1
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Kılıç M, Ensing B. Redox Properties of Flavin in BLUF and LOV Photoreceptor Proteins from Hybrid QM/MM Molecular Dynamics Simulation. J Phys Chem B 2024; 128:3069-3080. [PMID: 38518376 DOI: 10.1021/acs.jpcb.3c06245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Flavins play an important role in many oxidation and reduction processes in biological systems. For example, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are common cofactors found in enzymatic proteins that use the special redox properties of these flavin molecules for their catalytic or photoactive functions. The redox potential of the flavin is strongly affected by its (protein) environment; however, the underlying molecular interactions of this effect are still unknown. Using hybrid quantum mechanics/molecular mechanics (QM/MM) simulation techniques, we have studied the redox properties of flavin in the gas phase, aqueous solution, and two different protein environments, in particular, a BLUF and a LOV photoreceptor domain. By mapping the changes in electrostatic potential and solvent structure, we gain insight into how specific polarization of the flavin by its environment tunes the reduction potential. We find also that accurate calculation of the reduction potentials of these systems by using the hybrid QM/MM approach is hampered by a too limited sampling of the counterion configurations and by artifacts at the QM/MM boundary. We make suggestions for how these issues can be overcome.
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Affiliation(s)
- Murat Kılıç
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Park 904, Amsterdam 1098 XH, The Netherlands
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Park 904, Amsterdam 1098 XH, The Netherlands
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2
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Mitra S, Heuer A, Diddens D. Electron transfer reaction of TEMPO-based organic radical batteries in different solvent environments: comparing quantum and classical approaches. Phys Chem Chem Phys 2024; 26:3020-3028. [PMID: 38179667 DOI: 10.1039/d3cp04111e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
In this study, we delve into the complex electron transfer reactions associated with the redox-active (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO), a common component in organic radical batteries (ORBs). Our approach estimates quantum electron-transfer (ET) energies using Density Functional Theory (DFT) calculations by sampling from structures simulated classically. This work presents a comparative study of reorganization energies in ET reactions across different solvents. Furthermore, we investigate how changes in the electrolyte environment can modify the reorganization energy and, consequently, impact ET dynamics. We also explore the relationship between classical and quantum vertical energies using linear regression models. Importantly, this comparison between quantum and classical vertical energies underscores the role of quantum effects, like charge delocalization, in offering added stabilization post-redox reactions. These effects are not adequately represented by the classical vertical energy distribution. Our study shows that, although we find a significant correlation between the vertical energies computed by DFT and the classical force field, the regression parameters depend on the solvent, highlighting that classical methods should be benchmarked by DFT before applying them to novel electrolyte materials.
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Affiliation(s)
- Souvik Mitra
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, University of Münster, Corrensstraße 28/30, 48149 Münster, Germany
- Helmholtz-Institute Münster (IEK-12), Forschungszentrum Jülich GmbH, Corrensstraße 46, 48149 Münster, Germany.
| | - Diddo Diddens
- Helmholtz-Institute Münster (IEK-12), Forschungszentrum Jülich GmbH, Corrensstraße 46, 48149 Münster, Germany.
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3
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Mandal S, Kar R, Meyer B, Nair NN. Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe 2+ /Fe 3+ Redox Reaction. Chemphyschem 2023; 24:e202200617. [PMID: 36169153 DOI: 10.1002/cphc.202200617] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/27/2022] [Indexed: 02/03/2023]
Abstract
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe2+ /Fe3+ ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE). While hybrid functionals can minimize SIE, standard plane-wave based AIMD at that level of theory is typically 150 times slower than GGA for systems containing ∼100 atoms. Among several approaches reported to speed-up AIMD simulations with hybrid functionals, the noise-stabilized MD (NSMD) procedure, together with the use of localized orbitals to compute the required exchange integrals, is an attractive option. In this work, we demonstrate the application of the NSMD approach for studying the Fe2+ /Fe3+ redox reaction in water. It is shown here that long AIMD trajectories at the level of hybrid density functionals can be obtained using this approach. Redox properties of the aqueous Fe2+ /Fe3+ system computed from these simulations are compared with the available experimental data for validation.
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Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India.,Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, 91052, Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, 91058, Erlangen, Germany
| | - Ritama Kar
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India
| | - Bernd Meyer
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, 91052, Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, 91058, Erlangen, Germany
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), 208016, Kanpur, India
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4
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Ahart CS, Rosso KM, Blumberger J. Implementation and Validation of Constrained Density Functional Theory Forces in the CP2K Package. J Chem Theory Comput 2022; 18:4438-4446. [PMID: 35700315 PMCID: PMC9281399 DOI: 10.1021/acs.jctc.2c00284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Constrained density
functional theory (CDFT) is a powerful tool
for the prediction of electron transfer parameters in condensed phase
simulations at a reasonable computational cost. In this work we present
an extension to CDFT in the popular mixed Gaussian/plane wave electronic
structure package CP2K, implementing the additional force terms arising
from a constraint based on Hirshfeld charge partitioning. This improves
upon the existing Becke partitioning scheme, which is prone to give
unphysical atomic charges. We verify this implementation for a variety
of systems: electron transfer in (H2O)2+ in a vacuum, electron tunnelling
between oxygen vacancy centers in solid MgO, and electron self-exchange
in aqueous Ru2+–Ru3+. We find good agreement
with previous plane-wave CDFT results for the same systems, but at
a significantly lower computational cost, and we discuss the general
reliability of condensed phase CDFT calculations.
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Affiliation(s)
- Christian S Ahart
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
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5
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Gibson LD, Pfaendtner J, Mundy CJ. Probing the thermodynamics and kinetics of ethylene carbonate reduction at the electrode-electrolyte interface with molecular simulations. J Chem Phys 2021; 155:204703. [PMID: 34852482 DOI: 10.1063/5.0067687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the formation of the solid-electrolyte interphase (SEI) in lithium-ion batteries is an ongoing area of research due to its high degree of complexity and the difficulties encountered by experimental studies. Herein, we investigate the initial stage of SEI growth, the reduction reaction of ethylene carbonate (EC), from both a thermodynamic and a kinetic approach with theory and molecular simulations. We employed both the potential distribution theorem and the Solvation Method based on Density (SMD) to EC solvation for the estimation of reduction potentials of Li+, EC, and Li+-solvating EC (s-EC) as well as reduction rate constants of EC and s-EC. We find that solvation effects greatly influence these quantities of interest, particularly the Li+/Li reference electrode potential in EC solvent. Furthermore, we also compute the inner- and outer-sphere reorganization energies for both EC and s-EC at the interface of liquid EC and a hydroxyl-terminated graphite surface, where total reorganization energies are predicted to be 76.6 and 88.9 kcal/mol, respectively. With the computed reorganization energies, we estimate reduction rate constants across a range of overpotentials and show that EC has a larger electron transfer rate constant than s-EC at equilibrium, despite s-EC being more thermodynamically favorable. Overall, this manuscript demonstrates how ion solvation effects largely govern the prediction of reduction potentials and electron transfer rate constants at the electrode-electrolyte interface.
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Affiliation(s)
- Luke D Gibson
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, USA
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6
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Hpone Myint K, Ding W, Willard AP. The Influence of Spectator Cations on Solvent Reorganization Energy Is a Short-Range Effect. J Phys Chem B 2021; 125:1429-1438. [PMID: 33525875 DOI: 10.1021/acs.jpcb.0c09895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this manuscript, we use classical molecular dynamics simulation to explore the origin of specific cation effects on the rates of bulk-phase aqueous electron transfer (ET) reactions. We consider 0.6 M solutions of Cl- and a series of different cations: Li+, Na+, K+, Rb+, and Cs+. We evaluate the collective electrostatic fluctuations that drive Marcus-like ET and find that they are essentially unaffected by changes in the cationic species. This finding implies that the structure making/breaking properties of various cations do not exert a significant influence on bulk-phase ET reactions. We evaluate the role of ion pairing in these specific cation effects and find, unsurprisingly, that model redox anions that are more highly charged tend to pair more effectively with spectator cations than their monovalent counterparts. We demonstrate that this ion pairing significantly affects local electrostatic fluctuations for the anionic redox species and thus conclude that ion pairing is one of the likely sources of rate-dependent cation effects in aqueous ET reactions.
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Affiliation(s)
- Kyaw Hpone Myint
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wendu Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Blumberger J, Gaigeot MP, Sulpizi M, Vuilleumier R. Frontiers in molecular simulation of solvated ions, molecules and interfaces. Phys Chem Chem Phys 2020; 22:10393-10396. [PMID: 32352136 DOI: 10.1039/d0cp90091e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This themed collection is a collection of articles on frontiers in molecular simulation of solvated ions, molecules and interfaces.
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Affiliation(s)
- J Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, UK.
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8
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Kılıç M, Ensing B. Microscopic Picture of the Solvent Reorganization During Electron Transfer to Flavin in Water. J Phys Chem B 2019; 123:9751-9761. [PMID: 31647869 DOI: 10.1021/acs.jpcb.9b07250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The redox potential of molecular species is largely modulated by its molecular environment so that a change of the environment will lead to a different redox potential. However, a detailed molecular picture of reorganization of the environment upon reduction is still unclear. To unravel the details of the solvent reorganization during electron transfer, we have performed density functional theory-based molecular dynamics (DFT-MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of the reduction of lumiflavin. Previously, we have calculated the reduction free energy curves of the redox half reactions of lumiflavin in water as a function of the instantaneous gap energy (ΔE) ( J. Chem. Theory Comput. 2013 , 9 , 3889 - 3899 ). In this work, we focus on finding the changes in the solvent environment that correlate with this ΔE reaction coordinate. Comparing the QM/MM simulations, in which the solvent is modeled with an empirical force field, with the (full) DFT-MD simulations, we find that the response through electronic polarization plays a significant role in the latter case. Also a small charge transfer between flavin and solvent is observed in the full DFT treatment. As a result, we find only in the case of the QM/MM model a strong correlation between ΔE and the (pairwise computed) electrostatic potential (ESP) at the flavin due to the solvent. By analyzing the contribution of the ESP at the flavin per solvent molecule, we cannot only distinguish between the different modes of hydration by solvent molecules that coordinate at the hydrophilic and hydrophobic sides of the flavin molecule but also quantify their contribution to the reorganization free energy by measuring the ESP fluctuations per solvent molecule.
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Affiliation(s)
- Murat Kılıç
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Park 904 , 1098 XH , Amsterdam , The Netherlands
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Park 904 , 1098 XH , Amsterdam , The Netherlands
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9
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Behara PK, Dupuis M. Electron transfer in extended systems: characterization by periodic density functional theory including the electronic coupling. Phys Chem Chem Phys 2019; 22:10609-10623. [PMID: 31670326 DOI: 10.1039/c9cp05133c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We describe a new computer implementation of electron transfer (ET) theory in extended systems treated by periodic density functional theory (DFT), including the calculation of the electronic coupling transition element VAB. In particular, the development opens up the full characterization of electron transfer in the solid state. The approach is valid for any single-determinant wavefunction with localized character representing the electronic structure of the system, from Hartree-Fock (HF) theory, to density functional theory (DFT), hybrid DFT theory, DFT+U theory, and constrained DFT (cDFT) theory. The implementation in CP2K reuses the high-performance functions of the code. The computational cost is equivalent to only one iteration of an HF calculation. We present test calculations for electron transfer in a number of systems, including a 1D-model of ferric oxide, hematite Fe2O3, rutile TiO2, and finally bismuth vanadate BiVO4.
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Affiliation(s)
- Pavan Kumar Behara
- Department of Chemical and Biological Engineering, and Computational and Data-Enabled Science and Engineering Program, University at Buffalo, State of New York University, Buffalo, NY 14260, USA.
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10
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Kamat K, Peters B. Gibbs free-energy differences between polymorphs via a diabat approach. J Chem Phys 2018; 149:214106. [PMID: 30525715 DOI: 10.1063/1.5051448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Polymorph free-energy differences are critical to several applications. A recently proposed diabat interpolation framework estimated free-energy differences between polymorphs by quadratic interpolation of diabats. This work extends the Zwanzig-Bennett relation to the NPT ensemble so that the diabats directly give Gibbs free-energy differences. We also demonstrate how the approach can be used in cases where the diabats are not parabolic. We illustrate the diabat method for Gibbs free-energy difference of zirconium (BCC and HCP phases) and compare it with the conventional lattice switch Monte Carlo approach.
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Affiliation(s)
- Kartik Kamat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Baron Peters
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
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11
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Rozzi CA, Troiani F, Tavernelli I. Quantum modeling of ultrafast photoinduced charge separation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013002. [PMID: 29047450 DOI: 10.1088/1361-648x/aa948a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phenomena involving electron transfer are ubiquitous in nature, photosynthesis and enzymes or protein activity being prominent examples. Their deep understanding thus represents a mandatory scientific goal. Moreover, controlling the separation of photogenerated charges is a crucial prerequisite in many applicative contexts, including quantum electronics, photo-electrochemical water splitting, photocatalytic dye degradation, and energy conversion. In particular, photoinduced charge separation is the pivotal step driving the storage of sun light into electrical or chemical energy. If properly mastered, these processes may also allow us to achieve a better command of information storage at the nanoscale, as required for the development of molecular electronics, optical switching, or quantum technologies, amongst others. In this Topical Review we survey recent progress in the understanding of ultrafast charge separation from photoexcited states. We report the state-of-the-art of the observation and theoretical description of charge separation phenomena in the ultrafast regime mainly focusing on molecular- and nano-sized solar energy conversion systems. In particular, we examine different proposed mechanisms driving ultrafast charge dynamics, with particular regard to the role of quantum coherence and electron-nuclear coupling, and link experimental observations to theoretical approaches based either on model Hamiltonians or on first principles simulations.
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12
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Bouzid A, Pasquarello A. Redox Levels through Constant Fermi-Level ab Initio Molecular Dynamics. J Chem Theory Comput 2017; 13:1769-1777. [DOI: 10.1021/acs.jctc.6b01232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Assil Bouzid
- Chaire de Simulation à
l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alfredo Pasquarello
- Chaire de Simulation à
l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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13
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Mechanical polishing as an improved surface treatment for platinum screen-printed electrodes. SENSING AND BIO-SENSING RESEARCH 2016. [DOI: 10.1016/j.sbsr.2016.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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14
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Tiwari A, Ensing B. Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus' theory. Faraday Discuss 2016; 195:291-310. [DOI: 10.1039/c6fd00132g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Outer sphere electron transfer between two ions in aqueous solution is a rare event on the time scale of first principles molecular dynamics simulations. We have used transition path sampling to generate an ensemble of reactive trajectories of the self-exchange reaction between a pair of Ru2+ and Ru3+ ions in water. To distinguish between the reactant and product states, we use as an order parameter the position of the maximally localised Wannier center associated with the transferring electron. This allows us to align the trajectories with respect to the moment of barrier crossing and compute statistical averages over the path ensemble. We compare our order parameter with two typical reaction coordinates used in applications of Marcus theory of electron transfer: the vertical gap energy and the solvent electrostatic potential at the ions.
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Affiliation(s)
- Ambuj Tiwari
- Van't Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
- Amsterdam Center for Multiscale Modeling
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
- Amsterdam Center for Multiscale Modeling
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15
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Jono R, Tateyama Y, Yamashita K. A method to calculate redox potentials relative to the normal hydrogen electrode in nonaqueous solution by using density functional theory-based molecular dynamics. Phys Chem Chem Phys 2015; 17:27103-8. [PMID: 26412242 DOI: 10.1039/c5cp05029d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate the redox potential calculation relative to the normal hydrogen electrode (NHE) in nonaqueous solution using a density functional theory-based molecular dynamics (DFT-MD) simulation. The calculation of the NHE in nonaqueous solution consists of two processes: the first step is the equilibrated simulation for a proton in nonaqueous solution to determine the space for inserting a proton in solution, and the second step is the thermodynamic integration method to calculate the solvation energy of the proton in the nonaqueous solution. In this work, we apply the method for a cation and an anion, i.e., copper(ii)/copper(i) and iodine/iodide in acetonitrile solution, and show that the errors in the calculated redox potential from experiments are within 0.21 V.
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Affiliation(s)
- Ryota Jono
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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16
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Drechsel-Grau C, Sprik M. The temperature dependence of the symmetry factor for a model Fe3+(aq)/Fe2+(aq) redox half reaction. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1066897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Michiel Sprik
- Department of Chemistry, University of Cambridge , Cambridge, United Kingdom
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17
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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18
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Computational Redox Potential Predictions: Applications to Inorganic and Organic Aqueous Complexes, and Complexes Adsorbed to Mineral Surfaces. MINERALS 2014. [DOI: 10.3390/min4020345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Hosseini M, Rivera-Nazario DM, Echegoyen LA. Self-assembled monolayers of C60-triphenylamine dyads as photo-switched interfacial layers for potential application in photovoltaic cells. ACS APPLIED MATERIALS & INTERFACES 2014; 6:3712-3720. [PMID: 24524362 DOI: 10.1021/am500049q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
C60-Triphenylamine dyads were synthesized for incorporation as photoswitched interfacial layers in organic photovoltaic (OPV) cells. Self-assembled monolayers (SAMs) of these dyads on gold (through S-Au and C60-Au interactions) were prepared through one or two adsorption processes, and their packing densities were fully characterized. Analysis using quartz crystal microbalance (QCM) and electrochemical impedance spectroscopy (EIS) measurements indicated that all SAMs exhibit dense coverage on the gold surfaces. Electrochemical desorption in KOH confirmed that the cis-1 dyad is anchored to the gold surface through its thiol group. Impedance measurements in the absence and presence of UV irradiation were performed to observe the photoswitched properties of these surface confined dyads. Upon UV light exposure of the SAMs, the charge-transfer resistance decreased when Fe(CN)6(3-/4-) was used as the probe redox couple and increased with Ru(NH3)6(3+/2+), confirming the generation of positive charges on the surface upon UV irradiation.
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Affiliation(s)
- Mahsa Hosseini
- Department of Chemistry, University of Texas at El Paso , 500 W. University Avenue, El Paso, Texas 79968, United States
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20
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Kılıç M, Ensing B. First and Second One-Electron Reduction of Lumiflavin in Water—A First Principles Molecular Dynamics Study. J Chem Theory Comput 2013; 9:3889-99. [DOI: 10.1021/ct400088g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Murat Kılıç
- Van’t Hoff
Institute for Molecular Sciences,
University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The
Netherlands
| | - Bernd Ensing
- Van’t Hoff
Institute for Molecular Sciences,
University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The
Netherlands
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21
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Liu Y, Fan X, Jin Y, Hu X, Hu H. Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach. J Chem Theory Comput 2013; 9:4257-65. [DOI: 10.1021/ct400406v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yang Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Xiaoli Fan
- School of Materials Science
and Engineering, Northwestern Polytechnical University, Xi’an, Shannxi, 710072, China
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United
States
| | - Yingdi Jin
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United
States
| | - Hao Hu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
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22
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Sato H. A modern solvation theory: quantum chemistry and statistical chemistry. Phys Chem Chem Phys 2013; 15:7450-65. [DOI: 10.1039/c3cp50247c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Zeng X, Hu X, Yang W. Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru 2+-Ru 3+ Self-Exchange Electron Transfer. J Chem Theory Comput 2012; 8:4960-4967. [PMID: 23682243 PMCID: PMC3652472 DOI: 10.1021/ct300758v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A fragment-based fractional number of electron (FNE) approach, is developed to study entire electron transfer (ET) processes from the electron donor region to the acceptor region in condensed phase. Both regions are described by the density-fragment interaction (DFI) method while FNE as an efficient ET order parameter is applied to simulate the electron transfer process. In association with the QM/MM energy expression, the DFI-FNE method is demonstrated to describe ET processes robustly with the Ru2+-Ru3+ self-exchange ET as a proof-of-concept example. This method allows for systematic calculations of redox free energies, reorganization energies, and electronic couplings, and the absolute ET rate constants within the Marcus regime.
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Affiliation(s)
- Xiancheng Zeng
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Xiangqian Hu
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
- Department of Physics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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24
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Martin DR, Matyushov DV. Solvated dissipative electro-elastic network model of hydrated proteins. J Chem Phys 2012; 137:165101. [DOI: 10.1063/1.4759105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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25
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Iida K, Sato H. Theoretical study on ionization process in aqueous solution. J Chem Phys 2012; 136:144510. [DOI: 10.1063/1.3700225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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26
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Electron transfer studies of redox probes in bovine milk. J Colloid Interface Sci 2012; 370:124-31. [DOI: 10.1016/j.jcis.2011.12.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 12/26/2011] [Accepted: 12/27/2011] [Indexed: 11/19/2022]
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27
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Heck A, Woiczikowski PB, Kubař T, Giese B, Elstner M, Steinbrecher TB. Charge transfer in model peptides: obtaining Marcus parameters from molecular simulation. J Phys Chem B 2012; 116:2284-93. [PMID: 22260641 DOI: 10.1021/jp2086297] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist.
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Affiliation(s)
- Alexander Heck
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
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28
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Drechsel-Grau C, Sprik M. Activation energy for a model ferrous-ferric half reaction from transition path sampling. J Chem Phys 2012; 136:034506. [DOI: 10.1063/1.3677195] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Vuilleumier R, Tay KA, Jeanmairet G, Borgis D, Boutin A. Extension of Marcus Picture for Electron Transfer Reactions with Large Solvation Changes. J Am Chem Soc 2012; 134:2067-74. [DOI: 10.1021/ja2069104] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rodolphe Vuilleumier
- Ecole Normale Supérieure, Département
de Chimie, UMR 8640 ENS-CNRS-UPMC, 24 Rue Lhomond, 75005 Paris, France
| | - Kafui A. Tay
- Ecole Normale Supérieure, Département
de Chimie, UMR 8640 ENS-CNRS-UPMC, 24 Rue Lhomond, 75005 Paris, France
| | - Guillaume Jeanmairet
- Ecole Normale Supérieure, Département
de Chimie, UMR 8640 ENS-CNRS-UPMC, 24 Rue Lhomond, 75005 Paris, France
| | - Daniel Borgis
- Ecole Normale Supérieure, Département
de Chimie, UMR 8640 ENS-CNRS-UPMC, 24 Rue Lhomond, 75005 Paris, France
| | - Anne Boutin
- Ecole Normale Supérieure, Département
de Chimie, UMR 8640 ENS-CNRS-UPMC, 24 Rue Lhomond, 75005 Paris, France
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30
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Camarada MB, Jaque P, Díaz FR, del Valle MA. Oxidation potential of thiophene oligomers: Theoretical and experimental approach. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/polb.22360] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Zarzycki P, Kerisit S, Rosso K. Computational methods for intramolecular electron transfer in a ferrous–ferric iron complex. J Colloid Interface Sci 2011; 361:293-306. [DOI: 10.1016/j.jcis.2011.05.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 05/24/2011] [Indexed: 11/30/2022]
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32
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Koper MT. Thermodynamic theory of multi-electron transfer reactions: Implications for electrocatalysis. J Electroanal Chem (Lausanne) 2011. [DOI: 10.1016/j.jelechem.2010.10.004] [Citation(s) in RCA: 647] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Gates AJ, Kemp GL, To CY, Mann J, Marritt SJ, Mayes AG, Richardson DJ, Butt JN. The relationship between redox enzyme activity and electrochemical potential—cellular and mechanistic implications from protein film electrochemistry. Phys Chem Chem Phys 2011; 13:7720-31. [DOI: 10.1039/c0cp02887h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Kirchner B, di Dio PJ, Hutter J. Real-world predictions from ab initio molecular dynamics simulations. Top Curr Chem (Cham) 2011; 307:109-53. [PMID: 21842358 DOI: 10.1007/128_2011_195] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
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Affiliation(s)
- Barbara Kirchner
- Wilhelm-Ostwald Institute of Physical and Theoretical Chemistry, University of Leipzig, Linnéstr. 2, 04103 Leipzig, Germany.
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35
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Cheng J, Sulpizi M, Sprik M. Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics. J Chem Phys 2010; 131:154504. [PMID: 20568869 DOI: 10.1063/1.3250438] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pK(a)) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies.
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Affiliation(s)
- Jun Cheng
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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36
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Ayala R, Spezia R, Vuilleumier R, Martínez JM, Pappalardo RR, Sánchez Marcos E. An Ab Initio Molecular Dynamics Study on the Hydrolysis of the Po(IV) Aquaion in Water. J Phys Chem B 2010; 114:12866-74. [DOI: 10.1021/jp1010956] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Regla Ayala
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Riccardo Spezia
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Rodolphe Vuilleumier
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - José Manuel Martínez
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Rafael R. Pappalardo
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Enrique Sánchez Marcos
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
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37
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Lacaze-Dufaure C, Najjar F, André-Barrès C. First Computational Evidence of a Competitive Stepwise and Concerted Mechanism for the Reduction of Antimalarial Endoperoxides. J Phys Chem B 2010; 114:9848-53. [DOI: 10.1021/jp100718p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Corinne Lacaze-Dufaure
- Centre Interuniversitaire de Recherche et d’Ingénierie des Matériaux, CNRS UMR 5085, ENSIACET, 4 allée Emile Monso, BP 44362, 31432 Toulouse cedex 04, France, Laboratoire de Synthèse et Physicochimie de Molécules d’Intérêt Biologique, CNRS UMR 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France, and Faculty of Sciences-2, Lebanese University, Jdaidet el-Maten, B.P. 90656, Lebanon
| | - Fadia Najjar
- Centre Interuniversitaire de Recherche et d’Ingénierie des Matériaux, CNRS UMR 5085, ENSIACET, 4 allée Emile Monso, BP 44362, 31432 Toulouse cedex 04, France, Laboratoire de Synthèse et Physicochimie de Molécules d’Intérêt Biologique, CNRS UMR 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France, and Faculty of Sciences-2, Lebanese University, Jdaidet el-Maten, B.P. 90656, Lebanon
| | - Christiane André-Barrès
- Centre Interuniversitaire de Recherche et d’Ingénierie des Matériaux, CNRS UMR 5085, ENSIACET, 4 allée Emile Monso, BP 44362, 31432 Toulouse cedex 04, France, Laboratoire de Synthèse et Physicochimie de Molécules d’Intérêt Biologique, CNRS UMR 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France, and Faculty of Sciences-2, Lebanese University, Jdaidet el-Maten, B.P. 90656, Lebanon
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38
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Van Voorhis T, Kowalczyk T, Kaduk B, Wang LP, Cheng CL, Wu Q. The diabatic picture of electron transfer, reaction barriers, and molecular dynamics. Annu Rev Phys Chem 2010; 61:149-70. [PMID: 20055670 DOI: 10.1146/annurev.physchem.012809.103324] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Diabatic states have a long history in chemistry, beginning with early valence bond pictures of molecular bonding and extending through the construction of model potential energy surfaces to the modern proliferation of methods for computing these elusive states. In this review, we summarize the basic principles that define the diabatic basis and demonstrate how they can be applied in the specific context of constrained density functional theory. Using illustrative examples from electron transfer and chemical reactions, we show how the diabatic picture can be used to extract qualitative insight and quantitative predictions about energy landscapes. The review closes with a brief summary of the challenges and prospects for the further application of diabatic states in chemistry.
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Affiliation(s)
- Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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39
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Moens J, Seidel R, Geerlings P, Faubel M, Winter B, Blumberger J. Energy Levels and Redox Properties of Aqueous Mn2+/3+ from Photoemission Spectroscopy and Density Functional Molecular Dynamics Simulation. J Phys Chem B 2010; 114:9173-82. [DOI: 10.1021/jp101527v] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Moens
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium, Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Robert Seidel
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium, Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Paul Geerlings
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium, Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Manfred Faubel
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium, Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Bernd Winter
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium, Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Jochen Blumberger
- Faculty of Sciences, Department of General Chemistry, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium, Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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40
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Oberhofer H, Blumberger J. Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions. J Chem Phys 2009; 131:064101. [PMID: 19691372 DOI: 10.1063/1.3190169] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following the earlier work of Wu and Van Voorhis [Phys. Rev. A 72, 024502 (2005)], the density functional is minimized under the constraint that the charge difference between donor and acceptor is equal to a given value. The classical ion dynamics is propagated on the Born-Oppenheimer surface of the charge constrained state. We investigate the dependence of the constrained energy and of the energy gap on the definition of the charge and present expressions for the constraint forces. The method is applied to the Ru2+-Ru3+ electron self-exchange reaction in aqueous solution. Sampling the vertical energy gap along CDFT-MD trajectories and correcting for finite size effects, a reorganization free energy of 1.6 eV is obtained. This is 0.1-0.2 eV lower than a previous estimate based on a continuum model for solvation. The smaller value for the reorganization free energy can be explained by the fact that the Ru-O distances of the divalent and trivalent Ru hexahydrates are predicted to be more similar in the electron transfer complex than for the separated aqua ions.
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Affiliation(s)
- Harald Oberhofer
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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41
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Seidel R, Faubel M, Winter B, Blumberger J. Single-Ion Reorganization Free Energy of Aqueous Ru(bpy)32+/3+ and Ru(H2O)62+/3+ from Photoemission Spectroscopy and Density Functional Molecular Dynamics Simulation. J Am Chem Soc 2009; 131:16127-37. [DOI: 10.1021/ja9047834] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert Seidel
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Manfred Faubel
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Bernd Winter
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jochen Blumberger
- Helmholtz-Zentrum Berlin für Materialien und Energie, and BESSY, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany, Max-Planck-Institut für Dynamik and Selbstorganisation, Bunsenstrasse 10, D-37073 Göttingen, Germany, and Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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42
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Zeng X, Hu H, Hu X, Yang W. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method. J Chem Phys 2009; 130:164111. [PMID: 19405565 DOI: 10.1063/1.3120605] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
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Affiliation(s)
- Xiancheng Zeng
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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43
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Willard AP, Reed SK, Madden PA, Chandler D. Water at an electrochemical interface--a simulation study. Faraday Discuss 2009; 141:423-41; discussion 443-65. [PMID: 19227369 DOI: 10.1039/b805544k] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The results of molecular dynamics simulations of the properties of water in an aqueous ionic solution close to an interface with a model metallic electrode are described. In the simulations the electrode behaves as an ideally polarizable hydrophilic metal, supporting image-charge interactions with charged species, and it is maintained at a constant electrical potential with respect to the solution so that the model is a textbook representation of an electrochemical interface through which no current is passing. We show how water is strongly attracted to and ordered at the electrode surface. This ordering is different to the structure that might be imagined from continuum models of electrode interfaces. Further, this ordering significantly affects the probability of ions reaching the surface. We describe the concomitant motion and configurations of the water and ions as functions of the electrode potential, and we analyze the length scales over which ionic atmospheres fluctuate. The statistics of these fluctuations depend upon surface structure and ionic strength. The fluctuations are large--sufficiently so that the mean ionic atmosphere is a poor descriptor of the aqueous environment near a metal surface. The importance of this finding for a description of electrochemical reactions is examined by calculating, directly from the simulation, Marcus free-energy profiles for transfer of charge between the electrode and a redox species in the solution and comparing the results with the predictions of continuum theories. Significant departures from the electrochemical textbook descriptions of the phenomenon are found and their physical origins are characterized from the atomistic perspective of the simulations.
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Affiliation(s)
- Adam P Willard
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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Hu H, Yang W. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. ACTA ACUST UNITED AC 2009; 898:17-30. [PMID: 24146439 DOI: 10.1016/j.theochem.2008.12.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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.
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Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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Martin DR, Matyushov DV. Electrostatic fluctuations in cavities within polar liquids and thermodynamics of polar solvation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:041206. [PMID: 18999411 DOI: 10.1103/physreve.78.041206] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Indexed: 05/27/2023]
Abstract
We present the results of numerical simulations of the fluctuations of the electrostatic potential and electric field inside cavities created in the fluid of dipolar hard spheres. We found that the thermodynamics of polar solvation changes dramatically when the cavity size becomes about 4-5 times larger than the size of the liquid particle. The range of small cavities can be reasonably understood within the framework of current solvation models. On the contrary, the regime of large cavities is characterized by a significant softening of the cavity interface resulting in a decay of the fluctuation variances with the cavity size much faster than anticipated by both the continuum electrostatics and microscopic theories. For instance, the variance of the electrostatic potential at the cavity center decays with the cavity radius R0 approximately as 1R{0};{4-6} instead of the 1R{0} scaling expected from the standard electrostatics. Our results suggest that cores of nonpolar molecular assemblies in polar liquids lose solvation strength much faster than is traditionally anticipated.
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Affiliation(s)
- Daniel R Martin
- Center for Biological Physics, Arizona State University, P.O. Box 871604, Tempe, Arizona 85287-1604, USA
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Evans DH. One-Electron and Two-Electron Transfers in Electrochemistry and Homogeneous Solution Reactions. Chem Rev 2008; 108:2113-44. [DOI: 10.1021/cr068066l] [Citation(s) in RCA: 273] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Moens J, Jaque P, De Proft F, Geerlings P. The Study of Redox Reactions on the Basis of Conceptual DFT Principles: EEM and Vertical Quantities. J Phys Chem A 2008; 112:6023-31. [DOI: 10.1021/jp711652a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Moens
- Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium, and Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile
| | - Pablo Jaque
- Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium, and Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile
| | - Frank De Proft
- Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium, and Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile
| | - Paul Geerlings
- Eenheid Algemene Chemie, Faculteit Wetenschappen, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, Belgium, and Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile
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LeBard DN, Matyushov DV. Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation. J Chem Phys 2008; 128:155106. [DOI: 10.1063/1.2904879] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Kritayakornupong C. The Jahn-Teller effect of the Ag2+ ion in aqueous solution: A hybrid ab initio quantum mechanical/molecular mechanical molecular dynamics simulation. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.02.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zeng X, Hu H, Hu X, Cohen AJ, Yang W. Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach. J Chem Phys 2008; 128:124510. [PMID: 18376946 PMCID: PMC3730858 DOI: 10.1063/1.2832946] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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Affiliation(s)
- Xiancheng Zeng
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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