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

• dual function, viz., supply the phosphate ion in the phosphorolysis reaction and simultaneously accept the resulting PF-1Pi (e.g., QAE Sephadex A-25-nPi) and liberate it as a key substrate in the enzymatic synthesis of nucleosides. The use of dRib-1Pi (Ba2+) and dRib-1Pi bound to the QAE Sephadex A-25

• in cladribine synthesis The dual function of QAE Sephadex A-25 noted above was tested in the enzymatic synthesis of cladribine using dRib-1Pi as a barium salt and bound to the resin. Chemical synthesis of this nucleoside, which has a wide spectrum of pharmacological activities [6][63][64][65], is

• synthesis. On the contrary, Dowex-nPi can effectively carry out only the first function. The E. coli PNP-catalyzed reaction of N6-benzyladenine and Rib-1Pi bound by the test resin during the phosphorolysis of uridine was used to test the ability of the resin to transfer Rib-1Pi in terms of the amount of N6

Synthesis of 4-substituted azopyridine-functionalized Ni(II)-porphyrins as molecular spin switches

• Jannis Ludwig,
• Tobias Moje,
• Fynn Röhricht and
• Rainer Herges

Beilstein J. Org. Chem. 2020, 16, 2589–2597, doi:10.3762/bjoc.16.210

• diamagnetic (or the paramagnetic) species in the two photostationary states. The intermolecular association constants of pyridines as axial ligands to Ni-porphyrins as a function of their para substituents usually follow the Hammett relationship [5][12]. Hence, the association constants should also be

• collaborative research center 677 (SFB 677) “Function by Switching”.

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

• synthetic molecular machines. Developing switchable and specifically designed crown ethers enables the implementation of function into molecular assemblies. Seven tailor-made redox-active crown ethers incorporating tetrathiafulvalene (TTF) or naphthalene diimide (NDI) as redox-switchable building blocks are

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• [2][3]; the level of N-glycan expression regulates the adhesiveness of a cell [4]; glycosylation also plays a role in immune function [5] and cellular signalling [5][6]. At the forefront, glycosylation plays a significant role in influencing protein–protein interactions. For example, the influenza

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

• recent years, the focus of biochemical research and drug development has shifted from the inhibition of single enzymes to targeting protein-protein interactions [1][2], which play key roles in cellular function and dysfunction [3][4]. Enzymes usually bind their substrates in deep pockets with specific

• [8][9][10][11][12], and inhibit enzyme function [13] in vitro, they also exhibit interesting effects in vivo like the reversal of Alzheimer plaques in mice [14], tumor inhibition [15], and reduction of HIV infectivity [16], all while showing almost no toxic side effects [14][17]. In calixarenes with

• function and thus on its size. Small molecules <1000 g/mol show positive NOEs while large molecules like proteins exhibit negative NOEs. Around a molecular weight of ≈1000–1500 g/mol, the NOE passes through zero, meaning no NOE signal can be measured, even if molecules are in close enough proximity. A lot

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

• aspects of glycan identification, quantification and visualisation, some of which will be further developed throughout this article. Biological molecules express their function throughout their three-dimensional structures. For this reason, structural biology places great emphasis on the three-dimensional

• structure as a central element in the characterisation of biological function. An adequate understanding of biomolecular mechanisms inherently requires our ability to model and visualise them. Visualisation of molecular structures is thus one of the most common tasks performed by structural biologists. As

• several computer applications using a standardised notation. The earliest glycan editors allowed manual drawing similar to ChemDraw or used input files with glycan sequence KCF (KEGG Chemical Function) [9] in text format for similarity search against other structures deposited in the databases. Later

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• buffer solutions at different pH values. Sigmoid function obtained from dye 8 UV–vis absorption spectra during pH investigation. TGA curves of all synthetized dyes. Synthetic pathways of dyes 3–7 and Schiff base analogs 8–12. Photophysical properties of dyes 3–7 in various solvents with different

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

• (data not shown). Instead, for the conjugate Dex-1b the scattering was high with a well-confirmed autocorrelation function (Figure S5 in Supporting Information File 1). Thus, the DLS data confirmed that the conjugate Dex-1b forms aggregates or nanoparticles as previously reported [27]. The size

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

• microarray experiments provide needed information to develop new hypotheses about glycan recognition and function. In this article, we highlight some of the nuances of how fabrication of the glycan microarrays is done, along with tools currently available or in development to help with analysis and

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• molecules were dyes used for the DNA/RNA labelling or even monitoring or influencing DNA/RNA function [3][4]. However, due to the complexity of DNA-coded or RNA-coded processes, also including epigenetics, there is permanent need for novel dyes, differing in selectivity, colour, or method of monitoring [5

• for Ka and n given in Table 1 all have satisfactory correlation coefficients (>0.999). Thermal melting curves for DNA, RNA, and their complexes with the studied compound were determined as previously described [37] by following the absorption change at 260 nm as a function of temperature. The

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• can function as an energy donor to activate the relatively lower triplet energy of the energy acceptor through an overall PS TTET process [91][92][93][94][95][96][97][98][99][100]. In contrast to PRC, the mechanism of TTET occurs in a way that does not depend on the redox potential of the molecules or

• the respective products. Employing the optimum reaction conditions, Lectka and co-workers fluorinated phenylalanine-containing di- and tripeptides to give the products 70a–f in modest to excellent yield (34–84%, Scheme 29). The carboxylic acid function could be free or protected as an ester without

Synthesis of 6,13-difluoropentacene

• Matthias W. Tripp and
• Ulrich Koert

Beilstein J. Org. Chem. 2020, 16, 2136–2140, doi:10.3762/bjoc.16.181

• ) showed an n-type behavior. In their synthesis and structural as well as electronic characterization of F4PEN 3, Bettinger et al. showed that the electronic properties of pentacenes are not a simple linear function of the degree of fluorination [7][8]. They reported that the fluorination in the 2,3,9,10

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• -glycosylation; O-glycosylation; Python; Introduction Glycosylation is a key post-translational modification critical for protein folding and function in eukaryotes [1][2][3]. Diverse types of glycosylation are known, all involving modification of specific amino acid residues with complex carbohydrate

Azo-dimethylaminopyridine-functionalized Ni(II)-porphyrin as a photoswitchable nucleophilic catalyst

• Jannis Ludwig,
• Julian Helberg,
• Hendrik Zipse and
• Rainer Herges

Beilstein J. Org. Chem. 2020, 16, 2119–2126, doi:10.3762/bjoc.16.179

• efficiency. Conclusion A photoswitchable base catalyst for the nitroaldol (Henry) reaction was synthesized and investigated. Principle of function is the control of the basicity of a DMAP derivative by light-induced coordination/decoordination of an azo-DMAP unit covalently bound to a Ni-porphyrin. Upon

• chemical shift of the pure decoordinated (diamagnetic) system. The signals are broad because of paramagnetic line broadening of the coordinated species and fast ligand exchange. Conversion of 4-nitrobenzaldehyde (6) in the Henry reaction with nitroethane (5) as a function of time, using (a, left) 4 mM

• coordinated Ni complex in different solvents). Funding This work was funded by the Deutsche Forschungsgemeinschaft (DFG) within the collaborative research center 677 (SFB 677) “Function by Switching”.

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

• ; electropherogram; glycosylation; monoclonal antibodies; peak picking; process development; Introduction Glycosylation is important for the efficacy and function of a majority of the most dominant biologic drugs currently on the global market. In the case of antibody-based biotherapeutics, the absence of

• function allowed grouping of similar electropherograms and therefore clean the HappyTools calibration output. (A) HappyTools calibration of all 391 electropherograms was largely misaligned. This made peaks not well aligned and made it difficult to define the peak positions for quantitation. (B) The

• File 1, Table S3 as a function of % abundance. Glycans identified in anti-HER-2 samples using UPLC-MS and CE. (A) the UPLC chromatogram confirmed the 14 glycans using GU and mass. Green boxed glycans were also identified in CE. (B) Glucose units vs. migration time for all 391 CE electropherograms

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• differential recognition in glycan arrays [27]. Additionally, the different conformation of the arms explains the known difficulties in sialylating the (1-6) arm by ST6-Gal1, relatively to the (1-3) arm [28]. Also, the different 3D conformational propensity of the arms in function of sequence can have

• in a trajectory and heat maps for each dihedral were generated with a kernel density estimate (KDE) function. Statistical and clustering analysis was done with the R package and data were plotted with RStudio (https://www.rstudio.com). Further details on the simulation set-up and running protocol are

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

• function of temperature. Absorbance of the ligands was subtracted from every curve and the absorbance scale was normalized. The Tm values are the midpoints of the transition curves determined from the maximum of the first derivative and checked graphically by the tangent method [59]. The ΔTm values were

• respectively on the structure. (a) Melting curve of poly(dA-dT)2 alone and after the addition of NDI 3a,b, and 5 (r = 0.3 ([NDI]/[polynucleotide])) (sodium cacodylate buffer, pH 5.0, ionic strength (I) = 0.05 M). (b) First derivative function of absorption from temperature. Changes in fluorescence intensity

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• VIII was observed due to the difficulty of phosphorylation of the substrate by kinases [16]. The first kinase phosphorylation step is generally rate limiting, and the prior introduction of a phosphate or phosphonate function can circumvent this problem. The preparation of diols VIII was realized by

• ester function we expected the ring-opening reaction to proceed with the formation of additional products to alkenes E-13 and Z-13. In fact, two byproducts formed and were identified as β-hydroxymethyl-α-fluorolactone 14 and β-bromomethyl-α-fluorolactone 15 (Table 4) [30]. This ring expansion has been

• presence of BF3·Et2O only (Table 4, entries 1, 2, and 6). Of note in contrast to 8, when TBAB/BF3·Et2O was added we cannot exclude a control by steric or electronic repulsions between bromide ions and the ester function leading to Z-13 and 15 instead of expected alkene E-13 and to the lactone 18 from

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

• in PVC cylinders (outer diameter = 8 mm). The GC rods functioned as the electronic conductors and the PVC shells were used to both control the amount of exposed GC surface and to function as the substrate for the ISM to adhere to. Poly(3,4-ethylenedioxythiophene) doped with chloride (PEDOT-Cl) was

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• membrane proteins [11][12]. The captured proteins would be subsequently identified by mass spectrometry, and their function in MPD scrambling validated by biochemical and genetic approaches. A suitable molecular probe and mimic of MPD (Figure 1) can be subdivided into three essential components: a β-ᴅ

Tuneable access to indole, indolone, and cinnoline derivatives from a common 1,4-diketone Michael acceptor

• Dalel El-Marrouki,
• Sabrina Touchet,
• Abderrahmen Abdelli,
• Hédi M’Rabet,
• Mohamed Lotfi Efrit and
• Philippe C. Gros

Beilstein J. Org. Chem. 2020, 16, 1722–1731, doi:10.3762/bjoc.16.144

• . The reaction mechanism shown in Scheme 3 involves the formation of an imine upon the reaction of the primary amine with the most reactive carbonyl moiety (nonconjugated and exocyclic carbonyl function). Then, depending on the reaction conditions, the imine can react following a 1,2- or 1,4-addition

Microwave-assisted efficient one-pot synthesis of N²-(tetrazol-5-yl)-6-aryl/heteroaryl-5,6-dihydro-1,3,5-triazine-2,4-diamines

• Moustafa Sherief Moustafa,
• Ramadan Ahmed Mekheimer,
• Saleh Mohammed Al-Mousawi,
• Mohamed Abd-Elmonem,
• Hesham El-Zorba,
• Afaf Mohamed Abdel Hameed,
• Tahany Mahmoud Mohamed and
• Kamal Usef Sadek

Beilstein J. Org. Chem. 2020, 16, 1706–1712, doi:10.3762/bjoc.16.142

• NH, and triazine CH-2 protons in addition to two broad singlet signals at δ = 8.59 and 7.32 ppm for NH2 function as well as signals for the aromatic protons. The 13C NMR spectrum was in support of the proposed structure. Based on the established product, we revealed that two molecules of cyanamide 1

• favorable due to the high nucleophilicity of the exocyclic amino function attached to the electron-rich tetrazole ring [45]. In support of this assumption we stopped the reaction after 4 minutes of heating under microwave irradiation and inspected the prior formation of 9 via comparison with an authentic

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• , they are poorly suited for written communication. This function is fulfilled almost ideally by Gilbert Lewis’ structural formulae [13]. Lewis drew on a long history of depicting molecules in terms of their constituent atoms [14] and added a rationalization in terms of stable electron octets that

• give more constant results as the extent of the basis set increases. The basic problem, however, remains that where a basis function is centered in space has little to do with how to assign electron density to notional atoms. The second, smaller group of analysis techniques relies on partitioning space

• that this fundamental problem cannot be resolved because of the nature of the quantum mechanical wave function or electron density. All models that aim to derive Lewis-like concepts from quantum mechanical calculations are therefore arbitrary, however reasonable they may seem, and can only be judged on

Rearrangement of o-(pivaloylaminomethyl)benzaldehydes: an experimental and computational study

• Csilla Hargitai,
• Györgyi Koványi-Lax,
• Tamás Nagy,
• Péter Ábrányi-Balogh,
• András Dancsó,
• Gábor Tóth,
• Judit Halász,
• Angéla Pandur,
• Gyula Simig and
• Balázs Volk

Beilstein J. Org. Chem. 2020, 16, 1636–1648, doi:10.3762/bjoc.16.136

• under the same conditions in tetrahydrofuran (THF) instead of DCM, substantially less dimer-like product 3a or 3b was formed in favor of the rearranged aldehyde 2a or 2b. When starting from aldehyde 1c [2], containing the methoxy function in the ortho position of the formyl moiety and meta to the

Fluorohydration of alkynes via I(I)/I(III) catalysis

• Jessica Neufeld,
• Constantin G. Daniliuc and
• Ryan Gilmour

Beilstein J. Org. Chem. 2020, 16, 1627–1635, doi:10.3762/bjoc.16.135

• -fluoroketone motif from alkynes. Selectfluor®-mediated oxidation of p-TolI in the presence of an amine/HF source, which plays a dual function as fluoride source and Brønsted acid activator, enables in situ generation of p-TolIF2 (Figure 5). From these preliminary mechanistic investigations, conclusions