Liquid methanol from DFT and DFT/MM molecular dynamics simulations

Journal of Chemical Theory and Computation

Volumn 9, Issue 1, 2013, Pages 106-118

  Sieffert, Nicolas ^a   Bühl, Michael ^b   Gaigeot, Marie Pierre ^c,d   Morrison, Carole A ^e  

^a UNIV GRENOBLE ALPES   (France)

^b UNIVERSITY OF ST ANDREWS   (United Kingdom)

^c UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^d INSTITUT UNIVERSITAIRE DE FRANCE   (France)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872133331     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300784x     Document Type: Article

References (97)

1. Ahmed, M.; Dincer, I. Int. J.Energy Res. 2011, 35, 1213
2. Ludwig, R. ChemPhysChem 2005, 6, 1369
3. Blandamer, M. J.; Burgess, J. Transition Met. Chem. 1988, 13, 1
4. Chaumont, A.; Wipff, G. Phys. Chem. Chem. Phys. 2008, 10, 6940
5. Bühl, M.; Sieffert, N.; Chaumont, A.; Wipff, G. Inorg. Chem. 2011, 50, 299
6. Jorgensen, W. L. J. Am. Chem. Soc. 1980, 102, 543
7. Jorgensen, W. L. J. Phys. Chem. 1986, 90, 1276
8. Haughney, M.; Ferrario, M.; McDonald, I. R. J. Phys. Chem. 1987, 91, 4934
9. Dang, L. X.; Chang, T.-M. J. Chem. Phys. 2003, 119, 9851
10. Patel, S.; Brooks Iii, C. L. J. Chem. Phys. 2005, 122, 024508
11. Ishiyama, T.; Sokolov, V. V.; Morita, A. J. Chem. Phys. 2011, 134, 024509
12. Nielson, K. D.; van Duin, A. C. T.; Oxgaard, J.; Deng, W.-Q.; Goddard, W. A. J. Phys. Chem. A 2004, 109, 493
13. See for instance the case of hydrogen transfer at a ruthenium center: Handgraaf, J.-W.; Meijer, E. J. J. Am. Chem. Soc. 2007, 129, 3099
14. Bühl, M.; Kabrede, H. J. Chem. Theory Comput. 2006, 2, 1282
15. Waller, M. P.; Braun, H.; Hojdis, N.; Bühl, M. J. Chem. Theory Comput. 2007, 3, 2234
16. Bühl, M.; Reimann, C.; Pantazis, D. A.; Bredow, T.; Neese, F. J. Chem. Theory Comput. 2008, 4, 1449
17. Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2011, 7, 669
18. Handgraaf, J.-W.; van Erp, T. S.; Meijer, E. J. Chem. Phys. Lett. 2003, 367, 617
19. Handgraaf, J.-W.; Meijer, E. J.; Gaigeot, M.-P. J. Chem. Phys. 2004, 121, 10111
20. Kuo, I. F. W.; Mundy, C. J.; McGrath, M. J.; Siepmann, J. I. J. Phys. Chem. C 2008, 112, 15412
21. Pagliai, M.; Cardini, G.; Righini, R.; Schettino, V. J. Chem. Phys. 2003, 119, 6655
22. Morrone, J. A.; Tuckerman, M. E. J. Chem. Phys. 2002, 117, 4403
23. Grimme, S. J. Comput. Chem. 2004, 25, 1463
24. Grimme, S. J. Comput. Chem. 2006, 27, 1787
25. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. J. Chem. Phys. 2010, 132, 154104
26. Lin, I. C.; Seitsonen, A. P.; Coutinho-Neto, M. c. D.; Tavernelli, I.; Rothlisberger, U. J. Phys. Chem. B 2009, 113, 1127
27. Lin, I. C.; Seitsonen, A. P.; Tavernelli, I.; Rothlisberger, U. J. Chem. Theory Comput. 2012, 8, 3902-3910
28. Jonchiere, R.; Seitsonen, A. P.; Ferlat, G.; Saitta, A. M.; Vuilleumier, R. J. Chem. Phys. 2011, 135, 154503
29. Yoo, S.; Xantheas, S. S. J. Chem. Phys. 2011, 134, 121105
30. 2 has also been reported using a different approach for the description of dispersion effects. See: Balasubramanian, S.; Kohlmeyer, A.; Klein, M. L. J. Chem. Phys. 2009, 131, 144506
31. McGrath, M. J.; Kuo, I. F. W.; Ghogomu, J. N.; Mundy, C. J.; Siepmann, J. I. J. Phys. Chem. B 2011, 115, 11688
32. McGrath, M. J.; Kuo, I. F. W.; Siepmann, J. I. Phys. Chem. Chem. Phys. 2011, 13, 19943
33. Sieffert, N.; Bühl, M. Inorg. Chem. 2009, 48, 4622
34. Minenkov, Y.; Singstad, A.; Occhipinti, G.; Jensen, V. R. Dalton Trans. 2012, 41, 5526
35. Senn, H. M.; Thiel, W. Ang. Chem. Int. Ed. 2009, 48, 1198
36. VandeVondele, J.; Mohamed, F.; Krack, M.; Hutter, J.; Sprik, M.; Parrinello, M. J. Chem. Phys. 2005, 122, 014515
37. Kuo, I. F. W.; Mundy, C. J.; McGrath, M. J.; Siepmann, J. I. J. Chem. Theory Comput. 2006, 2, 1274
38. Kuo, I. F. W.; Mundy, C. J.; McGrath, M. J.; Siepmann, J. I.; VandeVondele, J.; Sprik, M.; Hutter, J.; Chen, B.; Klein, M. L.; Mohamed, F.; Krack, M.; Parrinello, M. J. Phys. Chem. B 2004, 108, 12990
39. Laio, A.; VandeVondele, J.; Rothlisberger, U. J. Chem. Phys. 2002, 116, 6941
40. Laio, A.; VandeVondele, J.; Rothlisberger, U. J. Phys. Chem. B 2002, 106, 7300
41. Laino, T.; Mohamed, F.; Laio, A.; Parrinello, M. J. Chem. Theory Comput. 2005, 1, 1176
42. Laino, T.; Mohamed, F.; Laio, A.; Parrinello, M. J. Chem. Theory Comput. 2006, 2, 1370
43. Yamaguchi, T.; Hidaka, K.; Soper, A. K. Mol. Phys. 1999, 96, 1159
44. Mol. Phys. 1999, 97, 603. Erratum
45. Holz, M.; Mao, X.-a.; Seiferling, D.; Sacco, A. J. Chem. Phys. 1996, 104, 669
46. McClellan, A. L., Tables of Experimental Dipole Moment; Rahara Enterprises, El Cerrito, CA (1989), as cited in: Dang, L. X.; Chang, T.-M. J. Chem. Phys. 2003, 119, 9851.
47. Serrallach, A.; Meyer, R.; Günthard, H. H. J. Mol. Spectrosc. 1974, 52, 94
48. Bertie, J. E.; Zhang, S. L. J. Mol. Struct. 1997, 413-414, 333
49. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham Iii, T. E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1
50. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668
51. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
52. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577
53. Ewald, P. P. Annalen der Physik 1921, 369, 253
54. Laino, T.; Hutter, J. J. Chem. Phys. 2008, 129, 074102
55. Toukmaji, A. Y.; Board, J. A. Comput. Phys. Commun. 1996, 95, 73
56. The experimental density of liquid methanol at P = 1.01325 bar is 24.79141 mol/L at T = 290 K, and 24.49774 mol/L at T = 300 K (see: Goodwin, R. D. J. Phys. Chem. Ref. Data 1987, 16, 799). In our study, the densities considered in the simulated systems are 24.75 mol/L (32 methanol molecules, cell lengh 12.9 Å), 24.53 mol/L (64 molecules, 16.3 Å) and 23.47 mol/L (1367 molecules, 45.9 Å).
57. Case, D.A.; Darden, T.A.; Cheatham, T.E.;, III; Simmerling, C.L.; Wang, J.; Duke, R.E.; Luo, R.; Crowley, M.; Walker, R.C.; Zhang, W.; Merz, K.M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; I. Kolossvaìry; Wong, K.F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S.R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D.H.; Seetin, M.G.; Sagui, C.; Babin, V.;; Kollman, P.A. (2008), AMBER 10, University of California, San Francisco.
58. Nosé, S. J. Chem. Phys. 1984, 81, 511
59. Martyna, G. J.; Klein, M. L.; Tuckerman, M. J. Chem. Phys. 1992, 97, 2635
60. Hoover, W. G. Phys. Rev. A 1985, 31, 1695
61. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471
62. CPMD Version 3.15.1, Copyright IBM Corp. 1990-2006, Copyright MPI für Festkörperforschung Stuttgart, 1997-2001
63. Becke, A. D. Phys. Rev. A 1988, 38, 3098
64. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785
65. Perdew, J. P. Phys. Rev. B 1986, 33, 8822
66. Perdew, J. P. Phys. Rev. B 1986, 34, 7406
67. Troullier, N.; Martins, J. L. Phys. Rev. B 1991, 43, 1993
68. Kleinman, L.; Bylander, D. M. Phys. Rev. Lett. 1982, 48, 1425
69. VandeVondele, J.; Krack, M.; Mohamed, F.; Parrinello, M.; Chassaing, T.; Hutter, J. Comput. Phys. Commun. 2005, 167, 103
70. For more information on CP2K see: http://www.cp2k.org (accessed October 17, 2012)
71. Schafer, A.; Huber, C.; Ahlrichs, R. J. Chem. Phys. 1994, 100, 5829
72. Goedecker, S.; Teter, M.; Hutter, J. Phys. Rev. B 1996, 54, 1703
73. Hartwigsen, C.; Goedecker, S.; Hutter, J. Phys. Rev. B 1998, 58, 3641
74. Krack, M. Theor. Chem. Acc. 2005, 114, 145
75. Becke, A. D. Phys. Rev. A 1988, 38, 3098
76. Perdew, J. P. Phys. Rev. B 1986, 33, 8822
77. Perdew, J. P. Phys. Rev. B 1986, 34, 7406
78. Scott, W. R. P.; Hünenberger, P. H.; Tironi, I. G.; Mark, A. E.; Billeter, S. R.; Fennen, J.; Torda, A. E.; Huber, T.; Krüger, P.; van Gunsteren, W. F. J. Phys. Chem. A 1999, 103, 3596
79. In practice, we employ the NVE ensemble for the study of vibrational properties of solutes (see Ref 59), whereas we employ the NVT ensemble for full DFT-MD studies of metal complexes in solution (see e.g. Bühl, M.; Sieffert, N.; Wipff, G. Chem. Phys. Lett. 2009, 467, 287). We therefore decided herein to test and validate our protocols in the same conditions, in view with their further applications.
80. Martyna, G. J.; Tuckerman, M. E. J. Chem. Phys. 1999, 110, 2810
81. Humphrey, W.; Dalke, A.; Schulten, K. J. Molec. Graphics 1996, 14, 33
82. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
83. Marzari, N.; Vanderbilt, D. Phys. Rev. B 1997, 56, 12847
84. Silvestrelli, P. L.; Parrinello, M. J. Chem. Phys. 1999, 111, 3572
85. Gaigeot, M.-P.; Sprik, M. J. Phys. Chem. B 2003, 107, 10344
86. A detailed description of the method we employed to compute IR spectra from DFT-MD simulations can be found in: Gaigeot, M.-P. Phys. Chem. Chem. Phys. 2010, 12, 3336
87. see e.g. Ong, S. W.; Tok, E. S.; Kang, H. C. Phys. Chem. Chem. Phys. 2010, 12, 14960
88. Ivash, E. V.; Dennison, D. M. J. Chem. Phys. 1953, 21, 1804
89. -1 with B97-D2. These values have been obtained by optimizing a (fully deuterated) methanol molecule in the gas phase using the def2-QZVPP basis set and computing the numerical frequencies with the Turbomole package. See: TURBOMOLE V6.4 2012, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com (accessed October 17, 2012)
90. Grabowski, S. Ç. J. Chem. Rev. 2011, 111, 2597
91. Kollman, P. A.; Allen, L. C. Chem. Rev. 1972, 72, 283
92. Morrone, J. A.; Tuckerman, M. E. Chem. Phys. Lett. 2003, 370, 406
93. Tu, Y.; Laaksonen, A. Phys. Rev. E 2001, 64, 026703
94. Rode, B.; Hofer, T.; Randolf, B.; Schwenk, C.; Xenides, D.; Vchirawongkwin, V. Theor. Chem. Acc. 2006, 115, 77
95. Bulo, R. E.; Ensing, B.; Sikkema, J.; Visscher, L. J. Chem. Theory Comput. 2009, 5, 2212
96. Pezeshki, S.; Lin, H. J. Chem. Theory Comput. 2011, 7, 3625
97. Bernstein, N.; Varnai, C.; Solt, I.; Winfield, S. A.; Payne, M. C.; Simon, I.; Fuxreiter, M.; Csanyi, G. Phys. Chem. Chem. Phys. 2012, 14, 646