Emerging trends in the optimization of organic synthesis through high-throughput tools and machine learning

• Pablo Quijano Velasco,
• Kedar Hippalgaonkar and
• Balamurugan Ramalingam

Beilstein J. Org. Chem. 2025, 21, 10–38, doi:10.3762/bjoc.21.3

• demands solutions that meet multiple targets, such as yield, selectivity, purity, cost, environmental impact, etc. In recent years, the advancement of artificial intelligence (AI), machine learning (ML), and automation has produced a paradigm shift for chemical synthesis optimization techniques. By

• consonant and/or conflicting targets. In addition, the incorporation of lab robotics into chemical synthesis has enabled the development of closed-loop optimization platforms capable of executing optimization campaigns rapidly with minimal human intervention, relieving experimenters from labor-intensive

• trends in the selection of optimization algorithms for chemical synthesis. Finally, we highlight the future directions and opportunities in the field. For an in-depth overview on the topic of chemical reaction optimization, the readers are referred to prominent reviews by Taylor et al. [5], Griffin et al

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

• an “azacorannulene”. Working from graph structures based on chemically stable (“group elementary”) nodes is a useful principle in molecular design and chemical synthesis. Such a perspective is important to understand fundamental physical organic molecular properties as well as to predict desirable

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

• (1O2) finds many applications in photochemistry and photobiology, e.g., for wastewater treatment, fine chemical synthesis, and photodynamic therapy (PDT) [79][80][81][82][83]. Additionally, after light excitation, porphyrins can also oxidize a substrate by accepting electrons from a substrate molecule

Enantioselective regiospecific addition of propargyltrichlorosilane to aldehydes catalyzed by biisoquinoline N,N’-dioxide

• Noble Brako,
• Sreerag Moorkkannur Narayanan,
• Amber Burns,
• Layla Auter,
• Valentino Cesiliano,
• Rajeev Prabhakar and
• Norito Takenaka

Beilstein J. Org. Chem. 2024, 20, 3069–3076, doi:10.3762/bjoc.20.255

• ; Introduction Enantioenriched α-allenic alcohols are an important class of chiral building blocks used for the chemical synthesis of biologically relevant molecules [1][2][3][4][5]. Their strength comes from the rich synthetic versatility [6][7][8][9] and biological relevance [10] of the allene functionality

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

• 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

5th International Symposium on Synthesis and Catalysis (ISySyCat2023)

• Anthony J. Burke and
• Elisabete P. Carreiro

Beilstein J. Org. Chem. 2024, 20, 2704–2707, doi:10.3762/bjoc.20.227

• fundamental to advancing technologies that address global challenges in health, sustainability, and beyond. By enabling the production of complex molecules with specific functions, chemical synthesis and catalysis play a key role in innovation across the above-mentioned fields and thus improve our quality of

Synthesis and cytotoxicity studies of novel N-arylbenzo[h]quinazolin-2-amines

• Battini Veeraiah,
• Kishore Ramineni,
• Dabbugoddu Brahmaiah,
• Nangunoori Sampath Kumar,
• Hélène Solhi,
• Rémy Le Guevel,
• Chada Raji Reddy,
• Frédéric Justaud and
• René Grée

Beilstein J. Org. Chem. 2024, 20, 2592–2598, doi:10.3762/bjoc.20.218

• describe a short and efficient synthesis for this type of novel skeleton and to prepare a focused library for these targets C. Further, we will report results on their cytotoxic activities. Results and Discussion Chemical synthesis For the preparation of our targets, we selected a flexible strategy which

• has not been used earlier, should offer attractive potentialities in bioorganic and medicinal chemistry. Extension of these studies are ongoing in our laboratories and corresponding results will be reported in due course. Experimental Chemical synthesis General information All reactions were performed

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

• the Open Reaction Database (ORD) [36], an open-source initiative to collect and standardize chemical synthesis data from various literature sources. The ORD allows chemists to upload reaction data associated with their publications, and aims to serve as a benchmark for ML development. However, the ORD

• capture of experimental records of chemical reactions from chemical synthesis papers. This development demonstrates significant advancements in streamlining the data extraction process for chemical research. Implicit data issues and data preprocessing tools The quality of training data is a crucial factor

• enhancing the overall chemical synthesis pathway. They demonstrated the predictive pathway for sonidegib synthesis, but it still required chemical insights to verify the compatibility of the solvents predicted by the global model with the reactants. Moreover, in a multistep synthesis route, the

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

• use the optimized conditions in entry 2, because reducing the amount of Bu4NBF4, for example, to 5 equiv is important from the viewpoint of eco-friendly chemical synthesis. The reaction time of 16 h also seems to be suitable for the investigation. Thus, the combination of Tf2NH and Bu4NBF4 might

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

• screening and rapid optimization [46][47]. Homogenous heating and mixing in flow reactors can lead to higher reaction rates and yields. In terms of photochemistry, continuous flow setups provide enhanced light irradiation as well [48][49]. These advantages make flow chemistry a powerful tool for chemical

• synthesis and industrial applications [50][51]. To assess the advantage of moving from batch to flow, the production of compounds 2b and 2i was carried out with the telescoped approach. Despite the difference in the yield being minimal, the rate of the transformation showed a significant improvement under

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

• approach" merging efficient enzymatic synthesis – traditionally employed in the biosynthesis of natural products by microorganisms and plants – with precise chemical synthesis conducted by chemists. Chemo-enzymatic total syntheses reported recently fall into three main categories based on the purpose for

• tricyclic scaffold was produced through scalable chemical synthesis. Subsequently, in vitro enzymatic oxidative functionalizations were carried out during the oxidation stage. The exploration of Bsc9 homologs and directed evolution expanded the scope of substrates of the dioxygenase beyond the natural

• biosynthetic intermediate 8 to its analogs 21, enabling the chemo-enzymatic total synthesis of 1. The chemical synthesis commenced with the preparation of two fragments and their subsequent coupling to assemble the core 5/8/5 tricyclic scaffold (Scheme 3A). The left-half fragment, aldehyde 14, was synthesized

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

• three main routes for the synthesis of methylated peptides: chemical synthesis [33][34], in vitro ribosomal synthesis [35], and enzymatic synthesis. Chemical synthesis. Three main categories of reactions are commonly used: reductive amination, reductive ring openings, and the use of methylating agents

• peptide methylation. Biocatalysis provides an efficient and sustainable alternative to chemical synthesis strategies. Both NRPS and RiPP biosynthetic machineries can be used for cell-based or in vitro strategies [53]. Especially well suited as biocatalysts are MTs from RiPP pathways, as they demonstrate

Generation of multimillion chemical space based on the parallel Groebke–Blackburn–Bienaymé reaction

• Evgen V. Govor,
• Vasyl Naumchyk,
• Ihor Nestorak,
• Dmytro S. Radchenko,
• Dmytro Dudenko,
• Yurii S. Moroz,
• Olexiy D. Kachkovsky and
• Oleksandr O. Grygorenko

Beilstein J. Org. Chem. 2024, 20, 1604–1613, doi:10.3762/bjoc.20.143

• purposes [1][2][3][4][5][6]. Isonitrile-based multicomponent reactions, such as the Groebke–Blackburn–Bienaymé (GBB) reaction, is an important tool in chemical synthesis providing easy access to a huge compound diversity and complexity [7][8][9][10][11][12][13][14][15][16][17]. Essentially, the GBB

Electrocatalytic hydrogenation of cyanoarenes, nitroarenes, quinolines, and pyridines under mild conditions with a proton-exchange membrane reactor

• Koichi Mitsudo,
• Atsushi Osaki,
• Haruka Inoue,
• Eisuke Sato,
• Naoki Shida,
• Mahito Atobe and
• Seiji Suga

Beilstein J. Org. Chem. 2024, 20, 1560–1571, doi:10.3762/bjoc.20.139

• ; quinoline; Introduction Nitrogen-containing molecules are important bioactive compounds and intermediates in chemical synthesis. Therefore, the chemical transformations of nitrogen-containing compounds have been widely studied in the field of organic synthesis [1][2][3][4]. For instance, the reduction of

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• product structures were experimentally determined, such as by crystallography, nuclear magnetic resonance (NMR) analysis or by chemical synthesis, were obtained for further analysis. The modules in PKSs were categorized as α-module (containing KS-AT-ACP tridomain), β-module (KS-AT-KR-ACP), γ-module (KS-AT

Generation of alkyl and acyl radicals by visible-light photoredox catalysis: direct activation of C–O bonds in organic transformations

• Mithu Roy,
• Bitan Sardar,
• Itu Mallick and
• Dipankar Srimani

Beilstein J. Org. Chem. 2024, 20, 1348–1375, doi:10.3762/bjoc.20.119

• Mithu Roy Bitan Sardar Itu Mallick Dipankar Srimani Department of Chemistry, Indian Institute of Technology-Guwahati, Kamrup, Assam 781039, India 10.3762/bjoc.20.119 Abstract Alkyl and acyl radicals play a critical role in the advancement of chemical synthesis. The generation of acyl and alkyl

Stability trends in carbocation intermediates stemming from germacrene A and hedycaryol

• Naziha Tarannam,
• Prashant Kumar Gupta,
• Shani Zev and
• Dan Thomas Major

Beilstein J. Org. Chem. 2024, 20, 1189–1197, doi:10.3762/bjoc.20.101

• germacrene A and hedycaryol and how this might affect product distribution in chemical synthesis and biosynthesis. Additionally, we compare the effect of the choice of DFT functional and basis set on the results. Methods The structures of all studied intermediate carbocations originating from germacrene A

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

• complexity of chemical synthesis towards novel drugs has almost doubled from eight chemical steps to an average of 14 in 2021 [1]. Therefore, the need for robust reactions compatible with many functional groups in complex molecules is an integral part in contemporary medicinal chemistry and drug development

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• -inflammatory properties, hepatorenal protection, and anticancer activity. They are often used as coloring and seasoning agents. Due to the limited content of crocins in plants and the high cost of chemical synthesis, the supply of crocins is insufficient to meet current demand. The biosynthetic pathways for

• cell suspension culture, heterologous biosynthesis, and total synthesis [16][17]. Crocins can be obtained from plant cell culture, but the production is prone to epigenetic silencing and toxic intermediates. The chemical synthesis of crocins is challenging due to the presence of numerous chiral centers

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• macrocyclizations (Scheme 1c). NAC thioester and other related mimics (such as coenzyme A (CoA), phosphopantetheine, and thiophenol) span the gap between the chemical synthesis and biosynthesis languages and expand the substrate promiscuity of TE domains. This bridge makes the in vitro TE-catalyzed macrocyclization

• contrast to Kang’s chemical synthesis route, this biotransformation provided a more efficient and productive strategy for the desoaminylation of macrolide aglycones. Combining in vitro and in vivo enzymatic reactions together, this chemoenzymatic platform exhibits the potential to access a broader range of

Regioselective quinazoline C2 modifications through the azide–tetrazole tautomeric equilibrium

• Dāgs Dāvis Līpiņš,
• Andris Jeminejs,
• Una Ušacka,
• Anatoly Mishnev,
• Māris Turks and
• Irina Novosjolova

Beilstein J. Org. Chem. 2024, 20, 675–683, doi:10.3762/bjoc.20.61

• of 4-azido-6,7-dimethoxy-2-sulfonylquinazoline derivatives 12 were proven by chemical synthesis of the regioisomers 15 (Scheme 7) and X-ray analysis of 12a (Scheme 6). 6,7-Dimethoxy-2,4-diazidoquinazoline (13) was synthesized from commercially available dichloroquinazoline 7 in 93% yield. Further

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• for 6000 years [1]. Initially, indigo has been extracted from the plant species, for example Indigofera tinctoria and Polygonum tinctorium in Asia and America, Isatis tinctoria or dyer’s woad in Europe [2] before the chemical synthesis of indigo was achieved by the German chemist Adolf von Baeyer [3

• ]. As an alternative to the chemical synthesis of indigo, environmentally friendly biological approaches towards constructing the indigo scaffold are also being developed for nearly a century [5][6][7][8]. The biosynthetic methods include production of indigo by microorganisms and enzymatic synthesis

Optimizations of lipid II synthesis: an essential glycolipid precursor in bacterial cell wall synthesis and a validated antibiotic target

• Milandip Karak,
• Cian R. Cloonan,
• Brad R. Baker,
• Rachel V. K. Cochrane and
• Stephen A. Cochrane

Beilstein J. Org. Chem. 2024, 20, 220–227, doi:10.3762/bjoc.20.22

• bacteria. Accessing this valuable cell wall precursor is important both for studying cell wall synthesis and for studying/identifying novel antimicrobial compounds. Herein, we describe optimizations to the modular chemical synthesis of lipid II and unnatural analogues. In particular, the glycosylation step

• ramoplanin [2]. It is also the target for a host of other antimicrobials (mostly non-ribosomal peptides), including the tridecaptins [3], nisin [4], teixobactin [5], clovibactin [6], malacidin [7], and cilagicin [8]. Despite significant progress in the chemical synthesis of lipid II and its analogues, the

• , the chemical, chemoenzymatic, or biochemical synthesis of lipid II and its variants has been achieved by several research groups [10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27]. Nonetheless, considering the current state of knowledge, the chemical synthesis approach emerges as

Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration

• Yipeng Yin,
• Reed Arneson,
• Alexander Apostle,
• Adikari M. D. N. Eriyagama,
• Komal Chillar,
• Emma Burke,
• Martina Jahfetson,
• Yinan Yuan and
• Shiyue Fang

Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146

• ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and

• have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex reaction mixture using the catching-by-polymerization (CBP) method. To determine the authenticity of the ODNs, 399 and

• to address all the aforementioned problems, such as generating sequences having highly stable secondary structures [18]. In this paper, we report a method to access long ODNs involving automated direct de novo chemical synthesis and isolation of full-length sequences using the catching-by

Photoredox catalysis enabling decarboxylative radical cyclization of γ,γ-dimethylallyltryptophan (DMAT) derivatives: formal synthesis of 6,7-secoagroclavine

• Alessio Regni,
• Francesca Bartoccini and
• Giovanni Piersanti

Beilstein J. Org. Chem. 2023, 19, 918–927, doi:10.3762/bjoc.19.70

• requires a multistep process in conventional chemical synthesis [39][40][41]. Among the various widely available and abundant substrates for photocatalyzed reactions, natural and unnatural α-amino acids play a very important role, given their paramount importance across several chemistry fields as well as