Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• of the tree is the glycan information, separated into glycan types. Each glycan also contains a list of sugars, with a range of validation information and a list of linkage with torsion angle information. Tree visualisation was created with jsoncrack.com. Left: Graphical representation of the

(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• equilibrium, n = 2. Structural insights into the binding mechanism of CMA1. (a, b) Overall representation of the N-terminal domain of CMA1 in complex with (a) LacNAc (Galβ1-4GlcNAc) [29] or (b) GalNAc [30]. Trefoil repeats are colored differently, and cadmium ions are represented as red spheres. (c, d) Close

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• ; irradiated with orange light (λirr > 520 nm): dash-dotted line. In all cases irradiation time t = 5 min. Reprinted with permission from ref. [38]. Copyright (1965) American Chemical Society. Photoisomerization of compound 18c upon irradiation with red light and schematic representation of the complexation of

• the Z-isomer with metal cations. Schematic representation of indigo-type (left) and amide-type (right) resonances in N,N'-acetylindigo (9a). Suggested intermediates for the double bond cleavage for the thermal relaxation of N,N'-diacylindigos: (A) a biradical transient species, (B) a dipolar transient

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions

• Matthias R. Steiner,
• Max Schmallegger,
• Larissa Donner,
• Johann A. Hlina,
• Christoph Marschner,
• Judith Baumgartner and
• Christian Slugovc

Beilstein J. Org. Chem. 2024, 20, 41–51, doi:10.3762/bjoc.20.6

• in these cases (Supporting Information File 1, Figures S54 and S74). Crystal structures The solid-state structures of 2a and 2f were determined by single-crystal X-ray diffraction. The crystals were grown from concentrated solutions in toluene. A representation of the molecular structure of 2a is

NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform

• Luc Patiny,
• Hamed Musallam,
• Alejandro Bolaños,
• Michaël Zasso,
• Julien Wist,
• Metin Karayilan,
• Eva Ziegler,
• Johannes C. Liermann and
• Nils E. Schlörer

Beilstein J. Org. Chem. 2024, 20, 25–31, doi:10.3762/bjoc.20.4

• platform for specialized data handling applications. This trend has not been withheld from science: With the advent of web tools for the online representation and manipulation of scientific data [14][15][16][17] and the development of software for spectroscopy visualization [18][19][20][21][22][23][24][25

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• µM and adding AvaA7 (final concentration: 0.2 µM) and NADPH (final concentration: 800 µM). Comparison of ava and cma clusters and the biosynthetic pathway of p-coumaric acid. A) Schematic representation of ava and cma clusters from Streptomyces sp. RI-77 and Kutzneria albida, respectively. They

• harbor similar gene components except for the genes encoding oxidoreductases (avaA8 and cmaG), transporter (avaC), and regulator (cmaR). B) The proposed biosynthetic pathway of p-coumaric acid by the cma cluster. Heterologous expression of the cma cluster in S. albus. A) Schematic representation of the

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• would be significantly smaller. Data analysis and its graphical representation were done with the R-package [49] and VMD [50]. Results In total, 14 US simulations were performed to investigate the specificity of GAG–protein interactions, capabilities of US simulations to dissociate and reassociate

• to relax the system and to check if the final pose was energetically stable or if it changed during the relaxation step. The data depicted in the graphs result from the analysis of merged US trajectories. While this representation is not entirely physically sound, as the outcomes for each US window

• to analyze them. Graphical representation of ligands (in licorice, hydrogen atoms not shown) used in this study. Ligands 1, 2, and 3 were used in complexes with basic fibroblast factor (as modifications of the 1BFC PDB structure) and acidic fibroblast factor (as modifications of the 2AXM PDB

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• structure was calculated with the Pymol tool [66]. ORTEP representation of the new N-acylhydrazones synthesized in the present work, drawn with thermal ellipsoids at 30% probability. Left: hdz-CH3 and right: hdz-NO2. (A) Superposition of molecular structures and stacked motifs of (B) hdz-CH3 and (C) hdz-NO2

Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration

• Ghenwa Nasr,
• Hélène Greige-Gerges,
• Sophie Fourmentin,
• Abdelhamid Elaissari and
• Nathalie Khreich

Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115

• methylated-β-CD (CRYSMEB), the hydroxypropyl-β-CD (HP-β-CD), and the sulfobutyl ether-β-CD (SBE-β-CD). A schematic representation of the chemical structure of the native CDs and their dimensions is depicted in Figure 1, reprinted with permission from [21]. The structures of β-CD derivatives and their degrees

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• representation of halogen bonding. Quantitative evaluation of σ-holes in monovalent iodine-containing compounds; and, qualitative molecular electrostatic potential (MEP) of I-3 from −0.052 to 0.052 e showing a single σ-hole (dark blue) [86]. Quantitative evaluation of σ-holes in hypervalent iodine-containing

Selective and scalable oxygenation of heteroatoms using the elements of nature: air, water, and light

• Damiano Diprima,
• Hannes Gemoets,
• Stefano Bonciolini and
• Koen Van Aken

Beilstein J. Org. Chem. 2023, 19, 1146–1154, doi:10.3762/bjoc.19.82

• . A) Effect of the addition of 1 equiv of various acids and bases to the standard solution. B) Effect of the addition of 1 equiv of various salts to the standard solution. Oxidation of heteroatoms. Graphical representation comparing A electrochemistry and B photoredox catalysis using a semiconductor

Synthesis of imidazo[4,5-e][1,3]thiazino[2,3-c][1,2,4]triazines via a base-induced rearrangement of functionalized imidazo[4,5-e]thiazolo[2,3-c][1,2,4]triazines

• Dmitry B. Vinogradov,
• Alexei N. Izmest’ev,
• Angelina N. Kravchenko,
• Yuri A. Strelenko and
• Galina A. Gazieva

Beilstein J. Org. Chem. 2023, 19, 1047–1054, doi:10.3762/bjoc.19.80

• spectra of compounds 4a and 5a in DMSO-d6 in the region of 4.3–9.0 ppm. 13C NMR GATED spectra of compounds 4a and 5a in DMSO-d6 in the region of 156.0–168.0 ppm. General view of 5a in the crystal in thermal ellipsoid representation (p = 80%). Base-induced transformations and rearrangements of

Linker, loading, and reaction scale influence automated glycan assembly

• Marlene C. S. Dal Colle,
• Manuel G. Ricardo,
• Nives Hribernik,
• José Danglad-Flores,
• Peter H. Seeberger and
• Martina Delbianco

Beilstein J. Org. Chem. 2023, 19, 1015–1020, doi:10.3762/bjoc.19.77

• of new linkers, more efficient cleaving procedures [34], and the implementation of post-AGA manipulation steps on resin. Schematic representation of the AGA process (A). Variables that can affect the AGA outcome investigated in this study (B). AGA of model glycan sequences analyzed in this study: α

Light-responsive rotaxane-based materials: inducing motion in the solid state

• Adrian Saura-Sanmartin

Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64

• ) Chemical structure of polyrotaxane 2; and (b) cartoon representation of the light-triggered degradation of rotaxane polymer 2 [52]. The key colour of the cartoon representation is analogous to that of the chemical structures. a) Chemical structures of rotaxanes (E)-3 and (Z)-3; b) stick representation of

• the solid structure of UMUMOF-(E)-3 showing a rhombohedral metallogrid; and (c) cartoon representation of the operation mode of UMUMOF-(E)-3 as a molecular nanodispenser [62]. Colour key of the solid structure: light blue = carbon atoms; purple = nitrogen atoms; red = oxygen atoms; and grey = copper

• atoms. The key colour of the cartoon representation is analogous to that of the chemical structures. Stick representations of the solid structures of: (a) U-CB[8]-MPyVB showing an interlocked ligand connected to two uranium clusters; and (b) the intertwined photodimerized product within the crystalline

Strategies in the synthesis of dibenzo[b,f]heteropines

• David I. H. Maier,
• Barend C. B. Bezuidenhoudt and
• Charlene Marais

Beilstein J. Org. Chem. 2023, 19, 700–718, doi:10.3762/bjoc.19.51

• coupling in dibenzo[b,f]oxepine synthesis. Wittig reaction and Ullmann coupling as key steps in dihydrobenz[b,f]oxepine synthesis. Pd-catalysed dibenzo[b,f]azepine synthesis via norbornene azepine intermediate 109. A simple representation of olefin metathesis resulting in transalkylidenation. Ring-closing

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• systems in various solvents [61][62][63]. 2D (left) and 3D (right) representation of fluorescence emission spectra of Phen-Py-1 (c = 2 × 10−6 mol dm−3) at different pH values (Na cacodylate, HCl, Ic = 0.05 mol dm−3 at 25 °C (λexc = 280 nm)). Most representative structures of the conjugates Phen-Py-1 and

Discrimination of β-cyclodextrin/hazelnut (Corylus avellana L.) oil/flavonoid glycoside and flavonolignan ternary complexes by Fourier-transform infrared spectroscopy coupled with principal component analysis

• Nicoleta G. Hădărugă,
• Gabriela Popescu,
• Dina Gligor (Pane),
• Cristina L. Mitroi,
• Sorin M. Stanciu and
• Daniel Ioan Hădărugă

Beilstein J. Org. Chem. 2023, 19, 380–398, doi:10.3762/bjoc.19.30

• of the data. The new axes are denominated Factors or Principal Components (PCs). The translation coordinates will provide the scores plots that reveal the similarities/dissimilarities between cases (samples), while the representation of the rotation coordinates of the axes (direction cosines) will

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

Investigation of cationic ring-opening polymerization of 2-oxazolines in the “green” solvent dihydrolevoglucosenone

• Solomiia Borova and
• Robert Luxenhofer

Beilstein J. Org. Chem. 2023, 19, 217–230, doi:10.3762/bjoc.19.21

• the [M]0/[I]0 ratio. In summary, even though the CROP of selected 2-oxazolines can be carried out in dihydrolevoglucosenone, it does not appear suitable to obtain well-defined poly(2-alkyl-oxazoline)s. Schematic representation of the mechanism of the cationic ring-opening polymerization (CROP) of 2

Combining the best of both worlds: radical-based divergent total synthesis

• Kyriaki Gennaiou,
• Antonios Kelesidis,
• Maria Kourgiantaki and
• Alexandros L. Zografos

Beilstein J. Org. Chem. 2023, 19, 1–26, doi:10.3762/bjoc.19.1

• discoveries, namely a photoredox-catalytic nitrogen-centered radical cascade [72], which has resulted in the impressive collective total synthesis of 33 alkaloids of three different classes of indole natural products (please see the inset of Scheme 11 for concise representation). Specifically, this included

Inline purification in continuous flow synthesis – opportunities and challenges

• Jorge García-Lacuna and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182

• ]. General purification scheme using the catch and release strategy. Exemplar catch and release purification of a stereoselective oxidation. Redrawn from [105]. Catch and release-type purification using conventional SiO2. Redrawn from [107]. Schematic representation of an industrial continuous

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• 2022) [20]. As the largest database of characterized BGCs, MIBiG is frequently used as a training data set for the development of genome mining algorithms. The imbalanced representation of NP BGCs in the database, however, might introduce a bias when it comes to the training of novel algorithms

One-pot double annulations to confer diastereoselective spirooxindolepyrrolothiazoles

• Juan Lu,
• Bin Yao,
• Desheng Zhan,
• Zhuo Sun,
• Yun Ji and
• Xiaofeng Zhang

Beilstein J. Org. Chem. 2022, 18, 1607–1616, doi:10.3762/bjoc.18.171

• eliminating the intermediate purification. It is an efficient way to build up novel spirooxindolepyrrolothiazoles for drug discovery screening. Bioactive Spirooxindole-pyrrolothiazoles. Graphical representation of the green metrics (AE, AEf, CE, RME, OE and MP) analysis for processes A and B. The higher the

• value, the greener the process. Graphical representation of the green metrics (PMI, E-factor, and SI) analysis for processes A and B. The lower value, the better the reaction process. The diastereoselective synthesis of spirooxindoles through MCRs. The synthesis of spirooxindolepyrrolothiazoles. Four

New triazole-substituted triterpene derivatives exhibiting anti-RSV activity: synthesis, biological evaluation, and molecular modeling

• Elenilson F. da Silva,
• Krist Helen Antunes Fernandes,
• Denise Diedrich,
• Jessica Gotardi,
• Marcia Silvana Freire Franco,
• Carlos Henrique Tomich de Paula da Silva,
• Ana Paula Duarte de Souza and
• Simone Cristina Baggio Gnoatto

Beilstein J. Org. Chem. 2022, 18, 1524–1531, doi:10.3762/bjoc.18.161

• with compound 8. (B) Viral load quantification by real-time PCR after treatment with compound 8. Superposition of the top-ranked docking solution of compound 8 (carbon atoms in yellow, in stick representation) with the crystallographic poses of IMP and inhibitor MAD1 (color by atoms in stick

• representation) inside the IMPDH active site from Mycobacterium tuberculosis (cartoon representation – PDB code 4ZQP), with selected residues and interactions here also represented. Synthesis of 1-azido-3-nitrobenzene (c). Synthesis of the triazole-substituted triterpene derivatives 7 and 8. Antiviral activity