Regioselective (thio)carbamoylation of 2,7-di-tert-butylpyrene at the 1-position with iso(thio)cyanates

• Anna Wrona-Piotrowicz,
• Marzena Witalewska,
• Janusz Zakrzewski and
• Anna Makal

Beilstein J. Org. Chem. 2017, 13, 1032–1038, doi:10.3762/bjoc.13.102

• reported an efficient method for the synthesis of pyrene-1-carbothioamides via reaction of pyrene with isothiocyanates in the presence of trifluoromethanesulfonic (triflic) acid (TfOH) [11][12]. Since 2 was used as a starting material in the syntheses of various pyrenyl fluorophores exhibiting unique

• (thio)cyanates occurs selectively at the 1- position, whereas Friedel–Crafts acylation promoted by this acid leads to 4-substitution. The reaction is less regioselective for aromatic iso(thio)cyanates. We believe that the described reaction opens up new synthetic routes to novel fluorophores having a

Energy down converting organic fluorophore functionalized mesoporous silica hybrids for monolith-coated light emitting diodes

• Markus Börgardts and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 768–778, doi:10.3762/bjoc.13.76

• Markus Borgardts Thomas J. J. Muller Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany 10.3762/bjoc.13.76 Abstract The covalent attachment of organic fluorophores in mesoporous silica matrices for

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• fluorophores, in addition to bright visible emission, have become particularly popular for their versatility as non-isotopic detection labels which are amenable to live cell imaging and immunoassay applications [7]. In particular, cadmium-based QDs (e.g., CdS, CdSe, CdSe/ZnS) are commonly used for in vitro

Novel β-cyclodextrin–eosin conjugates

• Gábor Benkovics,
• Damien Afonso,
• András Darcsi,
• Szabolcs Béni,
• Sabrina Conoci,
• Éva Fenyvesi,
• Lajos Szente,
• Milo Malanga and
• Salvatore Sortino

Beilstein J. Org. Chem. 2017, 13, 543–551, doi:10.3762/bjoc.13.52

• tentatively be attributed to populations of fluorophores probably interacting in a different way with the CD cavity. As outlined in the introduction, singlet oxygen, 1O2, is the key species involved in PDT and it is generated by energy transfer from the excited triplet state of a PS and the nearby molecular

A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

• Heidi-Kristin Walter,
• Bettina Olshausen,
• Ute Schepers and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2017, 13, 127–137, doi:10.3762/bjoc.13.16

• structure of double-helical DNA elucidates that the positioning of the fluorophores in the major groove may be improved by inversion of the configuration at the 2’-position of the anchor nucleoside sugar. In fact, arabino nucleic acids are an important class of antisense oligonucleotides [20] since their

• corresponding unmodified counterstrand. The four fluorophores D1 [23], a blue emitter excitable at 389 nm, D2 [24], D3 [19], and D4 [24], all green emitters excitable at 450–460 nm, that were “clicked” to the oligonucleotides DNA1a and DNA1r belong to our recently established class of cyanine-styryl dyes that

• -configured uridine 1. This rather small structural difference allows the attached fluorophores to point into the major groove. Thereby optimized dye–DNA orientations result in higher fluorescence quantum yields of these single dye modifications. The modified oligonucleotides with dyes D1–D4 were applied as

Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts

• Lukas J. Patalag and
• Daniel B. Werz

Beilstein J. Org. Chem. 2016, 12, 2739–2747, doi:10.3762/bjoc.12.270

• methods are commonly employed. Either unnatural fluorescent dyes are inserted into the membrane (e.g., pyrene) or the hydrophilic part of lipids is utilized for the covalent attachment of fluorophores. Another possibility is the use of fluorescently labelled antibodies which bind membrane components such

• −1 for fatty acid 11 with three conjugated double bonds (Table 1). Fluorescence excitation spectra (not shown) for all three fluorophores pretty much coincide with the corresponding absorption spectra in Figure 2, which allows the fluorescence to be switched on at the longest wavelengths respectively

Construction of bis-, tris- and tetrahydrazones by addition of azoalkenes to amines and ammonia

• Artem N. Semakin,
• Aleksandr O. Kokuev,
• Yulia V. Nelyubina,
• Alexey Yu. Sukhorukov,
• Petr A. Zhmurov,
• Sema L. Ioffe and
• Vladimir A. Tartakovsky

Beilstein J. Org. Chem. 2016, 12, 2471–2477, doi:10.3762/bjoc.12.241

• modulation of the molecular geometry, for example through coordination with metal cations, hydrogen bond formation or irradiation. These unique structural features of the hydrazone fragment have been successfully exploited in the design of various molecular switches, fluorophores and machines. Bis- and

DNA functionalization by dynamic chemistry

• Zeynep Kanlidere,
• Oleg Jochim,
• Marta Cal and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2016, 12, 2136–2144, doi:10.3762/bjoc.12.203

• metal ligands or fluorophores. Functional molecules of interest can be tethered post-synthetically in an irreversible manner as amide or reversibly as imine or thioester. Recent advances in dynamic combinatorial chemistry [29][30][31][32][33][34][35][36][37][38][39][40] have enabled the utilization of

Practical synthetic strategies towards lipophilic 6-iodotetrahydroquinolines and -dihydroquinolines

• David R. Chisholm,
• Garr-Layy Zhou,
• Ehmke Pohl,
• Roy Valentine and
• Andrew Whiting

Beilstein J. Org. Chem. 2016, 12, 1851–1862, doi:10.3762/bjoc.12.174

• (DHQ) are heterocyclic scaffolds that are ubiquitous in natural products, therapeutics, fluorophores and dyes [1]. Both are structures of great versatility, and their physical and chemical properties can be finely tuned using synthetic chemistry. Methods for their synthesis have been well studied, and

• range from the classic Skraup–Doebner–von Miller syntheses, to catalytic and asymmetric methods [2][3][4]. We required a straightforward synthesis of THQs and DHQs for the synthesis of a library of biocompatible fluorophores with the potential to be used in fluorescence microscopy applications. The

• mildly red shifted (to 376 nm). This behaviour indicates that 1,4-DHQ structures of this type may function as more effective donor chromophores in dyes and fluorophores than the corresponding THQs due to improved orbital overlap between the nitrogen lone pair and the aromatic π-system by virtue of the

Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• synthesis of conjugates of pyrrole–imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple

• part of the present article, we describe the synthesis of various linkers bearing different functional groups for simple and accessible introduction of azide and alkyne groups into biopolymers, fluorophores and ligands. Then, these linkers were introduced into the structure of MGBs and TFOs and used

• -NH2 and two fluorophores bearing an azide functional group: one cyanine TO (derivative of thiazole orange [18]), and one coumarine MM14 kindly provided by M. P. Teulade-Fichou (Figure 7). The conjugation was conducted in a microwave reactor as for the polyamide tandem synthesis [2]. The details of the

Synthesis, fluorescence properties and the promising cytotoxicity of pyrene–derived aminophosphonates

• Jarosław Lewkowski,
• Maria Rodriguez Moya,
• Anna Wrona-Piotrowicz,
• Janusz Zakrzewski,
• Renata Kontek and
• Gabriela Gajek

Beilstein J. Org. Chem. 2016, 12, 1229–1235, doi:10.3762/bjoc.12.117

• and show vibronic structure characteristic for monomeric fluorophores. The spectra of 5 are slightly shifted bathochromically (9 nm and 4 nm for the absorption and emission spectrum, respectively) in comparison to the spectra of pyrene. In this context, it should be noticed that spectra reported in [9

Synthesis and fluorosolvatochromism of 3-arylnaphtho[1,2-b]quinolizinium derivatives

• Phil M. Pithan,
• David Decker,
• Manlio Sutero Sardo,
• Giampietro Viola and
• Heiko Ihmels

Beilstein J. Org. Chem. 2016, 12, 854–862, doi:10.3762/bjoc.12.84

• emission energy to a different degree, thus denoting a major influence of hydrogen bonding on the stabilization of the ground and excited states. Based on these results it is concluded that the solvent-sensitive emission properties of biaryl-type quinolizinium fluorophores are a promising structural motif

Indenopyrans – synthesis and photoluminescence properties

• Andreea Petronela Diac,
• Ana-Maria Ţepeş,
• Albert Soran,
• Ion Grosu,
• Anamaria Terec,
• Jean Roncali and
• Elena Bogdan

Beilstein J. Org. Chem. 2016, 12, 825–834, doi:10.3762/bjoc.12.81

• lattice, along with an emission-band broadening, as compared to the solution fluorescence spectra. Keywords: indenopyran-3-ones; organic fluorophores; pyrones; solid-state emission spectra; solution emission spectra; UV–vis spectra; Introduction Indenopyrans are functionalized oxygen-containing

New synthetic strategies for xanthene-dye-appended cyclodextrins

• Milo Malanga,
• Andras Darcsi,
• Mihaly Balint,
• Gabor Benkovics,
• Tamas Sohajda and
• Szabolcs Beni

Beilstein J. Org. Chem. 2016, 12, 537–548, doi:10.3762/bjoc.12.53

• fluorophores for labeling in order to assess if these versatile molecules cross biological barriers (e.g., cell membrane, blood–brain barrier) and to follow their distribution in living matter [3]. Among the fluorescent dyes, the group of fluorophores based on xanthene scaffolds is one of the most popular. Two

• of this evergreen class of dyes is still an ongoing process [5][6]. Fluorescein is the most widely used fluorescent probe in biological applications and in particular for covalently labeling proteins. Rhodamine derivatives are robust dyes that find application as fluorophores for microscopy, in cell

Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

• Eric V. Anslyn

Beilstein J. Org. Chem. 2016, 12, 362–376, doi:10.3762/bjoc.12.40

• fluorophores bound in the cavity of cyclodextrins to measure Keq values, our idea was to instead exploit the displacement as the sensing modality. Thus, the idea of an indicator-displacement assay (IDA) was born [58][59]. As with so many “new” ideas in chemistry, the approach had actually been used before, by

Bright molecules for sensing, computing and imaging: a tale of two once-troubled cities

• A. Prasanna de Silva

Beilstein J. Org. Chem. 2015, 11, 2774–2784, doi:10.3762/bjoc.11.298

• position in a membrane–water interfacial region [52]. The second challenge is addressed with fluorophores which achieve charge-separated excited states [12][53] so that their interaction with the local dipoles of the neighbourhood causes shifts in the emission spectra. Simultaneous monitoring of wavelength

Learning from the unexpected in life and DNA self-assembly

• Jennifer M. Heemstra

Beilstein J. Org. Chem. 2015, 11, 2713–2720, doi:10.3762/bjoc.11.292

• these enantiomeric biosensors with orthogonal fluorophores (Figure 5). In our initial experiments, we utilized fluorescein (FAM) and cyanine 3 (Cy3), however, we observed that the difference in fluorophore structure resulted in an approximately two-fold difference in the equilibrium constants for the

• sensors. This was surprising, as the fluorophores are small molecules attached to the termini of much larger DNA molecules. However, we found this lesson very informative, as it showed that dyes and other functional groups that we frequently append to DNA are not as innocuous as we assume them to be

Synthesis and spectroscopic properties of β-triazoloporphyrin–xanthone dyads

• Dileep Kumar Singh and
• Mahendra Nath

Beilstein J. Org. Chem. 2015, 11, 1434–1440, doi:10.3762/bjoc.11.155

• ] including anti-oxidative [35], antihypertensive [36], anti-inflammatory [37] and antiplatelet agents [38]. They have also been used as fluorophores and exhibited good fluorescence properties when attached to a triazole ring [39][40]. Owing to the biological significance of porphyrins, 1,2,3-triazoles and

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

• compares with commercially available azide-modified fluorophores and a brominated one. The ease of synthesis, small size, stability, and the universal detection possibilities make it an ideal reporter for activity-based protein profiling and functional metabolic profiling. Keywords: activity-based protein

• introduced in this field and is still widely used in protein labeling [2]. Later, fluoresceins and rhodamines found applications in this area as well because of advantageous UV–vis absorption maxima (480–600 nm) and more bathochromic emission wavelengths (510–615 nm) [3]. A successful class of fluorophores

• to minimize the structural complexity of the fluorophores to achieve higher atom economy and reduce the interaction with biomacromolecules. In this context it was critical to realize that the thiazole moiety itself can also act as a fluorophore, especially the class of 4-hydroxythiazoles [4][5]. 4

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• available structural data on these complexes [7], it is possible to envisage that any pair of groups protruding from both thymines methyl groups of a TAT triplet and able to give rise to attractive interactions (Figure 1a) would stabilize the triplex. If these groups are aromatic fluorophores, changes in

• ), probably due to the quenching effect of nucleobase units; however, the most important data are related to changes in the fluorescence spectrum upon hybridization with DNA, since this property is strongly related to the environment around the fluorophores [38] and can reveal interactions between pyrene

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

• multichromophoric glucopyranoside 2 bearing three dicyanomethylenepyran (DCM) fluorophores and one diarylethene (DAE) photochrome has been prepared by Cu(I)-catalyzed alkyne–azide cycloaddition reaction. The fluorescence of 2 was switched off upon UV irradiation, in proportion with the open to closed form (OF to CF

• (photochrome and fluorophore) moieties have also been reported by other groups [5][6][7][8][9]. The fluorophore vs photochrome ratio in reported bifunctional systems is 1:1 [4][5][6][7] or 2:1 [8][9]. Other strategies to assemble interacting fluorophores and photochromes (supramolecular systems, nanoparticles

• fluorophores present within this distance. In a situation where one photochromic unit is surrounded by several fluorophores, we can take advantage of this phenomenon both to increase the brightness of the fluorescent molecular system and to turn “ON” and “OFF” several fluorophores with one given photochromic

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

Automated solid-phase peptide synthesis to obtain therapeutic peptides

• Veronika Mäde,
• Sylvia Els-Heindl and
• Annette G. Beck-Sickinger

Beilstein J. Org. Chem. 2014, 10, 1197–1212, doi:10.3762/bjoc.10.118

• . Following resin cleavage, radio labeling was performed with NHS-[2,3-3H]propionate (Figure 5) by the Bolton–Hunter reaction. Then, the Nvoc protecting groups could be removed by irradiation with UV light to obtain the fully deprotected, radio-labeled peptide [130]. Biotin and fluorophores such as CF (5(6

The Ugi four-component reaction as a concise modular synthetic tool for photo-induced electron transfer donor-anthraquinone dyads

• Sarah Bay,
• Gamall Makhloufi,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 1006–1016, doi:10.3762/bjoc.10.100

• approximation. Keywords: absorption spectroscopy; cyclic voltammetry; chromophores; fluorescence; multicomponent reactions; photo-induced electron transfer; Introduction Chromophores, fluorophores, and electrophores, are functional organic materials [1] and constitute active components in molecular

One-pot three-component synthesis and photophysical characteristics of novel triene merocyanines

• Christian Muschelknautz,
• Robin Visse,
• Jan Nordmann and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 599–612, doi:10.3762/bjoc.10.51

• reactions; Introduction Functional organic materials [1], such as chromophores, fluorophores, and electrophores, constitute the active components in molecular electronics [2], photonics [3], and bioanalytics [4][5][6]. Among many chromophores the class of merocyanines [7][8][9], i.e. α-donor-ω-acceptor