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Calculations of the exciton coupling elements between the DNA bases using the transition density cube method

J. Chem. Phys. 128, 035101 (2008); doi:10.1063/1.2821384

Published 15 January 2008

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Arkadiusz Czader
Department of Chemistry, University of Houston, Houston, Texas 77204, USA

Eric R. Bittner
Department of Chemistry, University of Houston, Houston, Texas 77204, USA and Cavendish Laboratory, Madingley Road, Cambridge CB3 0HE, United Kingdom
Excited states of the double-stranded DNA model (A)12·(T)12 were calculated in the framework of the Frenkel exciton theory. The off-diagonal elements of the exciton matrix were calculated using the transition densities and ideal dipole approximation associated with the lowest energy pipi* excitations of the individual nucleobases as obtained from time-dependent density functional theory calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal dipole approximation (IDA) methods were found to be significantly different for the small interchromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of structural fluctuations of the DNA chain on the magnitude of dipolar coupling were also found to be very significant. The difference between the maximum and minimum values was as large as 1000 and 300  cm−1 for the IDA and TDC methods, respectively. To account for these effects, the properties of the excited states were averaged over a large number of conformations obtained from the molecular dynamics simulations. Our calculations using the TDC method indicate that the absorption of the UV light creates exciton states carrying the majority of the oscillator strength that are delocalized over at least six DNA bases. Upon relaxation, the excitation states localize over at least four contiguous bases. ©2008 American Institute of Physics
History: Received 9 July 2007; accepted 12 November 2007; published 15 January 2008
Permalink: http://link.aip.org/link/?JCPSA6/128/035101/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.10.Tf
    Molecular dynamics simulation (biological/medical physics)
  • 87.14.gk
    DNA
  • 87.15.ap
    Molecular dynamics simulation in molecular biophysics
  • 87.15.B-
    Structure of biomolecules
  • YEAR: 2008

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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