Attachable solvatochromic fluorophores and bioconjugation studies

Domino Three-Component N-Acylation/[4 + 2] Cycloaddition/Alder-ene Synthesis of Polysubstituted Benzo[f]isoindole-4-carboxylic Acids

Diversely substituted, partially saturated benzo[f]isoindole-4-carboxylic acids were synthesized by a new three-component reaction (3CR) starting from cinnamic amines (3-arylallylamines), maleimides, and maleic anhydride. The process consists of N-acylation of the amines by maleic anhydride, intramolecular [4 + 2] cycloaddition in vinylarenes (the IMDAV reaction), and the concluding Alder-ene reaction between Diels-Alder intermediates and maleimides. All of the reaction steps proceed in a highly regio- and stereoselective manner, furnishing five adjacent chiral centers and leading to a single diastereoisomer of the title compound. The efficiency of the transformation is secured by thermal conditions or utilization of soft Lewis acids (Yb(OTf)3) as catalysts. The kinetics and mechanism of the 3CR were studied by using dynamic 19F NMR. Based on the NMR data and density functional theory (DFT) calculations, the IMDAV, not the Alder-ene, reaction is the rate-limiting step of the entire process.

Photocatalytic Cascade Cyclization of Aryl Haloalkynyl Ketones Forming Cyclopenta[b]naphthalene Derivatives

An efficient metal-free, photoredox-mediated cascade cyclization of aryl 1-haloalk-5-ynyl ketones has been developed. Using catalytic amounts of eosin Y (EY) and EtNMe₂ as a reductive quencher, various aryl 1-haloalk-5-ynyl ketones have been transformed into the corresponding cyclization products in up to 98% yield. As a result, synthetic access to differently α-functionalized cyclopenta[b]naphthones and direct construction of cyclopenta[b]naphtholes has been developed.

Intramolecular Diels-Alder Reactions of α-Bromostyrene-Functionalized Unsaturated Carboxamides

Intramolecular cycloaddition reactions of α-bromostyrene-functionalized amides of monomethyl fumarate were investigated. The reaction of the amides with Et₃N in toluene at 110 °C gave 1,4-dihydronaphthalenes. The 1,4-dihydronaphthalenes may be produced via the intramolecular Diels-Alder reaction, proton transfer, and dehydrobromination by a base, along with C═C bond isomerization by proton transfer. The reaction of amide derivatives with halogen on a benzene ring and alkali metal carbonates in toluene at 110 °C gave naphthalene derivatives directly. Dehydrogenation of various 1,4-dihydronaphthalenes with cesium or rubidium carbonate in toluene at 110 °C gave naphthalene derivatives. The retardation by TEMPO, acceleration by air for some substrates, and density functional theory calculations suggest a radical mechanism caused by intervention of molecular oxygen.

Facile synthesis of diverse hetero polyaromatic hydrocarbons (PAHs) via the styryl Diels–Alder reaction of conjugated diynes

The intramolecular styryl Diels–Alder reaction with conjugated diynes under thermally stable triazole-gold (TA–Au) catalytic conditions and the sequential transformation through alkyne activation to access various PAHs with high efficiency was reported for the first time.

Lewis Base Catalyzed, Sulfenium Ion Initiated Enantioselective, Spiroketalization Cascade

A Lewis base catalyzed, enantioselective sulfenocyclization of alkenes to afford [6,6]spiroketals has been developed. The method uses a chiral Lewis base catalyst with an electrophilic sulfur source to generate enantioenriched thiiranium ion with alkenes. Upon formation, the thiiranium ion is subsequently captured in a cascade-type reaction, wherein a ketone oxygen serves as the nucleophile to open the thiiranium ion and an alcohol provides the secondary cyclization to form biorelevant spiroketals. A variety of electron-rich and electron-neutral E-substituted styrenes form the desired spiroketals in good yields with excellent enantio- and diastereoselectivities. Alkyl-substituted and terminal alkenes participate in the cascade reaction, but with a limited scope compared to the styrenyl substrates. This method allows for rapid formation of highly substituted spiroketals in good yield and excellent enantioselectivity.

Small rings in the bigger picture: ring expansion of three- and four-membered rings to access larger all-carbon cyclic systems

The release of the inherent ring strain of cyclobutane and cyclopropane derivatives allows a rapid build-up of molecular complexity. This review highlights the state-of-the-art of the ring expansions of three- and four-membered cycles and is organised by types of reactions with emphasis on the reaction mechanisms. Selected examples are discussed to illustrate the synthetic potential of this elegant synthetic tool.

Rapid construction of cyclopenta[b]naphthalene frameworks from propargylic alcohol tethered methylenecyclopropanes

We have developed a new synthetic methodology for the rapid construction of cyclopenta[b]naphthalene frameworks from the reaction of propargylic alcohol tethered methylenecyclopropanes with mesyl chloride in the presence of triethylamine through cascade cyclization. The reaction can be performed under mild conditions without the use of transition metals, affording the target products in moderate to good yields, and this cyclization reaction process can be scaled up to a gram-scale synthesis.

Fluorescent amino acids as versatile building blocks for chemical biology

Fluorophores have transformed the way we study biological systems, enabling non-invasive studies in cells and intact organisms, which increase our understanding of complex processes at the molecular level. Fluorescent amino acids have become an essential chemical tool because they can be used to construct fluorescent macromolecules, such as peptides and proteins, without disrupting their native biomolecular properties. Fluorescent and fluorogenic amino acids with unique photophysical properties have been designed for tracking protein-protein interactions in situ or imaging nanoscopic events in real time with high spatial resolution. In this Review, we discuss advances in the design and synthesis of fluorescent amino acids and how they have contributed to the field of chemical biology in the past 10 years. Important areas of research that we review include novel methodologies to synthesize building blocks with tunable spectral properties, their integration into peptide and protein scaffolds using site-specific genetic encoding and bioorthogonal approaches, and their application to design novel artificial proteins, as well as to investigate biological processes in cells by means of optical imaging.

Lewis or Brønsted acid-catalysed reaction of propargylic alcohol-tethered alkylidenecyclopropanes with indoles and pyrroles for the preparation of polycyclic compounds tethered with indole or pyrrole motif

We developed a facile synthetic method to access the cyclopenta[b]naphthalene skeleton from Lewis or Brønsted acid-catalysed propargylic alcohol-tethered alkylidenecyclopropanes with indole and pyrrole derivatives.

1,5-Prodan Emits from a Planar Intramolecular Charge-Transfer Excited State

1-Propionyl-5-dimethylaminonaphthalene (8, 1,5-Prodan) and two derivatives where the amino group is constrained in a seven-membered (9) and five-membered (10) ring are prepared. All three exhibit strong fluorescence and similar degrees of solvatochromism. Their fluorescence is strongly quenched in alcohol solvents. Because the amino group in 9 and especially 10 is forced to be coplanar with the naphthalene ring, the similar photophysical behavior of all three suggests that emission arises from a planar excited state (planar intramolecular charge transfer).

Base-Promoted Selective Synthesis of 2H-Pyranones and Tetrahydronaphthalenes via Domino Reactions

A highly efficient domino protocol has been developed for the synthesis of 6-aryl-4-(methylthio/amine-1-yl)-2-oxo-2H-pyran-3-carbonitriles and 4-aryl-2-(amine-1-yl)-5,6,7,8-tetrahydronaphthalene-1-carbonitriles from simple and readily available α-aroylketene dithioacetals, malononitrile, secondary amines, and cyclohexanone. This elegant domino process involved consecutive addition-elimination, intramolecular cyclization, and ring opening and closing sequences. Notably, in situ generated 2-imino-4-(methylthio/amine-1-yl)-6-aryl-2H-pyran-3-carbonitrile plays multiple roles in the construction of various novel polyaromatic hydrocarbons.

Synthesis and photophysical studies of through-space conjugated [2.2]paracyclophane-based naphthalene fluorophores

New three-dimensional compact organic fluorophores with tunable photophysical properties are easily accessible from [2.2]paracyclophane using an intramolecular dehydrogenative Diels–Alder reaction as a key step.

Spectroscopic investigation of bio-mimetic solvolysis of 6-(N,N-dimethylamino)-2,3-naphthalic anhydride in confined nanocavities

Enzymes are biological catalysts that can vastly accelerate the reaction rate of a substrate by accommodating it within the active site.

Intramolecular [2 + 2] and [4 + 2] Cycloaddition Reactions of Cinnamylamides of Ethenetricarboxylate in Sequential Processes

Intramolecular [2 + 2] and [4 + 2] cycloaddition reactions of cinnamylamides of ethenetricarboxylate in sequential processes have been studied. Reaction of 1,1-diethyl 2-hydrogen ethenetricarboxylate and trans-cinnamylamines in the presence of EDCI/HOBt/Et₃N led to pyrrolidine products in one pot, via intramolecular [2 + 2], [4 + 2], and some other cyclizations. The types of the products depend on the substituents on the benzene ring and the reaction conditions. Reaction of cinnamylamines without substituents on the benzene ring and with halogens and OMe on the para position at room temperature gave cyclobutane-fused pyrrolidines as major products via [2 + 2] cycloaddition. The reaction at 80 °C in 1,2-dichloroethane gave δ-lactone fused pyrrolidines as major products, probably via ring-opening of the cyclobutanes. Interestingly, reaction of 1,1-diethyl 2-hydrogen ethenetricarboxylate and cinnamylamines bearing electron-withdrawing groups such as NO₂, CN, CO₂Me, CO₂Et, and CF₃ on ortho and para positions in the presence of EDCI/HOBt/Et₃N at room temperature or at 60-80 °C gave tetrahydrobenz[f]isoindolines via [4 + 2] cycloaddition as major products. DFT studies have been performed to explained the observed [2 + 2]/[4 + 2] selectivity.

Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions

A nucleoside bearing a solvatochromic push-pull fluorene fluorophore (dCFL ) was designed and synthesized by the Sonogashira coupling of alkyne-linked fluorene 8 with 5-iodo-2'-deoxycytidine. The fluorene building block 8 and labeled nucleoside dCFL exerted bright fluorescence with significant solvatochromic effect providing emission maxima ranging from 421 to 544 nm and high quantum yields even in highly polar solvents, including water. The solvatochromism of 8 was studied by DFT and ADC(2) calculations to show that, depending on the polarity of the solvent, emission either from the planar or the twisted conformation of the excited state can occur. The nucleoside was converted to its triphosphate variant dCFLTP which was found to be a good substrate for DNA polymerases suitable for the enzymatic synthesis of oligonucleotide or DNA probes by primer extension or PCR. The fluorene-linked DNA can be used as fluorescent probes for DNA-protein (p53) or DNA-lipid interactions, exerting significant color changes visible even to the naked eye. They also appear to be suitable for time-dependent fluorescence shift studies on DNA, yielding information on DNA hydration and dynamics.

Recent advances in the synthesis and application of fluorescent α-amino acids

The design and synthesis of new fluorescent α-amino acids as well as their application in imaging of biological systems has been reviewed.

Rational design of cyclopenta[b]naphthalenes for better optoelectronic applications and their photophysical properties using DFT/TD-DFT methods

The optical properties of cyclopenta[b]naphthalenes (CPNs) can be fine-tuned by suitable substitutions and DFT calculations show that they can make efficient OLEDs.

MediaChrom: Discovering a Class of Pyrimidoindolone-Based Polarity-Sensitive Dyes

A small library of six polarity-sensitive fluorescent dyes, nicknamed MediaChrom, was prepared. This class of dyes is characterized by a pyrimidoindolone core fitted out with a conjugated push-pull system and a carboxy linker for a conceivable coupling with biomolecules. The optimized eight-step synthetic strategy involves a highly chemo- and regioselective gold-catalyzed cycloisomerization reaction. The photophysical properties of MediaChrom dyes have been evaluated in-depth. In particular, the MediaChrom bearing a diethylamino as an electron-donating group and a trifluoromethyl as an electron-withdrawing group displays the most interesting and advantageous spectroscopic features (e.g., absorption and emission in the visible range and a good quantum yield). Promising results in terms of sensitivity have been obtained in vitro on this dye as a membrane/lipophilic probe and as a peptide fluorescent label.

Intramolecular didehydro-Diels-Alder reaction and its impact on the structure-function properties of environmentally sensitive fluorophores

Reaction discovery plays a vital role in accessing new chemical entities and materials possessing important function.1 In this Account, we delineate our reaction discovery program regarding the [4 + 2] cycloaddition reaction of styrene-ynes. In particular, we highlight our studies that lead to the realization of the diverging reaction mechanisms of the intramolecular didehydro-Diels-Alder (IMDDA) reaction to afford dihydronaphthalene and naphthalene products. Formation of the former involves an intermolecular hydrogen atom abstraction and isomerization, whereas the latter is formed via an unexpected elimination of H2. Forming aromatic compounds by a unimolecular elimination of H2 offers an environmentally benign alternative to typical oxidation protocols. We also include in this Account ongoing work focused on expanding the scope of this reaction, mainly its application to the preparation of cyclopenta[b]naphthalenes. Finally, we showcase the synthetic utility of the IMDDA reaction by preparing novel environmentally sensitive fluorophores. The choice to follow this path was largely influenced by the impact this reaction could have on our understanding of the structure-function relationships of these molecular sensors by taking advantage of a de novo construction and functionalization of the aromatic portion of these compounds. We were also inspired by the fact that, despite the advances that have been made in the construction of small molecule fluorophores, access to rationally designed fluorescent probes or sensors possessing varied and tuned photophysical, spectral, and chemical properties are still needed. To this end, we report our studies to correlate fluorophore structure with photophysical property relationships for a series of solvatochromic PRODAN analogs and viscosity-sensitive cyanoacrylate analogs. The versatility of this de novo strategy for fluorophore synthesis was demonstrated by showing that a number of functional groups could be installed at various locations, including handles for eventual biomolecule attachment or water-solubilizing groups. Further, biothiol sensors were designed, and we expect these to be of general utility for the study of lipid dynamics in cellular membranes and for the detection of protein-binding interactions, ideal applications for these relatively hydrophobic fluorophores. Future studies will be directed toward expanding this chemistry-driven approach to the rational preparation of fluorophores with enhanced photophysical and chemical properties for application in biological systems.