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DUGi: Item | DUGiDocs - Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

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

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

© Journal of Chemical Physics, 2008, vol. 128, núm. 11

American Institute of Physics

Author: Voityuk, Alexander A.
Date: 2008
Abstract: The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA
Format: application/pdf
Citation: Voityuk, A.A. (2008). Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study. Journal of Chemical Physics, 128 (11), 115101. Recuperat 28 març 2011,a http://link.aip.org/link/doi/10.1063/1.2841421
ISSN: 0021-9606 (versió paper)
1089-7690 (versió electrònica)
Document access: http://hdl.handle.net/10256/3315
Language: eng
Publisher: American Institute of Physics
Collection: Reproducció digital del document publicat a: http://dx.doi.org/10.1063/1.2841421
Articles publicats (D-Q)
Is part of: © Journal of Chemical Physics, 2008, vol. 128, núm. 11
Rights: Tots els drets reservats
Subject: ADN
Biologia molecular
Dinàmica molecular
Electrònica molecular
Quàntums, Teoria dels
Transferència de càrrega
Charge transfer
DNA
Molecular biology
Molecular dynamics
Molecular electronics
Quantum theory
Title: Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study
Type: info:eu-repo/semantics/article
Repository: DUGiDocs

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