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

• efficiency and effectiveness of reaction conditions design, and enable novel discoveries in synthetic chemistry. Keywords: data preprocessing; reaction conditions prediction; reaction data mining; reaction optimization; reaction representation; Introduction Machine learning (ML) techniques have been widely

• applied to various chemical-related tasks, such as computer-aided synthesis planning (CASP) [1][2][3][4], which can recommend possible synthetic routes for a target molecule and potentially improve the efficiency of developing new synthetic pathways. Many studies have shown that ML-based retrosynthesis

• -scale global models, descriptors with longer feature lengths and higher computational efficiency, such as the first four methods, are preferred. However, for small-scale local models, QM features can offer more compact and accurate information, but they require sampling and optimizing the 3D conformers

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

• reaction process of O-methylisouronium sulfate to improve the reaction efficiency and intrinsic safety. In recent years, continuous flow microreactors have been recognized due to their excellent mass and heat transfer performance, precise control over reaction parameters, and intrinsic safety [5][6][7][8

• shown in Figure S1 in Supporting Information File 1, the conversion of IO gradually increased as the molar ratio of HNO3 elevated. The molar ratio of HNO3 was established at 4.4 equiv, a value chosen to optimize both conversion and atom efficiency. Effect of two types of mixing equipment Upon achieving

• the elimination of mass transfer limitations. The improved mixing efficiency can be attributed to the mixer’s design features, such as its double reverse rotating vortex [27][28], large specific surface area [29], and the incorporation of obstacles within the flow channel [30][31]. Determining

Efficient one-step synthesis of diarylacetic acids by electrochemical direct carboxylation of diarylmethanol compounds in DMSO

• Hisanori Senboku and
• Mizuki Hayama

Beilstein J. Org. Chem. 2024, 20, 2392–2400, doi:10.3762/bjoc.20.203

• ), electrodes (Table 1, entries 2, 6, and 7), and electricity (Table 1, entries 2 and 8–10) were investigated. A current density between 10 and 30 mA/cm2 had little effect on the yield of 2a (Table 1, entries 1–3). Carboxylation of 1a also took place in DMF instead of DMSO as solvent. However, the efficiency

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

• . The limitations in the scope of this methodology include a poor stereoselectivity achieved with 5-membered cyclic 2,3-disubstituted silanes in contrast to the 6-membered analogues (53). A lower efficiency was recorded with 2-substituted allylsilanes bearing either a halogen or an alkyl group with

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

• dozens of kilodaltons. The main advantage of the gel shift assay is to obtain quantitative information of the protein’s probe modification extent, considering high efficiency of the click reaction. Given the bulkiness of the PEG–azide linker, the bioorthogonal reaction needs some optimization, including

• modified peptides can be used for side identification given the relatively high abundance and ionization efficiency due to remaining lysine. The use of the AzTB linker is practical for swift optimization of enrichment workflows, because after the probe–protein conjugates enrichment on the streptavidin

• solvent alone cleans the probe–protein conjugates from excess of ‘click’ reagents and non-protein components present in lysates with high efficiency. The fast sequence of the wash steps is performed on a magnet separating the magnetic beads with aggregated proteins from the wash solution. Next, the

Stereoselective mechanochemical synthesis of thiomalonate Michael adducts via iminium catalysis by chiral primary amines

• Michał Błauciak,
• Dominika Andrzejczyk,
• Błażej Dziuk and
• Rafał Kowalczyk

Beilstein J. Org. Chem. 2024, 20, 2313–2322, doi:10.3762/bjoc.20.198

• significant enhancement of catalytic system efficiency and results from the dramatic decrease in enantioselectivity observed in mill reactions. Additionally, the catalyst’s synthesis requires an extra synthetic step. We decided to conduct further investigations utilizing system A or its modifications. First

• guanidine motif in AA-3 compared to simple AA-1. Alterations in the thiol structure within thiomalonates significantly impact their stability and reactivity, thereby influencing both reaction efficiency and stereochemical outcome, as demonstrated in the case of catalysis employing bifunctional hydrogen bond

• efficiency. Motivated by our curiosity surrounding the reactivity of alicyclic enones with bis-thiomalonates, we embarked on a study to evaluate a chosen catalytic system's efficacy under both standard conditions and mechanochemical milling. We aimed to facilitate the nucleophilic addition of 1–4 to 4

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

• ). Increasing the reaction temperature negatively affected the efficiency of aziridination: Reactions performed at 30 or 50 °C afforded 3a in 50% and 43% yield, respectively (Table 1, entries 5 and 6). Replacing HFIP with 2,2,2-trifluoroethanol (TFE), which is also a commonly encountered fluorinated alcohol

• the generality of H-bond activation of iminoiodinanes for direct aziridination, albeit with modest efficiency for some substrates. The impact of the iminoiodinane structure on the efficiency of HFIP-promoted direct aziridination was next investigated (Scheme 3). For this purpose, cyclopentene was

• % yield. The N-Tces group (Tces = trichloroethylsulfamate) could also be transferred to afford 6f in 39% yield. Finally, the iminoiodinane derived from celecoxib (2i) could be used to transfer this drug moiety to furnish aziridine 6i in 46% yield. In general, the efficiency of aziridination correlates

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

• high efficiency under physiologically active conditions and the absence of any toxic metal ions. SpAAC is biorthogonal, which allows for the specific labeling and imaging of biomolecules even in living cells and organisms. Recently, a more rapid click reaction was desired and the strain-promoted

• ], and crosslinked polymers [14][15][16][17]. Since crosslinking polymers requires high reaction efficiency under mild conditions, developing such reactions is crucial. We previously reported the regioselective double azide addition to octadehydrodibenzo[12]annulene with hexyloxy substituents (DBA-OHex

Selective hydrolysis of α-oxo ketene N,S-acetals in water: switchable aqueous synthesis of β-keto thioesters and β-keto amides

• Haifeng Yu,
• Wanting Zhang,
• Xuejing Cui,
• Zida Liu,
• Xifu Zhang and
• Xiaobo Zhao

Beilstein J. Org. Chem. 2024, 20, 2225–2233, doi:10.3762/bjoc.20.190

• °C, the reaction efficiency significantly decreased (Table 1, entry 13). Alike 2a, the keto isomer of 3a was the dominant isomer, with a keto/enol ratio of 3:1. Then, we tested the effects of different bases on the reaction and found that the strong bases NaOH and KOH gave 3a in high yield (Table 1

Electrochemical allylations in a deep eutectic solvent

• Sophia Taylor and
• Scott T. Handy

Beilstein J. Org. Chem. 2024, 20, 2217–2224, doi:10.3762/bjoc.20.189

• starting material were recovered via extraction with methoxycyclopentane and the CC/EG used in another cycle. Through two recyclings, the reactions were similar in efficiency, although the DES became increasingly viscous as the tin byproducts built up and it became impractical to recycle the DES further

• demonstrate efficient and near quantitative recovery of the metal by electrolysis after product extraction and this recovered metal can be used again for further allylations. Further efforts to improve the efficiency and enable catalytic metal use are underway. Experimental Preparation of deep eutectic

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

• performance for paired approaches. For example, it has been shown that similarity-based pairing during training compound generation for Siamese neural networks can significantly improve model efficiency [36]. Additionally, active learning-based subsampling is an autonomous and adaptive approach that has been

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

• , providing a cost-effective alternative to traditional catalytic methods. The immobilisation of organocatalysts offers the potential to increase catalyst reusability and efficiency in organic reactions. This article reviews the key parameters that influence the effectiveness of immobilised organocatalysts

• supported organocatalyst whose catalytic efficiency can be reproduced over a sufficient number of reaction cycles. Despite the difficulty of the challenge, the design of heterogeneous, recyclable organocatalytic systems is of high interest [8]. The continued development of efficient catalytic recovery

• ]. The role of the polymers as supports for catalysts is not merely passive. These supports significantly influence the reaction environment and catalytic efficiency [42]. Attachment methods, spacer lengths, and polymer nature profoundly impact the catalyst's performance and recyclability. Various

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

• explore complex systems, including glycans, with ever-increasing accuracy and efficiency [44]. Tools for building structural models of carbohydrates Before going into details of the computational tools that can be used to dissect the 3D conformational features of glycans, an overview of the most useful

• simplify the transmission and efficiency of the communication within the scientific community. This led to the extensive use of the symbol nomenclature for glycans (SNFG) representation that is used in all the tools described below (Figure 3) [11][45]. Numerous computer applications have been developed to

• through molecular docking [110]. Advances in information technology and improved computational efficiency have made computational methods integral to modern biological research, and large-scale structure-based docking screens have become common, facilitating the exploration of vast chemical spaces and

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

• pH value. According to atomic force microscopy (AFM) data, the resulting particles had a domain structure and were similar in appearance to raspberries [20]. An interesting feature of the resulting particles was the high efficiency as Pickering emulsifiers: even at a concentration below 0.3 g/L

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

• efficiency of these reactions. In particular, traditional multistep syntheses of pyrazoles have considerably been extended by MCR. Progress has been made in the cyclocondensation of 1,3-dielectrophiles that are generated in situ. Limitations in the regioselectivity of cyclocondensation with 1,3-dicarbonyls

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

• %) would mean that there is less X-ray radiolysis, fewer catalysing species produced and therefore a lower effect on the Z–E reaction. Interestingly, it has been shown previously that the efficiency of electron or hole catalysis of Z–E isomerisation increases with increasing photoswitch concentration, due

• to the closer proximity leading to more efficient transfer of the catalysing species between molecules [40]. This suggests that there is a breakdown in the efficiency of the catalytic transfer at the concentrations studied here, or there is a critical water concentration needed to produce a

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

• aldehyde hydrazones and alkenes for the preparation of pyrazolines was proposed by Tong, Song, et al., achieving similar efficiency using oxone/KBr as an environmentally friendly oxidative system [59]. Most recently, Zhou and Ma et al. described the electrochemical access to 3‑aminopyrazoles 79 from

• -diphenylethylene proceeded with similar efficiency, thereby excluding any radical pathway. As such, it was proposed that the catalytic electrooxidation of iodide (ENH4I = 0.41 V and 0.75 V vs Ag/AgCl in dimethylacetamide for I−/I3− and I3−/I2 redox couples) into iodine provided a green and mild tool to in situ

• prepare 5-thioxo-1,2,4-triazolium inner salts 97. The electrolysis was conducted with two inexpensive graphite electrodes in the absence of additional supporting electrolyte. It could be easily performed on a gram scale, albeit with a slight decrease in the efficiency. It was compatible with a large array

Development of a flow photochemical process for a π-Lewis acidic metal-catalyzed cyclization/radical addition sequence: in situ-generated 2-benzopyrylium as photoredox catalyst and reactive intermediate

• Masahiro Terada,
• Zen Iwasaki,
• Ryohei Yazaki,
• Shigenobu Umemiya and
• Jun Kikuchi

Beilstein J. Org. Chem. 2024, 20, 1973–1980, doi:10.3762/bjoc.20.173

• continues to flow and the reaction can be quenched immediately when necessary, the decomposition of an unstable product under the reaction conditions can be avoided [22][23][24][25]. Furthermore, when a photoreaction is performed in a flow system, there is an advantage that the light irradiation efficiency

• : 50 °C) with half the amount of AgNTf2 (flow: 5 mol %, batch: 10 mol %), and the light irradiation time was shortened to only 2.5 minutes (batch: 1 h). Thus, under the optimal conditions (Table 1, entry 10), the flow reaction system proved extremely useful for improving the efficiency of the present

• batch reaction (Table 2, entry 4: 57% vs 10%). The reaction of 1e substituted with a strong electron-withdrawing trifluoromethyl group afforded the product 3e in high yield (Table 2, entry 5: 77%), again confirming the high efficiency of the flow reaction system (batch: 54%). Next, the effects of the

A new platform for the synthesis of diketopyrrolopyrrole derivatives via nucleophilic aromatic substitution reactions

• Vitor A. S. Almodovar and
• Augusto C. Tomé

Beilstein J. Org. Chem. 2024, 20, 1933–1939, doi:10.3762/bjoc.20.169

• purposes. This study not only contributes to the expansion of accessible N-substituted DPP derivatives but also reveals that such transformations can be achieved with outstanding efficiency and environmental sensitivity by employing mild reaction conditions. Experimental Chemicals and instrumentation The

Negishi-coupling-enabled synthesis of α-heteroaryl-α-amino acid building blocks for DNA-encoded chemical library applications

• Matteo Gasparetto,
• Balázs Fődi and
• Gellért Sipos

Beilstein J. Org. Chem. 2024, 20, 1922–1932, doi:10.3762/bjoc.20.168

• complexity of DELs, there is only limited opportunity to track the efficiency of individual reactions during library synthesis. Therefore, BBs need to pass validation before being used in library synthesis settings. For these bifunctional amino esters, we performed a three-step validation where they were

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• composite compared to the individual constituents tested separately. Solvent-free conditions afforded better yields than traditional solvents (water, toluene, DCM, EtOH, MeOH) and 12 adducts were synthetized in 84–96% yield. Finally, the catalyst was recycled six times with a slight decrease in efficiency

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• regio- and diastereocontrolled hydroxylation at C3, along with transposition of the double bond, to form the desired product 22 in approximately 20% yield with 50% conversion. To enhance efficiency of the enzymatic oxidation, Renata and co-workers conducted two approaches: homolog screening and enzyme

• , efficiency, and robustness of these biocatalysts are expected to enhance their usefulness and generality as synthetic tools. Apart from oxygenated terpenes and RiPPs, chemo-enzymatic approaches for polyketides and non-ribosomal peptides (NRPs) are considered more suitable for the second and third strategies

• novel paradigm for exploiting the inherent specificity and efficiency of enzymatic catalysts within synthetic sequences. The integration of designed substrate analogs that can be transformed by promiscuous enzymes provides a versatile synthetic platform towards natural products and their derivatives. In

Ring opening of photogenerated azetidinols as a strategy for the synthesis of aminodioxolanes

• Henning Maag,
• Daniel J. Lemcke and
• Johannes M. Wahl

Beilstein J. Org. Chem. 2024, 20, 1671–1676, doi:10.3762/bjoc.20.148

• starting from α-bromoacetophenones 4 and disubstituted amines 5 (Scheme 2b). Three different criteria were chosen to evaluate the photochemical cyclization (Scheme 2c). We hypothesized that changes in the π-system of the aromatic ring would have an impact on the efficiency of triplet generation (1 → 31

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• advance and are not recycled in the system. The amino acids are methylated either prior to tRNA binding or after. The efficiency of incorporating unnatural amino acids is lower, but Merryman and Green have demonstrated that an excess of tRNA can overcome this problem [47]. When attempting to incorporate

• system and must be prepared beforehand. The incorporation of unnatural amino acids by the ribosome is less efficient and leads to incomplete translation, resulting in shunt products. Additionally, ribosome recycling efficiency and synthesis of full length proteins declines with length of the primary

• with N-terminal alanine, serine, threonine, glycine, and methionine residues, as well as the antibiotics nisin and haloduracin with good efficiency. Nisin was methylated on its N-terminal isoleucine and on the side chain of Lys12, where two methylations occurred. It is important to note that N

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

• structural properties of the membranes restrain their stability and durability, their humidity and temperature application conditions, and their efficiency and consequently, the performance of fuel cells or eletrolysers [18][19]. Many organic polymers with acidic functional groups have been developed as