(233b) Modeling the Aggregation Behavior of Cyanine Dyes for Efficient Energy Transport

Authors: 
Bricker, W. P., Massachusetts Institute of Technology
Banal, J. L., Massachusetts Institute of Technology
Stone, M. B., Massachusetts Institute of Technology
Chen, W. J., Massachusetts Institute of Technology
Schlau-Cohen, G. S., Massachusetts Institute of Technology
Bathe, M., Massachusetts Institute of Technology
In natural photosynthetic systems, quantum coherent effects contribute to enhanced efficiency in energy transfer pathways when light-harvesting chromophores are closely packed or aggregated. We can mimic these effects synthetically by exploiting the J- and H-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 continuous A-tract 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 use density functional theory (DFT) to analyze the excitonic transport properties of the model PIC aggregates 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 neither parallel nor orthogonal 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-1 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. Also, H-aggregates of cyanine dimers and trimers can be engineered using covalent attachment to the backbone of DNA nanostructures. Using molecular dynamics, the H-aggregated structure of cyanine dimers and trimers can be analyzed, leading to improved estimates of spectral and excitonic properties of these systems. Both J- and H-aggregated templated dye molecules studied here can be further utilized in the rational design and optimization of DNA-dye excitonic circuits using PIC and related cyanine dyes.