Assessing Time-Dependent Density Functional Theory as a Computational Tool to Model Chromophores Intercalated into DNA Scaffolds

Understanding first-principles energy transport in organic molecules reveals novel energy harvesting systems, quantum computing, and solar power energy transportation and production. DiSC2(5), also named Cy5, exhibits bright fluorescence signals and has shown promising lossless exciton transport properties, as well as tunable energy absorption and emission when conjoined with DNA. This paper focuses on functional groups of organic molecules, specifically the chromophoric red dye DiSC2(5) and its interaction with Hand J-aggregates and with DNA. Density functional theory (DFT) and time dependent density functional theory (TD-DFT) are applied to investigate the chromophore Cy5 in vertically stacked (H-aggregates) and slipped assembly dyes (J-aggregates) arrangements in order to assess computational tools for the prediction of optimized structural characteristics and hypsochromic, bathochromic exciton behavior.