Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study

Voityuk, Alexander A.

doi:10.1063/1.2841421

Cited by 89 publications

(126 citation statements)

References 39 publications

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“…[31][32][33] The effect of polarization by the molecular environment surrounding a nucleobase on its ionization potential has been reported to be up to 0.4 eV. 33 Thus, accounting for these environmental effects is a major component of the modeling of charge transport in biological systems.…”

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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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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“…10 Keeping in mind the wide fluctuations of this coupling around its mean value, 5-9 the adopted t 0 can be regarded as a quite representative one, small enough as compared to the optimal transfer integral value t ‫ء‬ = 0.37 eV establishing the maximum physically acceptable value for this parameter. We have checked that the width of the different bands in the electronic spectrum linearly scales with the transfer integral value within the interval ͗t͘ Յ t Յ t ‫ء‬ .…”

Section: Twist Phonon Coupling Effects On the Energy Spectramentioning

confidence: 99%

“…5 Following this approach, a systematic study of those stack conformations leading to higher mobilities has been performed for several DNA duplex oligomers. 10 However, the analysis of the obtained molecular-dynamics snapshots does not provide a clear enough picture on the spatial stack structures showing the best hole mobility. Accordingly, some complementary approaches would be welcome in order to get a more detailed picture of the optimal DNA stack configurations.…”

Section: Introductionmentioning

confidence: 99%

“…9 In fact, recent studies have revealed that transfer integral values are extremely sensitive to conformational fluctuations, so that the transport efficiency calculated ignoring dynamical effects can be underestimated by several orders of magnitude. 5,10 Thus, depending on the DNA sequence composition, its length and effective temperature, reported transfer integral values can vary over a relatively broad interval, ranging from t = 0.01 to t = 0.4 eV. 6,[11][12][13][14][15][16][17][18][19][20][21] These figures imply charge migration time scales within the range ប / t Ӎ 2 -66 fs for coherent tunneling.…”

Section: Introductionmentioning

confidence: 99%

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π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

Maciá

2009

Phys. Rev. B

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The presence of synchronized, collective twist motions of the Watson-Crick base pairs in DNA duplexes ͑helicoidal standing waves͒ can efficiently enhance the -orbital overlapping between nonconsecutive base pairs via a long-range, phonon-correlated tunneling effect. The resulting structural patterns are described within the framework of dynamical phyllotaxis, providing a realistic treatment which takes into account both the intrinsic three-dimensional, helicoidal geometry of DNA, and the coupling between the electronic degrees of freedom and double-helix DNA molecular dynamics at low frequencies. The main features of the resulting electronic band structures are discussed for several resonance frequencies of interest, highlighting the possible biophysical implications of the obtained results.

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“…The INDO/s method has been used in the past to calculate the electronic properties of DNA, as well as those of carbon nanotubes [50,[67][68][69][70][71][72], and showed accuracy comparable to that of higher-level quantum calculations [65,73,74]. The INDO/s electronic structure was calculated for each of the 6200 frames of the 3.1 ns molecular dynamics (MD) simulation [40] of two intertwined (GT) 30 DNA chains wrapped around a 70 Å-long fragment of (6,5) SWNT (see Fig.…”

Section: Theory and Simulationsmentioning

confidence: 99%

Two-color spectroscopy of UV excited ssDNA complex with a single-wall nanotube photoluminescence probe: Fast relaxation by nucleobase autoionization mechanism

et al. 2016

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SWNT ssDNADNA is capable to recover after absorbing ultraviolet (UV) radiation, for example, by autoionization (AI). Singlewall carbon nanotube (SWNT) two-color photoluminescence spectroscopy was combined with quantum mechanical calculations to explain the AI in self-assembled complexes of DNA wrapped around SWNT. DNA autoionization is a fundamental process wherein UV-photoexcited nucleobases dissipate energy by charge transfer to the environment without undergoing chemical damage. Here, single-wall carbon nanotubes (SWNT) are explored as a photoluminescent reporter for studying the mechanism and rates of DNA autoionization. Two-color photoluminescence spectroscopy allows separate photoexcitation of the DNA and the SWNTs in the UV and visible range, respectively. A strong SWNT photoluminescence quenching is observed when the UV pump is resonant with the DNA absorption, consistent with charge transfer from the excited states of the DNA to the SWNT. Semiempirical calculations of the DNA-SWNT electronic structure, combined with a Green's function theory for charge transfer, show a 20 fs autoionization rate, dominated by the hole transfer. Rate-equation analysis of the spectroscopy data confirms that the quenching rate is limited by the thermalization of the free charge carriers transferred to the nanotube reservoir. The developed approach has a great potential for monitoring DNA excitation, autoionization, and chemical damage both in vivo and in vitro arXiv:1512.00710v1 [cond-mat.mes-hall] 2 Dec 2015 2

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Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study

Cited by 89 publications

References 39 publications

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

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

π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

Two-color spectroscopy of UV excited ssDNA complex with a single-wall nanotube photoluminescence probe: Fast relaxation by nucleobase autoionization mechanism

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