Classification and naming of polymethine dyes used as staining agents for microscopy. A short guide for biomedical investigators.

The scientific literature contains many accounts of application of polymethine dyes, including cyanine dyes, as imaging agents, i.e., "biological stains," for microscopic investigation of biological materials. Currently, many such dyes are used as probes for living cells, i.e., "fluorescent probes." Polymethine dyes are defined here by two criteria. First, they possess a conjugated chain of (2n + 1) sp2-hybridized carbon atoms that connect a terminal π-electron-accepting (π-electron withdrawing) group with a terminal π-electron-donating group. Second, they have an odd number (2n + 3) of π-centers and an even number (2n + 4) of π-electrons in this chain, where n equals the number of -CR2=CR3- groups, usually vinylene groups -CH=CH-. Commercialization of diverse chemical types of many polymethine dyes has been attempted. The dyes that have achieved wide application, however, are limited in number and it is these dyes that are emphasized here. Because these polymethine dyes sometimes have been described by confusing, and sometimes confused, names, we clarify here the chemical categories and names of such dyes for the nonchemist, biomedical end user of such imaging agents. Nevertheless, the nomenclature presented here is not intended to replace the traditional "chromophore" categories of dyestuff chemistry, because the latter are held in place both by wide usage and by venerable authorities, such as the Colour Index.

Correspondence on "Cyanine Dyes Containing Quinoline Moieties: History, Synthesis, Optical Properties and Applications".

In the review on "Cyanine Dyes Containing Quinoline Moieties: History, Synthesis, Optical Properties and Applications" (K. Ilina, M. Henary, Chem Eur. J. 2021, 27, 2430; https://doi.org/10.1002/chem.202003697), some essential aspects were incorrectly described and discussed. To avoid further confusion, this correspondence tries to clarify both the structures and the history of some cyanine and apocyanine dyes that were not presented sufficiently.

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0.

Cyanines derived from heptamethines were mainly discussed regarding their functionalization to broaden the solubility in different surroundings exhibiting either hydrophilic or hydrophobic properties and to tailor made the ΔG et photopysical properties with respect to absorption and fluorescence. Electrochemical properties were additionally considered for some selected examples. The cyanines chosen comprised as end groups either indolenine, benzo[e]- or benzo[cd]indolium pattern, which facilitated to shift the absorption between 750-1000 nm. This enabled their use in applications with light sources emitting in the near-infrared (NIR) region selected from high power LEDs or lasers with line-shaped focus. The absorbers considered were discussed regarding their function as sensitizer for applications related to Chemistry 4.0 standards. These were mainly photopolymer coatings, which can be found for applications in the graphic industry or to protect selected substrates. The huge release of heat on demand upon turning ON or OFF the NIR light source enables them for photothermal treatment in processes requesting heat to initiate either chemical (activated reactions) or physical (melting, evaporation) events.

Fine Structure in Electronic Spectra of Cyanine Dyes: Are Sub-Bands Largely Determined by a Dominant Vibration or a Collection of Singly Excited Vibrations?

This work critically examines attempts to model the fine structure apparent in electronic spectra of cyanine dyes and their analogues. Numerous computational studies reported over the past decade attribute the origin of sub-bands and their relative intensities to vibronic transitions in which the relevant electronic transition is coupled, irrespective of symmetry, with a collection of vibrations. It is contended that this type of approach is not supported by experimental evidence. An argument is reiterated for a more appropriate model that adheres closely to fundamental principles and fits the data. It stipulates that essentially just one symmetric vibration, carbon-carbon bond stretching of the cyanine polymethine chain, dominates the coupling and is responsible for the observed fine structure. Furthermore, it is pointed out that the intensities of the sub-bands are readily explained by means of the Franck-Condon principle.

Cyanine dyes as ratiometric fluorescence standards for the far-red spectral region.

Most quantitative fluorescence measurements report emission quantum yields by referring the integrated fluorescence profile to that of a well-known standard compound measured under carefully controlled conditions. This simple protocol works well provided an appropriate standard fluorophore is available and that the experimental conditions used for reference and unknown are closely comparable. Commercial fluorescence spectrophotometers tend to perform very well at wavelengths between 250 and 650 nm but are less responsive at longer wavelengths. There are no recognized emission standards for the far-red region. We now report fluorescence quantum yields for a series of commercially available cyanine dyes in methanol solution at room temperature. The compounds are selected to span the wavelength region from 600 to 850 nm, with absolute emission quantum yields being determined by thermal blooming spectrometry. Calibration of the instrument is made by reference to aluminium(iii) phthalocyanine tetrasulfonate and aza-BODIPY in methanol.

Potential-Energy Surfaces, the Born-Oppenheimer Approximations, and the Franck-Condon Principle: Back to the Roots.

The concept of a potential-energy surface (PES) is central to our understanding of spectroscopy, photochemistry, and chemical kinetics. However, the terminology used in connection with the basic approximations is variously, and somewhat confusingly, represented with such phrases as "adiabatic", "Born-Oppenheimer", or "Born-Oppenheimer adiabatic" approximation. Concerning the closely relevant and important Franck-Condon principle (FCP), the IUPAC definition differentiates between a classical and quantum mechanical formulation. Consequently, in many publications we find terms such as "Franck-Condon (excited) state", or a vertical transition to the "Franck-Condon point" with the "Franck-Condon geometry" that relaxes to the excited-state equilibrium geometry. The Born-Oppenheimer approximation and the "classical" model of the Franck-Condon principle are typical examples of misused terms and lax interpretations of the original theories. In this essay, we revisit the original publications of pioneers of the PES concept and the FCP to help stimulate a lively discussion and clearer thinking around these important concepts.

The effects of substituents and solvents on the ground-state π-electronic structure and electronic absorption spectra of a series of model merocyanine dyes and their theoretical interpretation.

Two series of new merocyanine dyes have been synthesised and the dependence of their electronic structure on substituents and solvents has been studied by NMR spectroscopy, by using both the NMR (13)C chemical shifts between adjacent C atoms in the polymethine chain and the (3)J(H,H) coupling constants for trans-vicinal protons. The widely used valence bond (VB) model based on two contributing structures cannot account theoretically for the observed alternating π-electron density in the polymethine chain. In addition, the prediction of zero-π-bond order alternation (or zero-bond length alternation) by this model is also incorrect. However, the results are consistent with the predictions of a qualitative VB model which considers the resonance of a positive charge throughout the whole polymethine chain. Based on this model and the Franck-Condon principle the effect of substituents and solvents on the fine structure of the electronic spectra of these dyes can be explained as vibronic transitions from the vibrational state v = 0 to v', where v is the vibrational quantum number of the totally symmetric C=C valence vibration of the polymethine chain in the electronic ground state and v' is that in the electronic excited state. In contrast, neither the effects of substituents or solvents on the electronic structure of merocyanines and their electronic spectra can be accounted for by the simple two state VB model.

Long-wavelength absorbing and fluorescent chameleon labels for proteins, peptides, and amines.

Long-wavelength absorbing labels that change their color and fluorescence upon conjugation to proteins and other biomolecules provide two critical advantages over the wealth of conventional amine-reactive labels. At first, the progress of the labeling reaction can be monitored continuously either visually or by spectrometry without prior purification. Then, the labeled biomolecule can be investigated with red or near-infrared light, which minimizes background interference in biological samples. These unique characteristics are met by a group of long-wavelength absorbing cyanine dyes carrying a reactive chloro substituent for nucleophilic substitution with primary amines, which is accompanied by a color change from green to blue. In addition to this so-called chameleon effect, the dyes display an increase in fluorescence during the labeling reaction. Despite their structural similarity, the reactivity of the dyes differs strongly. The fastest labeling kinetics is observed with dye S 0378 as its five-membered ring affords a stabilizing effect on the intermediate carbocation during an S(N)1-type of nucleophilic substitution. The reaction mechanism of the amine-reactive cyanine dyes provides a blueprint for the design of future long-wavelength absorbing chameleon dyes.

Relationship between the molecular structure of cyanine dyes and the vibrational fine structure of their electronic absorption spectra.

Electronic absorption spectra of symmetrical cyanine dyes show vibronic sub-bands, attributed to the symmetric C-C valence vibration of the polymethine chain in the electronic excited state. Displacements in the equilibrium configuration between electronic ground and excited states of cyanine dyes lead to longer C-C bonds in the excited state. Additionally, in the electronic ground state, a small degree of bond localisation always remains in the chain depending on the different heterocyclic terminal groups. Our investigations suggest that we can use (3)J(H,H) coupling constants in the polymethine chain to characterise the bond localisation within the chain. Based on these values and the Franck-Condon principle, the intensity distribution among the vibrational sub-bands can be explained.

Current developments in optical data storage with organic dyes.

The main motivation for the development of digital data storage has been the improvement in play-back quality and the increase in storage capacity. In 1982 Philips and Sony introduced the first technically and economically successful system based on this-the compact disc (CD) and a compatible player. A very broad diversity of optical data recording formats are available today, and a difference is drawn between prerecorded, recordable, and rewritable media. This Review gives an overview of the systems used, the main features of production, and then concentrates on the properties of the organic dyes that are used in recordable systems. Dyestuffs chemistry has gained the reputation of having become a mature field of activity. Is this prejudice or a justified swan song for dyestuffs chemistry? When applications in optical data storage are considered, it is evident that even today progresses such as CD-R and DVD/R would not be feasible without functional dyes.