Theoretical studies of proton-coupled electron transfer: Models and concepts relevant to bioenergetics

Hammes‐Schiffer, Sharon; Hatcher, Elizabeth; Ishikita, Hiroshi; Skone, Jonathan H.; Soudackov, Alexander V.

doi:10.1016/j.ccr.2007.07.019

Cited by 82 publications

(94 citation statements)

References 67 publications

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“…As pointed out previously, 31 in the absence of the quadratic term in the coupling expansion, the averaging of the squared coupling with the classical harmonic distribution function leads to a prefactor that coincides with the prefactor in the rate constant expression derived with the cumulant expansion approach in the low-frequency limit for the proton donoracceptor mode. When the quadratic term is included in the coupling expansion, the expressions given in Eqs.…”

Section: Thermal Averaging Over Proton Donor-acceptor Motionsupporting

confidence: 70%

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

Soudackov

Hammes‐Schiffer

2015

The Journal of Chemical Physics

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Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency proton donor-acceptor vibrational modes. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term in the framework of the cumulant expansion framework may significantly impact the rate constants at high temperatures for proton transfer interfaces with soft proton donor-acceptor modes that are associated with small force constants and weak hydrogen bonds. The effects of the quadratic term may also become significant in these regimes when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant. In this case, however, the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances sampled. The effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances. Additionally, the rigorous relation between the cumulant expansion and thermal averaging approaches is clarified. In particular, the cumulant expansion rate constant includes effects from dynamical interference between the proton donor-acceptor and solvent motions and becomes equivalent to the thermally averaged rate constant when these dynamical effects are neglected. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes. C 2015 AIP Publishing LLC. [http://dx

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Section: Thermal Averaging Over Proton Donor-acceptor Motionsupporting

confidence: 70%

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

Soudackov

Hammes‐Schiffer

2015

The Journal of Chemical Physics

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“…Many examples of PCET exist for different biological [24,25] and nonbiological [26,27] systems. They have been studied both experimentally [28,29] and theoretically [30][31][32]. The PCET formalism can be readily applied in the case of CcNiR since the electrons are supplied from the assisting hemes at the same time as protons are supplied through the inlet channel.…”

Section: Introductionmentioning

confidence: 99%

Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study

Bykov

Neese

2012

J Biol Inorg Chem

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Cytochrome c nitrite reductase catalyzes the six-electron, seven-proton reduction of nitrite to ammonia without release of any detectable reaction intermediate. This implies a unique flexibility of the active site combined with a finely tuned proton and electron delivery system. In the present work, we employed density functional theory to study the recharging of the active site with protons and electrons through the series of reaction intermediates based on nitrogen monoxide [Fe(II)-NO(+), Fe(II)-NO·, Fe(II)-NO(-), and Fe(II)-HNO]. The activation barriers for the various proton and electron transfer steps were estimated in the framework of Marcus theory. Using the barriers obtained, we simulated the kinetics of the reduction process. We found that the complex recharging process can be accomplished in two possible ways: either through two consecutive proton-coupled electron transfers (PCETs) or in the form of three consecutive elementary steps involving reduction, PCET, and protonation. Kinetic simulations revealed the recharging through two PCETs to be a means of overcoming the predicted deep energetic minimum that is calculated to occur at the stage of the Fe(II)-NO· intermediate. The radical transfer role for the active-site Tyr(218), as proposed in the literature, cannot be confirmed on the basis of our calculations. The role of the highly conserved calcium located in the direct proximity of the active site in proton delivery has also been studied. It was found to play an important role in the substrate conversion through the facilitation of the proton transfer steps.

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“…The quantity ΔŨ μν is defined to be ΔŨ μν ¼ ΔU μν þ k B T lnðQ II ∕Q I Þ, where ΔU μν is the energy difference between states ν and μ, and Q I and Q II are the vibrational partition functions of the reduced and oxidized solute complexes, respectively, in bulk solution. The quantities P μ , S μν , and ΔŨ μν depend on the proton donor-acceptor distance R. The effects of the proton donor-acceptor motion can be included by thermally averaging over the proton donor-acceptor distance (25)(26)(27):…”

Section: Resultsmentioning

confidence: 99%

Insights into proton-coupled electron transfer mechanisms of electrocatalytic H₂oxidation and production

Horvath

Fernandez

Soudackov

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

132

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The design of molecular electrocatalysts for H 2 oxidation and production is important for the development of alternative renewable energy sources that are abundant, inexpensive, and environmentally benign. Recently, nickel-based molecular electrocatalysts with pendant amines that act as proton relays for the nickel center were shown to effectively catalyze H 2 oxidation and production. We developed a quantum mechanical approach for studying protoncoupled electron transfer processes in these types of molecular electrocatalysts. This theoretical approach is applied to a nickelbased catalyst in which phosphorous atoms are directly bonded to the nickel center, and nitrogen atoms of the ligand rings act as proton relays. The catalytic step of interest involves electron transfer between the nickel complex and the electrode as well as intramolecular proton transfer between the nickel and nitrogen atoms. This process can occur sequentially, with either the electron or proton transferring first, or concertedly, with the electron and proton transferring simultaneously without a stable intermediate. The electrochemical rate constants are calculated as functions of overpotential for the concerted electron-proton transfer reaction and the two electron transfer reactions in the sequential mechanisms. Our calculations illustrate that the concerted electron-proton transfer standard rate constant will increase as the equilibrium distance between the nickel and nitrogen atoms decreases and as the pendant amines become more flexible to facilitate the contraction of this distance with a lower energy penalty. This approach identifies the favored mechanisms under various experimental conditions and provides insight into the impact of substituents on the nitrogen and phosphorous atoms.hydrogen evolution | heterogeneous catalysis | PCET E nvironmental and economic concerns about the use of fossil fuels have led to the development of new technologies that are more environmentally friendly but are also cost-effective alternatives to nonrenewable resources. An important example is the oxidation and production of H 2 for use in hydrogen-based fuel cells and functional storage devices for the energy harvested from solar, wind, and other environmentally benign processes (1). While efficient methods have been developed for H 2 oxidation and production, platinum catalysts are neither abundant enough nor cost effective enough for mass production and large-scale use (2). On the other hand, H 2 oxidation and production occur naturally in the hydrogenase class of enzymes. These biological systems could serve as the key to the design of effective synthetic catalysts because the catalytic center of the enzyme is comprised of iron and/or nickel, both of which are highly abundant and inexpensive metals.The presence of an amine ligand in the second coordination sphere is thought to contribute significantly to the high catalytic activity of the [FeFe] hydrogenase enzymes. These pendant amines may assist in the heterolytic cleavage of H 2 by facilitati...

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Theoretical studies of proton-coupled electron transfer: Models and concepts relevant to bioenergetics

Cited by 82 publications

References 67 publications

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study

Insights into proton-coupled electron transfer mechanisms of electrocatalytic H₂oxidation and production

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Theoretical studies of proton-coupled electron transfer: Models and concepts relevant to bioenergetics

Cited by 82 publications

References 67 publications

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

Reductive activation of the heme iron–nitrosyl intermediate in the reaction mechanism of cytochrome c nitrite reductase: a theoretical study

Insights into proton-coupled electron transfer mechanisms of electrocatalytic H2oxidation and production

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Insights into proton-coupled electron transfer mechanisms of electrocatalytic H₂oxidation and production