Unspeci!ed verticality of Franck–Condon transitions, absorption and emission spectra of cyanine dyes, and a classically inspired approximation

Joseph Alia, Joseph Flack

Research output: Contribution to journalArticlepeer-review

20 Downloads (Pure)


The computed vertical energy, Ev,a/f, from the equilibrium geometry of the initial electronic state is frequently considered as representative of the experimental excitation/emission energy, Eabs/! hc/lmax. Application of the quantum mechanical version of the Franck–Condon principle does not involve precise speci"cation of nuclear positions before, after, or during an electronic transition. Moreover, the duration of an electronic transition is not experimentally accessible in spectra with resolved vibrational structure. It is shown that computed vibronic spectra based on TDDFT methods and application of quantum mechanical FC analysis predict Eabs hc/lmax with a 10-fold improvement in accuracy compared to Ev,a for nine cyanine dyes. It is argued that part of the reason for accuracy when this FC analysis is compared to experiment as opposed to Ev,a/f is the unspeci"ed verticality of transitions in the context of the quantum version of the FC principle. Classical FC transitions that preserve nuclear kinetic energy before and after an electronic transition were previously found to occur at a weighted average of "nal and initial electronic state molecular geometries known as the r-centroid. Inspired by this approach a qualitative method using computed vertical and adiabatic energies and the harmonic approximation is developed and applied yielding a 5-fold improvement in accuracy compared to Ev,a. This improvement results from the dominance of low frequency vibronic transitions in the cyanine dye major band. The model gives insight into the nature of the redshift when qPCR dye EvaGreen is complexed to lDNA and is applicable to the low frequency band of similar non cyanine dyes such as curcumin. It is found that the computed vibronic cyanine dye spectra from time-dependent FC analysis at 0 K and 298 K show decreased intensity at higher temperature suggestive of increased intensity with restricted motion shown when cyanine dyes are used in biomedical imaging. A 2-layer ONIOM model of the DNA minor groove indicates restricted motion of the TC-1 dye excited state in this setting indicative of enhanced !uorescence.
Original languageEnglish (US)
Pages (from-to)43153-43167
Number of pages14
JournalRSC Advances
StatePublished - Nov 18 2020


  • Franck-Condon Principle
  • Uncertainty principle
  • Classical approximation
  • Molecular Spectroscopy
  • Computational quantum chemistry
  • Cyanine dyes
  • Vertical transition
  • Biomedical imaging


Dive into the research topics of 'Unspeci!ed verticality of Franck–Condon transitions, absorption and emission spectra of cyanine dyes, and a classically inspired approximation'. Together they form a unique fingerprint.

Cite this