Adaptive experimentation and optimization in organic chemistry

• Artur M. Schweidtmann and
• Philippe Schwaller

Beilstein J. Org. Chem. 2025, 21, 2367–2368, doi:10.3762/bjoc.21.180

• have enabled this transformation. High-throughput experimentation platforms can now rapidly test large numbers of reaction conditions [3]. Machine learning algorithms can process complex chemical data to identify promising directions [4]. Closed-loop systems can autonomously design, execute, and

• approaches across multiple areas. Quijano Velasco et al. review recent advances in high-throughput automated chemical reaction platforms and machine learning algorithms for reaction optimization, showing how these approaches reduce experimentation time and human intervention [8]. They also discuss current

Pathway economy in cyclization of 1,n-enynes

• Hezhen Han,
• Wenjie Mao,
• Bin Lin,
• Maosheng Cheng,
• Lu Yang and
• Yongxiang Liu

Beilstein J. Org. Chem. 2025, 21, 2260–2282, doi:10.3762/bjoc.21.173

• , this strategy has demonstrated remarkable potential in pharmaceutical synthesis, where the rapid generation of molecular diversity from simple precursors is paramount. Looking forward, the fusion of pathway economy with machine learning algorithms and high-throughput experimentation holds promise for

Rhodium-catalysed connective synthesis of diverse reactive probes bearing S(VI) electrophilic warheads

• Scott Rice,
• Julian Chesti,
• William R. T. Mosedale,
• Megan H. Wright,
• Stephen P. Marsden,
• Terry K. Smith and
• Adam Nelson

Beilstein J. Org. Chem. 2025, 21, 1924–1931, doi:10.3762/bjoc.21.150

• diverse co-substrates. A high-throughput approach was used to identify promising substrate/co-substrate/catalyst combinations which were then prioritised for purification by mass-directed HPLC to yield a total of thirty reactive probes. The structural diversity of the probe set was increased by the

• exploited. A high-throughput synthetic approach was harnessed to identify substrate/co-substrate/catalyst combinations, which led to the productive formation of intermolecular reaction products. Overall, the approach enabled the synthesis of thirty diverse reactive probes. The probes were screened for

Preparation of spirocyclic oxindoles by cyclisation of an oxime to a nitrone and dipolar cycloaddition

• Beth L. Ritchie,
• Alexandra Longcake and
• Iain Coldham

Beilstein J. Org. Chem. 2025, 21, 1890–1896, doi:10.3762/bjoc.21.146

• chromatography on silica gel. The structure of this isomer could not be ascertained with certainty from NOESY analysis and initial crystallisation attempts were unsuccessful. However, through use of encapsulated nanodroplet crystallisation (ENaCt), a high-throughput crystallisation technique which controls the

Photocatalysis and photochemistry in organic synthesis

• Timothy Noël and
• Bartholomäus Pieber

Beilstein J. Org. Chem. 2025, 21, 1645–1647, doi:10.3762/bjoc.21.128

• thematic issue that visible light increases the reaction rate of palladium-catalyzed Negishi cross-couplings [34]. The integration of enabling technologies has also contributed to the success of photocatalytic organic synthesis [35]. Automated reaction platforms, high-throughput experimentation techniques

Silver(I) triflate-catalyzed post-Ugi synthesis of pyrazolodiazepines

• Muhammad Hasan,
• Anatoly A. Peshkov,
• Syed Anis Ali Shah,
• Andrey Belyaev,
• Chang-Keun Lim,
• Shunyi Wang and
• Vsevolod A. Peshkov

Beilstein J. Org. Chem. 2025, 21, 915–925, doi:10.3762/bjoc.21.74

• synthetic methods to access diazepines fused with other nitrogen-containing heterocycles towards their broader exploration in high-throughput screening for identifying new drug candidates. Traditional synthetic methods for producing medium-ring nitrogen-containing heterocycles often involve complex

Synthesis and photoinduced switching properties of C₇-heteroatom containing push–pull norbornadiene derivatives

• Daniel Krappmann and
• Andreas Hirsch

Beilstein J. Org. Chem. 2025, 21, 807–816, doi:10.3762/bjoc.21.64

• various positions of the NBD scaffold were envisioned, although such modifications have primarily been investigated theoretically thus far [25][26][27][28]. Recently, high-throughput calculations were conducted to screen a wide array of hetero-substituted NBD species. These studies predominantly

Photocatalyzed elaboration of antibody-based bioconjugates

• Marine Le Stum,
• Eugénie Romero and
• Gary A. Molander

Beilstein J. Org. Chem. 2025, 21, 616–629, doi:10.3762/bjoc.21.49

• light control might also be improved using photochemical transformations. Importantly, optimization of bioconjugation reactions with technologies such as high-throughput experimentation has already been applied on antibodies [51]. Bioorthogonality Bioorthogonal chemistry has transformed our capability

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

• technique for high-throughput experimentation [83]. A further area of development would be the possibility of integrating options for the in-situ monitoring of reactions, such as X-ray and Raman techniques [47][48][84][85][86][87]. In conclusion, in recognizing that both photochemistry and mechanochemistry

New tandem Ugi/intramolecular Diels–Alder reaction based on vinylfuran and 1,3-butadienylfuran derivatives

• Yuriy I. Horak,
• Roman Z. Lytvyn,
• Andrii R. Vakhula,
• Yuriy V. Homza,
• Nazariy T. Pokhodylo and
• Mykola D. Obushak

Beilstein J. Org. Chem. 2025, 21, 444–450, doi:10.3762/bjoc.21.31

• reactions, for instance, have contributed to high-throughput screening for drug discovery, facilitating the identification of new therapeutic compounds. [9][10]. A notable example is ivosidenib, approved in 2018, which was synthesized using the Ugi reaction to target mutated IDH1 in acute myeloid leukemia

Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• therefore can be subjected to automated and high-throughput crystallization studies and, with Szczypiński, Slater, Cooper and co-workers, we were able to isolate all five calculated lowest-energy conformers of cage 1 in the solid state (see crystal cavity heights marked under conformers in Figure 9A) [40

• rational design, which depend on systematic access to incrementally varied experimental datasets, which are not always available for metastable systems. Further, without many-electron metals to model [208][376], high-throughput calculations of organic cages are facile [366][377][378][379][380][381][382

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

• intervention. Herein, we review the currently used state-of-the-art high-throughput automated chemical reaction platforms and machine learning algorithms that drive the optimization of chemical reactions, highlighting the limitations and future opportunities of this new field of research. Keywords: autonomous

• reactors; data processing; high-throughput experimentation; machine learning; reaction optimization; Introduction Organic synthesis plays a crucial role in drug discovery, polymer synthesis, materials science, agrochemicals, and specialty chemicals. Their synthesis and process optimization require

• review follows the steps presented in Figure 1. In the following section, we review the high-throughput platforms currently used to perform chemical reaction optimization. Thereafter, we discuss the development and use of analytical tools and data processing algorithms. After that, we discuss the latest

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 paper also identifies the current limitations and opportunities in this field, such as the data quality and availability, and the integration of high-throughput experimentation. The paper demonstrates how the combination of chemical engineering, data science, and ML algorithms can enhance the

• ]. However, the OFAT method is simplistic and may fail to identify the optimal reaction conditions, since it ignores the possible interactions among the experimental factors. With the rapid development of high-throughput experimentation (HTE) techniques and ML, it has become more feasible to collect large

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

• reduce the number of required experiments. As such, these methods contribute to the acceleration of catalyst discovery, for example through high-throughput virtual screening. Predating these computational techniques is the desire to understand and explain experimental outcomes in organic chemistry with

• a major challenge in organic chemistry and restricts the applicability of literature data for statistical modelling [30]. Despite emerging high-throughput experimentation (HTE) pipelines [44][45], large datasets of high-quality are still scarce. While multiple large datasets are available for

• inspired a manifold of other groups to develop new ML techniques, including graph neural networks. With the continued rise of high-throughput experimentation in organocatalysis [40], we expect ML to be applied to more data sets in this domain to aid in answering a wider variety of research questions. For

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

• ± 4% E-to-Z isomerisation for 10 and 90 wt % AAPTAB, respectively, as determined previously using 1H NMR [20]. SAXS SAXS measurements were performed at the high-throughput SAXS beamline B21, Diamond Light Source (Oxfordshire, UK) [47]. The X-ray beam energy was 13.0 keV and the detector distance set

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

• with the Negishi cross-coupling step in a continuous flow manner [41][42][43]. Continuous flow chemistry offers superior control over reaction parameters compared to traditional batch methods. This approach leads to reproducible reactions, improved safety features, and it can facilitate high-throughput

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

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

• peptide structures. The remaining challenges include combining various post-translational modifications and developing a medium to high throughput screening approach to subject interesting peptide drug candidates to various MTs and perform SAR studies (structure–activity relationship). Overall, RiPP MTs

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

• as high-throughput docking or machine learning [33][34][35][36][37]. In this work, we aimed at the implementation of the GBB reaction for the generation of such ultra-large chemical space, including experimental evaluation of the synthesis success rate (SSR, i.e., percentage of experiments that

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

• and post-translationally modified peptide (RiPP) natural products offer a valuable opportunity for bioinformatics-guided discovery in plants due to their short biosynthetic pathways and gene encoded substrates. Using a high-throughput approach to assemble and analyze 700 publicly available raw

• data in a high throughput manner, we created an automated pipeline. Raw Illumina sequencing data were downloaded using the NCBI SRA Toolkit, the transcriptome was then assembled with rnaSPAdes [15], and the open reading frames were detected with TransDecoder [16][17]. To search for putative precursor

Synthesis of substituted triazole–pyrazole hybrids using triazenylpyrazole precursors

• Simone Gräßle,
• Laura Holzhauer,
• Nicolai Wippert,
• Olaf Fuhr,
• Martin Nieger,
• Nicole Jung and
• Stefan Bräse

Beilstein J. Org. Chem. 2024, 20, 1396–1404, doi:10.3762/bjoc.20.121

• . It offers the additional benefits of chemistry on solid support: straightforward purification of the resin-bound intermediates by washing steps and a high throughput that allows for faster derivatization. Further research is necessary to establish a protocol for the cleavage of 4-substituted

Rhodium-catalyzed homo-coupling reaction of aryl Grignard reagents and its application for the synthesis of an integrin inhibitor

• Kazuyuki Sato,
• Satoki Teranishi,
• Atsushi Sakaue,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai,
• Hiroyuki Takeda,
• Tatsuo Kinashi and
• Masaaki Omote

Beilstein J. Org. Chem. 2024, 20, 1341–1347, doi:10.3762/bjoc.20.118

• developing novel inhibitors of integrin function, we identified a drug candidate (10n) through high throughput screening (HTS) that inhibits the integrin complex formation, which is an important step for integrin activation. The binding inhibitor 10n was effective as IC50 of 190 μM in AlphaScreen system, and

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

• . During preclinical research large screening libraries are integral part of the structure-based drug design and high-throughput screening and facile, efficient synthetic methods to explore diverse chemical spaces are of great help [2][3][4]. However, due to the vastness of chemical space, generation of

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• groups, using a ribosome engineering approach in Streptomyces sp. CB02009 (Figure 2d) [48]. Seyedsayamdost et al. developed the high-throughput elicitor screening (HiTES) approach, a forward chemical genetics method that identifies small-molecule inducers of silent natural products (Figure 2e) [49]. Han

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

• stability, etc. Emerging research methods on bioinformatics, computational modeling, deep learning, protein engineering, and high-throughput screening will accelerate the pace of enzyme discovery to provide a broader platform of tools for employing chemoenzymatic strategies [64][87][88][89]. More