Dyes in modern organic chemistry

• Heiko Ihmels

Beilstein J. Org. Chem. 2019, 15, 2798–2800, doi:10.3762/bjoc.15.272

• properties. Traditionally, organic dyes are the basis of well-established color indicators for qualitative and quantitative analysis. Nowadays, we cannot imagine research in the life sciences or in medical diagnostics without the sophisticated applications of organic dyes as fluorescent probes, dye labels

Emission solvatochromic, solid-state and aggregation-induced emissive α-pyrones and emission-tuneable 1H-pyridines by Michael addition–cyclocondensation sequences

• Natascha Breuer,
• Irina Gruber,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2019, 15, 2684–2703, doi:10.3762/bjoc.15.262

• prerequisites for the application of fluorescent substances in chemistry, medicine and materials science [1]. With this respect emissive small molecules [2], fluorescent proteins [3], and quantum dots have received considerable attention and remarkable progress in their synthesis and photophysics has been

• increasingly used in OLEDs [6][7][8][9][10] and LCDs [11][12][13] of mobile phones [14]. Fluorescent compounds often intensively emit in solution but only weakly or not in the solid state [15]. Dyes which fluoresce both in the solid state and in solution are still relatively rare, due to the fact that often

• considerably depending on the substituent pattern. The absorption and emission maxima are shifted bathochromically with increasing donor strength. α-Pyrones are only weakly fluorescent in solution. However, with distinct p-N,N-dimethylaminophenyl substitution in 6-position, an extraordinarily high fluorescence

Plasma membrane imaging with a fluorescent benzothiadiazole derivative

• Pedro H. P. R. Carvalho,
• Jose R. Correa,
• Karen L. R. Paiva,
• Daniel F. S. Machado,
• Jackson D. Scholten and
• Brenno A. D. Neto

Beilstein J. Org. Chem. 2019, 15, 2644–2654, doi:10.3762/bjoc.15.257

• , Brazil Laboratory of Molecular Catalysis, Institute of Chemistry, Graduate Program (PPGQ), Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil 10.3762/bjoc.15.257 Abstract This work describes a novel fluorescent 2,1,3-benzothiadiazole derivative designed to act as a water

• agreement with the experimental data and helped to understand the stabilizing intramolecular charge-transfer process from the first excited state. The new fluorescent derivative could be applied as selective bioprobe in several cell lines and displayed plasma-membrane affinity during the imaging experiments

• and by poor performances related to most of them. Therefore, many studies are still based on the use of WGA [16] (wheat germ agglutinin) or membrane proteins bearing fluorescent protein tags [11]. Water solubility is another issue that has to be considered. For the development of new fluorogenic dyes

Arylisoquinoline-derived organoboron dyes with a triaryl skeleton show dual fluorescence

• Vânia F. Pais,
• Tristan Neumann,
• Ignacio Vayá,
• M. Consuelo Jiménez,
• Abel Ros and
• Uwe Pischel

Beilstein J. Org. Chem. 2019, 15, 2612–2622, doi:10.3762/bjoc.15.254

• quenching effects, as the result of the formation of fluoroboronate complexes. In the case of the pyrenyl- and anthryl-substituted dyes a clear ratiometric behavior was noted. No quenching was seen for the addition of cyanide ions or bromide and chloride. This makes the new dyes selective fluorescent

A new approach to silicon rhodamines by Suzuki–Miyaura coupling – scope and limitations

• Thines Kanagasundaram,
• Antje Timmermann,
• Carsten S. Kramer and
• Klaus Kopka

Beilstein J. Org. Chem. 2019, 15, 2569–2576, doi:10.3762/bjoc.15.250

• functionalized with free acid moieties are directly accessible in contrast to previously described methods. Keywords: cross coupling; fluorescent dyes; near-infrared (NIR) dyes; silicon rhodamines; Suzuki–Miyaura coupling; Introduction Silicon rhodamines are versatile fluorescent dyes that found extensive use

α,ß-Didehydrosuberoylanilide hydroxamic acid (DDSAHA) as precursor and possible analogue of the anticancer drug SAHA

• Shital K. Chattopadhyay,
• Subhankar Ghosh,
• Sarita Sarkar and
• Kakali Bhadra

Beilstein J. Org. Chem. 2019, 15, 2524–2533, doi:10.3762/bjoc.15.245

• presence of ROS sensitive probe DCFH-DA (dichlorodihydrofluorescein hydrate diacetate) by using FACS (Figure 4). Cellular ROS levels were found to be increased with dose. The mean fluorescent intensities for four compounds were presented in Table 4 and maximum changed intensity for 11b was observed from

• with DAPI staining revealed a significant increase in nucleosomal fragmentation and nuclear condensation in 11b treated cells with increasing doses (Figure 6 upper panel) [39]. Furthermore, a cellular functional assay by JC-1 probe, a voltage sensitive fluorescent cationic dye, exhibits membrane

In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization

• Lei Zhang,
• Greta Linden and
• Olalla Vázquez

Beilstein J. Org. Chem. 2019, 15, 2500–2508, doi:10.3762/bjoc.15.243

• (TM) obtained by the first derivative of the data in A. Outline of the displacement assay principle, in which a photoswitchable PNA probe (blue) hybridizes to a complementary quencher-labelled single-stranded (ss) DNA (black) and replaces a fluorescent-labelled ssDNA (grey); F = fluorescein; Q = black

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• show that this can be a successful alternative to evaluate two-photon properties, particularly useful in case of non-fluorescent molecules. Results and Discussion Spectroscopic properties The UV–vis absorption spectrum of hydrazone 1 shows an intense absorption band peaked at 395 nm in toluene, as

• signal intensity slightly decreases on the 7.5 ps timescale, as the result of vibrational relaxation, and mostly recovers on a ca. 140 ps timescale. Transient absorption measurements upon 400 nm excitation were also performed in acetonitrile and methanol. While the Z-form is fluorescent in acetonitrile

Targeted photoswitchable imaging of intracellular glutathione by a photochromic glycosheet sensor

• Xianzhi Chai,
• Hai-Hao Han,
• Yi Zang,
• Jia Li,
• Xiao-Peng He,
• Junji Zhang and
• He Tian

Beilstein J. Org. Chem. 2019, 15, 2380–2389, doi:10.3762/bjoc.15.230

• obvious morphology of nanosheets which presented a large 2D and ultrathin plane with a diameter of ca. 200 nm (Figure 2B) [33][34]. By virtue of the expansive surface, 2D MnO2 nanosheets possess the ability to load dozens of fluorophores. An array of fluorescent reporters thus formed, which facilitate

• fluorescence spectroscopy. As shown in Figure S3A (Supporting Information File 1), GSH showed a distinct selectivity over other analytes, suggesting a specific GSH detection performance of Glyco-DTE@MnO2. A linear response of the normalized fluorescent intensity I/Imax at 535 nm within 0–0.4 mM GSH

• fluorescent sensors for detecting intracellular GSH or discriminative sensing of GSH with other common biothiols (e.g., Cys and Hcy) [45][46]. In this work, the highly accessible 2D MnO2 nanosheet is used as the GSH responsive site instead of traditional functional groups that require elaborate design for

Excited state dynamics for visible-light sensitization of a photochromic benzil-subsituted phenoxyl-imidazolyl radical complex

• Yoichi Kobayashi,
• Yukie Mamiya,
• Katsuya Mutoh,
• Hikaru Sotome,
• Masafumi Koga,
• Hiroshi Miyasaka and
• Jiro Abe

Beilstein J. Org. Chem. 2019, 15, 2369–2379, doi:10.3762/bjoc.15.229

• molecular design [25]. The wide ranges of thermal back reactions of photoswitches expand the potential applications of photochromic materials such as to dynamic holographic display [26][27][28], switchable fluorescent markers [29][30][31], and anticounterfeit inks. However, PIC is photosensitive only in the

Mono- and bithiophene-substituted diarylethene photoswitches with emissive open or closed forms

• A. Lennart Schleper,
• Mariano L. Bossi,
• Vladimir N. Belov and
• Stefan W. Hell

Beilstein J. Org. Chem. 2019, 15, 2344–2354, doi:10.3762/bjoc.15.227

• with mono- (Th1) and bithiophene (Th2) units attached to positions 6 and 6′ (Sy = symmetric) or only to position 6 (As = asymmetric). “Oxidized” compounds have highly fluorescent closed forms emitting in the visible region (yellow to red). The dyes with nonoxidized benzothiophenes possess fluorescent

• highly fluorescent “closed” forms combine photochromic and fluorescent entities in one molecule [1] and contain a perfluorocyclopentene bridge linking two 2-alkyl-1-benzothiophene-1,1-oxide residues with a C=C bond via C-3 and C-3′ atoms [2][3]. The “open” form of the DAE core (see graphical abstract and

• Table 1) is only weakly fluorescent (φFl ≈ 0.01) [4]. In general, diarylethenes with fluorescent open forms are rare, while photoswitchable compounds with highly fluorescent “open” and “closed” forms represent a yet unknown and unique class of ratiometric fluorophores. Recently, we demonstrated that

Fluorescent phosphorus dendrimers excited by two photons: synthesis, two-photon absorption properties and biological uses

• Anne-Marie Caminade,
• Artem Zibarov,
• Eduardo Cueto Diaz,
• Aurélien Hameau,
• Maxime Klausen,
• Kathleen Moineau-Chane Ching,
• Jean-Pierre Majoral,
• Jean-Baptiste Verlhac,
• Olivier Mongin and
• Mireille Blanchard-Desce

Beilstein J. Org. Chem. 2019, 15, 2287–2303, doi:10.3762/bjoc.15.221

• branches of the dendrimer structures, respectively. Also the functionalization in two compartments (core and surface, or branches and surface) was achieved. The consequences of the location of the fluorophores on the fluorescence and TPA properties have been studied. Several of these TPA fluorescent

• dendrimers have water-solubilizing functions as terminal groups, and fluorophores at the core or in the branches. They have been used as fluorescent tools in biology for different purposes, such as tracers for imaging blood vessels of living animals, for determining the phenotype of cells, for deciphering

• instance, fluorescein, which is a widely used fluorescent tracer for many applications, was synthesized for the first time in 1871 [1]. Besides this classical type of one-photon-induced fluorescence, a theoretical work by M. Göppert-Mayer in 1931 [2] predicted the possibility of the simultaneous absorption

Recent advances in transition-metal-catalyzed incorporation of fluorine-containing groups

• Xiaowei Li,
• Xiaolin Shi,
• Xiangqian Li and
• Dayong Shi

Beilstein J. Org. Chem. 2019, 15, 2213–2270, doi:10.3762/bjoc.15.218

Aggregation-induced emission effect on turn-off fluorescent switching of a photochromic diarylethene

• Luna Kono,
• Yuma Nakagawa,
• Ayako Fujimoto,
• Ryo Nishimura,
• Yohei Hattori,
• Toshiki Mutai,
• Nobuhiro Yasuda,
• Kenichi Koizumi,
• Satoshi Yokojima,
• Shinichiro Nakamura and
• Kingo Uchida

Beilstein J. Org. Chem. 2019, 15, 2204–2212, doi:10.3762/bjoc.15.217

• , diarylethene derivatives with photoswitchable fluorescent properties were prepared. They are applicable for fluorescence imaging including bio-imaging. On the other hand, a new system called “excited state intramolecular proton transfer (ESIPT)” is reported. In the system, absorption and emission bands are

• largely separated due to the proton transfer, hence it showed strong fluorescence even in the crystalline state. We aimed to construct the photochromic system incorporating the ESIPT mechanism. Results: A diarylethene incorporating a fluorescent moiety that exhibit ESIPT behavior was prepared. The ESIPT

• fluorescent turn-off behavior during photochromism in aprotic solvents as well as in crystalline state upon UV light irradiation. Furthermore, it showed AIE in THF/water mixtures with blue-shift of the emission. Keywords: AIE; diarylethene; ESIPT fluorescent switching; turn-off fluorescence; Introduction

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• enzyme assay. The long irradiation periods that were necessary to obtain significant amounts of the (Z)-isomers did not permit switching of the inhibitors in the enzyme assay mixture, as the fluorescent substrate and the enzyme would be harmed by long-term UV radiation. We envisioned to replace the

• a fluorescent readout. Inhibition was determined by comparing percentage substrate conversion to a DMSO control after subtraction of the blank fluorescence signal. All compounds were tested at 100 µM, 50 µM and 10 µM, respectively. For compounds that showed more than 50% inhibition at 10 µM an IC50

Synthesis and properties of sulfur-functionalized triarylmethylium, acridinium and triangulenium dyes

• Marco Santella,
• Eduardo Della Pia,
• Jakob Kryger Sørensen and
• Bo W. Laursen

Beilstein J. Org. Chem. 2019, 15, 2133–2141, doi:10.3762/bjoc.15.210

• of the ethylthiol substituents. For the triangulenium derivatives significant fluorescence was observed (Φf = 0.1 to Φf = 0.3). Keywords: acridinium dyes; aromatic nucleophilic substitution; fluorescent dyes; sulfur-functionalized dyes; triangulenium dyes; triarylmethylium; Introduction The design

• , synthesis and studies of organic fluorescent dyes have witnessed a revival in recent years, in particular due to their applications in imaging and biomedical assays and analytical techniques [1][2][3][4][5]. The desire to detect minute amounts of dye, ideally single molecules [6][7], in complex biological

• bichromophoric behavior has been studied in detail for the dialkylamino-substituted xanthenium/rhodamine system [45][46], and is also the likely reason for these compounds being non-fluorescent. The three sulfur-substituted trioxatriangulenium dyes 6, 8, and 9 all display a first absorption band around 480 nm

1,2,3,4-Tetrahydro-1,4,5,8-tetraazaanthracene revisited: properties and structural evidence of aromaticity loss

• Arnault Heynderickx,
• Sébastien Nénon,
• Olivier Siri,
• Vladimir Lokshin and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2019, 15, 2059–2068, doi:10.3762/bjoc.15.203

• ]. A strongly fluorescent compound, 3, has been isolated from the reaction of ethylenediamine with noradrenaline, 2-methylnoradrenaline, adrenolone, 3,4-dihydroxymandelic acid or catechol [8]. The reaction with 2,5-dihydroxy-p-benzoquinone (4) under a stream of air affording 3 in 50% yield was proposed

• fluorescent. Minimum two Pekarian functions are needed to reproduce the band shape of the salts 6 in ethanol indicating that at least two electronic transitions are involved (Supporting Information File 1, Figure S3). TD DFT calculations interprets the longest wavelength absorption bands of 3 and 6 to be

Reactions of 2-carbonyl- and 2-hydroxy(or methoxy)alkyl-substituted benzimidazoles with arenes in the superacid CF₃SO₃H. NMR and DFT studies of dicationic electrophilic species

• Dmitry S. Ryabukhin,
• Alexey N. Turdakov,
• Natalia S. Soldatova,
• Mikhail O. Kompanets,
• Alexander Yu. Ivanov,
• Irina A. Boyarskaya and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2019, 15, 1962–1973, doi:10.3762/bjoc.15.191

• –Crafts reaction; triflic acid; Introduction Imidazoles and benzimidazoles are important heterocyclic scaffolds in pharmaceuticals and agrochemicals [1][2][3][4][5][6][7][8][9][10]. They also have applications in the fields of dyes, chemo-sensing, and fluorescent materials [3]. (Benz)imidazoles are a

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• studied by us and others, there are only scarce reports on the biological activity of archangelolide. Here we present the preparation of its fluorescent derivative based on a dansyl moiety using azide–alkyne Huisgen cycloaddition having obtained the two sesquiterpene lactones from the seeds of Laserpitium

• fluorescent conjugate; sarco/endoplasmic reticulum calcium ATPase; sesquiterpene lactone; trilobolide analogue; Introduction Sesquiterpene lactones (SLs) have been attracting interest already for some time due to the plethora of biological effects they elicit. Various SLs show anticancer, antimicrobial

• these compounds for further work including synthetic modifications using azide–alkyne Huisgen cycloaddition. We previously showed the preparation of fluorescent trilobolide conjugates [8] that retained the activity of the parental compounds and proved to be useful for live-cell imaging. In this article

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

• Xiao Xie,
• Michela Zuffo,
• Marie-Paule Teulade-Fichou and
• Anton Granzhan

Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183

• ] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift

• rapid topological classification of G4-DNA structures. Keywords: fluorescent probes; G-quadruplex DNA; G-quadruplex RNA; nucleic acids; styryl dyes; Introduction Development of fluorescent probes for G-quadruplex (G4) DNA and RNA is an active research area. In fact, these non-canonical nucleic acid

• structures appear to be biologically relevant, although a complete understanding of their roles is still missing [1][2][3]. At the same time, they represent versatile building blocks for artificial nano-architectures and nanodevices [4][5]. In this context, small-molecule fluorescent probes find applications

A golden opportunity: benzofuranone modifications of aurones and their influence on optical properties, toxicity, and potential as dyes

• Joza Schmitt and
• Scott T. Handy

Beilstein J. Org. Chem. 2019, 15, 1781–1785, doi:10.3762/bjoc.15.171

• virtually the entirety of recorded history and yet the application of aurones as dyes or pigments has not been reported or studied [3]. Even the optical properties of aurones have had very minimal study. The reports that have appeared have all focused on fluorescent properties and have also been largely

• limited in scope to the influence of the benzylidene portion. Most noteworthy is the report by Bane and co-workers examining the UV–vis and fluorescent properties of a series of amino-substituted aurones [4]. Subsequently, Liu and co-workers explored the same series of aurones using computational methods

Synthesis, photophysical and electrochemical properties of pyridine, pyrazine and triazine-based (D–π–)₂A fluorescent dyes

• Keiichi Imato,
• Toshiaki Enoki,
• Koji Uenaka and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2019, 15, 1712–1721, doi:10.3762/bjoc.15.167

• Keiichi Imato Toshiaki Enoki Koji Uenaka Yousuke Ooyama Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan 10.3762/bjoc.15.167 Abstract The donor–acceptor–π-conjugated (D–π–)2A fluorescent dyes OUY-2, OUK-2

• characteristic band of the (D–π–)2A fluorescent dyes show bathochromic shifts in the order of OUY-2 < OUK-2 < OUJ-2. Moreover, the photoabsorption bands of the (D–π–)2A fluorescent dyes are nearly independent of solvent polarity, while the fluorescence bands showed bathochromic shifts with increasing solvent

• there is little difference in the HOMO energy level among the three dyes, but the LUMO energy levels decrease in the order of OUY-2 > OUK-2 > OUJ-2. Consequently, this work reveals that for the (D–π–)2A fluorescent dyes OUY-2, OUK-2 and OUJ-2 the bathochromic shifts of λmax,abs and λmax,fl and the

Host–guest interactions in nor-seco-cucurbit[10]uril: novel guest-dependent molecular recognition and stereoisomerism

• Xiaodong Zhang,
• Wei Wu,
• Zhu Tao and
• Xin-Long Ni

Beilstein J. Org. Chem. 2019, 15, 1705–1711, doi:10.3762/bjoc.15.166

• ]. Keywords: fluorescent; host–guest interaction; macrocycles; molecular recognition; nor-seco-cucurbit[10]uril; pyrene; Introduction Host–guest interactions that trigger molecular recognition are a current topic of interest. For example, understanding the protein–ligand molecular recognition is of paramount

Recent advances on the transition-metal-catalyzed synthesis of imidazopyridines: an updated coverage

• Gagandeep Kour Reen,
• Ashok Kumar and
• Pratibha Sharma

Beilstein J. Org. Chem. 2019, 15, 1612–1704, doi:10.3762/bjoc.15.165

Synthesis, enantioseparation and photophysical properties of planar-chiral pillar[5]arene derivatives bearing fluorophore fragments

• Guojuan Li,
• Chunying Fan,
• Guo Cheng,
• Wanhua Wu and
• Cheng Yang

Beilstein J. Org. Chem. 2019, 15, 1601–1611, doi:10.3762/bjoc.15.164

• quantum yield was significantly decreased to 46.4% compared with 78.2% for Py-6. We ascribed the decreased fluorescence of P5A-Py to the π–π stacking of the Py units caused by the high local concentration of perylene. For P5A-DPA, which also bears two DPA units in one macrocyclic host, the fluorescent

• quantum yield was only slightly decreased. This should be mainly due to the steric hindrance of the 9- and 10-phenyl groups, which inhibited the π–π stacking of the anthracene core in DPA. The fluorescent lifetimes of P5A-Py and P5A-DPA were compared with Py-6 and DPA-6. As shown in Figure 2, the lifetime

• was 4.8 ns, which is very similar to DPA-6 (5.0 ns) and the non-substituted DPA (5.3 ns) [42]. The fact that grafting DPA units in one host did not influence the fluorescent quantum yield together with the appealing host–guest properties make P5A-DPA an ideal candidate for applications as acceptor for