51
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Odella E, Mora SJ, Wadsworth BL, Huynh MT, Goings JJ, Liddell PA, Groy TL, Gervaldo M, Sereno LE, Gust D, Moore TA, Moore GF, Hammes-Schiffer S, Moore AL. Controlling Proton-Coupled Electron Transfer in Bioinspired Artificial Photosynthetic Relays. J Am Chem Soc 2018; 140:15450-15460. [DOI: 10.1021/jacs.8b09724] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emmanuel Odella
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - S. Jimena Mora
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Brian L. Wadsworth
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Mioy T. Huynh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joshua J. Goings
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Paul A. Liddell
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas L. Groy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Miguel Gervaldo
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal No. 3, 5800 Río Cuarto, Córdoba, Argentina
| | - Leónides E. Sereno
- Departamento de Química, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Agencia Postal No. 3, 5800 Río Cuarto, Córdoba, Argentina
| | - Devens Gust
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Thomas A. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Gary F. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ana L. Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
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52
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Hammes-Schiffer S. Controlling Electrons and Protons through Theory: Molecular Electrocatalysts to Nanoparticles. Acc Chem Res 2018; 51:1975-1983. [PMID: 30110147 DOI: 10.1021/acs.accounts.8b00240] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The development of renewable energy sources that are environmentally friendly and economical is of critical importance. The effective utilization of such energy sources relies on catalysts to facilitate the interconversion between electrical and chemical energy through multielectron, multiproton reactions. The design of effective catalysts for these types of energy conversion processes requires the ability to control the localization and movement of electrons and protons, as well as the coupling between them. Theoretical calculations, in conjunction with experimental validation and feedback, are playing a key role in these catalyst design efforts. A general theory has been developed for describing proton-coupled electron transfer (PCET) reactions, which encompass all reactions involving the coupled transfer of electrons and protons, including sequential and concerted mechanisms for multielectron, multiproton processes. In addition, computational methods have been devised to compute the input quantities for the PCET rate constant expressions and to generate free energy pathways for molecular electrocatalysts. These methods have been extended to heterogeneous PCET reactions to enable the modeling of PCET processes at electrode and nanoparticle surfaces. Three distinct theoretical studies of PCET reactions relevant to catalyst design for energy conversion processes are discussed. In the first application, theoretical calculations of hydrogen production catalyzed by hangman metalloporphyrins predicted that the porphyrin ligand is reduced, leading to dearomatization and proton transfer from the carboxylic acid hanging group to the meso carbon of the porphyrin rather than the metal center, producing a phlorin intermediate. Subsequent experiments isolated and characterized the phlorin intermediate, validating this theoretical prediction. These molecular electrocatalysts exemplify the potential use of noninnocent ligands to localize electrons and protons on different parts of the catalyst and to direct their motions accordingly. In the second application, theoretical calculations on substituted benzimidazole phenol molecules predicted that certain substituents would lead to multiple intramolecular proton transfer reactions upon oxidation. Subsequent experiments verified these multiproton reactions, as well as the predicted shifts in the redox potentials and kinetic isotope effects. These bioinspired molecular systems demonstrate the potential use of multiproton relays to enable the transport of protons over longer distances along specified pathways, as well as the tuning of redox potentials through this movement of positive charge. In the third application, theoretical studies of heterogeneous PCET in photoreduced ZnO nanoparticles illustrated the significance of proton diffusion through the bulk of the nanoparticle as well as interfacial PCET to an organic radical in solution at its surface. These theoretical calculations were consistent with prior experimental studies of this system, although theoretical methods for heterogeneous PCET have not yet attained the level of predictive capability highlighted for the molecular electrocatalysts. These examples suggest that theory will play a significant role in the design of both molecular and heterogeneous catalysts to control the movement and coupling of electrons and protons. The resulting catalysts will be essential for the development of renewable energy sources to address current energy challenges.
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Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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53
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Holmberg N, Laasonen K. Diabatic model for electrochemical hydrogen evolution based on constrained DFT configuration interaction. J Chem Phys 2018; 149:104702. [PMID: 30219020 DOI: 10.1063/1.5038959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accuracy of density functional theory (DFT) based kinetic models for electrocatalysis is diminished by spurious electron delocalization effects, which manifest as uncertainties in the predicted values of reaction and activation energies. In this work, we present a constrained DFT (CDFT) approach to alleviate overdelocalization effects in the Volmer-Heyrovsky mechanism of the hydrogen evolution reaction (HER). This method is applied a posteriori to configurations sampled along a reaction path to correct their relative stabilities. Concretely, the first step of this approach involves describing the reaction in terms of a set of diabatic states that are constructed by imposing suitable density constraints on the system. Refined reaction energy profiles are then recovered by performing a configuration interaction (CDFT-CI) calculation within the basis spanned by the diabatic states. After a careful validation of the proposed method, we examined HER catalysis on open-ended carbon nanotubes and discovered that CDFT-CI increased activation energies and decreased reaction energies relative to DFT predictions. We believe that a similar approach could also be adopted to treat overdelocalization effects in other electrocatalytic proton-coupled electron transfer reactions, e.g., in the oxygen reduction reaction.
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Affiliation(s)
- Nico Holmberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Kari Laasonen
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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54
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Soudackov AV, Hammes-Schiffer S. Proton-coupled electron transfer reactions: analytical rate constants and case study of kinetic isotope effects in lipoxygenase. Faraday Discuss 2018; 195:171-189. [PMID: 27735009 DOI: 10.1039/c6fd00122j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general theory has been developed for proton-coupled electron transfer (PCET), which is vital to a wide range of chemical and biological processes. This theory describes PCET reactions in terms of nonadiabatic transitions between reactant and product electron-proton vibronic states and includes the effects of thermal fluctuations of the solvent or protein environment, as well as the proton donor-acceptor motion. Within the framework of this general PCET theory, a series of analytical rate constant expressions has been derived for PCET reactions in well-defined regimes. Herein, the application of this theory to PCET in the enzyme soybean lipoxygenase illustrates the regimes of validity for the various rate constant expressions and elucidates the fundamental physical principles dictating PCET reactions. Such theoretical studies provide significant physical insights that guide the interpretation of experimental data and lead to experimentally testable predictions. A combination of theoretical treatments with atomic-level simulations is essential to understanding PCET.
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Affiliation(s)
- Alexander V Soudackov
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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55
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Gillet N, Elstner M, Kubař T. Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer. J Chem Phys 2018; 149:072328. [PMID: 30134697 DOI: 10.1063/1.5027100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.
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Affiliation(s)
- Natacha Gillet
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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56
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Amadei A, Aschi M. Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems. RSC Adv 2018; 8:27900-27918. [PMID: 35542751 PMCID: PMC9083445 DOI: 10.1039/c8ra03900c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/23/2018] [Indexed: 11/21/2022] Open
Abstract
In this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems.
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Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, Universita' di Roma 'Tor Vergata' Roma Italy +390672594905
| | - Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Universita' di L'Aquila L'Aquila Italy +390862433775
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57
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Mandal A, Shakib FA, Huo P. Investigating photoinduced proton coupled electron transfer reaction using quasi diabatic dynamics propagation. J Chem Phys 2018; 148:244102. [DOI: 10.1063/1.5030634] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Arkajit Mandal
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Farnaz A. Shakib
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
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58
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Tyburski R, Föhlinger J, Hammarström L. Light Driven Electron Transfer in Methylbipyridine/Phenol Complexes Is Not Proton Coupled. J Phys Chem A 2018; 122:4425-4429. [DOI: 10.1021/acs.jpca.8b02221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robin Tyburski
- Department of Chemistry, Ångström Laboratories, Uppsala University, Box 523, SE75120 Uppsala, Sweden
| | - Jens Föhlinger
- Department of Chemistry, Ångström Laboratories, Uppsala University, Box 523, SE75120 Uppsala, Sweden
| | - Leif Hammarström
- Department of Chemistry, Ångström Laboratories, Uppsala University, Box 523, SE75120 Uppsala, Sweden
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59
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Li P, Soudackov AV, Hammes-Schiffer S. Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations. J Am Chem Soc 2018; 140:3068-3076. [PMID: 29392938 PMCID: PMC5849423 DOI: 10.1021/jacs.7b13642] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proton-coupled electron transfer (PCET) reaction catalyzed by soybean lipoxygenase has served as a prototype for understanding hydrogen tunneling in enzymes. Herein this PCET reaction is studied with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The free energy surfaces are computed as functions of the proton donor-acceptor (C-O) distance and the proton coordinate, and the potential of mean force is computed as a function of the C-O distance, inherently including anharmonicity. The simulation results are used to calculate the kinetic isotope effects for the wild-type enzyme (WT) and the L546A/L754A double mutant (DM), which have been measured experimentally to be ∼80 and ∼700, respectively. The PCET reaction is found to be exoergic for WT and slightly endoergic for the DM, and the equilibrium C-O distance for the reactant is found to be ∼0.2 Å greater for the DM than for WT. The larger equilibrium distance for the DM, which is due mainly to less optimal substrate binding in the expanded binding cavity, is primarily responsible for its higher kinetic isotope effect. The calculated potentials of mean force are anharmonic and relatively soft at shorter C-O distances, allowing efficient thermal sampling of the shorter distances required for effective hydrogen tunneling. The primarily local electrostatic field at the transferring hydrogen is ∼100 MV/cm in the direction to facilitate proton transfer and increases dramatically as the C-O distance decreases. These simulations suggest that the overall protein environment is important for conformational sampling of active substrate configurations aligned for proton transfer, but the PCET reaction is influenced primarily by local electrostatic effects that facilitate conformational sampling of shorter proton donor-acceptor distances required for effective hydrogen tunneling.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave, Urbana, Illinois 61801; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Alexander V. Soudackov
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave, Urbana, Illinois 61801; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Ave, Urbana, Illinois 61801; Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
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60
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Weinstock IA, Schreiber RE, Neumann R. Dioxygen in Polyoxometalate Mediated Reactions. Chem Rev 2017; 118:2680-2717. [DOI: 10.1021/acs.chemrev.7b00444] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ira A. Weinstock
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Roy E. Schreiber
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ronny Neumann
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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61
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Jevtic S, Anders J. A qualitative quantum rate model for hydrogen transfer in soybean lipoxygenase. J Chem Phys 2017; 147:114108. [PMID: 28938801 DOI: 10.1063/1.4998941] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The hydrogen transfer reaction catalysed by soybean lipoxygenase (SLO) has been the focus of intense study following observations of a high kinetic isotope effect (KIE). Today high KIEs are generally thought to indicate departure from classical rate theory and are seen as a strong signature of tunnelling of the transferring particle, hydrogen or one of its isotopes, through the reaction energy barrier. In this paper, we build a qualitative quantum rate model with few free parameters that describes the dynamics of the transferring particle when it is exposed to energetic potentials exerted by the donor and the acceptor. The enzyme's impact on the dynamics is modelled by an additional energetic term, an oscillatory contribution known as "gating." By varying two key parameters, the gating frequency and the mean donor-acceptor separation, the model is able to reproduce well the KIE data for SLO wild-type and a variety of SLO mutants over the experimentally accessible temperature range. While SLO-specific constants have been considered here, it is possible to adapt these for other enzymes.
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Affiliation(s)
- S Jevtic
- Department of Mathematics, Huxley Building, Imperial College, London SW7 2AZ, United Kingdom
| | - J Anders
- CEMPS, Physics and Astronomy, University of Exeter, Exeter EX4 4QL, United Kingdom
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62
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Ghosh S, Castillo-Lora J, Soudackov AV, Mayer JM, Hammes-Schiffer S. Theoretical Insights into Proton-Coupled Electron Transfer from a Photoreduced ZnO Nanocrystal to an Organic Radical. NANO LETTERS 2017; 17:5762-5767. [PMID: 28846428 DOI: 10.1021/acs.nanolett.7b02642] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proton-coupled electron transfer (PCET) at metal-oxide nanoparticle interfaces plays a critical role in many photocatalytic reactions and energy conversion processes. Recent experimental studies have shown that photoreduced ZnO nanocrystals react by PCET with organic hydrogen atom acceptors such as the nitroxyl radical TEMPO. Herein, the interfacial PCET rate constant is calculated in the framework of vibronically nonadiabatic PCET theory, which treats the electrons and transferring proton quantum mechanically. The input quantities to the PCET rate constant, including the electronic couplings, are calculated with density functional theory. The computed interfacial PCET rate constant is consistent with the experimentally measured value for this system, providing validation for this PCET theory. In this model, the electron transfers from the conduction band of the ZnO nanocrystal to TEMPO concertedly with proton transfer from a surface oxygen of the ZnO nanocrystal to the oxygen of TEMPO. Moreover, the proton tunneling at the interface is gated by the relatively low-frequency proton donor-acceptor motion between the TEMPO radical and the ZnO nanocrystal. The ZnO nanocrystal and TEMPO are found to contribute similar amounts to the inner-sphere reorganization energy, implicating structural reorganization at the nanocrystal surface. These fundamental mechanistic insights may guide the design of metal-oxide nanocatalysts for a wide range of energy conversion processes.
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Affiliation(s)
- Soumya Ghosh
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Janelle Castillo-Lora
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Alexander V Soudackov
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - James M Mayer
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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63
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Tse ECM, Barile CJ, Kirchschlager NA, Li Y, Gewargis JP, Zimmerman SC, Hosseini A, Gewirth AA. Proton transfer dynamics control the mechanism of O2 reduction by a non-precious metal electrocatalyst. NATURE MATERIALS 2016; 15:754-9. [PMID: 27135859 DOI: 10.1038/nmat4636] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 01/28/2016] [Indexed: 05/25/2023]
Abstract
Many chemical and biological processes involve the transfer of both protons and electrons. The complex mechanistic details of these proton-coupled electron transfer (PCET) reactions require independent control of both electron and proton transfer. In this report, we make use of lipid-modified electrodes to modulate proton transport to a Cu-based catalyst that facilitates the O2 reduction reaction (ORR), a PCET process important in fuel cells and O2 reduction enzymes. By quantitatively controlling the kinetics of proton transport to the catalyst, we demonstrate that undesired side products such as H2O2 and O2(-) arise from a mismatch between proton and electron transfer rates. Whereas fast proton kinetics induce H2O2 formation and sluggish proton flux produces O2(-), proton transfer rates commensurate with O-O bond breaking rates ensure that only the desired H2O product forms. This fundamental insight aids in the development of a comprehensive framework for understanding the ORR and PCET processes in general.
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Affiliation(s)
- Edmund C M Tse
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Christopher J Barile
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nicholas A Kirchschlager
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ying Li
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - John P Gewargis
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ali Hosseini
- Manufacturing Systems Ltd., Auckland 0632, New Zealand
| | - Andrew A Gewirth
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- International Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka 819-0395, Japan
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64
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Shakib F, Hanna G. Mixed Quantum-Classical Liouville Approach for Calculating Proton-Coupled Electron-Transfer Rate Constants. J Chem Theory Comput 2016; 12:3020-9. [DOI: 10.1021/acs.jctc.6b00362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Farnaz Shakib
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gabriel Hanna
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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65
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González-Lafont À, Lluch JM. Kinetic isotope effects in chemical and biochemical reactions: physical basis and theoretical methods of calculation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química; Universitat Autònoma de Barcelona; Bellaterra, Barcelona Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química; Universitat Autònoma de Barcelona; Bellaterra, Barcelona Spain
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66
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Shakib FA, Hanna G. New insights into the nonadiabatic state population dynamics of model proton-coupled electron transfer reactions from the mixed quantum-classical Liouville approach. J Chem Phys 2016; 144:024110. [DOI: 10.1063/1.4939586] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Farnaz A. Shakib
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Gabriel Hanna
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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67
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Harshan A, Yu T, Soudackov AV, Hammes-Schiffer S. Dependence of Vibronic Coupling on Molecular Geometry and Environment: Bridging Hydrogen Atom Transfer and Electron-Proton Transfer. J Am Chem Soc 2015; 137:13545-55. [PMID: 26412613 PMCID: PMC4629534 DOI: 10.1021/jacs.5b07327] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/29/2022]
Abstract
The rate constants for typical concerted proton-coupled electron transfer (PCET) reactions depend on the vibronic coupling between the diabatic reactant and product states. The form of the vibronic coupling is different for electronically adiabatic and nonadiabatic reactions, which are associated with hydrogen atom transfer (HAT) and electron-proton transfer (EPT) mechanisms, respectively. Most PCET rate constant expressions rely on the Condon approximation, which assumes that the vibronic coupling is independent of the nuclear coordinates of the solute and the solvent or protein. Herein we test the Condon approximation for PCET vibronic couplings. The dependence of the vibronic coupling on molecular geometry is investigated for an open and a stacked transition state geometry of the phenoxyl-phenol self-exchange reaction. The calculations indicate that the open geometry is electronically nonadiabatic, corresponding to an EPT mechanism that involves significant electronic charge redistribution, while the stacked geometry is predominantly electronically adiabatic, corresponding primarily to an HAT mechanism. Consequently, a single molecular system can exhibit both HAT and EPT character. The dependence of the vibronic coupling on the solvent or protein configuration is examined for the soybean lipoxygenase enzyme. The calculations indicate that this PCET reaction is electronically nonadiabatic with a vibronic coupling that does not depend significantly on the protein environment. Thus, the Condon approximation is shown to be valid for the solvent and protein nuclear coordinates but invalid for the solute nuclear coordinates in certain PCET systems. These results have significant implications for the calculation of rate constants, as well as mechanistic interpretations, of PCET reactions.
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Affiliation(s)
| | | | - Alexander V. Soudackov
- Department of Chemistry, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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68
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Kretchmer JS, Miller TF. Tipping the Balance between Concerted versus Sequential Proton-Coupled Electron Transfer. Inorg Chem 2015; 55:1022-31. [PMID: 26440812 DOI: 10.1021/acs.inorgchem.5b01821] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joshua S. Kretchmer
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F. Miller
- Department of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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69
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Hammes-Schiffer S. Proton-Coupled Electron Transfer: Moving Together and Charging Forward. J Am Chem Soc 2015; 137:8860-71. [PMID: 26110700 PMCID: PMC4601483 DOI: 10.1021/jacs.5b04087] [Citation(s) in RCA: 291] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/24/2022]
Abstract
Proton-coupled electron transfer (PCET) is ubiquitous throughout chemistry and biology. This Perspective discusses recent advances and current challenges in the field of PCET, with an emphasis on the role of theory and computation. The fundamental theoretical concepts are summarized, and expressions for rate constants and kinetic isotope effects are provided. Computational methods for calculating reduction potentials and pKa's for molecular electrocatalysts, as well as insights into linear correlations and non-innocent ligands, are also described. In addition, computational methods for simulating the nonadiabatic dynamics of photoexcited PCET are discussed. Representative applications to PCET in solution, proteins, electrochemistry, and photoinduced processes are presented, highlighting the interplay between theoretical and experimental studies. The current challenges and suggested future directions are outlined for each type of application, concluding with an overall view to the future.
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Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry, University of
Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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70
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Shakib FA, Hanna G. An analysis of model proton-coupled electron transfer reactions via the mixed quantum-classical Liouville approach. J Chem Phys 2014; 141:044122. [DOI: 10.1063/1.4890915] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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71
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Solis BH, Hammes-Schiffer S. Proton-coupled electron transfer in molecular electrocatalysis: theoretical methods and design principles. Inorg Chem 2014; 53:6427-43. [PMID: 24731018 DOI: 10.1021/ic5002896] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Molecular electrocatalysts play an essential role in a wide range of energy conversion processes. The objective of electrocatalyst design is to maximize the turnover frequency and minimize the overpotential for the overall catalytic cycle. Typically, the catalytic cycle is dominated by key proton-coupled electron transfer (PCET) processes comprised of sequential or concerted electron and proton transfer steps. Theoretical methods have been developed to investigate the mechanisms, thermodynamics, and kinetics of PCET processes in electrocatalytic cycles. Electronic structure methods can be used to calculate the reduction potentials and pKa's and to generate thermodynamic schemes, free energy reaction pathways, and Pourbaix diagrams, which indicate the most stable species under certain conditions. These types of calculations have assisted in identifying the thermodynamically favorable mechanisms under specified experimental conditions, such as acid strength and overpotential. Such calculations have also revealed linear correlations among the thermodynamic properties, which can be used to predict the impact of modifying the ligands, substituents, or metal centers. The thermodynamic properties can be tuned with electron-withdrawing or electron-donating substituents. Ligand modification can exploit the role of noninnocent ligands. For example, ligand protonation typically decreases the overpotential. Calculations of rate constants for electron and proton transfer, as well as concerted PCET, have assisted in identifying the kinetically favorable mechanisms under specified conditions. The concerted PCET mechanism is thought to lower the overpotential required for catalysis by avoiding high-energy intermediates. Rate constant calculations have revealed that the concerted mechanism involving intramolecular proton transfer will be favored by designing more flexible ligands that facilitate the proton donor-acceptor motion while also maintaining a sufficiently short equilibrium proton donor-acceptor distance. Overall, theoretical methods have assisted in the interpretation of experimental data and the design of more effective molecular electrocatalysts.
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Affiliation(s)
- Brian H Solis
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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72
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Migliore A, Polizzi NF, Therien M, Beratan DN. Biochemistry and theory of proton-coupled electron transfer. Chem Rev 2014; 114:3381-465. [PMID: 24684625 PMCID: PMC4317057 DOI: 10.1021/cr4006654] [Citation(s) in RCA: 354] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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73
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Affiliation(s)
- Joshua P. Layfield
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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74
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Schwerdtfeger CA, Soudackov AV, Hammes-Schiffer S. Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales. J Chem Phys 2014; 140:034113. [DOI: 10.1063/1.4855295] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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75
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Savéant JM. Concerted proton-electron transfers: fundamentals and recent developments. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:537-560. [PMID: 25014349 DOI: 10.1146/annurev-anchem-071213-020315] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proton-coupled electron transfers (PCET) are ubiquitous in natural and synthetic processes. This review focuses on reactions where the two events are concerted. Semiclassical models of such reactions allow their kinetic characterization through activation versus driving force relationships, estimates of reorganization energies, effects of the nature of the proton acceptor, and H/D kinetic isotope effect as well as their discrimination from stepwise pathways. Several homogeneous reactions (through stopped-flow and laser flash-quench techniques) and electrochemical processes are discussed in this framework. Once the way has been rid of the improper notion of pH-dependent driving force, water appears as a remarkable proton acceptor in terms of reorganization energy and pre-exponential factor, thanks to its H-bonded and H-bonding properties, similarly to purposely synthesized "H-bond train" molecules. The most recent developments are in modeling and description of emblematic concerted proton-electron transfer (CPET) reactions associated with the breaking of a heavy-atom bond in an all-concerted process.
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Affiliation(s)
- Jean-Michel Savéant
- Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche, Université Paris Diderot, Sorbonne Paris Cité, CNRS 7591, 75205 Paris Cedex 13, France;
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76
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Koper MTM. Theory of the transition from sequential to concerted electrochemical proton-electron transfer. Phys Chem Chem Phys 2013; 15:1399-407. [PMID: 23011280 DOI: 10.1039/c2cp42369c] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A theory for the calculation of potential energy surfaces of electrochemical proton-coupled electron transfer is considered and parameterized on the basis of thermodynamic relations. The paper discusses the qualitatively different potential energy surfaces predicted by the theory, and their relation to the existence of sequential and concerted proton-electron transfer pathways. The concomitant activation energies for sequential and concerted PET are calculated. The applied overpotential may change the qualitative shape of the PES and therefore the mechanism of the proton-coupled electron transfer reaction.
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Affiliation(s)
- Marc T M Koper
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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77
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Kretchmer JS, Miller TF. Direct simulation of proton-coupled electron transfer across multiple regimes. J Chem Phys 2013; 138:134109. [DOI: 10.1063/1.4797462] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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78
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Bushnell EAC, Jamil R, Gauld JW. Gaining insight into the chemistry of lipoxygenases: a computational investigation into the catalytic mechanism of (8R)-lipoxygenase. J Biol Inorg Chem 2013; 18:343-55. [PMID: 23361122 DOI: 10.1007/s00775-013-0978-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
Abstract
Lipoxygenases (LOXs) are ubiquitous in nature and catalyze a range of life-essential reactions within organisms. In particular they are critical to the formation of eicosanoids, which are critical for normal cell function. However, a number of important questions about the reactivity and mechanism of these enzymes still remain. Specifically, although the initial step in the mechanism of LOXs has been well studied, little is known of subsequent steps. Thus, with use of a quantum mechanical/molecular mechanical approach, the complete catalytic mechanism of (8R)-LOX was investigated. The results have provided a better understanding of the general chemistry of LOXs as a whole. In particular, from comparisons with soybean LOX-1, it appears that the initial proton-coupled electron transfer may be very similar among all LOXs. Furthermore, LOXs appear to undergo multistate reactivity where potential spin inversion of an electron may occur either in the attack of O(2) or in the regeneration of the active site. Lastly, it is shown that with the explicit modeling of the environment, the regeneration of the active center likely occurs via the rotation of the intermediate followed by an outer-sphere [Formula: see text] transfer as opposed to the formation of a "purple intermediate" complex.
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Affiliation(s)
- Eric A C Bushnell
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, N9B 3P4, Canada
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79
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Tanimura Y. Reduced hierarchy equations of motion approach with Drude plus Brownian spectral distribution: Probing electron transfer processes by means of two-dimensional correlation spectroscopy. J Chem Phys 2012; 137:22A550. [DOI: 10.1063/1.4766931] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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80
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Weinberg DR, Gagliardi CJ, Hull JF, Murphy CF, Kent CA, Westlake BC, Paul A, Ess DH, McCafferty DG, Meyer TJ. Proton-Coupled Electron Transfer. Chem Rev 2012; 112:4016-93. [DOI: 10.1021/cr200177j] [Citation(s) in RCA: 1125] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David R. Weinberg
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
- Department of Physical and Environmental
Sciences, Colorado Mesa University, 1100 North Avenue, Grand Junction,
Colorado 81501-3122, United States
| | - Christopher J. Gagliardi
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Jonathan F. Hull
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Christine Fecenko Murphy
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Caleb A. Kent
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Brittany C. Westlake
- The American Chemical Society,
1155 Sixteenth Street NW, Washington, District of Columbia 20036,
United States
| | - Amit Paul
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Daniel H. Ess
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Dewey Granville McCafferty
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Thomas J. Meyer
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
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81
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Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study. J Biol Inorg Chem 2012; 17:741-60. [DOI: 10.1007/s00775-012-0893-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 03/05/2012] [Indexed: 01/08/2023]
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82
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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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83
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Soudackov AV, Hazra A, Hammes-Schiffer S. Multidimensional treatment of stochastic solvent dynamics in photoinduced proton-coupled electron transfer processes: Sequential, concerted, and complex branching mechanisms. J Chem Phys 2011; 135:144115. [DOI: 10.1063/1.3651083] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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84
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Sirjoosingh A, Hammes-Schiffer S. Diabatization Schemes for Generating Charge-Localized Electron–Proton Vibronic States in Proton-Coupled Electron Transfer Systems. J Chem Theory Comput 2011; 7:2831-41. [DOI: 10.1021/ct200356b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Andrew Sirjoosingh
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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85
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Impaired protein conformational landscapes as revealed in anomalous Arrhenius prefactors. Proc Natl Acad Sci U S A 2011; 108:10520-5. [PMID: 21670258 DOI: 10.1073/pnas.1104989108] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A growing body of data supports a role for protein motion in enzyme catalysis. In particular, the ability of enzymes to sample catalytically relevant conformational substates has been invoked to model kinetic and spectroscopic data. However, direct experimental links between rapidly interconverting conformations and the chemical steps of catalysis remain rare. We report here on the kinetic analysis and characterization of the hydride transfer step catalyzed by a series of mutant thermophilic alcohol dehydrogenases (ht-ADH), presenting evidence for Arrhenius prefactor values that become enormously elevated above an expected value of approximately 10(13) s(-1) when the enzyme operates below its optimal temperature range. Restoration of normal Arrhenius behavior in the ht-ADH reaction occurs at elevated temperatures. A simple model, in which reduced temperature alters the ability of the ht-ADH variants to sample the catalytically relevant region of conformational space, can reproduce the available data. These findings indicate an impaired landscape that has been generated by the combined condition of reduced temperature and mutation at a single, active-site hydrophobic side chain. The broader implication is that optimal enzyme function requires the maintenance of a relatively smooth landscape that minimizes low energy traps.
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86
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Auer B, Fernandez LE, Hammes-Schiffer S. Theoretical Analysis of Proton Relays in Electrochemical Proton-Coupled Electron Transfer. J Am Chem Soc 2011; 133:8282-92. [DOI: 10.1021/ja201560v] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Auer
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Laura E. Fernandez
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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87
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88
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Sirjoosingh A, Hammes-Schiffer S. Proton-Coupled Electron Transfer versus Hydrogen Atom Transfer: Generation of Charge-Localized Diabatic States. J Phys Chem A 2011; 115:2367-77. [DOI: 10.1021/jp111210c] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrew Sirjoosingh
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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89
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Hemant Kumar P, Prashanthi S, Bangal PR. Role of Hydrogen Bonding in the Photophysical Properties of Isomeric Tetrapyridylporphyrins in Aprotic Solvent. J Phys Chem A 2011; 115:631-42. [DOI: 10.1021/jp1045782] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Pippara Hemant Kumar
- Inorganic and Physical Chemistry Division, Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad, India 500607
| | - Suthari Prashanthi
- Inorganic and Physical Chemistry Division, Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad, India 500607
| | - Prakriti Ranjan Bangal
- Inorganic and Physical Chemistry Division, Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad, India 500607
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90
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Theory of proton coupled electron transfer reactions: Assessing the Born–Oppenheimer approximation for the proton motion using an analytically solvable model. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2010.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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91
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Hammes–Schiffer S, Stuchebrukhov AA. Theory of coupled electron and proton transfer reactions. Chem Rev 2010; 110:6939-60. [PMID: 21049940 PMCID: PMC3005854 DOI: 10.1021/cr1001436] [Citation(s) in RCA: 578] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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92
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Kumar A, Sevilla MD. Proton-coupled electron transfer in DNA on formation of radiation-produced ion radicals. Chem Rev 2010; 110:7002-23. [PMID: 20443634 PMCID: PMC2947616 DOI: 10.1021/cr100023g] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309
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93
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Hazra A, Soudackov AV, Hammes-Schiffer S. Role of Solvent Dynamics in Ultrafast Photoinduced Proton-Coupled Electron Transfer Reactions in Solution. J Phys Chem B 2010; 114:12319-32. [DOI: 10.1021/jp1051547] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anirban Hazra
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Alexander V. Soudackov
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
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94
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Snir O, Wang Y, Tuckerman ME, Geletii YV, Weinstock IA. Concerted Proton−Electron Transfer to Dioxygen in Water. J Am Chem Soc 2010; 132:11678-91. [DOI: 10.1021/ja104392k] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ophir Snir
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel, Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10003
| | - Yifeng Wang
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel, Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10003
| | - Mark E. Tuckerman
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel, Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10003
| | - Yurii V. Geletii
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel, Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10003
| | - Ira A. Weinstock
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel, Department of Chemistry, Emory University, Atlanta, Georgia 30322, and Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10003
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95
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Kiefer PM, Hynes JT. Theoretical aspects of tunneling proton transfer reactions in a polar environment. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1710] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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96
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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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97
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Edwards SJ, Soudackov AV, Hammes-Schiffer S. Impact of distal mutation on hydrogen transfer interface and substrate conformation in soybean lipoxygenase. J Phys Chem B 2010; 114:6653-60. [PMID: 20423074 PMCID: PMC2880924 DOI: 10.1021/jp100133p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The impact of distal mutation on the hydrogen transfer interface properties and on the substrate mobility, conformation, and orientation in soybean lipoxygenase-1 (SLO) is examined. SLO catalyzes a hydrogen abstraction reaction that occurs by a proton-coupled electron transfer mechanism. Mutation of isoleucine 553 to less bulky residues has been found experimentally to increase the magnitude and temperature dependence of the kinetic isotope effect for this reaction. This residue borders the linoleic acid substrate but is approximately 15 A from the active site iron. In the present study, we model these experimental data with a vibronically nonadiabatic theory and perform all-atom molecular dynamics simulations on the complete solvated wild-type and mutant enzymes. Our calculations indicate that the proton transfer equilibrium distance increases and the associated frequency decreases as residue 553 becomes less bulky. The molecular dynamics simulations illustrate that this mutation impacts the mobility, geometrical conformation, and orientation of the linoleic acid within the active site. In turn, these effects alter the proton donor-acceptor equilibrium distance and frequency, leading to the experimentally observed changes in the magnitude and temperature dependence of the kinetic isotope effect. This study provides insight into how the effects of distal mutations may be transmitted in enzymes to ultimately impact the catalytic rates.
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Affiliation(s)
- Sarah J. Edwards
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, PA 16802
| | - Alexander V. Soudackov
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, PA 16802
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, PA 16802
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98
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Hammes-Schiffer S. Theory of proton-coupled electron transfer in energy conversion processes. Acc Chem Res 2009; 42:1881-9. [PMID: 19807148 DOI: 10.1021/ar9001284] [Citation(s) in RCA: 261] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proton-coupled electron transfer (PCET) reactions play an essential role in a broad range of energy conversion processes, including photosynthesis and respiration. These reactions also form the basis of many types of solar fuel cells and electrochemical devices. Recent advances in the theory of PCET enable the prediction of the impact of system properties on the reaction rates. These predictions may guide the design of more efficient catalysts for energy production, including those based on artificial photosynthesis and solar energy conversion. This Account summarizes the theoretically predicted dependence of PCET rates on system properties and illustrates potential approaches for tuning the reaction rates in chemical systems. A general theoretical formulation for PCET reactions has been developed over the past decade. In this theory, PCET reactions are described in terms of nonadiabatic transitions between the reactant and product electron-proton vibronic states. A series of nonadiabatic rate constant expressions for both homogeneous and electrochemical PCET reactions have been derived in various well-defined limits. Recently this theory has been extended to include the effects of solvent dynamics and to describe ultrafast interfacial PCET. Analysis of the rate constant expressions provides insight into the underlying physical principles of PCET and enables the prediction of the dependence of the rates on the physical properties of the system. Moreover, the kinetic isotope effect, which is the ratio of the rates for hydrogen and deuterium, provides a useful mechanistic probe. Typically the PCET rate will increase as the electronic coupling and temperature increase and as the total reorganization energy and equilibrium proton donor-acceptor distance decrease. The rate constant is predicted to increase as the driving force becomes more negative, rather than exhibit turnover behavior in the inverted region, because excited vibronic product states associated with low free energy barriers and relatively large vibronic couplings become accessible. The physical basis for the experimentally observed pH dependence of PCET reactions has been debated in the literature. When the proton acceptor is a buffer species, the pH dependence may arise from the protonation equilibrium of the buffer. It could also arise from kinetic complexity of competing concerted and sequential PCET reaction pathways. In electrochemical PCET, the heterogeneous rate constants and current densities depend strongly on the overpotential. The change in equilibrium proton donor-acceptor distance upon electron transfer may lead to asymmetries in the Tafel plots and deviations of the transfer coefficient from the standard value of one-half at zero overpotential. Applications of this theory to experimentally studied systems illustrate approaches that can be utilized to tune the PCET rate. For example, the rate can be tuned by changing the pH or using different buffer species as proton acceptors. The rate can also be tuned with site-specific mutagenesis in biological systems or chemical modifications that vary the substituents on the redox species in chemical systems. Understanding the impact of these changes on the PCET rate may assist experimental efforts to enhance energy conversion processes.
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Affiliation(s)
- Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania 16802
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Johannissen LO, Irebo T, Sjödin M, Johansson O, Hammarström L. The Kinetic Effect of Internal Hydrogen Bonds on Proton-Coupled Electron Transfer from Phenols: A Theoretical Analysis with Modeling of Experimental Data. J Phys Chem B 2009; 113:16214-25. [DOI: 10.1021/jp9048633] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Linus O. Johannissen
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Tania Irebo
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Martin Sjödin
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Olof Johansson
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Leif Hammarström
- Department of Photochemistry and Molecular Science, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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100
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Edwards SJ, Soudackov AV, Hammes-Schiffer S. Driving force dependence of rates for nonadiabatic proton and proton-coupled electron transfer: conditions for inverted region behavior. J Phys Chem B 2009; 113:14545-8. [PMID: 19795899 PMCID: PMC2783471 DOI: 10.1021/jp907808t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The driving force dependence of the rate constants for nonadiabatic electron transfer (ET), proton transfer (PT), and proton-coupled electron transfer (PCET) reactions is examined. Inverted region behavior, where the rate constant decreases as the reaction becomes more exoergic (i.e., as DeltaG(0) becomes more negative), has been observed experimentally for ET and PT. This behavior was predicted theoretically for ET but is not well understood for PT and PCET. The objective of this Letter is to predict the experimental conditions that could lead to observation of inverted region behavior for PT and PCET. The driving force dependence of the rate constant is qualitatively different for PT and PCET than for ET because of the high proton vibrational frequency and substantial shift between the reactant and product proton vibrational wave functions. As a result, inverted region behavior is predicted to be experimentally inaccessible for PT and PCET if only the driving force is varied. This behavior may be observed for PT over a limited range of rates and driving forces if the solvent reorganization energy is low enough to cause observable oscillations. Moreover, this behavior may be observed for PT or PCET if the proton donor-acceptor distance increases as DeltaG(0) becomes more negative. Thus, a plausible explanation for experimentally observed inverted region behavior for PT or PCET is that varying the driving force also impacts other properties of the system, such as the proton donor-acceptor distance.
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