Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach.
ABSTRACT Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.
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ABSTRACT: Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes.Journal of Molecular Structure THEOCHEM 03/2009; 898(1-3):17-30. · 1.37 Impact Factor
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ABSTRACT: This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.Physical Chemistry Chemical Physics 06/2014; · 4.20 Impact Factor
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ABSTRACT: We developed a double-quantum mechanical/molecular mechanical (d-QM/MM) method for investigation of full outer-sphere electron transfer (ET) processes between a donor and an acceptor (DA) in condensed matter. In the d-QM/MM method, which employs the novel concept of multiple QM regions, one can easily specify the number of electrons, spin states and appropriate exchange-correlation treatment in each QM region, which is especially important in the cases of ET involving transition metal sites. We investigated Fe(2+/3+) self-exchange and Fe(3+) + Ru(2+) → Fe(2+) + Ru(3+) in aqueous solution as model reactions, and demonstrated that the d-QM/MM method gives reasonable accuracy for the redox potential, reorganization free energy and electronic coupling. In particular, the DA distance dependencies of those quantities are clearly shown at the density functional theory hybrid functional level. The present d-QM/MM method allows us to explore the intermediate DA distance region, important for long-range ET phenomena observed in electrochemistry (on the solid-liquid interfaces) and biochemistry, which cannot be dealt by the half-reaction scheme with the conventional QM/MM.Physical Chemistry Chemical Physics 08/2014; · 4.20 Impact Factor