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

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• biological material. SDFS main components and its work model. A) Schematic representation of the SDFS structure. Dotted lines indicate hexaethylene glycol linkers in T1 and T4, and polythymidines linker in T2 and T3; Dz1 and Dz2 – deoxyribozyme sequences. B) The detailed structure of the Dz catalytic core

The charge-assisted hydrogen-bonded organic framework (CAHOF) self-assembled from the conjugated acid of tetrakis(4-aminophenyl)methane and 2,6-naphthalenedisulfonate as a new class of recyclable Brønsted acid catalysts

• Svetlana A. Kuznetsova,
• Alexander S. Gak,
• Yulia V. Nelyubina,
• Vladimir A. Larionov,
• Han Li,
• Michael North,
• Vladimir P. Zhereb,
• Alexander F. Smol'yakov,
• Artem O. Dmitrienko,
• Michael G. Medvedev,
• Igor S. Gerasimov,
• Ashot S. Saghyan and
• Yuri N. Belokon

Beilstein J. Org. Chem. 2020, 16, 1124–1134, doi:10.3762/bjoc.16.99

• frameworks could be tuned by varying the ratio of anion/cation multitopic components and the basicity of the cation component. View of the crystal structure of F-1 (F-1a phase), with representation of atoms by thermal ellipsoids at a 30% probability level. The hydrogen atoms, except for those in NH groups

• and solvate water molecules, were omitted for clarity. Only the labels of symmetry-independent heteroatoms are shown. View of the crystal structure of F-1 (F-1a’ phase), with representation of the atoms via thermal ellipsoids at a 30% probability level. The hydrogen atoms, except for those in NH

Fabclavine diversity in Xenorhabdus bacteria

• Sebastian L. Wenski,
• Harun Cimen,
• Natalie Berghaus,
• Sebastian W. Fuchs,
• Selcuk Hazir and
• Helge B. Bode

Beilstein J. Org. Chem. 2020, 16, 956–965, doi:10.3762/bjoc.16.84

• our current study, future work is required to confirm fabclavines as the active compounds here as well (Table 3) [20]. General biosynthesis of fabclavine Ia (1) in X. budapestensis (A) and representation of a shortened fabclavine derivative from X. szentirmaii (B), resulting from the alternative

One-pot synthesis of dicyclopenta-fused peropyrene via a fourfold alkyne annulation

• Ji Ma,
• Yubin Fu,
• Junzhi Liu and
• Xinliang Feng

Beilstein J. Org. Chem. 2020, 16, 791–797, doi:10.3762/bjoc.16.72

• . Hydrogen atoms and solvent molecules are omitted for clarity. (d) Selected bond lengths (from the crystal structure) and calculated NICS(1) values of rings A–I in 1. (e) Clar valence structure representation of 1 with three benzeneoid rings. (a) UV–vis absorption spectra of precursor 5 and 1 in CH2Cl2

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54

• browser (signing in may be an impediment but not a stopper). These are thus distinct from commercial offerings where access has to be purchased. Relationship representation As outlined in the abstract the connectivity between documents, structures and bioactivity can be expressed in shorthand as “D-A-R-C

• to enable full DARCP representation in PubChem BioAssay for suitable data sets. 5.) The transfer of data from the literature into on-line open resources (by an individual or a curation enterprise) could conceivably come up against copyright issues. The complexities of permissions to mine scholarly

Recent developments in photoredox-catalyzed remote ortho and para C–H bond functionalizations

• Rafia Siddiqui and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 248–280, doi:10.3762/bjoc.16.26

• review article. Jablonski diagram. Photoredox catalysis via reductive or oxidative pathways. D = donor, A = acceptor, S = substrate, PC = photoredox catalyst, RDP = reductive quenching pathway, OQP = oxidative quenching pathway. Schematic representation of the combination of photoredox catalysis and

Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis

• Alonso Pardo-Vargas,
• Priya Bharate,
• Martina Delbianco and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288

• procedure B. For detailed procedures, see Tables S10 and S11 in Supporting Information File 1. Schematic representation of LAM and AM oligomers obtained using AGA. Schematic representation of AGA for oligomannosides and oligoarabinomannosides using building blocks 1–3. AGA of arabinomannosides 4–9