Squaraine Figure Eight (SF8) dyes are a unique class of deep-red fluorescent dyes with self-threaded molecular architecture that provides structural rigidity while simultaneously encapsulating and protecting the emissive fluorochrome. Previous cell microscopy and bulk phase studies of SF8 dyes indicated order of magnitude enhancements in photostability over conventional pentamethine cyanine dyes such as Cy5. Studies conducted at the single molecule level now reveal that these ensemble level enhancements carry over to the single molecule level in terms of enhanced emission quantum yields, longer times to photobleaching, and enhanced total photon yields. When compared to Cy5, the SF8-based dye SF8(D4) possesses a three-fold larger single molecule emission quantum yield, exhibits order of magnitude longer average times before photobleaching, and exhibits twenty times larger photon yields. Additional features such as water solubility, fluorochrome encapsulation to protect it against nucleophilic attack, and selective biomarker targeting capability make SF8-based dyes promising candidates for biological labeling and microscopy applications and single molecule tracking.

The phenomenal global upheaval caused by SARS-CoV-2 has produced amazing responses from science and healthcare, particularly in the rapid realisation and production of vaccines. However, until early 2020 global infection control research was highly focused on rapidly increasing rates of conventional antimicrobial resistance (AMR) and the supply of drugs to counter this. Antimicrobial dyes have been suggested by various authors for inclusion in this effort, usually with little return from responsible authorities, and normally on the basis of post-treatment staining or potential toxicity, but this does not deny the fact that such dyes, particularly with photoactivation, are the only class of agents with pan-microbial activity - i.e. against each of bacteria, viruses, fungi and protozoa - regardless of the organism's drug resistance status. Conventional antibacterials, antivirals etc. usually demonstrate activity against one particular section of pathogens only, and disinfectants such as chlorhexidine or benzalkonium salts are too toxic for internal use. This perspective reflects both the background utility of antimicrobial dyes and ways forward for their inclusion in 21st Century infection control protocols.

The ongoing pandemic of coronavirus disease 2019 (COVID-19) posed a major challenge to the public health. Currently, no proven antiviral treatment for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is available. Here we report compounds pentalysine β-carbonylphthalocyanine zinc (ZnPc5K) and chlorin e6 (ce6) potently inhibited the viral infection and replication in vitro with EC values at nanomolar level. These compounds were first identified by screening a panel of photosensitizers for photodynamic viral inactivation. Such viral inactivation strategy is implementable, and has unique advantages, including resistance to virus mutations, affordability compared to the monoclonal antibodies, and lack of long-term toxicity.

Near-infrared (NIR) emitting probes with very large Stokes' shifts play a crucial role in bioimaging applications, as the optical signals in this region exhibit high signal to background ratio and allow deeper tissue penetration. Herein we illustrate NIR-emitting probe with very large Stokes' shifts (Δλ ≈ 260 - 272 nm) by integrating the excited-state intramolecular proton transfer (ESIPT) unit 2-(2'-hydroxyphenyl)benzoxazole (HBO) into a pyridinium derived cyanine. The ESIPT not only enhances the Stokes' shifts but also improves the quantum efficiency of the probe (ф = 0.27 - 0.40 in DCM). The application of in live cells imaging reveals that compound stains mitochondria in eukaryotic cells, normal human lungs fibroblast (NHLF), Zebrafish's neuromast hair cells, and support cells, and inner plasma membrane in prokaryotic cells, ().

A novel aggregation-induced emission (AIE) structure containing a tetraphenylethene (TPE) unit covalently linked with a merocyanine (MC) unit was synthesized and investigated in semi-aqueous solutions with 90% water fraction. The open-form structure of red-emissive MC unit combined with TPE unit was utilized as a bi-fluorophoric sensor to detect lead(II) ion, which could be transformed from the close-form structure of non-emissive SP unit upon UV exposure. Moreover, the TPE unit as an energy donor with the blue-green photoluminescence (PL) emission at 480 nm was combined with the MC unit as an energy acceptor with the red PL emission at 635 nm. Due to the Förster resonance energy transfer (FRET) processes, the bi-fluorophoric sensor produced more efficient ratiometric PL behavior to induce a stronger red PL emission than that of the mono-fluorophoric MC unit. Hence, the PL sensor responses of the AIE bi-fluorophoric structure toward lead(II) ion could be further amplified via the FRET-OFF processes to turn off red PL emission of the coordinated MC acceptor and to recover blue-green PL emission of the TPE donor. Accordingly, the best LOD value for the AIE sensor detection toward Pb was 0.27 μM. The highest red MC emission with the optimum FRET process of AIE sensor could be utilized in cell viability tests to prove the non-toxic and remarkable bio-marker of AIE sensor to detect lead(II) ion in live cells. The developed FRET-OFF processes with ratiometric PL behavior of the bi-fluorophoric AIE sensor can be utilized for future chemo- and bio-sensor applications.

By performing a single-atom replacement within common fluorophores, we have developed a facile and general strategy to prepare a broad-spectrum class of colorimetric and fluorogenic probes for the selective detection of mercury ions in aqueous environments. Thionation of carbonyl groups from existing fluorophore cores results in a great reduction of fluorescence quantum yield and loss of fluorescence emission. The resulting thiocaged probes are efficiently desulfurized to their oxo derivatives in the presence of mercury ions, leading to pronounced changes in chromogenic and fluorogenic signals. Because these probes exhibit high selectivity, excellent sensitivity, good membrane-permeability, and rapid responses towards mercury ions, they are suitable for visualization of mercury in both aqueous and intracellular environments.

•Special Issue on 4th ICEM 2020.•Science, Techniques, Surveillance.•The importance of Science.•Fluorescent dyes.

A series of selenylated-oxadiazoles were prepared and their interaction with DNA was investigated. The photophysical studies showed that all the selenylated compounds presented absorption between 270 and 329 nm, assigned to combined n→π* and π→π* transitions, and an intense blue emission (325-380 nm) with quantum yield in the range of  = 0.1-0.4. DFT and TD-DFT calculations were also performed to study the likely geometry and the excited state of these compounds. Electrochemical studies revealed the ionization potential energies (-5.13 to -6.01 eV) and electron affinity energies (-2.25 to -2.83 eV), depending directly on the electronic effect (electron-donating or electron-withdrawing) of the substituent attached to the product. Finally, the UV-Vis DNA interaction experiments indicated that the compounds can interact with the DNA molecule due to intercalation, except for (which interacted via electrostatic interaction). Plasmid cleavage assay presented positive results only for that presented the strongest interaction results. These results made the tested selenylated-oxadiazoles as suitable structures for the development of drugs and the design of structurally-related therapeutics.

The computationally-aided photophysical and lasing properties of a selected battery of BOPHYs are described and compared to those of related BODIPY counterparts. The present joined theoretical-experimental study helps to put into context the weaknesses and strengths of both dye families under different irradiation conditions. The chemical versatility of the BOPHY scaffold has been also comparatively explored to modulate key photonic properties towards the development of red-emitting dyes, chiroptical dyes and singlet oxygen photosensitizers. Thus, BOPHY BINOLation by fluorine substitution with enantiopure BINOLs endows the BOPHY chromophore with chiroptical activity, as supporting by the simulated circular dichroism, decreasing deeply its fluorescent response due to the promotion of fluorescence-quenching intramolecular charge transfer (ICT). Interestingly, the sole alkylation of the BOPHY core strongly modulates the promotion of ICT, allowing the generation of highly bright BINOL-based BOPHY dyes. Moreover, 3,3'-dibromoBINOLating BOPHYs can easily achieve singlet-oxygen photogeneration, owing to spin-orbit coupling mediated by heavy-atom effect feasible in view of the theoretically predicted disposition of the bromines surrounding the chromophore. From this background, we have established the master guidelines to design bright fluorophores and laser dyes, photosensitizers for singlet oxygen production and chiroptical dyes based on BOPHYs. The possibility to finely mix and balance such properties in a given molecular scaffold outstands BOPHYs as promising dyes competing with the well-settled BODIPY dyes.

The endoplasmic reticulum (ER) of eukaryotic cells plays critical roles in the processing of secreted and transmembrane proteins. Defects in these functions are associated with a wide range of pathologies. To image this organelle, cells are often treated with fluorescent ER-Tracker dyes. Although these compounds are selective, existing red fluorescent probes of the ER are costly glibenclamide derivatives that inhibit ER-associated sulphonylurea receptors. To provide simpler and more cost-effective red fluorescent probes of the ER, we synthesized amino analogues of the fluorophore resorufin. By varying the polarity of linked substituents, we identified hexyl resorufamine (HRA) as a novel hydrophobic (cLogD (pH 7.4) = 3.8) red fluorescent (Ex. 565 nm; Em. 614 nm in ethanol) molecular probe. HRA is exceptionally bright in organic solvents (quantum yield = 0.70), it exclusively localizes to the ER of living HeLa cells as imaged by confocal microscopy, it is effective at concentrations as low as 100 nM, and it is non-toxic under these conditions. To examine its utility, we used HRA to facilitate visualization of small molecule-mediated release of a GFP-GPI fusion protein from the ER into the secretory pathway. HRA represents a potent, selective, and cost-effective probe for imaging and labeling the ER.

A series of geometrically well-defined cationic fluorophores were designed based on molecular mechanics. They contain biaryl linkers to impart rigidity preventing intramolecular folding between a conjugated biomolecule and fluorophore. All probes have absorption and emission maxima within 20 nm from Texas Red, as predicted by TDDFT calculations and validated experimentally.

A cationic azadioxatriangulenium (ADOTA) dye was entrapped in silica thin films obtained by the sol-gel process and in poly (vinyl) alcohol (PVA) thin films. Azadioxatriangulenium is a red emitting fluorophore with a long fluorescence lifetime of ~20 ns. The fluorescent properties of azadioxatriangulenium in silica thin films and PVA films were studied by means of steady-state and time resolved fluorescence techniques. We have found that the azadioxatriangulenium entrapped in silica thin film has a wider fluorescence lifetime distribution (Lorentzian distribution), lower fluorescence efficiencies, shorter lifetimes compared to Azadioxatriangulenium in a PVA film. The local environment of azadioxatriangulenium molecules in the silica thin film is rich with water and ethanol, which creates the possibility of forming excited state aggregates due to high concentration of dye within a small confined area. In contrast to the PVA matrices, the porous silica films allow restricted rotations of Azadioxatriangulenium molecules, which result in faster and complex fluorescence anisotropy decays suggesting energy migration among dye molecules.

A novel method for the preparation of β-fused porphyrin dyads was developed that exploits a one-pot reaction of 2,3-diaminoporphyrins with diethyl oxalate. This approach provides good yields of the zinc β-fused dyad and the corresponding free-base, opening the way for preparation of several metal derivatives to permit modulation of optoelectronic characteristics for commercial applications.

A high yield route to symmetric, conjugatable pentamethine carbocyanine dyes with far-red/near infrared (NIR) emission between 650 and 700 nm is reported. The dyes are prepared via condensation of indolium or benz[e]indolium inner salts with an alkyl carboxylic acid derivatized malonaldehyde dianil or alternatively in a one-pot reaction without isolation of the malonaldehyde intermediate. The fluorophores are water-soluble, have bright fluorescence emission, are easily prepared in good yield, and are promising candidates for use in a variety of biochemical and in vivo imaging applications.

The fundamental photophysical properties of three symmetrically substituted 3,9-perylene analogues were examined in a diverse range of solvents. All three compounds exhibited solvent-dependent fluorescence quantum yield, which was lower than that of perylene or its diimides. Whilst the absence of a large excited state dipole moment suggests that there is no preferential charge accumulation in one side of the molecules, the data suggest that intramolecular electron transfer occurs and that such an event causes additional photochemical mechanisms in chlorinated compounds where the fluorescence quantum yield is lower than in all other solvents and the values of the fluorescence decay change significantly. The dyes could be an interesting new class of fluorescence tags for labeling biomolecules and as dyes for organic photovoltaic materials.

Commercially available, near-infrared fluorescent squaraine dyes (Seta-635 and Seta-670) were covalently bound to antibodies and employed insurface enhanced immunoassay. From fluorescence intensity and lifetime changes determined for a surface which had been coated with silver nanoparticles as well as a non-coated glass surface, both labelled compounds exhibited a 15 to 20-fold enhancement of fluorescence on the silver coated surface compared to that achieved on the non-coated surface. In addition, the fluorescence lifetime changes drastically for both labels in the case of silver-coated surfaces. The fluorescence signal enhancement obtained for the two dyes was greater than that previously recorded for Rhodamine Red-X and AlexaFluor-647 labels.

We characterize the response of several boronic acid containing fluorophores, which are widely used for sugar determination, towards aqueous cyanide. In two recent reports we have shown that boronic acid containing fluorophores can be used to sense aqueous cyanide through physiological safeguard levels. In this report we show that our new sensing mechanism is not just specific to our recently reported probes, but is indeed generic to the boronic acid moiety itself. Subsequently a wide range of cyanide-sensitive probes can now be realized, offering several modalities for fluorescence based cyanide sensing such as: intensity, lifetime, ratiometric, polarization and modulation fluorescence sensing.

We characterize a new water soluble fluorescent probe sensitive to changes in pH. The new probe shows spectral shifts and intensity changes in different pH media, in a wavelength ratiometric and colorimetric manner. Subsequently, changes in pH can readily be determined around the physiological level. The new probe's response is based on the ability of the boronic acid group to interact with strong bases like OH, changing from the neutral form of the boronic acid group [R-B(OH)] to the anionic R-B(OH) form, which is an electron donating group. The presence of an electron deficient quaternary heterocyclic nitrogen center and a strong electron donating amino group in the 6-position, on the quinolinium backbone, provides for the spectral changes observed upon OH complexation. In addition, the presence of the amino group in the 6-position of the quinolinium backbone, suppresses the response of the boronic acid containing probe towards mono saccharides such as glucose and fructose, which are present in many biological fluids, allowing for the predominant pH sensitivity. Finally we compare our findings to those of a control compound that does not contain the boronic acid group.

We characterize two new water-soluble probes, - and -NBDPBA, which show notable changes in their absorption spectra in the presence of monosaccharides such as glucose and fructose. Subsequently glucose concentrations can readily be determined in the physiological glucose concentration range in a wavelength-ratiometric and colorimetric manner. -NBDPBA has a dissociation constant of 204 mM for glucose, which is not unlike other mono-phenyl boronic acid derived probes. In addition we have also synthesized a control compound, NBDP, which does not contain the boronic acid moiety and is therefore insensitive to sugars, to help rationale the spectral changes observed.