Distance Dependence of Electron Transfer in DNA:  The Role of the Reorganization Energy and Free Energy

Tavernier, H. L.; Fayer, M. D.

doi:10.1021/jp001362w

Cited by 126 publications

(152 citation statements)

References 47 publications

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“…This model appears to be rather crude, and it is not supported by the results of moleculardynamics simulations of DNA 18,19 or even by the more extended electrostatic models using a heterogeneous dielectric medium. 2,[6][7][8] As expected, the calculation carried out using 0 = 1 = 2 = 1.0 leads to quite delocalized hole states in ͑GC͒ n . For instance, we obtain that in ͑GC͒ 5 q 0 = 0.476, q ±1 = 0.251, q ±2 = 0.011.…”

Section: Resultssupporting

confidence: 76%

“…For instance, to estimate the reorganization energy for hole transfer in DNA, one applied the Poisson equation solver 6 to heterogeneous dielectric models consisting of several different dielectric zones surrounding the hole donor and acceptor sites. 2,5,7,8 The calculation results are quite different because of uncertainties concerning the construction of the dielectric model. 8 The surrounding polar medium affects also the delocalization of an electron hole in DNA over adjacent base pairs.…”

Section: Introductionmentioning

confidence: 99%

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Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects

Voityuk

2005

The Journal of Chemical Physics

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We include solvation effects in tight-binding Hamiltonians for hole states in DNA. The corresponding linear-response parameters are derived from accurate estimates of solvation energy calculated for several hole charge distributions in DNA stacks. Two models are considered: ͑A͒ the correction to a diagonal Hamiltonian matrix element depends only on the charge localized on the corresponding site and ͑B͒ in addition to this term, the reaction field due to adjacent base pairs is accounted for. We show that both schemes give very similar results. The effects of the polar medium on the hole distribution in DNA are studied. We conclude that the effects of polar surroundings essentially suppress charge delocalization in DNA, and hole states in ͑GC͒ n sequences are localized on individual guanines.

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Section: Resultssupporting

confidence: 76%

Section: Introductionmentioning

confidence: 99%

Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects

Voityuk

2005

The Journal of Chemical Physics

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“…The reorganization energy for DNA hole transfer is expected to increase with distance, and this dependence has been probed theoretically by several groups (19,(36)(37)(38). The reorganization energies at a given distance for the four families of data in Fig.…”

Section: Interpretation Of the Experimental Resultsmentioning

confidence: 88%

Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA

Lewis

Liu²,

Weigel

et al. 2002

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

164

168

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Electron transfer (ET) processes in DNA are of current interest because of their involvement in oxidative strand cleavage reactions and their relevance to the development of molecular electronics. Two mechanisms have been identified for ET in DNA, a single-step tunneling process and a multistep charge-hopping process. The dynamics of tunneling reactions depend on both the distance between the electron donor and acceptor and the nature of the molecular bridge separating the donor and acceptor. In the case of protein and alkane bridges, the distance dependence is not strongly dependent on the properties of the donor and acceptor. In contrast, we show here that the distance decay of DNA ET rates varies markedly with the energetics of the donor and acceptor relative to the bridge. Specifically, we find that an increase in the energy of the bridge states by 0.25 eV (1 eV ‫؍‬ 1.602 ؋ 10 ؊19 J) relative to the donor and acceptor energies for photochemical oxidation of nucleotides, without changing the reaction free energy, results in an increase in the characteristic exponential distance decay constant for the ET rates from 0.71 to 1.1 Å ؊1 . These results show that, in the small tunneling energy gap regime of DNA ET, the distance dependence is not universal; it varies strongly with the tunneling energy gap. These DNA ET reactions fill a ''missing link'' or transition regime between the large barrier (rapidly decaying) tunneling regime and the (slowly decaying) hopping regime in the general theory of bridge-mediated ET processes. E lectron transfer (ET) processes in which an electron donor and acceptor are separated by a molecular spacer or bridge (D-B-A systems) are encountered widely in biological systems (proteins and DNA; refs. 1-4) and molecular wires (5-7). The dynamics of such processes are known to depend, inter alia, on the length and nature of the bridge (8, 9). The dynamics of single-step photoinduced ET in D-B-A systems, a process referred to as tunneling, is generally found to display an exponential dependence on the D-A distance as described by Eq. 1,where k o is a temperature-dependent prefactor, r da is the D-A separation, and ␤ characterizes the steepness of the experimental distance dependence are observed for bridges consisting of conjugated polyenes (5, 12), which probably arise from delocalization of the donor and acceptor states onto the bridge. DNA systems apparently are unique in that a wide range of values of ␤ (0.1-1.5 Å Ϫ1 ) have been observed for similar duplex DNA bridge structures (13,14). The very smallest ␤ values for DNA ET may arise from an alternative ET mechanism, multistep hole hopping (15-18). The distance dependence of the reorganization energy may enhance some of the observed ␤ values (19). A question in DNA ET is how much the donor and acceptor energetics can influence the ␤ value by tuning the electronic coupling strength. By making donor-acceptor modifications that do not change the ETactivation free energies, we find that ␤ values can be changed by more than 50%. We interpret...

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“…However, the investigation of the transfer parameters, such as orbital overlapping [9,10,17] and activation energy for charge migration i.e. the IP and the reorganization energy [8,9,10,17,18,19,21], have been performed mostly for the nucleobases or/and base pairs.…”

Section: Introductionmentioning

confidence: 99%

Energetics of the hole transfer in DNA duplex oligomers

Berashevich

Chakraborty

2007

Chemical Physics Letters

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We report on our calculations of the inner-sphere reorganization energy and the interaction of the π orbitals within DNA oligomers. The exponential decrease of the electronic coupling between the highest and second highest occupied base orbitals of the intrastrand nucleobases in the (A-T)n and (G-C)n oligomers have been found with an increase of the sequence number n in the DNA structure. We conclude that for realistic estimation of the electronic coupling values between the nucleobases within the DNA molecule, a DNA chain containing at least four base pairs is required. We estimate the geometry relaxation of the base pairs within the (A-T)n and (G-C)n oligomers (n = 1 − 6) due to their oxidation. The decrease of the inner-sphere reorganization energy with elongation of the oligomer structure participating in the oxidation process have been observed. The maximum degree of geometry relaxation of the nucleobase structures and correspondingly the higher charge density in the oxidized state are found to be located close to the oligomer center.

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Distance Dependence of Electron Transfer in DNA: The Role of the Reorganization Energy and Free Energy

Cited by 126 publications

References 47 publications

Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects

Charge transfer in DNA: Hole charge is confined to a single base pair due to solvation effects

Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA

Energetics of the hole transfer in DNA duplex oligomers

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