(360a) Scaffolded DNA-Dye Complexes: Theory of Molecular Interactions for Synthetic Light Harvesting Applications

Natural photosynthetic systems utilize quantum coherent effects to enhance energy transfer efficiency when light-harvesting molecules are closely interacting. These natural photosynthetic complexes enable molecular packing and interaction by precise scaffolding within a protein environment. Likewise, synthetic DNA nanotechnology enables control of molecular interactions by rational attachment of photoactive dyes to DNA scaffolding. In both natural and synthetic systems, closely-interacting dyes may exhibit J- (red-shifted energies) and H-aggregation (blue-shifted energies) behavior, effects which are caused by excitonic delocalization of the molecular wavefunctions. Using model systems consisting of cyanine dyes attached or interacting with DNA scaffolding, we explore a range of excitonic and structural behavior using a combined quantum mechanics (QM) and molecular dynamics (MD) theoretical toolset. We explore complexes with cyanine dyes non-covalently bound to DNA, as well as complexes with cyanine dyes covalently attached to the DNA backbone. Using MD, we explore the dynamical motion of these cyanine-DNA complexes, and subsequently using QM, the visible absorption spectra and photoactive properties upon aggregation can be calculated and compared to experimental results. Thus, using theoretical tools, we can build a molecular exciton model to elucidate the environmental effect of DNA on aggregation and excitonic behavior of photoactive dyes. These excitonic and structural aggregation properties of cyanine-based DNA-dye complexes can be compared to natural light-harvesting complexes with protein-based scaffolding. Understanding the differences between natural and synthetic biological scaffolds are of major interest, and knowledge of excitonic behavior at the molecular level will enable directed bio-inspired design of scaffolded photoactive materials.