In natural photosynthetic systems, quantum coherent effects contribute to enhanced efficiency in energy transfer pathways using closely packed or aggregated light-harvesting chromophores. These effects may be mimicked synthetically by exploiting the J-aggregation behavior of certain dyes, such as cyanines. A proof-of-concept study has established that J-aggregated pseudoisocyanine (PIC) dyes can be rationally attached to DNA scaffolding, where they self-assemble in the minor groove of poly-A/T DNA sequences. In addition, in concentrated aqueous solution PIC forms homogeneous fibers with an average width of 2.89 nm, shown from a cryo-TEM analysis. To determine the physical mode of aggregation in aqueous solution, we first use density functional theory (DFT) to analyze the interaction energy landscape between PIC dimers. Next, excitonic transport properties of the model PIC aggregates are calculated to understand how the physical aggregation behavior of PIC influences its energy transfer efficiency. We note that a chiral-aggregate model in which PIC monomers are at oblique angles relative to the long-axis of the fiber replicates the experimental spectra most accurately, where the J-aggregate absorption band is red-shifted 1600 cm<sup>-1</sup> from the monomer band. This model of aggregation could be formed in concentrated aqueous solution by the sequential binding of PIC dimers and monomers to the ends of the fiber. In future work, we will analyze the binding energies of PIC in sequence-dependent DNA duplexes using a quantum mechanical / molecular mechanical (QM/MM) model in order to determine the physical binding mode of PIC when non-covalently templated on DNA scaffolds. These results will then be further utilized in the design and optimization of DNA-dye excitonic circuits using PIC and related cyanine dyes.

Superstructural aggregation behavior of cyanine dyes in aqueous solution

256th National Meeting (2018)

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