Ab initio molecular dynamics study of carbon dioxide and bicarbonate hydration and the nucleophilic attack of hydroxide on CO2

Journal of Physical Chemistry B

Volumn 111, Issue 17, 2007, Pages 4453-4459

  Leung, Kevin ^a   Nielsen, Ida M B ^b   Kurtz, Ira ^c  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b SANDIA NATIONAL LABORATORIES   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENERGY BARRIERS; FREE ENERGY; HYDRATION; HYDROPHOBICITY; MOLECULAR DYNAMICS;

BICARBONATES; GAS PHASE; NUCLEOPHILIC ATTACK;

CARBON DIOXIDE;

BICARBONATE; CARBON DIOXIDE; HYDROXIDE; HYDROXIDE ION; UNCLASSIFIED DRUG; WATER;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION;

BICARBONATES; CARBON DIOXIDE; COMPUTER SIMULATION; HYDROXIDES; WATER;

EID: 34249106035     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0684751     Document Type: Article

References (74)

1. Caldeira, K.; Wickett, M. E. Nature 2003, 425, 365.
2. Plane, J. M. C. Ann. Geophys. 2000, 18, 807.
3. Orr, J. C.; Fabry, V. J.; Aumont, O.; et al. Nature 2005, 437, 681.
4. Kurtz, I.; Petrasek, D.; Tatischev, S. J. Membr. Biol. 2004, 197, 77.
5. Pushkin, A.; Kurtz, I. Am. J. Physiol. 2006, 290, F580.
6. Pinsent, B. R. W.; Roughton, F. J. W. Trans. Faraday Soc. 1951, 47, 263.
7. Harned, H. S.; Davis, R., Jr. J. Am. Chem. Soc. 1943, 65, 2030.
8. Himmelblau, D. M.; Babb, A. L. AIChE J. 1958, 4, 143.
9. Pinsent, B. R. W.; Pearson, L.; Roughton, F. J. W. Trans. Faraday Soc. 1956, 52, 1512.
10. Danckwerts, P. V.; Melkersson, K. A. Trans. Faraday Soc. 1962, 58, 1832.
11. Pohorecki, R.; Moniuk, W. Chem. Eng. Sci. 1988, 43, 1677.
12. Falk, M.; Miller, A. G. Vib. Spectrosc. 1992, 4, 105.
13. Abashkin, Y.; Mele, F.; Russo, N.; Toscano, M. Int. J. Quantum Chem. 1994, 52, 1011.
14. Kuznetsova, T.; Kvamme, B. Phys. Chem. Chem. Phys. 2002, 4, 937.
15. da Rocha, S. R. P.; Johnston, K. P.; Westacott, R. E.; Rossky, P. J. J. Phys. Chem. B 2001, 105, 12092.
16. In Het Panhuis, M.; Patterson, C. H.; Lynden-Bell, R. M. Mol. Phys. 1998, 94, 963.
17. Jönsson, B.; Karlström, O.; Wannerström, H. J. Am. Chem. Soc. 1978, 100, 1658.
18. Davis, R. P. J. J. Am. Chem. Soc. 1958, 80, 1958.
19. Brär, M.; Péz-Lustres, J. L.; Westen, J.; Anders, E. Inorg. Chem. 2002, 41, 1454.
20. Merz, K. M., Jr.; Banci, L. J. Am. Chem. Soc. 1997, 119, 863.
21. Schroöder, D.; Schwarz, H.; Schenk, S.; Anders, E. Angew. Chem. 2003, 42, 5087.
22. Liang, J. Y.; Lipscomb, W. N. J. Am. Chem. Soc. 1986, 108, 5051.
23. Davidson, M. M.; Hillier, I. H.; Hall, R. J.; Burton, N. A. Mol. Phys. 1994, 83, 327.
24. Nemukhin, A. V.; Topol, I. A.; Grigorenko, B. L.; Burt, S. K. J. Phys. Chem. B 2002, 106, 1734.
25. Peng, Z.; Merz, K. M., Jr. J. Am. Chem. Soc. 1992, 114, 2733.
26. Peng, Z.; Merz, K. M., Jr. J. Am. Chem. Soc. 1993, 115, 9640.
27. See, for example: Leung, K.; Rempe, S. B. J. Am. Soc. Chem. 2004, 126, 344.
28. Kieke, M. L.; Schoppelrei, J. W.; Brill, T. B. J. Phys. Chem. 1996, 100, 7455.
29. Takemura, F.; Matsumoto, Y. Chem. Eng. Sci. 2000, 55, 3907.
30. See, for example: Chandler, D. Introduction to Modern Statistical Mechanics; Oxford University Press: New York, 1987.
31. Sprik, M. Chem. Phys. 2000, 259, 139.
32. Sprik, M. J. Phys.: Condens. Matter 2000, 12, A161.
33. Davis, J. E.; Doltsinis, N. L.; Kirby, A. J.; Roussev, C. D.; Sprik, M. J. Am. Chem. Soc. 2002, 124, 6594.
34. Ivanov, I.; Klein, M. L. J. Am. Chem. Soc. 2002, 124, 13380.
35. Leung, K.; Rempe, S. B. J. Chem. Phys. 2005, 122, 184506.
36. Lee, J. G.; Asciutto, E.; Babin, V.; Sagui, C.; Darden, T.; Roland, C. J. Phys. Chem. B 2006, 110, 2325.
37. For example, see: Meijer, E. J.; Sprik, M. J. Phys. Chem. A 1998, 102, 2893.
38. Blumberger, J.; Klein, M. L. Chem. Phys. Lett. 2006, 422, 210.
39. Møller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618.
40. Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry; McGraw-Hill: New York, 1989.
41. Pratt, L. R.; Asthagiri, D.; Kress, J. D. Phys. Rev. E 2003, 68, 041505.
42. Grossman, J. C.; Schwegler, E.; Draeger, E. W.; Gygi, F.; Galli, G. J. Chem. Phys. 2004, 120, 300.
43. VandeVondele, J.; Mohamed, F.; Krack, M.; Hutter, J.; Sprik, M.; Parrinello, M. J. Chem. Phys. 2005, 122, 014515.
44. Hammer, B.; Hansen, L. B.; Norskov, J. K. Phys. Rev. B 1999, 59, 7413.
45. Becke, A. D. Phys. Rev. A 1988, 38, 3098.
46. Lee, C. T.; Yang, W. T.; Parr, R. G. Phys. Rev. B 1998, 37, 785.
47. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865.
48. Asthagiri, D.; Pratt, L. R.; Kress, J. D.; Gomez, M. A. Proc. Natl. Acad. Sci. 2004, 101, 7229.
49. Tuckerman, M. E.; Marx, D.; Parrinello, M. Nature 2002, 417, 925.
50. Tuckerman, M. E; Chandra, A.; Marx, D. Acc. Chem. Res. 2006, 39, 151.
51. Tuckerman, M. E.; Marx, D.; Klein, M. L.; Parrinello, M. Science 1997, 275, 817.
52. Chen, B.; Ivanov, I.; Park, J. M.; Parrinello, M.; Klein, M. L. J. Phys. Chem. B 2002, 106, 12006.
53. Kresse, G.; Furthmüller, J. Phys. Rev. B 1996, 54, 11169;
54. Comput. Mater. Sci. 1996, 6, 15.
55. Blochl, P. E. Phys. Rev. B 1994, 50, 17954.
56. Kresse, G.; Joubert, D. Phys. Rev. B 1999, 59, 1758.
57. See http://cms.mpi.univie.ac.at/vasp/.
58. 2O in liquid water occurs at O(1) ps intervals, neither slow enough to be avoided on AIMD time scales nor fast enough to enable adequate sampling throughout the simulation cell.
59. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047.
60. /ω2), is negligible.
61. OH is close to zero, it should be well sampled within AIMD.
62. Hammes, G. G. Principles of Chemical Kinetics; Academic Press: New York, 1978; pp 52.
63. Frisch, M. J.; et al. Gaussian 03, revision C.02; Gaussian Inc.: Wallingford, CT, 2004.
64. Dunning, T. H., Jr. J. Chem. Phys. 1989, 90, 1007.
65. Kendall, R. A.; Dunning, T. H., Jr.; Harrison, R. J. J. Chem. Phys. 1992, 96, 6796.
66. Woon, D. E.; Dunning, T. H., Jr. J. Chem. Phys. 1994, 100, 2975.
67. Jensen, F. J. Chem. Phys. 1999, 110, 6601.
68. Halkier, A.; Helgaker, T.; Jørgensen, P.; Klopper, W.; Olsen, J. Chem. Phys. Lett. 1999, 302, 437.
69. Halkier, A.; Helgaker, T. Jørgensen, P.; Klopper, W.; Koch, H.; Olsen, J.; Wilson, A. K. Chem. Phys. Lett. 1998, 286, 243.
70. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553.
71. Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
72. We have neglected the difference in hydration free energies predicted by different quantum mechanical methods because these involve subtle balancing between water-solute and water-water interactions.
73. CO = 2.08 Å, but we expect the resulting differences to be negligible.
74. Chandler, D. J. Chem. Phys. 1978, 68, 2959.