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

• approaches to enable broader exploration New approaches have been developed to circumvent the aforementioned constraints and enable the exploration of a broader natural product chemical space. Existing approaches fall into two broad categories – sequence metagenomics (Figure 2a) and function metagenomics

• (Figure 2b). The former analyzes nucleic acid sequences to prioritize BGCs that are worth exploring [20]. For example, it has been shown that tracking characteristic biosynthetic or self-resistance gene(s) can facilitate the discovery of new congeners of a natural product family [21][22]. Function

• morphology of the host, etc. [25]. Sequence and function metagenomic approaches have been reviewed elsewhere and will not be covered herein [26][27][28]. This Perspective focuses on chemical structure metagenomics (Figure 2c), an emerging field that integrates bioinformatics, chemical synthesis, molecular

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

• in a high yield. In this reaction, the size of the end-capping agent is the key, as an extremely large reagent does not react well with the amino axle-end groups, whereas an extremely small reagent cannot function as an end-cap. This reaction exhibits the following multiple advantages compared with

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

• ,1H-NOESY spectrum of compound 1c in DMSO-d6. Absorption (left) and normalized emission spectra (right) of compound 1i in various solvents (c = 10−5 M). Solvatochromic behavior of compounds 1c and 1i: plots of arithmetic mean of emission/absorption wavenumbers vs Kawsk–Chamma–Viallet polarity function

Advances in radical peroxidation with hydroperoxides

• Oleg V. Bityukov,
• Pavel Yu. Serdyuchenko,
• Andrey S. Kirillov,
• Gennady I. Nikishin,
• Vera A. Vil’ and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2024, 20, 2959–3006, doi:10.3762/bjoc.20.249

• carried out as part of the investigation of the enzymatic function of cytochrome P-450 with low valent ruthenium complex catalysts. Various phenols 86 bearing para-substituents were transformed into the corresponding tert-butyldioxy dienones 87 smoothly using RuCl2(PPh3)3 as the catalyst (Scheme 31) [83

Synthesis of fluorinated acid-functionalized, electron-rich nickel porphyrins

• Mike Brockmann,
• Jonas Lobbel,
• Lara Unterriker and
• Rainer Herges

Beilstein J. Org. Chem. 2024, 20, 2954–2958, doi:10.3762/bjoc.20.248

• , see Scheme 1). In order to break the symmetry and to generate the acid function only on one side, benzyl protection was performed. From diols 1, 2, and 3 statistical mixtures of unprotected, mono-, and di-protected products were obtained, from which the isolation of the desired mono-protected products

Structure and thermal stability of phosphorus-iodonium ylids

• Andrew Greener,
• Stephen P. Argent,
• Coby J. Clarke and
• Miriam L. O’Duill

Beilstein J. Org. Chem. 2024, 20, 2931–2939, doi:10.3762/bjoc.20.245

• on ex situ analysis (1H, 31P NMR, ESI-MS) following aborted TGA experiments. (b–c) TGA and derivative plots for 1e and commercial samples of decomposition products 6 (Br− salt), 8 (Br− salt) and PPh3. (d–g) TGA thermograms replotted to show the molecular weight as a function of temperature assuming

The charge transport properties of dicyanomethylene-functionalised violanthrone derivatives

• Sondos A. J. Almahmoud,
• Joseph Cameron,
• Dylan Wilkinson,
• Michele Cariello,
• Claire Wilson,
• Alan A. Wiles,
• Peter J. Skabara and
• Graeme Cooke

Beilstein J. Org. Chem. 2024, 20, 2921–2930, doi:10.3762/bjoc.20.244

• that the three materials might function effectively as electron acceptors. OFET device studies The electrical characteristics were confirmed by the fabrication of OFETs. Compounds 3a–c were deposited by spin-coating onto n-doped Si/SiO2/Au substrates. The device performance parameters are summarised in

• −4.30 eV) of some of the most widely used fullerene-based acceptors such as PC60BM and PC70BM [35], which suggests that the three materials might function well as components in OPVs. Among the three materials the introduction of dicyanomethylene groups to compound 2b significantly improved the μh by 60

Recent advances in transition-metal-free arylation reactions involving hypervalent iodine salts

• Ritu Mamgain,
• Kokila Sakthivel and
• Fateh V. Singh

Beilstein J. Org. Chem. 2024, 20, 2891–2920, doi:10.3762/bjoc.20.243

• capability to function as radical initiators. The use of diaryliodonium salts as efficient electrophilic arylating reagents in a wide range of organic transformations is due to their unique features such as solid-state nature, excellent stability, and the presence of a robust leaving group [39][40][41][42

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

• Victor Levet Balu Ramesh Congyang Wang Tatiana Besset INSA Rouen Normandie, Univ Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, F-76000 Rouen, France Beijing National Laboratory for Molecular Sciences CAS key Laboratory of Molecular Recognition and Function CAS Research

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

• presence of the oxime group (Scheme 21). In fact, it represents one of the most active non-glycosylated indirubin derivatives against cancer [11][28]. It has been reported that the free NH function of the indirubin is crucial for CDK inhibition. The reaction of isatin with thiaindan-3-one has been reported

• mentioned above, that the free NH function of indirubin is important for CDK inhibition. We have shown in our group by enzyme studies that glycoside β-33b, lacking the free NH-function, does not act as a CDK inhibitor, despite its high activity against melanoma cells and other cancers [32]. These results

• point to a completely different mode of action. In fact, the exact function of glycosylation is not clear. However, it might be assumed that the carbohydrate moiety increases the water solubility of the indirubin which results in a higher bioavailability of the drug. It might be speculated that 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

• for the detection of both gaseous and/or aqueous H2S are shown in Figure 1 [12][16][17]. These sensors all function via the copper sequestration mechanism, where upon addition of hydrogen sulfide to the quenched bimetallic species, luminescence modulation occurs. In our quest for highly selective

• proposed to function by Cu2+ sequestration. The remaining report is of a terbium(III) complex [Tb(DPA-N3)3]3− (Figure 7), which contains an aryl azide-functionalized ligand. In this system the azide functionality prohibits the energy transfer to the lanthanide ion, effectively quenching luminescence. In

Computational design for enantioselective CO₂ capture: asymmetric frustrated Lewis pairs in epoxide transformations

• Maxime Ferrer,
• Iñigo Iribarren,
• Tim Renningholtz,
• Ibon Alkorta and
• Cristina Trujillo

Beilstein J. Org. Chem. 2024, 20, 2668–2681, doi:10.3762/bjoc.20.224

• performance, for example, the reaction rate, is displayed as a function of the catalyst–substrate interaction, for example, the adsorption energy when considering a heterogeneous catalyst (Figure 1A). The resulting plot exhibits a volcano-like shape consisting of at least two slopes with the best-performing

• determines a function such as E1 = f(E2, TS3). The quality of these correlations is assessed through the square of the Pearson coefficient. The pair of stationary points has to correlate with the energies of the six stationary points previously presented. The quality of the pair considered to describe well

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

• -hexadecylglycerol, as well as other common long-chain alcohols and amides. Although a general defensive function has been proposed for snake abdominal scent glands, the specific chemistry and moderate amounts of acids reported here may suggest a function in chemical signaling for the Mangshan pit viper. In addition

• common fatty acids, which allow for easier evaporation, make acids A–F suitable to be used in chemical communication of P. mangshanensis. However, actual proof of function can only be obtained by bioassays with synthetic material. Interestingly, there are a few structurally related compounds in the

• of several microderivatizations and finally confirmed structurally by synthesis. The structural uniqueness of the compounds, not found in other snake species, suggests a function, may it be in chemical communication, defense, or other traits. The other scent gland constituents are commonly found in

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

• is described in the first two papers in the series on the hydration of α-CD and β-CD, respectively [13][14]. The performed M062X/6-31G(d,p) frequency calculations for each structure ascertain that the wave function corresponds to a minimum on a potential energy hypersurface, but also yields the

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

• result of a photon or neutron of wavelength (λ) scattering off the sample at an angle of 2φ (Equation 1 and Figure 12). Typically, a 2D detector measures the scattered radiation to determine the scattering intensity (I(q)) and is measured as a function of q. The scattering vector has units of reciprocal

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

• are widely used in pharmacology due to their pronounced biological activities and low toxicities. The introduction of a hydroxy function into uracil and pyridine molecules has led to compounds with antioxidant, anti-inflammatory, and immunomodulatory activity (3-hydroxy-6-methyl-2-ethylpyridine, 5

• : oxidation; 6-methyluracil; peroxydisulfate; phthalocyanine catalysts; pyridine; Introduction The Elbs and Boyland–Sims peroxydisulfate oxidation reactions offer a convenient means of introducing the hydroxy function into phenols and aromatic amines [1]. The oxidation of phenol using peroxydisulfate was

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

• nodes and edges through recursive message passing and a readout function, resulting in a molecular representation. There are many variants of GNN models [140][141][142][143], most of which are based on the message passing neural network (MPNN) framework proposed by Gilmer et al. [144]. Encoding

• mapping (AAM) is a process that establishes the correspondence between atoms before and after a reaction, reflecting the reaction mechanism. AAM-exempted methods [145][146][147][148][149][150] apply graph convolutions to each reactant and product molecule separately, and then use a pooling function or

HFIP as a versatile solvent in resorcin[n]arene synthesis

• Hormoz Khosravi,
• Valeria Stevens and
• Raúl Hernández Sánchez

Beilstein J. Org. Chem. 2024, 20, 2469–2475, doi:10.3762/bjoc.20.211

• unique bowl-shape structures and self-assembly in solution have facilitated their widespread use as building blocks in nanomaterials [61][62]. Nevertheless, precisely due to their vast number of applications, functionalized resorcin[n]arenes are needed that meet the needs of the desired function. For

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

• . Determining the apparent reaction kinetics The variation in the conversion of IO (xIO) as the function of time (t) at different temperatures (30 °C, 35 °C, 40 °C) and H2SO4 mass fractions (88%, 90%, 92%, 94%, 96%, and 98%) is depicted in Figure S3 in Supporting Information File 1 and subsequently modeled

• type of compound, and Mc is the activity coefficient function introduced in the next section. By shifting the terms in Equation 9, Equation 10 can be obtained as: Therefore, by plotting as the vertical coordinate and Mc as the horizontal coordinate, the values of n and k0 can be obtained from the

• , specifically when the H2SO4 concentrations were between 15.2 and 18.4 mol/L. By fitting the predicted data, Mc as a function of the H2SO4 concentration at a given temperature was determined (Figure S4 in Supporting Information File 1). In addition, the values of Mc for different sulfuric acid concentrations at

Asymmetric organocatalytic synthesis of chiral homoallylic amines

• Nikolay S. Kondratyev and
• Andrei V. Malkov

Beilstein J. Org. Chem. 2024, 20, 2349–2377, doi:10.3762/bjoc.20.201

• , creating the desired syn-(2R,3S)-homoallylic amine 120 in high diastereo- and enantioselectivity. The reaction was tested with various aryl, benzyl, allyl, and alkyl-functionalised β-formyl N-morpholinyl amides 119; the amide function was also varied. Yields were scattered across the 31–90% range, with 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

• conjugate(s) and the desired analytical output with the information about the protein and conjugate identity. Thus, the linkers have not only the function to simply connect the probe scaffold with an affinity or reporter tag, but they carry previously underappreciated features enhancing the capabilities of

Hydrogen-bond activation enables aziridination of unactivated olefins with simple iminoiodinanes

• Phong Thai,
• Lauv Patel,
• Diyasha Manna and
• David C. Powers

Beilstein J. Org. Chem. 2024, 20, 2305–2312, doi:10.3762/bjoc.20.197

• ]. Iminoiodinanes (ArI=NR) are a subclass of hypervalent iodine reagents that function as nitrene equivalents in synthesis [5][6]. The direct reaction of iminoiodinanes with olefins, which could be envisioned to give rise to aziridines directly, is typically not observed and thus families of transition metal

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

• ]. While the accuracy of the model is paramount, interpretability is also highly desirable. In this regard, MLR bears the advantage that it yields a directly interpretable function which can be used for mechanistic inference. However, it is important to note that the caveat of correlation and causality

• their OSCAR [31] database, the authors used the NaviCatGA genetic algorithm [118] to find the most general catalysts. The fitness function comprised multiple objectives, including the median of the enantioselectivity and activity across the generality probing set. The usage of a multi-objective

Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression

• Tabea Bartsch,
• Stephan Lütz and
• Katrin Rosenthal

Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192

• of the intracellular environment on the function and cellular behavior of proteins are composition, viscosity, and macromolecular crowding [16], these parameters could have a strong impact on the protein synthesis performance using CFPS. For example, the addition of chemical chaperones, such as

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

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