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

• shifts for both 1H and 13C nuclei. Methylation of Lys and Arg occurs as posttranslational modification (PTM) of proteins in nature, often used as a switch to regulate protein interactions and thus their function [112][113]. The Crowley lab has used this advantage to study the binding of sulfonatocalix[4

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

• list of pre-built core N- and O-linked carbohydrate moieties, which are usually present in glycoproteins structures, can be used as a template for further modification. A shortlist of glycan epitopes is also included providing templates for drawing more complex molecules. The software uses the Symbol

Chan–Evans–Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

• Viktor M. Tkachuk,
• Oleh O. Lukianov,
• Mykhailo V. Vovk,
• Isabelle Gillaizeau and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2020, 16, 2304–2313, doi:10.3762/bjoc.16.191

• arylation of the nucleophilic nitrogen atom, known as the Ullmann [6][7] reaction, and its modification by Chan and Lam [8] are favored due to the several advantages they offer versus the Pd counterpart (i.e., the Buchwald–Hartwig reaction) such as the lower cost and lower toxicity of the metal as well as

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

• of ICT for electronic state modification in the excited state of the molecules [45]. In this state, all dyes have a notably higher dipole moment and a lower LUMO energy level as compared to their ground state [46][47][48][49]. Increasing the electron-donating strength of the various heterocyclic

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

• another, paving the synthetic roadmap to many natural and unnatural compounds. While C–H bonds are not normally considered as functional groups, these are, however, ubiquitous, for example, in hydrocarbon fuels and in alkyl groups of countless organic molecules. The modification of unactivated C–H

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

• Benjamin Jeffries,
• Zhong Wang,
• Robert I. Troup,
• Anaïs Goupille,
• Jean-Yves Le Questel,
• Charlene Fallan,
• James S. Scott,
• Elisabetta Chiarparin,
• Jérôme Graton and
• Bruno Linclau

Beilstein J. Org. Chem. 2020, 16, 2141–2150, doi:10.3762/bjoc.16.182

• groups is a common strategy in the drug optimization process. It is typically employed to ensure proper fitting of the part(s) of a ligand that interact with a receptor [1][2]. Apart from volume considerations, shape complementarity is regarded as important as well [3][4][5]. Hence, the modification of

• ]. Apart from a slight shape/volume alteration caused by the significant change in bond angles and the deletion of two hydrogen atoms, this bioisosteric modification also usually results in improved metabolic stability, increased rigidity and, due to its electron-withdrawing nature, pKa modulation of

• , which leads to a large logD7.4 increase (ΔlogD7.4 +0.73). The modification of a geminal dimethyl moiety to an oxetanyl group has also proven to be a useful biomimetic replacement leading to a significant logP decrease (compare 3 with 4) [16][17][18]. However, when an amino group is located in the α

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

• ]. This heterogeneity can take the form of variable occupancy, also known as macroheterogeneity – the presence or absence of modification at a particular site in a protein, due to inefficient transfer of the initial glycan structure [5]. In addition, the non-template-driven synthesis of glycan structures

• glycopeptides based on peptide sequence and glycan monosaccharide composition is comparatively reliable with modern LC–MS/MS and data analytics, it is much more difficult to unambiguously assign the precise site of modification within a glycopeptide. GlypNirO therefore provides two options for analysis: site

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

• modification, we have considered two biantennary systems, one terminating with β(1-2)-GlcNAc on both arms (ngf) and the other with terminal β(1-3)-Gal on both arms (gf), shown in Figure 1. In both glycoforms core α(1-3)-Fuc occupies a stable position, with one single conformer populated (100%), see Tables S1

• terminates with LeX, because of the non-complementary position of the α(1-3)-Fuc deoxy-C6. The analysis of all these different complex N-glycoforms clearly shows that every modification, addition or removal of a specific motif, can greatly affect the 3D architecture of the N-glycan, thus its accessibility

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• in the image (e.g., cells, cellular organelles, etc.) This can be achieved by using several steps of image curation and modification (e.g., deconvolution) and using several analysis modules adapted to the shape, size, and intensity of the object of interest. Once all masks are properly detected and

Three new O-isocrotonyl-3-hydroxybutyric acid congeners produced by a sea anemone-derived marine bacterium of the genus Vibrio

• Dandan Li,
• Enjuro Harunari,
• Tao Zhou,
• Naoya Oku and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1869–1874, doi:10.3762/bjoc.16.154

• , Tenacibaculum maritimum NBRC16015. Structural similarities among 1–4, the O-isocrotonylated 3-hydroxybutyrate oligomers 5, and microbial biopolymer polyhydroxyalkanoates (PHA) suggest the presence of a common biosynthetic machinery, and hence a possible dehydrative modification at the hydroxy terminus of PHA

• -chain 3-hydroxy acids are the common building blocks with PHA, the microbial storage polymer. The structural similarities among 1–5 and PHA suggest a quite similar or even the same biosynthetic origin of these molecules, and hence a potential dehydrative modification at the hydroxy terminus of PHA. MS

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• interactions as the native donor substrate and created only one strong interaction with the metal ion cofactor. So further modification of these four molecules can lead to the compounds with similar or higher affinities to the GlfT2 than UDP-Galf. Chemistry Within the structure of target compounds 1–3, the

One-pot and metal-free synthesis of 3-arylated-4-nitrophenols via polyfunctionalized cyclohexanones from β-nitrostyrenes

• Haruyasu Asahara,
• Minami Hiraishi and
• Nagatoshi Nishiwaki

Beilstein J. Org. Chem. 2020, 16, 1830–1836, doi:10.3762/bjoc.16.150

• various applications. In particular, 3-arylated-4-nitrophenols have attracted much attention from a biological viewpoint [1][2][3][4][5][6][7][8][9][10][11]; however, they cannot be synthesized by the direct modification of 4-nitrophenol because the ortho-directing hydroxy and the meta-directing nitro

• group hinder the electrophilic modification at the 3-position. Generally, the aryl group is introduced by a Suzuki–Miyaura cross-coupling reaction [4][5], for which 3-bromo-4-nitrophenol must be prepared by the nitration of 3-bromophenol [6][7]. An alternative approach is the nitration of 3-arylphenol

• (Scheme 2). Cyclohexanone 4a has acidic hydrogen atoms that can facilitate the aromatization by modification, e.g., by iodination. In order to obtain further insights into this possibility, 4a was heated with deuterium oxide, but no change was observed. In contrast, the signals assigned to the protons in

When metal-catalyzed C–H functionalization meets visible-light photocatalysis

• Lucas Guillemard and
• Joanna Wencel-Delord

Beilstein J. Org. Chem. 2020, 16, 1754–1804, doi:10.3762/bjoc.16.147

• lengths were potent substrates, affording the corresponding perfluoralkylated products in moderate to good yields, except for trifluoromethyl iodide, presumably due to the low boiling point of CF3I. Finally, the removal of the DG allowed the post-modification of the products into the corresponding

One-pot synthesis of isosorbide from cellulose or lignocellulosic biomass: a challenge?

• Isaline Bonnin,
• Raphaël Mereau,
• Thierry Tassaing and
• Karine De Oliveira Vigier

Beilstein J. Org. Chem. 2020, 16, 1713–1721, doi:10.3762/bjoc.16.143

• activity and recyclability of the catalyst was improved. A modification of the Ru/C hydrogenation catalyst’s surface by sulfonation and oxidative treatment was performed and had a significant effect on the catalyst properties in the isosorbide synthesis. Hence, strong acid sites are generated on the

Synthesis of Streptococcus pneumoniae serotype 9V oligosaccharide antigens

• Sharavathi G. Parameswarappa,
• Claney L. Pereira and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2020, 16, 1693–1699, doi:10.3762/bjoc.16.140

• vaccines. The serotype 9V is part of the currently marketed conjugate vaccine and contains an acetate modification. To better understand the importance of glycan modifications in general and acetylation in particular, defined oligosaccharide antigens are needed for serological and immunological studies

Mechanochemical green synthesis of hyper-crosslinked cyclodextrin polymers

• Alberto Rubin Pedrazzo,
• Fabrizio Caldera,
• Marco Zanetti,
• Silvia Lucia Appleton,
• Nilesh Kumar Dhakar and
• Francesco Trotta

Beilstein J. Org. Chem. 2020, 16, 1554–1563, doi:10.3762/bjoc.16.127

• in water and organic solvents and, unlike other types of NS, do not swell appreciably. In addition, they are nontoxic [1][3], stable up to 300 °C, and their structure allows modification through different functional groups before and/or after the synthesis. Carbonate nanosponges demonstrated

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• from our own group include the synthesis of a polystyrene gel with a photocatalytic cross-linking monomer, 4,7-bis(4-vinylphenyl)benzo[c][1,2,5]thiadiazole (St-BTZ) [47]. Additionally, we showed the direct synthesis of a BODIPY photocatalyst as a postsynthetic modification to an aldehyde-functionalised

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

• without a 3-methyl group, and the former lineages are unique to Burkholderia producers [28]. These metabolites are shown to be biosynthesized by head-to-head condensation of anthranilate and β-ketoacylate precursors, followed by a modification at C3 or nitrogen by putative monooxygenases or

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel–Hauser amides, and magnesium alkoxides

• Mateo Berton,
• Kevin Sheehan,
• Andrea Adamo and
• D. Tyler McQuade

Beilstein J. Org. Chem. 2020, 16, 1343–1356, doi:10.3762/bjoc.16.115

• Grignard and Knochel–Hauser base synthesis on the ODR prototype. Challenges: The changes in the reactor material from reusable glass to disposable perfluorinated columns and the modification in the bicomponent (Mg/LiCl) configuration from a single stratified column to two separated monocomponent columns

Distinctive reactivity of N-benzylidene-[1,1'-biphenyl]-2-amines under photoredox conditions

• Shrikant D. Tambe,
• Kwan Hong Min,
• Naeem Iqbal and
• Eun Jin Cho

Beilstein J. Org. Chem. 2020, 16, 1335–1342, doi:10.3762/bjoc.16.114

• hypothesized that the structural modification of the substrate might affect its reactivity, and to our delight, the introduction of an ortho-phenyl moiety on the N-benzylideneaniline species provided the desired 1,2-diamine product, wherein the N,N-dicyclohexylmethylamine (Cy2NMe) acted as both the coupling

Photocatalytic trifluoromethoxylation of arenes and heteroarenes in continuous-flow

• Alexander V. Nyuchev,
• Ting Wan,
• Borja Cendón,
• Carlo Sambiagio,
• Job J. C. Struijs,
• Michelle Ho,
• Moisés Gulías,
• Ying Wang and
• Timothy Noël

Beilstein J. Org. Chem. 2020, 16, 1305–1312, doi:10.3762/bjoc.16.111

• yields for the same compounds (64–92%). These experiments demonstrated that the addition of bases indeed represent an interesting modification of the previous protocol, despite being substrate-dependent. Conclusion In summary, we have developed the first continuous-flow trifluoromethoxylation of arenes

Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• molecular modification of the derivatives 1 and 2 through the bioisosteric replacement [20] of the amide functional group by an aliphatic or aromatic ester. The potential antiinflammatory activity of the new bisphosphonates was predicted using the Prediction of Activity Spectra for Substances (PASSOnline

• approximation, to study the effect of these structural modification on the pharmacodynamics, we performed a molecular docking over two MPPs. In Table 4, the interaction energy value (MolDock Score) [38] of each compound with the two different MMPs obtained from the docking calculation is displayed. Also, the

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• available, enabling utilisation and modification by other groups. Stress-Chip is a chip that allows the isolation of a hundred worms in single-worm arenas and monitoring as chemicals flow over the worms [153]. The CAD file for producing the microfluidic device has been made available on Figshare under the

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• available production and modification methods and possible characterization techniques. We evaluate the preparation methods for activated carbon materials with respect to its use as catalyst support and identify important parameters for metal loading. The considered carbon sources include coal, wood

• , agricultural wastes or biomass as well as ionic liquids, deep eutectic solvents or precursor solutions. The preparation of the activated carbon usually involves pre-treatment steps followed by physical or chemical activation and application dependent modification. In addition, highly porous materials can also

• compositions [2]. In general, activated carbon is an amorphous carbon modification with a high surface area and a well-developed porosity, which can be produced from a variety of carbon sources [3]. The preparation of activated carbons is already broadly covered in the literature. Therefore, we limit our brief

Development of fluorinated benzils and bisbenzils as room-temperature phosphorescent molecules

• Shigeyuki Yamada,
• Takuya Higashida,
• Yizhou Wang,
• Masato Morita,
• Takuya Hosokai,
• Kaveendra Maduwantha,
• Kaveenga Rasika Koswattage and
• Tsutomu Konno

Beilstein J. Org. Chem. 2020, 16, 1154–1162, doi:10.3762/bjoc.16.102

• (Figure 2A), which show prominent fluorescence not only in dilute solution, but also in the crystalline state [27][28][29][30][31]. As a powerful tool to develop novel pure organic phosphorescent molecules, we envisioned the structural modification of the carbon–carbon triple (C≡C) bond in fluorinated

• effects of structural modification (i.e., the benzil structure with a tolane vs bisbenzil moiety) and incorporation of fluorine atoms on the phosphorescence, the ratio between the peak intensities at ≈395 and ≈560 nm (I560/I395) was quantitatively calculated, and the results are summarized in Table 1. The