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Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer
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    A: Structure, Spectroscopy, and Reactivity of Molecules and Clusters

    Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer
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    The Journal of Physical Chemistry A

    Cite this: J. Phys. Chem. A 2023, 127, 45, 9530–9540
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    https://doi.org/10.1021/acs.jpca.3c06090
    Published November 7, 2023
    Copyright © 2023 American Chemical Society

    Abstract

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    The indocarbocyanine Cy3 dye is widely used to probe the dynamics of proteins and DNA. Excitonically coupled Cy3 dimers exhibit very unique spectral signatures that depend on the interchromophoric geometrical orientation induced by the environment, making them powerful tools to infer the dynamics of their surroundings. Understanding the origin of the dimeric spectral signatures is a necessity for an accurate interpretation of the experimental results. In this work, we simulate the vibronic spectrum of an experimentally well-studied Cy3 dimer, and we explain the origin of the experimental signatures present in its linear absorption spectrum. The Franck–Condon harmonic approximations, among other tests, are used to probe the factors contributing to the spectrum. It is found that the first peak in the absorption spectrum originates from the lower energy excitonic state, while the next two peaks are vibrational progressions of the higher energy excitonic state. The polar solvent plays a crucial role in the appearance of the spectrum, being responsible for the localized S1 minimum, which results in an increased intensity of the first peak.

    Copyright © 2023 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpca.3c06090.

    • Effect of temperature and removal of the methyl groups on the spectra, the natural transition orbitals corresponding to the vertical excitations from the ground state equilibrium structure, and coordinates of the ground state and first/second excited state equilibrium structures obtained from ωB97XD/Def2SVP optimizations in implicit methanol via PCM (PDF)

    • Movies of vibrational modes of the S1 minimum (ZIP)

    • Movies of the vibrational modes of the S2 minimum (ZIP)

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    Cited By

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    This article is cited by 2 publications.

    1. Mohammed I. Sorour, Kurt A. Kistler, Andrew H. Marcus, Spiridoula Matsika. Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA. The Journal of Physical Chemistry B 2024, 128 (32) , 7750-7760. https://doi.org/10.1021/acs.jpcb.4c03115
    2. Dayana Bashirova, Tim J. Zuehlsdorff. First-Principles Modeling of the Absorption Spectrum of Crystal Violet in Solution: The Importance of Environmentally Driven Symmetry Breaking. The Journal of Physical Chemistry A 2024, 128 (27) , 5229-5242. https://doi.org/10.1021/acs.jpca.4c00389

    The Journal of Physical Chemistry A

    Cite this: J. Phys. Chem. A 2023, 127, 45, 9530–9540
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jpca.3c06090
    Published November 7, 2023
    Copyright © 2023 American Chemical Society

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