Studies of Cy5 Chromophore Interactions – Excitonics for Quantum Computing
DNA-based nanoassemblies enable the arrangement of chromophores in well-defined configurations with sufficiently close spaces for coherent exciton energy transfer. Excitons are suggested to work as carriers of energy in biological solar energy harvesting systemsor as carriers of information in quantum computing systems. It is understood that spatial and energetic cascades play an impactful role on the final effectiveness of energy producing reaction centers. Density functional theory has shown sufficient results in calculating the special and energetic behavior of the Cy5 molecule and it’s interaction with the DNA system. We investigate Cy5 configurations in H- and J- aggregate formations utilizing local density approximations (LDA) and Perdew Burke Ernzerhoff (PBE) formalism of the general gradient approximations (GGA) as methods for structural optimization of a two Cy5 molecule motif. We present ground state configurations for three different models: H-assembly stacked (typical configuration), H-assembly flipped, and J-assembly (parallel). Resultant structural and electrical properties will be used in further time-dependent density functional theory (TD-DFT) studies to advance the understanding of experimentally derived absorption spectra and circular dichroism (CD) observations and guide future experiments.
Nelson, Eric and Correa Hernandez, Andres, "Studies of Cy5 Chromophore Interactions – Excitonics for Quantum Computing" (2017). 2017 Undergraduate Research and Scholarship Conference.