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

• ], glycosidic linkage stereochemistry [14] and torsion [15][16], and most recently, ring conformation [17]. Most of these issues have now been addressed as part of ongoing efforts to provide better software tools for structure determinations of glycoproteins, although the most difficult cases remain hard to

• stereochemistry [14], incorrect torsion [15][16], and unlikely high-energy ring conformations [17]. Early efforts in the validation of carbohydrate structures saw the introduction of online tools such as PDB-CARE [37] and CARP [16]; more recently, we released the Privateer software [24], which was the first

• terminal Man-(1→3)-GlcNAc [14]. Moreover, the proposed model contained systematic errors in the anomer annotations and carbohydrate stereochemistry. To this day, there is still no experimental evidence reported for these types of linkages and capping in an identical context. The new version of Privateer

Hierarchically assembled helicates as reaction platform – from stoichiometric Diels–Alder reactions to enamine catalysis

• David Van Craen,
• Jenny Begall,
• Johannes Großkurth,
• Leonard Himmel,
• Oliver Linnenberg,
• Elisabeth Isaak and
• Markus Albrecht

Beilstein J. Org. Chem. 2020, 16, 2338–2345, doi:10.3762/bjoc.16.195

• auxiliary, Lewis acid or catalyst. In the previously reported system two different induction pathways were conceivable: (1) A chiral ligand is located close to the diene and controls the stereochemistry of the cycloaddition. (2) The chiral ligand controls the helicity of the helicate (ΔΔ or ΛΛ) and the

• reaction yielded the racemic product after purification. Scheme 3 is showing that the induction of stereochemistry of the Diels–Alder reaction depends on the chirality at the chiral ligand and not at the helix. This allows improvement of the stereoselectivity by using more appropriate sterically hindered

• formed helicates with mixtures of ligands as platforms to control the stereochemistry of C–C bond-forming reactions. However, it would be of great advantage to transfer the findings to catalytic C–C bond-forming reactions which are catalyzed by hierarchical helicates containing chiral ligands for

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

• ) as a reagent; the thus obtained N1-styryl-substituted 4-trifluoromethylpyrimidin-2(1H)-one 5a obviously has considerable synthetic potential [49][50]. The stereochemistry of compound 5a was confirmed by a NOE NMR experiment, which demonstrated significant spatial interaction between the H6 and Hb

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

• , and HRMS analyses (Figures S1–S40 in Supporting Information File 1). Moreover, the stereochemistry of the double bonds was determined on the basis of the coupling constants of the vinylic hydrogens in the 1H NMR spectra (J ≈ 15–16 Hz) and revealed that the dyes are stable as E-stereoisomers [31

Reactions of 3-aryl-1-(trifluoromethyl)prop-2-yn-1-iminium salts with 1,3-dienes and styrenes

• Thomas Schneider,
• Michael Keim,
• Bianca Seitz and
• Gerhard Maas

Beilstein J. Org. Chem. 2020, 16, 2064–2072, doi:10.3762/bjoc.16.173

• -(1-phenylvinyl)indene 12 through an intramolecular iminium ion-induced 1,5-cyclization. The same cyclization type together with oxidative aromatization converts dihydronaphthalenes 16 into benzo[a]fluorenes 13. The stereochemistry of 12d can be explained by a stereoselective formation of trans-3,4

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

• invoked when discussing other biopolymers or complex carbohydrates. In the specific case of glycans, the structural complexity, in terms of the diversity of monosaccharides, the linkages’ stereochemistry and the branched scaffolds, makes the already difficult case even more intricate. Nevertheless, the

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

• . China The Environment and Resource Efficiency Cluster (EREC), Nazarbayev University, Nur-Sultan, Republic of Kazakhstan 10.3762/bjoc.16.163 Abstract In this report, we introduce a new strategy for controlling the stereochemistry in Ugi adducts. Instead of controlling stereochemistry directly during the

• major slow enantiomer was successfully established as S (Figure 1). Conclusion In summary, we have explored a new strategy for controlling the stereochemistry in the Ugi adducts through the enantioselective post-Ugi functionalization. Specifically, we have adapted the cinchona alkaloid-promoted

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• its analogues towards trans- and cis-amides [81]. An unsubstituted proline residue usually exhibits a preference to form a trans-amide. Fluoroprolines are notorious for the relative stabilization of the amide rotamers depending on the stereochemistry at the C4-atom. This is known as the chiral bias

• . Therefore, no difference was found in the solvation effects contributing to the rotation barriers in these molecules. Finally, the difference between the barriers in the diastereomers calls for an explanation. It is clear from the presented data that the stereochemistry at the C4-atom has an effect on 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

• afforded trace amounts of 3a and 4a, both of which were obtained as a mixture of diastereomeric isomers (Table 1, entry 1). The stereochemistry of the major product 4a was determined to be trans,trans (all-equatorial) by X-ray crystallography (Figure 1). Among the solvents tested, less polar solvents, such

Synthesis of the tetrasaccharide repeating unit of the O-specific polysaccharide of Azospirillum doebereinerae type strain GSF71^T using linear and one-pot iterative glycosylations

• Arin Gucchait,
• Pradip Shit and
• Anup Kumar Misra

Beilstein J. Org. Chem. 2020, 16, 1700–1705, doi:10.3762/bjoc.16.141

• ]. Repeating the reaction with disaccharide acceptor 5 using the same conditions, the stereoselective glycosylation with compound 3 furnished trisaccharide acceptor 6 in 70% yield. The desired stereochemistry of the newly formed glycosidic bond was confirmed by NMR spectroscopic analysis [appearance of signals

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

• EtOH/THF mixture at room temperature for 48 h afforded the desired O-acetylated pentasaccharide 5. The stereochemistry of each anomeric center during the respective glycosylation was confirmed using the 1H coupling constant and using coupled HSQC for the JC1,H1 coupling (see Supporting Information File

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

• one. The regio- and stereochemistry of this transformation is predictable, in most cases. Since this is an important issue throughout the review, a concise remark about the mechanism of this transformation is outlined below (Scheme 3). This mechanism was proposed by Magnus over 30 years ago and is

• Co–C bond. These electronic effects have been shown to be less important than steric ones, and are often overcome by the latter. Regarding the stereochemistry, exo-products are almost exclusively obtained for norbornene and norbornadiene. Many deviations from the classic reaction conditions have been

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

• structure for compounds 3b, 8a,b, and 23a, and the RR–SS structure for congener 23b. In order to get a better insight into the stereochemistry of compounds 23a and 23b, we calculated their refined stereostructure by means of DFT geometry optimization in a DCM solution. As a result, one minimal energy

Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)

• Cora Hertzer,
• Stefan Kehraus,
• Nils Böhringer,
• Fontje Kaligis,
• Robert Bara,
• Dirk Erpenbeck,
• Gert Wörheide,
• Till F. Schäberle,
• Heike Wägele and
• Gabriele M. König

Beilstein J. Org. Chem. 2020, 16, 1596–1605, doi:10.3762/bjoc.16.132

• -methylenedeoxoscalarin (relative stereochemistry depicted), isolated from Doriprismatica stellata nudibranchs, their egg ribbons and the dietary sponge Spongia cf. agaricina. Superimposed HPLC–MS chromatogram of Doriprismatica stellata nudibranch, egg ribbon, and Spongia cf. agaricina extracts, showing the presence of

An overview on disulfide-catalyzed and -cocatalyzed photoreactions

• Yeersen Patehebieke

Beilstein J. Org. Chem. 2020, 16, 1418–1435, doi:10.3762/bjoc.16.118

• stereochemistry of the product can be modulated by changing the stereochemical structure of the disulfide catalyst [10]. The simple reaction mechanism is shown in Scheme 4a. Thiyl radicals, which are generated under irradiation, trigger the reaction by adding to the methylenecyclopropane 4, which affords the

Synthesis of 3-substituted isoxazolidin-4-ols using hydroboration–oxidation reactions of 4,5-unsubstituted 2,3-dihydroisoxazoles

• Lívia Dikošová,
• Júlia Laceková,
• Ondrej Záborský and
• Róbert Fischer

Beilstein J. Org. Chem. 2020, 16, 1313–1319, doi:10.3762/bjoc.16.112

• isoxazolidines by means of dihydroxylation [9][10] and epoxidation [11][12] reactions. Regarding the stereochemistry, almost all of the realized additions proceed with an excellent trans stereoselectivity relative to the substituent at C-3, giving isoxazolidine-4,5-diols and isoxazolidinyl epoxides with a C-3/4

• lower values (2.08–3.30 ppm), and the signal for the H-5 proton can be found at 5.50 ppm due to the effect of the two oxygen atoms bound to the C5 carbon atom. Regarding the stereochemistry, the borane attack on the C=C double bond of the 2,3-dihydroisoxazole occurs from the sterically less hindered

• stereochemical results are consistent with our previous findings on the direct dihydroxylation and epoxidation reactions of 4,5-unsubstituted 2,3-dihydroisoxazoles [9][10][11][12]. To invert the relative C-3/4-trans stereochemistry, the isoxazolidin-4-ols 5a–c were first oxidized to the corresponding ketones

[3 + 2] Cycloaddition with photogenerated azomethine ylides in β-cyclodextrin

• Margareta Sohora,
• Leo Mandić and
• Nikola Basarić

Beilstein J. Org. Chem. 2020, 16, 1296–1304, doi:10.3762/bjoc.16.110

• the macrocyclic host affected the stereochemistry of the reaction. Moreover, we studied photodecarboxylation reactions initiated by the phthalimide chromophore [17][18][19] and applied them in cyclizations with memory of chirality [20] and diastereoselective peptide cyclizations [21

Palladium-catalyzed regio- and stereoselective synthesis of aryl and 3-indolyl-substituted 4-methylene-3,4-dihydroisoquinolin-1(2H)-ones

• Valeria Nori,
• Antonio Arcadi,
• Armando Carlone,
• Fabio Marinelli and
• Marco Chiarini

Beilstein J. Org. Chem. 2020, 16, 1084–1091, doi:10.3762/bjoc.16.95

• -assisted cyclization and reductive elimination from the resulting σ-indolylpalladium complex C (Scheme 5). The reaction led to the stereoselective formation of indole derivatives 6ba–fc (aryl, heteroaryl and vinyl groups were allowed in substrates 5) in good to high yield. The stereochemistry of compounds

Suzuki–Miyaura cross coupling is not an informative reaction to demonstrate the performance of new solvents

• James Sherwood

Beilstein J. Org. Chem. 2020, 16, 1001–1005, doi:10.3762/bjoc.16.89

• catalysed carbon–carbon bond formation, making it an obvious case study to validate the performance of novel solvents [1][2][3][4][5][6][7]. The polarity of the solvent is known to determine the structure and activity of catalytic intermediates, the rate determining step, and stereochemistry (where

Diversity-oriented synthesis of 17-spirosteroids

• Benjamin Laroche,
• Thomas Bouvarel,
• Martin Louis-Sylvestre and
• Bastien Nay

Beilstein J. Org. Chem. 2020, 16, 880–887, doi:10.3762/bjoc.16.79

• structure and stereochemistry of the products were determined by 2D NMR analysis. Taking 16b as an example, the key NOESY correlations between proton H-4' at 2.79 ppm and steroid protons H-12 at 1.33/1.65 ppm demonstrated that H-4' is on the α-face of the cyclohexene (Figure 3a). The endo character of the

• -ethynyl-17-hydroxysteroids 1–4 (top) and how they could be used to generate diversity (down). Structure of metathesis catalysts. Rationale for the observed stereochemistry: (a) NOESY correlations observed on compound 16b, showing key correlations between protons of the cyclohexene α-face and both protons

Efficient synthesis of dipeptide analogues of α-fluorinated β-aminophosphonates

• Marcin Kaźmierczak and
• Henryk Koroniak

Beilstein J. Org. Chem. 2020, 16, 756–762, doi:10.3762/bjoc.16.69

• Herein, we present an efficient synthesis of dipeptide analogues of α-fluorinated β-aminophosphonates. Each step of the synthesis was optimized to provide excellent yields. Moreover, the absolute configuration of the obtained compounds was determined by X-ray analysis, which proved the stereochemistry

• enzyme binding may depend on the C–F stereochemistry, the synthesis of such compounds with a specific configuration is very important [9][10][11]. α-Fluorinated phosphonates can be prepared by many different protocols [12][13][14][15][16]. Nucleophilic fluorination is one of the fundamental reactions in

• at room temperature. What is more, we attempted to crystallize at least one derivative to confirm the absolute stereochemistry of the obtained compounds. In order to obtain a single crystal suitable for X-ray diffraction studies, various crystallization techniques were tested [37][38

Combining enyne metathesis with long-established organic transformations: a powerful strategy for the sustainable synthesis of bioactive molecules

• Valerian Dragutan,
• Ileana Dragutan,
• Albert Demonceau and
• Lionel Delaude

Beilstein J. Org. Chem. 2020, 16, 738–755, doi:10.3762/bjoc.16.68

• the respective dienic compounds (Scheme 2) [52]. The reaction course is essential for directing the process towards the desired exo or endo isomer, in compliance with the required stereochemistry of the final product. For the intermolecular enyne metathesis reaction, the double bond of the alkene is

• contrast to the majority of steroids that are trans-fused, rhodexin A comprises cis-fused AB and CD rings. By carefully selecting the reaction conditions, they managed to impose this stereochemistry in all synthetic steps participating in the construction of the tetracyclic ring system of rhodexin A

Recent advances in Cu-catalyzed C(sp³)–Si and C(sp³)–B bond formation

• Balaram S. Takale,
• Ruchita R. Thakore,
• Elham Etemadi-Davan and
• Bruce H. Lipshutz

Beilstein J. Org. Chem. 2020, 16, 691–737, doi:10.3762/bjoc.16.67

• to products reflecting a complete inversion of stereochemistry. The screening showed that XPhos-Pd-G2 is the best pre-catalyst for these reactions and it was proposed that the reaction takes place through an SE2 pathway due to coordination of the carbonyl group of the nucleophile to the boronate

Synthesis of organic liquid crystals containing selectively fluorinated cyclopropanes

• Zeguo Fang,
• Nawaf Al-Maharik,
• Peer Kirsch,
• Matthias Bremer,
• Alexandra M. Z. Slawin and
• David O’Hagan

Beilstein J. Org. Chem. 2020, 16, 674–680, doi:10.3762/bjoc.16.65

• isomer 11b for subsequent analysis. Stereoisomer 11a was a crystalline solid and a suitable crystal was subject to X-ray structure analysis and the structure is shown in Scheme 4. In this way the stereochemistry of 11a and 11b could be confirmed unambiguously. Evaluation of liquid crystal candidates 8

• of the parameter was relatively low (Δε = −1.1). Thus the two isomers constitute two different classes of LC materials, entirely as a consequence of stereochemistry. The best compound of this series is 11a and it was of interest to get some insight into its conformational flexibility. Thus, a

• stereochemically clean sample of isomer 11b for experimental evaluation, theory predicts that it will have a modest negative dielectric value, indicating the importance of stereochemistry in dictating the class of LC material. We conclude too that the overall performance of prototype LCs 11a and 11b should not be

Towards the total synthesis of chondrochloren A: synthesis of the (Z)-enamide fragment

• Jan Geldsetzer and
• Markus Kalesse

Beilstein J. Org. Chem. 2020, 16, 670–673, doi:10.3762/bjoc.16.64

• (Cmc5) by the groups of Höfle and Reichenbach in 2003 [12]. This PKS/NRPS-derived natural product shows only weak antibiotic effects in agar diffusion tests against Micrococcus luteus, Schizosaccharomyces pombe, Bacillus subtilis and Staphylococcus aureus [12]. The relative and absolute stereochemistry