Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution
We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model,...
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- 2017
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- Repositorio UDEM
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| dc.title.spa.fl_str_mv |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| title |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| spellingShingle |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| title_short |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| title_full |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| title_fullStr |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| title_full_unstemmed |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| title_sort |
Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution |
| dc.contributor.affiliation.spa.fl_str_mv |
Caro, M.A., Department of Electrical Engineering and Automation, Aalto University, Espoo, Finland, COMP Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, Espoo, Finland Lopez-Acevedo, O., COMP Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, Espoo, Finland, Departamento de Facultad de Ciencias Básicas, Universidad de Medellín, Medellín, Colombia Laurila, T., Department of Electrical Engineering and Automation, Aalto University, Espoo, Finland |
| description |
We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr2+/3+, V2+/3+, Ru(NH3)62+/3+, Sn2+/4+, Cu1+/2+, FcMeOH0/1+, and Fe2+/3+ (in aqueous solution) and Fc0/1+ (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations. © 2017 American Chemical Society. |
| publishDate |
2017 |
| dc.date.accessioned.none.fl_str_mv |
2017-12-19T19:36:41Z |
| dc.date.available.none.fl_str_mv |
2017-12-19T19:36:41Z |
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2017 |
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Article |
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http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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http://purl.org/coar/resource_type/c_6501 http://purl.org/coar/resource_type/c_2df8fbb1 |
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info:eu-repo/semantics/article |
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15499618 |
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http://hdl.handle.net/11407/4253 |
| dc.identifier.doi.none.fl_str_mv |
10.1021/acs.jctc.7b00314 |
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reponame:Repositorio Institucional Universidad de Medellín |
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instname:Universidad de Medellín |
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15499618 10.1021/acs.jctc.7b00314 reponame:Repositorio Institucional Universidad de Medellín instname:Universidad de Medellín |
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http://hdl.handle.net/11407/4253 |
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eng |
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eng |
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https://www.scopus.com/inward/record.uri?eid=2-s2.0-85027228601&doi=10.1021%2facs.jctc.7b00314&partnerID=40&md5=e934b462e00f989f9f4e16ce4500392c |
| dc.relation.ispartofes.spa.fl_str_mv |
Journal of Chemical Theory and Computation Journal of Chemical Theory and Computation Volume 13, Issue 8, 8 August 2017, Pages 3432-3441 |
| dc.relation.references.spa.fl_str_mv |
Aarva, A., Laurila, T., & Caro, M. A. (2017). Doping as a means to probe the potential dependence of dopamine adsorption on carbon-based surfaces: A first-principles study. Journal of Chemical Physics, 146(23) doi:10.1063/1.4986521 Bard, A. J., & Faulkner, L. R. (1980). Electrochemical Methods: Fundamentals and Applications. Berens, P. H., Mackay, D. H. J., White, G. M., & Wilson, K. R. (1983). Thermodynamics and quantum corrections from molecular dynamics for liquid water. The Journal of Chemical Physics, 79(5), 2375-2389. Blöchl, P. E. (1994). Projector augmented-wave method. Physical Review B, 50(24), 17953-17979. doi:10.1103/PhysRevB.50.17953 Cannes, C., Kanoufi, F., & Bard, A. J. (2003). Cyclic voltammetry and scanning electrochemical microscopy of ferrocenemethanol at monolayer and bilayer-modified gold electrodes. Journal of Electroanalytical Chemistry, 547(1), 83-91. doi:10.1016/S0022-0728(03)00192-X Caro, M. A. (2017). Solvation shells and radial distribution functions of transition metal complexes in aqueous solution: Results from ab initio molecular dynamics. Zenodo. Caro, M. A., Laurila, T., & Lopez-Acevedo, O. (2016). Accurate schemes for calculation of thermodynamic properties of liquid mixtures from molecular dynamics simulations. Journal of Chemical Physics, 145(24) doi:10.1063/1.4973001 Caro, M. A., Määttä, J., Lopez-Acevedo, O., & Laurila, T. (2015). Energy band alignment and electronic states of amorphous carbon surfaces in vacuo and in aqueous environment. Journal of Applied Physics, 117(3) doi:10.1063/1.4905915 Cheng, J., Liu, X., VandeVondele, J., Sulpizi, M., & Sprik, M. (2014). Redox potentials and acidity constants from density functional theory based molecular dynamics. Accounts of Chemical Research, 47(12), 3522-3529. doi:10.1021/ar500268y Christ, C. D., Mark, A. E., & Van Gunsteren, W. F. (2010). Basic ingredients of free energy calculations: A review. Journal of Computational Chemistry, 31(8), 1569-1582. doi:10.1002/jcc.21450 Dudarev, S. L., Botton, G. A., Savrasov, S. Y., Humphreys, C. J., & Sutton, A. P. (1998). Electron-energy-loss spectra and the structural stability of nickel oxide: An LSDA+U study. Physical Review B - Condensed Matter and Materials Physics, 57(3), 1505-1509. Gagne, R. R., Koval, C. A., & Lisensky, G. C. (1980). Ferrocene as an internal standard for electrochemical measurements. Inorganic Chemistry, 19(9), 2854-2855. doi:10.1021/ic50211a080 Gillan, M. J., Alfè, D., & Michaelides, A. (2016). Perspective: How good is DFT for water? Journal of Chemical Physics, 144(13) doi:10.1063/1.4944633 Heyd, J., Scuseria, G. E., & Ernzerhof, M. (2003). Hybrid functionals based on a screened coulomb potential. Journal of Chemical Physics, 118(18), 8207-8215. doi:10.1063/1.1564060 Holmberg, N., & Laasonen, K. (2015). Ab initio electrochemistry: Exploring the hydrogen evolution reaction on carbon nanotubes. Journal of Physical Chemistry C, 119(28), 16166-16178. doi:10.1021/acs.jpcc.5b04739 Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review A, 31(3), 1695-1697. doi:10.1103/PhysRevA.31.1695 House, C. I., & Kelsall, G. H. (1984). Potential-pH diagrams for the Sn/H2OCl system. Electrochimica Acta, 29(10), 1459-1464. doi:10.1016/0013-4686(84)87028-0 Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926-935. Kresse, G., & Furthmüller, J. (1996). Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Physical Review B - Condensed Matter and Materials Physics, 54(16), 11169-11186. Kresse, G., & Joubert, D. (1999). From ultrasoft pseudopotentials to the projector augmented-wave method. Physical Review B - Condensed Matter and Materials Physics, 59(3), 1758-1775. Lai, P. -., Hsieh, C. -., & Lin, S. -. (2012). Rapid determination of entropy and free energy of mixtures from molecular dynamics simulations with the two-phase thermodynamic model. Physical Chemistry Chemical Physics, 14(43), 15206-15213. doi:10.1039/c2cp42011b Lee, C., Yang, W., & Parr, R. G. (1988). Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37(2), 785-789. doi:10.1103/PhysRevB.37.785 Lin, S. -., Blanco, M., & Goddard III, W. A. (2003). The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of lennard-jones fluids.Journal of Chemical Physics, 119(22), 11792-11805. doi:10.1063/1.1624057 Lin, S. -., Maiti, P. K., & Goddard III, W. A. (2010). Two-phase thermodynamic model for efficient and accurate absolute entropy of water from molecular dynamics simulations. Journal of Physical Chemistry B, 114(24), 8191-8198. doi:10.1021/jp103120q Lindahl, E., Bjelkmar, P., Larsson, P., Cuendet, M. A., & Hess, B. (2010). Implementation of the charmm force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459-466. doi:10.1021/ct900549r Lucking, M., Sun, Y. -., West, D., & Zhang, S. (2014). Absolute redox potential of liquid water: A first-principles theory. Chemical Science, 5(3), 1216-1220. doi:10.1039/c3sc52287c Makov, G., & Payne, M. C. (1995). Periodic boundary conditions in ab initio calculations. Physical Review B, 51(7), 4014-4022. doi:10.1103/PhysRevB.51.4014 Nosé, S. (1984). A unified formulation of the constant temperature molecular dynamics methods. The Journal of Chemical Physics, 81(1), 511-519. Pascal, T. A., & Goddard, W. A. (2012). Hydrophobic segregation, phase transitions and the anomalous thermodynamics of water/methanol mixtures. Journal of Physical Chemistry B, 116(47), 13905-13912. doi:10.1021/jp309693d Pavlishchuk, V. V., & Addison, A. W. (2000). Conversion constants for redox potentials measured versus different reference electrodes in acetonitrile solutions at 25°C. Inorganica Chimica Acta, 298(1), 97-102. doi:10.1016/S0020-1693(99)00407-7 Perdew, J. P., Burke, K., & Ernzerhof, M. (1996). Generalized gradient approximation made simple. Physical Review Letters, 77(18), 3865-3868. doi:10.1103/PhysRevLett.77.3865 Post, K., & Robins, R. G. (1976). Thermodynamic diagrams for the vanadium-water system at 298·15K. Electrochimica Acta, 21(6), 401-405. doi:10.1016/0013-4686(76)85115-8 Rossmeisl, J., Nørskov, J. K., Taylor, C. D., Janik, M. J., & Neurock, M. (2006). Calculated phase diagrams for the electrochemical oxidation and reduction of water over pt(111). Journal of Physical Chemistry B, 110(43), 21833-21839. doi:10.1021/jp0631735 Rossmeisl, J., Skúlason, E., Björketun, M. E., Tripkovic, V., & Nørskov, J. K. (2008). Modeling the electrified solid-liquid interface. Chemical Physics Letters, 466(1-3), 68-71. doi:10.1016/j.cplett.2008.10.024 Rusnak, A. J., Pinnick, E. R., Calderon, C. E., & Wang, F. (2012). Static dielectric constants and molecular dipole distributions of liquid water and ice-ih investigated by the PAW-PBE exchange-correlation functional. Journal of Chemical Physics, 137(3) doi:10.1063/1.4734594 Skúlason, E., Karlberg, G. S., Rossmeisl, J., Bligaard, T., Greeley, J., Jónsson, H., & Nørskov, J. K. (2007). Density functional theory calculations for the hydrogen evolution reaction in an electrochemical double layer on the pt(111) electrode. Physical Chemistry Chemical Physics, 9(25), 3241-3250. doi:10.1039/b700099e Stradi, D., Martinez, U., Blom, A., Brandbyge, M., & Stokbro, K. (2016). General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium green's function. Physical Review B, 93(15) doi:10.1103/PhysRevB.93.155302 Tkatchenko, A., & Scheffler, M. (2009). Accurate molecular van der waals interactions from ground-state electron density and free-atom reference data. Physical Review Letters, 102(7) doi:10.1103/PhysRevLett.102.073005 Trasa'tti, S. (1986). The absolute electrode potential: An explanatory note (recommendations 1986). Pure and Applied Chemistry, 58(7), 955-966. doi:10.1351/pac198658070955 Tsierkezos, N. G. (2007). Cyclic voltammetric studies of ferrocene in nonaqueous solvents in the temperature range from 248.15 to 298.15 K. Journal of Solution Chemistry, 36(3), 289-302. doi:10.1007/s10953-006-9119-9 Tsierkezos, N. G., & Ritter, U. (2010). Electrochemical impedance spectroscopy and cyclic voltammetry of ferrocene in acetonitrile/acetone system. Journal of Applied Electrochemistry, 40(2), 409-417. doi:10.1007/s10800-009-0011-3 Van De Walle, C. G., & Martin, R. M. (1986). Theoretical calculations of heterojunction discontinuities in the Si/Ge system. Physical Review B, 34(8), 5621-5634. doi:10.1103/PhysRevB.34.5621 Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701-1718. doi:10.1002/jcc.20291 Wang, L. -., & Van Voorhis, T. (2012). A polarizable QM/MM explicit solvent model for computational electrochemistry in water. Journal of Chemical Theory and Computation, 8(2), 610-617. doi:10.1021/ct200340x Wang, Y., Rogers, E. I., & Compton, R. G. (2010). The measurement of the diffusion coefficients of ferrocene and ferrocenium and their temperature dependence in acetonitrile using double potential step microdisk electrode chronoamperometry. Journal of Electroanalytical Chemistry, 648(1), 15-19. doi:10.1016/j.jelechem.2010.07.006 Wu, Y., Chan, M. K. Y., & Ceder, G. (2011). Prediction of semiconductor band edge positions in aqueous environments from first principles. Physical Review B - Condensed Matter and Materials Physics, 83(23) doi:10.1103/PhysRevB.83.235301 Zhang, C., Spanu, L., & Galli, G. (2011). Entropy of liquid water from ab initio molecular dynamics. Journal of Physical Chemistry B, 115(48), 14190-14195. doi:10.1021/jp204981y Zhang, S. B., Tománek, D., Louie, S. G., Cohen, M. L., & Hybertsen, M. S. (1988). Quasiparticle calculation of valence band offset of AlAs-GaAs(001). Solid State Communications, 66(6), 585-588. doi:10.1016/0038-1098(88)90213-X |
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American Chemical Society |
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Facultad de Ciencias Básicas |
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Scopus |
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Repositorio Institucional Universidad de Medellin |
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2017-12-19T19:36:41Z2017-12-19T19:36:41Z201715499618http://hdl.handle.net/11407/425310.1021/acs.jctc.7b00314reponame:Repositorio Institucional Universidad de Medellíninstname:Universidad de MedellínWe present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr2+/3+, V2+/3+, Ru(NH3)62+/3+, Sn2+/4+, Cu1+/2+, FcMeOH0/1+, and Fe2+/3+ (in aqueous solution) and Fc0/1+ (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations. © 2017 American Chemical Society.engAmerican Chemical SocietyFacultad de Ciencias Básicashttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85027228601&doi=10.1021%2facs.jctc.7b00314&partnerID=40&md5=e934b462e00f989f9f4e16ce4500392cJournal of Chemical Theory and ComputationJournal of Chemical Theory and Computation Volume 13, Issue 8, 8 August 2017, Pages 3432-3441Aarva, A., Laurila, T., & Caro, M. A. (2017). Doping as a means to probe the potential dependence of dopamine adsorption on carbon-based surfaces: A first-principles study. Journal of Chemical Physics, 146(23) doi:10.1063/1.4986521Bard, A. J., & Faulkner, L. R. (1980). Electrochemical Methods: Fundamentals and Applications.Berens, P. H., Mackay, D. H. J., White, G. M., & Wilson, K. R. (1983). Thermodynamics and quantum corrections from molecular dynamics for liquid water. The Journal of Chemical Physics, 79(5), 2375-2389.Blöchl, P. E. (1994). Projector augmented-wave method. Physical Review B, 50(24), 17953-17979. doi:10.1103/PhysRevB.50.17953Cannes, C., Kanoufi, F., & Bard, A. J. (2003). Cyclic voltammetry and scanning electrochemical microscopy of ferrocenemethanol at monolayer and bilayer-modified gold electrodes. Journal of Electroanalytical Chemistry, 547(1), 83-91. doi:10.1016/S0022-0728(03)00192-XCaro, M. A. (2017). Solvation shells and radial distribution functions of transition metal complexes in aqueous solution: Results from ab initio molecular dynamics. Zenodo.Caro, M. A., Laurila, T., & Lopez-Acevedo, O. (2016). Accurate schemes for calculation of thermodynamic properties of liquid mixtures from molecular dynamics simulations. Journal of Chemical Physics, 145(24) doi:10.1063/1.4973001Caro, M. A., Määttä, J., Lopez-Acevedo, O., & Laurila, T. (2015). Energy band alignment and electronic states of amorphous carbon surfaces in vacuo and in aqueous environment. Journal of Applied Physics, 117(3) doi:10.1063/1.4905915Cheng, J., Liu, X., VandeVondele, J., Sulpizi, M., & Sprik, M. (2014). Redox potentials and acidity constants from density functional theory based molecular dynamics. Accounts of Chemical Research, 47(12), 3522-3529. doi:10.1021/ar500268yChrist, C. D., Mark, A. E., & Van Gunsteren, W. F. (2010). Basic ingredients of free energy calculations: A review. Journal of Computational Chemistry, 31(8), 1569-1582. doi:10.1002/jcc.21450Dudarev, S. L., Botton, G. A., Savrasov, S. Y., Humphreys, C. J., & Sutton, A. P. (1998). Electron-energy-loss spectra and the structural stability of nickel oxide: An LSDA+U study. Physical Review B - Condensed Matter and Materials Physics, 57(3), 1505-1509.Gagne, R. R., Koval, C. A., & Lisensky, G. C. (1980). Ferrocene as an internal standard for electrochemical measurements. Inorganic Chemistry, 19(9), 2854-2855. doi:10.1021/ic50211a080Gillan, M. J., Alfè, D., & Michaelides, A. (2016). Perspective: How good is DFT for water? Journal of Chemical Physics, 144(13) doi:10.1063/1.4944633Heyd, J., Scuseria, G. E., & Ernzerhof, M. (2003). Hybrid functionals based on a screened coulomb potential. Journal of Chemical Physics, 118(18), 8207-8215. doi:10.1063/1.1564060Holmberg, N., & Laasonen, K. (2015). Ab initio electrochemistry: Exploring the hydrogen evolution reaction on carbon nanotubes. Journal of Physical Chemistry C, 119(28), 16166-16178. doi:10.1021/acs.jpcc.5b04739Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review A, 31(3), 1695-1697. doi:10.1103/PhysRevA.31.1695House, C. I., & Kelsall, G. H. (1984). Potential-pH diagrams for the Sn/H2OCl system. Electrochimica Acta, 29(10), 1459-1464. doi:10.1016/0013-4686(84)87028-0Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926-935.Kresse, G., & Furthmüller, J. (1996). Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Physical Review B - Condensed Matter and Materials Physics, 54(16), 11169-11186.Kresse, G., & Joubert, D. (1999). From ultrasoft pseudopotentials to the projector augmented-wave method. Physical Review B - Condensed Matter and Materials Physics, 59(3), 1758-1775.Lai, P. -., Hsieh, C. -., & Lin, S. -. (2012). Rapid determination of entropy and free energy of mixtures from molecular dynamics simulations with the two-phase thermodynamic model. Physical Chemistry Chemical Physics, 14(43), 15206-15213. doi:10.1039/c2cp42011bLee, C., Yang, W., & Parr, R. G. (1988). Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Physical Review B, 37(2), 785-789. doi:10.1103/PhysRevB.37.785Lin, S. -., Blanco, M., & Goddard III, W. A. (2003). The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of lennard-jones fluids.Journal of Chemical Physics, 119(22), 11792-11805. doi:10.1063/1.1624057Lin, S. -., Maiti, P. K., & Goddard III, W. A. (2010). Two-phase thermodynamic model for efficient and accurate absolute entropy of water from molecular dynamics simulations. Journal of Physical Chemistry B, 114(24), 8191-8198. doi:10.1021/jp103120qLindahl, E., Bjelkmar, P., Larsson, P., Cuendet, M. A., & Hess, B. (2010). Implementation of the charmm force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459-466. doi:10.1021/ct900549rLucking, M., Sun, Y. -., West, D., & Zhang, S. (2014). Absolute redox potential of liquid water: A first-principles theory. Chemical Science, 5(3), 1216-1220. doi:10.1039/c3sc52287cMakov, G., & Payne, M. C. (1995). Periodic boundary conditions in ab initio calculations. Physical Review B, 51(7), 4014-4022. doi:10.1103/PhysRevB.51.4014Nosé, S. (1984). A unified formulation of the constant temperature molecular dynamics methods. The Journal of Chemical Physics, 81(1), 511-519.Pascal, T. A., & Goddard, W. A. (2012). Hydrophobic segregation, phase transitions and the anomalous thermodynamics of water/methanol mixtures. Journal of Physical Chemistry B, 116(47), 13905-13912. doi:10.1021/jp309693dPavlishchuk, V. V., & Addison, A. W. (2000). Conversion constants for redox potentials measured versus different reference electrodes in acetonitrile solutions at 25°C. Inorganica Chimica Acta, 298(1), 97-102. doi:10.1016/S0020-1693(99)00407-7Perdew, J. P., Burke, K., & Ernzerhof, M. (1996). Generalized gradient approximation made simple. Physical Review Letters, 77(18), 3865-3868. doi:10.1103/PhysRevLett.77.3865Post, K., & Robins, R. G. (1976). Thermodynamic diagrams for the vanadium-water system at 298·15K. Electrochimica Acta, 21(6), 401-405. doi:10.1016/0013-4686(76)85115-8Rossmeisl, J., Nørskov, J. K., Taylor, C. D., Janik, M. J., & Neurock, M. (2006). Calculated phase diagrams for the electrochemical oxidation and reduction of water over pt(111). Journal of Physical Chemistry B, 110(43), 21833-21839. doi:10.1021/jp0631735Rossmeisl, J., Skúlason, E., Björketun, M. E., Tripkovic, V., & Nørskov, J. K. (2008). Modeling the electrified solid-liquid interface. Chemical Physics Letters, 466(1-3), 68-71. doi:10.1016/j.cplett.2008.10.024Rusnak, A. J., Pinnick, E. R., Calderon, C. E., & Wang, F. (2012). Static dielectric constants and molecular dipole distributions of liquid water and ice-ih investigated by the PAW-PBE exchange-correlation functional. Journal of Chemical Physics, 137(3) doi:10.1063/1.4734594Skúlason, E., Karlberg, G. S., Rossmeisl, J., Bligaard, T., Greeley, J., Jónsson, H., & Nørskov, J. K. (2007). Density functional theory calculations for the hydrogen evolution reaction in an electrochemical double layer on the pt(111) electrode. Physical Chemistry Chemical Physics, 9(25), 3241-3250. doi:10.1039/b700099eStradi, D., Martinez, U., Blom, A., Brandbyge, M., & Stokbro, K. (2016). General atomistic approach for modeling metal-semiconductor interfaces using density functional theory and nonequilibrium green's function. Physical Review B, 93(15) doi:10.1103/PhysRevB.93.155302Tkatchenko, A., & Scheffler, M. (2009). Accurate molecular van der waals interactions from ground-state electron density and free-atom reference data. Physical Review Letters, 102(7) doi:10.1103/PhysRevLett.102.073005Trasa'tti, S. (1986). The absolute electrode potential: An explanatory note (recommendations 1986). Pure and Applied Chemistry, 58(7), 955-966. doi:10.1351/pac198658070955Tsierkezos, N. G. (2007). Cyclic voltammetric studies of ferrocene in nonaqueous solvents in the temperature range from 248.15 to 298.15 K. Journal of Solution Chemistry, 36(3), 289-302. doi:10.1007/s10953-006-9119-9Tsierkezos, N. G., & Ritter, U. (2010). Electrochemical impedance spectroscopy and cyclic voltammetry of ferrocene in acetonitrile/acetone system. Journal of Applied Electrochemistry, 40(2), 409-417. doi:10.1007/s10800-009-0011-3Van De Walle, C. G., & Martin, R. M. (1986). Theoretical calculations of heterojunction discontinuities in the Si/Ge system. Physical Review B, 34(8), 5621-5634. doi:10.1103/PhysRevB.34.5621Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701-1718. doi:10.1002/jcc.20291Wang, L. -., & Van Voorhis, T. (2012). A polarizable QM/MM explicit solvent model for computational electrochemistry in water. Journal of Chemical Theory and Computation, 8(2), 610-617. doi:10.1021/ct200340xWang, Y., Rogers, E. I., & Compton, R. G. (2010). The measurement of the diffusion coefficients of ferrocene and ferrocenium and their temperature dependence in acetonitrile using double potential step microdisk electrode chronoamperometry. Journal of Electroanalytical Chemistry, 648(1), 15-19. doi:10.1016/j.jelechem.2010.07.006Wu, Y., Chan, M. K. Y., & Ceder, G. (2011). Prediction of semiconductor band edge positions in aqueous environments from first principles. Physical Review B - Condensed Matter and Materials Physics, 83(23) doi:10.1103/PhysRevB.83.235301Zhang, C., Spanu, L., & Galli, G. (2011). Entropy of liquid water from ab initio molecular dynamics. Journal of Physical Chemistry B, 115(48), 14190-14195. doi:10.1021/jp204981yZhang, S. B., Tománek, D., Louie, S. G., Cohen, M. L., & Hybertsen, M. S. (1988). Quasiparticle calculation of valence band offset of AlAs-GaAs(001). Solid State Communications, 66(6), 585-588. doi:10.1016/0038-1098(88)90213-XScopusRedox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous SolutionArticleinfo:eu-repo/semantics/articlehttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1Caro, M.A., Department of Electrical Engineering and Automation, Aalto University, Espoo, Finland, COMP Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, Espoo, FinlandLopez-Acevedo, O., COMP Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, Espoo, Finland, Departamento de Facultad de Ciencias Básicas, Universidad de Medellín, Medellín, ColombiaLaurila, T., Department of Electrical Engineering and Automation, Aalto University, Espoo, FinlandCaro M.A.Lopez-Acevedo O.Laurila T.Department of Electrical Engineering and Automation, Aalto University, Espoo, FinlandCOMP Centre of Excellence in Computational Nanoscience, Department of Applied Physics, Aalto University, Espoo, FinlandDepartamento de Facultad de Ciencias Básicas, Universidad de Medellín, Medellín, ColombiaWe present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr2+/3+, V2+/3+, Ru(NH3)62+/3+, Sn2+/4+, Cu1+/2+, FcMeOH0/1+, and Fe2+/3+ (in aqueous solution) and Fc0/1+ (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations. © 2017 American Chemical Society.http://purl.org/coar/access_right/c_16ec11407/4253oai:repository.udem.edu.co:11407/42532020-05-27 16:24:40.954Repositorio Institucional Universidad de Medellinrepositorio@udem.edu.co |