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

• . Chemical reagents and solvents were purchased in the highest available quality from commercial suppliers (Merck/Sigma-Aldrich, ABCR) and used without further purification. Analytical thin-layer chromatography (TLC) was performed on Macherey-Nagel Polygram® SIL G/UV254 plates. 0.2 mm silica gel 60 for

• Na2SO4 and concentrated to dryness. Finally, the crude compound was purified via silica gel chromatography using 50–70% ethyl acetate in cyclohexane as gradient. General procedure B. The product obtained in general procedure A was dissolved in ethanol mixed with 4-cyanophenylacetonitrile and 8 drops of

• obtained in general procedure B was dissolved in dichloromethane and cooled to 0 °C under argon atmosphere. Then, triphenylphosphine and carbon tetrabromide were added and stirred at room temperature for two hours. Afterwards, the entire mixture was loaded on a silica gel column and eluted with 100

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 carried out on aluminum plates coated with silica gel 60 F254 (Merck, Darmstadt, Germany). The TLC plates were analyzed using UV light at 254 nm. Flash chromatography was performed on silica gel 60 M from Macherey-Nagel (grain size of 40−63 μm). The conditions are given in the form “(A/B = a:b

• , Torrance, CA, USA) was used. H2O and MeCN, both containing 0.1% (v/v) TFA, served as eluents. Fmoc-protected amino acids were detected at 220 nm. For a chiral analysis, a CHIRALPAK ZWIX(−) column ((R,R)-ACHSA immobilized on 3 μm silica gel, 250 × 4 mm, Chiral Technologies Europe, Illkirch Cedex, France

Entry to 2-aminoprolines via electrochemical decarboxylative amidation of N‑acetylamino malonic acid monoesters

• Olesja Koleda,
• Janis Sadauskis,
• Darja Antonenko,
• Edvards Janis Treijs,
• Raivis Davis Steberis and
• Edgars Suna

Beilstein J. Org. Chem. 2025, 21, 630–638, doi:10.3762/bjoc.21.50

• quench of a transient N-acyliminium species was found to be a major side-reaction as evidenced by the formation of an open-chain hemiaminal 10a (the hemiaminal could not be isolated due to the instability on silica gel). Screening of other supporting electrolytes revealed that basic salts (K2CO3, Na2CO3

Deep-blue emitting 9,10-bis(perfluorobenzyl)anthracene

• Long K. San,
• Sebastian Balser,
• Brian J. Reeves,
• Tyler T. Clikeman,
• Yu-Sheng Chen,
• Steven H. Strauss and
• Olga V. Boltalina

Beilstein J. Org. Chem. 2025, 21, 515–525, doi:10.3762/bjoc.21.39

• Barnstead NANOpure Ultrapure Water system, producing water with a final resistance of at least 18 MΩ); and silica gel (Sigma-Aldrich, 70–230 mesh, 60 Å). For HPLC separations: acetonitrile (Fisher Scientific ACS grade); toluene (Fisher Scientific, ACS grade); and heptane (Mallinckrodt Chemicals, ACS grade

• were extracted with Et2O and washed four to six times with doubly distilled water removing the aqueous layer each time. Anhydrous MgSO4 was added to the organic layer and passed through silica gel with DCM as the eluent. The organic layer was then concentrated to dryness. Yield (isolated): 9-H-10-BnF

Unprecedented visible light-initiated topochemical [2 + 2] cycloaddition in a functionalized bimane dye

• Metodej Dvoracek,
• Brendan Twamley,
• Mathias O. Senge and
• Mikhail A. Filatov

Beilstein J. Org. Chem. 2025, 21, 500–509, doi:10.3762/bjoc.21.37

• chlorine gas, with the reaction conducted by stirring the pyrazolinone with TCICA in DCM for 18 hours. Bimanes can be purified easily using column chromatography with silica gel as the stationary phase, with the compounds Cl2B, Me2B, and Me4B only requiring neat DCM as the eluent. After chromatographic

Organocatalytic kinetic resolution of 1,5-dicarbonyl compounds through a retro-Michael reaction

• James Guevara-Pulido,
• Fernando González-Pérez,
• José M. Andrés and
• Rafael Pedrosa

Beilstein J. Org. Chem. 2025, 21, 473–482, doi:10.3762/bjoc.21.34

• its enantioselectivity, aliquots of the reaction mixture were taken at defined time intervals and analyzed by HPLC using a chiral column after passing them through a short silica gel pad. Some interesting conclusions can be made from the data in Table 1. Firstly, the retro-Michael reaction occurs, to

• a one dm path length, and concentration was given in grams per 100 mL. TLC analysis was performed on glass-backed plates coated with silica gel 60 and an F254 indicator and visualized by either UV irradiation or staining with phosphomolybdic acid solution. Flash chromatography uses silica gel (230

• added to a solution of enal (2.5 mmol) and 2-phenylacetophenone (3.0 mmol) in dichloromethane (20 mL), and the mixture was stirred until the reaction was completed. Then, the solvent was removed under reduced pressure, and the residue was purified by silica gel column chromatography using hexane/ethyl

Photomechanochemistry: harnessing mechanical forces to enhance photochemical reactions

• Francesco Mele,
• Ana M. Constantin,
• Andrea Porcheddu,
• Raimondo Maggi,
• Giovanni Maestri,
• Nicola Della Ca’ and
• Luca Capaldo

Beilstein J. Org. Chem. 2025, 21, 458–472, doi:10.3762/bjoc.21.33

• (9.1) (Scheme 9) [75]. In this case the authors used a ball-mill reactor equipped with a blue LED, and the reaction was run in a glass vial with two transparent PMMA balls. The authors noted that fluorination of the vial and the use of silica gel to adjust texture were needed to prevent reagent

• investigated. When o-terphenyl (10.1) was milled (30 Hz, PTFE balls) and irradiated (λ = 270 nm) in the presence of silica gel (bulking agent), I2 (1 equiv) as an oxidant, and K2CO3 (1 equiv) as a base in the presence of toluene, the expected product 10.2 was obtained in 81% yield after isolation upon 181 h of

Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• able to adapt this chemistry to work in situ, allowing soluble metastable imine frameworks to be trapped as amides [38]. The adapted cages were soluble, and were now stable enough to be purified by gel-permeation (size-exclusion) chromatography (useful when precipitation is not possible), which is

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

• to generate an inseparable byproduct. By contrast, the byproduct derived from Boc-protected amines has a significantly different retention time on HPLC and could be removed by regular silica gel chromatography. Because the formation of 5‒7 posts a significant purification challenge, we sought to

• silica gel column chromatography. The LUMO and electrostatic charges of thalidomide and its derivatives by DFT calculation at the ωB97X-D/6-311+G** level. The synthetic route for iVeliparib-AP6. The conversion of byproduct 6 to 10 to facilitate its removal. Effects of the length and functionalization of

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

• (15 g) was analyzed by LC–MS. Thereafter, it was fractionated by vacuum liquid chromatography (VLC) using silica gel as a stationary phase. The elution procedure was performed using a chromatographic scheme of two different gradients as follows: 1) n-heptane/EtOAc (1:0, 7:3, 3:7, 0:1) followed by

Three-component reactions of conjugated dienes, CH acids and formaldehyde under diffusion mixing conditions

• Dmitry E. Shybanov,
• Maxim E. Kukushkin,
• Eugene V. Babaev,
• Nikolai V. Zyk and
• Elena K. Beloglazkina

Beilstein J. Org. Chem. 2025, 21, 262–269, doi:10.3762/bjoc.21.18

• days (TLC or NMR control). After completion of the reaction, the solvent was removed under reduced pressure, and the residue was purified by column chromatography on silica gel using chloroform as eluent. ((1S,4S)-Bicyclo[2.2.1]hept-5-ene-2,2-diyl)bis(phenylmethanone) (8) and phenyl((4aR,7aS)-2-phenyl

Effect of substitution position of aryl groups on the thermal back reactivity of aza-diarylethene photoswitches and prediction by density functional theory

• Misato Suganuma,
• Daichi Kitagawa,
• Shota Hamatani and
• Seiya Kobatake

Beilstein J. Org. Chem. 2025, 21, 242–252, doi:10.3762/bjoc.21.16

• solution, extracted with ether, washed with brine, dried over MgSO4, filtered, and concentrated in vacuo. The crude product was purified by column chromatography on silica gel using n-hexane and ethyl acetate 95:5 to give 1.4 g of I2(a) in 50% yield. 1H NMR (300 MHz, CDCl3, TMS) δ = 2.55 (d, JHF = 3.2 Hz

• brine, dried over MgSO4, filtered, and concentrated in vacuo. The crude product was purified by column chromatography on silica gel using n-hexane to give 2.8 g of I4(a) in 56% yield. 1H NMR (300 MHz, CDCl3, TMS) δ = 2.42 (s, 3H, CH3), 7.29–7.34 (m, 1H, aromatic H), 7.40–7.46 (m, 1H, aromatic H), 7.49

• reaction mixture was neutralized by HCl aqueous solution, extracted with ether, washed with brine, dried over MgSO4, filtered, and concentrated in vacuo. The crude product was purified by column chromatography on silica gel using n-hexane and ethyl acetate 8:2 and recycling HPLC using chloroform as the

Nickel-catalyzed cross-coupling of 2-fluorobenzofurans with arylboronic acids via aromatic C–F bond activation

• Takeshi Fujita,
• Haruna Yabuki,
• Ryutaro Morioka,
• Kohei Fuchibe and
• Junji Ichikawa

Beilstein J. Org. Chem. 2025, 21, 146–154, doi:10.3762/bjoc.21.8

• JMS-T100GCV or a JEOL JMS-T200GC spectrometer. All the reactions were conducted under argon or nitrogen. Materials: Column chromatography was conducted on silica gel (Silica Gel 60 N, Kanto Chemical Co., Inc.). Toluene and N,N-dimethylformamide (DMF) were purified by a solvent-purification system

• . After removal of the solvent under reduced pressure, the residue was purified by silica gel column chromatography (hexane/EtOAc = 10:1) to give 3bb (76 mg, 98%) as a white solid. 1H NMR (500 MHz, CDCl3) δ 8.15 (d, J = 8.2 Hz, 1H), 7.93 (d, J = 8.2 Hz, 1H), 7.75–7.67 (m, 4H), 7.58 (ddd, J = 8.2, 6.9, 1.2

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

• products once experiments are performed. Despite this bottleneck, the landscape is evolving, with various practical tools emerging to streamline purification processes. From prepacked silica gel tubes to the precision semipreparative liquid chromatography and the versatile capabilities of various scavenger

Intramolecular C–H arylation of pyridine derivatives with a palladium catalyst for the synthesis of multiply fused heteroaromatic compounds

• Yuki Nakanishi,
• Shoichi Sugita,
• Kentaro Okano and
• Atsunori Mori

Beilstein J. Org. Chem. 2024, 20, 3256–3262, doi:10.3762/bjoc.20.269

• dichloromethane (2 mL) three times. The combined organic extracts were repeatedly washed with water (20 mL) and brine (20 mL). The organic layer was dried over anhydrous sodium sulfate and concentrated under reduced pressure to give a crude material, which was purified by silica gel column chromatography (hexane

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

• , after which the extract was partitioned between EtOAc and H2O. The EtOAc-soluble fraction was subjected to silica gel column chromatography. A detailed analysis of the 1H NMR spectrum of the fraction eluted after the one containing ceratinadins E and F revealed signals corresponding to psammaplysin F (2

• sponge Pseudoceratina sp. (order Verongida; family Aplysinellidae), collected in Okinawa, Japan (0.4 kg, wet weight), was obtained following the method described in [8]. In a manner similar to [8], a portion of the EtOAc-soluble material (1.45 g) was fractionated by silica gel column chromatography

• [silica gel 60N (spherical, neutral, 40–50 µm), Kanto Chemical Co., Inc.; 38 × 350 mm; eluent CHCl3/MeOH 100:0 to 0:100], yielding 18 fractions (Fr. 1–18). A portion (17.0 mg) of the fraction Fr. 14 (32.5 mg) was further separated by C18 HPLC (COSMOSIL 5C18-AR-II, 10 × 250 mm, Nacalai tesque Inc.; eluent

Direct trifluoroethylation of carbonyl sulfoxonium ylides using hypervalent iodine compounds

• Radell Echemendía,
• Carlee A. Montgomery,
• Fabio Cuzzucoli,
• Antonio C. B. Burtoloso and
• Graham K. Murphy

Beilstein J. Org. Chem. 2024, 20, 3182–3190, doi:10.3762/bjoc.20.263

• vial was quickly capped with a Teflon microwave cap. The reaction was heated to 70 ºC for 10 min. The crude mixture was dissolved with DCM (3 mL), the solvent was removed under reduced pressure to furnish a crude product that was purified by flash column chromatography, using silica gel 60 (200–400

Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• applications of rotaxane-based polymers Polymer materials having rotaxane structures exhibit unique properties compared with conventional materials owing to the higher molecular mobility of the former [76][77][78]. In this regard, one of the most successful material applications is the slide ring gel, which

• consists of the rotaxane crosslinking structure, as a tough material or ultra-stretchable/swelling polymer [79][80]. A typical slide ring gel has a network structure of polyrotaxane, which consists of a linear polymer chain like PEG and many α-CD rings on it, meaning that the crosslinking points are made

• articles have covered the study of slide ring gel, this review does not go into the details of this topic. Meanwhile, the structural control of this slide ring gel has been generally conducted in a rough regulation, meaning further development could be considered by the precise structural control as

gem-Difluorovinyl and trifluorovinyl Michael acceptors in the synthesis of α,β-unsaturated fluorinated and nonfluorinated amides

• Monika Bilska-Markowska,
• Marcin Kaźmierczak,
• Wojciech Jankowski and
• Marcin Hoffmann

Beilstein J. Org. Chem. 2024, 20, 2946–2953, doi:10.3762/bjoc.20.247

• products. These highly stable compounds were isolated after purification on silica gel in good yields (Scheme 2) and characterized by spectroscopic methods. The reaction proceeded with very high Z-stereoselectivity (Scheme 2, compounds 9a–d). In the 19F NMR spectra of crude mixtures, only trace amounts of

C–H Trifluoromethylthiolation of aldehyde hydrazones

• Victor Levet,
• Balu Ramesh,
• Congyang Wang and
• Tatiana Besset

Beilstein J. Org. Chem. 2024, 20, 2883–2890, doi:10.3762/bjoc.20.242

• collected separately, dried over MgSO4, and concentrated in vacuo. The crude was purified by column chromatography on silica gel, flash chromatography to afford the desired product 2–6. State of the art and this work. Reaction conditions: hydrazone (0.3 mmol, 1.0 equiv), NBS (0.33 mmol, 1.1 equiv), in CH3CN

Synthesis of pyrrole-fused dibenzoxazepine/dibenzothiazepine/triazolobenzodiazepine derivatives via isocyanide-based multicomponent reactions

• Marzieh Norouzi,
• Mohammad Taghi Nazeri,
• Ahmad Shaabani and
• Behrouz Notash

Beilstein J. Org. Chem. 2024, 20, 2870–2882, doi:10.3762/bjoc.20.241

• reaction mixture was stirred at temperatures of 100 or 80 °C for 2 h using a magnetic stirrer. After making sure that the reactions were completed (monitored by TLC), the reaction mixture was cooled to ambient temperature. Then, the crude mixture was purified using a silica gel chromatography column and

Synthesis of tricarbonylated propargylamine and conversion to 2,5-disubstituted oxazole-4-carboxylates

• Kento Iwai,
• Akari Hikasa,
• Kotaro Yoshioka,
• Shinki Tani,
• Kazuto Umezu and
• Nagatoshi Nishiwaki

Beilstein J. Org. Chem. 2024, 20, 2827–2833, doi:10.3762/bjoc.20.238

•  3) [13][14]. To a dry THF solution of adduct 4a, butyllithium was added, and the reaction mixture was stirred at −78 °C for 5 min. Following the addition of acetic acid, the reaction mixture was concentrated and subjected to silica gel column chromatography, resulting in the isolation of ethyl 5

• ), the mixture was concentrated under reduced pressure. The residue was purified by column chromatography on silica gel (eluent: hexane/ethyl acetate 70:30, Rf 0.55) to afford diethyl 2-[(4-methylbenzoyl)amino]-2-(phenylethynyl)propanedioate (4a, 122 mg, 0.31 mmol, 78% yield) as yellow oil. 1H NMR (400

• acetic acid (0.1 mL), the solvent was removed under reduced pressure. The residue was purified by column chromatography on silica gel (eluent: hexane/ethyl acetate 70:30, eluent for TLC: hexane/ethyl acetate 80:20, Rf 0.61) to afford ethyl 2-(4-methylphenyl)-5-(phenylmethyl)oxazole-4-carboxylate (5a

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

• . (b) Effect of 1-pyrenebutyric acid (PyBA) addition at various concentrations to liposomes without catC60 and C60. The gel-to-liquid crystalline phase transition for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes was observed at 25 °C. All the measurements were performed with liposome

Synthesis of spiroindolenines through a one-pot multistep process mediated by visible light

• Francesco Gambuti,
• Jacopo Pizzorno,
• Chiara Lambruschini,
• Renata Riva and
• Lisa Moni

Beilstein J. Org. Chem. 2024, 20, 2722–2731, doi:10.3762/bjoc.20.230

• yield of 88% each step). Since, during the optimization of the reaction conditions, we have noticed a certain instability of the spiro-compounds through chromatography on silica gel, we have initially carried out the purifications using alumina as the stationary phase. However, during the scope studies

• the solvent and using Et3N as additive for the eluent of the chromatography on silica gel. With these improvements, we have demonstrated that the yields are comparable to those obtained with purification on alumina but reaching significantly higher degrees of purity of the final products (see

• %) due to difficulties in the purification. IR spectra were recorded as solid, oil, or foamy samples, with the ATR (attenuated total reflectance) method. TLC analyses were carried out on pre-coated Merck silica gel 60 F254 plates or Aluminum oxide on TLC-plates and viewed at UV (254 nm) and developed

Synthesis of benzo[f]quinazoline-1,3(2H,4H)-diones

• Ruben Manuel Figueira de Abreu,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 2708–2719, doi:10.3762/bjoc.20.228

• -Flight (TOF) LC–MS. The solvent, toluene, was purchased as dry solvent and applied without further purification. Other reagents, catalysts, ligands, acids, and bases were used as purchased from commercial suppliers. Column chromatography was performed on Merck Silica gel 60 (particle size 63–200 μm