Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• ). Optical micrographs and corresponding size distribution of the perfluorohexane-stabilized microbubbles with a shell of a) DPPC, b) DPPC/F-lipopeptide 3, and c) DPPC/hydrocarbon analog 4. Half-lives of microbubbles (25 °C) containing F-lipopeptides 1–3 and hydrocarbon analog 4. a) Schematic representation

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• cationic polyelectrolyte in neural to acidic solution. Overview of the different states of the multi-switchable system consisting of Flavy, 1N36S, and poly(allylamine) (simplified schematic representation displaying one molecule of each component per assembly only). A: The protonated photoacid and Flavy in

Tuning the solid-state emission of liquid crystalline nitro-cyanostilbene by halogen bonding

• Subrata Nath,
• Alexander Kappelt,
• Matthias Spengler,
• Bibhisan Roy,
• Jens Voskuhl and
• Michael Giese

Beilstein J. Org. Chem. 2021, 17, 124–131, doi:10.3762/bjoc.17.13

• comprehensive study investigating the potential of halogen bonding in fluorescent liquid crystalline materials. Schematic representation of the modular approach towards halogen-bonded fluorescent liquid crystals. Representative POM images of NO2-C10 at 94 °C (a) and NO2-C10∙∙∙F4Az at 61.5 °C (b) upon cooling

• from the isotropic melt. Comparison of the mesomorphic properties of NO2-Cn, NO2-Cn∙∙∙F4St, and NO2-Cn∙∙∙F4Az (n = 8–11). The transition temperatures were obtained by DSC upon cooling from the isotropic state. Mesophase ranges are given in black numbers. Graphical representation of the calculated

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• distance between the carboxylic groups of two PDIs. E) Schematic representation of the assembly structuring. Cryo-TEM images of 1 × 10−4 M compound 1 in THF/water solutions after one minute of aging. A) 5% THF: monomolecular 1D π-stack fibers and B) 10% THF: crystalline platelets. Transient kinetics at

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• for Direct Fluorescence “Switch‐On” Detection of Nucleic Acid in Cells”, Chem. – Eur. J. © 2017 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim. A) Molecular structure of 6; B) possible binding mode of pyrene termini of 6 to CB[8] according to molecular modeling; C) cartoon representation of ratiometric

Construction of pillar[4]arene[1]quinone–1,10-dibromodecane pseudorotaxanes in solution and in the solid state

• Xinru Sheng,
• Errui Li and
• Feihe Huang

Beilstein J. Org. Chem. 2020, 16, 2954–2959, doi:10.3762/bjoc.16.245

• , chloroform-d, 298 K). Normalized UV–vis spectra: H (black); H upon adding 0.5 equiv of G (red); and H upon adding 1 equiv of G (blue). [H] = 3.00 mM. Chemical structures and schematic representation of (a) the pillar[4]arene[1]quinone H; (b) 1,10-dibromodecane (G); and (c) schematic representation of the

Controlled decomposition of SF₆ by electrochemical reduction

• Sébastien Bouvet,
• Bruce Pégot,
• Stéphane Sengmany,
• Erwan Le Gall,
• Eric Léonel,
• Anne-Marie Goncalves and
• Emmanuel Magnier

Beilstein J. Org. Chem. 2020, 16, 2948–2953, doi:10.3762/bjoc.16.244

• Parstat 2273 potentiostat was also used with its internal «Powersuite» software. For all cyclic voltammetries, the conventional representation of anodic currents is reported as positive values and cathodic currents as negative values. SF6 electrolysis was performed in acetonitrile with a constant

One-pot multicomponent green Hantzsch synthesis of 1,2-dihydropyridine derivatives with antiproliferative activity

• Giovanna Bosica,
• Kaylie Demanuele,
• José M. Padrón and
• Adrián Puerta

Beilstein J. Org. Chem. 2020, 16, 2862–2869, doi:10.3762/bjoc.16.235

• measured at 530 (primary) and 620 nm (secondary). The antiproliferative activity, expressed as GI50 values, was calculated according to the NCI formulas [30]. Optimization trials with the selected solid catalysts. Graphical representation of the results obtained in the reusability test. The classical

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• hydrogen-bonded octameric and tetrameric tubes. (c) A representation of the complex mixture after combining the monomers 5 and 6 in CDCl3. (d) The partial separation of the mixture upon the selective C60 complexation by monomer 5. The guest-induced rearrangement results in an incomplete self-sorted mixture

Dirhamnolipid ester – formation of reverse wormlike micelles in a binary (primerless) system

• David Liese,
• Hans Henning Wenk,
• Xin Lu,
• Jochen Kleinen and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2020, 16, 2820–2830, doi:10.3762/bjoc.16.232

• Information File 1) shows the thermal reversibility of the gel formation process. The phase transition temperature can be obtained from the temperature sweeps and is defined as the temperature where the dynamic moduli intercept. In an alternative representation, the phase transition temperature can also be

• viscoelastic solid. Both moduli intercept at γ = 35%, which marks the point where the sample turns from a viscoelastic solid to a viscous fluid. In a representation where the phase angle is plotted against the amplitude (Figure 4, right), it becomes apparent that the deformation processes are similar for the

• motion for cylindrical micelles [33][34]. Another representation is the so-called Cole–Cole plot [35], where the normalized value for the loss modulus (G''/G''max) is plotted against the storage modulus (G'/G''max), is depicted in Figure 5. The semicircular arrangement centered at G'/G''max is the result

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• of ATP, ADP, AMP, PPi and Pi in a buffer (each at 50 µM) and c) with only ATP (50 µM) (A) and a mixture of ATP, ADP, AMP, PPi and Pi (50 µM of each) (B) in buffer. d) Emission spectra of PBIm12 (100 μM) upon the addition of ATP in a buffer containing 150 mM NaCl. Schematic representation of ATP

A heterobimetallic tetrahedron from a linear platinum(II)-bis(acetylide) metalloligand

• Matthias Hardy,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2020, 16, 2701–2708, doi:10.3762/bjoc.16.220

• ). Schematic representation of symmetry-considerations concerning possible diastereomeric tetrahedra. The figure summarizes the cage symmetries and the expected observations in the 1H and 31P NMR spectra, looking at one chemically equivalent position. The colored dots represent chemically and magnetically

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• clear glycan representation accessible to both computers and humans. Linear Code, a linearized and readily parsable glycan structure representation, is such a language. For this reason, Linear Code was adapted to represent reaction rules, but the syntax has drifted from its original description to

• compliance with FAIR standards. Here, we present Linear Code for Reaction Rules (LiCoRR), version 1.0, an unambiguous representation for describing glycosylation reactions in both literature and code. Keywords: glycoinformatics; linear code; systems glycobiology; Introduction Glycans are predominantly

• that benefit from an unambiguous representation with human readability. For example, graphical denotation is one of the most human-understandable representations to describe reaction rules [18][19][20]. While graphical representations are intuitive and extremely accessible to a human reader, they are

Anion exchange resins in phosphate form as versatile carriers for the reactions catalyzed by nucleoside phosphorylases

• Julia N. Artsemyeva,
• Ekaterina A. Remeeva,
• Tatiana N. Buravskaya,
• Irina D. Konstantinova,
• Roman S. Esipov,
• Anatoly I. Miroshnikov,
• Natalia M. Litvinko and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2020, 16, 2607–2622, doi:10.3762/bjoc.16.212

• ). The conversion of the obtained resins to the phosphate form was carried out in the usual manner. A graphical representation and fitting of the data were performed in the online editor Plotly Chart Studio https://plotly.com/chart-studio/ The recombinant E. coli thymidine phosphorylase (TP, specific

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• spectroelectrochemical measurements (0.1 M n-Bu4PF6, CH2Cl2/CH3CN 1:1, 298 K) of a) NDIC7 (0.5 mM), b) NDIC8 (0.5 mM), and c) NDIRot (1 mM). Potentials are referenced against a silver wire pseudo-reference electrode. Schematic representation of synthetic routes towards TTFC7, exTTFC7, NDIC7, and NDIC8. Thermodynamic

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• view of the features in the system under observation, could be readily applied to other binding problems as part of a general strategy in drug design or mechanistic analysis. A representation of mucin glycopeptide bound to AR20.5 antibody. Chain A is represented as a molecular surface colored by

• secondary structure, chain B is represented in cartoon and colored by secondary structure. The mucin peptide is represented as licorice. The Tn glycan (N-acetylgalactosamine) is represented as licorice, and the sugar ring is highlighted with the paper chain representation [18][19]. A comparison of root mean

• drawn as a green ribbon with first cluster conformation in opaque green. The sugar is drawn without hydrogens in licorice and the sugar ring is highlighted with the paper chain representation [18][19]. Supporting Information Supporting Information File 464: Additional molecular dynamics analyses

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• labeling of only Lys has been used to monitor tweezer binding to full-length tau with 44 lysines, showing that the tweezers can bind to multiple of them and thus interfering with tau aggregation. A schematic representation of a 15N-HSQC spectrum of a shorter tauF4 construct with uniform vs. lysine-specific

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visualisation and modelling of glycans. The article also provides details on the standard representation of glycans, and

• glycoconjugates, which helps the communication of structure details within the scientific community. We highlight the comparative analysis of the available tools which could help researchers to perform various tasks related to structure representation and model building of glycans. These tools can be useful for

• glycobiologists or any researcher looking for a ready to use, simple program for the sketching or building of glycans. Keywords: bioinformatics; carbohydrate; glycan; glycobiology; nomenclature; oligosaccharide; polysaccharide; representation; structure; Introduction Glycoscience is a rapidly surfacing and

Design and synthesis of a bis-macrocyclic host and guests as building blocks for small molecular knots

• Elizabeth A. Margolis,
• Rebecca J. Keyes,
• Stephen D. Lockey IV and
• Edward E. Fenlon

Beilstein J. Org. Chem. 2020, 16, 2314–2321, doi:10.3762/bjoc.16.192

• -atom trefoil [10]. (c) Target 73 backbone-atom trefoil knot of this work using host 1 and guest 2. Schematic representation of the second-generation TLC approach to a 73 backbone atom trefoil knot. Two routes to azidobromide 6. Initial route to core diester 13. aLigand = tris(2-benzimidazolylmethyl

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• under vacuum to obtain 360 mg of Dex-1d as light orange-solid FTIR data are given in Figure S10 of Supporting Information File 1. ICP-AES boron content 0.09 mg/g. Structure of PBA-BODIPY (1) and schematic representation of dextran (Dex) and PBA-BODIPY conjugated dextran Dex-1a–d. The structure of Dex-1a

• representation of dextran/PBA-BODIPY bioconjugations in: A. conventional solution-based conditions to prepare the Dex-1a conjugate (using roughly 1 equiv of 1). B. Ball milling conditions to prepare conjugates Dex-1b (using roughly 1 equiv of 1), Dex-1c (using roughly 0.5 equiv of 1), and Dex-1d (using roughly

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• would not account for terminal motifs. CCARL customizes the frequent subtree mining approach by extending the glycan notation to include terminal node information by including additional nodes in the graph representation to indicate the absence or presence of linkage at particular backbone carbon

Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 2212–2259, doi:10.3762/bjoc.16.186

• article which covers almost all the unsuccessful as well as successful efforts towards the synthesis of sumanene and its congeners. The ball-and-stick representation, bowl fragments and the chemical structures of corannulene (1) and sumanene (2) are displayed in the Figure 1. 2 Synthesis of sumanene and

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• compared qualitatively and quantitatively. For capillary electrophoresis-based glycomics data processing, this is complicated by heterogenous glycan peaks which may not fit under a Gaussian approximation. As such, automated Gaussian fitting of these peaks will yield inaccurate representation of the glycans