Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 DimerClick to copy article linkArticle link copied!
- Mohammed I. Sorour*Mohammed I. Sorour*Email: [email protected]Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United StatesMore by Mohammed I. Sorour
- Andrew H. Marcus*Andrew H. Marcus*Email: [email protected]Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United StatesMore by Andrew H. Marcus
- Spiridoula Matsika*Spiridoula Matsika*Email: [email protected]Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United StatesMore by Spiridoula Matsika
Abstract
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.
Cited By
This article is cited by 2 publications.
- 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
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, 7750-7760. https://doi.org/10.1021/acs.jpcb.4c03115
- 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
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, 5229-5242. https://doi.org/10.1021/acs.jpca.4c00389
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