Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA. Keywords: amino acid–fluorophore conjugate; circular dichroism; DNA/RNA recognition; fluorescence; intercalation; naphthalene diimide

• ; Introduction The interplay of non-covalent interactions between nucleic acids and proteins or peptides is the basis of life and is also often used for the design of artificial small molecules, aiming for sensing or control of biorelevant processes. Many naturally occurring bioactive molecules contain a short

• [9]). One of the approaches relies on amino acids conjugated with various DNA/RNA-binding chromophores, thereby yielding effective spectrometric sensing systems due to their interactions with DNA. In this approach, chromophores can be combined with peptide sequences in various ways, thus giving

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• , Laboratory of Molecular Science and Engineering, Åbo Akademi University, Biskopsgatan 8, FI-20500 Turku/Åbo, Finland 10.3762/bjoc.16.157 Abstract Carboxylate sensing solid-contact ion-selective electrodes (ISEs) were created to provide a proof-of-concept ISE development process covering all aspects from in

• directed our efforts towards sensing carboxylates. The detection of these analytes is important in a number of areas and there is an obvious lack of easy-to-use sensing methods. Carboxylates are challenging analytes for two reasons. Firstly, binding is mainly achieved through either ion–ion interactions or

• -life sensing, also influences binding [4]. Within an ion-selective electrode (ISE), lipophilicity is mostly contributed by the low polarity membrane, which is commonly based on plasticized PVC [5]. One possible receptor family for carboxylates is based on the biscarbazolylurea moiety (Figure 1). This

Clickable azide-functionalized bromoarylaldehydes – synthesis and photophysical characterization

• Dominik Göbel,
• Marius Friedrich,
• Enno Lork and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2020, 16, 1683–1692, doi:10.3762/bjoc.16.139

• ][8], biological imaging [9][10][11][12] and chemical sensing [13][14][15]. Referring to the Jablonski diagram (see Scheme 1a) [16][17], upon excitation from the singlet ground state (S0) to higher singlet states (Sn), followed by internal conversion (IC), either non-radiative or radiative decay to S0

4-Hydroxy-3-methyl-2(1H)-quinolone, originally discovered from a Brassicaceae plant, produced by a soil bacterium of the genus Burkholderia sp.: determination of a preferred tautomer and antioxidant activity

• Dandan Li,
• Naoya Oku,
• Yukiko Shinozaki,
• Yoichi Kurokawa and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1489–1494, doi:10.3762/bjoc.16.124

• rutaceous plants [9]. Examples from microbes include chymase inhibitors SF2809-I to VI from an actinomycete of the genus Dactylosporangium [10], a quorum sensing signaling molecule 2,4-dihydroxyquinoline (DHQ, 4) from Gram-negative bacteria Pseudomonas aeruginosa and Burkholderia thailandensis, [7], and 4-O

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• 4 °C for 24 h. These results were consistent with our hypothesis on facilitating the ease of access to target 60-AR_RNA by cutting a short 27-nt fragment from the full target sequence by deoxyribozymes, thus increasing the local concentration of this fragment near to the sensing part of SDFS (Figure

Synthesis of triphenylene-fused phosphole oxides via C–H functionalizations

• Md. Shafiqur Rahman and
• Naohiko Yoshikai

Beilstein J. Org. Chem. 2020, 16, 524–529, doi:10.3762/bjoc.16.48

• extended π-system. These included, in particular, those fused with polycyclic aromatic hydrocarbons (PAHs) for possible applications in organic electronics, bioimaging and sensing, and asymmetric catalysis (Figure 1). To name a few examples, Yamaguchi et al. described synthetic routes to novel phosphorus

The reaction of arylmethyl isocyanides and arylmethylamines with xanthate esters: a facile and unexpected synthesis of carbamothioates

• Narasimhamurthy Rajeev,
• Toreshettahally R. Swaroop,
• Ahmad I. Alrawashdeh,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Seegehalli M. Anil,
• Kuppalli R. Kiran,
• Chandra,
• Paris E. Georghiou,
• Kanchugarakoppal S. Rangappa and
• Maralinganadoddi P. Sadashiva

Beilstein J. Org. Chem. 2020, 16, 159–167, doi:10.3762/bjoc.16.18

• , Manasagangothri, Mysuru, Karnataka 570 006, India Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador A1B3X7, Canada Aramco Laboratory for Applied Sensing Research, King Abdullah Institute for Nanotechnology, King Saudi University, Riyadh, Saudi Arabia Surface, and

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• Mai Hoang for the proofreading of the manuscript. This work used Dr. Bharate’s thesis “Automated Glycan Assembly of Oligomannose Glycans for Sensing Applications” as a source.

A chiral self-sorting photoresponsive coordination cage based on overcrowded alkenes

• Constantin Stuckhardt,
• Diederik Roke,
• Wojciech Danowski,
• Edwin Otten,
• Sander J. Wezenberg and
• Ben L. Feringa

Beilstein J. Org. Chem. 2019, 15, 2767–2773, doi:10.3762/bjoc.15.268

• is essential for the application of SCCs towards chiral recognition and sensing [34][35][36][37]. To the best of our knowledge no self-sorted responsive SCCs have been reported so far. Molecular motors based on overcrowded alkenes are unique photoswitches that are able to undergo unidirectional

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

• ], BASHY dyes [10][11] or Boranils [12][13]) often feature quite rigid structures which contribute to high fluorescence quantum yields. These dyes have been applied for example in optoelectronics [14][15][16], sensing [17][18][19][20], and bioimaging [6][20][21][22][23][24][25][26]. On the other hand

Synthesis of novel sulfide-based cyclic peptidomimetic analogues to solonamides

• José Brango-Vanegas,
• Luan A. Martinho,
• Lucinda J. Bessa,
• Andreanne G. Vasconcelos,
• Alexandra Plácido,
• Alex L. Pereira,
• José R. S. A. Leite and
• Angelo H. L. Machado

Beilstein J. Org. Chem. 2019, 15, 2544–2551, doi:10.3762/bjoc.15.247

• analogues were prepared in moderate overall yields and did not show toxic effects on Staphylococcus aureus growth and were not toxic to human fibroblasts. Two of them inhibited the hemolytic activity of S. aureus, suggesting an interfering action in the bacterial quorum sensing similar to the one already

• , methicillin-resistant S. aureus (MRSA) is considered an endemic cause of nosocomial infections and has spread into the community and livestock animals as well [8]. Expression of many S. aureus virulence factors is controlled by a sophisticated intercellular chemical signalling pathway named quorum-sensing (QS

• exert an effect on S. aureus quorum sensing. To evaluate this hypothesis, we are now rationally designing new solonamide analogues, based on the SN2’ strategy reported here, to be tested for AgrC-inhibitory activity. Chemical structure of solonamides and autoinducing peptides (AIP). Effect of compounds

Formation of alkyne-bridged ferrocenophanes using ring-closing alkyne metathesis on 1,1’-diacetylenic ferrocenes

• Celine Bittner,
• Dirk Bockfeld and
• Matthias Tamm

Beilstein J. Org. Chem. 2019, 15, 2534–2543, doi:10.3762/bjoc.15.246

• sensing. ORTEP diagram of 1a with thermal displacement parameters drawn at 50% probability; hydrogen atoms are omitted for clarity; occupation Fe 74%, Fe’ 26%. Selected bond lengths [Å] and angles [°]: Fe–Ct1 1.6947(12), Fe-Ct11 1.6695(12), Ct1-Fe-Ct11 176.96(8), C9–C10 1.186(11), C8–C9–C10 177.2(9), C19

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

• signals has been developed, aiming at reducing interferences and improving sensing precision in complex physiological environments [9][10][11][12][13][14][15][16][17]. This photoresponsive design presents several advantages over conventional probes: 1) The light-activation mode endows the probe with light

• precise outputs can be obtained for targeted analytes even at low concentrations. Though promising, common “photochromophore–fluorophore”-type sensors require elaborate designs to integrate multifunctionality (e.g., photoswitching, fluorescence sensing, targetability, water solubility, etc.) into one

• , indicating the successful coating of MnO2 nanosheets with the Glyco-DTE reporter [25]. An increasing Zeta potential was also observed after the assembly, confirming again the successful fabrication of Glyco-DTE@MnO2 glycosheet (Figure 2D) [26]. GSH sensing and fluorescence photoswitching of Glyco-DTE@MnO2

1,2,3-Triazolium macrocycles in supramolecular chemistry

• Mastaneh Safarnejad Shad,
• Pulikkal Veettil Santhini and
• Wim Dehaen

Beilstein J. Org. Chem. 2019, 15, 2142–2155, doi:10.3762/bjoc.15.211

• have led to applications in molecular recognition, sensing, molecular machines and devices, supramolecular polymers, stimuli-responsive materials, supramolecular catalysis and drug-delivery systems [4][5][6][7]. Inspired by the attractive role of various N-heterocyclic building blocks such as

• results in the sensing of anions. In fact, strictly speaking this interaction is not a hydrogen bonding interaction seen as there is no X···H–Y unit (X, Y = O, N, F) but these interactions are often referred to as such in the literature. The anion binding can be enhanced by the alkylation of 1,2,3

• selectivity of this receptor for chloride anion is due to the cavity size (see Figure 3) [37]. 2.2. Optical anion sensing by 1,2,3-triazolium macrocycles within porphyrin cages Various porphyrin-based host supramolecules containing hydrogen-bond donor groups such as integrated amide, urea, pyrrole, ammonium

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

• aromatic analytes afford strongly induced circular dichroism (ICD) signals in the near-UV and visible regions [18]. Endo-functionalized molecular tubes, first reported by the Glass group [19], were used by the Jiang group for molecular recognition and chiroptical sensing of epoxides in water. The absolute

Tautomerism as primary signaling mechanism in metal sensing: the case of amide group

• Vera Deneva,
• Georgi Dobrikov,
• Aurelien Crochet,
• Daniela Nedeltcheva,
• Katharina M. Fromm and
• Liudmil Antonov

Beilstein J. Org. Chem. 2019, 15, 1898–1906, doi:10.3762/bjoc.15.185

• , Switzerland 10.3762/bjoc.15.185 Abstract The concept for sensing systems using the tautomerism as elementary signaling process has been further developed by synthesizing a ligand containing 4-(phenyldiazenyl)naphthalene-1-ol as a tautomeric block and an amide group as metal capturing antenna. Although it has

• solvents. Strong bathochromic and hyperchromic effects in the visible spectra accompany the 1:1 formation of complexes with some alkaline earth metal ions. Keywords: amide group; azo dye; molecular sensor; sidearm; tautomerism; Introduction The design of new organic sensing systems is an undividable part

• )2 and Mg(ClO4)2. Conceptual idea for tautomeric metal sensing. 4-(Phenyldiazenyl)naphthalen-1-ol (1) and tautomeric ligands based on it. Synthetic route of 6. Absorption maxima of the complexes with different alkaline-earth metal ions and stability constants of the complexes of 6 in acetonitrile

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

• governing their interaction with DNA and sensing capabilities. In fact, although it is known in broad terms that some molecular features (e.g., size and shape of the aromatic scaffold, charge, redox potential) influence the interaction of dyes with G4-DNA, a thorough assessment of such phenomena by

• comparative studies is lacking in most reports. In this work, we address this gap within the family of styryl dyes, trying to establish how to construct an optimized dye for G4 sensing. In particular, we studied the optical properties and the fluorimetric response of 61 in-house synthesized compounds against

• propensity of cationic dyes to accumulate in mitochondria. At the same time, our work establishes an approach to optimize the structure of renowned scaffolds and achieve maximal performances in G4 sensing. Some di- and mono-styryl dyes previously reported as fluorescent “light-up” probes for G4-DNA and RNA

Novel macrocycles – and old ones doing new tricks

• Wei Jiang and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2019, 15, 1838–1839, doi:10.3762/bjoc.15.178

• diversified. They are not only tools for studying molecular recognition and molecular machines, but are also key components for sensing, supramolecular catalysis, (chiral) separation, drug delivery, or smart materials. Many new macrocycles have recently been reported, with pillararenes being one of the most

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

• chemical introduction of chromophores onto the rims of pillar[5]arene has been applied to allow its use as receptors for molecular sensing or biological applications [30][31][32][33]. It occurred to us that connecting fluorophores with strong absorptions in the visible range and with a high fluorescence

• adding water into the THF solution. This work presented a new strategy for achieving versatile planar chiral hosts, and these hosts will have potential applications in various fields such as supramolecular sensing, host–guest recognition and triplet–triplet annihilation upconversion. Experimental General

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• far, a series of receptors based on these macrocycles were synthesized. They have been designed for the selective recognition of sulfate ions [4][5][6], di- and triphosphate ions [7], for sensing of pyrophosphate ions in aqueous solutions [8], as receptors for phenols [9], α-chiral primary

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 with four amide NH residues have been studied for ca. three decades and used in a wide range of fields including molecular recognition, optical sensing, molecular machine etc. [2][3][4][5][6][7][8][9][10][11][12][13]. The amide N−H groups directed into the cavity could form hydrogen

Reversible end-to-end assembly of selectively functionalized gold nanorods by light-responsive arylazopyrazole–cyclodextrin interaction

• Maximilian Niehues,
• Patricia Tegeder and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2019, 15, 1407–1415, doi:10.3762/bjoc.15.140

• sensing properties [4][5]. In particular, noble metal nanoparticles of sizes smaller than the wavelength of the incident light show interesting optical behavior as a result of collective oscillations of the valence electrons. This leads to surface plasmon resonance (SPR), which is highly dependent on size

• 20-fold higher binding constant to β-CD (6.5 × 104 M−1) [32] than unmodified azobenzenes (2.5 × 103 M−1) [33]. Therefore, the competitive binding of CTAB to β-CD has been applied previously, e.g., in sensing applications [34] or to enhance the water solubility of a cyclodextrin polymer [35]. On

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

• 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

• -consuming syntheses. Alternatively, supramolecular chemistry provides a non-covalent approach to achieve fluorescence sensing [2]. An elegant supramolecular strategy, named indicator displacement assay (IDA), was established and popularized by Anslyn and co-workers (Scheme 1a) [3][4]. The complexation of a

• fluorophores through supramolecular encapsulation using artificial macrocyclic hosts has always been an active research area [10][11][12]. The complexes of macrocycles with luminescent dyes not only act as reporter pairs for sensing [13][14][15], but also offer various applications in bioimaging [16][17

Selective detection of DABCO using a supramolecular interconversion as fluorescence reporter

• Indrajit Paul,
• Debabrata Samanta,
• Sudhakar Gaikwad and
• Michael Schmittel

Beilstein J. Org. Chem. 2019, 15, 1371–1378, doi:10.3762/bjoc.15.137

• machinery [22]. In contrast, the actual contribution seeks to explore the utility of supramolecular rearrangements [23] for sensing and detection, in particular with an emphasis on high selectivity. As a notable example of the latter category, Nitschke recently reported the guest-induced transformation of

• porphyrin edge capsules to cone-shaped inclusion complexes depending on the presence of C60/C70, however, a process that was not selective for one of the guests [24]. A spectacular case of guest sensing, but not guest-induced recognition, was demonstrated by Clever in a supramolecular cage-to-cage

• to the fact, that the interconversion is accompanied by a diagnostic change in the fluorescence spectra, the present system represents a supramolecular reporter for the selective detection of DABCO. It is thus a rare example of DABCO sensing by luminescence [41]. Molecular structures of ligands 1, 2