Synthesis of BODIPY-pyrrolo[3,4-b]pyridin-5-ones via Ugi-Zhu/cascade reactions and studies of fluorescence response toward viscosity

A series of seven new meso-phenyl BODIPY-pyrrolo[3,4-b]pyridin-5-one conjugates were synthesized in one experimental step by using a Sc(III)-catalyzed Ugi-Zhu three-component reaction coupled to a cascade sequence (aza Diels-Alder/N-acylation/aromatization) as post-MCR functionalization process. Further experimental studies were performed behind understanding the fluorescence response toward viscosity. All compounds exhibited a linear response between increasing viscosity (DMSO and glycerol mixtures) and fluorescence intensity. The different substituents also influenced the photophysical properties. Furthermore, in DMSO all compounds exhibited dual emission. Each band is attributed to the pyrrolo[3,4-b]pyridin-5-one and BODIPY moieties, respectively. The electronic structure of all compounds was computed by DFT and TD-DFT calculations, allowing to determine the molecular orbitals involved in the electronic transitions.

BODIPY Dimers with a Fused and Coplanar Structure: Photophysical Comparison, Low Threshold for Amplified Spontaneous Emission, and Deep-Red Bio-Imaging/Photodynamic Therapy Application

Boron dipyrromethene (BODIPY)-derived dyes are generally superior emitters, but their absorption and emission fail to match the bio-active optical window (650-900 nm). In this work, we explored four bisBODIPY dyes (PB1-PB4) with easy-to-go synthesis, good solubility, high photostability, and high emission quantum yield in the deep-red region. Methyl and ethyl groups were introduced in these BODIPY dyes to improve their solubility. PB4 having a fused coplanar plane was synthesized and compared to PB1-PB3 having a non-fused structure. Their geometric structure was confirmed by single-crystal analysis, and their electronic structure, along with one-photon and two-photon absorptions, was analyzed by time-dependent functional theory calculation. Their absorption/emission spectra, emission quantum yields, and lifetimes were compared. It was found that the fused coplanar structure successfully red shifted PB4 absorption/emission to the deep-red region (698/720 nm), with a quantum yield of 0.58. PB4 showed an amplified spontaneous emission effect with an output efficiency of 6.0% at a pumping power of 3000 μJ. An improved photodynamic therapy (PDT) performance was observed from PB4 via in vitro and in vivo experiments. The practical PDT performance was evaluated by cell availability. Upon a 980 nm laser radiation of 5 min, the cell viability was decreased to ∼15%.

Intermolecular dark resonance energy transfer (DRET): upgrading fluorogenic DNA sensing

The sensitivity of FRET-based sensing is usually limited by the spectral overlaps of the FRET donor and acceptor, which generate a poor signal-to-noise ratio. To overcome this limitation, a quenched donor presenting a large Stokes shift can be combined with a bright acceptor to perform Dark Resonance Energy Transfer (DRET). The consequent fluorogenic response from the acceptor considerably improves the signal-to-noise ratio. To date, DRET has mainly relied on a donor that is covalently bound to the acceptor. In this context, our aim was to develop the first intermolecular DRET pair for specific sensing of nucleic acid sequences. To this end, we designed DFK, a push-pull probe based on a fluorenyl π-platform that is strongly quenched in water. DFK was incorporated into a series of oligonucleotides and used as a DRET donor with Cy5-labeled complementary sequences. In line with our expectations, excitation of the dark donor in the double-labeled duplex switched on the far-red Cy5 emission and remained free of cross-excitation. The DRET mechanism was supported by time-resolved fluorescence measurements. This concept was then applied with binary probes, which confirmed the distance dependence of DRET as well as its potency in detecting sequences of interest with low background noise.

Carbazole Substituted BODIPYs

Difluoroboron-dipyrromethenes (BODIPYs) are highly popular fluorescent dyes with applications as NIR probes for bioimaging, fluorescent tags/sensors and as photosensitizers in cancer therapy and organic photovoltaics. This review concentrates on the synthesis and spectral properties of BODIPY dyes conjugated with carbazole heterocycle. The carbazole is an electron rich tricyclic compound and due to its excellent electronic properties, it is extensively used in the production of electroluminescent materials and polymers. This review highlights the recent progress made on the series of BODIPY derivatives containing carbazole ring at alpha, beta, and meso-positions of the BODIPY skeleton. Carbazole based hybrid BODIPYs, carbazole linked aza-BODIPYs and carbazole-fused BODIPYs are also discussed.

Towards Efficient and Photostable Red-Emitting Photonic Materials Based on Symmetric All-BODIPY-Triads, -Pentads, and -Hexads

The development of efficient and stable red and near-IR emitting materials under hard radiation doses and/or prolonged times is a sought-after task due to their widespread applications in optoelectronics and biophotonics. To this aim, novel symmetric all-BODIPY-triads, -pentads, and -hexads have been designed and synthesized as light-harvesting arrays. These photonic materials are spectrally active in the 655-730 nm region and display high molar absorption across UV-visible region. Furthermore, they provide, to the best of our knowledge, the highest lasing efficiency (up to 68 %) and the highest photostability (tolerance >1300 GJ mol^-1 ) in the near-IR spectral region ever recorded under drastic pumping conditions. Additionally, the modular synthetic strategy to access the cassettes allows the systematic study of their photonic behavior related to structural factors. Collectively, the outstanding behavior of these multichromophoric photonic materials provides the keystone for engineering multifunctional systems to expedite the next generation of effective red optical materials.

A red-emitting fluorescent probe with large Stokes shift for real-time tracking of cysteine over glutathione and homocysteine in living cells

Fluorescent probes with high quality for highly selective detection of cysteine (Cys) are still urgently in demand because of the indispensable roles Cys plays in the biological systems. Herein, a red-emitting fluorescent probe CP was developed for the highly selective detection of Cys over glutathione (GSH) and homocysteine (Hcy) by incorporating acryloyl group as the recognition unit into the 2-(2-(4-hydroxystyryl)-6-methyl-4H-pyran-4-ylidene) malononitrile (P-OH) fluorophore which is characterized by red emission, noteworthy Stokes shift, and appreciable photostability. Basically, CP demonstrated appreciable sensing performance toward Cys including short response time of 4 min, high sensitivity with approximately 147-fold emission enhancement, low detection limit of 41.696 nM, and good selectivity both in the solution and living cells, indicating its promising potential of visualizing Cys in biological systems.

Visualizing biofilm by targeting eDNA with long wavelength probe CDr15

We developed a small molecule CDr15, which has eDNA selectivity of bacterial biofilm.

A NIR fluorescent sensor for biothiols based on a dicyanoisophorone derivative with a large Stokes shift and high quantum yield

Probe N-Bio exhibited rapid response, high sensitivity and strong NIR fluorescence in the detection of biothiols in living cells.

Diphenylacrylonitrile-connected BODIPY dyes: fluorescence enhancement based on dark and AIE resonance energy transfer

This study focuses on the construction of novel diphenylacrylonitrile-connected BODIPY dyes with high fluorescence in both solution and an aggregated state by combining DRET and FRET processes in a single donor-acceptor system. The first BODIPY derivatives with one, two, or three AIE-active diphenylacrylonitrile groups were designed and synthesized in moderate yields. Strong fluorescence emissions were observed in the THF solution under excitation at the absorption wavelength of non-emissive diphenylacrylonitrile chromophores, implying the existence of the DRET process between the dark diphenylacrylonitrile donor and the emissive BODIPY acceptor. In the THF/H₂O solution, the fluorescence intensity of the novel BODIPY derivatives gradually increased under excitation at the absorption wavelength of diphenylacrylonitrile chromophores, suggesting a FRET process between diphenylacrylonitrile and BODIPY moieties. A greater number of diphenylacrylonitrile units led to higher energy-transfer efficiencies. The pseudo-Stokes shift for both DRET and FRET processes was as large as 190 nm.

A NIR fluorescent probe for the detection and visualization of hydrogen sulfide using the aldehyde group assisted thiolysis of dinitrophenyl ether strategy

A NIR fluorescent probe exploiting the aldehyde group assisted thiolysis of dinitrophenyl ether strategy for H₂S imaging in cells, tissues and mice.

A silica supported tricarbocyanine based pH nanosensor with a large Stokes shift and a near infrared fluorescence response: performance in vitro and in live cells

We report the synthesis of a near-infrared (NIR) fluorescent pH probe with a remarkable Stokes shift (∼135 nm) based on a tricarbocyanine (Cy-PIP).

Novel Dual BODIPY-Carbazole Conjugates with Various Linkers

Four dual BODIPY-carbazole conjugates (BDPa–d, BODIPY is 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene), with various π bridges, including none, phenyl, thiophene, and furan, were designed and synthesized. The results suggest that the π bridges have significant effect on the thermal, photophysical, and electrochemical properties of the conjugates. BDPc and BDPd, with a five-membered heterocycle as a π bridge possessing more coplanar molecular geometry, exhibit broader and red-shifted absorption with an obvious charge transfer shoulder peak, as well as red-shifted emission. UV-visible absorption spectroscopy and cyclic voltammetry results show that the extension of the π-conjugated system leads to a reduction in the optical gap with a decrease of the LUMO level. All conjugates display remarkable Stokes shifts (107–216 nm) and low fluorescence quantum yields. BDPc and BDPd, which essentially possess broad and intense absorption, and suitable HOMO–LUMO energy levels, are potential candidates for light-harvesting and photovoltaic applications.

AIEgens for dark through-bond energy transfer: design, synthesis, theoretical study and application in ratiometric Hg2+ sensing

A novel dark through-bond energy transfer (DTBET) strategy is proposed and applied as the design strategy to develop ratiometric Hg²⁺ sensors with high performance. Tetraphenylethene (TPE) derivatives with aggregation-induced emission (AIE) characteristics are selected as dark donors to eliminate emission leakage from the donors. The TBET mechanism has been adopted since it experiences less influence from spectral overlapping than Förster resonance energy transfer (FRET), making it more flexible for developing cassettes with large pseudo-Stokes shifts. In this work, energy transfer from the TPE derivatives (dark donor) to a rhodamine moiety (acceptor) was illustrated through photophysical spectroscopic studies and the energy transfer efficiency (ETE) was found to be up to 99%. In the solution state, no emission from the donors was observed and large pseudo-Stokes shifts were achieved (>280 nm), which are beneficial for biological imaging. Theoretical calculations were performed to gain a deeper mechanistic insight into the DTBET process and the structure-property relationship of the DTBET cassettes. Ratiometric Hg²⁺ sensors were rationally constructed based on the DTBET mechanism by taking advantage of the intense emission of TPE aggregates. The Hg²⁺ sensors exhibited well resolved emission peaks. >6000-fold ratiometric fluorescent enhancement is also achieved and the detection limit was found to be as low as 0.3 ppb. This newly proposed DTBET mechanism could be used to develop novel ratiometric sensors for various analytes and AIEgens with DTBET characteristics will have great potential in various areas including light harvesting materials, environmental science, chemical sensing, biological imaging and diagnostics.

A Simple BODIPY-Based Viscosity Probe for Imaging of Cellular Viscosity in Live Cells

Intracellular viscosity is a fundamental physical parameter that indicates the functioning of cells. In this work, we developed a simple boron-dipyrromethene (BODIPY)-based probe, BTV, for cellular mitochondria viscosity imaging by coupling a simple BODIPY rotor with a mitochondria-targeting unit. The BTV exhibited a significant fluorescence intensity enhancement of more than 100-fold as the solvent viscosity increased. Also, the probe showed a direct linear relationship between the fluorescence lifetime and the media viscosity, which makes it possible to trace the change of the medium viscosity. Furthermore, it was demonstrated that BTV could achieve practical applicability in the monitoring of mitochondrial viscosity changes in live cells through fluorescence lifetime imaging microscopy (FLIM).

Synthesis and spectroscopic properties of β,β'-dibenzo-3,5,8-triaryl-BODIPYs

A series of β,β'-bicyclo-3,5-diaryl-BODIPYs were synthesized from the corresponding β,β'-bicyclo-3,5-diiodo-BODIPYs (1a,b) via Pd(0)-mediated Suzuki cross-coupling reactions in 82-92% yields. Subsequent aromatization with DDQ afforded the corresponding β,β'-dibenzo-aryl-BODIPYs, which showed red-shifted absorptions and emissions in the near-IR range. The dibenzo-appended BODIPYs showed characteristic 1H-, 13C-, 11B- and 19F-NMR shifts, and nearly planar conformations by X-ray crystallography.

The first porphyrin–subphthalocyaninatoboron(iii)-fused hybrid with unique conformation and intramolecular charge transfer behavior

The first porphyrin–subphthalocyaninatoboron(iii)-fused hybrid with unique conformation and intramolecular charge-transfer behaviour has been isolated and structurally characterized.

Non-symmetric benzo[b]-fused BODIPYs as a versatile fluorophore platform reaching the NIR: a systematic study of the underlying structure–property relationship

Ten newly synthesized non-symmetric benzo[b]-fused BODIPYs are compared with an extended series of nine related families (23 compounds) to gain insights into their structure–property relationship.

From Dark to Light to Fluorescence Resonance Energy Transfer (FRET): Polarity-Sensitive Aggregation-Induced Emission (AIE)-Active Tetraphenylethene-Fused BODIPY Dyes with a Very Large Pseudo-Stokes Shift

The work presented herein is devoted to the fabrication of large Stokes shift dyes in both organic and aqueous media by combining dark resonance energy transfer (DRET) and fluorescence resonance energy transfer (FRET) in one donor-acceptor system. In this respect, a series of donor-acceptor architectures of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) dyes substituted by one, two, or three tetraphenylethene (TPE) luminogens were designed and synthesised. The photophysical properties of these three chromophore systems were studied to provide insight into the nature of donor-acceptor interactions in both THF and aqueous media. Because the generation of emissive TPE donor(s) is strongly polarity dependent, due to its aggregation-induced emission (AIE) feature, one might expect the formation of appreciable fluorescence emission intensity with a very large pseudo-Stokes shift in aqueous media when considering FRET process. Interestingly, similar results were also recorded in THF for the chromophore systems, although the TPE fragment(s) of the dyes are non-emissive. The explanation for this photophysical behaviour lies in the DRET. This is the first report on combining two energy-transfer processes, namely, FRET and DRET, in one polarity-sensitive donor-acceptor pair system. The accuracy of the dark-emissive donor property of the TPE luminogen is also presented for the first time as a new feature for AIE phenomena.

Discovery, understanding, and bioapplication of organic fluorophore: a case study with an indolizine-based novel fluorophore, Seoul-Fluor

Owing to its high sensitivity and great applicability, the fluorescence phenomenon has been considered as an inevitable research tool in the modern scientific fields of chemistry, biology, materials science, biomedical science, and their interfaces. Many strategies have been pursued to understand and manipulate the photophysical properties of fluorescent materials, but the scientific community has been focused on the repeated application of existing organic fluorophores or the identification of unique fluorescence properties in a trial-and-error basis without systematic studies. Moreover, recent studies are emphasizing the necessity of deeper understanding about the structure-photophysical property relationship of organic fluorophores for the development of better fluorescent probes. Herein, we provide an overview of a novel fluorescent molecular framework, Seoul-Fluor, which can be rationally engineered to furnish a wide variety of fluorophores in terms of the photophysical properties. Seoul-Fluor is built on an indolizine-based fluorescent platform with three different positions to introduce various substituents: R(1) and R(2) substituents for electronic perturbation; R(3) substituent as a functional handle for bioconjugation. Over the past decade, we have demonstrated that the Seoul-Fluor system has (i) tunable and predictable emission wavelength covering a full visible-color range; (ii) controllable quantum yield via photoinduced electron transfer phenomenon; and (iii) environment-sensitive fluorogenic properties that can be modified through intramolecular charge transfer processes. We convincingly demonstrated the prediction of photophysical properties, that is, emission wavelength and quantum yield, through the construction of a systematic set of analogues and the subsequent analysis of their photophysical properties without the highly sophisticated theoretical support. Guided by quantifiable parameters such as the Hammett substituent constants or energy levels of the molecular orbitals, this unique organic fluorophore can serve as a versatile molecular platform for the development of novel fluorescent switchable biosensors and fluorogenic bioprobes. In this Account, we will discuss the discovery and recent progress made on Seoul-Fluor, the rational design of Seoul-Fluor-based bioprobes, and their practical applications to specific biological processes that are facilitated by systematic studies of the structure-photophysical property relationships.

Fusion and planarization of bisBODIPY: a new family of photostable near infrared dyes

A new family of directly-fused bisBODIPY BBP was developed by fusion and planarization of bisBODIPY 4 through a FeCl₃-mediated intramolecular oxidative cyclodehydrogenation reaction, showing intriguing electrochemical and spectroscopic properties.

Synthesis and use of “clickable” bay-region tetrasubstituted perylene tetracarboxylic tetraesters and a perylene monoimide diester as energy acceptors

Novel perylene derivatives are ready to be used as functional energy acceptors in light-harvesting systems.

Synthesis and systematic evaluation of dark resonance energy transfer (DRET)-based library and its application in cell imaging

In this paper, we report a new strategy for constructing a dye library with large Stokes shifts. By coupling a dark donor with BODIPY acceptors of tunable high quantum yield, a novel dark resonance energy transfer (DRET)-based library, named BNM, has been synthesized. Upon excitation of the dark donor (BDN) at 490 nm, the absorbed energy is transferred to the acceptor (BDM) with high efficiency, which was tunable in a broad range from 557 nm to 716 nm, with a high quantum yield of up to 0.8. It is noteworthy to mention that the majority of the non-radiative energy loss of the donor was converted into the acceptor's fluorescence output with a minimum leak of donor emission. Fluorescence imaging tested in live cells showed that the BNM compounds are cell-permeable and can also be employed for live-cell imaging. This is a new library which can be excited through a dark donor allowing for strong fluorescence emission in a wide range of wavelengths. Thus, the BNM library is well suited for high-throughput screening or multiplex experiments in biological applications by using a single laser excitation source.