Representing the potential-energy surface of protonated water clusters by high-dimensional neural network potentials

Physical Chemistry Chemical Physics

Volumn 17, Issue 13, 2015, Pages 8356-8371

  Kondati Natarajan, Suresh ^a   Morawietz, Tobias ^a   Behler, Jörg ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PROTON; WATER;

ARTIFICIAL NEURAL NETWORK; CHEMISTRY; HYDROGEN BOND; MOLECULAR DYNAMICS; THERMODYNAMICS;

HYDROGEN BONDING; MOLECULAR DYNAMICS SIMULATION; NEURAL NETWORKS (COMPUTER); PROTONS; THERMODYNAMICS; WATER;

EID: 84925707827     PISSN: 14639076     EISSN: None     Source Type: Journal    
DOI: 10.1039/c4cp04751f     Document Type: Article

References (89)

1. P. Ball, Life's matrix: a biography of water, Univ. of California Press, 2001
2. R. Ludwig Angew. Chem., Int. Ed. 2001 40 1808
3. N. Agmon Acc. Chem. Res. 2012 45 63
4. R. Bukowski K. Szalewicz G. C. Groenenboom A. van der Avoird Science 2007 315 1249
5. B. Guillot J. Mol. Liq. 2002 101 219
6. A. Tokmakoff Science 2007 317 54
7. Y. Zubavicus M. Grunze Science 2004 304 974
8. P. Wernet D. Nordlund U. Bergmann M. Cavalleri M. Odelius H. Ogasawara L. Å. Näslund T. K. Hirsch L. Ojamäe P. Glatzel L. G. M. Pettersson A. Nilsson Science 2004 304 995
9. H. Helmholtz Annu. Rev. Phys. Chem. 1853 LXXXIX 211
10. W. Schmickler Chem. Rev. 1996 96 3177
11. N. Agmon Chem. Phys. Lett. 1995 244 456
12. D. Marx ChemPhysChem 2006 7 1848
13. M. E. Tuckerman A. Chandra D. Marx Acc. Chem. Res. 2006 39 151
14. D. Marx A. Chandra M. E. Tuckerman Chem. Rev. 2010 110 2174
15. D. Marx and J. Hutter, Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods, Cambridge University Press, 2009
16. R. Car M. Parrinello Phys. Rev. Lett. 1985 55 2471
17. W. L. Jorgensen J. Chandrasekhar J. D. Madura R. W. Impey M. L. Klein J. Chem. Phys. 1983 79 926
18. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren and J. Hermans, Intermolecular Forces, Reidel, Dordrecht, 1981, p. 331
19. F. H. Stillinger A. Rahman J. Chem. Phys. 1974 60 1545
20. C. Vega J. L. F. Abascal Phys. Chem. Chem. Phys. 2011 13 19663
21. T. James D. J. Wales J. Chem. Phys. 2005 122 134306
22. R. Kumar R. A. Christie K. D. Jordan J. Phys. Chem. B 2009 113 4111
23. U. W. Schmitt G. A. Voth J. Phys. Chem. B 1998 102 5547
24. C. Knight G. A. Voth Acc. Chem. Res. 2012 45 101
25. R. E. Kozack P. C. Jordan J. Chem. Phys. 1992 96 3131
26. M. P. Hodges A. J. Stone J. Chem. Phys. 1999 110 6766
27. X. C. Huang B. J. Braams J. M. Bowman J. Chem. Phys. 2005 122 044308
28. A. P. Bartók M. C. Payne R. Kondor G. Csányi Phys. Rev. Lett. 2010 104 136403
29. A. P. Bartók M. J. Gillan F. R. Manby G. Csányi Phys. Rev. B: Condens. Matter Mater. Phys. 2013 88 054104
30. P. Pinski G. Csanyi J. Chem. Theory Comput. 2014 10 68 75
31. T. S. Zwier Science 2004 304 1119
32. D. Marx M. E. Tuckerman J. Hutter M. Parrinello Nature 1999 397 601
33. D. H. Zhang M. A. Collins S. Y. Lee Science 2000 290 961
34. K. R. Asmis N. L. Pivonka G. Santambrogio M. Bruemmer C. Kaposta D. M. Neumark L. Woeste Science 2003 299 1375
35. M. H. Begemann C. S. Gudeman J. Pfaff R. J. Saykally Phys. Rev. Lett. 1983 51 554
36. D. J. Wales J. Chem. Phys. 1999 110 10403
37. D. J. Wales J. Chem. Phys. 1999 111 8429
38. M. Jieli M. Aida J. Phys. Chem. A 2009 113 1586
39. J. Dai Z. Bacic X. Huang S. Carter J. M. Bowman J. Chem. Phys. 2003 119 6571
40. Y. Xie R. B. Remington H. F. Schaefer III J. Chem. Phys. 1994 101 4878
41. D. Wei D. R. Salahub J. Chem. Phys. 1994 101 7633
42. S. W. Charoensak Lao-ngam P. Asawakun K. Sagarik Phys. Chem. Chem. Phys. 2011 13 4562
43. G. M. Chaban J. O. Jung R. B. Gerber J. Phys. Chem. A 2000 104 2772
44. J. M. Headrick E. G. Diken R. S. Walters N. I. Hammer R. A. Christie J. Cui E. M. Myshakin M. A. Duncan M. A. Johnson K. D. Jordan Science 2005 308 1765
45. H. Gassner M. Probst A. Lauenstein K. Hermansson J. Phys. Chem. A 1998 102 4596
46. S. Manzhos X. Wang R. Dawes T. Carrington J. Phys. Chem. A 2006 110 5295
47. K. T. No B. H. Chang S. Y. Kim M. S. Jhon H. A. Scheraga Chem. Phys. Lett. 1997 271 152
48. K. W. Cho K. T. No H. A. Scheraga J. Mol. Struct. 2002 641 77
49. C. M. Handley P. L. A. Popelier J. Chem. Theory Comput. 2009 5 1474
50. C. M. Handley G. I. Hawe D. B. Kell P. L. A. Popelier Phys. Chem. Chem. Phys. 2009 11 6365
51. J. Behler M. Parrinello Phys. Rev. Lett. 2007 98 146401
52. J. Behler J. Phys.: Condens. Matter 2014 26 183001
53. T. Morawietz V. Sharma J. Behler J. Chem. Phys. 2012 136 064103
54. T. Morawietz J. Behler J. Phys. Chem. A 2013 117 7356
55. T. Morawietz J. Behler Z. Phys. Chem. 2013 227 1559
56. R. J. Bartlett M. Musiał Rev. Mod. Phys. 2007 79 291
57. Y. Wang J. M. Bowman Chem. Phys. Lett. 2010 491 1
58. C. M. Handley J. Behler Eur. Phys. J. B 2014 87 152
59. J. Ischtwan M. A. Collins J. Chem. Phys. 1994 100 8080
60. A. Brown B. J. Braams K. Christoffel Z. Jin J. M. Bowman J. Chem. Phys. 2003 119 8790
61. M. Rupp A. Tkatchenko K. R. Müller O. A. von Lilienfeld Phys. Rev. Lett. 2012 108 058301
62. T. B. Blank S. D. Brown A. W. Calhoun D. J. Doren J. Chem. Phys. 1995 103 4129
63. C. M. Bishop, Neural Networks for Pattern Recognition, Oxford University Press, 1996
64. C. M. Handley P. L. A. Popelier J. Phys. Chem. A 2010 114 3371
65. J. Behler Phys. Chem. Chem. Phys. 2011 13 17930
66. J. Behler J. Chem. Phys. 2011 134 074106
67. J. Behler R. Martonák D. Donadio M. Parrinello Phys. Rev. Lett. 2008 100 185501
68. N. Artrith B. Hiller J. Behler Phys. Status Solidi B 2013 250 1191
69. N. Artrith J. Behler Phys. Rev. B: Condens. Matter Mater. Phys. 2012 85 045439
70. N. Artrith T. Morawietz J. Behler Phys. Rev. B: Condens. Matter Mater. Phys. 2011 83 153101
71. G. C. Sosso G. Miceli S. Caravati J. Behler M. Bernasconi Phys. Rev. B: Condens. Matter Mater. Phys. 2012 85 174103
72. H. Eshet R. Z. Khaliullin T. D. Kühne J. Behler M. Parrinello Phys. Rev. B: Condens. Matter Mater. Phys. 2010 81 184107
73. R. Z. Khaliullin H. Eshet T. D. Kühne J. Behler M. Parrinello Phys. Rev. B: Condens. Matter Mater. Phys. 2010 81 100103
74. K. V. Jovan Jose N. Artrith J. Behler J. Chem. Phys. 2012 136 194111
75. V. Blum R. Gehrke F. Hanke P. Havu V. Havu X. Ren K. Reuter M. Scheffler Comput. Phys. Commun. 2009 180 2175
76. J. P. Perdew K. Burke M. Ernzerhof Phys. Rev. Lett. 1996 77 3865
77. J. P. Perdew K. Burke M. Ernzerhof Phys. Rev. Lett. 1997 78 1396
78. Y. Sugita Y. Okamoto Chem. Phys. Lett. 1999 314 141
79. M. P. Hodges D. J. Wales Chem. Phys. Lett. 2000 324 279
80. J. W. Ponder F. M. Richards J. Comput. Chem. 1987 8 1016
81. E. S. Penev S. Lampoudi J. E. Shea Comput. Phys. Commun. 2009 180 2013
82. T. B. Blank S. D. Brown J. Chemom. 1994 8 391
83. J. Behler, RuNNer-A Software Package for Constructing High-Dimensional Neural Network Potentials, Ruhr-Universität Bochum, 2007-2014
84. O. M. Becker M. Karplus J. Chem. Phys. 1997 106 1495
85. D. Wales, Energy Landscapes: Applications to Clusters, Biomolecules and Glasses, Cambridge University Press, 2004
86. T. Morawietz, A. Singraber, C. Dellago and J. Behler, in preparation
87. E. Schwegler J. C. Grossman F. Gygi G. Galli J. Chem. Phys. 2004 121 5400
88. D. Marx M. E. Tuckerman M. Parrinello J. Phys.: Condens. Matter 2000 12 A153 A159
89. The MD simulations have been carried out using the LAMMPS code (S. Plimpton, J. Comp. Phys., 1995, 117, 1-19, http://lammps.sandia.gov), which has been extended by a NN potential module by Andreas Singraber, Computational Physics, University of Vienna, Austria