Design, synthesis and investigation of water-soluble hemi-indigo photoswitches for bioapplications

• Daria V. Berdnikova

Beilstein J. Org. Chem. 2019, 15, 2822–2829, doi:10.3762/bjoc.15.275

• new biocompatible photochromes with complementary properties is highly desirable to speed up the progress in this important field. In this context, an emerging class of hemi-indigo photoswitches attracted special attention [12][13][14][15][16][17]. Despite the fact that the hemi-indigo dyes are known

• responsible for the rate of thermal E–Z isomerization pointing out the importance of the Coulomb interactions between hemi-indigo and buffer components. A possible explanation of this observation can be provided by the comparison with structurally related hemi(thio)indigo dyes [22]. Thus, in the case of hemi

Dyes in modern organic chemistry

• Heiko Ihmels

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

• Heiko Ihmels University of Siegen, Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany 10.3762/bjoc.15.272 Keywords: dyes; Research on organic dyes constitutes a cornerstone in organic chemistry. It started

• between research on dyes and industrial chemistry [2][3][4]. As a result, the success and strength of several chemical companies are originally based on dye chemistry. Although the traditional dyeing of textiles, hair, food, cosmetics, photography or printer colors, etc. is still highly relevant, organic

• dyes also contribute as essential components in modern applications such as in OLEDs [5][6], solar cells [7][8], organic semiconductors [9], NLO materials [10], photopolymerization [11], or Chemistry 4.0 [12]. From its very beginning, dye chemistry is strongly connected to the scientific developments

Diversity-oriented synthesis of spirothiazolidinediones and their biological evaluation

• Sambasivarao Kotha,
• Gaddamedi Sreevani,
• Lilya U. Dzhemileva,
• Milyausha M. Yunusbaeva,
• Usein M. Dzhemilev and
• Vladimir A. D’yakonov

Beilstein J. Org. Chem. 2019, 15, 2774–2781, doi:10.3762/bjoc.15.269

• , phosphatidylserine molecules appear on the cell surface but the membrane is still impermeable for DNA-binding dyes (such as propidium iodide). The membrane integrity is lost at later stages of the cell death. Thus, while detecting the apoptosis, one can distinguish four types of cells: living cells (annexin V−/PI

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

• 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

• fluorophores [19], in particular on aggregation-induced emissive polar dyes [20]. Conceptually, many of these consecutive multicomponent syntheses rely on transition-metal-catalyzed heterocyclic syntheses [21]. By virtue of catalytic generation of alkynones [22] we have recently disclosed consecutive

Synthesis of aryl-substituted thieno[3,2-b]thiophene derivatives and their use for N,S-heterotetracene construction

• Nadezhda S. Demina,
• Nikita A. Kazin,
• Nikolay A. Rasputin,
• Roman A. Irgashev and
• Gennady L. Rusinov

Beilstein J. Org. Chem. 2019, 15, 2678–2683, doi:10.3762/bjoc.15.261

• light-harvesting dyes for dye-sensitized solar cells [1], electron-donating materials for bulk heterojunction solar cells [2][3][4], and p-type semiconductors for organic field-effect transistors [5][6][7]. Within the same context of organic semiconductor development, the bicyclic TT subunit has been

A photochemical determination of luminescence efficiency of upconverting nanoparticles

• Baptiste Amouroux,
• Clément Roux,
• Jean-Claude Micheau,
• Fabienne Gauffre and
• Christophe Coudret

Beilstein J. Org. Chem. 2019, 15, 2671–2677, doi:10.3762/bjoc.15.260

• diamminetetrakis(thiocyanato)chromate(III)), photochromic dyes have been proposed for such a purpose, mainly from the azobenzene, fulgide or diarylethene families [22]. The latter two are particularly attractive for visible light wavelengths above 400 nm. However, their use is conditioned by their availability and

• (Figure 1) [25][27]. Switching of such diarylethene dyes in both directions (ring closure/coloration or ring opening/discoloration) by UCNPs has been documented for years, with a seminal work reported in 2009 by the team of Branda [28]. In the following we will show how this photochromic compound can be

• particles (70 nm) [34] and recruiting the flavin-containing coenzymes as 1O2 sensitizers. In the skin, typical number of dyes per femtoliter is expected to be 750. This would correspond to an absorbance of 0.0014 in 1 cm of pure water according to a molar extinction coefficient of ca. 11300 L mol−1 cm−1. To

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

• transduction, apoptosis and even necrosis [8][9][10]. The monitoring of plasma membranes, their biophysical properties, endocytosis/exocytosis of several types of molecules, as well as their dynamic changes, may be performed by using fluorogenic organic dyes or derivatives thereof [11][12][13][14][15]. The

• 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

• ][62]. These organelles are formed by plasma membrane invaginations sustaining the structure and composition of the original component. The use of lipophilic dyes for plasma membrane staining will therefore afford additional cytoplasm markers due to endosome formation from the plasma membrane

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

• , 41012 Seville, Spain 10.3762/bjoc.15.254 Abstract Four new dyes that derive from borylated arylisoquinolines were prepared, containing a third aryl residue (naphthyl, 4-methoxynaphthyl, pyrenyl or anthryl) that is linked via an additional stereogenic axis. The triaryl cores were synthesized by Suzuki

• couplings and then transformed into boronic acid esters by employing an Ir(I)-catalyzed reaction. The chromophores show dual emission behavior, where the long-wavelength emission band can reach maxima close to 600 nm in polar solvents. The fluorescence quantum yields of the dyes are generally in the range

• of 0.2–0.4, reaching in some cases values as high as 0.5–0.6. Laser-flash photolysis provided evidence for the existence of excited triplet states. The dyes form fluoroboronate complexes with fluoride anions, leading to the observation of the quenching of the long-wavelength emission band and

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

• intraoperative imaging of cancerous lesions, we were interested in silicon rhodamines due to their fluorescence properties in the biological window (650 nm to 1350 nm). While clinically approved fluorescence dyes like ICG (indocyanine green, Mw = 775 g/mol) have a high molecular weight and could therefore alter

• dyes Cy5.5 and Alexa Fluor® 680 [23]. Moreover, silicon rhodamines demonstrated in in vivo imaging experiments excellent fluorescence properties and biostabilities [23] as well as exhibited high quantum efficiencies with high tolerance to photobleaching [24]. A silicon rhodamine antibody conjugate

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

• large fluorescence quantum yield, compound SyOTh1 emerged as a candidate for single-molecule based super-resolution fluorescence microscopy. Keywords: diarylethenes; dyes; fluorescence; organic synthesis; photochromism; photoswitching; Introduction Reversibly photoswitchable diarylethenes (DAEs) with

• (φOF→CF); the oxidized compounds showed an opposite trend. As a result, the degree of conversion in the photostationary state found for nonoxidized compounds was moderate <70% (ca. 30% for asymmetric and 70% for symmetric dyes), but the oxidized analogs show complete conversions (>98%). Interestingly

Synthesis of a dihalogenated pyridinyl silicon rhodamine for mitochondrial imaging by a halogen dance rearrangement

• Jessica Matthias,
• Thines Kanagasundaram,
• Klaus Kopka and
• Carsten S. Kramer

Beilstein J. Org. Chem. 2019, 15, 2333–2343, doi:10.3762/bjoc.15.226

• .15.226 Abstract Background: Since their first synthesis, silicon xanthenes and the subsequently developed silicon rhodamines (SiR) gained a lot of attention as attractive fluorescence dyes offering a broad field of application. We aimed for the synthesis of a fluorinable pyridinyl silicon rhodamine for

• ; mitochondrial probe; near-infrared (NIR) dyes; one-pot reaction; silicon rhodamines; Introduction Since their first synthesis by Fu and co-workers in 2008 [1], silicon xanthenes and the subsequently developed silicon rhodamines (SiR) have drawn a lot of attention as attractive fluorescence dyes offering a

• microscopy [2][3][4][5][6][7][8][9], as direct probes for various biomolecules [10][11][12][13] or as sensors for metal ions [14][15][16][17][18], pH [16], voltage [19] or metabolites [20][21][22][23]. Several attempts were made, partially supported by DFT calculations, to correlate the dyes’ structural

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

• studies proposed a binding mode in which 2a mimics the nicotinamide residue of NAD+, whereas aromatic amino acid residues of the selectivity pocket stabilize the dimethylphenol ring [35]. As photoisomerization in stilbenes and azo dyes is accompanied by a perpendicular twist of the phenyl ring towards the

• stilbene motive of selected stilbene 2c by a diazeno group, because photoisomerization of azo dyes was anticipated to proceed fast and reversible by application of UV irradiation and visible light, respectively in this analogue. 5-Diazenylnicotinamide 11 was synthetically accessible in two steps through

• state, as envisioned. Possible reasons could be assigned to substituent effects as demonstrated by Simeth et al. [62]. As recently reported by Schehr et al., reducing agents like DTT, used to prevent enzyme oxidation in crystallization mixtures or in vitro assays, can reduce azo dyes to hydrazine

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

• Marco Santella Eduardo Della Pia Jakob Kryger Sorensen Bo W. Laursen Nano-Science Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark 10.3762/bjoc.15.210 Abstract Triangulenium dyes functionalized with one, two or three ethylthiol

• bridges leading to sulfur-functionalized acridinium, xanthenium or triangulenium dyes. For all the dye classes the sulfur functionalities are found to lead to intensely absorbing dyes in the visible range (470 to 515 nm), quite similar to known analogous dye systems with dialkylamino donor groups in place

• 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

α-Photooxygenation of chiral aldehydes with singlet oxygen

• Dominika J. Walaszek,
• Magdalena Jawiczuk,
• Jakub Durka,
• Olga Drapała and
• Dorota Gryko

Beilstein J. Org. Chem. 2019, 15, 2076–2084, doi:10.3762/bjoc.15.205

• ], TEMPO [4], or benzoyl peroxide [5][6][7][8]. Therefore, the use of environmentally friendly reagents instead is highly desirable. Along this line, singlet oxygen by being easily photochemically generated from triplet oxygen in the presence of organic dyes seems promising. Despite its high reactivity and

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

• rigid and the molecules can become more or less planar to adopt the constrains of the molecular packing. Thus, the structures of salts 6a and 7a resemble more those of cyanine dyes and the structure of 3 those of merocyanines. The protonation positions of 3 are correctly predicted by the calculations

Naphthalene diimides with improved solubility for visible light photoredox catalysis

• Barbara Reiß and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2019, 15, 2043–2051, doi:10.3762/bjoc.15.201

• light range between 520 nm and 640 nm. The irradiation by visible light together with the use of an organic dye instead of a transition metal complex as photoredox catalyst improve the sustainability and make photoredox catalysis “greener”. Keywords: chromophore; dyes; electrochemistry; photochemistry

• conclusively showed that there is no universal photoredox catalyst for different organic transformations. Instead, each photoredox catalyst has its own reactivity profile and scope. In order to apply organic dyes in advanced photoredox catalysts in a versatile way, it is crucial that modifications can be

• easily incorporated into the core structure in order to tune optical and redox properties. Naphthalene diimides (NDIs) as the smallest possible rylene dyes are such an important class of organic dyes. In contrast to their bigger homologs perylene diimides which were rarely used for photoredox catalysis

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

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• , Supporting Information File 1). It should be noted that chirality induction can be exploited to design chirality sensing ensembles [17]. This strategy was successfully implemented by the Nau group for sensing of chiral aromatic compounds. Ternary complexes between cucurbit[8]uril, dicationic dyes, and chiral

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

• cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of

• common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4

• analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide

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

• . In this study, the influence of substitution in the benzofuranone ring on the UV–vis spectrum is explored, as well as an initial screening of their toxicity and a qualitative preliminary study of their potential to act as fabric dyes. Keywords: aurone; dyeing; dyes; substitution effect; toxicity; UV

• 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

• system, we chose to study the potential for aurones to be used as dyes as well as a more extensive study of the impact of substitution in the benzofuranone portion of the molecule on its optical properties. Results and Discussion Synthesis We have previously reported the synthesis of a significant number

Functional panchromatic BODIPY dyes with near-infrared absorption: design, synthesis, characterization and use in dye-sensitized solar cells

• Quentin Huaulmé,
• Cyril Aumaitre,
• Outi Vilhelmiina Kontkanen,
• David Beljonne,
• Alexandra Sutter,
• Gilles Ulrich,
• Renaud Demadrille and
• Nicolas Leclerc

Beilstein J. Org. Chem. 2019, 15, 1758–1768, doi:10.3762/bjoc.15.169

• Polymères Université de Mons - UMONS / Materia Nova Place du Parc, 20, B-7000 Mons, Belgium ICPEES – UMR7515, CNRS-Université de Strasbourg, 25 rue Becquerel, 67087 Strasbourg CEDEX 02, France 10.3762/bjoc.15.169 Abstract We report two novel functional dyes based on a boron-dipyrromethene (BODIPY) core

• displaying a panchromatic absorption with an extension to the near-infrared (NIR) range. An innovative synthetic approach for preparing the 2,3,5,6-tetramethyl-BODIPY unit is disclosed, and a versatile way to further functionalize this unit has been developed. The optoelectronic properties of the two dyes

• were computed by density functional theory modelling (DFT) and characterized through UV–vis spectroscopy and cyclic voltammetry (CV) measurements. Finally, we report preliminary results obtained using these functional dyes as photosensitizers in dye-sensitized solar cells (DSSCs). Keywords: boron

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

• properties of the three dyes were investigated by photoabsorption and fluorescence spectroscopy, Lippert–Mataga plots, cyclic voltammetry and density functional theory calculations. The photoabsorption maximum (λmax,abs) and the fluorescence maximum (λmax,fl) for the intramolecular charge-transfer

• 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

A heteroditopic macrocycle as organocatalytic nanoreactor for pyrroloacridinone synthesis in water

• Piyali Sarkar,
• Sayan Sarkar and
• Pradyut Ghosh

Beilstein J. Org. Chem. 2019, 15, 1505–1514, doi:10.3762/bjoc.15.152

• ; pyrroloacridinones; sustainable chemistry; water; Introduction Acridines are a renowned heterocyclic entity not only for their biological activities but also for their fluorescence and chemiluminescence properties. Acridine dyes (e.g., acridine orange, acridine yellow, etc.), are predominantly used in staining of

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• tetralactam macrocycles [14][15][16]. The Smith group has used tetralactam macrocycles to encapsulate and stabilize deep-red fluorescent squaraine dyes for biomedical applications [17][18][19][20]. By introducing water-soluble groups to tetralactam macrocycles, Davis and co-workers realized selective

Complexation of a guanidinium-modified calixarene with diverse dyes and investigation of the corresponding photophysical response

• Yu-Ying Wang,
• Yong Kong,
• Zhe Zheng,
• Wen-Chao Geng,
• Zi-Yi Zhao,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2019, 15, 1394–1406, doi:10.3762/bjoc.15.139

• luminescent dyes. Fluorescein, eosin Y, rose bengal, tetraphenylporphine sulfonate and sulfonated aluminum phthalocyanine were employed as classical aggregation-induced quenching dyes. 2-(p-Toluidinyl)naphthalene-6-sulfonic acid and 1-anilinonaphthalene-8-sulfonic acid were selected as representatives of

• intramolecular charge-transfer dyes. Phosphated tetraphenylethylene was involved as the classical aggregation-induced emission dye. Sulfonated acedan representing one example of two-photon fluorescent probes, was also investigated. A ruthenium(II) complex with carboxylated bipyridyl ligands was included as a

• and potential applications according to the diverse photophysical responses are provided. Keywords: calixarene; host–guest complexation; luminescent dyes; macrocycles; photophysical properties; Introduction Fluorescence sensing represents a powerful detection methodology due to its low cost, ease of