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

• scarcity and diversity, as they need to cover a vast reaction space [26][27]. However, collecting data relevant to chemical reactions represents a significant challenge. While specific molecular properties can be precisely computed using existing simulation methods like quantum chemical calculations

• ]. Most of the existing methods were originally designed for predicting reaction properties (such as activation energy, reaction enthalpy, etc.) or classifying reactions, but they can be potentially adapted for reaction conditions prediction by modifying the output layer of the model. Both global reaction

• of molecules using density functional theory (DFT) calculations, which are computationally expensive and time-consuming [62]. To overcome this challenge, some studies have proposed to pre-generate QM properties datasets and train ML models to serve as fast feature generators for new molecules [16

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

• ][41][42][43]. The inhibitory activity of β-lactamases is exhibited by those congeners with a (3R,5R)-configuration, such as clavulanic acid (1), whereas clavams with other configurations are not lactamase inhibitors, although some of these have antifungal or antibacterial properties [35]. In the

• ) 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

• , enhances charge transfer by stabilizing the mesityl moiety. Conversely, the introduction of tert-butyl groups increases the life time of the excited state [52][53][54][55][56]. As a consequence, the PC IV is a strong oxidant in the excited state and displays unique oxidizing properties (E1/2[*PC+/PC

Synthesis and conformational analysis of pyran inter-halide analogues of ᴅ-talose

• Olivier Lessard,
• Mathilde Grosset-Magagne,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2024, 20, 2442–2454, doi:10.3762/bjoc.20.208

• -tetrahalohexanediols. Conformational analysis and lipophilicities of the latter compounds were determined and trihalogenated alkanes were incorporated into piperidines of pitolisant [23]. This work was an extension of our synthetic routes to multivicinal organofluorines to unveil some of their unique properties [24

• order to decipher the key physical properties of complex pyran inter-halides, we performed 19F NMR analysis of halogenated talose analogues 12–15 (Figure 2). First, all analogues adopt standard 4C1-like conformations. Comparison of the vicinal and geminal coupling constants for each organohalogen

Phenylseleno trifluoromethoxylation of alkenes

• Clément Delobel,
• Armen Panossian,
• Gilles Hanquet,
• Frédéric R. Leroux,
• Fabien Toulgoat and
• Thierry Billard

Beilstein J. Org. Chem. 2024, 20, 2434–2441, doi:10.3762/bjoc.20.207

• specific properties of the fluorine atom [1][2][3], fluorinated compounds are now present in a wide range of applications, from materials to life sciences [4][5][6][7][8][9][10][11]. In order to propose new molecules with specific properties for targeted applications, the development of new fluorinated

• moieties is an active research field [12]. Among these emerging fluorinated groups, the association of the CF3 moiety with chalcogens is an interesting approach. In particular, the trifluoromethoxy group (CF3O) possesses valuable properties such as electronegativity [13][14], lipophilicity [15][16

• human physiology [30][31]. Moreover, several selenylated molecules have found applications in various fields such as materials or bioactive compounds [32][33][34][35][36][37][38][39][40][41][42][43]. Some selenylated compounds exhibit fascinating biological properties. Despite these separate converging

Synthesis, electrochemical properties, and antioxidant activity of sterically hindered catechols with 1,3,4-oxadiazole, 1,2,4-triazole, thiazole or pyridine fragments

• Daria A. Burmistrova,
• Andrey Galustyan,
• Nadezhda P. Pomortseva,
• Kristina D. Pashaeva,
• Maxim V. Arsenyev,
• Oleg P. Demidov,
• Mikhail A. Kiskin,
• Andrey I. Poddel’sky,
• Nadezhda T. Berberova and
• Ivan V. Smolyaninov

Beilstein J. Org. Chem. 2024, 20, 2378–2391, doi:10.3762/bjoc.20.202

• antioxidant properties were determined using the reaction with synthetic radicals, the cupric reducing antioxidant capacity assay, the inhibition process of superoxide radical anion formation by xanthine oxidase, and the process of lipid peroxidation of rat liver (Wistar) homogenates in vitro. Keywords

• neuroprotective, antihypoxic effects, act as antiparkinsonian agents [3][4][5], exhibit antitumor and antibacterial activity [6][7][8], possess antioxidant properties for regulating free radical processes [9][10][11]. The functionalization of polyphenolic compounds by introducing various substituents or

• properties [28]. Anti-tuberculosis activity was identified for 5-substituted 2-mercapto-1,3,4-oxadiazoles [29], 5-substituted-2-[(3,5-dinitrobenzyl)-sulfanyl]-1,3,4-oxadiazoles and 1,3,4-thiadiazoles [30]. Some derivatives of 5-(4-tert-butylphenyl)-1,3,4-oxadiazole-2(3H)-thione showed antiproliferative

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

• ; rearrangement; Introduction Nitrogen-containing organic compounds (sometimes referred to as alkaloids due to their basic properties) are of critical importance in medicinal chemistry because of their unique binding properties to biomolecules [1]. Out of 55 drug candidates, approved by the FDA in 2023, 28 (51

Tandem diazotization/cyclization approach for the synthesis of a fused 1,2,3-triazinone-furazan/furoxan heterocyclic system

• Yuri A. Sidunets,
• Valeriya G. Melekhina and
• Leonid L. Fershtat

Beilstein J. Org. Chem. 2024, 20, 2342–2348, doi:10.3762/bjoc.20.200

• , anticancer, non-steroidal anti-inflammatory, antihypertensive, antipsychotic, anxiolytic and in other pharmaceuticals [3][4][5]. Therefore, considering the diversity of biological properties, development of reliable approaches for the synthesis of new nitrogen heterocyclic systems is a highly urgent goal

• high-energy materials [8][9][10][11][12][13]. Moreover, furazan derivatives possess antiproliferative, antibacterial, antiparasitic and antiviral activity [14][15][16]. On the other hand, furoxans referred to as unique heterocyclic compounds that exhibit NO-releasing properties under physiological

• various diseases [17][18][19][20]. Therefore, due to their NO-releasing abilities, furoxan derivatives also demonstrate anticancer, antiplatelet, antiviral and antiparasitic properties [21][22][23][24][25][26][27][28][29][30][31][32]. Another valuable nitrogen heterocyclic scaffold in medicinal chemistry

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

• discuss the properties and applications of different chemical proteomics linkers with special focus on their fragmentation releasing diagnostic ions and how these may improve the confidence in identified active compound–peptide conjugates. The application of advanced search options improves the

• , the linkers were proposed and designed to mainly facilitate the enrichment of the probe–protein or probe–peptide conjugates and their selective release after enrichment. In this review we would like to highlight the fragmentation properties of the different linkers and resulting ions as the valuable

• , the physicochemical properties are highly similar as well as the mass of the conjugate leading to coelution from LC and cofragmentation during MS/MS. The case study of the adamantane-based probe revealed at least five probe-derived diagnostic ions from labile search, which are summarized in Figure 11B

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

• energies of relevant species either via force field or quantum chemical methods to assess the properties of a reaction such as activation energies or selectivity. Irrespective of the degree of automation, in silico calculations are often less time-sensitive than wet-lab experiments and can be used to

• by observing the influence of substituents on a reaction outcome. However, Hammett parameters have shown to not fully describe observed trends. Therefore, complementary representations capturing other properties of a molecule have been derived (vide infra) [28]. While traditional linear free energy

• properties and thus makes it suited towards the accelerated design of chemicals and materials, including organocatalysts [29]. Due to this potential, an increasing number of research groups have used ML to predict and develop new organocatalytic reactions. This review aims to provide a critical overview of

gem-Difluorination of carbon–carbon triple bonds using Brønsted acid/Bu₄NBF₄ or electrogenerated acid

• Mizuki Yamaguchi,
• Hiroki Shimao,
• Kengo Hamasaki,
• Keiji Nishiwaki,
• Shigenori Kashimura and
• Kouichi Matsumoto

Beilstein J. Org. Chem. 2024, 20, 2261–2269, doi:10.3762/bjoc.20.194

• Organofluorine compounds have attracted great attention in various fields, such as organic materials and pharmaceuticals [1][2][3], because fluorinated compounds sometimes show specific properties [4]. So far, several methods have been developed for the synthesis of fluorinated compounds. Using nucleophilic

• also been proposed [19][20]. Thus, the synthesis of fluorinated compounds is an active research field. Among these compounds, skeletons bearing CF2 units are important [21][22][23][24], because such molecules can change the physical properties and biological activity. They can also serve as building

Synthesis and reactivity of the di(9-anthryl)methyl radical

• Tomohiko Nishiuchi,
• Kazuma Takahashi,
• Yuta Makihara and
• Takashi Kubo

Beilstein J. Org. Chem. 2024, 20, 2254–2260, doi:10.3762/bjoc.20.193

• , electrical properties, and reactivity. The generation of the DAntM radical was confirmed by its ESR spectrum, which showed two broad signals. The unpaired electron is primarily localized on the central sp2 carbon and slightly delocalized over the two anthryl moieties. Although the DAntM radical undergoes

• the field of radical chemistry. However, reducing the reactivity of radical species can mean losing one of their most attractive properties. Therefore, it is very important to explore aromatic hydrocarbon radicals that are sufficiently stable for handling, yet reactive under specific conditions

• site, head-to-head σ-dimerization of the DAntM radical could yield 1,1,2,2-tetra(9-anthryl)ethane, which is a new anthracene embedded ethane [30] and would be a good candidate for the synthesis of overcrowded ethylene [31][32][33][34][35][36]. Herein, we report the synthesis and properties of the DAntM

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

• nucleotides and amino acids, as well as energy molecules, salts, buffer, etc., are added. After successful protein synthesis, further substrates can be added for an enzyme activity assay. Although mimicking of cell-like conditions is an approach for optimization, the physical and chemical properties of CFPS

• -physiological conditions have been tested to date that would expand the parameter space in which CFPS can be performed. In this study, the properties of an Escherichia coli extract-based CFPS system are evaluated, and the parameter space is extended to high viscosities, concentrations of inorganic ion and

• some of the gaps in the consideration of the general physical properties and potential effects on the performance of Escherichia coli-based CFPS. We use technical additives, such as water-soluble macromolecular polymers and salts, which are commonly used as deep eutectic solvents (DES) and extend the

Metal-free double azide addition to strained alkynes of an octadehydrodibenzo[12]annulene derivative with electron-withdrawing substituents

• Naoki Takeda,
• Shuichi Akasaka,
• Susumu Kawauchi and
• Tsuyoshi Michinobu

Beilstein J. Org. Chem. 2024, 20, 2234–2241, doi:10.3762/bjoc.20.191

• , DBAs substituted with electron-withdrawing groups have been little studied [19], and their chemical stability and physical properties are not well understood. In this paper, a new DBA substituted with ester groups was synthesized, and the double azide addition was comprehensively investigated. Finally

• , the double azide addition reaction was applied to polymer crosslinking and the mechanical properties of the self-standing polymer films were compared. Results and Discussion Strain-promoted azide–alkyne cycloaddition Octadehydrodibenzo[12]annulene (DBA) with electron-withdrawing carbonyl substituents

• outer side (in-out-ts), but the thermodynamically stable final product is a regioselective “in-in” adduct, i.e., compound 6a. Optical properties Absorption and emission spectra of 6a were measured in CH2Cl2 (Figure 5). The conjugation is changed and a highly-twisted macrocyle forms by the double azide

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

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

• , and in textiles. Although the parent alternariol and the plethora of compounds biosynthetically derived from alternariol are very diverse and show numerous detrimental but also beneficial biological properties, they have never been comprehensively surveyed in a review. Nevertheless, quite a number of

• Trichoderma (Hypocrea) sp. [157]. It is quite astonishing that this assumed main intermediate in the biosynthetic downstream of alternariol was identified as natural product only recently (2021) and that no biological properties were established. The respective 4-hydroxy derivative of 9-O-methylalternariol

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

• –80%) along with their preliminary photophysical (absorption, emission and time resolved fluorescence lifetime) properties. The condensation reaction for assembling the required DPMs were catalyzed with trifluoroacetic acid (TFA) at 0 °C to room temperature (rt), and the stable dipyrromethanes were

• electron transfer processes etc. [26][27][28]. On the other front, doping with heteroatom(s) to the truxene skeleton drastically modulate its unique physical as well as chemical properties besides the geometrical structure, as well [29]. After successful construction of truxene and its asymmetrical isomer

• plethora of hetero-analogues of both truxene and isotruxene have been reported with altered physiochemical properties [30][34][35]. To our best knowledge, derivatizations of the truxene core with heterocycles are limited [33][36][37][38] and needs to be explored for diverse promising applications. Keeping

Finding the most potent compounds using active learning on molecular pairs

• Zachary Fralish and
• Daniel Reker

Beilstein J. Org. Chem. 2024, 20, 2152–2162, doi:10.3762/bjoc.20.185

• properties (‘exploitative’) [18], or a combination of both (‘balanced’) [8]. Explorative active learning provides diverse chemical structures to support model learning while exploitative approaches instead bias towards rapid identification of favorable compounds. As such, explorative strategies may not

O,S,Se-containing Biginelli products based on cyclic β-ketosulfone and their postfunctionalization

• Kateryna V. Dil and
• Vitalii A. Palchykov

Beilstein J. Org. Chem. 2024, 20, 2143–2151, doi:10.3762/bjoc.20.184

• oxidations of rare Biginelli products are discussed in Supporting Information File 1 using compound 2a as an example. In silico evaluation of ADMET parameters and biological profile We performed in silico screening of the biological properties of Biginelli products 2a–r and their postfunctionalized

• derivatives 3–7 using SwissADME (http://www.swissadme.ch) [44], ProTox 3.0 (https://tox-new.charite.de) [45], and MolPredictX (https://www.molpredictx.ufpb.br) [46] free online software. Considering ADMET [47] and other crucial properties, we found that all compounds (except for the nitro derivative 2e) do

Factors influencing the performance of organocatalysts immobilised on solid supports: A review

• Zsuzsanna Fehér,
• Dóra Richter,
• Gyula Dargó and
• József Kupai

Beilstein J. Org. Chem. 2024, 20, 2129–2142, doi:10.3762/bjoc.20.183

• influence on the properties and thus performance of the resulting heterogeneous catalyst. However, immobilisation and structural modification introduce additional steps in the synthesis of the catalyst. Moreover, the catalytic activity and selectivity of immobilised catalysts are often lower than those of

• generated by altering the reaction conditions during synthesis [52][53][54][55][56][57] or by using potassium chloride or ammonium fluoride salts as additives [58][59][60]. In a comprehensive study [61], the catalytic properties of three types (rope, rod and fibre) of mesoporous silica Santa Barbara

• catalyst closer to the support, impacting electronic properties and ligand conformation. With large catalyst molecules, the pores of an ordered mesoporous material being similar in size to the catalyst can create significant diffusion barriers as the catalyst attempts to enter the pores. As a result, the

From perfluoroalkyl aryl sulfoxides to ortho thioethers

• Yang Li,
• Guillaume Dagousset,
• Emmanuel Magnier and
• Bruce Pégot

Beilstein J. Org. Chem. 2024, 20, 2108–2113, doi:10.3762/bjoc.20.181

• strategy to improve or modulate their physicochemical and biological properties [41][42][43][44][45], only few publications have reported a [3,3]-rearrangement with fluorinated molecules (Scheme 1c). In 2020, Wang and co-workers have developed a one-pot [3,3]-sigmatropic rearrangement/Haller–Bauer reaction

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• associated constants designed to reproduce the molecular geometry and selected properties of a system, as well as the naming and labelling of the system atoms, vary from one force field to another; therefore, it is important to ensure compatibility between the input file of the tested structure and the

• have been developed over the years [64][65][66][67][68], to date, the most widely used force field for carbohydrates is GLYCAM, which is continuously updated and improved to accurately describe their peculiar and complex set of conformational and energetic properties [61][69]. For specific studies

Cage-like microstructures via sequential Ugi reactions in aqueous emulsions

• Rita S. Alqubelat,
• Yaroslava A. Menzorova and
• Maxim A. Mironov

Beilstein J. Org. Chem. 2024, 20, 2078–2083, doi:10.3762/bjoc.20.179

• structures existed only within a narrow pH range: when the pH value dropped below 5.5, the chitosan easily dissolved, and when the pH value was above 7, the CMC domains swelled and lost their properties. It is known that the Ugi reaction can be successfully used to obtain cross-linked gels based on

Multicomponent syntheses of pyrazoles via (3 + 2)-cyclocondensation and (3 + 2)-cycloaddition key steps

• Ignaz Betcke,
• Alissa C. Götzinger,
• Maryna M. Kornet and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2024, 20, 2024–2077, doi:10.3762/bjoc.20.178

• agrochemical uses of pyrazoles [13] include insecticides [14], herbicides [15], and fungicides [16]. Furthermore, they are widely applied for the assembly of supramolecular ensembles [17] and molecular systems capable of photoinduced electron transfer [18]. Due to their pertinent photophysical properties [19

Diastereoselective synthesis of highly substituted cyclohexanones and tetrahydrochromene-4-ones via conjugate addition of curcumins to arylidenemalonates

• Deepa Nair,
• Abhishek Tiwari,
• Banamali Laha and
• Irishi N. N. Namboothiri

Beilstein J. Org. Chem. 2024, 20, 2016–2023, doi:10.3762/bjoc.20.177

• properties such as anticancer, anti-HIV protease, anti-ageing, anti-inflammatory and anti-oxidant, to name a few [12][13][14][15][16][17][18][19][20][21][22][23]. Considering the fact that curcumin’s uniqueness is associated with its ability to function as a multifunctional substrate in various organic

Understanding X-ray-induced isomerisation in photoswitchable surfactant assemblies

• Beatrice E. Jones,
• Camille Blayo,
• Jake L. Greenfield,
• Matthew J. Fuchter,
• Nathan Cowieson and
• Rachel C. Evans

Beilstein J. Org. Chem. 2024, 20, 2005–2015, doi:10.3762/bjoc.20.176

• of smart materials whose properties can be controlled using external stimuli is of significant interest for diverse applications spanning soft robotics [1], energy storage [2] and drug delivery [3]. Light is an ideal stimulus as it is non-invasive and can be administered selectively with high

• hydrophilicity [6]. This, in turn, affects the interfacial and self-assembly properties of the PS [4][5][6]. The uniquely tuneable properties of these photoswitchable molecules have led to their successful application in areas such as DNA compaction [8], photorheological fluids [9][10] and micellar catalysis [11

• phototuneable interfacial [16][17][18] and self-assembly properties [19][20]. However, further understanding of factors which affect the isomerisation of these new surfactants, and the effect this has on their self-assembled structures, is still needed to tailor them towards application. Small-angle scattering

Harnessing the versatility of hydrazones through electrosynthetic oxidative transformations

• Aurélie Claraz

Beilstein J. Org. Chem. 2024, 20, 1988–2004, doi:10.3762/bjoc.20.175

• -methoxymethylpyrrolidine)hydrazones could be also key intermediates for the asymmetric synthesis of α-substituted aldehydes and ketones [18][19]. Interestingly, depending on the substitution pattern, the C=N bond can feature different electronic properties [20]. For instance, various hydrazones have been employed for the

• regardless of the electronic properties of the substituents on the N-phenyl ring. When dissymmetric diaryl ketone-derived substrates were employed, the C–N bond formation occurred selectively on the most electron rich aromatic ring. According to the proposed mechanism, this dehydrogenative cyclization of

• substituents on the aromatic moiety regardless of their electronic properties. However, 4,5-disubstituted 1,2,3-thiadiazoles could not be accessed with this methodology. Mechanistically, control experiments with radical trapping agent such as TEMPO ((2,2,6,6-tetramethylpiperidin-1-yl)oxyl) or 1,1