Emission wavelength prediction of a full-color-tunable fluorescent core skeleton, 9-aryl-1,2-dihydropyrrolo[3,4-b]indolizin-3-one

In this paper we report on a novel fluorescent core skeleton, 9-aryl-1,2-dihydropyrrolo[3,4-b]indolizin-3-one, which we named Seoul-Fluor, having tunable and predictable photophysical properties. Using a concise and practical one-pot synthetic procedure, a 68-member library of new fluorescent compounds was synthesized with diverse substituents. In Seoul-Fluor, the electronic characteristics of the substituents, as well as their positional changes, have a close correlation with their photophysical properties. The systematic perturbation of electronic densities on the specific positions of Seoul-Fluor, guided with the Hammett constant, allows emission wavelength tunability covering the full color range. On the basis of these observations and a computational analysis, we extracted a simple first-order correlation of photophysical properties with the theoretical calculation and accurately predicted the emission wavelength of Seoul-Fluors through the rational design. In this study, we clearly demonstrate that Seoul-Fluor can provide a powerful gateway for the generation of desired fluorescent probes without the need for a tiresome synthesis and trial-and-error process.     

Distyryl-boradiazaindacenes: facile synthesis of novel near IR emitting fluorophores

Boradiazaindacenes with methyl substituents at 3 and 5 positions were for the first time shown to undergo efficient double condensation reactions with an aromatic aldehyde yielding a series of extended conjugation dyes. These new fluorophores have absorption maxima in the range of 650-660 nm. The dyes reported here have large quantum yields with 20 nm Stokes' shifted emission peaks. The straightforward synthesis of such red shifted BODIPY derivatives is important in relation to the synthesis of novel and useful fluorescent chemosensors. In addition, this facile transformation may make these new fluorophores' building blocks in the construction of large functional supramolecular systems.     

Synthesis and Photophysical Properties of a Series of Cyclopenta[b]naphthalene Solvatochromic Fluorophores

The synthesis and photophysical properties of a series of naphthalene-containing solvatochromic fluorophores are described within. These novel fluorophores are prepared using a microwave-assisted dehydrogenative Diels-Alder reaction of styrene, followed by a palladium-catalyzed cross coupling reaction to install an electron donating amine group. The new fluorophores are structurally related to Prodan. Photophysical properties of the new fluorophores were studied and intriguing solvatochromic behavior was observed. For most of these fluorophores, high quantum yields (60-99%) were observed in methylene chloride in addition to large Stokes shifts (95-226 nm) in this same solvent. As the solvent polarity increased, so did the observed Stokes shift with one derivative displaying a Stokes shift of ～300 nm in ethanol. All fluorophore emission maxima, and nearly all absorption maxima were significantly red-shifted when compared to Prodan. Shifting the absorption and emission maxima of a fluorophore into the visible region increases its utility in biological applications. Moreover, the cyclopentane portion of the fluorophore structure provides an attachment point for biomolecules that will minimize disruptions of the photophysical properties.     

Unnatural amino acid mutagenesis of green fluorescent protein

Unnatural amino acid mutagenesis has been used to selectively substitute tyrosine 66 of green fluorescent protein (GFP) with five novel amino acids: p-amino-L-phenylalanine, p-methoxy-L-phenylalanine, p-iodo-L-phenylalanine, p-bromo-L-phenylalanine, and L-3-(2-naphthyl)alanine. The absorbance and emission maxima of the resulting mutant GFPs span the range from 375 to 435 nm and 428 to 498 nm, respectively. The spectral properties of the mutant GFPs, including the absorbance and fluorescence maxima and quantum yields, correlate with the structural and electronic properties of the substituents on the amino acids.     

Donor and Ring-Fusing Engineering for Far-Red to Near-Infrared Triphenylpyrylium Fluorophores with Enhanced Fluorescence Performance for Sensing and Imaging

Fluorescent probes have become an indispensable tool in the detection and imaging of biological and disease-related analytes due to their sensitivity and technical simplicity. In particular, fluorescent probes with far-red to near-infrared (FR-NIR) emissions are very attractive for biomedical applications. However, many available FR-NIR fluorophores suffer from small Stokes shifts and sometimes low quantum yields, resulting in self-quenching and low contrast. In this work, we describe the rational design and engineering of FR-NIR 2,4,6-triphenylpyrylium-based fluorophores ( TPP-Fluors ) with the help of theoretical calculations. Our strategy is based on the appending of electron-donating substituents and fusing groups onto 2,4,6-triphenylpyrylium. In contrast to the parent TPP with short emission wavelength, weak quantum yields, and low chemical stability, the obtained novel TPP-Fluors display some favorable properties, such as long-wavelength emission, large Stokes shifts, moderate to high quantum yields, and chemical stability. TPP-Fluors demonstrate their biological value as mitochondria-specific labeling reagents due to their inherently positive nature. In addition, TPP-Fluors can also be applied to develop ratiometric fluorescent probes, as the electron-donating ability of the 2,6-phenyl substituents is closely correlated with their emission wavelength. A proof-of-concept ratiometric probe has been developed by derivatizing the amino groups of TPP-Fluor for the detection and imaging of nitroreductase in vitro and in hypoxic cells.     

A near-infrared fluorescent calcium probe: a new tool for intracellular multicolour Ca2+ imaging

We report a novel near-infrared fluorescent calcium probe (KFCA), which has good optical properties such as intense NIR fluorescence emission (670 nm, QY: 0.24), excellent ON/OFF ratio (120-fold), and good wavelength-compatibility with visible-light-emissive fluorophores (Fluo-4, DsRed2), and which is applicable for real-time dual-colour intracellular Ca(2+) imaging.     

Magnesium azaphthalocyanines: an emerging family of excellent red-emitting fluorophores

Magnesium(II), zinc(II), and metal-free phthalocyanines (Pcs) and azaphthalocyanines (AzaPcs) containing alkylsulfanyl, aryloxy, and dialkylamino peripheral substituents have been synthesized. The complexation of magnesium(II) by metal-free Pcs and AzaPcs has been studied in detail to determine the optimal reaction conditions necessary to ensure a complete conversion. Photophysical and photochemical measurements in tetrahydrofuran showed that magnesium(II) AzaPcs with aryloxy and alkylsulfanyl substituents have excellent fluorescent properties (Φ(F) up to 0.73) and that the corresponding zinc(II) Pcs are efficient singlet oxygen producers (Φ(Δ) up to 0.68). The presence of dialkylamino substituents causes intramolecular charge transfer within the molecule that competes with fluorescence and singlet oxygen formation. Alkylsulfanyl MgAzaPc and ZnAzaPc were the most photostable compounds among the series of studied derivatives. In addition, high molar absorption coefficients (ε ～ 300,000 M(-1) cm(-1)), absorption (λ(max) ～ 650 nm), and emission (λ(em) ～ 660 nm, high Φ(F)) in the red region suggest that these molecules are potential fluorescent probes that are superior to the commercial red cyanine dye Cy5. MgAzaPc, when incorporated into lipidic bilayers of liposomes, maintains excellent fluorescence properties (Φ(F) = 0.64). Water-soluble MgAzaPc with quaternary ammonium peripheral substituents retained a high fluorescence quantum yield even in water (Φ(F) = 0.25). The described properties show that magnesium(II) AzaPcs are excellent red-emitting fluorophores with potential applications as fluorescent probes in sensing or in vitro imaging applications.     

Synthesis of fluorinated benzophenones, xanthones, acridones, and thioxanthones by iterative nucleophilic aromatic substitution

Fluorination of fluorophores can substantially enhance their photostability and improve spectroscopic properties. To facilitate access to fluorinated fluorophores, bis(2,4,5-trifluorophenyl)methanone was synthesized by treatment of 2,4,5-trifluorobenzaldehyde with a Grignard reagent derived from 1-bromo-2,4,5-trifluorobenzene, followed by oxidation of the resulting benzyl alcohol. This hexafluorobenzophenone was subjected to sequential nucleophilic aromatic substitution reactions, first at one or both of the more reactive 4,4'-fluorines, and second by cyclization through substitution of the less reactive 2,2'-fluorines, using a variety of oxygen, nitrogen, and sulfur nucleophiles, including hydroxide, methoxide, amines, and sulfide. This method yields symmetrical and asymmetrical fluorinated benzophenones, xanthones, acridones, and thioxanthones and provides scalable access to known and novel precursors to fluorinated analogues of fluorescein, rhodamine, and other derivatives. Spectroscopic studies revealed that several of these precursors are highly fluorescent, with tunable absorption and emission spectra, depending on the substituents. This approach should allow access to a wide variety of novel fluorinated fluorophores and related compounds.     

Large Stokes shift fluorescent dyes based on a highly substituted terephthalic acid core

The synthesis of dyes based on a highly substituted terephthalic acid core is described, starting from readily available 2,5-dihydroxy-terephthalic acid diethyl ester. The dyes are highly colored, soluble in organic solvents and reasonably fluorescent in solution and in the solid state. The maxima for absorption and emission are around 402 and 502 nm, respectively. The fluorophores are readily cyclized to generate compounds which comprise the basic 6,13-dihydroxy-chromeno[2,3-b]xanthene-7,14-dione unit. These new derivatives are nonfluorescent.     

A Simple Central Seven-Membered BOPYIN: Synthesis,Structural, Spectroscopic Properties,and Cellular Imaging Application

A two-step, one-flask synthesis of central seven-membered borondifluoride-3,3-dimethyl-2-[2-(2-pyrrolyl)ethenyl] indole (BOPYIN) ligands has been developed by using the unexplored 3,3-dimethyl-2-[2-(2-pyrrolyl)ethenyl] indole. The simple synthetic approach has enabled modification of the electronic structure by changing the substituents on the indole unit. X-ray analysis indicated that conformations of the seven-membered BF₂ complex including BOPYIN and diazaborepin differ from that of the five- and six-membered organoboron complexes. Interestingly, the bond angle of the N⋅⋅⋅B−N bond increases with the number of atoms in the core ring, based on Baeyer strain theory. These unsymmetric BOPYIN derivatives have excellent photophysical properties, including high fluorescence quantum yields, except for BOPYIN- 4 in the solution state, large Stokes shifts, and good molar absorptivity. The dipole moment of BOPYIN- 3 in the first excited singlet state and ground state was demonstrated by a linear Lippert–Mataga plot. The absorption and emission spectra were not mirror images for BOPYIN- 1 – 3 and 5 , in contradiction to Kasha's rule, as determined by TDDFT. The synthesized BOPYINs have been shown to be biocompatible fluorophores in cell bioimaging.     

Systematic Exploration of Furoindolizine-Based Molecular Frameworks towards a Versatile Fluorescent Platform

The photophysical behaviors of fluorescent molecules largely determine their major utility in biological studies. Despite their well-defined characteristics, classical fluorophores have often been challenged by their limited synthetic methodology and tunability in adjusting intrinsic optical properties. A novel heterocyclic core equipped with modular functional groups could offer the flexibility to control its photophysical properties with a minimum synthetic effort. By conducting a systematic analysis guided by quantum calculations, we proposed the furoindolizine-based molecular framework as a unique fluorescent platform capable of providing versatile photophysical properties with minimal structural modification. A broad tunability of furoindolizine derivatives′ photophysical properties such as emission wavelength, Stokes shift, fluorescent brightness, and charge transfer characteristics was achieved through synergistic interaction between two functional moieties. Furthermore, this modular platform led to live-cell imaging probes with two distinct optical features simply by reorganizing a pair of functional moieties.     

Hetero-Substituted αβ-Fused BODIPY

Here, we report the synthesis and properties of heterosubtituted αβ-fused BODIPY fluorophores. The compounds were obtained in good yields by sequential and selective Stille cross-coupling reactions from 2,3,5,6-tetrahalo-BODIPY, allowing the introduction of different substituents at the 3,5 and 2,6 positions of the BODIPY ring. The final fused compounds were synthesized using oxidative cyclisation with ferrous chloride. The fully fused compounds show a strong bathochromically shifted emission along with a hyperchromic shift of the absorption maxima. The fluorescence quantum yields remain relatively large for compounds emitting in this wavelength range. Computational studies have been carried out to fully understand the photophysical behaviour of these dyes.     

Heterocyclic quinol-type fluorophores: synthesis, X-ray crystal structures, and solid-state photophysical properties of novel 5-hydroxy-5-substituent-benzo[b]naphtho[1,2-d]furan-6-one and 3-hydroxy-3-substituent-benzo[kl]xanthen-2-one derivatives

Novel heterocyclic quinol-type fluorophores (4 a-c) and (5 a-c) that contain substituents (R = Me, Bu, Ph) with nonconjugated linkages to the chromophore skeleton have been synthesized and their photophysical properties have been investigated in solution and in the solid state. Considerable differences in the absorption and fluorescence spectra were observed between the two states. Quinols 4 a-c and 5 a-c exhibited almost the same absorption and fluorescence spectra in solution; however, their solid-state fluorescence excitation and emission spectra in the crystalline state were quite different. We performed X-ray crystallographic analyses to elucidate the dramatic effect of the substituents of the nonconjugated linkage on the solid-state fluorescence excitation and emission spectra. The relationships between the solid-state photophysical properties and the chemical and crystal structures of 4 a-c and 5 a-c are discussed on the basis of the X-ray crystal structures.     

Bioluminescence resonance energy transfer from aequorin to a fluorophore: an artificial jellyfish for applications in multianalyte detection

In nature, the green light emission observed in the jellyfish Aequorea victoria is a result of a non-radiative energy transfer from the excited-state aequorin to the green fluorescent protein. In this work, we have modified the photoprotein aequorin by attaching selected fluorophores at a unique site on the protein. This will allow for in vitro transfer of bioluminescent energy from aequorin to the fluorophore thus creating an artificial jellyfish. The fluorophores are selected such that the excitation spectrum of the fluorophore overlaps with the emission spectrum of aequorin. By modifying aequorin with different fluorophores, bioluminescent labels with different emission maxima are produced, which will allow for the simultaneous detection of multiple analytes. By examining the X-ray crystal structure of the protein, four different sites for introduction of the unique cysteine residue were evaluated. Two fluorophores with differing emission maxima were attached individually to the mutants through the sulfhydryl group of the cysteine molecule. Two of the fluorophore-labeled mutants showed a peak corresponding to fluorophore emission thus indicating resonance energy transfer from aequorin to the fluorophore.     

Benzothiazoles with tunable electron-withdrawing strength and reverse polarity: a route to triphenylamine-based chromophores with enhanced two-photon absorption

A series of dipolar and octupolar triphenylamine-derived dyes containing a benzothiazole positioned in the matched or mismatched fashion have been designed and synthesized via palladium-catalyzed Sonogashira cross-coupling reactions. Linear and nonlinear optical properties of the designed molecules were tuned by an additional electron-withdrawing group (EWG) and by changing the relative positions of the donor and acceptor substituents on the heterocyclic ring. This allowed us to examine the effect of positional isomerism and extend the structure-property relationships useful in the engineering of novel heteroaromatic-based systems with enhanced two-photon absorption (TPA). The TPA cross-sections (δ(TPA)) in the target compounds dramatically increased with the branching of the triphenylamine core and with the strength of the auxiliary acceptor. In addition, a change from the commonly used polarity in push-pull benzothiazoles to a reverse one has been revealed as a particularly useful strategy (regioisomeric control) for enhancing TPA cross-sections and shifting the absorption and emission maxima to longer wavelengths. The maximum TPA cross-sections of the star-shaped three-branched triphenylamines are ～500-2300 GM in the near-infrared region (740-810 nm); thereby the molecular weight normalized δ(TPA)/MW values of the best performing dyes within the series (2.0-2.4 GM·g(-1)·mol) are comparable to those of the most efficient TPA chromophores reported to date. The large TPA cross-sections combined with high emission quantum yields and large Stokes shifts make these compounds excellent candidates for various TPA applications, including two-photon fluorescence microscopy.     

Oligodeoxyfluorosides: Strong Sequence Dependence of Fluorescence Emission

We describe the properties of a series of oligomeric polyfluorophores assembled on the DNA backbone. The 11 oligomers (oligodeoxyfluorosides, ODFs), 4-7 monomers in length, were composed of only two fluorescent monomers and a spacer in varied sequences, and were designed to test how fluorescent nucleobases can interact electronically to yield complexity in fluorescence emission. The monomer fluorophores were deoxyribosides of pyrene and perylene, which emit light in violet and blue wavelengths, respectively. The experiments show that simple variation in sequence and spacing can dramatically change fluorescence, yielding emission maxima ranging from 380 to 557 nm and visible colors from violet to orange-red. Fluorescence lifetime data, excitation spectra, and absorption data point to a number of multi-fluorophore electronic interactions, including pyrene-pyrene and perylene-perylene excimers, pyrene-perylene exciplexes, as well as monomer dye emissions, contributing to the final spectral outcomes. Thus, two simple fluorophores can be readily combined to give emissions over much of the visible spectrum, all requiring only a single excitation. The results demonstrate that fluorescent nucleobases in oligomeric form can act cooperatively as electronic units, and that fluorophore sequence in such oligomers is as important as fluorophore composition in determining fluorescence properties.     

Coumarin-based two-photon AIE fluorophores: Photophysical properties and biological application

Based on the coumarin skeleton, we deliberately designed two groups of fluorophores, termed as Coum-R and Naph-Coum-R, using the diphenylamino group as the electron donor, which displayed long-wavelength emissions (red spectral region), large Stokes shift (up to 204 nm), superior AIE performance, and large two-photon absorbance cross-sections (as high as 365 GM). The electron-withdrawing substituents at the 3-position of these dyes could induce a significant red-shift in their emission spectra. Preliminary imaging experiments demonstrated the capability of these dyes as two-photon fluorophores for specifically staining lipid droplets in living cells.     

Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels

The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.     

Novel fluorophores: efficient synthesis and photophysical study

[structure: see text] We have synthesized novel fluorophores by using Sonogashira reactions of 1,4-bis(dibromovinyl)benzene and 2,5-bis(dibromovinyl)thiophene with various aromatic bromides. The emission maxima of these fluorophores vary from the indigo blue to the reddish-orange region, depending on the structures of aromatic nuclei and peripheral moieties.     

Oligonucleotide-stabilized Ag nanocluster fluorophores

Single-stranded oligonucleotides stabilize highly fluorescent Ag nanoclusters, with emission colors tunable via DNA sequence. We utilized DNA microarrays to optimize these scaffold sequences for creating nearly spectrally pure Ag nanocluster fluorophores that are highly photostable and exhibit great buffer stability. Five different nanocluster emitters have been created with tunable emission from the blue to the near-IR and excellent photophysical properties. Ensemble and single molecule fluorescence studies show that oligonucleotide encapsulated Ag nanoclusters exhibit significantly greater photostability and higher emission rates than commonly used cyanine dyes.