Quantum trajectory-electronic structure approach for exploring nuclear effects in the dynamics of nanomaterials

Journal of Chemical Theory and Computation

Volumn 9, Issue 12, 2013, Pages 5221-5235

  Garashchuk, Sophya ^a   Jakowski, Jacek ^b   Wang, Lei ^a   Sumpter, Bobby G ^c  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84890502790     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct4006147     Document Type: Article

References (84)

1. Wang, Q.; Challa, S. R.; Sholl, D. S.; Johnson, J. K. Phys. Rev. Lett. 1999, 82, 956-959
2. Niimura, S.; Fujimori, T.; Minami, D.; Hattori, Y.; Abrams, L.; Corbin, D.; Hata, K.; Kaneko, K. J. Am. Chem. Soc. 2012, 134, 18483-18486
3. FitzGerald, S. A.; Pierce, C. J.; Rowsell, J. L. C.; Bloch, E. D.; Mason, J. A. J. Am. Chem. Soc. 2013, 135, 9458-9464
4. Martinez-Mesa, A.; Zhechkov, L.; Yurchenko, S. N.; Heine, T.; Seifert, G.; Rubayo-Soneira, J. J. Phys. Chem. C 2012, 116, 19543-19553
5. Hayes, R. L.; Paddison, S. J.; Tuckerman, M. E. J. Phys. Chem. B 2009, 113, 16574-16589
6. Hayes, R. L.; Paddison, S. J.; Tuckerman, M. E. J. Phys. Chem. A 2011, 115, 6112-6124
7. Dellago, C.; Naor, M. M.; Hummer, G. Phys. Rev. Lett. 2003, 90, 105902
8. Dimitrakakis, G. K.; Tylianakis, E.; Froudakis, G. E. Nano Lett 2008, 8, 3166-3170
9. Krstic, P. S.; Allain, J. P.; Taylor, C. N.; Dadras, J.; Maeda, S.; Morokuma, K.; Jakowski, J.; Allouche, A.; Skinner, C. H. Phys. Rev. Lett. 2013, 110, 105001
10. Ito, A.;; Wang, Y.;; Irle, S.;; Morokuma, K.;; Nakamura, H. Molecular dynamics simulation of hydrogen atom sputtering on the surface of graphite with defect and edge. Proceedings of the 18th International Conference on Plasma-Surface Interactions in Controlled Fusion Device, Toledo, Castilla-La Mancha, Spain, May 26-30, 2008; Journal of Nuclear Materials, 2009; pp 183-187.
11. Schedin, F.; Geim, A. K.; Morozov, S. V.; Hill, E. W.; Blake, P.; Katsnelson, M. I.; Novoselov, K. S. Nat. Mater. 2007, 6, 652-655
12. Ehemann, R. C.; Krstic, P. S.; Dadras, J.; Kent, P. R. C.; Jakowski, J. Nanoscale Res. Lett. 2012, 7, 1-14
13. Voth, G. A. Acc. Chem. Res. 2006, 39, 143-150
14. Hummer, G.; Rasaiah, J. C.; Noworyta, J. P. Nature 2001, 414, 188-190
15. Garberoglio, G. Eur. Phys. J. D 2009, 51, 185-191
16. Garberoglio, G. J. Chem. Phys. 2008, 128, 134109
17. Beenakker, J.; Borman, V.; Krylov, S. Chem. Phys. Lett. 1995, 232, 379-382
18. Hathorn, B. C.; Sumpter, B. G.; Noid, D. W. Phys. Rev. A 2001, 64, 022903
19. Manzhos, S. Aust. J. Chem. 2013, 66, 1021-2028
20. Shao, M.; Keum, J.; Xiao, K.; Hong, K.; Chen, J.; He, Y.; Chen, W.; Browning, J.; Jakowski, J.; Sumpter, B. G.; Ilia, N.; Ivanov, I. N.; Ma, Y.; Rouleau, C. M.; Geohegan, D. B. Nature Comm. (submitted).
21. Ito, A.; Nakamura, H.; Takayama, A. J. Phys. Soc. Jpn. 2008, 77, 114602
22. Sakong, S.; Kratzer, P. J. Chem. Phys. 2010, 133, 054505
23. Spirko, V.; Rubes, M.; Bludsky, O. J. Chem. Phys. 2010, 132, 194708
24. Casolo, S.; Livvik, O. M.; Martinazzo, R.; Tantardini, G. F. J. Chem. Phys. 2009, 130, 054704
25. Haberer, D.; Giusca, C. E.; Wang, Y.; Sachdev, H.; Fedorov, A. V.; Farjam, M.; Jafari, S. A.; Vyalikh, D. V.; Usachov, D.; Liu, X.; Treske, U.; Grobosch, M.; Vilkov, O.; Adamchuk, V. K.; Irle, S. Adv. Mater. 2011, 23, 4497
26. Wang, Y.; Qian, H.-J.; Morokuma, K.; Irle, S. J. Phys. Chem. A 2012, 116, 7154-7160
27. Karplus, M.; Sharma, R. D.; Porter, R. N. J. Chem. Phys. 1964, 40, 2033
28. Zhu, X.; Lopes, P.; MacKerell, A. D. Wiley interdis. rev.-Comput. Mol. Sci. 2012, 2, 167-185
29. Cha, Y.; Murray, C. J.; Klinman, J. P. Science 1989, 243, 1325-1330
30. Dekker, C.; Ratner, M. A. Phys. World 2001, 14, 29-33
31. Knapp, M. J.; Klinman, J. P. Eur. J. Biochem. 2002, 269, 3113-3121
32. Killelea, D. R.; Campbell, V. L.; Shuman, N. S.; Utz, A. L. Science 2008, 319, 790-793
33. Zhang, W.; Kawamata, H.; Liu, K. Science 2009, 325, 303-306
34. Han, Y.-C.; Bowman, J. M. Chem. Phys. Lett. 2013, 556, 39-43
35. Czako, G.; Kaledin, A. L.; Bowman, J. M. J. Chem. Phys. 2010, 132, 164103
36. Czako, G.; Kaledin, A. L.; Bowman, J. M. Chem. Phys. Lett. 2010, 500, 217-222
37. Light, J. C.; Carrington, T., Jr. Adv. Chem. Phys. 2000, 114, 263-310
38. Herman, M. F.; Kluk, E. Chem. Phys. 1984, 91, 27
39. Kay, K. G. J. Chem. Phys. 1994, 100, 4377-4392
40. Miller, W. H. J. Phys. Chem. A 2001, 105, 2942-2955
41. Ben-Nun, M.; Quenneville, J.; Martinez, T. J. J. Chem. Phys. 2001, 104, 5161-5175
42. Kim, S. Y.; Hammes-Schiffer, S. J. Chem. Phys. 2006, 124, 244102
43. Prezhdo, O.; Kisil, V. Phys. Rev. A 1997, 56, 162-175
44. Hone, T. D.; Izvekov, S.; Voth, G. A. J. Chem. Phys. 2005, 122, 054105
45. Gao, J.; Truhlar, D. G. Annu. Rev. Phys. Chem. 2002, 53, 467-505
46. Náray-Szabó, G.; Warshel, A., Eds. Computational approaches to biochemical reactivity; Understanding chemical reactivity; Kluwer Academic Publishers, 1997; Vol. 19.
47. Gindensperger, E.; Meier, C.; Beswick, J. A. J. Chem. Phys. 2000, 113, 9369-9372
48. Craig, I. R.; Manolopoulos, D. E. J. Chem. Phys. 2005, 122, 084106
49. Habershon, S.; Manolopoulos, D. E. J. Chem. Phys. 2009, 131, 244302
50. Tuckerman, M. E.; Berne, B. J.; Martyna, G. J.; Klein, M. L. J. Chem. Phys. 1993, 99, 2796-2808
51. Hetenyi, B.; Rabani, E.; Berne, B. J. J. Chem. Phys. 1999, 110, 6143-6153
52. Geneste, G.; Dammak, H.; Hayoun, M.; Thiercelin, M. Phys. Rev. B 2013, 87, 014113
53. Stuart, S. J.; Nugawela, D.; Hadri, B.; Jakowski, J.; Krstic, P.; Garashchuk, S.; Irle, S. Optimization of Density Functional Tight-Binding and Classical Reactive Molecular Dynamics for High-Throughput Simulations of Carbon Materials. Conference proceedings of XSEDE12, Chicago, July 16-19, 2012.
54. Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Phys. Rev. B 1998, 58, 7260-7268
55. Porezag, D.; Frauenheim, T.; Kãuhler, T.; Seifert, G.; Kaschner, R. Phys. Rev. B 1995, 51, 12947
56. Zheng, G.; Lundberg, M.; Jakowski, J.; Vreven, T.; Frisch, M. J.; Morokuma, K. Int. J. Quantum Chem. 2009, 109, 1841-1854
57. Garashchuk, S.; Volkov, M. V. Mol. Phys. 2012, 110, 985-993
58. Garashchuk, S.; Rassolov, V.; Prezhdo, O. Reviews in Computational Chemistry; Wiley, 2011; Vol. 27, Chapter Semiclassical Bohmian dynamics, pp 111-210.
59. Prezhdo, O. V.; Brooksby, C. Phys. Rev. Lett. 2001, 86, 3215-3219
60. Ohrn, N. Y. J. Phys. Chem. A 2001, 105, 2660-2667
61. Jakowski, J.; Morokuma, K. J. Chem. Phys. 2009, 130 224106
62. Iyengar, S. S.; Jakowski, J. J. Chem. Phys. 2005, 122
63. Rassolov, V. A.; Garashchuk, S.; Schatz, G. C. J. Phys. Chem. A 2006, 110, 5530-5536
64. Madelung, E. Z. Phys. 1927, 40, 322-326
65. Bohm, D. Phys. Rev. 1952, 85, 166-193
66. Garashchuk, S.; Rassolov, V. A. Chem. Phys. Lett. 2002, 364, 562-567
67. Garashchuk, S.; Rassolov, V. A. Chem. Phys. Lett. 2003, 376, 358-363
68. Ehrenfest, P. Z. Physik 1927, 45, 455
69. Gindensperger, E.; Meier, C.; Beswick, J. A.; Heitz, M. C. J. Chem. Phys. 2002, 116, 10051-10059
70. Slater, J. C.; Koster, G. F. Phys. Rev. 1954, 94, 1498-1524
71. Mermin, N. D. Phys. Rev. A 1965, 137, 1441
72. Sokoloff, J. Ann. Phys. 1967, 45, 186-190
73. Huang, J.; Jakowski, J.; Beste, A.; Younker, J.; Vazquez-Mayagoitia, A.; Cruz-Silva, E.; Fuentes-Cabrera, M.; Lopez-Bezanilla, A.; Meunier, V.; Sumpter, B. In Practical Aspects of Computational Chemistry II; Leszczynski, J.; Shukla, M. K., Eds.; Springer: Netherlands, 2012; pp 209-278.
74. Weinert, M.; Davenport, J. W. Phys. Rev. B 1992, 45, 13709
75. Wentzcovitch, R. M.; Martins, J. L.; Allen, P. B. Phys. Rev. B 1992, 45, 11372
76. Press, W. H.; Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T. Numerical Recipes: The Art of Scientific Computing, 2 nd ed.; Cambridge University Press: Cambridge, 1992.
77. Lee, C.; Yang, W.; Parr, R. Phys. Rev. B 1988, 37, 785-789
78. Becke, A. J. Chem. Phys. 1993, 98, 5648-5652
79. Shao, Y. Phys. Chem. Chem. Phys. 2006, 8, 3172-3191
80. Irle, S., private communicaton.
81. Feit, M. D.; Fleck, J. A., Jr.; Steiger, A. J. Comput. Phys. 1982, 47, 412-433
82. Kosloff, R. J. Phys. Chem. 1988, 92, 2087-2100
83. Mazzuca, J.; Garashchuk, S.; Jakowski, J. Chem. Phys. Lett. 2012, 542, 153-158
84. Garashchuk, S.; Volkov, M. V. J. Chem. Phys. 2012, 137, 074115