Charge Transfer in Model Peptides: Obtaining Marcus Parameters from Molecular Simulation

Heck, Alexander; Woiczikowski, P. Benjamin; Kubař, Tomáš; Giese, Bernd; Elstner, Marcus; Steinbrecher, Thomas

doi:10.1021/jp2086297

Cited by 38 publications

(47 citation statements)

References 139 publications

(232 reference statements)

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“…Concerning the fragments that are involved in the transfer, it may be necessary to consider not only the amino acid side chains but also the p-electron systems of the peptide bonds [128], and this represents another technical challenge because of the difficult definition of the QM/MM boundary. Our preliminary study of hole transfer in these peptides focused on the basic characterization of the transfer and the calculation of parameters of the Marcus theory [129]. An interesting result is the outer sphere RE for the sequential transfer 1 !…”

Section: Hole Transfer In Peptidesmentioning

confidence: 99%

A hybrid approach to simulation of electron transfer in complex molecular systems

Kubař

Elstner

2013

J. R. Soc. Interface.

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130

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Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors.

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Section: Hole Transfer In Peptidesmentioning

confidence: 99%

A hybrid approach to simulation of electron transfer in complex molecular systems

Kubař

Elstner

2013

J. R. Soc. Interface.

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130

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“…If water is allowed to enter the internal space of the protein, it, being unscreened in confined regions, provides a highly solvating medium. The reorganization energies for redox reactions in aqueous solutions are much higher, at the level of eV (or even higher 30 ). In addition, water can trap the charge by solvating a certain redox cofactor.…”

Section: Introductionmentioning

confidence: 99%

Electron-transfer chain in respiratory complex I

Martin

Matyushov

2017

Sci Rep

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Complex I is a part of the respiration energy chain converting the redox energy into the cross-membrane proton gradient. The electron-transfer chain of iron-sulfur cofactors within the water-soluble peripheral part of the complex is responsible for the delivery of electrons to the proton pumping subunit. The protein is porous to water penetration and the hydration level of the cofactors changes when the electron is transferred along the chain. High reaction barriers and trapping of the electrons at the iron-sulfur cofactors are prevented by the combination of intense electrostatic noise produced by the protein-water interface with the high density of quantum states in the iron-sulfur clusters caused by spin interactions between paramagnetic iron atoms. The combination of these factors substantially lowers the activation barrier for electron transfer compared to the prediction of the Marcus theory, bringing the rate to the experimentally established range. The unique role of iron-sulfur clusters as electron-transfer cofactors is in merging protein-water fluctuations with quantum-state multiplicity to allow low activation barriers and robust operation. Water plays a vital role in electron transport energetics by electrowetting the cofactors in the chain upon arrival of the electron. A general property of a protein is to violate the fluctuation-dissipation relation through nonergodic sampling of its landscape. High functional efficiency of redox enzymes is a direct consequence of nonergodicity.

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“…This can have several reasons: First, the calculated λ values 44 are in the order of 2 eV, which is very large compared to values found for proteins, 86 and determine the slow computed rates. It is likely that the computational approaches to estimate λ tend to overestimate its value.…”

Section: ■ Discussion and Conclusionmentioning

confidence: 93%

“…44 In that work, however, we only could study the direct CT between donor and acceptor neglecting the bridge within the FO approach, other pathways have been investigated using an empirical pathway model. Now, we also include the peptide backbone into the FO description.…”

Section: ■ Introductionmentioning

confidence: 99%

Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals

et al. 2014

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Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult to access experimentally, different modeling strategies have been successfully applied to study these processes in the past. These can be based on a simple empirical pathway model, efficient tight binding type atomic orbital Hamiltonians or ab initio and density functional calculations. An interesting strategy, which allows an efficient calculations of charge transfer parameters, is based on a fragmentation of the system into functional units. While this works well for systems like DNA, where the charge transfer pathway is naturally divided into distinct molecular fragments, this is less obvious for charge transfer along peptide and protein backbones. In this work, we develop and access a strategy for an effective fragmentation approach, which allows one to compute electronic couplings for large systems along nanosecond time scale molecular dynamics trajectories. The new methodology is applied to a solvated peptide, for which charge transfer properties have been studied recently using an empirical pathway model. As could be expected, dynamical effects turn out to be important, which emphasizes the importance of using effective quantum approaches which allow for sufficient sampling. However, the computed rates are orders of magnitude smaller than experimentally determined, which indicates the shortcomings of present modeling approaches. ■ INTRODUCTIONCharge transfer (CT) in biomolecules is a fundamental process that has been subject of intense scientific study for more than 50 years.1−4 It is highly relevant in the understanding of functional as well as pathological cellular processes, ranging from respiration and photosynthesis to DNA damage and repair.5−7 Our theoretical understanding of molecular CT has increased tremendously since the pioneering studies by Marcus and others, 8−16 but a complete detailed description on the molecular level remains elusive.Several approaches exist to compute the electronic couplings, ranging from empirical pathway models, 17−19 over tight-binding based 20,21 to ab initio or density functional calculations. 22−25Most of these quantum approaches are based on an atomic orbital description to compute charge transfer parameters, which becomes very costly for large systems, even when using extended Huckel or tight-binding Hamiltonians, because the computer time scales cubic with the number of atomic orbitals involved. An additional computational challange is the need for sampling along MD trajectories. The biochemical transfer of electrons over many nanometers through large protein assemblies involves dynamical changes that occur on time scales ranging from subpicosecond changes in electronic structure to microsecond or even slower conformational changes. Especially the interplay between the atomic structural fluctuations and the electron dynamics has bec...

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Charge Transfer in Model Peptides: Obtaining Marcus Parameters from Molecular Simulation

Cited by 38 publications

References 139 publications

A hybrid approach to simulation of electron transfer in complex molecular systems

A hybrid approach to simulation of electron transfer in complex molecular systems

Electron-transfer chain in respiratory complex I

Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals

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