Calculations of the Exciton Coupling Elements Between the DNA Bases Using the Transition Density Cube Method

TL;DR

This paper compares the transition density cube method and ideal dipole approximation for calculating exciton coupling in DNA, showing that IDA overestimates coupling at small distances and emphasizing the importance of structural fluctuations.

Contribution

It introduces the use of transition density cubes for more accurate exciton coupling calculations in DNA and highlights the limitations of the ideal dipole approximation.

Findings

Transition density cube method yields different coupling values than IDA.

IDA significantly overestimates coupling at small inter-chromophore distances.

Structural fluctuations affect exciton coupling calculations.

Abstract

Excited states of the of the double-stranded DNA model (A)$_{12}\cdot$(T)_{12} were calculated in the framework of the 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 $\pi\pi^{*}$ excitations of the individual nucleobases obtained from TDDFT calculations. The values of the coupling calculated with the transition density cubes (TDC) and ideal-dipole approximation (IDA) methods were found significantly different for the small inter-chromophore distances. It was shown that the IDA overestimates the coupling significantly. The effects of the structural fluctuations were incorporated by averaging the properties of the excited states over a large number of conformations obtained from the MD simulations.