Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime

Tesar, Sarah L.; Leveritt, John M.; Kurnosov, Arkady A.; Burin, Alexander L.

doi:10.1016/j.chemphys.2011.11.017

Cited by 11 publications

(25 citation statements)

References 47 publications

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“…Slower time constants are observed for DNA1 , 2 , 4 , and 5 , when the temperature is decreased. In addition, the retrieved activation energy matches the experimental results of the temperature dependence for charge‐hopping rates between adjacent CG pairs, and can be well described by an Arrhenius‐type law with an activation energy of 0.12 eV 33. 34 One may argue that the determination of an activation energy by only two different temperatures is not meaningful.…”

Section: Resultssupporting

confidence: 62%

Fluorescence Quenching over Short Range in a Donor‐DNA‐Acceptor System

et al. 2013

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A new donor-DNA-acceptor system has been synthesized containing Nile red-modified 2'-deoxyuridine as charge donor and 6-N,N-dimethylaminopyrene-modified 2'-deoxyuridine as acceptor to investigate the charge transfer in DNA duplexes using fluorescence spectroscopy and time-resolved femtosecond pump-probe techniques. Fluorescence quenching experiments revealed that the quenching efficiency of Nile red depends on two components: 1) the presence of a charge acceptor and 2) the number of intervening CG and AT base pairs between donor and acceptor. Surprisingly, the quenching efficiency of two base pairs (73% for CG and the same for AT) is higher than that for one base pair (68% for CG and 37% for AT), while at a separation of three base pairs less than 10% quenching is observed. A comparison with the results of time-resolved measurements revealed a correlation between quenching efficiency and the first ultrafast time constant suggesting that quenching proceeds via a charge transfer from the donor to the acceptor. All transients are satisfactorily described with two decays: a rapid charge transfer with 600 fs (∼10(12) s(-1)) that depends strongly and in a non-linear fashion on the distance between donor and acceptor, and a slower time constant of a few picoseconds (∼10(11) s(-1)) with weak distance dependence. A third time constant on a nanosecond time scale represents the fluorescence lifetime of the donor molecule. According to these results and time-dependent density functional theory (TDDFT) calculations a combination of single-step superexchange and multistep hopping mechanisms can be proposed for this short-range charge transfer. Furthermore, significantly less quenching efficiency and slower charge transfer rates at very short distances indicate that the direct interaction between donor and acceptor leads to a local structural distortion of DNA duplexes which may provide some uncertainty in identifying the charge transfer rates in short-range systems.

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Section: Resultssupporting

confidence: 62%

Fluorescence Quenching over Short Range in a Donor‐DNA‐Acceptor System

et al. 2013

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“…As found recently [23], the rearrangement of molecular geometry caused by the change of the charge state may occur via tunnelling-an exclusively QM mechanism. If that is the case then the usual classical way of calculating l i as mentioned earlier would yield values overestimated by a factor of as much as 2.…”

Section: Intra-fragment Interactionsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

“…1 (iii) The mechanism of transfer is known (adiabatic or non-adiabatic, solvent-controlled, etc.). A good indicator may be the relation of V and l [35], although the distinction may not always be easy to make use of [23]. An alternative solution is to perform an unbiased simulation of ET using a non-adiabatic MD scheme and high-level electronic structure calculations [36], yet such methods are limited to several tens of atoms and time intervals of up to a picosecond.…”

Section: Introductionmentioning

confidence: 99%

“…A rather accurate estimation of these parameters is required because of their appearance in the argument of an exponential, and the RE is particularly challenging to determine. It can be decomposed into two parts: the inner sphere RE l i , which is also sensitive to quantum effects [23], and the solvent contribution to the outer sphere RE l s , which can be calculated with classical MD simulations [24][25][26][27]; the effects of several structural and dynamic factors on l s have been discussed previously [28,29].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Kubař

Elstner

2013

J. R. Soc. Interface.

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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DNA as a Molecular Wire: Distance and Sequence Dependence

2013

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Functional nanowires and nanoelectronics are sought for their use in next generation integrated circuits, but several challenges limit the use of most nanoscale devices on large scales. DNA has great potential for use as a molecular wire due to high yield synthesis, near-unity purification, and nanoscale self-organization. Nonetheless, a thorough understanding of ground state DNA charge transport (CT) in electronic configurations under biologically relevant conditions, where the fully base-paired, double-helical structure is preserved, is lacking. Here, we explore the fundamentals of CT through double-stranded DNA monolayers on gold by assessing 17 base pair bridges at discrete points with a redox active probe conjugated to a modified thymine. This assessment is performed under temperature-controlled and biologically relevant conditions with cyclic and square wave voltammetry, and redox peaks are analyzed to assess transfer rate and yield. We demonstrate that the yield of transport is strongly tied to the stability of the duplex, linearly correlating with the melting temperature. Transfer rate is found to be temperature-activated and to follow an inverse distance dependence, consistent with a hopping mechanism of transport. These results establish the governing factors of charge transfer speed and throughput in DNA molecular wires for device configurations, guiding subsequent application for nanoscale electronics.

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Temperature dependence for the rate of hole transfer in DNA: Nonadiabatic regime

Cited by 11 publications

References 47 publications

Fluorescence Quenching over Short Range in a Donor‐DNA‐Acceptor System

Fluorescence Quenching over Short Range in a Donor‐DNA‐Acceptor System

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

DNA as a Molecular Wire: Distance and Sequence Dependence

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