Effect of a photoswitchable rotaxane on membrane permeabilization across lipid compositions

• Udyogi N. K. Conthagamage,
• Lilia Lopez,
• Zuliah A. Abdulsalam and
• Víctor García-López

Beilstein J. Org. Chem. 2025, 21, 2498–2512, doi:10.3762/bjoc.21.192

• modulate membrane permeability in large unilamellar vesicles (LUVs) of varying lipid compositions. Upon photoisomerization, the rotaxane significantly enhanced the release of the hydrophilic dye sulforhodamine B in vesicles composed of EYPC/Chol 8:2, with release increasing from 29% (non-irradiated) to 59

• % (irradiated). Moreover, gel-phase DPPC bilayers also exhibited an increase in release from 7% to 14%. On the contrary, highly fluid pure EYPC bilayers showed high baseline release upon rotaxane incorporation (64%), with photoswitching producing only a slight increase (70%), as most dye was released within the

• permeabilization was assessed by monitoring the release of encapsulated sulforhodamine B dye, serving as a reporter for membrane perturbation. Specifically, we examined LUVs in the liquid-disordered (Ld), liquid-ordered (Lo), and gel (Lβ) phases. As control molecules, we also investigated the membrane perturbation

Insoluble methylene-bridged glycoluril dimers as sequestrants for dyes

• Suvenika Perera,
• Peter Y. Zavalij and
• Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 2302–2314, doi:10.3762/bjoc.21.176

• (Figure 2) from water. Subsequently, we present the X-ray crystal structures of G2W1 and G2W3 which helps rationalize the results from the dye sequestration experiments. Finally, we present a detailed investigation into the methylene blue removal efficiency using H2 [39] (Figure 1) and the methylene

• consistent with the depicted C2v-symmetry. Comparison of the dye removal efficiency of hosts H2, G2W1–G2W4 After firmly establishing the structures of the new water-insoluble acyclic CB[n] receptors G2W1–G2W4, we turned our attention to determining their efficiency as solid state sequestrants for the panel

• . Before use, samples of H2, G2W1–G2W4 were repeatedly washed with water to remove TFA (monitored by 19F NMR) and activated by grinding and heating overnight at 90 °C under high vacuum. Experimentally, we incubated equimolar amounts (7.2 μmol) of each host with aqueous solutions of each dye (240 μM, 1 mL

Enantioselective radical chemistry: a bright future ahead

• Anna C. Renner,
• Sagar S. Thorat,
• Hariharaputhiran Subramanian and
• Mukund P. Sibi

Beilstein J. Org. Chem. 2025, 21, 2283–2296, doi:10.3762/bjoc.21.174

• engineered thiamine diphosphate-dependent lyase) working together with an organic dye (eosin Y) that served as a photoredox catalyst [77]. Highly diastereo- and enantioselective three-component couplings were catalyzed by an evolved pyridoxal decarboxylase and a small-molecule photoredox catalyst (rose

C2 to C6 biobased carbonyl platforms for fine chemistry

• Jingjing Jiang,
• Muhammad Noman Haider Tariq,
• Florence Popowycz,
• Yanlong Gu and
• Yves Queneau

Beilstein J. Org. Chem. 2025, 21, 2103–2172, doi:10.3762/bjoc.21.165

• al. also synthesized HFO from furan by thermocatalytic oxidation (Scheme 36b) [119]. Salomon and co-workers reported the conversion of 2-substituted furans to HFO using NaClO2 as oxidizing agent (Scheme 36c) [120]. The conversion of furfural to HFO by a dye-sensitized photooxidation reaction with

• amination of levulinic acid: The reductive amination of levulinic acid and its esters leads to the formation of N-substituted 5-methyl-2-pyrrolidinones (5MPs) which are used in many fields including pharmaceutical and dye industries. Zhang reviewed the synthesis of 5MPs from levulinates and different

Photoswitches beyond azobenzene: a beginner’s guide

• Michela Marcon,
• Christoph Haag and
• Burkhard König

Beilstein J. Org. Chem. 2025, 21, 1808–1853, doi:10.3762/bjoc.21.143

• choice of aldehyde and amine will determine the direction of the imine bond and the geometry of the Z-isomer. Examples Non-ionic bithienylpyrrole push–pull azo dye 32 was successfully introduced in liquid-crystalline matrices with thermal relaxation in the µs order, making them among the fastest liquid

• already known as dye [89] have only been studied very recently. Exchanging the C=C bond for a C=N bond gives a new subclass of extremely short-lived T-type photoswitches with visible light activation, thermal half-lives in the µs range, and very large spectral separation. The study of iminothioindoxyl

Research progress on calixarene/pillararene-based controlled drug release systems

• Liu-Huan Yi,
• Jian Qin,
• Si-Ran Lu,
• Liu-Pan Yang,
• Li-Li Wang and
• Huan Yao

Beilstein J. Org. Chem. 2025, 21, 1757–1785, doi:10.3762/bjoc.21.139

• further utilized this feature to achieve reversible transformation of amphiphilic guest molecules between micellar and vesicular states and have successfully applied it to the controlled release of dye molecules. Notably, the system can also effectively neutralize the toxicity of paraquat through host

Ambident reactivity of enolizable 5-mercapto-1H-tetrazoles in trapping reactions with in situ-generated thiocarbonyl S-methanides derived from sterically crowded cycloaliphatic thioketones

• Grzegorz Mlostoń,
• Małgorzata Celeda,
• Marcin Palusiak,
• Heinz Heimgartner,
• Marta Denel-Bobrowska and
• Agnieszka B. Olejniczak

Beilstein J. Org. Chem. 2025, 21, 1508–1519, doi:10.3762/bjoc.21.113

• tetrazolium structure in the MTT dye results in the formation of a coloured formazan that can be detected by spectrophotometry. Cytotoxic properties of the studied compounds were assessed on non-cancer as well as cancer cell lines. Cytotoxicity was established by measurement of 50% inhibition of cell growth

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

• with an electrophilic handle for the covalent attachment of the surrogate to the RNA. The resulting irreversibly tethered dye–RNA complexes have opened up new avenues for RNA imaging in live cells. Here, we report the syntheses of such modified HBC530 ((4-((2-hydroxyethyl)(methyl)amino)benzylidene

• have shown that this feature can be exploited to construct a covalent bond between the fluorophore and the RNA by replacing the N-hydroxyethyl group of the dye with an electrophilic handle, resulting in efficient RNA alkylation at the N7 of G41 [11]. Synthesis and evaluation of Pepper dyes with an

• 14 (Figure 2). Synthesis of a bifunctional Pepper dye Encouraged by the efficient attachment of the bromo- and mesyloxypropyl-modified HBC fluorophores to the Pepper aptamer, we generated a bifunctional HBC ligand with a second handle that is available for bioorthogonal reactions. The original

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

Synthesis, structure, ionochromic and cytotoxic properties of new 2-(indolin-2-yl)-1,3-tropolones

• Yurii A. Sayapin,
• Eugeny A. Gusakov,
• Inna O. Tupaeva,
• Alexander D. Dubonosov,
• Igor V. Dorogan,
• Valery V. Tkachev,
• Anna S. Goncharova,
• Gennady V. Shilov,
• Natalia S. Kuznetsova,
• Svetlana Y. Filippova,
• Tatyana A. Krasnikova,
• Yanis A. Boumber,
• Alexey Y. Maksimov,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2025, 21, 358–368, doi:10.3762/bjoc.21.26

• equation formalism (IEFPCM) [38]. Biological experiments The MTT colorimetric test for cell viability assessment is based on the reduction by NADPH-H-dependent cellular oxidoreductase enzymes of the tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, which has yellow color, into

Red light excitation: illuminating photocatalysis in a new spectrum

• Lucas Fortier,
• Corentin Lefebvre and
• Norbert Hoffmann

Beilstein J. Org. Chem. 2025, 21, 296–326, doi:10.3762/bjoc.21.22

• therapeutic methods [78][79][80]. Such reactions can be performed at particular locations such as DNA or tubulin, when the photocatalyst is placed via a tethered ligand (Scheme 17) [81]. In the present case, the triarylmethine dye 67 was used as sensitizer. It is in equilibrium with the lactone form 68 and

Quantifying the ability of the CF₂H group as a hydrogen bond donor

• Matthew E. Paolella,
• Daniel S. Honeycutt,
• Bradley M. Lipka,
• Jacob M. Goldberg and
• Fang Wang

Beilstein J. Org. Chem. 2025, 21, 189–199, doi:10.3762/bjoc.21.11

• established methods, including 1H NMR-based hydrogen bond acidity determination, UV–vis spectroscopy titration with Reichardt's dye, and 1H NMR titration using tri-n-butylphosphine oxide as a hydrogen bond acceptor. Our experiments reveal that the direct attachment of the CF2H group to cationic aromatic

• Reichardt's dye [53][54][55] as an indicator. These experiments measure the blue shift of Reichardt's dye upon complexation with an HB donor (Figure 3A, and Figures S13–S18 in Supporting Information File 1), from which the dissociation constant (Kd) of the HB complex can be determined. A smaller Kd value

• corresponds to a more stable complex, indicating a stronger HB donor. We employed this protocol to investigate a series of HB donors in anhydrous acetonitrile (Figure 3B). Acetonitrile is weakly HB accepting (α = 0.19) [51] and was thus chosen to attenuate the competition between the solvent and the dye with

Multicomponent reactions driving the discovery and optimization of agents targeting central nervous system pathologies

• Lucía Campos-Prieto,
• Aitor García-Rey,
• Eddy Sotelo and
• Ana Mallo-Abreu

Beilstein J. Org. Chem. 2024, 20, 3151–3173, doi:10.3762/bjoc.20.261

• channel blockade was determined by the measure of Ca2+ influx induced by K+-depolarization in SH-SY5Y neuroblastoma cells, previously loaded with the fluorescent dye Fluo-4AM. On the other hand, the antioxidant activity of the DHPs was evaluated using the ORAC-FL method. The most potent compounds

Advances in the use of metal-free tetrapyrrolic macrocycles as catalysts

• Mandeep K. Chahal

Beilstein J. Org. Chem. 2024, 20, 3085–3112, doi:10.3762/bjoc.20.257

• applied in various fields, including organometallic catalysis, dye-sensitized solar cells, sensing, artificial olfactory systems, photodynamic therapy (PDT), anticancer drugs, biochemical probes, and electrochemical devices. Relevant examples of these two pyrrolic macrocycles as metal-free organocatalysts

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

• reported that in the case of the dye molecule existing inside the CD cavity, the plus Cotton effect was observed when the dipole was directed along the axle of the cavity, whereas it became minus when the dipole was directed perpendicular to this axle (Figure 6, left) [59]. When the dye molecule was

• the entire solution derived from the release of the dumbbell 13 after the decrosslinking. This fluorescence wavelength change was induced by the solvation of the dye moieties. Since the dumbbell contains the push-pull type substituents on the biphenyl structure, this dye showed solvatochromism

Tunable full-color dual-state (solution and solid) emission of push–pull molecules containing the 1-pyrindane moiety

• Anastasia I. Ershova,
• Sergey V. Fedoseev,
• Konstantin V. Lipin,
• Mikhail Yu. Ievlev,
• Oleg E. Nasakin and
• Oleg V. Ershov

Beilstein J. Org. Chem. 2024, 20, 3016–3025, doi:10.3762/bjoc.20.251

• materials [14][20][21][22][23][24][25][26][27][28][29][30][31][32][33]. For example, organic π-systems whose main structural unit is stilbazole are used as active compounds in organic light-emitting diodes (OLEDs) [20], dye-sensitized solar cells (DSSCs) [21], nonlinear optics (NLO) materials [22][23

N-Glycosides of indigo, indirubin, and isoindigo: blue, red, and yellow sugars and their cancerostatic activity

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 2840–2869, doi:10.3762/bjoc.20.240

• photophysical materials. While unsubstituted (parent) indigo (1a) is not a natural product, Tyrian purple (also known as Shellfish purple) is present in nature and represents, besides indigo, an important indigo derivative used as a dye for thousands of years [4]. Several types of cancers, Alzheimer's disease

• be inactive. The activities of β-33b and 34 on the cell viability was independently studied by using crystal violet as a dye for viable cells following a 48 h incubation of A375 melanoma cells and A431 squamous carcinoma cells. Interestingly, a concentration-dependent cytotoxicity was again observed

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

• , meaning no drying is required of the material, the material itself needs to be fluorescent (but not quenching upon assembly) or the addition of a dye is required. Such dyes need to be able to stick with the fibres, rather than sitting in the pores. Therefore, the fluorescent material is either chemically

Transition-metal-free synthesis of arylboronates via thermal generation of aryl radicals from triarylbismuthines in air

• Yuki Yamamoto,
• Yuki Konakazawa,
• Kohsuke Fujiwara and
• Akiya Ogawa

Beilstein J. Org. Chem. 2024, 20, 2577–2584, doi:10.3762/bjoc.20.216

• are one of the fundamental aryl compounds in organic synthesis, especially in cross-coupling reactions [1][2][3][4][5][6][7][8][9], and their applications are widespread, including dye synthesis, pharmaceutical and agrochemical synthesis, and industrial manufacturing [10][11]. In recent years, a

A review of recent advances in electrochemical and photoelectrochemical late-stage functionalization classified by anodic oxidation, cathodic reduction, and paired electrolysis

• Nian Li,
• Ruzal Sitdikov,
• Ajit Prabhakar Kale,
• Joost Steverlynck,
• Bo Li and
• Magnus Rueping

Beilstein J. Org. Chem. 2024, 20, 2500–2566, doi:10.3762/bjoc.20.214

• [70]. The mildness of this reaction was demonstrated through the late-stage C–H trifluoromethylation of ascapheine, pentoxifylline, doxophylline, theobromine, methylethrone, and tryptophan derivatives. During the reaction, irradiation of the organic dye Mes-Acr+ leads to the formation of its oxidized

Machine learning-guided strategies for reaction conditions design and optimization

• Lung-Yi Chen and
• Yi-Pei Li

Beilstein J. Org. Chem. 2024, 20, 2476–2492, doi:10.3762/bjoc.20.212

• . Guo et al. [186] used a synthesis strategy that combines Monte Carlo Tree Search (MCTS) with reinforcement learning to model the retrosynthesis game, aiming to identify high-value synthetic pathways. Recently, Koscher et al. [21] have shown the simultaneous design and synthesis of dye molecules

Photoredox-catalyzed intramolecular nucleophilic amidation of alkenes with β-lactams

• Valentina Giraldi,
• Giandomenico Magagnano,
• Daria Giacomini,
• Pier Giorgio Cozzi and
• Andrea Gualandi

Beilstein J. Org. Chem. 2024, 20, 2461–2468, doi:10.3762/bjoc.20.210

• the cis-isomer. The optimal PC for the reaction was acridinium salt IV (Table 1, entry 1), while the Fukuzumi catalyst (I), commonly employed by Nicewicz et al., was less effective (Table 1, entry 9). 3CzClIPN, an organic dye belonging to the class of thermally activated delayed fluorescence (TADF

• ) dyes commonly employed nowadays in photoredox catalysis [47], was tested in our reaction. This dye was chosen due to its oxidizing properties, and it ranks among the most oxidizing agents within this class of compounds (E1/2[*PC/PC•−] = +1.56 V vs SCE) [48], but it proved ineffective in our reaction

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

• the SDS-PAGE. This approach also accounts for the protein-level identification; the exact modification site remains unknown. Here we show an example of the most used and commercially available rhodamine-derived dye (TAMRA-azide, Figure 6A). The bioorthogonal reaction between probe-labeled proteins and

Novel truxene-based dipyrromethanes (DPMs): synthesis, spectroscopic characterization and photophysical properties

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2024, 20, 2163–2170, doi:10.3762/bjoc.20.186

• ][12][13]. The most promising applications of truxene-based systems have been found in organic photovoltaics (OPVs), dye‐sensitized solar cells (DSSCs), fluorescent probes, organic thin‐film transistors (OTFTs), lasers, organic light emitting diodes (OLEDs), liquid crystals, non-linear optical (NLO

Efficacy of radical reactions of isocyanides with heteroatom radicals in organic synthesis

• Akiya Ogawa and
• Yuki Yamamoto

Beilstein J. Org. Chem. 2024, 20, 2114–2128, doi:10.3762/bjoc.20.182

• metal complex or functional dye as a photocatalyst (PC) [19][20]. Recently, some important reviews summarize and discuss the use of method 3 in synthetic organic chemistry [21][22]; in contrast, there is little detailed and coherent literature on the overall research trends regarding the latest research