys. Rev. Lett. 57, 2607 (1986). 10.1103/PhysRevLett.57.2607
3. D. Earl and M. W. Deem, Phys. Chem. Chem. Phys. 7, 3910 (2005). 10.1039/b509983h
4. R. Zhou and B. J. Berne, J. Chem. Phys. 107, 9185 (1997). 10.1063/1.475210
5. U. H. E. Hansmann and Y. Okamoto, Curr. Opin. Struct. Biol. 9, 177 (1999). 10.1016/S0959-440X(99)80025-6
6. F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001). 10.1103/PhysRevLett.86.2050
7. W. Watanabe and W. P. Reinhardt, Phys. Rev. Lett. 65, 3301 (1990). 10.1103/PhysRevLett.65.3301
8. I. Andricioaei, J. E. Straub, and A. F. Voter, J. Chem. Phys. 114, 6994 (2001). 10.1063/1.1358861
9. J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. 97, 050601 (2006). 10.1103/PhysRevLett.97.050601
10. V. A. Sharapov and V. A. Mandelshtam, J. Phys. Chem. A 111, 10284 (2007). 10.1021/jp072929c
11. V. A. Sharapov, D. Meluzzi, and V. A. Mandelshtam, Phys. Rev. Lett. 98, 105701 (2007). 10.1103/PhysRevLett.98.105701
12. J. Kim, T. Keyes, and J. E. Straub, J. Chem. Phys. 135, 061103 (2011). 10.1063/1.3626150
13. J. Kim, J. E. Straub, and T. Keyes, J. Phys. Chem. B 116, 8646 (2012). 10.1021/jp300366j
14. P. J. Ortoleva, T. Keyes, and M. Tuckerman, J. Phys. Chem. B 116, 8335 (2012). 10.1021/jp304524b
15. G. A. Huber and S. Kim, Biophys. J. 70, 97 (1996). 10.1016/S0006-3495(96)79552-8
16. D. Bhatt, B. W. Zhang, and D. M. Zuckerman, J. Chem. Phys. 133, 014110 (2010). 10.1063/1.3456985
17. D. J. Wales, Mol. Phys. 100, 3285 (2002). 10.1080/00268970210162691
18. C. Dellago, P. G. Bolhuis, and D. Chandler, J. Chem. Phys. 108, 9236 (1998). 10.1063/1.476378
19. D. Passerone and M. Parrinello, Phys. Rev. Lett. 87, 108302 (2001). 10.1103/PhysRevLett.87.108302
20. W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002). 10.1103/PhysRevB.66.052301
21. S. T. Chill, J. Stevenson, V. Ruehle, C. Shang, P. Xiao, J. D. Farrell, D. J. Wales, and G. Henkelman, J. Chem. Theory Comput. 10, 5476 (2014). 10.1021/ct5008718
22. F. Calvo, Mol. Phys. 100, 3421 (2002). 10.1080/00268970210158632
23. K. Arora and C. L. Brooks, Proc. Natl. Acad. Sci. U. S. A. 104, 18496 (2007). 10.1073/pnas.0706443104
24. P. I. Zhuravlev, S. Wu, D. A. Potoyan, M. Rubinstein, and G. A. Papoian, Methods 52, 115 (2010). 10.1016/j.ymeth.2010.05.003
25. D. A. Potoyan, P. I. Zhuravlev, and G. A. Papoian, J. Phys. Chem. B 116, 1709 (2012). 10.1021/jp209980b
26. P. Tao, A. J. Sodt, Y. Shao, G. König, and B. R. Brooks, J. Chem. Theory Comput. 10, 4198 (2014). 10.1021/ct500342h
27. W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005). 10.1021/jp0455430
28. E. Vanden-Eijnden and M. Venturoli, J. Chem. Phys. 130, 194101 (2009). 10.1063/1.3129843
29. D. J. Wales, Mol. Phys. 102, 891 (2004). 10.1080/00268970410001703363
30. D. J. Wales, Int. Rev. Phys. Chem. 25, 237 (2006). 10.1080/01442350600676921
31. W. E and E. Vanden-Eijnden, J. Stat. Phys. 123, 503 (2006). 10.1007/s10955-005-9003-9
32. P. Metzner, C. Schutte, and E. Vanden-Eijnden, J. Chem. Phys. 125, 084110 (2006). 10.1063/1.2335447
33. P. Metzner, C. Schütte, and E. Vanden-Eijnden, Multiscale Model. Simul. 7, 1192 (2009). 10.1137/070699500
34. Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. U. S. A. 84, 6611 (1987). 10.1073/pnas.84.19.6611
35. D. J. Wales and J. P. K. Doye, J. Phys. Chem. A 101, 5111 (1997). 10.1021/jp970984n
36. D. J. Wales and H. A. Scheraga, Science 285, 1368 (1999). 10.1126/science.285.5432.1368
37. D. Asenjo, J. D. Stevenson, D. J. Wales, and D. Frenkel, J. Phys. Chem. B 117, 12717 (2013). 10.1021/jp312457a
38. J. D. Bryngelson, J. N. Onuchic, N. D. Socci, and P. G. Wolynes, Proteins: Struct., Funct., Bioinf. 21, 167 (1995). 10.1002/prot.340210302
39. J. N. Onuchic, Z. Luthey-Schulten, and P. G. Wolynes, Annu. Rev. Phys. Chem. 48, 545 (1997). 10.1146/annurev.physchem.48.1.545
40. J. P. K. Doye, M. A. Miller, and D. J. Wales, J. Chem. Phys. 110, 6896 (1999). 10.1063/1.478595
41. M. T. Oakley, R. L. Johnston, and D. J. Wales, Phys. Chem. Chem. Phys. 15, 3965 (2013). 10.1039/c3cp44332a
42. D. J. Wales, Chem. Phys. Lett. 285, 330 (1998). 10.1016/S0009-2614(98)00044-X
43. D. Schebarchov and D. J. Wales, J. Chem. Phys. 139, 221101 (2013). 10.1063/1.4843956
44. D. Schebarchov and D. J. Wales, Phys. Rev. Lett. 113, 156102 (2014). 10.1103/PhysRevLett.113.156102
45. C. Tsallis, J. Stat. Phys. 52, 479 (1988). 10.1007/BF01016429
46. C. Shang and D. J. Wales, J. Chem. Phys. 141, 071101 (2014). 10.1063/1.4893344
47. V. Rühle, H. Kusumaatmaja, D. Chakrabarti, and D. J. Wales, J. Chem. Theory Comput. 9, 4026 (2013). 10.1021/ct400403y
48. D. Chakrabarti, H. Kusumaatmaja, V. Ruhle, and D. J. Wales, Phys. Chem. Chem. Phys. 16, 5014 (2014). 10.1039/C3CP52603H
49. K. Mochizuki, C. S. Whittleston, S. Somani, H. Kusumaatmaja, and D. J. Wales, Phys. Chem. Chem. Phys. 16, 2842 (2014). 10.1039/C3CP53537A
50. H. Kusumaatmaja, C. S. Whittleston, and D. J. Wales, J. Chem. Theory Comput. 8, 5159 (2012). 10.1021/ct3004589
51. D. J. Wales, Philos. Trans. R. Soc., A 363, 357 (2005). 10.1098/rsta.2004.1497
52. D. Chakrabarti and D. Wales, Phys. Chem. Chem. Phys. 11, 1970 (2009). 10.1039/b818054g
53. F. H. Stillinger and T. A. Weber, Science 225, 983 (1984). 10.1126/science.225.4666.983
54. D. J. Wales, Mol. Phys. 78, 151 (1993). 10.1080/00268979300100141
55. F. H. Stillinger, Science 267, 1935 (1995). 10.1126/science.267.5206.1935
56. B. Strodel and D. J. Wales, Chem. Phys. Lett. 466, 105 (2008). 10.1016/j.cplett.2008.10.085
57. P. G. Mezey, Theor. Chim. Acta 58, 309 (1981). 10.1007/BF02426907
58. P. G. Mezey, Potential Energy Hypersurfaces (Elsevier, Amsterdam, 1987).
59. S. Martiniani, J. D. Stevenson, D. J. Wales, and D. Frenkel, Phys. Rev. X 4, 031034 (2014). 10.1103/physrevx.4.031034
60. J. Skilling, Bayesian Anal. 1, 833 (2006). 10.1214/06-BA127
61. H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 116, 9058 (2002). 10.1063/1.1472510
62. V. A. Mandelshtam, P. A. Frantsuzov, and F. Calvo, J. Phys. Chem. A 110, 5326 (2006). 10.1021/jp055839l
63. D. J. Wales, Chem. Phys. Lett. 584, 1 (2013). 10.1016/j.cplett.2013.07.066
64. D. Earl and M. W. Deem, Phys. Chem. Chem. Phys. 7, 3910 (2005). 10.1039/b509983h
65. J. Geyer, in Computing Science and Statistics, Proceedings of the 23rd Symposium on the Interface, American Statistical Association, New York, 1991, p. 156. 10.1039/tf9686400371
66. D. J. Wales, J. Chem. Phys. 130, 204111 (2009). 10.1063/1.3133782
67. F. Rao and A. Caflisch, J. Mol. Biol. 342, 299 (2004). 10.1016/j.jmb.2004.06.063
68. F. Noé and S. Fischer, Curr. Opin. Struct. Biol. 18, 154 (2008). 10.1016/j.sbi.2008.01.008
69. D. Prada-Gracia, J. Gómez-Gardenes, P. Echenique, and F. Fernando, PLoS Comput. Biol. 5, e1000415 (2009). 10.1371/journal.pcbi.1000415
70. D. J. Wales, Curr. Opin. Struct. Biol. 20, 3 (2010). 10.1016/j.sbi.2009.12.011
71. D. A. Evans and D. J. Wales, J. Chem. Phys. 118, 3891 (2003). 10.1063/1.1540099
72. J. M. Carr and D. J. Wales, J. Chem. Phys. 123, 234901 (2005). 10.1063/1.2135783
73. J. M. Carr and D. J. Wales, J. Phys. Chem. B 112, 8760 (2008). 10.1021/jp801777p
74. J. M. Carr and D. J. Wales, Phys. Chem. Chem. Phys. 11, 3341 (2009). 10.1039/b820649j
75. J. D. Stevenson and D. J. Wales, J. Chem. Phys. 141, 041104 (2014). 10.1063/1.4891356
76. K. J. Laidler, Chemical Kinetics (Harper & Row, New York, 1987).
77. D. J. Wales and J. M. Carr, J. Chem. Theory Comput. 8, 5020 (2012). 10.1021/ct3004832
78. F. H. Stillinger and T. A. Weber, Phys. Rev. A 25, 978 (1982). 10.1103/PhysRevA.25.978
79. D. J. Wales and J. P. K. Doye, J. Chem. Phys. 119, 12409 (2003). 10.1063/1.1625644
80. O. M. Becker and M. Karplus, J. Chem. Phys. 106, 1495 (1997). 10.1063/1.473299
81. D. J. Wales, M. A. Miller, and T. R. Walsh, Nature 394, 758 (1998). 10.1038/29487
82. V. K. de Souza and D. J. Wales, J. Chem. Phys. 129, 164507 (2008). 10.1063/1.2992128
83. J. P. K. Doye and D. J. Wales, J. Chem. Phys. 111, 11070 (1999). 10.1063/1.480465
84. B. Friedrich, Z. Herman, R. Zahradnik, and Z. Havlas, Adv. Quantum Chem. 19, 247 (1988). 10.1016/s0065-3276(08)60617-6
85. A. Banerjee and N. P. Adams, Int. J. Quantum Chem. 43, 855 (1992). 10.1002/qua.560430610
86. D. J. Wales, J. Chem. Phys. 113, 3926 (2000). 10.1063/1.1288003
87. W. Quapp, J. Chem. Phys. 114, 609 (2001). 10.1063/1.1330237
88. N. D. Socci, J. N. Onuchic, and P. G. Wolynes, J. Chem. Phys. 104, 5860 (1996). 10.1063/1.471317
89. R. B. Best and G. Hummer, Proc. Natl. Acad. Sci. U. S. A. 107, 1088 (2010). 10.1073/pnas.0910390107
90. E. R. Henry, R. B. Best, and W. A. Eaton, Proc. Natl. Acad. Sci. U. S. A. 110, 17880 (2013). 10.1073/pnas.1317105110
91. G. Hummer, J. Chem. Phys. 120, 516 (2004). 10.1063/1.1630572
92. R. B. Best and G. Hummer, Proc. Natl. Acad. Sci. U. S. A. 102, 6732 (2005). 10.1073/pnas.0408098102
93. R. B. Best and G. Hummer, Phys. Chem. Chem. Phys. 13, 16902 (2011). 10.1039/c1cp21541h
94. L. Onsager, Phys. Rev. 54, 554 (1938). 10.1103/PhysRev.54.554
95. A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005). 10.1021/jp045546c
96. B. Qi, S. Muff, A. Caflisch, and A. R. Dinner, J. Phys. Chem. B 114, 6979 (2010). 10.1021/jp101476g
97. Y. M. Rhee and V. S. Pande, J. Phys. Chem. B 109, 6780 (2005). 10.1021/jp045544s
98. W. E, W. Ren, and E. Vanden-Eijnden, Chem. Phys. Lett. 413, 242 (2005). 10.1016/j.cplett.2005.07.084
99. G. Ciccotti, R. Kapral, and E. Vanden-Eijnden, ChemPhysChem 6, 1809 (2005). 10.1002/cphc.200400669
100. M. J. Morelli, S. Tanase-Nicola, R. J. Allen, and P. R. t. Wolde, Biophys. J. 94, 3413 (2008). 10.1529/biophysj.107.116699
101. A. K. Faradjian and R. Elber, J. Chem. Phys. 120, 10880 (2004). 10.1063/1.1738640
102. S. Kirmizialtin and R. Elber, J. Phys. Chem. A 115, 6137 (2011). 10.1021/jp111093c
103. P. G. Bolhuis, J. Phys.: Condens. Matter 15, S113 (2002). 10.1088/0953-8984/15/1/314
104. B. Peters and B. L. Trout, J. Chem. Phys. 125, 054108 (2006). 10.1063/1.2234477
105. E. E. Borrero and F. A. Escobedo, J. Chem. Phys. 127, 164101 (2007). 10.1063/1.2776270
106. S. L. Quaytman and S. D. Schwartz, Proc. Natl. Acad. Sci. U. S. A. 104, 12253 (2007). 10.1073/pnas.0704304104
107. B. Peters, G. T. Beckham, and B. L. Trout, J. Chem. Phys. 127, 034109 (2007). 10.1063/1.2748396
108. J. Juraszek and P. G. Bolhuis, Biophys. J. 95, 4246 (2008). 10.1529/biophysj.108.136267
109. S. V. Krivov and M. Karplus, Proc. Natl. Acad. Sci. U. S. A. 105, 13841 (2008). 10.1073/pnas.0800228105
110. C. Velez-Vega, E. E. Borrero, and F. A. Escobedo, J. Chem. Phys. 130, 225101 (2009). 10.1063/1.3147465
111. W. Lechner, J. Rogal, J. Juraszek, B. Ensing, and P. G. Bolhuis, J. Chem. Phys. 133, 174110 (2010). 10.1063/1.3491818
112. P. V. Banushkina and S. V. Krivov, J. Chem. Theory Comput. 9, 5257 (2013). 10.1021/ct400651z
113. P. Májek and R. Elber, J. Chem. Theory Comput. 6, 1805 (2010). 10.1021/ct100114j
114. B. W. Zhang, D. Jasnow, and D. M. Zuckerman, Proc. Natl. Acad. Sci. U. S. A. 104, 18043 (2007). 10.1073/pnas.0706349104
115. J. D. Bryngelson and P. G. Wolynes, J. Phys. Chem. 93, 6902 (1989). 10.1021/j100356a007
116. C. J. Camacho and D. Thirumalai, Proc. Natl. Acad. Sci. U. S. A. 90, 6369 (1993). 10.1073/pnas.90.13.6369
117. S. S. Plotkin and P. G. Wolynes, Phys. Rev. Lett. 80, 5015 (1998). 10.1103/PhysRevLett.80.5015
118. D. Beece, L. Eisenstein, H. Frauenfelder, D. Good, M. C. Marden, L. Reinisch, A. H. Reynolds, L. B. Sorensen, and K. T. Yue, Biochemistry 19, 5147 (1980). 10.1021/bi00564a001
119. A. Ansari, C. M. Jones, E. R. Henry, J. Hofrichter, and W. A. Eaton, Science 256, 1796 (1992). 10.1126/science.1615323
120. T. Cellmer, E. R. Henry, J. Hofrichter, and W. A. Eaton, Proc. Natl. Acad. Sci. U. S. A. 105, 18320 (2008). 10.1073/pnas.0806154105
121. S. J. Hagen, Curr. Protein Pept. Sci. 11, 385 (2010). 10.2174/138920310791330596
122. H. S. Chung and W. A. Eaton, Nature 502, 685688 (2013). 10.1038/nature12649
123. J. C. F. Schulz, L. Schmidt, R. B. Best, J. Dzubiella, and R. R. Netz, J. Am. Chem. Soc. 134, 6273 (2012). 10.1021/ja211494h
124. I. Echeverria, D. E. Makarov, and G. A. Papoian, J. Am. Chem. Soc. 136, 8708 (2014). 10.1021/ja503069k
125. D. de Sancho, A. Sirur, and R. B. Best, Nat. Commun. 5, 1 (2014). 10.1038/ncomms5307
126. P. N. Mortenson and D. J. Wales, J. Chem. Phys. 114, 6443 (2001). 10.1063/1.1343486
127. P. N. Mortenson, D. A. Evans, and D. J. Wales, J. Chem. Phys. 117, 1363 (2002). 10.1063/1.1484389
128. D. Chandler, Introduction to Modern Statistical Mechanics (Oxford University Press, Oxford, 1987).
129. N. G. van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1981).
130. H. A. Kramers, Physica 7, 284 (1940). 10.1016/S0031-8914(40)90098-2
131. J. Langer, Ann. Phys. 54, 258 (1969). 10.1016/0003-4916(69)90153-5
132. A. M. Berezhkovskii, E. Pollak, and V. Y. Zitserman, J. Chem. Phys. 97, 2422 (1992). 10.1063/1.463081
133. R. F. Grote and J. T. Hynes, J. Chem. Phys. 73, 2715 (1980). 10.1063/1.440485
134. R. F. Grote and J. T. Hynes, J. Chem. Phys. 74, 4465 (1981). 10.1063/1.441634
135. R. F. Grote and J. T. Hynes, J. Chem. Phys. 75, 2191 (1981). 10.1063/1.442331
136. A. Nitzan, J. Chem. Phys. 86, 2734 (1987). 10.1063/1.452076
137. J. J. Portman, S. Takada, and P. G. Wolynes, J. Chem. Phys. 114, 5069 (2001). 10.1063/1.1334662
138. N. Singhal, C. D. Snow, and V. S. Pande, J. Chem. Phys. 121, 415 (2004). 10.1063/1.1738647
139. J. D. Chodera, K. A. Dill, N. Singhal, V. S. Pande, W. C. Swope, and J. W. Pitera, J. Chem. Phys. 126, 155101 (2007). 10.1063/1.2714538
140. G. R. Bowman, K. A. Beauchamp, G. Boxer, and V. S. Pande, J. Chem. Phys. 131, 124101 (2009). 10.1063/1.3216567
141. J. H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J. D. Chodera, C. Schutte, and F. Noe, J. Chem. Phys. 134, 174105 (2011). 10.1063/1.3565032
142. T. J. Lane, G. R. Bowman, K. Beauchamp, V. A. Voelz, and V. S. Pande, J. Am. Chem. Soc. 133, 18413 (2011). 10.1021/ja207470h
143. J. Nocedal, Math. Comput. 35, 773 (1980). 10.1090/S0025-5718-1980-0572855-7
144. D. C. Liu and J. Nocedal, Math. Program. 45, 503 (1989). 10.1007/BF01589116
145. D. J. Wales, " gmin: A program for basin-hopping global optimisation and basin-sampling thermodynamics," online at http://www-wales.ch.cam.ac.uk/software.html.
146. D. J. Wales, " optim: A program for optimizing geometries and cal culating reaction pathways," online at http://www-wales.ch.cam.ac.uk/OPTIM/.
147. S. K. Kearsley, Acta Crystallogr., Sect. A 45, 208 (1989). 10.1107/S0108767388010128
148. R. Jonker and A. Volgenant, Computing 38, 325 (1987). 10.1007/BF02278710
149. B. J. Schulz, K. Binder, M. Müller, and D. P. Landau, Phys. Rev. E 67, 067102 (2003). 10.1103/PhysRevE.67.067102
150. G. M. Torrie and J. P. Valleau, Chem. Phys. Lett. 28, 578 (1974). 10.1016/0009-2614(74)80109-0
151. D. Frenkel and B. Smit, Understanding Molecular Simulation, 2nd ed. (Academic Press, London, 2002).
152. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988). 10.1103/PhysRevLett.61.2635
153. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989). 10.1103/PhysRevLett.63.1195
154. P. Labastie and R. L. Whetten, Phys. Rev. Lett. 65, 1567 (1990). 10.1103/PhysRevLett.65.1567
155. S. Weerasinghe and F. G. Amar, J. Chem. Phys. 98, 4967 (1993). 10.1063/1.464952
156. F. Calvo and P. Labastie, Chem. Phys. Lett. 247, 395 (1995). 10.1016/S0009-2614(95)01226-5
157. F. Calvo, Phys. Rev. E 82, 046703 (2010). 10.1103/PhysRevE.82.046703
158. J. E. Jones and A. E. Ingham, Proc. R. Soc. A 107, 636 (1925). 10.1098/rspa.1925.0047
159. J. P. Neirotti, F. Calvo, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 112, 10340 (2000). 10.1063/1.481671
160. F. Calvo, J. P. Neirotti, D. L. Freeman, and J. D. Doll, J. Chem. Phys. 112, 10350 (2000). 10.1063/1.481672
161. R. M. Sehgal, D. Maroudas, and D. M. Ford, J. Chem. Phys. 140, 104312 (2014). 10.1063/1.4866810
162. M. Picciani, M. Athenes, J. Kurchan, and J. Tailleur, J. Chem. Phys. 135, 034108 (2011). 10.1063/1.3609972
163. S. V. Krivov and M. Karplus, J. Phys. Chem. B 110, 12689 (2006). 10.1021/jp060039b
164. P. J. Steinhardt, D. R. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983). 10.1103/PhysRevB.28.784
165. J. S. van Duijneveldt and D. Frenkel, J. Chem. Phys. 96, 4655 (1992). 10.1063/1.462802
166. R. M. Lynden-Bell and D. J. Wales, J. Chem. Phys. 101, 1460 (1994). 10.1063/1.467771
167. P. Poulain, F. Calvo, R. Antoine, M. Broyer, and P. Dugourd, Phys. Rev. E 73, 056704 (2006). 10.1103/PhysRevE.73.056704
168. V. A. Mandelshtam and P. A. Frantsuzov, J. Chem. Phys. 124, 204511 (2006). 10.1063/1.2202312
169. D. J. Wales, L. J. Munro, and J. P. K. Doye, J. Chem. Soc., Dalton Trans. 1996, 611. 10.1039/DT9960000611
170. J. P. K. Doye, M. A. Miller, and D. J. Wales, J. Chem. Phys. 111, 8417 (1999). 10.1063/1.480217
171. G. C. Boulougouis and D. N. Theodorou, J. Chem. Phys. 127, 084903 (2007). 10.1063/1.2753153
172. N. P. Kopsias and D. N. Theodorou, J. Chem. Phys. 109, 8573 (1998). 10.1063/1.477522
173. G. S. Jas, W. A. Eaton, and J. Hofrichter, J. Phys. Chem. B 105, 261 (2001). 10.1021/jp0022048
174. D. J. Wales, Science 293, 2067 (2001). 10.1126/science.1062565
175. See https://github.com/pele-python/pele for Pele: Python energy landscape explorer.