ArticleThe journal of physical chemistry. A2021
Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3.
Article in The journal of physical chemistry. A, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- The intrinsically disordered C-terminal domain of bacteriophage T4 gp32 amplifies pre-existing conformational heterogeneity at DNA replication junctions.bioRxiv : the preprint server for biology · 2026Article
- Multiconfigurational Excitonic Couplings in Homo- and Heterodimer Stacks of Azobenzene-Derived Dyes.The journal of physical chemistry. A · 2024Article
- Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA.The journal of physical chemistry. B · 2024Article
- Article
- Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites.Nucleic acids research · 2024Article
- Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer.The journal of physical chemistry. A · 2023Article
- Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy.Annual review of physical chemistry · 2023Review
- Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching.Nano letters · 2022Article
- Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3.Molecules (Basel, Switzerland) · 2022Article
- Light-Harvesting Crystals Formed from BODIPY-Proline Biohybrid Conjugates: Antenna Effects and Excitonic Coupling.The journal of physical chemistry. A · 2022Article
- Temperature-dependent local conformations and conformational distributions of cyanine dimer labeled single-stranded-double-stranded DNA junctions by 2D fluorescence spectroscopy.The Journal of chemical physics · 2022Article
- Studies of DNA breathing in exciton-coupled (iCy3)Proceedings of SPIE--the International Society for Optical EngineeringArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments. Many methods have been used to model the excitonic coupling in molecules with varying degrees of accuracy. The atomic transition charge model offers a high-accuracy and cost-effective way to calculating the excitonic coupling. The main focus of this work is to generate high-quality atomic transition charges that can accurately model the Cy3 dye's transition density. The transition density of the excitation of the ground to first excited state is calculated using configuration-interaction singles and time-dependent density functional theory and is benchmarked against the algebraic diagrammatic construction method. Using the transition density we derived the atomic transition charges using two approaches: Mulliken population analysis and charges fitted to the transition electrostatic potential. The quality of the charges is examined, and their ability to accurately calculate the excitonic coupling is assessed via comparison to experimental data of an artificial biscyanine construct. Theoretical comparisons to the supermolecule
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