Data accessibility in the chemical sciences: an analysis of recent practice in organic chemistry journals

• Sally Bloodworth,
• Cerys Willoughby and
• Simon J. Coles

Beilstein J. Org. Chem. 2025, 21, 864–876, doi:10.3762/bjoc.21.70

• data guidance. We suggest first steps that researchers can take to move towards a positive culture of data sharing in organic chemistry. Routine actions that we encourage as standard practice include deposition of raw and metadata to open repositories, and inclusion of machine-readable structure

• ., by selection of 20 random integers and matching of these to a chronological list of the articles. Assessment of the data objects associated with the selected articles was then carried out. The inclusion of 18 possible data types generated in each research article was recorded using Yes/No binary

Acyclic cucurbit[n]uril bearing alkyl sulfate ionic groups

• Christian Akakpo,
• Peter Y. Zavalij and
• Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 717–726, doi:10.3762/bjoc.21.55

• important role driving the inclusion of Me6CHDA inside of C1 to form the C1·Me6CHDA complex. Of course, the inclusion of the hydrophobic cyclohexyl moiety inside the cavity of C1 provides a hydrophobic driving force for complexation in water. Given that C1 is a tetraanion and that Me6CHDA is a dication, an

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

• are crucial for product formation. Lastly, the author noted that the inclusion of acetonitrile as a LAG agent enabled the transformation even without the presence of a photocatalyst [72][74]. In 2023, Braunschweig and co-workers reported the photomechanochemical [2 + 2] cycloaddition of acenaphthylene

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

• o-chloranil depends on the reaction conditions and can proceed with or without the inclusion of a dehydrochlorination stage and leads to 5,6,7-trichloro- or 4,5,6,7-tetrachlorotropones, respectively [5][25]. The present work reports the synthesis of new 2-(indolin-2-yl)-1,3-tropolones by the

Synthesis, characterization, antimicrobial, cytotoxic and carbonic anhydrase inhibition activities of multifunctional pyrazolo-1,2-benzothiazine acetamides

• Ayesha Saeed,
• Shahana Ehsan,
• Muhammad Zia-ur-Rehman,
• Erin M. Marshall,
• Sandra Loesgen,
• Abdus Saleem,
• Simone Giovannuzzi and
• Claudiu T. Supuran

Beilstein J. Org. Chem. 2025, 21, 348–357, doi:10.3762/bjoc.21.25

• autoimmune diseases [18], osteoarthritis [29], hemorrhage [25], and cardiac diseases [30]. Pyrazole moieties have a wide spectrum of pharmacological efficiencies. One known example is celecoxib®, a clinically used anti-inflammatory and COX-2 enzyme-inhibiting drug [31]. In some cases, inclusion of a pyrazole

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

• phosphite were ineffective (Table 1, entry 5), the inclusion of chelating dienes improved the yield of 3bb (Table 1, entries 6–8). Among these, 5 mol % of 1,5-cyclooctadiene (cod) proved to be the most effective additive, affording 3bb in 95% yield (Table 1, entry 8). Additionally, by reducing the

Surprising acidity for the methylene of 1,3-indenocorannulenes?

• Shi Liu,
• Märt Lõkov,
• Sofja Tshepelevitsh,
• Ivo Leito,
• Kim K. Baldridge and
• Jay S. Siegel

Beilstein J. Org. Chem. 2024, 20, 3144–3150, doi:10.3762/bjoc.20.260

• . Access to the dianion of BFC presages an interesting diradical and this was achieved by inclusion of mesityl protecting groups [27]. Extension of the BFC model with thiophene provides further interesting materials [28]. A reasonable corollary to this behavior would assert that derivatives of TBF and

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

• substituted benzene ring, and γ-CD can host further bigger guest molecules, such as pyrene or two aliphatic chains, in one cavity. The ability of CD to form an inclusion complex structure is drastically affected by the cavity size or the modification strategy for the hydroxy groups on CD. To evaluate the

• formation of this inclusion complex, circular dichroism spectroscopy represents a powerful tool when combined with nuclear magnetic resonance (NMR) and X-ray single-crystal analysis. This is because the induced circular dichroism (ICD) can be observed on the guest molecule of the inclusion complex derived

• methods are more popular than the slipping method. However, this end-capping method must fulfill the following seven points to appropriately realize a rotaxane framework, and this causes several complexities (Figure 3): (1) The axle molecule must form a stable inclusion complex with CD, (2) the axle

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• Sciences, 1113 Sofia, Bulgaria, University of Chemical Technology and Metallurgy, 8 St. Kliment Ohridski Blvd, 1756 Sofia, Bulgaria 10.3762/bjoc.20.221 Abstract Cyclodextrins (CDs) are host systems with inherent capability for inclusion complex formation with various molecular entities, mostly hydrophobic

• sides, unlike the internal cavity, are hydrophilic, decorated with primary (narrow rim) and secondary (wider rim) hydroxy groups. Van der Waals (vdW) and hydrophobic interactions have been identified as the main driving forces for CDs inclusion complex formation [2][3][4]. Electrostatic interactions and

• hydrogen bonding, although generally not dominant, can influence the complex formation as well [5]. Cyclodextrins form inclusion complexes with polar and non-polar substances of various aggregate states. This incredible versatility, combined with the enhanced stability against oxidation, as well as

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

Efficient modification of peroxydisulfate oxidation reactions of nitrogen-containing heterocycles 6-methyluracil and pyridine

• Alfiya R. Gimadieva,
• Yuliya Z. Khazimullina,
• Aigiza A. Gilimkhanova and
• Akhat G. Mustafin

Beilstein J. Org. Chem. 2024, 20, 2599–2607, doi:10.3762/bjoc.20.219

• product is observed with a high rate of APS disappearance, possibly due to side reactions [38]. To create the necessary aerobic conditions, we hypothesize that the inclusion of H2O2 in the binary oxidation mixture is favorable. This phenomenon occurs as a consequence of the reaction between H2O2 and the

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

• , with the selective release of modified peptide–probe conjugates afterwards. The frequently used enzymatically cleaved TEV-linker contains a peptide sequence, which is recognized by Tobacco Etch Virus nuclear inclusion A peptidase, which is orthogonal to trypsin and chymotrypsin cleavage – two most

Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis

• Stefan P. Schmid,
• Leon Schlosser,
• Frank Glorius and
• Kjell Jorner

Beilstein J. Org. Chem. 2024, 20, 2280–2304, doi:10.3762/bjoc.20.196

• based on a manual analysis of the probed substrates. The inclusion of electronic parameters led to a considerable improvement in predicting the enantioselectivity of a peptide-catalysed bisphenol desymmetrisation compared to their omission, showcasing the importance of capturing relevant molecular

• the ML model by being considered as a nucleophile or electrophile, depending on the reaction mechanism. Descriptors allowed for the inclusion of a variety of co-catalysts, ranging from Fe-piano stool complexes to copper complexes. The consideration of co-catalysis into model development further

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

• reductive cleavage of the C4a–O5 bond in alternariol derivatives leads to biaryls which are thus no longer lactones, the respective derivatives are obviously derived from alternariol and their inclusion in this review seems to be reasonable. Even derivatives downstream in the alternariol biosynthesis, which

A fiber-optic spectroscopic setup for isomerization quantum yield determination

• Anouk Volker,
• Jorn D. Steen and
• Stefano Crespi

Beilstein J. Org. Chem. 2024, 20, 1684–1692, doi:10.3762/bjoc.20.150

• . The inclusion of a temperature-controlled cuvette holder and the possibility for simultaneous UV–vis absorption spectroscopy makes this setup ideally suitable for a wide range of photoswitches, including those with fast thermal back isomerization. Our setup was tested by determining the quantum yields

New triazinephosphonate dopants for Nafion proton exchange membranes (PEM)

• Fátima C. Teixeira,
• António P. S. Teixeira and
• C. M. Rangel

Beilstein J. Org. Chem. 2024, 20, 1623–1634, doi:10.3762/bjoc.20.145

• that these dopants can act both as a source of protons and proton acceptors, facilitating the intermolecular proton conduction. The rational of the strategy behind the use of amino- and hydroxyphenyl spacers is twofold: i) their inclusion in the structure separates the bulky phosphonate groups from the

Mining raw plant transcriptomic data for new cyclopeptide alkaloids

• Draco Kriger,
• Michael A. Pasquale,
• Brigitte G. Ampolini and
• Jonathan R. Chekan

Beilstein J. Org. Chem. 2024, 20, 1548–1559, doi:10.3762/bjoc.20.138

• precursor peptides, we removed any transcript that had contained a BURP domain as determined by the public HMM model (PFAM 03181) with an E-value of 0.1 inclusion threshold. The BURP domain itself is named after the four founding members BNM2, USP-like, RD22, and PG1β, which were bioinformatically described

• ). rnaSPAdes was used to assemble the raw reads using the default settings [15]. This software package was chosen primarily for its speed (≈1.5 h per transcriptome), which was essential for this large analysis effort. Our custom HMM was used to search for potential precursor peptides using an E-value inclusion

• threshold of 0.1. These results are present in Supporting Information File 4 compressed archive file. To remove fused burpitide cyclases, the HMM for the BURP domain (PFAM 03181) was also run against the assembled transcriptomes using the same 0.1 E-value inclusion threshold. Transcriptomes that indicated a

A comparison of structure, bonding and non-covalent interactions of aryl halide and diarylhalonium halogen-bond donors

• Nicole Javaly,
• Theresa M. McCormick and
• David R. Stuart

Beilstein J. Org. Chem. 2024, 20, 1428–1435, doi:10.3762/bjoc.20.125

• half-life it would be very challenging to synthesize astatine analogs of diarylhalonium salts and almost no experimental data exists on halogen bonding with astatine for comparison with DFT-generated data. However, the inclusion of molecules containing At in this study provides an opportunity to expand

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

• . Photostability measurements have also demonstrated that the inclusion of a triplet quencher like stilbene significantly enhances the longevity of the Aza-H chromophores, outperforming other well-known organic and metal-based photocatalysts such as 4CzIPN, riboflavin and [Ru(bpy)3](PF6)2 (Figure 5C and Supporting

Novel route to enhance the thermo-optical performance of bicyclic diene photoswitches for solar thermal batteries

• Akanksha Ashok Sangolkar,
• Rama Krishna Kadiyam and
• Ravinder Pawar

Beilstein J. Org. Chem. 2024, 20, 1053–1068, doi:10.3762/bjoc.20.93

• Perdew–Burke–Ernzerhof (PBE) functional along with the inclusion of the Grimme’s D3 dispersion correction. (a) Previously studied BBD-based photoswitches, (b) recently reported protocol to synthesize a BBD structure with elongated unsaturated bridge [37], (c) BBD-based photoswitches studied in the

Innovative synthesis of drug-like molecules using tetrazole as core building blocks

• Jingyao Li,
• Ajay L. Chandgude,
• Qiang Zheng and
• Alexander Dömling

Beilstein J. Org. Chem. 2024, 20, 950–958, doi:10.3762/bjoc.20.85

• due to the protected nature of the tetrazol. Additionally, inclusion of a strategically placed tetrazole and bioisostere replacement of MCR substrate with tetrazole may give rise to molecules with improved drug-like characteristics with nominal weight or size difference. This tetrazole building block

(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• activity, if not an improvement [1]. Often-used bioisosteres include the tetrazole group for a carboxylic acid [2][3][4][5] and fluorine atoms in place of hydrogens [6][7]. The inclusion of fluorine can alter the polarity of a molecule and can also be used to prevent epimerisation, as seen in

Skeletal rearrangement of 6,8-dioxabicyclo[3.2.1]octan-4-ols promoted by thionyl chloride or Appel conditions

• Martyn Jevric,
• Julian Klepp,
• Johannes Puschnig,
• Oscar Lamb,
• Christopher J. Sumby and
• Ben W. Greatrex

Beilstein J. Org. Chem. 2024, 20, 823–829, doi:10.3762/bjoc.20.74

• skeletal rearrangement (vide infra). Inclusion of the soft-nucleophile allyltrimethylsilane in the reaction of 10b to trap potential oxocarbenium ion intermediates also resulted in a complex mixture. During the isolation of the chloroalkyl ether products 11a–f, it was apparent that hydrolysis occurred

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• Hyg17 sequences with other members of the oxidoreductase family and inositol dehydrogenases and discuss specialized genome mining approaches using these sequences to identify new natural product biosynthetic clusters. Results and Discussion Hyg17 enzyme activity We found that Hyg17 formed inclusion

Enhanced host–guest interaction between [10]cycloparaphenylene ([10]CPP) and [5]CPP by cationic charges

• Eiichi Kayahara,
• Yoshiyuki Mizuhata and
• Shigeru Yamago

Beilstein J. Org. Chem. 2024, 20, 436–444, doi:10.3762/bjoc.20.38

• between the most stable calculated structure 1 and the crystalline structure is likely due to crystal packing forces, the presence of the counterion, and the inclusion of solvent molecules. The interfacial distances between the nearest neighbor centroid of a paraphenylene unit of [10]CPP and [5]CPP were