The high potential of methyl laurate as a recyclable competitor to conventional toxic solvents in [3 + 2] cycloaddition reactions

• Ayhan Yıldırım and
• Mustafa Göker

Beilstein J. Org. Chem. 2025, 21, 2389–2415, doi:10.3762/bjoc.21.184

• the time- and labor-intensive nature of traditional multistep synthesis strategies. For instance, this methodology has been demonstrated to be highly advantageous in the synthesis of numerous pharmaceutical compounds, biological probes, insecticides, alkaloids, and other intricate natural compounds

Conformational effects on iodide binding: a comparative study of flexible and rigid carbazole macrocyclic analogs

• Guang-Wei Zhang,
• Yong Zhang,
• Le Shi,
• Chuang Gao,
• Hong-Yu Li and
• Lei Xue

Beilstein J. Org. Chem. 2025, 21, 2369–2375, doi:10.3762/bjoc.21.181

• fluorescence quenching efficiency upon iodide binding compared to the rigid WDG (KPBG/KWDG = 22.78), demonstrating its potential as a highly sensitive optical probe and offering a novel strategy for engineering dynamic supramolecular receptors. Two carbazole-based macrocyclic probes, PBG (flexible benzene ring

Rotaxanes with integrated photoswitches: design principles, functional behavior, and emerging applications

• Jullyane Emi Matsushima,
• Khushbu,
• Zuliah Abdulsalam,
• Udyogi Navodya Kulathilaka Conthagamage and
• Víctor García-López

Beilstein J. Org. Chem. 2025, 21, 2345–2366, doi:10.3762/bjoc.21.179

• Michael addition taking place at the active site (C=C−C=N+) in the merocyanine unit in the presence of sulfite ions, resulting in color changes from red to green. This work represents a substantial advancement in the development of rotaxane-based fluorescent probes, providing highly sensitive and

Research towards selective inhibition of the CLK3 kinase

• Vinay Kumar Singh,
• Frédéric Justaud,
• Dabbugoddu Brahmaiah,
• Nangunoori Sampath Kumar,
• Blandine Baratte,
• Thomas Robert,
• Stéphane Bach,
• Chada Raji Reddy,
• Nicolas Levoin and
• René L. Grée

Beilstein J. Org. Chem. 2025, 21, 2250–2259, doi:10.3762/bjoc.21.172

• kinases” because of the lack of functional annotations and high-quality molecular probes for functional investigations [7][8]. Thus, new studies are still required for the discovery of selective inhibitors for each of these kinases in order to better clarify their mechanisms of action and their roles in

• . However, these derivatives remain still less potent on CLK3 than on the other CLKs. Therefore, they cannot be qualified as bona fide chemical probes for this CLK3 kinase. Structural and biochemical studies have been undertaken to find more selective CLKs inhibitors. Particularly, a detailed study has

A m-quaterphenyl probe for absolute configurational assignments of primary and secondary amines

• Yuka Takeuchi,
• Mutsumi Kobayashi,
• Yuuka Gotoh,
• Mari Ikeda,
• Yoichi Habata,
• Tomohiko Shirai and
• Shunsuke Kuwahara

Beilstein J. Org. Chem. 2025, 21, 2211–2219, doi:10.3762/bjoc.21.168

• , exciton-coupled CD has emerged as a powerful chiroptical method, providing a non-empirical correlation between the sign of the Cotton effect and the spatial arrangement of the electric transition dipole moments of interacting chromophores [7]. More recently, CD-based chiroptical probes have been developed

• configurations of chiral amines were determined. Reported chiroptical probes for determining the absolute configuration of chiral compounds only used the sign of the Cotton effect in CD. This method uses not only the sign but also the intensity of the Cotton effect in CD to determine the absolute configuration

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

• polyamides possess unusual intrinsic luminescence and high and selective affinity towards Fe2+ and Fe3+ metal ions, which could be used as fluorescent probes in the biomedical field [195]. Heptamethine cyanine Cy7 is a very important class of intermediates in the fields of biology and photomedicine. The

Rhodium-catalysed connective synthesis of diverse reactive probes bearing S(VI) electrophilic warheads

• Scott Rice,
• Julian Chesti,
• William R. T. Mosedale,
• Megan H. Wright,
• Stephen P. Marsden,
• Terry K. Smith and
• Adam Nelson

Beilstein J. Org. Chem. 2025, 21, 1924–1931, doi:10.3762/bjoc.21.150

• may be enabled by screening diverse sets of reactive probes. Most existing sets of reactive probes are armed with cysteine-directed warheads, a limitation that we sought to address. A connective synthesis was developed in which α-diazoamide substrates, armed with a S(VI) warhead, were reacted with

• diverse co-substrates. A high-throughput approach was used to identify promising substrate/co-substrate/catalyst combinations which were then prioritised for purification by mass-directed HPLC to yield a total of thirty reactive probes. The structural diversity of the probe set was increased by the

• multiplicity of reaction types between rhodium carbenoids and the many different co-substrate classes, and the catalyst-driven selectivity between these pathways. The probes were screened for activity against Trypanosma brucei, and four probes with promising anti-trypanosomal activity were identified

Fe-catalyzed efficient synthesis of 2,4- and 4-substituted quinolines via C(sp²)–C(sp²) bond scission of styrenes

• Prafull A. Jagtap,
• Manish M. Petkar,
• Vaishnavi R. Sawant and
• Bhalchandra M. Bhanage

Beilstein J. Org. Chem. 2025, 21, 1799–1807, doi:10.3762/bjoc.21.142

• probes for sensing and bioimaging applications (Figure 1) [16][17]. Quinoline-derived metal complexes have also demonstrated broad utility, functioning as effective catalysts in organic synthesis and finding applications across medicinal chemistry, materials science, photovoltaics, and chemical sensing

On the aromaticity and photophysics of 1-arylbenzo[a]imidazo[5,1,2-cd]indolizines as bicolor fluorescent molecules for barium tagging in the study of double-beta decay of ¹³⁶Xe

• Eric Iván Velazco-Cabral,
• Fernando Auria-Luna,
• Juan Molina-Canteras,
• Miguel A. Vázquez,
• Iván Rivilla and
• Fernando P. Cossío

Beilstein J. Org. Chem. 2025, 21, 1627–1638, doi:10.3762/bjoc.21.126

• efficiency of crown ethers as components in cation-selective fluorescent probes has been extensively explored [7][30], to the best of our knowledge no previous computational DFT studies on the selectivity of crown ethers of different sizes with Ba2+ have been reported. Therefore, we explored (Scheme 2A) the

pH-Controlled isomerization kinetics of ortho-disubstituted benzamidines: E/Z isomerism and axial chirality

• Ryota Kimura,
• Satoshi Ichikawa and
• Akira Katsuyama

Beilstein J. Org. Chem. 2025, 21, 1568–1576, doi:10.3762/bjoc.21.120

• various fields, such as functional materials, biological probes, and drugs. a) Structural features of DiBA. b) Resonance structure of the amide moiety of DiBA. c) Molecular form and protonated structure of ortho-disubstituted benzamidine. Rotational barriers of 2-bromo-N,N,6-trimethylbenzimidamide and its

Highly distinguishable isomeric states of a tripodal arylazopyrazole derivative on graphite through electron/hole-induced switching at ambient conditions

• Himani Malik,
• Sudha Devi,
• Debapriya Gupta,
• Ankit Kumar Gaur,
• Sugumar Venkataramani and
• Thiruvancheril G. Gopakumar

Beilstein J. Org. Chem. 2025, 21, 1496–1507, doi:10.3762/bjoc.21.112

• tapping mode and an ATM300 from RHK Technology, respectively. Aluminum-coated silicon cantilevers from Nanosensors (PPP-NCHR) were used as AFM probes. The force constant and resonance frequency of the cantilevers during the imaging were 30–34 N/m and ≈300 kHz, respectively. A Pt/Ir (80:20) tip was

Biobased carbon dots as photoreductants – an investigation by using triarylsulfonium salts

• Valentina Benazzi,
• Arianna Bini,
• Ilaria Bertuol,
• Mariangela Novello,
• Federica Baldi,
• Matteo Hoch,
• Alvise Perosa and
• Stefano Protti

Beilstein J. Org. Chem. 2025, 21, 1024–1030, doi:10.3762/bjoc.21.84

• photoreductants, and we considered triarylsulfonium salts Ar3S+X− as suitable probes. Such derivatives are photoreactive molecules characterized by a positively charged sulfur atom bonded to three aromatic moieties [20][21][22][23], mainly employed as photoacid generators in cationic polymerization [19]. Apart

Light-enabled intramolecular [2 + 2] cycloaddition via photoactivation of simple alkenylboronic esters

• Lewis McGhie,
• Hannah M. Kortman,
• Jenna Rumpf,
• Peter H. Seeberger and
• John J. Molloy

Beilstein J. Org. Chem. 2025, 21, 854–863, doi:10.3762/bjoc.21.69

• . Herein, we demonstrate the sensitization of alkenylboronates to enable efficient intramolecular [2 + 2] cycloaddition using high energy photosensitizers (Figure 1C). Sensitization was quickly established and explored through the use of alkene scrambling (geometrical isomerization) reaction probes, to

• process (Figure 2B) [19]. In a bid to translate sensitization reaction probes to meaningful synthetic transformations, conventional intermolecular [2 + 2] cycloaddition reactions were initially trialled (Figure 3A). Preliminary reactions using styrene or methyl acrylate were unsuccessful, with no [2 + 2

• activation (Table 2) [59][60]. As anticipated, guided by alkene scrambling reaction probes (Table 1), iridium sensitizers were unsuccessful (Table 2, entries 1 and 2). Thioxanthone provided the cyclobutyl product 4b in 10% yield (Table 2, entry 3), indicating catalysis with poor overlap between the catalyst

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

• have promising applications in optoelectronics. For example, investigation of the photophysical and electronic properties of ANTH began in the 1960s [1][2][3], and since then many new ANTH derivatives have been synthesized and explored for their use as fluorescent probes, organic semiconductors, and

• [20][21] and are not suitable as emitters for OLEDs or fluorescent probes. A family of perfluorobenzylated derivatives of another PAH, viz. perylene (PERY), was recently reported by our group [22]. We showed that the acceptor strength of PERY(BnF)n derivatives (n = 1–5) significantly increased with

Synthesis of electrophile-tethered preQ₁ analogs for covalent attachment to preQ₁ RNA

• Laurin Flemmich and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 483–489, doi:10.3762/bjoc.21.35

• reasonably fast labeling kinetics and up to quantitative conversion under quasi-physiological conditions [4]. Obviously, the rapid dissemination and widespread acceptance of such labeling methods depend on fast and simple access to the small molecule probes. Here, we report efficient synthetic routes to

Streamlined modular synthesis of saframycin substructure via copper-catalyzed three-component assembly and gold-promoted 6-endo cyclization

• Asahi Kanno,
• Ryo Tanifuji,
• Satoshi Yoshida,
• Sota Sato,
• Saori Maki-Yonekura,
• Kiyofumi Takaba,
• Jungmin Kang,
• Kensuke Tono,
• Koji Yonekura and
• Hiroki Oguri

Beilstein J. Org. Chem. 2025, 21, 226–233, doi:10.3762/bjoc.21.14

• avenues for the development of fluorescent probes based on the bis-THIQ alkaloidal scaffold. Further efforts to develop a concise and modular synthetic process for saframycins are currently underway. Representative bis-tetrahydroisoquinoline (THIQ) alkaloids and their analogues. Oxygen atoms on both the A

Synthesis of acenaphthylene-fused heteroarenes and polyoxygenated benzo[j]fluoranthenes via a Pd-catalyzed Suzuki–Miyaura/C–H arylation cascade

• Merve Yence,
• Dilgam Ahmadli,
• Damla Surmeli,
• Umut Mert Karacaoğlu,
• Sujit Pal and
• Yunus Emre Türkmen

Beilstein J. Org. Chem. 2024, 20, 3290–3298, doi:10.3762/bjoc.20.273

• fluorescent chemosensors and probes [4][5][6], as well as materials for applications in organic light-emitting diodes (OLEDs) [7][8][9], organic field-effect transistors (OFETs) [10], and perovskite solar cells [11]. In this respect, replacing either one or more of the carbons or rings of a fluoranthene with

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

Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond

• Thomas Ma and
• John Chu

Beilstein J. Org. Chem. 2024, 20, 3050–3060, doi:10.3762/bjoc.20.253

• traditional medicine formulations [2]. Modern science has found that natural products are uniquely suited as the starting point for the development of new drugs [3][4]. They may serve as chemical probes and help confirm laboratory findings [5]; furthermore, entirely new physical and chemical principles are

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

• ], positron emission tomography (PET) imaging [24], fluorescent probes and labels [25][26][27] detecting H2S in foodstuff, water, and living cells [28], Fe3+ ions [29], Hg2+ ions [30], and cyanide anions [31], for acid–base vapor sensing [32], and as candidate material for photonics devices, optical switches

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

• not exhibit any discernible increase in luminescence. As far as we are aware, there are only three reports of lanthanide-based probes for the detection of gaseous hydrogen sulfide. Two are the europium(III) complexes from our group ([Eu(triazole-DPA)3·Cu]3+ and [Eu(DO2A)(triazole-DPA)·Cu]+), which are

Young investigators in natural products chemistry, biosynthesis, and enzymology

• Jeffrey D. Rudolf,
• Lena Barra and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 2720–2721, doi:10.3762/bjoc.20.229

• clusters, and enzymes, development of chemical probes, biocatalysis and chemoenzymatic total synthesis, enzymatic mechanisms, and computational investigations of chemical structures and reactions. All of the major classes of natural products are represented here: nonribosomal peptides, ribosomally

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

• use of fluorescence probes should be used in tandem with CLSM. For example, Raeburn et al. showed that the addition of molecular rotors and fluorescent dyes affects the bulk network of self-assembled materials using rheology. The co-packing was observed to alter rheological properties of the materials

• arising, for example, from differences in the rate of fibre growth and entanglements. The change in rheological properties when comparing the material and its co-assembly with the probe shows that addition of such probes may lead to measurements which do not truly represent the system of interest [19

• proportions of fluorescent probes in the self-assembled material will be much smaller than the example discussed here, it is important to use appropriate methods to show that the addition of any co-assembling component does not impact the nanoscale structure and bulk network. To our knowledge there are very

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

• study several small molecule probes were used including propargylamine, a glutamine derivative, N6-propargyladenosine and a tyrosine derivative to document the thiotriazole formation during CuAAC. The two selected examples of adenosine and glutamine-derived diagnostic ions are shown in Figure 8E. Since

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