Coordination-driven self-assembly of discrete Ru₆–Pt₆ prismatic cages

• Aderonke Ajibola Adeyemo and
• Partha Sarathi Mukherjee

Beilstein J. Org. Chem. 2018, 14, 2242–2249, doi:10.3762/bjoc.14.199

• donors and transition metals as electron-deficient acceptors. Diverse functionalities embedded in these homometallic architectures have found useful applications in chemical sensing [24][25][26][27][28][29][30][31][32][33][34][35], catalysis [11][36][37][38][39][40][41][42][43][44][45][46], drug delivery

Calix[6]arene-based atropoisomeric pseudo[2]rotaxanes

• Carmine Gaeta,
• Carmen Talotta and
• Placido Neri

Beilstein J. Org. Chem. 2018, 14, 2112–2124, doi:10.3762/bjoc.14.186

• interesting properties as nanodevices for catalysis [5][6][7][8], recognition, and sensing [9][10][11][12][13]. Beyond these ascertained potentialities, interpenetrated architectures show fascinating structures that still stimulate the imagination of scientists. An amazing aspect of rotaxanes and catenanes is

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• for nucleotides sensing through a dye replacement procedure. It is unusual that disubstituted macrocycles 10a,b bind more effectively a less charged adenosine 5'-diphosphate (ADP) than adenosine 5'-triphosphate (ATP). A simple colorimetric method based on polydiacetylene vesicles decorated with 10b

• attention to the synthesis of host molecules with high affinity to biologically important anions [1][2][3][4][5]. Among these anions, nucleotide recognition and sensing represents an especially important research area due to the great biological significance of these anions. Adenine-containing nucleotides

• sensing purposes. Thereby, premicellar concentrations of calixarenes 10a,b (6 and 4 µM, respectively) and 12a,b (4 and 2 µM, respectively) were selected to design a receptor system based on the principle of competitive EY displacement by the guests. At these concentrations, a bathochromic shift

Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• Mohammad A. Alnajjar Jurgen Bartelmess Robert Hein Pichandi Ashokkumar Mohamed Nilam Werner M. Nau Knut Rurack Andreas Hennig Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany Chemical and Optical Sensing Division, Bundesanstalt für

• fluorescent dyes directly enables (bio)sensing applications through the indicator displacement principle [16][17]. Therein, the fluorescence properties of a dye are altered when encapsulated by the host, and when a competitive binder displaces the dye from the cavity, the properties of the non-encapsulated

• sufficient for the desired sensing applications (Table 1) [20][53]. Surprisingly, and despite the hexaalkylated core was used, the fluorescence quantum yields of protonated as well as unprotonated 3 were more than 100-fold lower than the quantum yields of the other derivatives. Such reduced quantum yields

Recent advances in materials for organic light emitting diodes

• Eli Zysman-Colman

Beilstein J. Org. Chem. 2018, 14, 1944–1945, doi:10.3762/bjoc.14.168

• (LEECs), two types of electroluminescent devices; (ii) sensing materials employed in electro-chemiluminescence; and (iii) photocatalysts employed in photoredox catalytic reactions.

Strong binding and fluorescence sensing of bisphosphonates by guanidinium-modified calix[5]arene

• Jie Gao,
• Zhe Zheng,
• Lin Shi,
• Si-Qi Wu,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2018, 14, 1840–1845, doi:10.3762/bjoc.14.157

• , Tianjin 300071, China 10.3762/bjoc.14.157 Abstract Based on the indicator displacement assay (IDA) approach, we herein report the fluorescence “switch-on” sensing and quantitative detection of bisphosphonates (BPs), a class of drugs extensively used in the treatment of patients with various skeletal

• BPs in buffer solution, and more importantly, in artificial urine. Calibration lines were therefore set up in untreated artificial urine, allowing for quantifying the concentrations of BPs in the biologically relevant low range. Keywords: bisphosphonate; calixarene; fluorescence sensing; macrocyclic

• in view of low cost, ease of use and high sensitivity of optical sensing modalities, but remains a challenge since BPs are considered as unlabeled analytes. With the development of the host–guest concept in supramolecular chemistry, the indicator displacement assay (IDA), pioneered by Prof. Anslyn

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• States 10.3762/bjoc.14.151 Abstract Quorum sensing (QS) is a cell–cell communication mechanism that enables bacteria to assess their population density and alter their behavior upon reaching high cell number. Many bacterial pathogens utilize QS to initiate an attack on their host, thus QS has attracted

• stimulating peptide (CSP); protein–peptide interactions; quorum sensing; Streptococcus pneumoniae; structure–activity relationships (SAR); Introduction Quorum sensing (QS), a cell-density mechanism utilized by bacteria to assess their population density through the detection of diffusible signal molecules

Synthesis and photophysical studies of a multivalent photoreactive Ru^II-calix[4]arene complex bearing RGD-containing cyclopentapeptides

• Sofia Kajouj,
• Lionel Marcelis,
• Alice Mattiuzzi,
• Adrien Grassin,
• Damien Dufour,
• Pierre Van Antwerpen,
• Didier Boturyn,
• Eric Defrancq,
• Mathieu Surin,
• Julien De Winter,
• Pascal Gerbaux,
• Ivan Jabin and
• Cécile Moucheron

Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150

• 10.3762/bjoc.14.150 Abstract Photoactive ruthenium-based complexes are actively studied for their biological applications as potential theragnostic agents against cancer. One major issue of these inorganic complexes is to penetrate inside cells in order to fulfil their function, either sensing the

Recent applications of chiral calixarenes in asymmetric catalysis

• Mustafa Durmaz,
• Erkan Halay and
• Selahattin Bozkurt

Beilstein J. Org. Chem. 2018, 14, 1389–1412, doi:10.3762/bjoc.14.117

• upper and/or lower rims of the molecular skeleton, they have been widely used for construction of artificial host molecules and found applications in various fields like molecular recognition, sensing, self-assembly, catalysis, nanoscience, drug delivery and separation science [7][8][9][10][11][12][13

Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria

• Lisa Ziesche,
• Jan Rinkel,
• Jeroen S. Dickschat and
• Stefan Schulz

Beilstein J. Org. Chem. 2018, 14, 1309–1316, doi:10.3762/bjoc.14.112

• /bjoc.14.112 Abstract N-Acylhomoserine lactones (AHLs) are important bacterial messengers, mediating different bacterial traits by quorum sensing in a cell-density dependent manner. AHLs are also produced by many bacteria of the marine Roseobacter group, which constitutes a large group within the marine

• ; fatty acid composition; N-acylhomoserine lactones; quorum sensing; Phaeobacter inhibens; Introduction The Roseobacter group, a subgroup of the Rhodobacteraceae family, constitutes an important class of Gram-negative marine bacteria, occurring in many different habitats [1][2], in fresh water as well as

• on surfaces [3]. They can produce a variety of secondary metabolites, including antibiotics [4][5], volatile compounds [6][7], oligohydroxybutyrates [8] and a range of N-acylhomoserine lactones (AHLs) [8][9][10]. AHLs are quorum-sensing signaling compounds that are used for cell–cell communication to

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• recognize the minor groove by sufficiently distorting the DNA structures leading to the opening of the minor groove [2]. In addition to the conventional direct and indirect readout mechanism, proteins have also been proposed to recognize the DNA minor groove by sensing variations in the shape and

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• . Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum. Keywords: ATP sensing; base-pairing; fluorescent probes; 3-hydroxyflavone

• recognition and sensing of ATP has therefore paramount importance in the understanding of biological processes. Amongst the numerous solutions [5][6][7][8][9], fluorescent chemosensors using either indicator displacement assays [10][11][12][13][14][15], cation-based recognition units [16][17][18][19][20

• ], metal-complexes [21][22][23][24][25][26][27] and other direct sensing systems [28][29][30] have significant advantages over the classical, separation-based methods. The primary difficulties in the design of an ATP chemosensor are the structural similarity of ATP to other nucleotides (i.e., to guanosine

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• better specificity than DNA beacons. A PNA beacon has been used as a sensing probe for PCR amplicons in a droplet-based microfluidic device [78], while an integrated microfluidic device that combined sample preparation, hybridization and confocal fluorescence spectroscopy allowed amplification-free

• probes [129]. Combination of PNA probes with nanomaterials as external quenchers/FRET partners Graphene oxide (GO) has been used extensively in combination with dye-labeled DNA for fluorescence-based DNA/RNA sensing [130][131]. Although ssDNA interacts strongly with GO via a combination of multiple

• into the DNA duplex allows the use of a PNA–GO sensing platform for the direct detection of dsDNA targets without requiring denaturation. Using three different labeled PNA probes, multiplex detection of short synthetic dsDNA that corresponded to the DNA sequences of HVA (hepatitis A Val17 polyprotein

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

• . The receptors of the innate immune system can detect particular components present in bacteria, viruses or fungi which are designated as “pathogen associated molecular patterns” (PAMPs) [1]. These receptors, termed pattern recognition receptors (PRRs), are able of sensing and responding to PAMPs. The

• to a similar extent as its parent LPS. Thus, it could be confirmed, that lipid A having at least one Kdo residue attached at position 6’ of the diglucosamine backbone represents the minimum structural requirement needed for the full activation of the LPS-sensing receptor TLR4. Comparison of

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• mechanism of sensing involves Hg(II) ion coordination to two thymine moieties followed by pyrene excimer formation [19]. Furthermore, compound A2 and adenine derivative A3 were reported to act as fluorescent sensors for thymine and adenine [23]. To the best of our knowledge, pyrene–nucleobases have not been

Structure–property relationships and third-order nonlinearities in diketopyrrolopyrrole based D–π–A–π–D molecules

• Jan Podlesný,
• Lenka Dokládalová,
• Oldřich Pytela,
• Adam Urbanec,
• Milan Klikar,
• Numan Almonasy,
• Tomáš Mikysek,
• Jaroslav Jedryka,
• Iwan V. Kityk and
• Filip Bureš

Beilstein J. Org. Chem. 2017, 13, 2374–2384, doi:10.3762/bjoc.13.235

• -emitting diodes (OLED), fluorophores, probes for ion sensing, functional polymers, and more recently also chromophores with nonlinear optical (NLO) activity. The latter property is mostly dictated by their conjugated character, electron-accepting behavior of the DPP scaffold, strong emissive character, and

One-pot syntheses of blue-luminescent 4-aryl-1H-benzo[f]isoindole-1,3(2H)-diones by T3P^® activation of 3-arylpropiolic acids

• Melanie Denißen,
• Alexander Kraus,
• Guido J. Reiss and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2017, 13, 2340–2351, doi:10.3762/bjoc.13.231

• , sensing and display applications [41]. 4-Phenylnaphtho[2,3-c]furan-1,3-diones can well serve as reactive intermediates in multicomponent reactions, e.g., for synthesizing the corresponding imides. A particularly intriguing access to 4-phenylnaphtho[2,3-c]furan-1,3-diones is the intramolecular [4 + 2

New bio-nanocomposites based on iron oxides and polysaccharides applied to oxidation and alkylation reactions

• Daily Rodríguez-Padrón,
• Alina M. Balu,
• Antonio A. Romero and
• Rafael Luque

Beilstein J. Org. Chem. 2017, 13, 1982–1993, doi:10.3762/bjoc.13.194

• nanocomposites with diverse applications in catalysis, sensing, drug delivery and adsorption [25][26][27][28]. In addition, mechanochemical protocols have also been employed to functionalize the surfaces of magnetic nanoparticles (MNPs) with monosaccharides [29] and to obtain bio-nanocomposites based on proteins

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• in bioenergetics, but also of phosphate in cellular sensing and, in general, in the composition of some essential synthetic cellular products also suggest a common origin for the involvement of phosphate, that is, a form of synthetic contiguity [28]. This ubiquity of phosphoesters, mostly as

Synthesis and metal binding properties of N-alkylcarboxyspiropyrans

• Alexis Perry and
• Christina J. Kousseff

Beilstein J. Org. Chem. 2017, 13, 1542–1550, doi:10.3762/bjoc.13.154

• with the facile elaboration of the spiropyran core, have made spiropyran–merocyanine systems a common motif in molecular switch and sensing applications [2]. In this respect, the difference in optical properties between colourless, non-fluorescent spiropyran and coloured, fluorescent merocyanine has

BODIPY-based fluorescent liposomes with sesquiterpene lactone trilobolide

• Ludmila Škorpilová,
• Silvie Rimpelová,
• Michal Jurášek,
• Miloš Buděšínský,
• Jana Lokajová,
• Roman Effenberg,
• Petr Slepička,
• Tomáš Ruml,
• Eva Kmoníčková,
• Pavel B. Drašar and
• Zdeněk Wimmer

Beilstein J. Org. Chem. 2017, 13, 1316–1324, doi:10.3762/bjoc.13.128

• [14][15][16], drugs [17], cell organelle markers, for antibody, peptide and nucleic acid labelling [18][19][20], for pH [21], metal [22][23] and redox potential sensing (well-reviewed in Boens et al. [24]), as well as for the development of photodynamically active agents [25][26]. In this work, we

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• inserted into membranes is a thriving domain of research [13]. Membranes serve a variety of functions such as transport, sensing, protection or supporting movement. They are also involved in energy production via vectorial transport of ions, generally protons. Transport and management of energy imply

• construction of cells, as well as transport across membranes, movement for exploration (including predation), protection against accidents and management of competition, but also repair, sensing and regulation. Almost all of these actions are operated by proteins in extant living organisms. A major question

Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

• Chinmay A. Shukla and
• Amol A. Kulkarni

Beilstein J. Org. Chem. 2017, 13, 960–987, doi:10.3762/bjoc.13.97

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

• relevant molecules have become very useful for drug delivery, sensing and catalysis to name just a few applications. As a result, nanomaterials exhibiting novel electronic and optical properties, having controlled size, geometry, surface distribution and functionality have been developed as materials for

• , chemical sensing, biosensing, bioimaging and nanomedicine, due to their unique tuneable photoluminescence (PL) properties, chemical inertness, high water solubility, ease and low cost fabrication and more importantly, low toxicity profiles. The latter makes these fluorescent nanomaterials attractive for a

• traditionally difficult to detect. The team was able to show significant quenching of the CDs via tryptophan oxidation of the exposed residues on the surface of CDs (Scheme 5). Post-oxidation fluorescence is compromised and therefore can be used as a signal for selectively sensing peroxynitrite up to

Posttranslational isoprenylation of tryptophan in bacteria

• Masahiro Okada,
• Tomotoshi Sugita and
• Ikuro Abe

Beilstein J. Org. Chem. 2017, 13, 338–346, doi:10.3762/bjoc.13.37

• the thiol groups of proteins in eukaryotes. In contrast, the Bacillus quorum sensing peptide pheromone, the ComX pheromone, possesses a posttranslationally modified tryptophan residue, and the tryptophan residue is isoprenylated with either a geranyl or farnesyl group at the gamma position to form a

• ; isoprenylation; post-translational modification; quorum sensing; tryptophan; Introduction Posttranslational modification is the chemical modification of proteins after their translation from mRNAs to the corresponding polypeptide chains synthesized by ribosomes. Since a posttranslational modification generates

• tryptophan residue of the quorum sensing pheromone from Bacillus subtilis, the ComX pheromone [13]. Quorum sensing is a specific gene expression system dependent on the cell density [14]. In terms of a competition for survival, the cell population density is one of the largest factors for microorganisms