Anthracene−BODIPY Dyads as Fluorescent Sensors for Biocatalytic Diels−Alder Reactions

In Situ Visualization of Reversible Diels-Alder Reactions with Self-Reporting Aggregation-Induced Emission Luminogens

The dynamic reversible Diels-Alder (DA) reactions play essential roles in both academic and applied fields. Currently, in situ visualization and direct monitoring of the formation and cleavage of covalent bonds in DA reactions are hampered by finite compatibility and expensive precise instruments, especially limited in solid reactions. We herein report a fluorescence system capable of in situ visualization by naked eyes and monitoring DA/retro-DA reactions. With the fluorescence quenching effect, the synthesized TPEMI could work as an innovative self-indicator for both DA termination and retro-DA occurrence. The fluorescence increases during DA reactions, and the mechanism is investigated to establish qualitative and quantitative relations. Besides rapid screening of reaction conditions and monitoring of DA exchange processes, the TPEMI fluorescence system can visualize heterogeneous and solid-state reactions with the AIE character. The TPEMI platform is expected to offer novel insights into reversible DA processes and dynamic covalent chemistry.

Lessons in Organic Fluorescent Probe Discovery

Fluorescent probes have gained profound use in biotechnology, drug discovery, medical diagnostics, molecular and cell biology. The development of methods for the translation of fluorophores into fluorescent probes continues to be a robust field for medicinal chemists and chemical biologists, alike. Access to new experimental designs has enabled molecular diversification and led to the identification of new approaches to probe discovery. This review provides a synopsis of the recent lessons in modern fluorescent probe discovery.

Trends in the Diels-Alder reaction in polymer chemistry

The Diels-Alder (DA) reaction is regarded as quite a useful strategy in organic and macromolecular syntheses. The reversibility of this reaction and the advent of self-repair technology, as well as other applications in controlled macromolecular architectures and crosslinking, have strongly boosted the research activity, which is still attracting a huge interest in both academic and industrial research. The DA reaction is a simple and scalable toolbox. Though it is well-established that furan/maleimide is the most studied diene/dienophile couple, this perspective article reports strategies using other reversible systems with deeper features on other types of diene/dienophile pairs being either petro-sourced (cyclopentadiene, anthracene) or bio-sourced (muconic and sorbic acids, myrcene and farnesene derivatives, eugenol, cardanol). This review is composed of four sections. The first one briefly recalls the background on the DA reactions involving cyclodimerizations, dienes, and dienophiles, parameters affecting the reaction, while the second part deals with the furan/maleimide reaction. The third one deals with petro-sourced and bio-sourced (or products becoming bio-sourced) reactants involved in DA reactions are also listed and discussed. Finally, the authors' opinion is given on the potential future of the crosslinking-decrosslinking reaction, especially regarding the process (e.g., key temperatures of decrosslinking) or possibly monocomponents. It presents both fundamental and applied research on the DA reaction and its applications.

Conjugated-linker dependence of the photophysical properties and electronic structure of chlorin dyads

The synthesis, photophysical properties and electronic structure of seven new chlorin dyads and associated benchmark monomers are described. Each dyad contains two identical chlorins linked at the macrocycle [Formula: see text]-pyrrole 13-position. The extent of electronic communication between chlorin constituents depends on the nature of the conjugated linker. The communication is assessed by modification of prominent ground-state absorption and redox properties, rate constants and yields of excited-state decay processes, and molecular-orbital characteristics. Relative to the benchmark monomers, the chlorin dyads in toluene exhibit a substantial bathochromic shift of the long-wavelength absorption band (30 nm average), two-fold increased radiative rate constant [average (10 ns)[Formula: see text] vs. (22 ns)[Formula: see text]], reduced singlet excited-state lifetimes (average 5.0 ns vs. 8.2 ns), and increased fluorescence quantum yields (average 0.56 vs. 0.42). The excited-state lifetime and fluorescence yield for the chlorin dyad with a benzothiadiazole linker are reduced substantially in benzonitrile vs. toluene due largely to [Formula: see text]25-fold accelerated internal conversion. The results aid design strategies for molecular architectures that may find utility in solar-energy conversion and photomedicine.

Quintuple-Decker Heteroleptic Phthalocyanine Heterometallic Samarium-Cadmium Complexes. Synthesis, Crystal Structure, Electrochemical Behavior, and Spectroscopic Investigation

A one-pot synthesis methodology was employed for obtaining diverse quintuple-decker phthalocyanine heterometallic lanthanide-cadmium complexes. By using the reaction of a double-decker homoleptic/heteroleptic phthalocyanine samarium compound with metal-free phthalocyanine and cadmium acetate in 1,2,4-trichlorobenzene at 200 °C, two novel quintuple-decker heteroleptic phthalocyanine heterometallic samarium-cadmium compounds, {(Pc)Sm(Pc)Cd(Pc*)Cd(Pc)Sm(Pc)} (1) and {(Pc)Sm(Pc*)Cd(Pc*)Cd(Pc*)Sm(Pc)} (2), together with one homoleptic phthalocyanine species, {(Pc*)Sm(Pc*)Cd(Pc*)Cd(Pc*)Sm(Pc*)} (3), were successfully fabricated, where H₂Pc and H₂Pc* represent unsubstituted phthalocyanine and 2,3,9,10,16,17,23,24-octakis(n-pentyloxy)phthalocyanine, respectively. Their quintuple-decker structures have been disclosed by various spectroscopic techniques and single-crystal X-ray diffraction. In addition, valence tautomerization of these three quintuple-decker complexes has been achieved by the addition of phenoxathiin hexachloroantimonate, giving three oxidized forms including one-, two-, and three-electron oxidation products. From 1 to 3 with the same oxidation state, the increased number of n-pentyloxy substituents of phthalocyanine ligands induces the blue shift of electronic absorption in the IR region due to the increased gap associated with the introduction of electron-donating substituents. In particular, the electronic absorption spectra of one- and two-electron oxidation products for 1 exhibit a rare band in the middle-IR region around 3000 nm, being one of the farthest electronic transitions captured by UV-vis spectroscopy. The three-electron oxidation product of 1 displays two bands at 2231 and 2740 nm, respectively. These data are well confirmed by IR spectroscopic data and theoretical calculation results.

Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage

Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure-property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage's cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments.

Quantitative Structure-Retention Relationships for Polycyclic Aromatic Hydrocarbons and their Oligoalkynyl-Substituted Derivatives

Reversed‐phase high‐performance liquid chromatography (RP‐HPLC) has been carried out for a series of unsubstituted polycyclic aromatic hydrocarbons (PAHs) and the corresponding ethynyl, 1,3‐butadiynyl, and 1,3,5‐hexatriynyl derivatives. Theoretical values of the isotropic polarizability and several polarity descriptors have been computed for each compound by using semiempirical models and density functional theory (DFT), with the aim of evaluating linear functions as quantitative structure–retention relationships (QSRRs). The polarity has been described by using either the permanent electric dipole moment, the subpolarity, or a topological electronic index. Three types of partial atomic charges have been used to calculate the subpolarity and a topological index. The choice of the theoretical model, of the polarity descriptor, and of the partial atomic charges is discussed and the resulting QSRRs are compared. Calculating the retention times from the polarizability and the topological electronic index (AM1, PM3, or DFT‐B3LYP/6–31+G(d,p)) gives the best agreement with the experimental values.

Amphiphilic BODIPY-Hydroporphyrin Energy Transfer Arrays with Broadly Tunable Absorption and Deep Red/Near-Infrared Emission in Aqueous Micelles

BODIPY-hydroporphyrin energy transfer arrays allow for development of a family of fluorophores featuring a common excitation band at 500 nm, tunable excitation band in the deep red/near-infrared window, and tunable emission. Their biomedical applications are contingent upon retaining their optical properties in an aqueous environment. Amphiphilic arrays containing PEG-substituted BODIPY and chlorins or bacteriochlorins were prepared and their optical and fluorescence properties were determined in organic solvents and aqueous surfactants. The first series of arrays contains BODIPYs with PEG substituents attached to the boron, whereas in the second series, PEG substituents are attached to the aryl at the meso positions of BODIPY. For both series of arrays, excitation of BODIPY at 500 nm results in efficient energy transfer to and bright emission of hydroporphyrin in the deep-red (640-660 nm) or near-infrared (740-760 nm) spectral windows. In aqueous solution of nonionic surfactants (Triton X-100 and Tween 20) arrays from the second series exhibit significant quenching of fluorescence, whereas properties of arrays from the first series are comparable to those observed in polar organic solvents. Reported arrays possess large effective Stokes shift (115-260 nm), multiple excitation wavelengths, and narrow, tunable deep-red/near-IR fluorescence in aqueous surfactants, and are promising candidates for a variety of biomedical-related applications.

Synthesis, structures, and properties of 2,5-dianthrylthiophene derivatives

The title thiophene derivatives bearing two 9-, 1-, or 2-anthryl groups were synthesized by cyclization of the corresponding 1,3-diynes with sodium sulfide or by Suzuki–Miyaura coupling. X-ray analysis and DFT calculations revealed that the molecules adopt nonplanar conformations depending on the steric demand of the anthryl groups. The dihedral angles between the arene units are an important contributor to the photophysical properties in the electronic spectra as well as the electrochemical data.

Rigid tetrazine fluorophore conjugates with fluorogenic properties in the inverse electron demand Diels-Alder reaction

1,2,4,5-Tetrazine fluorophore derivatives with structurally rigid molecular designs were synthesized using Sonogashira and Stille cross-coupling as well as copper-catalyzed azide-alkyne cycloaddition. The synthesized bichromophoric systems exhibit low fluorescence quantum yields due to quenching by the tetrazine. The extent of fluorescence quenching observed for those systems was shown to depend on the distance between the fluorophore and the tetrazine. The decreased fluorescence is "turned on" by conversion of the tetrazine in the inverse electron demand Diels-Alder cycloaddition. Time resolved spectroscopy indicated resonance energy transfer between BODIPY and the tetrazine as the underlying quenching mechanism. The synthesized conjugates were successfully applied in protein labeling experiments.

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.

A Luminescent Nitrogen-Containing Polycyclic Aromatic Hydrocarbon Synthesized by Photocyclodehydrogenation with Unprecedented Regioselectivity

We present a nitrogen-containing polycyclic aromatic hydrocarbon (N-PAH), namely 12-methoxy-9-(4-methoxyphenyl)-5,8-diphenyl-4-(pyridin-4-yl)pyreno[1,10,9-h,i,j]isoquinoline (c-TPE-ON), which exhibits high quantum-yield emission both in solution (blue) and in the solid state (yellow). This molecule was unexpectedly obtained by a three-fold, highly regioselective photocyclodehydrogenation of a tetraphenylethylene-derived AIEgen. Based on manifold approaches involving UV/Vis, photoluminescence, and NMR spectroscopy as well as HRMS, we propose a reasonable mechanism for the formation of the disk-like N-PAH that is supported by density functional theory calculations. In contrast to most PAHs that are commonly used, our system does not suffer from entire fluorescence quenching in the solid state due to the peripheral aromatic rings preventing π-π stacking interactions, as evidenced by single-crystal X-ray analysis. Moreover, its rod-like microcrystals exhibit excellent optical waveguide properties. Hence, c-TPE-ON comprises a N-PAH with unprecedented luminescent properties and as such is a promising candidate for fabricating organic optoelectronic devices. Our design and synthetic strategy might lead to a more general approach to the preparation of solution- and solid-state luminescent PAHs.

Unravelling RNA-substrate interactions in a ribozyme-catalysed reaction using fluorescent turn-on probes

The Diels-Alder reaction is one of the most important C-C bond-forming reactions in organic chemistry, and much effort has been devoted to controlling its enantio- and diastereoselectivity. The Diels-Alderase ribozyme (DAse) catalyses the reaction between anthracene dienes and maleimide dienophiles with multiple-turnover, stereoselectivity, and up to 1100-fold rate acceleration. Here, a new generation of anthracene-BODIPY-based fluorescent probes was developed to monitor catalysis by the DAse. The brightness of these probes increases up to 93-fold upon reaction with N-pentylmaleimide (NPM), making these useful tools for investigating the stereochemistry of the ribozyme-catalysed reaction. With these probes, we observed that the DAse catalyses the reaction with >91% de and >99% ee. The stereochemistry of the major product was determined unambiguously by rotating-frame nuclear Overhauser NMR spectroscopy (ROESY-NMR) and is in agreement with crystallographic structure information. The pronounced fluorescence change of the probes furthermore allowed a complete kinetic analysis, which revealed an ordered bi uni type reaction mechanism, with the dienophile binding first.

Fluorescent properties of 8-phenylBODIPY in ethanol - ethylene glycol mixed solutions

Fluorescent characteristics of two BODIPY dyes in solutions were investigated under the viscosity variations. Investigated dyes differ in the nature of 8-substituent of ligand molecule. Viscosity variation was achieved by changing of solvent composition in the binary system ethanol - ethylene glycol and solvent temperature. 8-Phenyl substituted BODIPY is found to exhibit properties of molecular rotor, i.e. its fluorescent characteristics are highly dependent on the viscosity or rigidity of the microenvironment. Increased temperature leads to a linear decrease of fluorescence parameters unlike the solvent composition variation where fluorescence change is nonlinear. The highest specific change in the fluorescence was observed in pure ethanol. Change in the nonradiative decay rate constant values with the increasing of viscosity indicates that the analyzed phenyl substituted complex is a true molecular rotor. Investigated 8-phenylBODIPY could be recommended as promising viscosity sensor in different organic media.

Design, synthesis and photophysical studies of dipyrromethene-based materials: insights into their applications in organic photovoltaic devices

This review article presents the most recent developments in the use of materials based on dipyrromethene (DPM) and azadipyrromethenes (ADPM) for organic photovoltaic (OPV) applications. These chromophores and their corresponding BF2-chelated derivatives BODIPY and aza-BODIPY, respectively, are well known for fluorescence-based applications but are relatively new in the field of photovoltaic research. This review examines the variety of relevant designs, synthetic methodologies and photophysical studies related to materials that incorporate these porphyrinoid-related dyes in their architecture. The main idea is to inspire readers to explore new avenues in the design of next generation small-molecule and bulk-heterojunction solar cell (BHJSC) OPV materials based on DPM chromophores. The main concepts are briefly explained, along with the main challenges that are to be resolved in order to take full advantage of solar energy.

BODIPY dyes functionalized with 2-(2-dimethylaminophenyl)ethanol moieties as selective OFF–ON fluorescent chemodosimeters for the nerve agent mimics DCNP and DFP

Hand held sensing kits for detecting nerve agents simulants.

Microscale thermophoresis provides insights into mechanism and thermodynamics of ribozyme catalysis

The analysis of binding interactions between small molecules and biopolymers is important for understanding biological processes. While fluorescence correlation spectroscopy (FCS) requires fluorescence labeling on the small molecule, which often interferes with binding, in microscale thermophoresis (MST) the label can be placed on the biopolymer. Ribozymes have not been analyzed by MST so far. The Diels-Alderase ribozyme (DAse) is a true catalyst, facilitating the Diels-Alder reaction between two free small substrates, anthracene dienes, and maleimide dienophiles. Despite high efforts, the determination of the dissociation constant (KD) of maleimide dienophiles to the DAse by FCS has been unsuccessful. Here, we determined the binding interactions of the DAse to its substrates and the Diels-Alder product using MST. The results supported a positive cooperativity for substrate binding to the DAse. By varying the temperature, we furthermore studied the thermodynamics of dienophile dissociation. The entropic contribution was found to be the energetic driving force for the binding of the dienophile to the DAse.

Single-molecule FRET studies of RNA folding: a Diels-Alderase ribozyme with photolabile nucleotide modifications

Enzymology at the single-molecule level by using fluorescence resonance energy transfer (smFRET) offers unprecedented insight into mechanistic aspects of catalytic reactions. Implementing spatiotemporal control of the reaction by using an external trigger is highly valuable in these challenging experiments. Here, we have incorporated a light-cleavable caging moiety into specific nucleotides of the Diels-Alderase (DAse) ribozyme. In this way, the folding energy landscape was significantly perturbed, and the catalytic activity was essentially suppressed. A careful smFRET efficiency histogram analysis at various Mg(2+) ion concentrations revealed an additional intermediate state that is not observed for the unmodified DAse ribozyme. We also observed that only a fraction of DAse molecules returns to the native state upon cleavage of the caged group by UV light. These constructs are attractive model RNA systems for further real-time single-molecule observation of the coupling between conformational changes and catalytic activity.

Synthesis, Photophysics, Electrochemistry and Electrogenerated Chemiluminescence of PEG-Modified BODIPY dyes in Organic and Aqueous Solutions

A set polyethylene glycol (PEG) appended BODIPY architectures (BOPEG1 - BOPEG3) have been prepared and studied in CH2Cl2, H2O:CH3CN (1:1) and aqueous solutions. BOPEG1 and BOPEG2 both contain a short PEG chain and differ in substitution about the BODIPY framework. BOPEG3 is comprised of a fully substituted BODIPY moiety linked to a PEG polymer that is roughly 13 units in length. The photophysics and electrochemical properties of these compounds have been thoroughly characterized in CH2Cl2 and aqueous CH3CN solutions. The behavior of BOPEG1 - BOPEG3 correlates with established rules of BODIPY stability based on substitution about the BODIPY moiety. ECL for each of these compounds was also monitored. BOPEG1, which is unsubstituted at the 2- and 6-positions dimerized upon electrochemical oxidation while BOPEG2, which contains ethyl groups at the 2- and 6-positions, was much more robust and served as an excellent ECL luminophore. BOPEG3 is highly soluble in water due to the long PEG tether and demonstrated modest ECL activity in aqueous solutions using tri-n-propylamine (TPrA) as a coreactant. As such, BOPEG3 represents the first BODIPY derivative that has been shown to display ECL in water without the need for an organic cosolvent, and marks an important step in the development of BODIPY based ECL probes for various biosensing applications.

Electrochemistry and electrogenerated chemiluminescence of BODIPY dyes

BODIPY (boron dipyrromethene) dyes are unique materials with spectroscopic and electrochemical properties comparable to those of aromatic hydrocarbons. Electrochemical studies are useful in understanding the redox properties of these materials and finding structure-stability relations for the radical ions; along with spectroscopy, these studies help researchers design novel compounds with desired properties. This Account represents our attempt at a full description of the electrochemical and electrogenerated chemiluminescence (ECL) properties of the BODIPY dyes. When the dyes are completely substituted with alkyl or other groups, the radical ions of BODIPY dyes are highly stable. But if they include unsubstituted positions, the radical ions can undergo dimerization or other reactions. BODIPY dyes also show unusually large separations, ~1.0 V, between the first and second cyclic voltammetric (CV) waves for both oxidation and reduction half-reactions. Alkyl-substituted BODIPY dyes show good photoluminescence (PL) quantum efficiencies, and radical ion electron transfer annihilation in these molecules produces electrogenerated chemiluminescence (ECL), the intensity of which depends on the structure of the dye. The large separation between waves and the presence of strong ECL signals are both important in the design of stable ECL-based materials. The ECL spectra provide a fast method of monitoring the electrochemical formation of dimers and aggregates from the monomers. BODIPY dyes are particularly good systems for studying stepwise electron transfer in their chemically synthesized oligomers and polymers because of the small separation between the first oxidation and first reduction waves, generally about 2.0-2.4 V, and their relative ease of reduction compared with many other aromatic compounds. The larger separation between consecutive waves for oxidation compared with reduction is noticeable for all BODIPY dimers and trimers. We also observe a more difficult addition or extraction of a third electron compared with the second for the trimers, signaling the importance of electrostatic interactions. In general, BODIPY dyes combine interesting electrochemical and spectroscopic properties that suggest useful analytical applications.

Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme

Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels-Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7-8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels-Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function.

Direct structural analysis of modified RNA by fluorescent in-line probing

Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5′-terminal ³²P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels–Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as ‘duplexing’ allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure.