title: Calculations of the exciton coupling elements between the DNA bases using the transition density cube method.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Houston, Houston, Texas 77204, USA. aczader@uh.edu
authors.forename: Arkadiusz
authors.initials: A
authors.lastname: Czader
authors.forename: Eric R
authors.initials: ER
authors.lastname: Bittner
mesh_terms: D001482:Base Composition; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004735:Energy Transfer; D007202:Indicators and Reagents / Q000737:chemistry; D008956:Models, Chemical; D015233:Models, Statistical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D013053:Spectrophotometry; D013816:Thermodynamics; D014466:Ultraviolet Rays
chemical_list: D007202:Indicators and Reagents; D004247:DNA