Intra-molecular electron transfer and electric conductance via sequential hopping: Unified theoretical description

Berlin, Yu. A.; Ratner, Mark A.

doi:10.1016/j.radphyschem.2005.04.004

Cited by 63 publications

(91 citation statements)

References 58 publications

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“…In addition, a number of configurations with shiftϾ 2 Å were generated. Figure 5 presents the parameter values of stack configurations where the electronic coupling squared for HT between G:C pairs is at least an order of magnitude larger than the average value ͗V 2 ͘ = 0.0065 eV 2 found for the 15 ns trajectory of G 15 . As expected, there are many configurations with small twist angles ͑see diagrams twist= 0°and twist = 10°in Fig.…”

Section: Screening Of Stack Conformationmentioning

confidence: 87%

“…Let us consider fluctuations of V 2 between the G 7 and G 8 base pairs computed for the 15 ns MD trajectory of the duplex G 15 . To exclude end effects, we consider the coupling of hole states localized on the middle BPs of the oligonucleotide.…”

Section: Electronic Couplings Computed For MD Trajectory Of G 15mentioning

confidence: 99%

“…Using the approach suggested by Berlin and Ratner, 15 we can estimate the electrical conduction of G 15 stacks of different conformations. The following model has been used: ͑1͒ all site energies and intersite couplings are assumed to be identical; ͑2͒ the reorganization energy is taken to be 0.7 eV, in line with experimental estimates; 45 ͑3͒ the gap between the bridge energy and the Fermi level of the electrode is set to 0.1 eV.…”

Section: Estimation Of Electrical Conductance Of the G 15 Duplexmentioning

confidence: 99%

“…9 High-level calculations ͑CAS-PT2͒ show that an excess charge in stacks is quite localized on single nucleobases, 10 and therefore, hopping mechanism for hole transfer ͑HT͒ can be applied. 11,12 It has been shown that the electrical conduction of single molecules is closely related to the electron transfer rate [13][14][15] being determined by electronic coupling and nuclear FranckCondon factors. 16,17 The efficiency of hole transport depends both on the structure of DNA sequence and mutual orientation of base pairs ͑BPs͒, and its environment.…”

Section: Introductionmentioning

confidence: 99%

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Conformations of poly{G}–poly{C} π stacks with high hole mobility

Voityuk

2008

The Journal of Chemical Physics

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Charge transfer properties of DNA depend strongly on the stack conformation. In the present paper, we identify conformations of homogeneous poly-͕G͖-poly-͕C͖ stacks that should exhibit high charge mobility. Two different computational approaches were applied. First, we calculated the electronic coupling squared, V 2 , between adjacent base pairs for all 1 ps snapshots extracted from 15 ns molecular dynamics trajectory of the duplex G 15 . The average value of the coupling squared ͗V 2 ͘ is found to be 0.0065 eV 2 . Then we analyze the base-pair and step parameters of the configurations in which V 2 is at least an order of magnitude larger than ͗V 2 ͘. To obtain more consistent data, ϳ65 000 configurations of the ͑G:C͒ 2 stack were built using systematic screening of the step parameters shift, slide, and twist. We show that undertwisted structures ͑twistϽ 20°͒ are of special interest, because the stack conformations with strong electronic couplings are found for a wide range of slide and shift. Although effective hole transfer can also occur in configurations with twist= 30°and 35°, large mutual displacements of neighboring base pairs are required for that. Overtwisted conformation ͑twistജ 38°͒ seems to be of limited interest in the context of effective hole transfer. The results may be helpful in the search for DNA based elements for nanoelectronics.

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Section: Screening Of Stack Conformationmentioning

confidence: 87%

Section: Electronic Couplings Computed For MD Trajectory Of G 15mentioning

confidence: 99%

Section: Estimation Of Electrical Conductance Of the G 15 Duplexmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Conformations of poly{G}–poly{C} π stacks with high hole mobility

Voityuk

2008

The Journal of Chemical Physics

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“…Kinetic constants in the hopping regime, instead, follow a power law decay. [50][51][52][53] In this work, we calculate effective donor-acceptor hole transfer couplings and fit them to Eq. (3).…”

Section: Introductionmentioning

confidence: 99%

Quantifying Environmental Effects on the Decay of Hole Transfer Couplings in Biosystems

Ramos

Pavanello

2014

J. Chem. Theory Comput.

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In the past two decades, many research groups worldwide have tried to understand and categorize simple regimes in the charge transfer of such biological systems as DNA. Theoretically speaking, the lack of exact theories for electron-nuclear dynamics on one side, and poor quality of the parameters needed by model Hamiltonians and nonadiabatic dynamics alike (such as couplings and site energies) on the other, are the two main difficulties for an appropriate description of the charge transfer phenomena. In this work, we present an application of a previously benchmarked and linear-scaling subsystem DFT method for the calculation of couplings, site energies and superexchange decay factors (β ) of several biological donor-acceptor dyads, as well as double stranded DNA oligomers comprised of up to 5 base pairs. The calculations are all-electron, and provide a clear view of the role of the environment on superexchange couplings in DNA -they follow experimental trends and confirm previous semiempirical calculations. The subsystem DFT method is proven to be an excellent tool for long-range, bridge-mediated coupling and site energy calculations of embedded molecular systems.

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