Direct Simulation of Electron Transfer Reactions in DNA Radical Cations

Steinbrecher, Thomas; Koslowski, Thorsten; Case, David A.

doi:10.1021/jp8076134

Cited by 52 publications

(98 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In comparison, assuming throughspace coupling between amino acid side chains at slightly smaller separation distance in the protein E. coli DNA photolyase or between neighboring nucleobases in DNA radical cations yielded ET rates in good agreement to experiment in recent studies. 52,54,122,140,141 With direct ET between donor and acceptor ruled out, future studies of the system can focus on the role of the medium between two charge carrying side chains in more detail than the empirical pathway model allows. The peptide backbone may mediate charge movement along the PPII helix or even allow transient localization, and explicitly including these effects could lead to higher predicted transfer rates.…”

Section: ■ Discussionmentioning

confidence: 99%

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

et al. 2012

View full text Add to dashboard Cite

Charge transfer within and between biomolecules remains a highly active field of biophysics. Due to the complexities of real systems, model compounds are a useful alternative to study the mechanistic fundamentals of charge transfer. In recent years, such model experiments have been underpinned by molecular simulation methods as well. In this work, we study electron hole transfer in helical model peptides by means of molecular dynamics simulations. A theoretical framework to extract Marcus parameters of charge transfer from simulations is presented. We find that the peptides form stable helical structures with sequence dependent small deviations from ideal PPII helices. We identify direct exposure of charged side chains to solvent as a cause of high reorganization energies, significantly larger than typical for electron transfer in proteins. This, together with small direct couplings, makes long-range superexchange electron transport in this system very slow. In good agreement with experiment, direct transfer between the terminal amino acid side chains can be dicounted in favor of a two-step hopping process if appropriate bridging groups exist. ■ INTRODUCTIONCharge transfer is a fundamental phenomenon in physical chemistry, enjoying strong and consistent scientific interest for more than fifty years. 1 Understanding charge transfer in complex and flexible biomolecules is crucial for a huge variety of processes, from cellular respiration and photosynthesis to DNA damage and repair. 2−4 Describing it accurately has turned out to be particularly challenging, both to experimentalists and theoreticians. Biochemical charge transfer involves the directed movement of electrons over large distances (multiple nanometers) through macromolecules, typically proteins or large heterogeneous multiprotein assemblies. These processes involve dynamical changes that occur on a time scale spanning multiple orders of magnitude, from subpicosecond changes in electronic structure to microsecond or even slower conformational changes. Only recently has the complicated interplay between atomic structural fluctuations and electron dynamics become a focus for charge transfer studies in biochemical systems, 5−9 building onto earlier work on model systems. 10−15 This fact, combined with the large system dimensions and difficult experimental conditions, explains why many open questions on electron transfer (ET) in biomolecules remain. Therefore, simpler model systems to study some aspects of ET have gained popularity, and theoretical models based on computer simulations have become important tools to help interpret experiments and gain a better understanding of the structure and function of the involved molecules. 16−22 An important model system in the study of charge transfer processes has always been peptide systems. Extensive experimental work was done by Isied et al., who have studied ET over distances of 8−32 Å via spectroscopical techniques and determined the properties of polyproline II helices as ET bridges. 27−34 This wo...

show abstract

Section: ■ Discussionmentioning

confidence: 99%

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

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Generally, the quantum delocalizing effect competes with the localizing forces of the solvent [56]. A certain consensus of a spatially localized hole has been reached recently in the theoretical and computational community [39,40,104,105]. It is possible to understand how peculiar the question of delocalization is by noticing the qualitative change over time of the results reported by several researchers.…”

Section: Rsifroyalsocietypublishingorg J R Soc Interface 10: 20130415mentioning

confidence: 99%

“…The response of the environment was taken into account in the DFT-based work in Mantz et al [37], but the observation of a localized hole was actually forced by the biased simulation protocol. So, the only work from that time which involved most of the interactions between the excess charge and the environment seems to be that in the study by Steinbrecher et al [40], in which a parametrized model of the electronic structure was used, making nanosecond simulations possible. Still, the model was not quite correct, as it left out the description of inner sphere reorganization.…”

Section: Rsifroyalsocietypublishingorg J R Soc Interface 10: 20130415mentioning

confidence: 99%

See 1 more Smart Citation

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

Kubař

Elstner

2013

J. R. Soc. Interface.

130

View full text Add to dashboard Cite

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.

show abstract

“…Steinbrecher et al reported direct simulations of charge migration in DNA radical cations [37]. They used a hybrid Quantum Chemistry/Molecular Mechanics (QM/MM) energy in which the p electrons of the purines were treated with a tight binding Hamiltonian, including a screened Coulomb potential to account for the effect of the environment (other DNA atoms and water).…”

Section: Direct Simulation Of Electron Transfersmentioning

confidence: 99%

Progress and challenges in simulating and understanding electron transfer in proteins

Lande

Gillet

Chen

et al. 2015

Archives of Biochemistry and Biophysics

View full text Add to dashboard Cite

Direct Simulation of Electron Transfer Reactions in DNA Radical Cations

Cited by 52 publications

References 47 publications

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

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

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

Progress and challenges in simulating and understanding electron transfer in proteins

Contact Info

Product

Resources

About