Computational Modeling of Dyes for Excitonic Applications

Cyanine dyes attached to DNA scaffolds have been shown to exhibit molecular aggregation and exciton delocalization. The molecular aggregation and exciton delocalization of dyes are useful for the development of excitonic devices, such as quantum computers utilizing molecular exciton wires. The functionality of excitonic devices is determined by the dynamics of excitons on the aggregate, such as exciton exchange and exciton-exciton interaction. Thus, it is necessary to understand how dyes orient and interact electronically when aggregated. The orientation and electronic properties of cyanine dyes when bound to DNA scaffolds were studied using density functional theory (DFT), time dependent (TD-) DFT, and molecular dynamics (MD) methods. Using DFT and TD-DFT, dye monomer static dipole differences and transition dipole moments, both of which contribute to exciton dynamics, were calculated. MD simulations of the dyes covalently bound to DNA scaffolds were done to examine the orientations of the dyes when aggregated. Using the static dipole differences and transition dipole moments together with dye orientations, excitonic coupling and interaction energies were calculated.