Keto-polymethines: a versatile class of dyes with outstanding spectroscopic properties for in cellulo and in vivo two-photon microscopy imaging

Design and Photonics of Merocyanine Dyes

Merocyanines, thanks to their easily adjustable electronic structure, appear to be the most versatile and promising functional dyes. Their D-π-A framework offers ample opportunities for custom design through variations in both donor/acceptor end-groups and the π-conjugated polymethine chain, and leads to a broad range of practical properties, including noticeable solvatochromism, high polarizability/hyperpolarizabilities, and the ability to sensitize various physicochemical processes. Accordingly, merocyanines are applied and extensively studied in various fields, such as light-converting materials for optoelectronics, nonlinear optics, optical storage, solar cells, fluorescent probes, and antitumor agents in photodynamic therapy. This review encompasses both classical and novel more important publications on the structure-property relationships in merocyanines, with particular emphasis on the results by A.  I. Kiprianov and his followers in Institute of Organic Chemistry in Kyiv, Ukraine.

Theoretical Study of Structure and Photophysics of Homologous Series of Bis(arylydene)cycloalkanones

Photophysical properties of a series of bis(arylydene)cycloalkanone dyes with various donor substituents are studied using quantum chemistry. Their capacity for luminescence and nonradiative relaxation through trans-cis isomerization is related to their structure, in particular, to the donor capacity of the substituents and the degree of conjugation due to the central cycloalkanone moiety. It is shown that cyclohexanone central moiety introduces distortions and disrupts the conjugation, thus leading to a nonmonotonic change in their properties. The increasing donor capacity of the substituents causes increase in the HOMO energy (rise in the oxidation potential) and decrease in the HOMO-LUMO gap, which results in the red shift of the absorption spectra. The ability of the excited dye to relax through fluorescence or through trans-cis isomerization is governed by the height of the barrier between the Franck-Condon and S1-S0 conical intersection regions on the potential energy surface of the lowest π-π* excited state. This barrier also correlates with the donor capacity of the substituents and the degree of conjugation between the central and donor moieties. The calculated fluorescence and trans-cis isomerization rates are in good agreement with the observed fluorescence quantum yields.

Unraveling the Chemistry of meso-Cl Tricarbocyanine Dyes in Conjugation Reactions for the Creation of Peptide Bonds

Tricarbocyanine dyes have become popular tools in life sciences and medicine. Their near-infrared (NIR) fluorescence makes them ideal agents for imaging of thick specimens or in vivo imaging, e.g., in fluorescence-guided surgery. Among other types of cyanine dyes, meso-Cl tricarbocyanine dyes have received a surge of interest, as it emerged that their high reactivity makes them inherently tumor-targeting. As such, significant research efforts have focused on conjugating these to functional moieties. However, the syntheses generally suffer from low yields. Hereby, we report on the reaction of meso-Cl dyes with a small selection of coupling reagents to give the corresponding keto-polymethines, potentially explaining low yields and the prevalence of monofunctionalized cyanine conjugates in the current state of the art of functional near-infrared dyes. We present the synthesis and isolation of the first keto-polymethine-based conjugate and present preliminary investigation in the prostate cancer cell lines PC3 and DU145 by confocal microscopy and discuss changes to optical properties in biological media.

Two-Photon Absorption: An Open Door to the NIR-II Biological Window?

The way in which photons travel through biological tissues and subsequently become scattered or absorbed is a key limitation for traditional optical medical imaging techniques using visible light. In contrast, near-infrared wavelengths, in particular those above 1000 nm, penetrate deeper in tissues and undergo less scattering and cause less photo-damage, which describes the so-called “second biological transparency window”. Unfortunately, current dyes and imaging probes have severely limited absorption profiles at such long wavelengths, and molecular engineering of novel NIR-II dyes can be a tedious and unpredictable process, which limits access to this optical window and impedes further developments. Two-photon (2P) absorption not only provides convenient access to this window by doubling the absorption wavelength of dyes, but also increases the possible resolution. This review aims to provide an update on the available 2P instrumentation and 2P luminescent materials available for optical imaging in the NIR-II window.

Assembly of Aggregation-Induced Emission Active Bola-Amphiphilic Macromolecules into Luminescent Nanoparticles Optimized for Two-Photon Microscopy In Vivo

The (Z) and (E)-isomers of an extended tetraphenylethylene-based chromophore with optimized two-photon-induced luminescence properties are separated and functionalized with water-solubilizing pendant polymer groups, promoting their self-assembly in physiological media in the form of small, colloidal stable organic nanoparticles. The two resulting fluorescent suspensions are then evaluated as potential two-photon luminescent contrast agents for intravital epifluorescence and two-photon fluorescence microscopy. Comparisons with previously reported works involving similar fluorophores devoid of polymer side chains illustrate the benefits of later functionalization regarding the control of the self-assembly of the nano-objects and ultimately their biocompatibility toward the imaged organism.

Counterion Pairing Effects on a Flavylium Heptamethine Dye

Polymethine fluorophores have facilitated the advance of biological and material sciences, due to their advantageous photophysical properties. However, the need to maintain a monomeric state can severely limit the utility and processability of dyes. High concentrations of fluorophore can lead to aggregation and negate the beneficial photophysical properties of monomers. Another concern is "crossing the cyanine limit" in which delocalization within the polymethine scaffold is broken, producing the presence of an asymmetric state diminishing its photophysical behavior. Herein, we attempt to overcome these limitations by exploring anion exchange on a cationic flavylium heptamethine scaffold. By increasing the size and hydrophobicity of the anion, we can effectively tune the degree of ion pairing within the polymethine dye. Interestingly, we found that the effect of ion pairing on photophysical properties was subtle for the flavylium heptamethine scaffold in comparison to the more commonly used indolenine cyanine dye. Utilizing larger weakly coordinating anions enabled solubility of the flavylium heptamethine fluorophore in nonpolar solvents, which could otherwise not be achieved. Even with more subtle effects than classic cyanine dyes, anion exchange on flavylium polymethine dyes holds potential for further manipulation of the properties of these low energy dyes.

Rational design of a large Stokes shift xanthene-benzothiozolium dyad for probing cysteine in mitochondria

Xanthene-modified cyanine dyes are considered to be an effective means to extend the emission wavelength and improve the photo-stability of cyanine dyes. However, the fluorophores obtained by this strategy generally have narrow Stokes shifts, which severely limits their application in biological imaging. Herein, a reasonable design strategy is adopted to provide an effective strategy to commendably improve the Stokes shift of xanthene-benzothiozolium fluorophores via the simultaneous expansion of a molecular π-conjugated system and heteroatomic substitution. Combined with density functional theory calculation guidance, the O atom is replaced with the S atom in the xanthene moiety and a π-conjugated benzene ring is introduced in the benzothiozolium moiety. Surprisingly, the results of the spectroscopic experiment showed that the fluorescence emission wavelength of PhCy-OH was extended to 803 nm, and the Stokes shift was improved to 68 nm. PhCy-Cys can effectively distinguish Cys from homocysteine (Hcy) and glutathione (GSH) with an extremely low detection limit of 0.166 μM. Importantly, PhCy-Cys has the ability to image endogenous Cys in mitochondria, providing the potential for exploring the specific function and mechanism of Cys in regulating oxidative stress in mitochondria.

Modified Indulines: From Dyestuffs to In Vivo Theranostic Agents

The efficient, versatile, and straightforward synthesis of the first N-alkyl analogues of induline 3B (8a and 8b) is reported. Thanks to the introduction of lipophilic substituents and their attractive photophysical properties (far-red emission and production of singlet oxygen), phenazinium 8b can be used as a theranostic agent and shows, at very low concentrations (100 nM), a remarkable ability to (i) image cells and zebrafish embryos with high quality under both mono- (514 nm) and biphotonic (790 and 810 nm) excitations, (ii) efficiently and quickly penetrate cancer cells rather than healthy fibroblasts, and (iii) induce a total or almost total cancer cell death in vitro and in vivo after illumination (λ_exc = 540-560 nm). The molecular structure of 8b is based on a triamino-phenazinium core only, with no need for additional components, highlighting the emergence of a minimalistic and versatile class of fluorescent probes for targeted photodynamic cancer therapy.

Explorations into the Effect of meso-Substituents in Tricarbocyanine Dyes: A Path to Diverse Biomolecular Probes and Materials

Polymethine cyanine dyes have been widely recognized as promising chemical tools for a range of life science and biomedical applications, such as fluorescent staining of DNA and proteins in gel electrophoresis, fluorescence guided surgery, or as ratiometric probes for probing biochemical pathways. The photophysical properties of such dyes can be tuned through the synthetic modification of the conjugated backbone, for example, by altering aromatic cores or by varying the length of the conjugated polymethine chain. Alternative routes to shaping the absorption, emission, and photostability of dyes of this family are centered around the chemical modifications on the polymethine chain. This Minireview aims to discuss strategies for the introduction of substituents in the meso-position, their effect on the photophysical properties of these dyes and some structure-activity correlations which could help overcome common limitations in the state of the art in the synthesis.

Rational design of near-infrared fluorophores with a phenolic D–A type structure and construction of a fluorescent probe for cysteine imaging

The structural modulation of phenolic D–A type fluorophores and a NIR fluorescent probe for cysteine imaging in vitro and in vivo.

Near-infrared dyes for two-photon absorption in the short-wavelength infrared: strategies towards optical power limiting

The recent advances in the field of two-photon absorbing chromophores in the short-wavelength infrared spectral range (SWIR 1100–2500 nm) are summarized, highlighting the development of optical power limiting devices in this spectral range.

High-Yielding Water-Soluble Asymmetric Cyanine Dyes for Labeling Applications

A simple and efficient microwave-assisted synthesis of asymmetric pentamethine cyanine dyes with various functional groups was developed, which allows high-yielding results. The synthesized dyes are modifiable and suitable for single-molecule imaging in biological and medical sciences by application of click chemistry or classic esterification and amidation.

Deeply coloured and highly fluorescent dipolar merocyanines based on tricyanofuran

TCF as the acceptor group of merocyanines, having its own extended π-system, gives access to deeply coloured dyes exhibiting good fluorescence efficiency in the red and near-IR spectral range.

Solvent-Free Synthesis of 2,5Bis((dimethylamino)methylene)cyclopentanone

Available protocols for the synthesis of ketocyanine dyes precursor 2,5-bis((dimethylamino)methylene)cyclopentanone are not straightforward and the reported yields are low to moderate. The important feature in the synthesis of this product through organocatalyzed condensation of cyclopentanone and N,N-Dimethylformamide dimethyl acetal is the removal of methanol produced during the reaction. By studying the reaction profile, in particular the selectivity for the formation of mono- and bis-condensation products, a high yield of the desired product can be obtained through an operationally simple and solvent-free protocol.

Interaction of Polymethine Dyes with Detonation Nanodiamonds

Among cationic, anionic, and merocyanine polymethine dyes, the binding to detonation nanodiamond (DND) colloid particles in hydrosol occurs only for negatively charged dye species. This, in view of the positive ζ-potential of the DND used in this study, suggests the predominance of electrostatic interactions over other intermolecular forces in such systems. Indeed, after decorating the merocyanine and the cationic dye by one and two negatively charged sulfopropyl groups, respectively, so that the net charge of their colored species becomes negative, the compounds also demonstrate affinity to the DND particles. In all cases, the binding of dyes to DND is accompanied by a decrease in fluorescence intensity and a bathochromic shift of their absorption and fluorescence bands. A quantitative study of the dyes adsorption on the DND nanoparticles as performed using the Küster-Freundlich and Langmuir equations reveals some peculiarities of their attaching to the DND aggregates and allows estimating the specific area of the DND particles at a concentration of 0.0212 wt/vol %.

Selective parallel G-quadruplex recognition by a NIR-to-NIR two-photon squaraine

Fluorescence imaging probes for specific G-quadruplex (G4) conformations are of considerable interest in biomedical research. Herein, we present the synthesis and the binding properties of a new water-soluble near-infrared (NIR) amphiphilic squaraine dye (CAS-C1) which is capable of selective detection of parallel over non-parallel and non G4 topologies. The striking changes in its linear optical response upon binding to parallel G4s give rise to high fluorescence quantum yields (Φ f ≈ 0.7) and one-photon molecular brightness in the far-red-NIR region. The outstanding recognition process of CAS-C1 for parallel G4s via end-stacking provides binding constants in the nanomolar regime (K b = 107 to 108 M-1) awarding it as one of the most potent parallel G4 binders currently available. Moreover, the CAS-C1-parallel G4 system exhibits large two-photon absorption (TPA) cross-sections and molecular brightness in the second NIR biological transparency window (λ ≈ 1275 nm), making it an ideal candidate for NIR-to-NIR ultrasensitive two-photon procedures.

Two-Photon Excited FRET Dyads for Lysosome-Targeted Imaging and Photodynamic Therapy

Two-photon excitable fluorescent dyes with integrated functions of targeted imaging and photodynamic therapy (PDT) are highly desired for the development of cancer theranostic agents. Herein, fluorescence resonance energy transfer (FRET) dyads, AceDAN-H₂Por-Lyso (1a) and AceDAN-ZnPor-Lyso (1b), were developed for two-photon excited (TPE) lysosome-targeted fluorescence imaging and PDT of cancer cells. Under one-photon or two-photon excitation, the AceDAN donor can effectively transfer the excited state energy to the porphyrin acceptor via high efficient FRET, leading to the generation of deep-red fluorescence and singlet oxygen for cell imaging and PDT, respectively. 1a and 1b exhibit high photocytotoxicity and low dark cytotoxicity, in addition to strong lysosomal targeting capability in living cells. By taking the advantages of the two-photon absorption properties of the AceDAN donor and the properly distributed S₁ and T₁ states of the porphyrin acceptor, the AceDAN-porphyrin dyads 1a and 1b have been successfully applied to TPE-fluorescence imaging for tracking the significant morphology changes of cancer cells under two-photon laser irradiation.

Specific Recognition of G-Quadruplexes Over Duplex-DNA by a Macromolecular NIR Two-Photon Fluorescent Probe

The implication of guanine-rich DNA sequences in biologically important roles such as telomerase dysfunction and the regulation of gene expression has prompted the search for structure-specific G-quadruplex agents for targeted diagnostic and therapeutic applications. Herein, we report on a near-infrared (NIR) two-photon poly(cationic) anthracene-based macromolecule able to selectively target G-quadruplexes (G4s) over genomic double-stranded DNA. In particular, the striking changes in its linear and third-order nonlinear optical properties, combined with the emergence of a strong induced electronic circular dichroism (ECD) signal upon binding to canonical and noncanonical DNA secondary structures allowed for a highly specific detection of several different G4s. Furthermore, through a detailed computational analysis we bring compelling evidence that our probe intercalation within G4s is a thermodynamically favored event, and we fully rationalize the spectroscopic evolution resulting from this complexation event by providing a reasonable explanation regarding the origin of the peculiar ECD effect that accompanies it.

Development of a unique family of two-photon full-color-tunable fluorescent materials for imaging in live subcellular organelles, cells, and tissues

We outline the rational design, synthesis, optical property studies, and biological imaging studies of a unique family of two-photon full-color-tunable functional fluorescent materials.

Tuning excited-state-intramolecular-proton-transfer (ESIPT) process and emission by cocrystal formation: a combined experimental and theoretical study

The formation of two-component molecular cocrystals can lead to the tunable excited state intramolecular proton transfer (ESIPT) process and emission, as first confirmed by both experimental and computational studies.