Geometry Relaxation-Induced Large Stokes Shift in Red-Emitting Borondipyrromethenes (BODIPY) and Applications in Fluorescent Thiol Probes

A two-photon fluorescent probe for highly selective detection of Cys over GSH and Hcy based on the Michael addition and transcyclization mechanism and its application in bioimaging and protein straining in SDS-PAGE

BACKGROUND

Cysteine (Cys), glutathione (GSH), and homocysteine (Hcy), as three major biothiols are involved in a variety of physiological processes and play a crucial role in plant growth. Abnormal levels of Cys can cause plants to fail to grow properly. To date, although a very large number of fluorescent probes have been reported for the detection of biothiols, very few of them can be used for the selective discrimination of Cys from GSH and Hcy due to their structural similarity, and only a few of them can be used for plant imaging.

RESULTS

Here, three fluorescent probes (o-/m-/p-TMA) based on TMN fluorophore and the ortho-/meta-/para-substituted maleimide recognition groups were constructed to investigate the selective response effect of Cys. Compared to the o-/m-TMA, p-TMA can selectively detect Cys over GSH and Hcy with a rapid response time (10 min) and a low detection limit (0.26 μM). The theoretical calculation confirmed that the intermediate p-TMA-Cys-int has shorter interatomic reaction distances (3.827 Å) compared to o-/m-TMA-Cys (5.533/5.287 Å), making it more suitable for further transcyclization reactions. Additionally, p-TMA has been employed for selective tracking of exogenous and endogenous Cys in Arabidopsis thaliana using both single-/two-photon fluorescence imaging. Furthermore, single cell walls produced obvious two-photon fluorescence signals, indicating that p-TMA can be used for high-concentration Cys analysis in single cells. Surprisingly, p-TMA can be used as a fluorescent dye for protein staining in SDS-PAGE with higher sensitivity (7.49 μg/mL) than classical Coomassie brilliant blue (14.11 μg/mL).

SIGNIFICANCE

The outstanding properties of p-TMA make it a promising multifunctional molecular tool for the highly selective detection of Cys over GSH and Hcy in various complex environments, including water solutions, zebrafish, and plants. Additionally, it has the potential to be developed as a fluorescent dye for a simple and fast SDS-PAGE fluorescence staining method.

Structural Analysis of the Large Stokes Shift Red Fluorescent Protein tKeima

The Keima family comprises large Stokes shift fluorescent proteins that are useful for dual-color fluorescence cross-correlation spectroscopy and multicolor imaging. The tKeima is a tetrameric large Stokes shift fluorescent protein and serves as the ancestor fluorescent protein for both dKeima and mKeima. The spectroscopic properties of tKeima have been previously reported; however, its structural basis and molecular properties have not yet been elucidated. In this study, we present the crystallographic results of the large Stokes shift fluorescent protein tKeima. The purified tKeima protein spontaneously crystallized after purification without further crystallization. The crystal structure of tKeima was determined at 3.0 Å resolution, revealing a β-barrel fold containing the Gln-Tyr-Gly chromophores mainly with cis-conformation. The tetrameric interfaces of tKeima were stabilized by numerous hydrogen bonds and salt-bridge interactions. These key residues distinguish the substituted residues in dKeima and mKeima. The key structure-based residues involved in the tetramer formation of tKeima provide insights into the generation of a new type of monomeric mKeima. This structural analysis expands our knowledge of the Keima family and provides insights into its protein engineering.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

Rational Design of Cost-Effective 4-Styrylcoumarin Fluorescent Derivatives for Biomolecule Labeling

Fluorescent labels are key tools in a wide range of modern scientific applications, such as fluorescence microscopy, flow cytometry, histochemistry, direct and indirect immunochemistry, and fluorescence in situ hybridization (FISH). Small fluorescent labels have important practical advantages as they allow maximizing the fluorescence signal by binding multiple fluorophores to a single biomolecule. At present, the most widely used fluorescent labels available present small Stokes shifts and are too costly to be used in routine applications. In this work we present four new coumarin derivatives, as promising and inexpensive fluorescent labels for biomolecules, obtained through a cost-effective, efficient, and straightforward synthetic strategy. Density functional theory and time-dependent density functional theory calculations of the electronic ground and lowest-lying singlet excited states were carried out in order to gain insights into the observed photophysical properties.

Adjustable Fluorescence Emission of J-Aggregated Tricarbocyanine in the Near-Infrared-II Region

Near-infrared (NIR) J-aggregates attract increasing attention in many areas, especially in biomedical applications, as they combine the advantages of NIR spectroscopy with the unique J-aggregation properties of organic dyes. They enhance light absorption and have been used as effective biological imaging and therapeutic agents to achieve high-resolution imaging or effective phototherapy in vivo. In this work, we present novel J-aggregates composed of the well-known cyanine molecules. Cyanines are one of the few types of molecules whose absorption and emission can be shifted over a broad spectral range, from the ultraviolet (UV) to the NIR regime. They can easily transform into J-aggregates with narrow absorption and emission peaks, which is accompanied by a red shift in their spectra. In this work, we show, for the first time, that the tricarbocyanine dye (IR 820) has two sharp fluorescence emission bands in the NIR-II region with high photostability. These emission bands can be tuned to a desired wavelength in the range of 1150-1560 and 1675 nm, with a linear dependence on the excitation wavelength. Cryogenic transmission electron microscopy (cryo-TEM) images are presented, and combined with molecular modeling analysis, they confirm IR 820 π-stacked self-assembled fibrous structures.

Bodipy Dimer for Enhancing Triplet-Triplet Annihilation Upconversion Performance

Triplet-triplet annihilation upconversion (TTA-UC) has considerable potential for emerging applications in bioimaging, optogenetics, photoredox catalysis, solar energy harvesting, etc. Fluoroboron dipyrrole (Bodipy) dyes are an essential type of annihilator in TTA-UC. However, conventional Bodipy dyes generally have large molar extinction coefficients and small Stokes shifts (<20 nm), subjecting them to severe internal filtration effects at high concentrations, and resulting in low upconversion quantum efficiency of TTA-UC systems using Bodipy dyes as annihilators. In this study, a Bodipy dimer (B-2) with large Stokes shifts was synthesized using the strategy of dimerization of an already reported Bodipy annihilator (B-1). Photophysical characterization and theoretical chemical analysis showed that both B-1 and B-2 can couple with the red light-activated photosensitizer PdTPBP to fulfill TTA-UC; however, the higher fluorescence quantum yield of B-2 resulted in a higher upconversion efficiency (η_UC) for PdTPBP/B-2 (10.7%) than for PdTPBP/B-1 (4.0%). This study proposes a new strategy to expand Bodipy Stokes shifts and improve TTA-UC performance, which can facilitate the application of TTA-UC in photonics and biophotonics.

A turn-on fluorescent probe based on ESIPT and AIEE mechanisms for the detection of butyrylcholinesterase activity in living cells and in non-alcoholic fatty liver of zebrafish

Butyrylcholinesterase (BChE) and acetylcholinesterase (AChE) are two important cholinesterase enzymes in human metabolism which are closely related to various diseases of the liver. BChE and AChE are difficult to be distinguished due to their similarity in biochemical properties. Therefore, developing BChE-specific probes with high sensitivity and low background reading is desirable for the relevant biological applications. Herein, we reported the design and synthesis of a fluorescent probe HBT-BChE for biological detection and imaging of BChE. The probe is triggered by BChE-mediated hydrolysis, releasing a fluorophore that holds AIEE and ESIPT properties with large Stokes shift (>100 nm), rendering the probe features of low background interference and high sensitivity. The probe can also distinguish BChE from AChE with a low detection limit of 7.540 × 10^-4 U/mL. Further in vitro studies have shown the ability of HBT-BChE to detect intracellular BChE activity, as well as to evaluate the efficiency of the BChE inhibitor. More importantly, the in vivo studies of imaging the BChE activity level in liver tissues using zebrafish as the model animal demonstrated the potential of HBT-BChE as a powerful tool for non-alcoholic fatty liver disease.

Mechanosynthesis of Triazolyl-bis(indolyl)methane Pharmacophores via Gold Catalysis: A Prelude to Their Molecular Electronic Properties and Biological Potency

Chemical structures possessing both 1,2,3-triazole and bis(indolyl)methane fragments gained considerable interest in drug synthesis owing to their established biological efficacies. However, 1,2,3-triazoles linked at the bridging position of bis(indolyl)methane is a logical and unexplored design approach. In this regard, nine new triazolyl-bis(indolyl)methane conjugates under AuCl catalyzed ball-milling conditions were accomplished. Comparative evaluation on absorptive and emissive properties of the synthesized dyads were also analyzed. To unravel the influence of different peripheral substituents on the electronic structure and π-orbital properties, theoretical investigations were performed. Screening of molecules for free radical scavenging, anti-inflammatory and antidiabetic showed comparable potency against reference drugs. In particular, compounds 7 h, 7 d and 7 a displayed good efficiency of α-amylase inhibition. The DNA gyrase inhibitory potential of all compounds were assessed in silico which revealed high binding affinity (ΔG=-8.99 Kcal/mol) for 7 i followed by 7 h (ΔG=-7.80 Kcal/mol) with the targeted protein.

Tris(boranil) Columnar Liquid Crystalline Fluorophores: pseudo-Triphenylene Boron(III) Complexes with Peripheral N-B-O Linkages

The borate complexes derived from salicylaldimine ligands, called boranils, possess a wide range of photophysical and electronic characteristics intrinsically. The unique combination of molecular rigidity, rendered by four-coordinate boron bridges, and extended π-conjugation enable them to serve as technically feasible fluorescent materials (dyes). The incorporation of liquid crystallinity in these boron(III) complexes, especially the columnar (Col) mesomorphism, which is overlooked hitherto, would provide a new dimension to these complexes. Herein, we report the first examples of tris(boranil) discotic liquid crystal (LC) dyes that have been readily synthesized by treating tris(N-salicylideneaniline)s, (TSAN)s, with BF₃ .Et₂ O in the presence of an acid quencher. These C₃ -symmetric borate complexes self-assemble into the Col phase, existing over a wide thermal span including room temperature. The 2D periodic order of the Col phases shows dependence on the length of the peripheral tails. The photophysical measurements reveal the fluorescence emission in their two condensed states viz., solid and Col phase, and in solution. Their electrochemical, two-step oxidation process coupled with the aforesaid features upholds their significance in applied research.

Rational development of an ESIPT-based fluorescent probe with large Stokes shift for imaging of hydrogen sulfide in live cells

It is crucial to monitor hydrogen sulfide (H2S) because H2S plays a vital role in the regulation of many physiology and pathology processes. Many evidences indicate that endogenous H2S is closely associated with many diseases such as inflammation and cancers. Herein, we reported a novel fluorescent probe BTDI to monitor the fluctuation of H2S based on the excited-state intramolecular proton transfer (ESIPT) mechanism both ex vivo and in vivo. The selectivity of BTDI for H2S is significantly higher than that for biothiols and other potential anions. After the probe responded to H2S, the nucleophilic addition reaction of the H2S with probe BTDI resulted the shifting of maximum emission peak from 630 nm to 542 nm and the fluorescent signals change from red to green emission along with a large Stokes shift (240 nm). Moreover, BTDI can be successfully applied to detect extracellular and endogenous H2S in living cells through fluorescent cell-imaging, which provides a promising tool for the specific recognition of H2S in complex biological systems.

Construction of novel coumarin-carbazole-based fluorescent probe for tracking of endogenous and exogenous H2S in vivo with yellow-emission and large Stokes shift

Recent medical studies have confirmed that endogenous H₂S serves as the third gas-messenger besides nitric oxide (NO) and carbon monoxide (CO), which is produced by enzyme-catalyzed metabolism of cysteine and takes part in multiple physiological processes. The abnormal levels induced by H₂S overproduction in mammals can destroy tissues and organ systems, which lead to certain serious diseases, such as neurodegenerative diseases, cardiovascular diseases, and various cancers. In this work, we developed a novel coumarin-carbazole fluorescent probe COZ-DNB with yellow emission and a large Stokes shift for H₂S detection. In probe COZ-DNB, the newly dye COZ-OH as a luminophore and the 2,4-dinitrophenyl ether moiety was chosen as a trigger group for H₂S. Probe COZ-DNB itself displayed nearly non-fluorescent. However, COZ-DNB gave the remarkable fluorescence with an 83-fold enhancement in the yellow region after interaction with H₂S. The sensing mechanism of COZ-DNB toward H₂S was checked by means of UHPLC, HRMS and DFT/TD-DFT calculations. What's more, probe COZ-DNB also exhibited fast response (2.0 min), high sensitivity (65.0 nM), a large Stokes shift (161.0 nm), high stability and excellent selectivity. Furthermore, COZ-DNB was applied for imaging of exogenous and endogenous H₂S in living HeLa cells and zebrafish with satisfactory performances. We anticipate COZ-DNB would be served as a potential tool for investigating the biological functions of H₂S in pathological processes.

Colorimetric and fluorescent detection of synthetic cathinones in oral fluid with meso-aryl BODIPYs and Cu(ii)

Synthetic cathinones are a class of new psychoactive substances whose consumption has increased a lot and is widespread throughout the world. Thus, there is currently a need for rapid and simple detection of these drugs. In particular, detection of synthetic cathinones in oral fluid in drivers can be of great importance in preventing traffic accidents. Herein, we report two probes, based on BODIPY derivatives combined with Cu(ii), which are able to detect these drugs both in water and in oral fluid, by changes in color and fluorescence. The determined limits of detection for ephedrone (as a model drug) are lower than the usual concentrations in saliva after intake of this type of drug. The sensing mechanism seems to be related to the cathinone induced reduction of Cu(ii) to Cu(i) with concomitants changes in the BODIPY structure.

Real-Time Fluorescence Imaging of the Abscisic Acid Receptor Allows Nondestructive Visualization of Plant Stress

Environmental stress greatly decreases crop yield. The application of noninvasive techniques is one of the most practical and feasible ways of monitoring the health condition of plants under stress. However, it remains largely unsolved. A chemical fluorescent probe can be applied as a typical nondestructive method, but it has not been applied in living plants for stress detection to date. The abscisic acid (ABA) receptor plays a central role in conferring tolerance to environmental stresses and is an excellent target for developing fluorescent probes. Herein, we developed a fluorescence molecular imaging technology to monitor live plant stress by visualizing the protein expression level of the ABA receptor PYR1. A computer-aided designed indicator dye, flubactin, exhibited an 8-fold enhancement in fluorescence intensity upon interaction with PYR1. In vitro and in vivo experiments showed that flubactin is suitable to be used to detect salt stress in plants in real time. Moreover, the low toxicity of flubactin promotes its application in the future. Our work opens a new era for the nondestructive visualization of plant stress in vivo.

2,2'-Bipyridine derived doubly B ← N fused bisphosphine-chalcogenides, [C5H3N(BF2){NCH2P(E)Ph2}]2 (E = O, S, Se): tuning of structural features and photophysical studies

2,2'-Bipyridine based bisphosphine [C₅H₃N{N(H)CH₂PPh₂}]₂ (1) and its bischalcogenide derivatives [C₅H₃N{N(H)CH₂P(E)Ph₂}]₂ (2, E = O; 3, E = S; 4, E = Se) were synthesized, and further reacted with BF₃·Et₂O/Et₃N to form doubly B ← N fused compounds [C₅H₃N(BF₂){NCH₂P(E)Ph₂}]₂ (5, E = O; 6, E = S; 7, E = Se) in excellent yields. The influence of the PE bonds on the electronic properties of the doubly B ← N fused systems and their structural features were investigated in detail, supported by extensive experimental and computational studies. Compound 6 exhibited a very high quantum yield of ϕ = 0.56 in CH₂Cl₂, whereas compound 7 showed a least quantum yield of ϕ = 0.003 in acetonitrile. Density functional theory (DFT) calculations demonstrated that the LUMO/HOMO of compounds 5-7 mostly delocalized over the entire π-conjugated frameworks. The involvement of PE bonds in the HOMO energy level of these compounds follows the order: PO < PS < PSe. Time-correlated single photon counting (TCSPC) experiments of compounds 5-7 revealed the singlet lifetime of 4.26 ns for 6, followed by 4.03 ns for 5 and a lowest value of 2.18 ns (τ₁) and 0.47 ns (τ₂) with a double decay profile for 7. Our findings provide important strategies for the design of highly effective B ← N bridged compounds and tuning their photophysical properties by oxidizing phosphorus with different chalcogens. Compounds 5 and 6 have been employed as green emitters (λ_em = 515 nm) in fluorescent organic light-emitting diodes (OLEDs). For compound 5, doped into the poly(9-vinylcarbazole) (PVK) matrix with 5 wt% doping concentration, nearly 90 Cd m^-2 luminance with 0.022% external quantum efficiency (EQE) was achieved. The best performance was observed for compound 6 doped into PVK by 1 wt% having a maximum luminance of 350 Cd m^-2 and a similar EQE value.

Recent Advances in BODIPY Compounds: Synthetic Methods, Optical and Nonlinear Optical Properties, and Their Medical Applications

Organoboron compounds are attracting immense research interest due to their wide range of applications. Particularly, low-coordinate organoboron complexes are receiving more attention due to their improbable optical and nonlinear optical properties, which makes them better candidates for medical applications. In this review, we summarize the various synthetic methods including multicomponent reactions, microwave-assisted and traditional pathways of organoboron complexes, and their optical and nonlinear properties. This review also includes the usage of organoboron complexes in various fields including biomedical applications.

New Red-Shifted 4-Styrylcoumarin Derivatives as Potential Fluorescent Labels for Biomolecules

Important scientific areas, such as cellular biology, medicine, pharmacy, and environmental sciences, are dependent on very sensitive analytical techniques to track and detect biomolecules. In this work, we develop a simple, low-cost and effective synthetic strategy to produce new red-shifted 4-styrylcoumarin derivatives as promising inexpensive fluorescent labels for biomolecules. The extension of the delocalized π-electron system results in bathochromic shifts in these new coumarin derivatives, which also present large Stokes shifts. In addition, density functional theory and time-dependent density functional theory calculations helped to rationalize the photophysical properties observed by the experimental results.

Development of new 2-piperidinium-4-styrylcoumarin derivatives with large Stokes shifts as potential fluorescent labels for biomolecules

New 2-piperidinium-4-styrylcoumarin derivatives, with large Stokes shifts and high fluorescence quantum yields, as potential fluorescent labels for biomolecules.

O-BODIPYs as fluorescent labels for sugars: glucose, xylose and ribose

Fluorescent 1 : 1, 1 : 2 and 1 : 3 sugar-O-BODIPY conjugates of glucose, xylose and ribose were characterised by 1H–11B HMBC and 11B NMR to discriminate between boron bound to 1,2-, 1,3- or 1,4-diol sites and furanose/pyranose sugar forms.

A deep-red-emission antimony(III) chloride with dual-cations: extremely large Stokes shift due to high [SbCl6] distortion

Compound [C₅mim][Mim]₂[SbCl₆] (1; [C₅mim]⁺ = 1-pentyl-3-methylimidazolium; [Mim]⁺ = N-methylimidazolium) with dual cations exhibits the first case of deep-red emission in [SbCl₆]^3--based 0D OIMHs. Anion distortion due to high disequilibrium of supramolecular interactions is revealed to be responsible for the extremely large Stokes shift of 335 nm and FWHM of 210 nm in the emission.

Benchmarking Density Functional Approximations for Excited-State Properties of Fluorescent Dyes

This study presents an extensive analysis of the predictive power of time-dependent density functional theory in determining the excited-state properties of two groups of important fluorescent dyes, difluoroboranes and hydroxyphenylimidazo[1,2-a]pyridine derivatives. To ensure statistically meaningful results, the data set is comprised of 85 molecules manifesting diverse photophysical properties. The vertical excitation energies and dipole moments (in the electronic ground and excited states) of the aforementioned dyes were determined using the RI-CC2 method (reference) and with 18 density functional approximations (DFA). The set encompasses DFAs with varying amounts of exact exchange energy (EEX): from 0% (e.g., SVWN, BLYP), through a medium (e.g., TPSSh, B3LYP), up to a major contribution of EEX (e.g., BMK, MN15). It also includes range-separated hybrids (CAM-B3LYP, LC-BLYP). Similar error profiles of vertical energy were obtained for both dye groups, although the errors related to hydroxyphenylimidazopiridines are significantly larger. Overall, functionals including 40-55% of EEX (SOGGA11-X, BMK, M06-2X) ensure satisfactory agreement with the reference vertical excitation energies obtained using the RI-CC2 method; however, MN15 significantly outperforms them, providing a mean absolute error of merely 0.04 eV together with a very high correlation coefficient (R2 = 0.98). Within the investigated set of functionals, there is no single functional that would equally accurately determine ground- and excited-state dipole moments of difluoroboranes and hydroxyphenylimidazopiridine derivatives. Depending on the chosen set of dyes, the most accurate μGS predictions were delivered by MN15 incorporating a major EEX contribution (difluoroboranes) and by PBE0 containing a minor EEX fraction (hydroxyphenylimidazopiridines). Reverse trends are observed for μES, i.e., for difluoroboranes the best results were obtained with functionals including a minor fraction of EEX, specifically PBE0, while in the case of hydroxyphenylimidazopiridines, much more accurate predictions were provided by functionals incorporating a major EEX contribution (BMK, MN15).

Radiative lifetime of a BODIPY dye as calculated by TDDFT and EOM-CCSD methods: solvent and vibronic effects

The radiative emission lifetime and associated S₁ excited state properties of a BODIPY dye are investigated with TDDFT and EOM-CCSD calculations. The effects of a solvent are described with the polarizable continuum model using the linear response (LR) approach as well as state-specific methods. The Franck-Condon (FC), Herzberg-Teller (HT) and Duschinsky vibronic effects are evaluated for the absorption and emission spectra, and for the radiative lifetime. The transition energies, spectra shapes and radiative lifetime are assessed with respect to experimental results. It is found that the TDDFT transition energies are overestimated by about 0.4-0.5 eV, whereas EOM-CCSD improves the vertical emission energy by about 0.1 eV in comparison to TDDFT. The solvatochromic and Stokes shifts are better reproduced by the state-specific solvation methods, which show that these methods are more suited than the LR model to describe the solvent effects on the BODIPY dye. The vibronic effects lead to an increase of the radiative lifetime of about 0.4 to 1.0 ns depending on the theoretical approach, which highlights the importance of such effects. Moreover, the HT effects are negligible on both the spectra and lifetime, which demonstrates that the FC approximation is accurate for the BODIPY dye. Finally, the comparison with experimental data shows that the radiative lifetimes predicted by EOM-CCSD and TDDFT have comparable accuracy.

Pseudospectral implementations of long-range corrected density functional theory

We have implemented pseudospectral density-functional theory (DFT) with long-range corrected DFT functionals (PS-LRC) in quantum mechanics package Jaguar, and applied it in the calculations of geometry optimizations, dimmer interaction energies, polarizabilities and first-order hyperpolarizabilities, harmonic vibrational frequencies, S₁ and T₁ excitation energies, singlet-triplet gaps, charge transfer numbers, oscillator strengths, reaction barrier heights, electron-transfer couplings, and charge-transfer excitation energies. From our accuracy benchmark analysis, PS grids, PS dealiasing functions, PS atomic corrections, PS multigrid strategy, PS length scales, and PS cutoff scheme perform well in PS DFT with LRC density functionals with very small and ignorable deviations when compared to the conventional spectral (CS) method. The timing benchmark study of S₁ excitation energy calculations of fullerenes (C_n , n up to 540) demonstrates that PS-LRC achieves 1.4-8.4-fold speedups in SCF, 22-32-fold speedups in Tamm-Dancoff approximation, and 6-15-fold speedups in total wall clock time with an average error 0.004 eV of excitation energies compared to the CS method.

Planar hexaphyrin-like macrocycles turning into bis-BODIPYs with box-shaped structures exhibiting excitonic coupling

Planar carbazole based hexaphyrin-like macrocycles with bis-coordinating cores and box-shaped cyclic BODIPYs were synthesized. Solution and solid-state structure analysis of the free macrocycles indicates an inversion of two pyrrole rings, resulting in a two-dipyrrin-like environment. The BF₂ complexes show large Stokes shifts and exhibit excitonic coupling, fine-tuned by the meso-substituents.

Azulene Bridged π-Distorted Chromophores: The Influence of Structural Symmetry on Optoelectrochemical and Photovoltaic Parameters

Conjugated chromophores possessing π-twisted functionality such as tetracyanobutadiene (TCBD) have emerged as promising active layer materials for organic photovoltaics (OPVs). In this study, we disclose the synthesis of two azulenyl chromophores containing one and two TCBD groups. The symmetrical and unsymmetrical structural characteristics of these molecules inflict dissimilar optoelectronic and electrochemical properties. Based on molar absorptivity, aggregation behavior, HOMO-LUMO energies and other quantum chemical parameters, the symmetrical molecule (TATC2) appears to be a better non-fullerene acceptor (NFA) compared to its unsymmetrical counterpart (TATC1). For instance, higher absorptivity and deeper HOMO-LUMO levels for TATC2 (23950 M-1  cm-1 ; -6.01 eV/-3.86 eV) over TATC1 (12200 M1  cm-1 ; -5.46 eV/-3.64 eV) was observed. Validating this structure-property relationship on solar cell prototypes exhibited higher photovoltaic parameters (VOC =0.54 V, FF=0.48, JSC =6.42 mA/cm2 ) for TATC2 than TATC1 (VOC =0.47 V, FF=0.38, JSC =5.77 mA/cm2 ). Though the device parameters are not high, this work uncovers the intrinsic properties of azulene-tethered twisted chromophores as potential π-semiconductor choice for NFA solar cells. In particular, this report explores the utility of azulene-based π-twisted semiconductors as acceptor material for OPVs with cell efficiencies of 1.70 and 1.04 % for TATC2 and TATC1 respectively.

Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase

The incredible potential for fluorescent proteins to revolutionize biology has inspired the development of a variety of design strategies to address an equally broad range of photophysical characteristics, depending on potential applications. Of these, fluorescent proteins that simultaneously exhibit high quantum yield, red-shifted emission, and wide separation between excitation and emission wavelengths (Large Stokes Shift, LSS) are rare. The pursuit of LSS systems has led to the formation of a complex, obtained from the marriage of a rationally engineered protein (human cellular retinol binding protein II, hCRBPII) and different fluorogenic molecules, capable of supporting photobase activity. The large increase in basicity upon photoexcitation leads to protonation of the fluorophore in the excited state, dramatically red-shifting its emission, leading to an LSS protein/fluorophore complex. Essential for selective photobase activity is the intimate involvement of the target protein structure and sequence that enables Excited State Proton Transfer (ESPT). The potential power and usefulness of the strategy was demonstrated in live cell imaging of human cell lines.

Relief of excited-state antiaromaticity enables the smallest red emitter

It is commonly accepted that a large π-conjugated system is necessary to realize low-energy electronic transitions. Contrary to this prevailing notion, we present a new class of light-emitters utilizing a simple benzene core. Among different isomeric forms of diacetylphenylenediamine (DAPA), o- and p-DAPA are fluorescent, whereas m-DAPA is not. Remarkably, p-DAPA is the lightest (FW = 192) molecule displaying red emission. A systematic modification of the DAPA system allows the construction of a library of emitters covering the entire visible color spectrum. Theoretical analysis shows that their large Stokes shifts originate from the relief of excited-state antiaromaticity, rather than the typically assumed intramolecular charge transfer or proton transfer. A delicate interplay of the excited-state antiaromaticity and hydrogen bonding defines the photophysics of this new class of single benzene fluorophores. The formulated molecular design rules suggest that an extended π-conjugation is no longer a prerequisite for a long-wavelength light emission.

Highly efficient implementation of the analytical gradients of pseudospectral time-dependent density functional theory

The accuracy and efficiency of time-dependent density functional theory (TDDFT) excited state gradient calculations using the pseudospectral method are presented. TDDFT excited state geometry optimizations of the G2 test set molecules, the organic fluorophores with large Stokes shifts, and the Pt-complexes show that the pseudospectral method gives average errors of 0.01-0.1 kcal/mol for the TDDFT excited state energy, 0.02-0.06 pm for the bond length, and 0.02-0.12° for the bond angle when compared to the results from conventional TDDFT. TDDFT gradient calculations of fullerenes (C_n, n up to 540) with the B3LYP functional and 6-31G** basis set show that the pseudospectral method provides 8- to 14-fold speedups in the total wall clock time over the conventional methods. The pseudospectral TDDFT gradient calculations with a diffuse basis set give higher speedups than the calculations for the same basis set without diffuse functions included.

Cyclopropyl Substituents Transform the Viscosity-Sensitive BODIPY Molecular Rotor into a Temperature Sensor

A quantitative fluorescent probe that responds to changes in temperature is highly desirable for studies of biological environments, particularly in cellulo. Here, we report new cell-permeable fluorescence probes based on the BODIPY moiety that respond to environmental temperature. The new probes were developed on the basis of a well-established BODIPY-based viscosity probe by functionalization with cyclopropyl substituents at α and β positions of the BODIPY core. In contrast to the parent BODIPY fluorophore, α-cyclopropyl-substituted fluorophore displays temperature-dependent time-resolved fluorescence decays showing greatly diminished viscosity dependence, making it an attractive sensor to be used with fluorescence lifetime imaging microscopy (FLIM). We performed theoretical calculations that help rationalize the effect of the cyclopropyl substituents on the photophysical behavior of the new BODIPYs. In summary, we designed an attractive new quantitative FLIM-based temperature probe that can be used for temperature sensing in live cells.

Torsion-Induced Nonradiative Relaxation of the Singlet Excited State of meso-Thienyl Bodipy and Charge Separation, Charge Recombination-Induced Intersystem Crossing in Its Compact Electron Donor/Acceptor Dyads

We prepared a series of meso-thienyl boron-dipyrromethene (Bodipy) derivatives to investigate the spin-orbit charge transfer intersystem crossing (SOCT-ISC). The photophysical properties of the compounds were studied by steady-state and femtosecond/nanosecond transient absorption spectroscopy, as well as density functional theory (DFT) computations. Different from the meso-phenyl Bodipy analogues, the meso-thienyl Bodipy are weakly fluorescent. Based on femtosecond transient absorption and DFT computations, we propose that the torsion of the thienyl group and the distortion of the Bodipy core (19.7 ps) in the S₁ state lead to a conical intersection on the potential energy surface as an efficient nonradiative decay channel (408 ps), which is responsible for the observed weak fluorescence as compared to the meso-phenyl analogue. The increased fluorescence quantum yield (from 5.5 to 14.5%) in viscous solvents supports this hypothesis. With the electron donor 4'-hydroxylphenyl moiety attached to the meso-thienyl unit, the fast charge separation (CS, 15.3 ps) and charge recombination (CR, 238 ps) processes outcompete the torsion-induced nonradiative decay and induce fast ISC through the SOCT-ISC mechanism. The triplet quantum yield of the electron donor/acceptor dyad is highly dependent on solvent polarity (Φ_T = 1.9-45%), which supports the SOCT-ISC mechanism, and the triplet-state lifetime is up to 247.3 μs. Using the electron donor-acceptor dyad showing SOCT-ISC as a triplet photosensitizer, efficient triplet-triplet annihilation (TTA) upconversion was observed with a quantum yield of up to 6.0%.

White light employing luminescent engineered large (mega) Stokes shift molecules: a review

Large (mega) Stokes shift molecules have shown great potential in white light emission for optoelectronic applications, such as flat panel display technology, light-emitting diodes, photosensitizers, molecular probes, cellular and bioimaging, and other applications. This review aims to summarize recent developments of white light generation that incorporate a large Stokes shift component, key approaches to designing large Stokes shift molecules, perspectives on future opportunities, and remaining challenges confronting this emerging research field. After a brief introduction of feasible pathways in generating white light, exemplifications of large Stokes shift molecules as white light candidates from organic and inorganic-based materials are illustrated. Various possible ways to design such molecules have been revealed by integrating the photophysical mechanisms that are essential to produce red-shifted emission upon photoexcitation, such as excited state intramolecular proton transfer (ESIPT), intramolecular charge transfer (ICT), excited state geometrical relaxation or structural deformation, aggregation-induced emission (AIE) alongside the different formations of aggregates, interplay between monomer and excimer emission, host-guest interaction, and lastly metal to ligand charge transfer (MLCT) via harvesting triplet state. Furthermore, previously reported fluorescent materials are described and categorized based on luminescence behaviors on account of the Stokes shifts value. This review will serve as a rationalized introduction and reference for researchers who are interested in exploring large or mega Stokes shift molecules, and will motivate new strategies along with instigation of persistent efforts in this prominent subject area with great avenues.

BODIPY-based monofunctional Pt (II) complexes for specific photocytotoxicity against cancer cells

Photodynamic therapy (PDT) has attracted extensive attention in cancer treatment because of its minimum trauma, less side effects, and so on. Photosensitizers, as one of the core elements of PDT, usually have to face problems such as poor water solubility and light stability, lack of targeting, and other problems, which seriously affect the therapeutic effect. In this work, two BODIPY (boron-dipyrromethene)-based monofunctional Pt (II) complexes, 1a and 2a, were designed and synthesized, and their PDT effect was studied. The Pt atom improved the singlet oxygen quantum yield (0.19 for 1a and 0.14 for 2a, respectively), which effectively improves the efficiency of PDT. MTT assay confirmed that the short time photo-irradiation distinctly promoted antitumor cytotoxicity of Pt (II) compounds against different cell lines. For 1a under irradiation, the IC₅₀ value of cancer cell lines were 13.1 μM for HeLa cells and 7.6 μM for MCF-7 cells, while those of normal cell lines were 32.4 μM for HBL-100 cells and 48.6 μM for L02 cells. The results demonstrated that 1a showed specific phototoxicity to cancer cells. This specific selectivity could be attributed to the synergistic effect of increased cellular uptake (determined by ICP-MS) and higher ROS generation (detected by Cell ROX Deep Red) in cancer cells after irradiation. This study laid the foundation for the future design and synthesis of effective PDT photosensitizers.

A novel copper ion sensing fluorescent probe for fast detection of pyrophosphate and alkaline phosphatase

A Cu²⁺ sensing fluorescent probe is synthesized via a Mannich reaction and is applied in the fluorescence detection of pyrophosphate and alkaline phosphatase.

Full Visible Spectrum and White Light Emission with a Single, Input-Tunable Organic Fluorophore

The blue emission of M2biQ can be tuned to specific wavelengths throughout the visible region by changing the identity of the cation it interacts with. These optical properties are observed in MeCN solution and the solid state. White light is obtained in MeCN by using either the proper ratio of zinc ions or acid. Thus, M2biQ acts as a nearly universal emitter (λem = 468-690 nm) with large Stokes shifts (116-306 nm, Δν̃ = 7,042-11,823 cm-1). Full spectral profiles as well as quantum yields, lifetimes, and the crystal structures of key RGB and yellow emitters are reported. Emission wavelengths correlate with cationic radius, and TD-DFT calculations show that, for 1:1 complexes, the smaller the ion, the shorter the N-cation bond, and the greater the bathochromic emission shift.

Near infrared absorption/emission perylenebisimide fluorophores with geometry relaxation-induced large Stokes shift

The dyes (P-1 and P-2) of perylenebisimide (PBI) conjugated with 2-(2-hydroxyphenyl)benzothiazole (HBT) were prepared by Sonogashira coupling reaction. The new compounds have special photophysical properties, such as near infrared absorption/emission and large Stokes shift. The UV-vis absorption (range from 651 nm to 690 nm) and emission wavelength (range from 732 nm to 756 nm) of P-1 and P-2 extend to near infrared range. Importantly, they have much larger Stokes shifts (range from 73 nm to 105 nm) compared with the conventional PBI derivatives, such as 7 (from 19 nm to 65 nm) and 9 (from 81 nm to 86 nm). TD-DFT calculation was used to rationalize UV-vis absorption, emission and especially large Stokes shift from the theoretical point of view. We found geometry relaxation of P-1 and P-2 in the excited state is an important reason for the origin of large Stokes shift besides intramolecular electron transfer (ICT).

The dyes with near infrared absorption/emission and large stokes shifts induced by geometry relaxation were prepared.

Elucidating the Magnitude of Internal Reorganization Energy of Molecular Excited States from the Perspective of Transition Density

Quantifying vibronic couplings in molecular excited states is crucial for the elucidation of a broad range of photophysical phenomena. In this study, we compare different theoretical approaches for the calculation of reorganization energy, a measure of vibronic coupling strength, and provide a rigorous derivation to show that molecular transition density characterizing electron-hole excitation could be used to quantify the magnitude of reorganization energy. The theory enables a descriptor based on molecular-orbital coefficients and atomic transition densities to quantify the magnitude of reorganization energies in molecular excited states. Applying the approach to low-lying excited states of polyacenes, we demonstrate that transition density distribution explains the difference in the magnitude of the reorganization energy of different excited states. Furthermore, to clarify the applicability of the transition density descriptor in molecular design for small-reorganization energy molecules, we investigate a broad range of molecular chromophores to show the effectiveness of the proposed theory. With this perspective on the relationship between reorganization energy and transition density, we successfully provide a quantitative rule to identify π-conjugated systems with small reorganization energy in the excited state, which should be useful for the development of novel optoelectronic materials.

Dual Emission: Classes, Mechanisms, and Conditions

There has been much interest in dual-emission materials in the past few years for materials and life science applications; however, a systematic overview of the underlying processes is so-far missing. We resolve this issue herein by classifying dual-emission (DE) phenomena as relying on one emitter with two emitting states (DE1), two independent emitters (DE2), or two correlated emitters (DE3). Relevant DE mechanisms for materials science are then briefly described together with the electronic and/or geometrical conditions under which they occur. For further reading, references are given that offer detailed insight into the complex mechanistic aspects of the various DE processes or provide overviews on materials families or their applications. By avoiding ambiguities and misinterpretations, this systematic, insightful Review might inspire future targeted designs of DE materials.

Development of alkyne-BODIPYs as viscosity sensitive fluorescent probes for enumeration of bacterial cells

We report a series of alkyne-functionalized meso-aryl boron dipyrrin (BODIPY) molecular rotors sensitive to viscosity. The planar and twisted conformation within the molecular structure decides the viscosity-dependent behavior. The variations in fluorescence lifetime and intensity were appreciable to the local viscosity. Hence, the dye has been successfully employed in the enumeration of microbes by considering the proportionate fluorescence intensity of the BODIPYs as an index of the number of cells per mL. With increasing cells per mL, the viscosity of the bacterial solution is increased. Consequently, the fluorescence intensity of the sample containing BODIPY tends to increase due to the restricted rotation in the viscous medium. The BODIPY probe offers high sensitivity and is easier than other conventional techniques of colony-forming unit (CFU) determination. The theoretical studies indicate that intramolecular charge transfer is responsible for the enhanced fluorescence intensity in a highly viscous solvent.

Development of an Unsymmetrical Cyclopropenimine-Guanidine Platform for Accessing Strongly Basic Proton Sponges and Boron-Difluoride Diaminonaphthalene Fluorophores

An unsymmetrical guanidine-cyclopropenimine proton sponge DAGUN and the related BF₂ -chelate DAGBO are reported. Insight into the structural, electronic, bonding and photophysical properties of these two molecules are presented. Joint experimental and theoretical studies reveal the protonated form of DAGUN possesses an intramolecular N⋅⋅⋅H-N hydrogen bond which affords a high experimental pK_BH+ of 26.6 (computed=26.3). Photophysical studies show that in solution DAGUN displays a green emission at 534 nm, with a large Stokes shift of 235 nm (14,718 cm^-1 ). In contrast, the conjugate acid DAGUN-H⁺ is only weakly emissive due to attenuated intramolecular charge transfer. X-ray diffraction studies reveal that DAGBO contains a stable tetracoordinate boronium cation, reminiscent of the well-established BODIPY family of dyes. In solution, DAGBO exhibits a strong blue emission at 450 nm coupled with a large Stokes shift (Δλ=158 nm, Δν=11,957 cm^-1 ) and quantum yield of 62 %, upon excitation at 293 nm. DAGBO sets the stage as the first entry into a new class of boron-difluoride diaminonaphthalenes (BOFDANs) that represent highly fluorescent and tunable next-generation dyes with future promise for biosensing and bioimaging applications.

TDDFT study on the photophysical properties of coumarinyl chalcones and sensing mechanism of a derived fluorescent probe for hydrogen sulfide

Coumarin-chalcone hybrids have attracted much attention in recent years due to their important optical properties. Herein, the photophysical properties of a series of coumarinyl chalcones and the sensing mechanism for H₂S of a related fluorescent probe CC-DNP were investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The predicted spectral properties agree well with the experimental results, which allowed an assignment of the spectra. Our calculations successfully clarified the experimental observed fluorescence "off-on" effect and the fluorescent quenching mechanism of the probe. The results revealed that the first excited state (S₁) of the probe CC-DNP is a dark state with obvious charge transfer from coumarin unit to 2,4-dinitrophenyl (DNP) moiety, which results in the fluorescence quenching via the nonradiative photoinduced electron transfer (PET) process. On the other hand, the excited state S₁ in the thiolysis product CC-OH decayed directly to S₀, and thus the fluorescence is recovered.

Reduced Nonradiative Voltage Loss in Terpolymer Solar Cells

The dissociation of hybrid local exciton and charge transfer excitons (LE-CT) in efficient bulk-heterojunction nonfullerene solar cells contributes to reduced nonradiative photovoltage loss, a mechanism that still remains unclear. Herein we studied the energetic and entropic contribution in the hybrid LE-CT exciton dissociation in devices based on a conjugated terpolymer. Compared with reference devices based on ternary blends, the terpolymer devices demonstrated a significant reduction in the nonradiative photovoltage loss, regardless of the acceptor molecule, be it fullerene or nonfullerene. Fourier transform photocurrent spectroscopy revealed a significant LE-CT character in the terpolymer-based solar cells. Temperature-dependent hole mobility and photovoltage confirm that entropic and energetic effects contribute to the efficient LE-CT dissociation. The energetic disorder value measured in the fullerene- or nonfullerene-based terpolymer devices suggested that this entropic contribution came from the terpolymer, a signature of higher disorder in copolymers with multiple aromatic groups. This gives new insight into the fundamental physics of efficient LE-CT exciton dissociation with smaller nonradiative recombination loss.

Revealing the Real Size of a Porphyrin Molecule with Quantum Confinement Probing via Temperature-Dependent Photoluminescence Spectroscopy

The confinement energy of electrons in an aromatic molecule was studied by indirect and direct methods, namely, temperature-dependent photoluminescence (TDPL) spectroscopy and scanning tunneling microscopy (STM). We observed a decrease in the tetraphenylporphyrin (H₂TPP) PL intensity with increasing temperature. The increase in temperature provides kinetic energy for the electrons to overcome the confinement energy barrier, making recombination via nonradiative pathways more favorable. The results of fitting the integrated TDPL intensity with a modified Arrhenius equation suggest two confinement energy values. We propose that these energy values are related to the size of the delocalized electron cloud along the plane and thickness of the H₂TPP ring. These values quantitatively express an abstract form of the size of the aromatic ring system. These results are in good agreement with the topography images of single H₂TPP molecules and monolayer H₂TPP obtained by a direct probing method using STM. These results are also supported by the porphyrin ring orientation relative to the excited crystal face during the TDPL measurements.