Steering dark state formation in molecular aggregates with DNA scaffolds: The interplay between Coulombic and charge transfer interactions

DNA-scaffolded dye aggregates have emerged as a promising platform for designing tractable model systems to understand the function of delocalized excitons in light harvesting, as the DNA provides a diverse molecular toolbox to control the spatial relationships of the dyes. However, in tightly packed aggregates Charge Transfer (CT) interactions can arise through spatial overlap of molecular orbitals between monomers and can destructively interfere with long-range Coulombic interactions, leading to significant quenching of measured fluorescence. Here we investigated the interference between short-range CT and long-range Coulombic interactions by studying indolenine squaraine dimers scaffolded on duplex DNA. Molecular dynamics and quantum mechanical simulations were performed on different squaraine-DNA arrangements to reveal the underlying molecular mechanisms on how this interplay is affected by the scaffolding. Paired with time-resolved fluorescence and transient absorption spectroscopy experiments, our results demonstrate how DNA scaffolds can influence the excited-state decay pathways of molecular dimers, which is critical for designing molecular aggregates for light-harvesting and computing applications.