Cyanines during the 1990s: A Review

Davydov Split Aggregates of Cyanine Dyes on Self-Assembled Nanotubes

The Davydov splitting of dye aggregates represents unique molecular excitons. In this paper, we report the formation of Davydov split aggregates of 3,3'-diethylthiacarbocyanine iodide (DiSC₂ (3)) and 3,3'-diethylthiadicarbocyanine iodide (DiSC₂ (5)) templated by the helical nanotubes of lithocholic acid (LCA). The templated Davydiv split aggregates show a strong J-band and a weak H-band in the adsorption spectra. As the LCA helical nanotubes transform into a straight shape, the relative intensities of the J-band and the H-band of the templated Davydov split aggregates become roughly equal. The twisted angle change of the transition moment of DiSC₂ (3) and DiSC₂ (5) molecules in the templated Davydov split aggregates in response to the helical-to-straight shape transformation of LCA nanotubes is estimated. The templated Dvaydov split aggregates with well-defined shapes and molecular excitons are of interest for artificial light-harvesting and optoelectronic devices.

Smart J-aggregate of cyanine photosensitizer with the ability to target tumor and enhance photodynamic therapy efficacy

Photodynamic therapy (PDT) has been demonstrated to be effective for cancer treatment. Design of photosensitizers (PS) featuring tumor targeting, long excitation wavelengths, and high singlet oxygen quantum yields (Φ(¹O₂)) is the crucial point of highly efficient PDT. However, it is especially difficult to integrate above features into one photosensitizer. Herein, we put forwards a PS J-aggregation method, simultaneously endowing PS with the ability of tumor targeting, the red-shift of spectra, and the increase of Φ(¹O₂). Cyanine PS 4-((E)-3-((E)-5-iodo-1,3,3-trimethylindolin-2-ylidene)prop-1-en-1-yl)-1-methylquinolin-1-ium iodide (IDMQ) is firstly designed and synthesized by us. IDMQ can form smart response-type J-aggregates under the control of negatively charge in microenvironments. In blood, IDMQ J-aggregates target tumor via "enhanced permeability and retention (EPR)" effect. Then the intracellular IDMQ J-aggregates assembled by RNA facilitate the red shift of absorption peak with deeper penetration, and compared to free state IDMQ, improve the Φ(¹O₂), resulting in the bathochromic shift of optimal PDT wavelength from 630 (free state IDMQ) to 700 nm (IDMQ J-aggregates). This intelligent J-aggregation method establishes a promising way for endowing photosensitizer with the ability of tumor-targeting and the synchronous improvement of PDT efficacy and further boosts the development of PDT.

Prediction of Molecular Electronic Transitions Using Random Forests

Fluorescent molecules, fluorophores or dyes, play essential roles in bioimaging. Effective bioimaging requires fluorophores with diverse colors and high quantum yields for better resolution. An essential computational component to design novel dye molecules is an accurate model that predicts the electronic properties of molecules. Here, we present statistical machines that predict the excitation energies and associated oscillator strengths of a given molecule using the random forest algorithm. The excitation energies and oscillator strengths of a molecule are closely related to the emission spectrum and the quantum yields of fluorophores, respectively. In this study, we identified specific molecular substructures that induce high oscillator strengths of molecules. The results of our study are expected to serve as new design principles for designing novel fluorophores.

Recent Advances of Organic Near-Infrared II Fluorophores in Optical Properties and Imaging Functions

Near-infrared (NIR) fluorescence imaging (FI) has become a research hotspot because of its distinctive imaging properties: high temporal resolution and sensitivity. Especially in recent years, with the research focus of NIR FI shifting to the NIR-II region, which has better imaging performance, it is expected that NIR FI will find significant applications in the field of in vivo imaging. One of the most crucial directions for research into NIR-II FI is the promotion of novel NIR-II fluorophores with superior imaging properties. The remarkable advantages of organic NIR-II fluorophores in biosafety make them more promising than other fluorescent materials in certain applications. But serious defects in their fluorescence performance preclude particular imaging effects and limit imaging functions. In this review, we summarize and discuss the recent leading literature on overcoming the defects of organic NIR-II fluorophores, demonstrating the potential for further improving their imaging properties. In addition, we cover the functions of NIR-II FI that are promoted by the development of fluorophores, notably including its outlook on molecular imaging in vivo.

Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers. Here, we study an amphiphilic cyanine dye (C8S3) that is known to self-assemble into double-walled, hollow, nanotubes with interesting optical properties. The molecular packing of the dyes inside the nanotubes, however, remains elusive. To reveal the structural features of the C8S3 nanotubes, we performed atomistic Molecular Dynamics simulations of preformed bilayers and nanotubes. We find that different packing arrangements lead to stable structures, in which the tails of the C8S3 molecules are interdigitated. Our results are verified by SAXS experiments. Together our data provide a detailed structural characterization of the C8S3 nanotubes. Furthermore, our approach was able to resolve the ambiguity inherent from cryo-TEM measurements in calculating the wall thickness of similar systems. The insights obtained are expected to be generally useful for understanding and designing other supramolecular assemblies.

Cyanine-Like Boronic Acid-Derived Salicylidenehydrazone Complexes (Cy-BASHY) for Bioimaging Applications

Boronic acid-derived salicylidenehydrazone complex (BASHY) dyes with a polymethine backbone were designed to yield efficient red-emitting and two-photon absorbing fluorophores that can be used as markers for astrocytes. The dyes are chemically stable in aqueous solution and do not undergo photodecomposition. Their photophysical properties can be electronically fine-tuned and thereby adapted to potentially different imaging situations and requirements.

A Review of Endogenous and Exogenous Contrast Agents Used in Photoacoustic Tomography with Different Sensing Configurations

Optical-based sensing approaches have long been an indispensable way to detect molecules in biological tissues for various biomedical research and applications. The advancement in optical microscopy is one of the main drivers for discoveries and innovations in both life science and biomedical imaging. However, the shallow imaging depth due to the use of ballistic photons fundamentally limits optical imaging approaches’ translational potential to a clinical setting. Photoacoustic (PA) tomography (PAT) is a rapidly growing hybrid imaging modality that is capable of acoustically detecting optical contrast. PAT uniquely enjoys high-resolution deep-tissue imaging owing to the utilization of diffused photons. The exploration of endogenous contrast agents and the development of exogenous contrast agents further improve the molecular specificity for PAT. PAT’s versatile design and non-invasive nature have proven its great potential as a biomedical imaging tool for a multitude of biomedical applications. In this review, representative endogenous and exogenous PA contrast agents will be introduced alongside common PAT system configurations, including the latest advances of all-optical acoustic sensing techniques.

Cause, Regulation and Utilization of Dye Aggregation in Dye-Sensitized Solar Cells

As an important member of third generation solar cell, dye-sensitized solar cells (DSSCs) have the advantages of being low cost, having an easy fabrication process, utilizing rich raw materials and a high-power conversion efficiency (PCE), prompting nearly three decades as a research hotspot. Recently, increasing the photoelectric conversion efficiency of DSSCs has proven troublesome. Sensitizers, as the most important part, are no longer limited to molecular engineering, and the regulation of dye aggregation has become a widely held concern, especially in liquid DSSCs. This review first presents the operational mechanism of liquid and solid-state dye-sensitized solar cells, including the influencing factors of various parameters on device efficiency. Secondly, the mechanism of dye aggregation was explained by molecular exciton theory, and the influence of various factors on dye aggregation was summarized. We focused on a review of several methods for regulating dye aggregation in liquid and solid-state dye-sensitized solar cells, and the advantages and disadvantages of these methods were analyzed. In addition, the important application of quantum computational chemistry in the study of dye aggregation was introduced. Finally, an outlook was proposed that utilizing the advantages of dye aggregation by combining molecular engineering with dye aggregation regulation is a research direction to improve the performance of liquid DSSCs in the future. For solid-state dye-sensitized solar cells (ssDSSCs), the effects of solid electrolytes also need to be taken into account.

Fluorous Soluble Cyanine Dyes for Visualizing Perfluorocarbons in Living Systems

The bioorthogonal nature of perfluorocarbons provides a unique platform for introducing dynamic nano- and microdroplets into cells and organisms. To monitor the localization and deformation of the droplets, fluorous soluble fluorophores that are compatible with standard fluorescent protein markers and applicable to cells, tissues, and small organisms are necessary. Here, we introduce fluorous cyanine dyes that represent the most red-shifted fluorous soluble fluorophores to date. We study the effect of covalently appended fluorous tags on the cyanine scaffold and evaluate the changes in photophysical properties imparted by the fluorous phase. Ultimately, we showcase the utility of the fluorous soluble pentamethine cyanine dye for tracking the localization of perfluorocarbon nanoemulsions in macrophage cells and for measurements of mechanical forces in multicellular spheroids and zebrafish embryonic tissues. These studies demonstrate that the red-shifted cyanine dyes offer spectral flexibility in multiplexed imaging experiments and enhanced precision in force measurements.

Tetrazine-Derived Near-Infrared Dye as a Facile Reagent for Developing Targeted Photoacoustic Imaging Agents

A new photoacoustic (PA) dye was developed as a simple-to-use reagent for creating targeted PA imaging agents. The lead molecule was prepared via an efficient two-step synthesis from an inexpensive commercially available starting material. With the dye's innate albumin-binding properties, the resulting tetrazine-derived dye is capable of localizing to tumor and exhibits a biological half-life of a few hours, allowing for an optimized distribution profile. The presence of tetrazine in turn makes it possible to link the albumin-binding optoacoustic signaling agent to a wide range of targeting molecules. To demonstrate the utility and ease of use of the platform, a novel PA probe for imaging calcium accretion was generated using a single-step bioorthogonal coupling reaction where high-resolution PA images of the knee joint in mice were obtained as early as 1 h post injection. Whole-body distribution was subsequently determined by labeling the probe with ^99mTc and performing tissue counting following necropsy. These studies, along with tumor imaging and in vitro albumin binding studies, revealed that the core PA contrast agent can be imaged in vivo and can be easily linked to targeting molecules for organ-specific uptake.

Antineoplastic Drug-Free Anticancer Strategy Enabled by Host-Defense-Peptides-Mimicking Synthetic Polypeptides

An antineoplastic drug-free anticancer strategy enabled by host defense peptides (HDPs)-mimicking synthetic polypeptides is reported. The polypeptide exhibits a broad spectrum of anticancer activity in 12 cancer cell lines, including drug-resistant and highly metastatic tumor cells. Detailed mechanistic studies reveal that the cationic anticancer polypeptide (ACPP) can directly induce rapid necrosis of cancer cells within minutes through a membrane-lytic mechanism. Moreover, a pH-sensitive zwitterionic derivative of ACPP (DA-ACPP) is prepared for in vivo application. DA-ACPP shows negligible hemolysis under neutral physiological conditions, and can be converted back to ACPP in slightly acidic tumor environments, resulting in selective killing of cancer cells. Consequently, DA-ACPP shows an effective inhibition of tumor growth in both 4T1 orthotopic breast tumor models and B16-F10 melanoma pulmonary metastatic models. Overall, these findings demonstrate that synthetic HDPs-mimicking polypeptides represent safe and effective antineoplastic agents, which sheds new light on the development of drug-free synthetic polymers for cancer therapy.

Molecular Fluorophores for Deep-Tissue Bioimaging

Fluorescence imaging has made tremendous inroads toward understanding the complexity of biological systems, but in vivo deep-tissue imaging remains a great challenge due to the optical opacity of biological tissue. Recent improvements in laser and detector manufacturing have allowed the expansion of nonlinear and linear fluorescence imaging to the underexplored "tissue-transparent" second near-infrared (NIR-II; 1000-1700 nm) window, opening up new opportunities for optical access deep inside opaque tissue. Molecular fluorophores have historically played a major role in fluorescence bioimaging. It is increasingly important to design new molecular fluorophores to fully unlock the potential of NIR-II imaging techniques. In this outlook, we give an overview of the novel molecular fluorophores developed for deep-tissue bioimaging in the past five years and discuss their pros and cons in applications. Guidelines for designing new molecular fluorophores with the desirable properties are also provided.

Role of MLCT States in the Franck-Condon Region of Neutral, Heteroleptic Cu(I)-4H-imidazolate Complexes: A Spectroscopic and Theoretical Study

The impact of the electronic structure of a series of 4H-imidazolate ligands in neutral, heteroleptic Cu(I) complexes is investigated. Remarkable broad and strong ligand-dependent absorption in the visible range of the electromagnetic spectrum renders the studied complexes promising photosensitizers for photocatalytic applications. The electronic structure of the Cu(I) complexes and the localization of photoexcited states in the Franck-Condon region are unraveled by means of UV-vis absorption and resonance Raman (rR) spectroscopy supported by time-dependent density functional theory (TD-DFT) calculations. The visible absorption bands stem from a superposition of bright metal-to-ligand charge-transfer (MLCT) and π-π* as well as weakly absorbing MLCT states. Additionally, the analysis of involved molecular orbitals and rR spectra upon excitation of MLCT and π-π* states highlights the impact of the electronic structure of the 4H-imidazolate ligands on the properties of the corresponding Cu(I) complexes to avail a toolbox for predictive studies and efficient complex design.

Nanoparticle Formulation of Indocyanine Green Improves Image-Guided Surgery in a Murine Model of Breast Cancer

PURPOSE

Negative surgical margins (NSMs) have favorable prognostic implications in breast tumor resection surgery. Fluorescence image-guided surgery (FIGS) has the ability to delineate surgical margins in real time, potentially improving the completeness of tumor resection. We have recently developed indocyanine green (ICG)-loaded self-assembled hyaluronic acid (HA) nanoparticles (NanoICG) for solid tumor imaging, which were shown to enhance intraoperative contrast.

PROCEDURES

This study sought to assess the efficacy of NanoICG on completeness of breast tumor resection and post-surgical survival. BALB/c mice bearing iRFP+/luciferase+ 4T1 syngeneic breast tumors were administered NanoICG or ICG, underwent FIGS, and were compared to bright light surgery (BLS) and sham controls.

RESULTS

NanoICG increased the number of complete resections and improved tumor-free survival. This was a product of improved intraoperative contrast enhancement and the identification of a greater number of small, occult lesions than ICG and BLS. Additionally, NanoICG identified chest wall invasion and predicted recurrence in a model of late-stage breast cancer.

CONCLUSIONS

NanoICG is an efficacious intraoperative contrast agent and could potentially improve surgical outcomes in breast cancer.

Fluorescence-guided lymphadenectomy in gastric cancer: a prospective western series

BACKGROUND

Indocyanine green (ICG) has been recently introduced in clinical practice as a fluorescent tracer. Lymphadenectomy is particularly challenging in gastric cancer surgery, owing to the complex anatomical drainage.

AIM

The primary outcomes of this study were the feasibility and usefulness of ICG-guided lymphadenectomy in gastric cancer surgery, considering both the success rate and improved understanding of the surgical anatomy of nodal basins. The secondary outcome was the diagnostic ability of ICG to predict the presence of nodal metastases.

PATIENTS AND METHODS

We conducted a single-center prospective trial comprising 13 patients with gastric cancer. ICG was injected the afternoon prior to surgery or intraoperatively via the submucosal or subserosal route. Standard lymphadenectomy was performed in all patients, according to patient age and tumor stage, as usual, but after standard lymphadenectomy the residual ICG + nodes were harvested and analyzed. Each nodal station and each dissected node was recorded and classified as ICG + or ICG- (both in vivo and back table evaluation was utilized for classification). After pathological analysis, each nodal station and each dissected node was recorded as metastatic or nonmetastatic (E&E staining).

RESULTS

The feasibility rate was 84.6% (11/13). The mean number of dissected lymph nodes per patient was 37.9. Focusing on the 11 patients in whom ICG-guided nodal navigation was successfully performed, 81 lymph node stations were removed, for a total of 417 lymph nodes. Sixty-six stations (81.48%), comprising a total of 336 lymph nodes, exhibited fluorescence. No IC- node was metastatic; all 54 metastatic nodes were ICG + . A total of 282 ICG + nodes were nonmetastatic. In two cases, some nodes outside D2 areas were harvested, being ICG + (1 case of metastatic node).

CONCLUSIONS

Fluorescence lymphography-guided lymphadenectomy is a promising new technique that combines a high feasibility rate with considerable ease of use. Regarding its diagnostic value, the key finding from this prospective series is that no metastatic nodes were found outside fluorescent lymph node stations. Further studies are needed to investigate whether this technique can help surgeons performing standard lymphadenectomy and selecting cases for D2 + lymphadenectomy.

Photodynamic effect of novel hexa-iodinated quinono-cyanine dye on Staphylococcus aureus

BACKGROUND

Staphylococcus aureus (S. aureus) is a Gram-positive bacteria and major human pathogen which can cause a wide variety of serious infections when it enters the bloodstream or internal tissues. Antimicrobial photodynamic therapy (APDT) utilizing a light-activated dye (photosensitizer) is a powerful method for in vitro and in vivo eradication of S. aureus and other pathogenic bacteria. However, the development of highly efficient, long-wavelength photosensitizers showing high phototoxicity to pathogens and low dark toxicity is still challenging.

AIM

To develop a highly efficient, long-wavelength photosensitizer for photodynamic inactivation of S. aureus.

METHOD

Synthesis of the new photosensitizer, hexa-iodinated quinono-cyanine dye IQCy and investigation of the dark and light-induced toxicity of this dye compared to known photosensitizers Chlorin e6 (Ce6) and HITC towards S. aureus.

RESULTS

When exposed to 14.9 J/cm² white LED light, 0.5 μM of IQCy, Ce6 and HITC inactivate, respectively, 99 %, 40 % and 30 % of S. aureus and at 0.05 μM and 27.9 J/cm² - 71 %, 18 % and 9%, which is much better compared to Ce6 and HITC. IQCy exhibits no dark toxicity at least at 10 μM dye concentration.

CONCLUSIONS

IQCy demonstrates a more pronounced photodynamic inactivation of S. aureus as compared to Ce6 and HITC and can be employed for the eradication of these bacteria at lower concentration and reduced light dose.

Two Isomeric Azulene-Decorated Naphthodithiophene Diimide-based Triads: Molecular Orbital Distribution Controls Polarity Change of OFETs Through Connection Position

Altering the charge carrier transport polarities of organic semiconductors by molecular orbital distribution has gained great interest. Herein, we report two isomeric azulene-decorated naphthodithiophene diimide (NDTI)-based triads (e.g., NDTI-B2Az and NDTI-B6Az), in which two azulene units were connected with NDTI at the 2-position of the azulene ring in NDTI-B2Az, whereas two azulene units were incorporated with NDTI at the 6-position of the azulene ring in NDTI-B6Az. The two isomeric triads were excellently soluble in common organic solvents. Density functional theory calculations on the molecular orbital distributions of the triads reveal that the lowest unoccupied molecular orbitals are completely delocalized over the entire molecule for both NDTI-B2Az and NDTI-B6Az, indicating great potential for n-type transport behavior, whereas the highest occupied molecular orbitals are mainly delocalized over the entire molecule for NDTI-B2Az or only localized at the two terminal azulene units for NDTI-B6Az, implying great potential for p-type transport behavior for the former and a disadvantage of hole carrier transport for the latter. Under ambient conditions, solution-processed bottom-gate top-contact transistors based on NDTI-B2Az showed ambipolar field-effect transistor (FET) characteristics with high electron and hole mobilities of 0.32 (effective electron mobility ≈0.14 cm² V^-1 s^-1 according to a reliability factor of 43%) and 0.03 cm² V^-1 s^-1 (effective hole mobility ≈0.01 cm² V^-1 s^-1 according to a reliability factor of 33%), respectively, whereas a typically unipolar n-channel behavior is found for a film of NDTI-B6Az with a high electron mobility up to 0.13 cm² V^-1 s^-1 (effective electron mobility ≈0.06 cm² V^-1 s^-1 according to a reliability factor of 43%). The results indicate that the polarity change of organic FETs based on the two isomeric triads could be controlled by the molecular orbital distributions through the connection position between the azulene unit and NDTI.

Dye-Loaded Quatsomes Exhibiting FRET as Nanoprobes for Bioimaging

Fluorescent organic nanoparticles (FONs) are emerging as an attractive alternative to the well-established fluorescent inorganic nanoparticles or small organic dyes. Their proper design allows one to obtain biocompatible probes with superior brightness and high photostability, although usually affected by low colloidal stability. Herein, we present a type of FONs with outstanding photophysical and physicochemical properties in-line with the stringent requirements for biomedical applications. These FONs are based on quatsome (QS) nanovesicles containing a pair of fluorescent carbocyanine molecules that give rise to Förster resonance energy transfer (FRET). Structural homogeneity, high brightness, photostability, and high FRET efficiency make these FONs a promising class of optical bioprobes. Loaded QSs have been used for in vitro bioimaging, demonstrating the nanovesicle membrane integrity after cell internalization, and the possibility to monitor the intracellular vesicle fate. Taken together, the proposed QSs loaded with a FRET pair constitute a promising platform for bioimaging and theranostics.

Supramolecular β-Sheet Forming Peptide Conjugated with Near-Infrared Chromophore for Selective Targeting, Imaging, and Dysfunction of Mitochondria

Herein, conjugation of the amyloid-β (Aβ) peptide fragment, Lys-Leu-Val-Phe-Phe (KLVFF, fragment of Aβ_16-20), with an unsymmetrical near-infrared (NIR) cyanine-5 (Cy-5) chromophore is achieved using microwave-assisted solid phase synthesis on 2-chlorotrityl chloride resin. Selective mitochondria tracking and staining in human carcinoma cells are accomplished by the KLVFF/Cy-5 conjugate containing triphenylphosphonium functionality, and this is compared to a control molecule KLVFF/Cy-5c. Mitochondrial target specificity of KLVFF/Cy-5 is established by the colocalization assay using mitochondria selective probe MitoTracker Red, which is monitored by confocal laser scanning microscope and shows a high Pearson's correlation coefficient. The KLVFF/Cy-5 conjugate has high photostability, NIR absorption/emission, high molar extinction coefficient, narrow absorption/emission band, high fluorescence lifetime, and high fluorescence quantum yield. Moreover, mitochondria targeting KLVFF/Cy-5 conjugate reaches the critical aggregation concentration inside the mitochondria of cancer cells due to the strong negative inner mitochondrial membrane potential [(ΔΨ_m)_cancer -220 mV] and self-assembles to form amyloid fibrils at the target site, which is responsible for the mitochondrial dysfunction and cytotoxicity. Annexin V-FITC/PI apoptosis detection assay is used to determine the signal pathway of mitochondria targeted cellular dysfunction.

Cyanine dyes

Cyanine dyes are characterized by an odd number 2n + 3 of π-centers and 2n + 4 π-electrons (where n is the number of vinyl groups –CH = CH–). This special feature has a marked impact on their electronic structure and thus their equilibrium structure in the electronic ground state as well their color and electronic spectrum, respectively. Their first technical application was the use as spectral sensitizers in silver halide photography. Today they have numerous of applications in digital optical data storage, Computer-to-Plate lithographic printing plates, bio-analysis and medical diagnostics.

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.

Photobleaching of organic fluorophores: quantitative characterization, mechanisms, protection

Photochemical stability is one of the most important parameters that determine the usefulness of organic dyes in different applications. This Review addresses key factors that determine the dye photostability. It is shown that photodegradation can follow different oxygen-dependent and oxygen-independent mechanisms and may involve both ¹S₁-³T₁ and higher-energy ¹S_n-³T_n excited states. Their involvement and contribution depends on dye structure, medium conditions, irradiation power. Fluorescein, rhodamine, BODIPY and cyanine dyes, as well as conjugated polymers are discussed as selected examples illustrating photobleaching mechanisms. The strategies for modulating and improving the photostability are overviewed. They include the improvement of fluorophore design, particularly by attaching protective and anti-fading groups, creating proper medium conditions in liquid, solid and nanoscale environments. The special conditions for biological labeling, sensing and imaging are outlined.

Selective Colorimetric "Turn-On" Probe for Efficient Engineering of Iminium Biocatalysis

The efficient engineering of iminium biocatalysis has drawn considerable attention, with many applications in pharmaceutical synthesis. Here, we report a tailor-made iminium-activated colorimetric "turn-on" probe, specifically designed as a prescreening tool to facilitate engineering of iminium biocatalysis. Upon complexation of the probe with the catalytic Pro-1 residue of the model enzyme 4-oxalocrotonate tautomerase (4-OT), a brightly colored merocyanine-dye-type structure is formed. 4-OT mutants that formed this brightly colored species upon incubation with the probe proved to have a substantial activity for the iminium-based Michael-type addition of nitromethane to cinnamaldehyde, whereas mutants that showed no staining by the probe exhibited no or very low-level "Michaelase" activity. This system was exploited in a solid-phase prescreening assay termed as activated iminium colony staining (AICS) to enrich libraries for active mutants. AICS prescreening reduced the screening effort up to 20-fold. After two rounds of directed evolution, two artificial Michaelases were identified with up to 39-fold improvement in the activity for the addition of nitromethane to cinnamaldehyde, yielding the target γ-nitroaldehyde product with excellent isolated yield (up to 95%) and enantiopurity (up to >99% ee). The colorimetric activation of the turn-on probe could be extended to the class I aldolase 2-deoxy-d-ribose 5-phosphate aldolase, implicating a broader application of AICS in engineering iminium biocatalysis.

Recent Progress in NIR-II Contrast Agent for Biological Imaging

Fluorescence imaging technology has gradually become a new and promising tool for in vivo visualization detection. Because it can provide real-time sub-cellular resolution imaging results, it can be widely used in the field of biological detection and medical detection and treatment. However, due to the limited imaging depth (1-2 mm) and self-fluorescence background of tissue emitted in the visible region (400-700 nm), it fails to reveal biological complexity in deep tissues. The traditional near infrared wavelength (NIR-I, 650-950 nm) is considered as the first biological window, because it reduces the NIR absorption and scattering from blood and water in organisms. NIR fluorescence bioimaging's penetration is larger than that of visible light. In fact, NIR-I fluorescence bioimaging is still interfered by tissue autofluorescence (background noise), and the existence of photon scattering, which limits the depth of tissue penetration. Recent experimental and simulation results show that the signal-to-noise ratio (SNR) of bioimaging can be significantly improved at the second region near infrared (NIR-II, 1,000-1,700 nm), also known as the second biological window. NIR-II bioimaging is able to explore deep-tissues information in the range of centimeter, and to obtain micron-level resolution at the millimeter depth, which surpass the performance of NIR-I fluorescence imaging. The key of fluorescence bioimaging is to achieve highly selective imaging thanks to the functional/targeting contrast agent (probe). However, the progress of NIR-II probes is very limited. To date, there are a few reports about NIR-II fluorescence probes, such as carbon nanotubes, Ag2S quantum dots, and organic small molecular dyes. In this paper, we surveyed the development of NIR-II imaging contrast agents and their application in cancer imaging, medical detection, vascular bioimaging, and cancer diagnosis. In addition, the hotspots and challenges of NIR-II bioimaging are discussed. It is expected that our findings will lay a foundation for further theoretical research and practical application of NIR-II bioimaging, as well as the inspiration of new ideas in this field.

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

It was demonstrated that styrylquinolizinium derivatives may be applied as photoswitchable DNA ligands. At lower ligand:DNA ratios (≤1.5), these compounds bind to duplex DNA by intercalation, with binding constants ranging from K b = 4.1 × 104 M to 2.6 × 105 M (four examples), as shown by photometric and fluorimetric titrations as well as by CD and LD spectroscopic analyses. Upon irradiation at 450 nm, the methoxy-substituted styrylquinolizinium derivatives form the corresponding syn head-to-tail cyclobutanes in a selective [2 + 2] photocycloaddition, as revealed by X-ray diffraction analysis of the reaction products. These photodimers bind to DNA only weakly by outside-edge association, but they release the intercalating monomers upon irradiation at 315 nm in the presence of DNA. As a result, it is possible to switch between these two ligands and likewise between two different binding modes by irradiation with different excitation wavelengths.

A Fast-Response Red Shifted Fluorescent Probe for Detection of H2S in Living Cells

Near-infrared (NIR) fluorescent probes are attractive tools for bioimaging applications because of their low auto-fluorescence interference, minimal damage to living samples, and deep tissue penetration. H2S is a gaseous signaling molecule that is involved in redox homeostasis and numerous biological processes in vivo. To this end, we have developed a new red shifted fluorescent probe 1 to detect physiological H2S in live cells. The probe 1 is based on a rhodamine derivative as the red shifted fluorophore and the thiolysis of 7-nitro 1,2,3-benzoxadiazole (NBD) amine as the H2S receptor. The probe 1 displays fast fluorescent enhancement at 660 nm (about 10-fold turn-ons, k2 = 29.8 M-1s-1) after reacting with H2S in buffer (pH 7.4), and the fluorescence quantum yield of the activated red shifted product can reach 0.29. The probe 1 also exhibits high selectivity and sensitivity towards H2S. Moreover, 1 is cell-membrane-permeable and mitochondria-targeting, and can be used for imaging of endogenous H2S in living cells. We believe that this red shifted fluorescent probe can be a useful tool for studies of H2S biology.

Single-Virus Tracking: From Imaging Methodologies to Virological Applications

Uncovering the mechanisms of virus infection and assembly is crucial for preventing the spread of viruses and treating viral disease. The technique of single-virus tracking (SVT), also known as single-virus tracing, allows one to follow individual viruses at different parts of their life cycle and thereby provides dynamic insights into fundamental processes of viruses occurring in live cells. SVT is typically based on fluorescence imaging and reveals insights into previously unreported infection mechanisms. In this review article, we provide the readers a broad overview of the SVT technique. We first summarize recent advances in SVT, from the choice of fluorescent labels and labeling strategies to imaging implementation and analytical methodologies. We then describe representative applications in detail to elucidate how SVT serves as a valuable tool in virological research. Finally, we present our perspectives regarding the future possibilities and challenges of SVT.

Construction and bioimaging application of novel indole heptamethine cyanines containing functionalized tetrahydropyridine rings

IR780 as a commercially available dye with near-infrared emission has been extensively applied in fluorescent probes and bioimaging.

The origin of the solvent dependence of fluorescence quantum yields in dipolar merocyanine dyes

Fluorophores with high quantum yields are desired for a variety of applications. Optimization of promising chromophores requires an understanding of the non-radiative decay channels that compete with the emission of photons. We synthesized a new derivative of the famous laser dye 4-dicyanomethylen-2-methyl-6-p-dimethylaminostyryl-4H-pyran (DCM), i.e., merocyanine 4-(dicyanomethylene)-2-tert-butyl-6-[3-(3-butyl-benzothiazol-2-ylidene)1-propenyl]-4H-pyran (DCBT). We measured fluorescence lifetimes and quantum yields in a variety of solvents and found a trend opposite to the energy gap law. This motivated a theoretical investigation into the possible non-radiative decay channels. We propose that a barrier to a conical intersection exists that is very sensitive to the solvent polarity. The conical intersection is characterized by a twisted geometry which allows a subsequent photoisomerization. Transient absorption measurements confirmed the formation of a photoisomer in unpolar solvents, while the measurements of fluorescence quantum yields at low temperature demonstrated the existence of an activation energy barrier.

About the origin of the large Stokes shift in aminoalkyl substituted heptamethine cyanine dyes

Aminoalkyl-substituted heptamethine cyanine dyes are characterized by a large Stokes shift, an uncommon feature for cyanine molecules yet very promising for their application as fluorescent probes in bioimaging and as light harvesting antennas in biohybrid systems for solar energy conversion. The origin of this photophysical feature has not been adequately explored so far, and a combined experimental and theoretical work is herein provided to shed light on the role played by the central aminoalkyl substituent bound to the heptamethine cyanine backbone in defining the unusual properties of the dye. The spectra recorded in solvents of different polarities point to a marginal role of the medium in the definition of the Stokes shift, which conversely can be ascribed to the relaxation of the molecular geometry upon photoexcitation. This hypothesis is supported by an extensive theoretical investigation of the ground and excited states of the dye. TD-DFT results on the aminoalkyl-substituted dye and its unsubstituted precursor demonstrate a very similar cyanine-like structure for both molecules in the relaxed excited state. Conversely, in the ground state the amino substitution disrupts the conjugation in the polymethine chain, leading to a broken-symmetry, non-planar structure.

Acyl radical to rhodacycle addition and cyclization relay to access butterfly flavylium fluorophores

Transition metal-catalyzed C–H activation and radical reactions are two versatile strategies to construct diverse organic skeletons. Here we show the construction of a class of flavylium fluorophores via the merge of radical chemistry and C–H activation starting from (hetero)aryl ketones and alkynes. This protocol is not only applicable to aryl ketones but also to heteroaryl ketones such as thiophene, benzothiophene and benzofuran, thus leading to structural diversity. Mechanism studies, including control experiments, intermediate separation, radical trapping, EPR and ESI-HRMS experiments, demonstrate that the key step lies in the addition of the acyl radical generated by the copper-catalyzed C–C bond cleavage of aryl ketone to the rhodacycle formed via the C–H activation of aryl ketone. The flavylium fluorophores feature butterfly symmetrical configuration, nearly planar skeleton and delocalized positive charge, and exhibit intriguing photophysical properties, such as tunable absorption and emission wavelengths and high quantum yields.

Structural diversity of organic fluorophores is of importance for several applications (fluorescent markers, photosensitizers, etc.). Here the authors report a method to merge radical chemistry with C–H activation to construct a brand-new class of flavylium fluorophores starting from (hetero)aryl ketones and alkynes.

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.