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

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

• structural units of monosaccharides (glycoblocks) that regulate the 3D architecture and dynamics of complex biantennary N-glycans from plants and invertebrate sources and hybrid mammalian constructs. The SFNG representation of each glycoblock is indicated in the first column from the left, 3D structures from

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

• ). Schematic representation of the alignment of the intercalating 3a (left) and 3b (right) between the base pairs of the oligonucleotide. The complex with 3b was prepared analogously to the NDI analogue [53] by replacing the threading intercalator in PDB258D [54] with 3b, and performing MM2 minimisation in

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

• . Schematic representation of binding models between organic cations (simple ammonium, guanidinium, Schmuck cation) and oxoanions. From Schmuck cations to cell-penetrating dipeptides, with schematic representation of the binding model between GCPs and GAGs on the cell surface, and with DNA. Peptide tweezers

Controlling the stereochemistry in 2-oxo-aldehyde-derived Ugi adducts through the cinchona alkaloid-promoted electrophilic fluorination

• Yuqing Wang,
• Gaigai Wang,
• Anatoly A. Peshkov,
• Ruwei Yao,
• Muhammad Hasan,
• Manzoor Zaman,
• Chao Liu,
• Stepan Kashtanov,
• Olga P. Pereshivko and
• Vsevolod A. Peshkov

Beilstein J. Org. Chem. 2020, 16, 1963–1973, doi:10.3762/bjoc.16.163

• the analogous reactions with Selectfluor. Having these results in hand, we moved to investigating the scope and limitation of this procedure with the Ugi adducts 8 obtained previously (Table 4). In order to have a more balanced representation we decided to test most of these substrates 8 with eight

• asymmetric electrophilic fluorination for derivatizing the 2-oxo-aldehyde-derived Ugi adducts. This allowed us to obtain the post-Ugi products fluorinated at the peptidyl position with the enantiomeric excess values in several instances reaching more than 70%. Molecular representation of the X-ray crystal

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

• the potential of the in silico methods for the design of new GlfT2 inhibitors. Target ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones 1‒3. Molecular representation of the best binding poses of the four compounds with the predicted highest affinity. (A) 1bα, (B) 2c, (C) 3c and (D) 1cβ. The molecule

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

• catalysis involving two catalysts and two catalytic cycles acting in a cooperative way to create a new bond, turned out to be a powerful strategy. According to a simplified representation, synergistic catalysis involves the concurrent activation of a nucleophile and an electrophile by means of two distinct

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

• minutes. a) Schematic depiction of the Jablonski diagram. b) Schematic representation of El-Sayed’s rule. Reaction conditions for para-bromobenzaldehyde 3: a) 1) 2-amino-2-methylpropan-1-ol, 4 Å MS, CH2Cl2, 25 °C, 18 h; 2) NBS, CH2Cl2, 25 °C, 5 h, 91%; b) 1) TMPMgCl·LiCl, THF, 25 °C, 4 h; 2) DMF, THF, 0

Pauson–Khand reaction of fluorinated compounds

• Jorge Escorihuela,
• Daniel M. Sedgwick,
• Alberto Llobat,
• Mercedes Medio-Simón,
• Pablo Barrio and
• Santos Fustero

Beilstein J. Org. Chem. 2020, 16, 1662–1682, doi:10.3762/bjoc.16.138

• this review will definitely pave the way for future applications in the fluoro-PKR, and put this emerging reaction at the forefront of drug design. Schematic representation of the Pauson–Khand reaction. Substrates included in this review. Commonly accepted mechanism for the Pauson–Khand reaction

Models of necessity

• Timothy Clark and
• Martin G. Hicks

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

• ; chemical structure representation; chemical structure models; language of chemistry; quantum chemistry; Introduction This article originally arose out of our discussions for the 2020 Beilstein Bozen Meeting “Models of Convenience” [1], which had to be postponed due to Covid-19 pandemic. It essentially

• needs to be able to define molecular structures uniquely within a common language and to use this language to develop a classification scheme that can deal with many millions of different molecules (compounds) and, even worse, reactions. This need is more fundamental than looking for a representation of

• survives in an extended form to this day and bears his name. Not only do these formulae provide the basis for fundamental concepts such as functional groups but also for just about every cheminformatics representation of molecular structures. Figure 3 shows the Lewis formula of clozapine (the molecule

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

• inversion of the local electronic environment, or the precise deletion of hydrogen-bond donors, respectively, with minimal steric variation [7]. The latter aspect is a crucial determinant in enabling fluorinated materials to adopt intriguing conformations which are a manifest representation of stabilising

NHC-catalyzed enantioselective synthesis of β-trifluoromethyl-β-hydroxyamides

• Alyn T. Davies,
• Mark D. Greenhalgh,
• Alexandra M. Z. Slawin and
• Andrew D. Smith

Beilstein J. Org. Chem. 2020, 16, 1572–1578, doi:10.3762/bjoc.16.129

• support. dMolecular representation of the X-ray crystal structure of 12. The unit cell of 12 contained two molecules of 12, with only one shown for clarity. Proposed mechanism. Optimization of the NHC-catalyzed formal [2 + 2] cycoaddition.a Supporting Information Supporting Information File 335

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

In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions

• Liwei Cao,
• Mikhail Kabeshov,
• Steven V. Ley and
• Alexei A. Lapkin

Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122

• and the appropriate mechanism, but also provides information for further kinetic studies and process development, thus contributing to the development of robust new chemical transformations. An approximate energy map for the electrophilic aromatic substitution mechanism. Schematic representation of

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

• molecules inside the catalytic site allowed the coordination through the ester groups rather than through the phosphonate moieties. The calculated distances from the Zn2+ ion and the different sites at the ligand and the protein are summarized in Table 6. In Figure 4, a schematic representation of the