Cyanine dyes covalently bound in DNA complexes have been studied for their
exciton delocalization properties that include J and H-aggregate behavior and
Davydov splitting [1,2]. The self assembly properties of DNA can bring dyes within
distances (≤ 2nm) that induce shifts in absorption maxima. Thus, DNA is used as a
scaffold, allowing the manipulation of dyes.
- Dye dimer orientation determines allowed energetic transitions (shown in Fig. 1)
- Control of dye orientations is crucial for the viability of dye-DNA excitonic
applications - Density functional theory (DFT) can be used to optimize the structures of
molecular systems and therefore perfect to explore dye orientations - Proper choice of exchange-correlation (XC) functionals is necessary to model
systems accurately
Goal of study: Determine XC-functional effects on ground state orientations and
excited state properties of Cy5 dye molecules (shown in Fig. 1).
monomer, J-dimer, H-dimer, and an oblique (J/H) dimer. The
colored ovals represent relative transition dipole orientations of
each aggregate. Allowed transitions are represented as solid
lines and forbidden transitions are dashed
tetramethylindocarbocyanine). Linkers are attached at R sites.