Star-shaped tetrathiafulvalene oligomers towards the construction of conducting supramolecular assembly

• Masahiko Iyoda and
• Masashi Hasegawa

Beilstein J. Org. Chem. 2015, 11, 1596–1613, doi:10.3762/bjoc.11.175

• functional dyes [22][23]. Furthermore, various multifunctional TTF-based supramolecular architectures have been designed and synthesized to realize molecular sensors, redox switches, multi-input systems for logic gates, electrochemically-driven conformational controls, molecular clips and tweezers, and redox

Preparative semiconductor photoredox catalysis: An emerging theme in organic synthesis

• David W. Manley and
• John C. Walton

Beilstein J. Org. Chem. 2015, 11, 1570–1582, doi:10.3762/bjoc.11.173

• , uncommon reaction sequences. Homogeneous PRCs form one class that encompasses soluble organic dyes [1] as well as transition metal complexes; particularly those of Ru and Ir. Study of the latter markedly escalated from 2008 thanks to papers from the groups of MacMillan [2], Yoon [3] and Stephenson [4]. The

• opportunity for surface modification of the semiconductors with metals or dyes to extend the capability into the visible light region. This is a step nearer to directly channeling the Sun’s energy into synthetic chemistry. Though not proven beyond doubt, the likelihood is that surface OH groups on the

Deproto-metallation of N-arylated pyrroles and indoles using a mixed lithium–zinc base and regioselectivity-computed CH acidity relationship

• Mohamed Yacine Ameur Messaoud,
• Ghenia Bentabed-Ababsa,
• Madani Hedidi,
• Aïcha Derdour,
• Floris Chevallier,
• Yury S. Halauko,
• Oleg A. Ivashkevich,
• Vadim E. Matulis,
• Laurent Picot,
• Valérie Thiéry,
• Thierry Roisnel,
• Vincent Dorcet and
• Florence Mongin

Beilstein J. Org. Chem. 2015, 11, 1475–1485, doi:10.3762/bjoc.11.160

• , vincamine, ergotamine, lysergic acid), as well as in pharmaceuticals (e.g., indomethacin, iprindole), agrochemicals (e.g., auxins, pyroquilon), and dyes and pigments (e.g., indigo, indocyanines) [1][2]. The deprotonative metallation [3][4][5][6][7] is a valuable tool for the regioselective functionalization

New palladium–oxazoline complexes: Synthesis and evaluation of the optical properties and the catalytic power during the oxidation of textile dyes

• Rym Hassani,
• Mahjoub Jabli,
• Yakdhane Kacem,
• Jérôme Marrot,
• Damien Prim and
• Béchir Ben Hassine

Beilstein J. Org. Chem. 2015, 11, 1175–1186, doi:10.3762/bjoc.11.132

• gap energy values (Eg) ranging between 2.34 and 3.21 eV. Their catalytic activities were tested for the degradation of Eriochrome Blue Black B (a model of azo dyes) in the presence of an ecological oxidant (H2O2). The efficiency of the decolorization has been confirmed via UV–visible spectroscopic

• rise to more air- and possibly water-stable catalysts [9]. Commonly, difficulties arise when trying to treat waste waters containing dyes because the dyes are recalcitrant molecules, often resistant to aerobic digestion, and stable to light, heat, and oxidizing agents [10][11]. Recently, the catalytic

• oxidation was recognized as an effective method to treat colored waters [12]. In fact, the treatment of colored waters remains a serious environmental topic. Many industries such as textile, leather and paper discharge various dyes during their processing operations [13][14]. These dyes are toxic, mutagenic

A hybrid electron donor comprising cyclopentadithiophene and dithiafulvenyl for dye-sensitized solar cells

• Gleb Sorohhov,
• Chenyi Yi,
• Michael Grätzel,
• Silvio Decurtins and
• Shi-Xia Liu

Beilstein J. Org. Chem. 2015, 11, 1052–1059, doi:10.3762/bjoc.11.118

• ]. Although devices with the most commonly used dyes based on polypyridyl transition-metal complexes show excellent photovoltaic performances with high power conversion efficiencies of over 11% [4], metal-free organic dyes have significant advantages in several aspects. These comprise for example large molar

• extinction coefficients, ease of synthesis, fine-tuning of structural and electronic properties, and low-cost production [1][2][3][4]. Particularly, the hitherto best DSSC based on organic sensitizers shows an efficiency of 10.3% [5]. Among the most efficient organic dyes are those featured with an electron

• view, can be treated as half of a TTF unit. DTF-based D–π–A sensitizers have been proven quite promising with high power conversion efficiencies of up to 8.3% [18][19]. Taking into account all these considerations, we set ourselves the synthetic task to prepare two new molecular dyes (Figure 1

A new and convenient synthetic way to 2-substituted thieno[2,3-b]indoles

• Roman A. Irgashev,
• Arseny A. Karmatsky,
• Gennady L. Rusinov and
• Valery N. Charushin

Beilstein J. Org. Chem. 2015, 11, 1000–1007, doi:10.3762/bjoc.11.112

• compounds which can be applied in organic optoelectronic materials. Indeed, we have recently reported the synthesis of novel push–pull dyes IK-1,2 based on the thieno[2,3-b]indole ring system, as a donating part of dye-sensitized solar cells [8] (Figure 1). It should be noted that thieno[2,3-b]pyrrole and

• analogues. This two-step approach provides an easy access to compounds of the family of electron-rich thieno[2,3-b]indoles, which are regarded as promising building-blocks for the development of new photo- and electrosensitive molecules, e.g., novel push–pull dyes for dye-sensitized solar cells

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• a third component fluorescent dyes [10] were coupled to the polymers simultaneously with the bioactive and the cell-penetrating peptides in order to enable the monitoring of cellular uptake and intracellular distribution of the peptide–polymer conjugate. Until now, various polymer carriers have been

Design, synthesis and photochemical properties of the first examples of iminosugar clusters based on fluorescent cores

• Mathieu L. Lepage,
• Antoine Mirloup,
• Manon Ripoll,
• Fabien Stauffert,
• Anne Bodlenner,
• Raymond Ziessel and
• Philippe Compain

Beilstein J. Org. Chem. 2015, 11, 659–667, doi:10.3762/bjoc.11.74

• . Difluoroboradiaza-s-indacenes, commonly named boron-dipyrromethene dyes (F-BODIPY), were logically selected for the construction of the probes. These compounds indeed combine high fluorescence quantum yields and high molar extinction coefficients, strong chemical and photochemical stability in solution and in solid

• substitution at the boron has less influence on the spectroscopic properties of the dyes [42]. So far, major endeavors have been dedicated to the preparation of classical F-BODIPY structures and less common E-BODIPY (E for ethynyl) and the examination of their spectroscopic and salient physical properties [43

• ethynyl tetra(ethylene glycol)methyl groups [58][59]. Synthesis of the BODIPY precursors The synthesis of the tris-iodo functionalized BODIPY dyes and their acetylenic derivatives is sketched in Scheme 1. The synthesis of derivatives 7 and 8 have previously been reported using a regioselective iodination

Photocatalytic nucleophilic addition of alcohols to styrenes in Markovnikov and anti-Markovnikov orientation

• Martin Weiser,
• Sergej Hermann,
• Alexander Penner and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2015, 11, 568–575, doi:10.3762/bjoc.11.62

• light sources, the research field of photoredox catalysis has tremendously grown over the past decade [1][2][3][4][5][6][7]. Transition metal complexes, mainly [Ru(bpy)3]2+ [7], were most often used as photocatalysts, whereas the potential of organic compounds and dyes has not yet been fully exploited

Eosin Y-catalyzed visible-light-mediated aerobic oxidative cyclization of N,N-dimethylanilines with maleimides

• Zhongwei Liang,
• Song Xu,
• Wenyan Tian and
• Ronghua Zhang

Beilstein J. Org. Chem. 2015, 11, 425–430, doi:10.3762/bjoc.11.48

• and not sustainable. Similar to the redox properties of these organometallic complexes, some metal-free organic dyes such as Eosin Y, Rose Bengal, Fluorescein, and Methylene Blue, have shown superiority of their applications as photocatalysts, which are easy to handle, environmentally friendly

• light (two 9 W blue LEDs) at room temperature. Gratifyingly, the desired product tetrahydroquinoline 3a was obtained in 82% yield after 18 h (Table 1, entry 1). We screened a number of metal-free organic dyes for photocatalysts. Of the dyes screened, Eosin Y showed the highest efficiency (Table 1, entry

2-(1-Hydroxypropyn-2-yl)-1-vinylpyrroles: the first successful Favorsky ethynylation of pyrrolecarbaldehydes

• A. V. Ivanov,
• V. S. Shcherbakova,
• I. A. Ushakov,
• L. N. Sobenina,
• O. V. Petrova,
• A. I. Mikhaleva and
• B. A. Trofimov

Beilstein J. Org. Chem. 2015, 11, 228–232, doi:10.3762/bjoc.11.25

• intermediates [4]. Also, 2-(1-hydroxypropyn-2-yl)pyrroles could serve as intermediates for the synthesis of meso-ethynyl-substituted boradiazoindacene (BODIPY) dyes, which have been shown to be potential components of light-harvesting compositions [5]. Until now, 2-(1-hydroxypropyn-2-yl)pyrroles have been

Efficient deprotection of F-BODIPY derivatives: removal of BF₂ using Brønsted acids

• Mingfeng Yu,
• Joseph K.-H. Wong,
• Cyril Tang,
• Peter Turner,
• Matthew H. Todd and
• Peter J. Rutledge

Beilstein J. Org. Chem. 2015, 11, 37–41, doi:10.3762/bjoc.11.6

• derivatives incorporating fluorescent dyes for sensing applications [22][23][24][25]. Looking to extend these systems to incorporate an F-BODIPY motif, we have synthesized the Boc-protected triazolyl-cyclam/F-BODIPY derivatives 3 and 4 from 2,4-dimethyl-1H-pyrrole (5), 4-nitrobenzaldehyde (6, Scheme 2A) and 4

Synthetic strategies for the fluorescent labeling of epichlorohydrin-branched cyclodextrin polymers

• Milo Malanga,
• Mihály Bálint,
• István Puskás,
• Kata Tuza,
• Tamás Sohajda,
• László Jicsinszky,
• Lajos Szente and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 3007–3018, doi:10.3762/bjoc.10.319

• , we report the controlled, regioselective fluorescent labeling of neutral and cationic epichlorohydrin branched β-CD polymer with four different dyes (rhodamine, fluorescein, coumarin and nitrobenzofurazan). Our goal was the development of versatile synthetic strategies, yielding key intermediates of

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• fluorimetric monitoring of the temperature-dependent Förster resonance energy transfer (FRET) between the dyes [29]. In sodium cacodylate buffer (10 mM Na+, 10 mM K+, 90 mM Li+) the melting curve of the DNA has a weak transition at 50 °C and a more pronounced one at Tm = 71.0 °C (Figure 4). The results of the

• case of thiazole orange (6) whose emission intensity increases by a factor of I/I0 = 1766. Within the series of heptamethine cyanine dyes 1a–e, the derivative 1d exhibits the largest light-up factor with I/I0 = 128. In contrast, the emission of coralyne (2), bis-quinolinium derivative 3 and the

• used (vide supra). On the other hand, a larger concentration of K+ was used during the fluorimetric titration leading to a higher fraction of the antiparallel form [9][10]. Apart from the derivatives 1c and 6 the binding constants of the cyanine dyes with the ILPR-DNA are larger than those observed

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• RNA dyes. Another large series of phenanthridinium-homodimers was constructed by linking two ethidium bromide subunits by peptide-like linkers of variable flexibility and rich in hydrogen-bonding possibilities within the DNA grooves (Figure 5). The resulting bis-intercalators (in comparison to the

• determination of binding contributions, which would clarify the observed selectivity. Although only the current widespread biochemical application is focused on ethidium bromide/propidium iodide dyes for DNA dyeing and cell viability tests, results summarised in this review pointed out the intriguing potential

• of the phenanthridine/phenanthridinium system for chemical and biochemical research. Widely used fluorimetric dyes, such as cyanine derivatives, are non-fluorescent in the free state but give tremendous fluorescence emission upon binding to biomacromolecular targets. However, many of these dyes show

Synthesis and properties of novel star-shaped oligofluorene conjugated systems with BODIPY cores

• Clara Orofino-Pena,
• Diego Cortizo-Lacalle,
• Joseph Cameron,
• Muhammad T. Sajjad,
• Pavlos P. Manousiadis,
• Neil J. Findlay,
• Alexander L. Kanibolotsky,
• Dimali Amarasinghe,
• Peter J. Skabara,
• Tell Tuttle,
• Graham A. Turnbull and
• Ifor D. W. Samuel

Beilstein J. Org. Chem. 2014, 10, 2704–2714, doi:10.3762/bjoc.10.285

• have found numerous applications as laser dyes [5][6][7], labels for biological imaging [8][9][10] and low band-gap polymers [11][12][13]. Being efficient emitters in solution, small molecule BODIPY compounds often show signs of aggregation at high concentration and in solid films [14][15], which

• lowers the luminescence efficiency of the material. Due to this aggregation and a low Stokes shift, BODIPY dyes with efficient emission in the solid state are still rare [16]. One of the strategies to suppress the aggregation of π-functional emissive units is to incorporate them into star-shaped

Solution processable diketopyrrolopyrrole (DPP) cored small molecules with BODIPY end groups as novel donors for organic solar cells

• Diego Cortizo-Lacalle,
• Calvyn T. Howells,
• Upendra K. Pandey,
• Joseph Cameron,
• Neil J. Findlay,
• Anto Regis Inigo,
• Tell Tuttle,
• Peter J. Skabara and
• Ifor D. W. Samuel

Beilstein J. Org. Chem. 2014, 10, 2683–2695, doi:10.3762/bjoc.10.283

• derivatives (e.g., selenophene) [20][21][22][23], often in combination with other heterocyclic units; the best performing systems are push–pull molecules or dyes [14]. In the last few years the diketopyrrolopyrrole (DPP, 1, Figure 1) core has been widely incorporated in conjugated polymers for both OPVs and

Host–guest-driven color change in water: influence of cyclodextrin on the structure of a copper complex of poly((4-hydroxy-3-(pyridin-3-yldiazenyl)phenethyl)methacrylamide-co-dimethylacrylamide)

• Nils Retzmann,
• Gero Maatz and
• Helmut Ritter

Beilstein J. Org. Chem. 2014, 10, 2480–2483, doi:10.3762/bjoc.10.259

• studied extensively, causing for example a blue to red color transition of polydiacetylenes (PDAS) due to the formation of inclusion complexes [6][7]. Azo dyes, with their remarkable ability to form stable azo–metal chelate complexes with outstanding thermal and optical properties have been studied widely

• and led to an increased usage of dyes in the field of optical recording media [8][9]. However, up to now, only little is known about the interactions of azo–metal chelate complexes in supramolecular structures with CD as a modulator for macromolecular effects. Few reports dealt with the reversibility

• addition. Assuming an intermolecular aggregating effect due to ionic interactions between the covalently attached azo dyes in 7 and Cu ions in solution, dynamic light scattering (DLS) experiments in a water/methanol solution were carried out (Figure 3). It was found that, by introducing copper ions to 7

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• profiling (ABPP); bioorthogonal; click chemistry; mass defect; molecular probe; Introduction Fluorescent dyes are widely used for detection and monitoring in the fields of chemistry, biochemistry, molecular biology, medicine and material sciences. Due to sensitive and selective detection methods and

• unproblematic toxicology they have almost completely replaced radioactive tags. Widely used representatives include dansyl chloride, fluoresceins, rhodamines and boron-dipyrromethenes (BODIPYs) [1]. Dansyl chloride, with a maximum UV–vis absorption at 369 nm, is one of the first extrinsic fluorescent dyes

Oxidative phenylamination of 5-substituted 1-hydroxynaphthalenes to N-phenyl-1,4-naphthoquinone monoimines by air and light “on water”

• Julio Benites,
• Juan Meléndez,
• Cynthia Estela,
• David Ríos,
• Luis Espinoza,
• Iván Brito and
• Jaime A. Valderrama

Beilstein J. Org. Chem. 2014, 10, 2448–2452, doi:10.3762/bjoc.10.255

• of their properties as dyes for optical devices [15], antioxidants [16], anticancer agents [17] and precursors of liquid crystalline materials [18]. With regard to the synthesis of N-phenyl-1,4-naphthoquinone monoimines, Bukhtoyarova et al. [19], has described their preparation by reaction of 1,5-DHN

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• fluorescent dyes – intercalating Sybr Green I and pending cyanine-5 (Figure 5). For the scenario of experiment F (Figure 2) the complex formation kinetics drops even further, but the brightness reaches a plateau at ≈2 × 105 kHz. The by far slowest complex formation is observed in case of experiment D (Figure

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• tracts by length and composition. This has been demonstrated, for instance, by the inability to distinguish between longer tracts (more than 20–30 base pairs) of homo and alternating distribution of AT base pairs. Our recent studies revealed a novel class of cyanine dyes characterized by bulky

• phosphonium substituents as intriguing AT binders, which showed very rare kinetic differentiation between alternating- and homo-AT-DNA sequences [6]. Moreover, these dyes efficiently entered cells and were shown to be non-toxic, mitochondria-specific fluorescent markers [7]. Previous studies also revealed the

• importance of AT tracts and the selectivity of cyanine dyes. On this basis, we were inspired to prepare the novel binders AP5 with a DBTAA–adenine linker length between AP3 (oligo dT specific) and AP6 (oligo-dT inert) and AP3am, in which pyridinium is exchanged by a permethylated amine, with the aim of

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• biomolecular interactions [1][2][3]. Traditionally, the biological macromolecules are labeled with two or more dyes which can interact in a conformation/distant-dependent manner via Förster resonance energy transfer (FRET) [4][5][6]. Alternatively, the FRET pairs can be replaced by an environmentally sensitive

• fashion. PNA–DNA duplexes have different structural morphology and electrostatic potential surfaces from DNA–DNA duplexes and therefore they are interacting differently with DNA-binding dyes [23][24][25]. We had recently introduced a new conformationally constrained pyrrolidinyl PNA known as acpcPNA that

Multichromophoric sugar for fluorescence photoswitching

• Stéphane Maisonneuve,
• Rémi Métivier,
• Pei Yu,
• Keitaro Nakatani and
• Juan Xie

Beilstein J. Org. Chem. 2014, 10, 1471–1481, doi:10.3762/bjoc.10.151

• -OF shows a very weak blue emission band between 400 nm and 500 nm from the diarylethene unit, and a rather strong red emission band peaking at 610 nm from the three DCM dyes (Figure 3f). This dual emission will be discussed further, by a careful analysis of excitation spectra (vide infra). Figure 4a

Microwave-assisted Cu(I)-catalyzed, three-component synthesis of 2-(4-((1-phenyl-1H-1,2,3-triazol-4-yl)methoxy)phenyl)-1H-benzo[d]imidazoles

• Yogesh Kumar,
• Vijay Bahadur,
• Anil K. Singh,
• Virinder S. Parmar,
• Erik V. Van der Eycken and
• Brajendra K. Singh

Beilstein J. Org. Chem. 2014, 10, 1413–1420, doi:10.3762/bjoc.10.145

• inhibition activity [5][6]. They have also been used to synthesize dyes [7], chemosensitizers [8] and fluorophores [9]. Triazole derivatives have shown antifungal [10], anticancer [11] antituberculosis [12] and antimicrobial [13] activities. Recently, hybrid molecules, connecting two or more distinct drug