Hybrid quantum mechanics/molecular mechanics solvation scheme for computing free energies of reactions at metal-water interfaces

Journal of Chemical Theory and Computation

Volumn 10, Issue 8, 2014, Pages 3354-3368

  Faheem, Muhammad ^a   Heyden, Andreas ^a  

^a The Department of Mechanical Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84906257605     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500211w     Document Type: Article

References (78)

1. Rossmeisl, J.; Logadottir, A.; Norskov, J. K. Electrolysis of water on (oxidized) metal surfaces Chem. Phys. 2005, 319, 178-184
2. 2 catalyst: NMR diffusion and relaxation studies Chem.-Eur. J. 2012, 18, 14426-14433
3. 4 cluster Phys. Chem. Chem. Phys. 2010, 12, 614-620
4. Hou, R.; Wang, T.; Lan, X. Enhanced selectivity in the hydrogenation of acetylene due to the addition of a liquid phase as a selective solvent Ind. Eng. Chem. Res. 2013, 52, 13305-13312
5. Hibbitts, D. D.; Loveless, B. T.; Neurock, M.; Iglesia, E. Mechanistic role of water on the rate and selectivity of Fischer-Tropsch synthesis on ruthenium catalysts Angew. Chem., Int. Ed. 2013, 52, 12273-12278
6. Okamoto, Y. Density-functional calculations of atomic and molecular adsorptions on 55-atom metal clusters: Comparison with (111) surfaces Chem. Phys. Lett. 2005, 405, 79-83
7. Okamoto, Y. Comparison of hydrogen atom adsorption on Pt clusters with that on Pt surfaces: A study from density-functional calculations Chem. Phys. Lett. 2006, 429, 209-213
8. Iftimie, R.; Minary, P.; Tuckerman, M. E. Ab initio molecular dynamics: Concepts, recent developments, and future trends Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6654-6659
9. Mattsson, T. R.; Paddison, S. J. Methanol at the water-platinum interface studied by ab initio molecular dynamics Surf. Sci. 2003, 544, L697-L702
10. Otani, M.; Hamada, I.; Sugino, O.; Morikawa, Y.; Okamoto, Y.; Ikeshoji, T. Structure of the water/platinum interface-A first principles simulation under bias potential Phys. Chem. Chem. Phys. 2008, 10, 3609-3612
11. Yang, J.; Dauenhauer, P. J.; Ramasubramaniam, A. The role of water in the adsorption of oxygenated aromatics on Pt and Pd J. Comput. Chem. 2013, 34, 60-66
12. Cramer, C. J.; Truhlar, D. G. Implicit solvation models: Equilibria, structure, spectra, and dynamics Chem. Rev. 1999, 99, 2161-2200
13. Tomasi, J.; Mennucci, B.; Cammi, R. Quantum mechanical continuum solvation models Chem. Rev. 2005, 105, 2999-3093
14. Klamt, A.; Schuurmann, G. COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient J. Chem. Soc., Perkin Trans. 2 1993, 799-805
15. Jacob, T.; Goddard, W. A. Water formation on Pt and Pt-based alloys: A theoretical description of a catalytic reaction ChemPhysChem 2006, 7, 992-1005
16. 2O interface from periodic DFT calculations integrated with a continuum solvation model J. Phys. Chem. C 2009, 113, 17502-17508
17. Faheem, M.; Suthirakun, S.; Heyden, A. New implicit solvation scheme for solid surfaces J. Phys. Chem. C 2012, 116, 22458-22462
18. Behtash, S.; Lu, J.; Faheem, M.; Heyden, A. Solvent effects on the hydrodeoxygenation of propanoic acid over Pd(111) model surfaces Green Chem. 2014, 16, 605-616
19. Toney, M. F.; Howard, J. N.; Richer, J.; Borges, G. L.; Gordon, J. G.; Melroy, O. R.; Wiesler, D. G.; Yee, D.; Sorensen, L. B. Voltage-dependent ordering of water molecules at an electrode-electrolyte interface Nature 1994, 368, 444-446
20. Henderson, M. A. The interaction of water with solid surfaces: Fundamental aspects revisited Surf. Sci. Rep. 2002, 46, 1-308
21. Hodgson, A.; Haq, S. Water adsorption and the wetting of metal surfaces Surf. Sci. Rep. 2009, 64, 381-451
22. Cao, D.; Lu, G. Q.; Wieckowski, A.; Wasileski, S. A.; Neurock, M. Mechanisms of methanol decomposition on platinum: A combined experimental and ab initio approach J. Phys. Chem. B 2005, 109, 11622-11633
23. Zope, B. N.; Hibbitts, D. D.; Neurock, M.; Davis, R. J. Reactivity of the gold/water interface during selective oxidation catalysis Science 2010, 330, 74-78
24. Senn, H. M.; Thiel, W. QM/MM methods for biomolecular systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
25. Meng, S.; Wang, E. G.; Gao, S. W. Water adsorption on metal surfaces: A general picture from density functional theory studies Phys. Rev. B 2004, 69, 195404
26. Torrie, G. M.; Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling J. Comput. Phys. 1977, 23, 187-199
27. Straatsma, T. P.; Berendsen, H. J. C. Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations J. Chem. Phys. 1988, 89, 5876-5886
28. Riccardi, D.; Schaefer, P.; Yang, Y.; Yu, H. B.; Ghosh, N.; Prat-Resina, X.; Konig, P.; Li, G. H.; Xu, D. G.; Guo, H.; Elstner, M.; Cui, Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes J. Phys. Chem. B 2006, 110, 6458-6469
29. Kastner, J.; Senn, H. M.; Thiel, S.; Otte, N.; Thiel, W. QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: Application to an enzymatic reaction J. Chem. Theory Comput. 2006, 2, 452-461
30. Hu, H.; Yang, W. T. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods Annu. Rev. Phys. Chem. 2008, 59, 573-601
31. Zwanzig, R. W. High-temperature equation of state by a perturbation method. 1. Nonpolar gases J. Chem. Phys. 1954, 22, 1420-1426
32. Senn, H. M.; Thiel, W. QM/MM methods for biological systems Top. Curr. Chem. 2007, 268, 173-290
33. Field, M. J.; Bash, P. A.; Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations J. Comput. Chem. 1990, 11, 700-733
34. Zhang, Y. K.; Lee, T. S.; Yang, W. T. A pseudobond approach to combining quantum mechanical and molecular mechanical methods J. Chem. Phys. 1999, 110, 46-54
35. Murphy, R. B.; Philipp, D. M.; Friesner, R. A. Frozen orbital QM/MM methods for density functional theory Chem. Phys. Lett. 2000, 321, 113-120
36. Lu, Z. Y.; Yang, W. T. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations J. Chem. Phys. 2004, 121, 89-100
37. Hu, H.; Lu, Z. Y.; Yang, W. T. QM/MM minimum free-energy path: Methodology and application to triosephosphate isomerase J. Chem. Theory Comput. 2007, 3, 390-406
38. Hu, H.; Lu, Z. Y.; Parks, J. M.; Burger, S. K.; Yang, W. T. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: Sequential sampling and optimization on the potential of mean force surface J. Chem. Phys. 2008, 128, 034105
39. Hu, H.; Yang, W. T. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes J. Mol. Struct.: THEOCHEM 2009, 898, 17-30
40. Kresse, G.; Furthmuller, J. Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set Comput. Mater. Sci. 1996, 6, 15-50
41. Kresse, G.; Furthmuller, J. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set Phys. Rev. B 1996, 54, 11169-11186
42. Kresse, G.; Joubert, D. From ultrasoft pseudopotentials to the projector augmented-wave method Phys. Rev. B 1999, 59, 1758-1775
43. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple Phys. Rev. Lett. 1996, 77, 3865-3868
44. Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized gradient approximation made simple [Phys. Rev. Lett. 77, 3865, (1996)] Phys. Rev. Lett. 1997, 78, 1396-1396 Erratum
45. Monkhorst, H. J.; Pack, J. D. Special points for Brillouin-zone integrations Phys. Rev. B 1976, 13, 5188-5192
46. Makov, G.; Payne, M. C. Periodic boundary conditions in ab initio calculations Phys. Rev. B 1995, 51, 4014-4022
47. Methfessel, M.; Paxton, A. T. High-precision sampling for Brillouin-zone integration in metals Phys. Rev. B 1989, 40, 3616-3621
48. Henkelman, G.; Uberuaga, B. P.; Jonsson, H. A climbing image nudged elastic band method for finding saddle points and minimum energy paths J. Chem. Phys. 2000, 113, 9901-9904
49. Henkelman, G.; Jonsson, H. Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points J. Chem. Phys. 2000, 113, 9978-9985
50. Henkelman, G.; Jonsson, H. A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives J. Chem. Phys. 1999, 111, 7010-7022
51. Heyden, A.; Bell, A. T.; Keil, F. J. Efficient methods for finding transition states in chemical reactions: Comparison of improved dimer method and partitioned rational function optimization method J. Chem. Phys. 2005, 123, 224101
52. TURBOMOLE V6.4 2012, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007.
53. Ahlrichs, R.; Bar, M.; Haser, M.; Horn, H.; Kolmel, C. Electronic structure calculations on workstation computers: The program system TURBOMOLE Chem. Phys. Lett. 1989, 162, 165-169
54. Treutler, O.; Ahlrichs, R. Efficient molecular numerical integration schemes J. Chem. Phys. 1995, 102, 346-354
55. Von Arnim, M.; Ahlrichs, R. Performance of parallel TURBOMOLE for density functional calculations J. Comput. Chem. 1998, 19, 1746-1757
56. Schafer, A.; Horn, H.; Ahlrichs, R. Fully optimized contracted Gaussian basis sets for atoms Li to Kr J. Chem. Phys. 1992, 97, 2571-2577
57. Schafer, A.; Huber, C.; Ahlrichs, R. Fully optimized contracted Gaussian basis sets of triple-Χ valence quality for atoms Li to Kr J. Chem. Phys. 1994, 100, 5829-5835
58. Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R. Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials Theor. Chem. Acc. 1997, 97, 119-124
59. Weigend, F.; Ahlrichs, R. Balanced basis sets of split valence, triple-Χ valence and quadruple-Χ valence quality for H to Rn: Design and assessment of accuracy Phys. Chem. Chem. Phys. 2005, 7, 3297-3305
60. Eichkorn, K.; Treutler, O.; Ohm, H.; Haser, M.; Ahlrichs, R. Auxiliary basis sets to approximate Coulomb potentials Chem. Phys. Lett. 1995, 240, 283-289
61. Weigend, F. Accurate Coulomb-fitting basis sets for H to Rn Phys. Chem. Chem. Phys. 2006, 8, 1057-1065
62. Klamt, A.; Jonas, V. Treatment of the outlying charge in continuum solvation models J. Chem. Phys. 1996, 105, 9972-9981
63. Schafer, A.; Klamt, A.; Sattel, D.; Lohrenz, J. C. W.; Eckert, F. COSMO implementation in TURBOMOLE: Extension of an efficient quantum chemical code towards liquid systems Phys. Chem. Chem. Phys. 2000, 2, 2187-2193
64. Klamt, A. Conductor-like screening model for real solvents: A new approach to the quantitative calculation of solvation phenomena J. Phys. Chem. 1995, 99, 2224-2235
65. Klamt, A.; Jonas, V.; Burger, T.; Lohrenz, J. C. W. Refinement and parametrization of COSMO-RS J. Phys. Chem. A 1998, 102, 5074-5085
66. Klamt, A. COSMO-RS: From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design; Elsevier Science Ltd.: Amsterdam, The Netherlands, 2005.
67. Perdew, J. P. Density-functional approximation for the correlation energy of the inhomogeneous electron gas Phys. Rev. B 1986, 33, 8822-8824
68. Becke, A. D. Density-functional exchange-energy approximation with correct asymptotic behavior Phys. Rev. A 1988, 38, 3098-3100
69. 2 investigated by the periodic electrostatic embedded cluster method J. Chem. Phys. 2009, 130, 174710
70. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
71. Reed, A. E.; Weinstock, R. B.; Weinhold, F. Natural population analysis J. Chem. Phys. 1985, 83, 735-746
72. Todorov, I. T.; Smith, W.; Trachenko, K.; Dove, M. T. DL-POLY-3: New dimensions in molecular dynamics simulations via massive parallelism J. Mater. Chem. 2006, 16, 1911-1918
73. Smith, W.; Forester, T. R. Parallel macromolecular simulations and the replicated data strategy. 2. The RD-SHAKE algorithm Comput. Phys. Commun. 1994, 79, 63-77
74. Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
75. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A smooth particle mesh Ewald method J. Chem. Phys. 1995, 103, 8577-8593
76. Spohr, E. Computer simulation of the water/platinum interface J. Phys. Chem. 1989, 93, 6171-6180
77. Jorgensen, W. L. Optimized intermolecular potential functions for liquid alcohols J. Phys. Chem. 1986, 90, 1276-1284
78. Geerke, D. P.; Van Gunsteren, W. F. The performance of non-polarizable and polarizable force-field parameter sets for ethylene glycol in molecular dynamics simulations of the pure liquid and its aqueous mixtures Mol. Phys. 2007, 105, 1861-1881