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

• and conformational errors over time and resolution. Conclusion In conclusion, the new Privateer database encompasses the carbohydrate validation capabilities of Privateer in an easily accessible pre-prepared form. The database contains all validation metrics calculated by Privateer as well as

• in the deposited model. The table contains information of the carbohydrate type, PDB code, linkage, frequency, and resolution, as well as a link to the Privateer database report for each PDB entry. Plot showing trends in deposition in the PDB over time from 1975 to the present. Grey bars show the

Synthesis and properties of 6-alkynyl-5-aryluracils

• Ruben Manuel Figueira de Abreu,
• Till Brockmann,
• Alexander Villinger,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 898–911, doi:10.3762/bjoc.20.80

• spectra were recorded on a Cary 60 UV–vis spectrophotometer and emission spectra were recorded on an Agilent Cary Eclipse fluorescence spectrophotometer. Basic and high-resolution mass spectra (MS/HRMS) were measured on instruments coupled to a preceding gas chromatograph (GC) or liquid chromatograph (LC

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari

• Fumito Sato,
• Terutaka Sonohara,
• Shunta Fujiki,
• Akihiro Sugawara,
• Yohei Morishita,
• Taro Ozaki and
• Teigo Asai

Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65

• GGPP, followed by hydrolysis by acid phosphatase. GC–MS analysis revealed that AsCPS synthesizes the same product to ObCPS_11g (see Supporting Information File 1, Figure S4A and B). It should be noted that the stereochemistry of CPP needs further verification due to the lack of chiral resolution of our

Enhanced reactivity of Li⁺@C₆₀ toward thermal [2 + 2] cycloaddition by encapsulated Li⁺ Lewis acid

• Hiroshi Ueno,
• Yu Yamazaki,
• Hiroshi Okada,
• Fuminori Misaizu,
• Ken Kokubo and
• Hidehiro Sakurai

Beilstein J. Org. Chem. 2024, 20, 653–660, doi:10.3762/bjoc.20.58

• mode high-resolution matrix-assisted laser desorption ionization mass spectra showed the formation of the monoadducts at m/z 875.10431 (5a) and 861.08866 (5b), which were assigned to each molecular ion ([M]+ calcd for C70H12OLi (5a): 875.10427 and C69H10OLi (5b): 861.08862, respectively). The UV–vis

• , external standard), and carbon of the solvent for 13C (53.84 ppm, CD2Cl2). High-resolution matrix-assisted laser desorption ionization (HR-MALDI) mass spectra were obtained on a Bruker solariX 12T mass spectrometer with dithranol as a matrix. UV–vis absorption spectra were measured on a JASCO V-670 and a

Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae

• Jia Tang,
• Yixiang Zhang and
• Yudai Matsuda

Beilstein J. Org. Chem. 2024, 20, 638–644, doi:10.3762/bjoc.20.56

• four enzymes in the Aspergillus oryzae NSARU1 strain [19]. Consequently, the A. oryzae transformant yielded two metabolites 1 and 2, which were absent in the host strain (Figure 2B, traces i and ii). Although we were unable to isolate compounds 1 and 2 because of their instability, high-resolution mass

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

Mono or double Pd-catalyzed C–H bond functionalization for the annulative π-extension of 1,8-dibromonaphthalene: a one pot access to fluoranthene derivatives

• Nahed Ketata,
• Linhao Liu,
• Ridha Ben Salem and
• Henri Doucet

Beilstein J. Org. Chem. 2024, 20, 427–435, doi:10.3762/bjoc.20.37

• III 400 MHz and Bruker Avance neo 500 MHz spectrometers. High-resolution mass spectra were measured on a Bruker MaXis 4G spectrometer. Melting points were determined with a Kofler hot bench system. Chromatography purifications were performed using a CombiFlash NextGen 300 with Buchi FlashPure

Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters

• Carlos R. Azpilcueta-Nicolas and
• Jean-Philip Lumb

Beilstein J. Org. Chem. 2024, 20, 346–378, doi:10.3762/bjoc.20.35

• substitution with alcohol 94 in the presence of lithium phthalimide 95 leads to product 96 and turns over the catalytic cycle. Importantly, species 93 can be detected by high resolution mass spectrometry, when the reaction is carried out without nucleophile and using stoichiometric amounts of PTH1. H. Fu and

Discovery of unguisin J, a new cyclic peptide from Aspergillus heteromorphus CBS 117.55, and phylogeny-based bioinformatic analysis of UngA NRPS domains

• Sharmila Neupane,
• Marcelo Rodrigues de Amorim and
• Elizabeth Skellam

Beilstein J. Org. Chem. 2024, 20, 321–330, doi:10.3762/bjoc.20.32

• min−1). High-resolution mass spectra were recorded on an ABSciex TripleTOF 6600+ mass spectrometer. Direct infusion of compounds 1 and 2 through the high-resolution mass spectrometry (HRMS) was performed using a flow rate of 10 μL min−1 which the samples were diluted at 10 ppm with a solution of MeCN

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

• confirmed and quantified this binding specificity in solution. Finally, we solved the high-resolution structure of the CMA1 N-terminal domain using X-ray crystallography, supporting our functional findings at the molecular level. Our study provides a comprehensive understanding of CMA1, laying the

• experiments, thermal shift assays, and high-resolution X-ray crystallography not only confirms its classification as a functional R-type lectin but also provides a deep dive into its unique glycan-binding profile and high-resolution 3D structure. Overall, we present a deeply characterized new lectin with a

• for the N-terminal domain (Figure S3, Supporting Information File 2). High-resolution diffraction of the crystals allowed us to solve the CMA1-Nter structure in complex with LacNAc at 1.3 Å and GalNAc at 1.55 Å (see data and refinement statistics in Table 1). All residues of the N-terminal construct

Synthesis of π-conjugated polycyclic compounds by late-stage extrusion of chalcogen fragments

• Aissam Okba,
• Pablo Simón Marqués,
• Kyohei Matsuo,
• Naoki Aratani,
• Hiroko Yamada,
• Gwénaël Rapenne and
• Claire Kammerer

Beilstein J. Org. Chem. 2024, 20, 287–305, doi:10.3762/bjoc.20.30

• tip of a scanning tunneling microscope (STM) [11][34][35][36]. Owing to the subatomic resolution now available with scanning probe microscopy techniques (STM and non-contact atomic force microscopy, nc-AFM), the “precursor approach” has opened the way for in-depth structural and electronic

• -resolution STM and AFM images, revealing the linear fusion of benzene rings with a zigzag edge (Figure 3), and their electronic properties were investigated at the single-molecule scale, with a particular attention devoted to the evolution of the HOMO–LUMO gap along the incremental series of acenes

• domains were employed to resolve the Au(111) lattice as well as the adsorbed molecule with atomic resolution. Adapted with permission from [85], J. Krüger et al., “Decacene: On-Surface Generation”, Angew. Chem., Int. Ed., with permission from John Wiley and Sons. Copyright © 2017 Wiley-VCH Verlag GmbH

Chiral phosphoric acid-catalyzed transfer hydrogenation of 3,3-difluoro-3H-indoles

• Yumei Wang,
• Guangzhu Wang,
• Yanping Zhu and
• Kaiwu Dong

Beilstein J. Org. Chem. 2024, 20, 205–211, doi:10.3762/bjoc.20.20

• great attention in organic synthesis. Various methods [9], including reductive hydrogenation [10][11], kinetic resolution [12][13][14], functionalization of indole [15], and de novo construction of chiral 2-substituted indolines, have been developed [16][17][18][19][20]. In recent years, the metal

Comparison of glycosyl donors: a supramer approach

• Anna V. Orlova,
• Nelly N. Malysheva,
• Maria V. Panova,
• Nikita M. Podvalnyy,
• Michael G. Medvedev and
• Leonid O. Kononov

Beilstein J. Org. Chem. 2024, 20, 181–192, doi:10.3762/bjoc.20.18

• treated with 90% aq trifluoroacetic acid in CH2Cl2 to give diol 7 (70% yield) that was formed due to migration of a chloroacetyl group from O-7 to O-9. The structure of diol 7 was established by NMR spectroscopy, high-resolution mass spectrometry and X-ray diffraction analysis (see the Experimental

• CFCl3 (δF 0.0). Assignments of the signals in the NMR spectra were performed using 2D-spectroscopy (COSY, HSQC, HMBC) and DEPT-135 experiments. For the copies of NMR spectra for all new compounds see Supporting Information File 1. High resolution mass spectra (electrospray ionization, HRESIMS) were

Synthesis of the 3’-O-sulfated TF antigen with a TEG-N₃ linker for glycodendrimersomes preparation to study lectin binding

• Mark Reihill,
• Hanyue Ma,
• Dennis Bengtsson and
• Stefan Oscarson

Beilstein J. Org. Chem. 2024, 20, 173–180, doi:10.3762/bjoc.20.17

• reported to one decimal point unless an additional digit was required to distinguish overlapping peaks. Software for data processing: MestReNova, version 11.0.0–17609 (MestReLab Research S.L.). High-resolution mass spectrometry (HRMS) data were recorded on a Waters Micromass LCT LC–TOF instrument using

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• in TCBDs and DCNQs and their optical resolutions were first realized in 2010 through their conjugation with methylated fullerenes, as shown in Figure 2 [130]. The optical resolution was realized using a chiral high-performance liquid chromatography (HPLC) system equipped with an (S,S)-WHELK-O1 column

• when the TCBD moiety was incorporated at the axial position of the subphthalocyanine (SubPc) core (Figure 3) [131]. Axially chiral SubPc–TCBD–aniline conjugates 59 and 60 were characterized via optical-resolution analysis through chiral HPLC using a Chiralpak IC column. The researchers unequivocally

• types of subporphyrin derivatives 61 and 62, wherein the subporphyrin skeleton was functionalized at its meso or axial position with the TCBD moiety (Figure 3). Although the optical resolution of 61 failed, they succeeded in achieving the optical resolution of 62 via chiral HPLC using a Chiralpak IC

Visible-light-induced radical cascade cyclization: a catalyst-free synthetic approach to trifluoromethylated heterocycles

• Chuan Yang,
• Wei Shi,
• Jian Tian,
• Lin Guo,
• Yating Zhao and
• Wujiong Xia

Beilstein J. Org. Chem. 2024, 20, 118–124, doi:10.3762/bjoc.20.12

• NMR (Figure S3 in Supporting Information File 1) [30] and high-resolution mass spectrometry. You and co-workers proposed a reaction pathway involving the combination of the indole substrate and Umemoto’s reagent to form an electron donor–acceptor (EDA) complex [31]. We excluded the possibility of an

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• current: 3.5 kV, capillary temperature: 300 °C, capillary voltage: 45 V, injection rate: 5 μL/min, scanning range: 150−750 m/z, and resolution: ultra-high) and processed with the software Xcalibur. The CHNS analysis data were determined in-house with a HEKAtech EuroEA combustion analyzer. The melting

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• molecules on surfaces like graphene or carbon nanotubes have allowed the scientific community to visualize at atomic resolution the structural changes of molecules in situ by single-molecule atomic-resolution real-time TEM imaging (SMART-TEM) [1][2][3][4][5]. Since the initial discovery [2], many movies

Optimizing reaction conditions for the light-driven hydrogen evolution in a loop photoreactor

• Pengcheng Li,
• Daniel Kowalczyk,
• Johannes Liessem,
• Mohamed M. Elnagar,
• Dariusz Mitoraj,
• Radim Beranek and
• Dirk Ziegenbalg

Beilstein J. Org. Chem. 2024, 20, 74–91, doi:10.3762/bjoc.20.9

• substrate and allowed to dry at room temperature. To improve the conductivity and achieve higher resolution SEM imaging, a 20 nm thick layer of Au was sputtered onto the sample surface. For EDS mapping, the samples were not sputtered with Au to avoid interference during the determination of Pt. UV–vis

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

• and zero-filling are now applied automatically by common software packages using presets. While this provides convenience, it also leads to a loss of knowledge for new users on their impact on properties such as resolution and signal-to-noise ratio and the balance between them. For teaching labs

Cycloaddition reactions of heterocyclic azides with 2-cyanoacetamidines as a new route to C,N-diheteroarylcarbamidines

• Pavel S. Silaichev,
• Tetyana V. Beryozkina,
• Vsevolod V. Melekhin,
• Valeriy O. Filimonov,
• Andrey N. Maslivets,
• Vladimir G. Ilkin,
• Wim Dehaen and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2024, 20, 17–24, doi:10.3762/bjoc.20.3

• effect on the yield of the final compounds 3 observed. The structures of compounds 3a–u were confirmed by IR, 1H and 13C NMR spectroscopy (Figures S1‒S44 in Supporting Information File 1) as well as by high-resolution mass spectrometry (HRMS). X-ray data obtained for compound 3g gave us final proof of

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

• result indicated that CmaG is a component of Cma PKS. From NMR analysis and high-resolution (HR)MS analysis ([M + H]+ ion at m/z = 222.0766, which corresponds to C11H12NO4+, calcd. 222.0761) of purified 6, the structure of 6 was determined as N-acetyl-3-aminocoumaric acid (Figures S9–S13 and Table S1 in

Substituent-controlled construction of A₄B₂-hexaphyrins and A₃B-porphyrins: a mechanistic evaluation

• Seda Cinar,
• Dilek Isik Tasgin and
• Canan Unaleroglu

Beilstein J. Org. Chem. 2023, 19, 1832–1840, doi:10.3762/bjoc.19.135

• certain time intervals within 2 hours and examined by ESI LC–MS. Throughout the high-resolution electrospray-ionization time-of-flight (HRESI–TOF) mass analysis of the reaction mixture at 0 °C, the following peaks were observed: m/z = 246.0366 ([M + H]+ calcd for C11H5F5N, 246.0337), m/z = 857.1468 ([M

• predominately observed (Figure S48 in Supporting Information File 1). According to high-resolution electrospray-ionization time-of-flight (HRESI–TOF) analysis, at the beginning of the reaction, mass peaks of intermediates II and IV arose as a result of tripyrrane 1 addition to N-tosylimine 2d. Further

• aryl-bearing N-tosylimines, but a 4-(CF3)C6H4 group led only to the formation of porphyrin compounds. A mechanistic perspective for the formation of porphyrinic products was acquired via a set of high-resolution mass analyses of selected model reactions. The results indicated that azafulvene-ended

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• ), thus providing valuable additional isomer resolution [4]. We demonstrated that this multidimensional MS–IR molecular fingerprint is unique to each carbohydrate building block and can be used to resolve their full sequence, including their monosaccharide content and the detail of their linkages

• a change in binning. To take this into account, data were binned with downgraded resolution then re-binned with 1 cm−1 step. The down sampling factor was randomly picked in a range from 1 to 5. Small variations of the calibration of the laser wavenumber may occur from day to day, leading to a shift

• a maximum accuracy variation of 0.5%. We demonstrated that the neural network is suitable for MS–IR classification in experimental conditions with variable resolution, noise or energy jitter. The question remains on how to discriminate unknown molecules or to identify problematic spectra, such as

A novel recyclable organocatalyst for the gram-scale enantioselective synthesis of (S)-baclofen

• Gyula Dargó,
• Dóra Erdélyi,
• Balázs Molnár,
• Péter Kisszékelyi,
• Zsófia Garádi and
• József Kupai

Beilstein J. Org. Chem. 2023, 19, 1811–1824, doi:10.3762/bjoc.19.133

• on a Bruker 300 Avance spectrometer (at 300 and 75.5 MHz for the 1H and 13C spectra, respectively) or on a Bruker Avance III HD (at 600 MHz for 1H and at 150 MHz for 13C spectra) at specified temperatures. High-resolution MS was measured on a Bruker MicroTOF II instrument using positive electrospray