Overcoming aggregation-induced quenching in DNA-assembled rhodamine dimers

Abstract

Collective effects in molecular aggregates, such as absorption band narrowing and superradiance, are fundamentally interesting and can be leveraged to enhance function. There are lesser well-known collective effects, such as aggregation-induced quenching (AIQ), that can frustrate fundamental studies and inhibit function. In this work, we use DNA to assemble rhodamine aggregates that are either susceptible to or that overcome AIQ. Specifically, we use four-way DNA junctions to assemble dimers of ethyl and azetidinyl rhodamine derivatives. Using steady-state and transient optical spectroscopy, we show that certain configurations either permit or inhibit AIQ. We provide structural insight into the dimer packing and surrounding environment via a combination of optical simulations, ab initio calculations, and molecular dynamics simulations. Our results suggest it may be possible to use biomolecules, such as DNA, to tailor the environment of molecular aggregates and thereby overcome and better understand AIQ.