Optimized synthesis of aroyl-S,N-ketene acetals by omission of solubilizing alcohol cosolvents

• Julius Krenzer and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2025, 21, 1201–1206, doi:10.3762/bjoc.21.97

• presumed byproducts in the addition–elimination sequence in the presence of an excess of ethanol as a cosolvent are the ethyl ester formed by Einhorn acylation [7] of the acid chloride under the standard conditions and deep colored polar byproducts (according to TLC detection) that arise from self

Harnessing tethered nitreniums for diastereoselective amino-sulfonoxylation of alkenes

• Shyam Sathyamoorthi,
• Appasaheb K. Nirpal,
• Dnyaneshwar A. Gorve and
• Steven P. Kelley

Beilstein J. Org. Chem. 2025, 21, 947–954, doi:10.3762/bjoc.21.78

• single regioisomer and diastereomer of B was formed (within the limits of 1H NMR detection), attesting to very selective reactivity. Here and in related projects, we found that many I(III) sources could generate a nitrenium ion, including iodosobenzene (PhIO) and iodomesitylene diacetate. However, unless

A convergent synthetic approach to the tetracyclic core framework of khayanolide-type limonoids

• Zhiyang Zhang,
• Jialei Hu,
• Hanfeng Ding,
• Li Zhang and
• Peirong Rao

Beilstein J. Org. Chem. 2025, 21, 926–934, doi:10.3762/bjoc.21.75

• single product, with no detection of 34 (Table 1, entry 11). This result presumably arises from the minimization of dipole–dipole repulsions between the carbonyl of the dienone moiety and the C14-OMe within the desired transition state (more details were discussed in our group’s previous work [29

Dicarboxylate recognition based on ultracycle hosts through cooperative hydrogen bonding and anion–π interactions

• Wen-Hui Mi,
• Teng-Yu Huang,
• Xu-Dong Wang,
• Yu-Fei Ao,
• Qi-Qiang Wang and
• De-Xian Wang

Beilstein J. Org. Chem. 2025, 21, 884–889, doi:10.3762/bjoc.21.72

• ]. Additionally, dicarboxylates like tartrate, adipate or citrate are widely used as food additives [23][24]. Furthermore, functional materials based on dicarboxylates are expected to play a significant role in future technologies [25]. Therefore, the recognition and detection of dicarboxylates are of great

Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• fluorescent protein (GFP), has revolutionized genetics by providing highly accurate real-time detection of fusion proteins in vitro and in vivo [1]. Pioneering work on GFP-tagged proteins for real-time monitoring of gene expression was first reported by Chalfie and co-workers in 1994 [2]. For a long time

Asymmetric synthesis of fluorinated derivatives of aromatic and γ-branched amino acids via a chiral Ni(II) complex

• Maurizio Iannuzzi,
• Thomas Hohmann,
• Michael Dyrks,
• Kilian Haoues,
• Katarzyna Salamon-Krokosz and
• Beate Koksch

Beilstein J. Org. Chem. 2025, 21, 659–669, doi:10.3762/bjoc.21.52

• ) was used. MeCN/MeOH/H2O mixture with 50 mM formic acid and 25 mM diethylamine was used as eluent. A flow rate of 0.5 mL/min was applied and the detection of the respective compounds occurred at 280 nm. Data analysis was carried out with the EZChrom ELITE software (version 3.3.2 SP2, Agilent). Ni(II

Photocatalyzed elaboration of antibody-based bioconjugates

• Marine Le Stum,
• Eugénie Romero and
• Gary A. Molander

Beilstein J. Org. Chem. 2025, 21, 616–629, doi:10.3762/bjoc.21.49

• antibodies in disease detection and treatment is that they are adorned with functional units (e.g., fluorophores, radionuclides, toxic payloads) that must be efficiently and selectively installed through compatible synthetic methods. Dozens of ADCs have been approved for clinical uses, and to date all are

Semisynthetic derivatives of massarilactone D with cytotoxic and nematicidal activities

• Rémy B. Teponno,
• Sara R. Noumeur and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 607–615, doi:10.3762/bjoc.21.48

• -UV system [column 2.1 × 50 mm, 1.7 μm, C18 Acquity UPLC BEH (Waters), solvent A: H2O + 0.1% formic acid; solvent B: ACN + 0.1% formic acid, gradient: 5% B for 0.5 min, increasing to 100% B in 19.5 min, maintaining 100% B for 5 min, RF = 0.6 mL/min, UV–vis detection 200–600 nm]. NMR spectra were

• ), solvent A: H2O + 0.1% formic acid; solvent B: acetonitrile (ACN) + 0.1% formic acid, gradient: 5% B for 0.5 min, increasing to 100% B in 20 min, maintaining isocratic conditions at 100% B for 10 min, flow = 0.6 mL/min, UV–vis detection 190–600 nm]. Preparative HPLC was achieved at room temperature on an

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

Tailored charge-neutral self-assembled L₂Zn₂ container for taming oxalate

• David Ocklenburg and
• David Van Craen

Beilstein J. Org. Chem. 2024, 20, 3007–3015, doi:10.3762/bjoc.20.250

• development of effective receptors for their detection. In particular, the smallest dicarboxylate, oxalate, presents a significant importance due to its widespread presence in nature and its association with various diseases. Yet, very little attention was devoted to the recognition of oxalate with metal

• calcium oxalate [6][7][8]. Unsurprisingly, the detection of oxalate was studied with numerous classic organic receptors involving acyclic hosts [9][10][11][12][13][14][15][16][17][18][19][20][21], macrocycles [22][23][24][25][26][27][28][29][30][31][32][33], and cages [34][35][36][37][38][39][40][41][42

• disassembly of the host structure. Guest-driven decomplexation events can also be utilized as detection method [65][68][69][70][71][72][73] but such processes are generally not desired for containers or cages because guest binding is anticipated to take place by encapsulation while the structure of the

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