Identification and removal of a cryptic impurity in pomalidomide-PEG based PROTAC

• Bingnan Wang,
• Yong Lu and
• Chuo Chen

Beilstein J. Org. Chem. 2025, 21, 407–411, doi:10.3762/bjoc.21.28

• of 6 can evade detection if unaware of this issue. However, the amount of 6 can increase to as much as 20% when conducting the reaction at 0.1–0.3 M, the concentrations generally used for preparative work. Notably, because the SNAr reaction of 1 proceeded slowly, 4-(dimethylamino)thalidomide also

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• gradient elution was applied using a mobile phase consisting of solvent A: H2O + 0.1% formic acid (v/v) and solvent B: acetonitrile (MeCN) + 0.1% formic acid (v/v). The gradient started at 5% B, gradually increasing to 100% B over 20 min, followed by a 10 min hold at 100% B, with UV–vis detection in the

Hydrogen-bonded macrocycle-mediated dimerization for orthogonal supramolecular polymerization

• Wentao Yu,
• Zhiyao Yang,
• Chengkan Yu,
• Xiaowei Li and
• Lihua Yuan

Beilstein J. Org. Chem. 2025, 21, 179–188, doi:10.3762/bjoc.21.10

• noncovalent bonding interactions. It also confers on supramolecular assemblies with higher complexity and multilevel ordering [9][10][11], leading to a vast number of applications, for example, for use in detection and separation [12], sensing [13], photocatalysis [14], release [15], and as thermochromic and

Emerging trends in the optimization of organic synthesis through high-throughput tools and machine learning

• Pablo Quijano Velasco,
• Kedar Hippalgaonkar and
• Balamurugan Ramalingam

Beilstein J. Org. Chem. 2025, 21, 10–38, doi:10.3762/bjoc.21.3

• analysis facilitates rapid decision-making, enabling researchers to continuously monitor and analyze data as it is generated and allows for immediate adjustments to process parameters during experiments. (ii) Early detection of trends or anomalies are made possible through real-time analysis, providing

• quantification, and use various quality criteria to curate the compiled data. For the quantification and calibration of chromatographic peaks, the user can either input a peak list containing the retention time window of the target chemicals, or the tool can use an automated peak detection algorithm, removing

• the need of user input. The peak detection algorithm was developed using a loop to attain the user-specified cut-off value of the highest-intensity peak. A new univariate spline is fitted for each iteration, from which the local maxima and minima are determined. Overall, HappyTools showed similar or

Ceratinadin G, a new psammaplysin derivative possessing a cyano group from a sponge of the genus Pseudoceratina

• Shin-ichiro Kurimoto,
• Kouta Inoue,
• Taito Ohno and
• Takaaki Kubota

Beilstein J. Org. Chem. 2024, 20, 3215–3220, doi:10.3762/bjoc.20.267

• MeCN/H2O/TFA 45:55:0.1; flow rate 2.5 mL/min; UV detection at 254 nm), yielding psammaplysin F (2, tR 14 min, 6.9 mg, 0.0056% wet weight) and ceratinadin G (1, tR 56 min, 0.4 mg, 0.00032% wet weight). Ceratinadin G (1): colorless amorphous solid; [α]D27 −71.0 (c 0.02, MeOH); UV (MeOH) λmax, nm: 207 (ε

Investigation of a bimetallic terbium(III)/copper(II) chemosensor for the detection of aqueous hydrogen sulfide

• Parvathy Mini,
• Michael R. Grace,
• Genevieve H. Dennison and
• Kellie L. Tuck

Beilstein J. Org. Chem. 2024, 20, 2818–2826, doi:10.3762/bjoc.20.237

• /bjoc.20.237 Abstract The chemosensor properties of a bimetallic terbium(III)/copper(II) complex functionalized with a 4-(2-pyridyl)-1,2,3-triazole ligand for the detection of Cu2+ ions and, aqueous and gaseous hydrogen sulfide was investigated. The 4-(2-pyridyl)-1,2,3-triazole ligand functions both as

• an antenna chromophore and a receptor for Cu2+ ions; the Cu2+ complex was shown to be a chemosensor for the detection of aqueous hydrogen sulfide. The chemosensor exhibited significant reversibility over multiple cycles, observed with the sequential addition of Na2S followed by Cu2+ ions. The limit

• of detection for aqueous hydrogen sulfide was 0.63 μM (20 ppb). No luminescent changes of the bimetallic terbium(III)/copper(II) complex were observed in the presence of gaseous hydrogen sulfide, and thus this sensor can only be used for the detection of aqueous hydrogen sulfide. Keywords

Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines

• Dmitriy Yu. Vandyshev,
• Daria A. Mangusheva,
• Khidmet S. Shikhaliev,
• Kirill A. Scherbakov,
• Oleg N. Burov,
• Alexander D. Zagrebaev,
• Tatiana N. Khmelevskaya,
• Alexey S. Trenin and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236

• hemisulfate to its basic form in situ. Thin-layer chromatography (TLC) and high-performance liquid chromatography with mass-spectrometric detection (HPLC–MS) were used to monitor the reaction and to identify the products obtained. It should be noted that in the case of HPLC–MS analysis, the signals registered

Interaction of a pyrene derivative with cationic [60]fullerene in phospholipid membranes and its effects on photodynamic actions

• Hayato Takagi,
• Çetin Çelik,
• Ryosuke Fukuda,
• Qi Guo,
• Tomohiro Higashino,
• Hiroshi Imahori,
• Yoko Yamakoshi and
• Tatsuya Murakami

Beilstein J. Org. Chem. 2024, 20, 2732–2738, doi:10.3762/bjoc.20.231

• as a •OH adduct of DMPO (DMPO-OH, Figure 5b(ii)) revealing that electron transfer reaction was also occurring. Using DEPMPO as a spin trapping reagent, detection of O2•– was tried and some radical adducts were detected, but without being clearly identified (Figure 5c(i), (ii)). The reason of the

• inability of O2•– detection is not known at present. Upon addition of dimethyl sulfoxide (DMSO) to this system, an adduct of DEPMPO and •CH3 (DEPMPO-CH3), which was presumably generated from the reaction of •OH and DMSO, was clearly observed, further confirming the generation of •OH (Figure 5b(iii)). At the

The scent gland composition of the Mangshan pit viper, Protobothrops mangshanensis

• Jonas Holste,
• Paul Weldon,
• Donald Boyer and
• Stefan Schulz

Beilstein J. Org. Chem. 2024, 20, 2644–2654, doi:10.3762/bjoc.20.222

• investigated by direct inlet atmospheric solids analysis probe-atmospheric mass spectrometry (ASAP-APCI-MS), which allows the detection of secondary metabolites up to a molecular mass of 1,500 Da, but no additional compounds were detected. A more detailed description of the use of this method in natural

Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

• the primary fibres, however, the discrepancy between cryo-TEM and SEM indicates that SEM was not representative of the fibrous network. The observation of fibres associating in the cryo-TEM as well as the detection of larger aggregates in SEM shows that there also existed some higher-order aggregates

Phenylseleno trifluoromethoxylation of alkenes

• Clément Delobel,
• Armen Panossian,
• Gilles Hanquet,
• Frédéric R. Leroux,
• Fabien Toulgoat and
• Thierry Billard

Beilstein J. Org. Chem. 2024, 20, 2434–2441, doi:10.3762/bjoc.20.207

• nucleophilic than chloride in an aprotic solvent such as acetonitrile. Gratifyingly, an excellent yield was obtained (Table 1, entry 6) without detection of the brominated by-product. To facilitate purification, the amount of DNTFB was reduced to 2 equiv without significantly changing the result (Table 1

Facile preparation of fluorine-containing 2,3-epoxypropanoates and their epoxy ring-opening reactions with various nucleophiles

• Yutaro Miyashita,
• Sae Someya,
• Tomoko Kawasaki-Takasuka,
• Tomohiro Agou and
• Takashi Yamazaki

Beilstein J. Org. Chem. 2024, 20, 2421–2433, doi:10.3762/bjoc.20.206

• detection of benzaldehyde which was considered to be formed by the NaClO-mediated oxidation of benzyl alcohol generated by hydrolysis. Changing the oxidizing reagent to crystalline NaClO·5H2O nicely solved the problem with the realization of 86% isolated yield of 2b by the utilization of this oxidant (2

• in high to excellent yields without detection of any regio- as well as stereoisomers. The chirality contained in amines did not work efficiently for the stereochemical induction of the products (entries 6 and 7 in Table 2). In the case of secondary amines, the sterically demanding dibenzylamine

• (Table 5, entry 3), and 1.6 and 3.2 equiv of CuI and n-C10H21MgBr, respectively, were concluded as the best amounts for the synthesis of the nucleophilic species (entries 3–5). The shorter reaction time led to a slightly better ratio of 11a to 12a with a lower combined yield along with the detection of

Homogeneous continuous flow nitration of O-methylisouronium sulfate and its optimization by kinetic modeling

• Jiapeng Guo,
• Weike Su and
• An Su

Beilstein J. Org. Chem. 2024, 20, 2408–2420, doi:10.3762/bjoc.20.205

• concentration that is too low may fall beneath the detection threshold, compromising the reliability of the experimental data. To strike a balance, the initial concentration of IO was set to 0.5 mol/L in the reaction mixture. In addition, the effect of the molar ratio between the two reactants was examined. As

• was collected and analyzed by high-performance liquid chromatography (HPLC, ThermoFisher Ulcel3000), and the conversion of the samples was derived from the external standard method based on the regression equation of the HPLC standard curve. HPLC detection conditions: C18 column (10 μm, 4.6 × 250 mm

• , Welch Materials Shanghai, China), the mobile phase was 80% MeOH and 20% ultrapure water at a flow rate of 1 mL/min, and the detection wavelength was 195 nm. The conversion of IO was calculated by the following equation: The residence time was calculated as follows: where t is the reaction residence time

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• provide unprecedented depth of proteome coverage and the possibility to detect desired modified peptides with high sensitivity. The chemical ‘linker’ connecting an active compound–protein conjugate with a detection tag is the critical component of all chemical proteomic workflows. In this review, we

• source of information steering the site identifications and increasing the confidence in those identifications in MS-based chemical proteomics. In-gel chemical proteomics The detection of the probe–protein conjugate(s) is based on the enhanced signal stemming from the probe–protein conjugate above the

• background from total protein present in the lysate. The detection can be done in several different ways. To obtain an overview of how many proteins are labeled in total and what is the intensity of the labeling, the probe–protein–tag conjugates are separated on sodium dodecyl sulfate polyacrylamide gel (SDS

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• ]. Docking calculations can be conducted in two distinct ways: blind dockings, which explore the entire protein surface [112], and directed docking, typically employed when prior knowledge of the binding pocket exists and performed within a predefined box. Blind dockings are performed using cavity detection

• programs and online servers, as follows: 1. CB-Dock2 [113]: Cavity-detection guided Blind Docking 2 (https://cadd.labshare.cn/cb-dock2/index.php) is an online protein–ligand docking program designed to perform blind docking at predicted sites instead of the entire surface of a protein. Thus CB-Dock

• automatically recognises putative binding sites to determine their centre and size, with the aim to adjust the docking box to suit specific query ligands. Finally, molecular docking calculations are performed with Autodock Vina (see below). 2. Fpocket [114]: It is an open-source pocket detection package based

Allostreptopyrroles A–E, β-alkylpyrrole derivatives from an actinomycete Allostreptomyces sp. RD068384

• Marwa Elsbaey,
• Naoya Oku,
• Mohamed S. A. Abdel-Mottaleb and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2024, 20, 1981–1987, doi:10.3762/bjoc.20.174

• , 5:5, 6:4, 7:3, and 8:2, v/v). The third (4:6) and fourth fractions (5:5) contained the peaks of our target, which were combined (35 mg) and purified by ODS-HPLC (Cosmosil C18 AR-II, 10 × 250 mm, 4 mL/min, UV detection at 254 nm) eluted with 33% MeCN/0.1% HCO2H solution to yield 1 (1.2 mg, tR 10.1

Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

• Moisés Alejandro Alejo Hernandez,
• Katia Pamela Villavicencio Sánchez,
• Rosendo Sánchez Morales,
• Karla Georgina Hernández-Magro Gil,
• David Silverio Moreno-Gutiérrez,
• Eddie Guillermo Sanchez-Rueda,
• Yanet Teresa-Cruz,
• Brian Choi,
• Armando Hernández Garcia,
• Alba Romero-Rodríguez,
• Oscar Juárez,
• Siseth Martínez-Caballero,
• Mario Figueroa and
• Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

• enzymes from the clostridial clade were downloaded from the BV-BRCPATRIC platform in FASTA format. Subsequently, the genomes were analyzed using AntiSMASH 6.0 [3] with the following parameters: Detection stringency: relaxed; additional features: all turned on, including BLAST with known sets, BLAST of

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• through alumina or molecular sieves-containing cartridges using a solvent purificator MBRAUN SPS-800. All the reactions with azobenzene-containing substrates were carried out in the dark. Reactions were monitored by TLC on Silica Gel 60F-254 plates with detection by UV (254 nm or 365 nm) or by spraying

• with 10% H2SO4 in EtOH and heating about 30 s at 400–600 °C. Column chromatography purification was performed on CombiFlash® Rf+ and RediSep® RF or RF Gold normal phase silica columns (with UV detection at 254 and 350 nm for all azobenzene derivatives), or by flash column chromatography employing

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis

• Johannes Rocker,
• Till J. B. Zähringer,
• Matthias Schmitz,
• Till Opatz and
• Christoph Kerzig

Beilstein J. Org. Chem. 2024, 20, 1236–1245, doi:10.3762/bjoc.20.106

• recorded with an LFP setup using 355 nm pulses (20 mJ) of ≈5 ns duration (see Supporting Information File 1 for experimental details). A delay of 250 ns was used between excitation and detection, which is sufficiently long to avoid the detection of the singlet-excited state (Figure 1B, black). Two broad TA

• in equilibrium with the dimeric solvent radical anion in MeCN, it weakly absorbs in our detection window and this species is rather short-lived compared to the triplet as well as the radical cation [71]. The oscillator strengths for the electronic transitions of 3Aza-H (purple) and the radical cation

• contribution of the radical cation to the TA signal at 640 nm is only minor, which allows us to estimate a triplet lifetime of ≈28 µs at this detection wavelength. Based on our observations, an isolated triplet spectrum can be obtained from the spectral difference between the black and the red spectrum in

Kinetically stabilized 1,3-diarylisobenzofurans and the possibility of preparing large, persistent isoacenofurans with unusually small HOMO–LUMO gaps

• Qian Liu and
• Glen P. Miller

Beilstein J. Org. Chem. 2024, 20, 1099–1110, doi:10.3762/bjoc.20.97

• modified cardboard box were utilized for detection of TLC spots. Melting points were determined in open capillary tubes using a Mel-Temp apparatus, and are uncorrected. Proton nuclear magnetic resonance (1H NMR) spectra and carbon nuclear magnetic resonance (13C NMR) spectra were recorded on either a

A Diels–Alder probe for discovery of natural products containing furan moieties

• Alyssa S. Eggly,
• Namuunzul Otgontseren,
• Carson B. Roberts,
• Amir Y. Alwali,
• Haylie E. Hennigan and
• Elizabeth I. Parkinson

Beilstein J. Org. Chem. 2024, 20, 1001–1010, doi:10.3762/bjoc.20.88

• supernatant. There are two main types of molecular probes based on their detection methods: imaging and UV–vis (Figure 2A). An imaging probe contains a mass spectrometry (MS) tag, oftentimes a halogen with a distinct isotopic ratio such as chlorine or bromine. A UV–vis probe contains a UV-tag, such as an

• natural products containing furan moieties, it was tested with crude cell supernatants. Experiments were first performed to determine the limit of detection of the cycloadduct in the cell extracts when run on a UPLC-MS (Figure S23 in Supporting Information File 1). Specifically, a cell supernatant from a

• determine the limit of detection for both the starting material 14, as well as the cycloadduct product in the complete cell supernatant. The reactions were run at various concentrations of compound 14 ranging from 71 mM to 17 µM. Gratifyingly, the cycloadduct has 260-fold increase in sensitivity compared to

Carbonylative synthesis and functionalization of indoles

• Alex De Salvo,
• Raffaella Mancuso and
• Xiao-Feng Wu

Beilstein J. Org. Chem. 2024, 20, 973–1000, doi:10.3762/bjoc.20.87

• -arylindoles by reductive carbonylation of unfunctionalized nitroarenes in the presence of arylalkynes and Pd(phen)2(BF4)2 as catalyst has been demonstrated by Cenini's group. The reaction was regioselective, with no detection of 2-arylindole byproducts. No prefunctionalization of the ortho position of the

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• allows for release and subsequent detection of heme-ligated iron [47]. Protein concentration was determined using bicinchoninic acid protein quantification assay (Pierce). The oligomeric state was determined by processing the protein through Superdex 200 Increase 10/300 GL analytical size exclusion

Discovery and biosynthesis of bacterial drimane-type sesquiterpenoids from Streptomyces clavuligerus

• Dongxu Zhang,
• Wenyu Du,
• Xingming Pan,
• Xiaoxu Lin,
• Fang-Ru Li,
• Qingling Wang,
• Qian Yang,
• Hui-Min Xu and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2024, 20, 815–822, doi:10.3762/bjoc.20.73

• positions of drimenol (Figure 3d). However, the remaining two P450 enzymes, CavE and CavG, appear to be non-functional either in the native S. clavuligerus or heterologous expression systems. Given the detection of two terpene cyclases (CavC and CavF) and the exclusive DMTs generated, we also speculated

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• . Sixteen of the abovementioned strains were randomly selected and cultured on five different media to obtain metabolic profile data according to culture temperature. This analysis resulted in the detection of newly isolated metabolites, metabolites exhibiting enhanced production, metabolites exhibiting