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

• Keith G. Andrews Department of Chemistry, Durham University, Lower Mount Joy, South Rd, Durham, DH1 3LE, UK 10.3762/bjoc.21.30 Abstract The bespoke environments in enzyme active sites can selectively accelerate chemical reactions by as much as 1019. Macromolecular and supramolecular chemists have

• between a simple, highly symmetrical, often hydrophobic pocket of a typical coordination cage host system and the complex, highly unsymmetrical and largely polar environment of an enzyme active site is a moot point… [since]… the mechanisms which an enzyme utilizes to accelerate chemical reactions are in

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

• and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore 10.3762/bjoc.21.3 Abstract The discovery of the optimal conditions for chemical reactions is a labor-intensive, time-consuming task that requires exploring a high-dimensional parametric space. Historically

• , the optimization of chemical reactions has been performed by manual experimentation guided by human intuition and through the design of experiments where reaction variables are modified one at a time to find the optimal conditions for a specific reaction outcome. Recently, a paradigm change in

• 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

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

• product biosynthesis, along with all the information an organism needs, are encoded in its genome. Genetic information is transcribed and translated into proteins that carry out chemical reactions that sustain life, which include both primary metabolism and the biosynthesis of natural products. Direct

Young investigators in natural products chemistry, biosynthesis, and enzymology

• Jeffrey D. Rudolf,
• Lena Barra and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 2720–2721, doi:10.3762/bjoc.20.229

• . Their privileged structures have led organic and bioorganic chemists to develop methods to construct them. Our fundamental knowledge in enzymology is continually expanded by enzymes involved in natural products biosynthesis, as their production requires evolved enzymes to perform chemical reactions

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

• /bjoc.20.212 Abstract This review surveys the recent advances and challenges in predicting and optimizing reaction conditions using machine learning techniques. The paper emphasizes the importance of acquiring and processing large and diverse datasets of chemical reactions, and the use of both global

• 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

• – allowing for the generation of extensive data through large-scale simulations – chemical reactions pose a much greater difficulty for accurate simulation. The development of systematic theoretical calculations to model correlations between reaction yields and various substrates and catalysts requires

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

• catalyst and reaction design The design of chemical reactions encompasses various aspects, from the choice of the employed catalyst to the selection of ideal reaction conditions. While traditionally, all of this has been performed by chemical knowledge, intuition and rational design, the last years have

Synthesis of polycyclic aromatic quinones by continuous flow electrochemical oxidation: anodic methoxylation of polycyclic aromatic phenols (PAPs)

• Hiwot M. Tiruye,
• Solon Economopoulos and
• Kåre B. Jørgensen

Beilstein J. Org. Chem. 2024, 20, 1746–1757, doi:10.3762/bjoc.20.153

• Information File 1). Naphthalene-1-ol (1b) gave a well-defined oxidation peak at 0.95 V (vs Fe/Fe+) while naphthalene-2-ol (1a) showed an oxidation peak at 1.14 V (vs Fe/Fe+). The oxidation peak potential difference between 1b and 1a was 190 mV. PAHs undergo rapid irreversible chemical reactions upon electron

Synthesis of cyclic β-1,6-oligosaccharides from glucosamine monomers by electrochemical polyglycosylation

• Md Azadur Rahman,
• Hirofumi Endo,
• Takashi Yamamoto,
• Shoma Okushiba,
• Norihiko Sasaki and
• Toshiki Nokami

Beilstein J. Org. Chem. 2024, 20, 1421–1427, doi:10.3762/bjoc.20.124

• polymerization of organic molecules is an important strategy for the preparation of functional materials, such as conducting polymers [1][2][3][4][5]. Electrochemical reactions can be controlled by electric potential or current, electrodes, and electrolytes, which are not available in conventional chemical

• reactions. Therefore, electrochemical polymerizations can be utilized for selective synthesis. Cyclic oligosaccharides are an important class of host molecules, and some natural cyclic oligosaccharides are produced by enzymatic processes. However, the corresponding chemical syntheses are still primitive [6

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

• facilitate important chemical reactions. Thus, we will focus on the reports detailing organic transformations that proceed via visible-light-induced deoxygenative generation of acyl radicals from carboxylic acids and acid anhydrides that have appeared since 2019. Review General mechanism of photoredox

• targeted absorption wavelength, and the overall efficacy. Researchers continue to explore and design photocatalysts to enhance the performance in various photocatalytic applications. Visible-light-induced photoredox catalysis has been used in a variety of chemical reactions, including C–C, C–N, C–O, and C

• light, a sustainable and abundant energy source, to initiate chemical reactions. This approach offers milder reaction conditions, which often result in improved selectivity and functional group compatibility. Additionally, it allows the activation of typically inert bonds and can enable the development

Oxidative hydrolysis of aliphatic bromoalkenes: scope study and reactivity insights

• Amol P. Jadhav and
• Claude Y. Legault

Beilstein J. Org. Chem. 2024, 20, 1286–1291, doi:10.3762/bjoc.20.111

• alternative reaction pathway. Keywords: bromoalkenes; bromoketones; hypervalent iodine; oxidative hydrolysis; Ritter-type; Introduction Organic synthesis heavily relies on oxidative transformations to facilitate chemical reactions. One popular method for achieving these transformations is using redox-active

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• of green chemistry. Organocatalysis is the acceleration of chemical reactions with the use of small organic compounds, which do not contain any amounts of enzyme or inorganic elements [37][38][39]. The benefits of solid acid catalysis render them as an appealing choice, compared to their liquid

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• have been published that record the dynamic behavior of a wide range of molecules and chemical reactions. One such process was the dimerization of C60 fullerene in a carbon nanotube peapod, i.e., hybrid structures consisting of fullerene molecules encapsulated in single-walled carbon nanotubes (SWCNT

1-Butyl-3-methylimidazolium tetrafluoroborate as suitable solvent for BF₃: the case of alkyne hydration. Chemistry vs electrochemistry

• Marta David,
• Elisa Galli,
• Richard C. D. Brown,
• Marta Feroci,
• Fabrizio Vetica and
• Martina Bortolami

Beilstein J. Org. Chem. 2023, 19, 1966–1981, doi:10.3762/bjoc.19.147

• ]. Considering the intrinsic ionic nature of ILs, they act as very different chemical medium compared to molecular solvents, having the possibility of stabilizing charged or dipolar intermediates. Therefore, ILs can be used to modulate outcomes for some chemical reactions [82][83]. There are only a few reported

Selectivity control towards CO versus H₂ for photo-driven CO₂ reduction with a novel Co(II) catalyst

• Lisa-Lou Gracia,
• Philip Henkel,
• Olaf Fuhr and
• Claudia Bizzarri

Beilstein J. Org. Chem. 2023, 19, 1766–1775, doi:10.3762/bjoc.19.129

• solvents and with water, it has been used in a large variety of (electro)chemical reactions [53]. The hydroxy group of this alcohol has a pKa of 9.3 [54][55], so we can expect that it is a suitable proton donor for this kind of reaction. We performed the photocatalytic CO2 reduction by dissolving in 5 mL 1

Benzoimidazolium-derived dimeric and hydride n-dopants for organic electron-transport materials: impact of substitution on structures, electrochemistry, and reactivity

• Swagat K. Mohapatra,
• Khaled Al Kurdi,
• Samik Jhulki,
• Georgii Bogdanov,
• John Bacsa,
• Maxwell Conte,
• Tatiana V. Timofeeva,
• Seth R. Marder and
• Stephen Barlow

Beilstein J. Org. Chem. 2023, 19, 1651–1663, doi:10.3762/bjoc.19.121

• wide range of semiconductors, they must exhibit low ionization energies and thus air sensitivity. One approach to circumvent this issue is to identify systems where the electron-transfer process is coupled to other chemical reactions, increasing the kinetic stability of the dopant to air, and thus

Radical chemistry in polymer science: an overview and recent advances

• Zixiao Wang,
• Feichen Cui,
• Yang Sui and
• Jiajun Yan

Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116

• a higher energy level or even the vacuum, generating radical species. The energy of UV photons is comparable to the energy of chemical bonds [163], and therefore photons are particularly suitable for driving chemical reactions on polymer surfaces. Benzophenone is the best-established source of

Photoredox catalysis harvesting multiple photon or electrochemical energies

• Mattia Lepori,
• Simon Schmid and
• Joshua P. Barham

Beilstein J. Org. Chem. 2023, 19, 1055–1145, doi:10.3762/bjoc.19.81

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• biochemical reaction and the many chemical reactions that accompany it is the hydrolysis reaction of ATP (adenosine 5’-triphosphate) to {ADP (adenosine 5’-diphosphate) + phosphate}: The apparent reaction quotient for this reaction is And the apparent equilibrium constant is Here, (aq) denotes that the

• individual chemical reactions. And, the value of ΔrN(H+) for the (overall) biochemical reaction can be calculated by using appropriate weighting factors for the values of ΔrN(H+) for each chemical reaction in this ensemble of chemical reactions. Thus, in general, ΔrN(H+) does not have an integral value

• . Corresponding to each of these chemical reactions, there is an equilibrium constant K. Thus, for Equation 5 where a is the activity of the specified species. Note that the determination of K′ relies on measured total concentrations and should be reported without any corrections for activity coefficients

Friedel–Crafts acylation of benzene derivatives in tunable aryl alkyl ionic liquids (TAAILs)

• Swantje Lerch,
• Stefan Fritsch and
• Thomas Strassner

Beilstein J. Org. Chem. 2023, 19, 212–216, doi:10.3762/bjoc.19.20

• compounds, acylation is possible by an organic acid chloride/acid anhydride and a Lewis acid [6][7]. In the course of the development of ionic liquids (ILs) as a reaction medium for chemical reactions [8][9], the Friedel–Crafts reaction was also examined [10][11][12][13][14][15][16]. First protocols were

Revisiting the bromination of 3β-hydroxycholest-5-ene with CBr₄/PPh₃ and the subsequent azidolysis of the resulting bromide, disparity in stereochemical behavior

• Christian Schumacher,
• Jas S. Ward,
• Kari Rissanen,
• Carsten Bolm and
• Mohamed Ramadan El Sayed Aly

Beilstein J. Org. Chem. 2023, 19, 91–99, doi:10.3762/bjoc.19.9

• leaving group at the 3β-position, have a unique feature in their chemical reactions. In these steroids, the breaking of the C3–X bond is facilitated by the formation of a cationic strained cyclopropane intermediate, which is formed by translocation of the C5–π bond electrons to the homoallylic carbon atom

Combining the best of both worlds: radical-based divergent total synthesis

• Kyriaki Gennaiou,
• Antonios Kelesidis,
• Maria Kourgiantaki and
• Alexandros L. Zografos

Beilstein J. Org. Chem. 2023, 19, 1–26, doi:10.3762/bjoc.19.1

• chemoselective manner [3]. The development of persistent radicals [4] as synthons in chemical synthesis, coupled with the advancements in generating and manipulating transient radicals [5] as cross-coupling partners in an array of chemical reactions, gives access to a wide variety of “new” retrosynthetic

Inline purification in continuous flow synthesis – opportunities and challenges

• Jorge García-Lacuna and
• Marcus Baumann

Beilstein J. Org. Chem. 2022, 18, 1720–1740, doi:10.3762/bjoc.18.182

• flexibility at low cost or exploit standardized flow reactor modules readily available from various vendors. The growing popularity of flow chemistry over the last two decades has led to many developments to streamline important chemical reactions, overcome limitations due to highly unstable intermediates

• ][19] due to the advantageous dimensioning inherent in flow chemistry setups. With further advances in these fields underway, many applications also achieve more sustainable chemical processing by intensifying chemical reactions, reducing solvent and energy consumption, and replacing stoichiometric

• process. One question which is thereby of great importance is whether inline purification is required to improve the overall process. This is an important question as the removal of impurities and spent reagents typically facilitates subsequent chemical reactions in a telescoped multistep sequence. In

Supramolecular approaches to mediate chemical reactivity

• Pablo Ballester,
• Qi-Qiang Wang and
• Carmine Gaeta

Beilstein J. Org. Chem. 2022, 18, 1463–1465, doi:10.3762/bjoc.18.152

• , Salerno, Italy 10.3762/bjoc.18.152 Nature continuously inspires scientists to design novel prototypes of artificial systems with more and more advanced functions and properties [1][2]. In this regard, one of the greatest innovations was the discovery that small molecules can catalyze/mediate chemical

• reactions by a biomimetic approach [3][4]. Very recently, many efforts have been devoted to study supramolecular catalysis processes [5][6][7][8][9][10][11][12][13][14] in which macrocyclic hosts, self-assembled capsules and metallo-cages were employed as catalysts or nanocontainers. The primary

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• with such information, the use of modern chemical reactions as well as the reinvestigation of old synthetic pathways and the help of modern purification and analytical tools are likely to provide new insights and opportunities to reach new chemical entities. The series of books [276] on heterocycle

• [288][289][290][291][292][293]. Moreover, the use/design of new chemical reactions may lead to hard-to-get and original analogues possibly better than the one reported. One example, depicted in Scheme 2, would be the fluorination, under superacid conditions [294], of the highly elaborated anticancer

Cyclodextrin-based Schiff base pro-fragrances: Synthesis and release studies

• Attila Palágyi,
• Jindřich Jindřich,
• Juraj Dian and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2022, 18, 1346–1354, doi:10.3762/bjoc.18.140

• industry, the covalent bond that links the fragrance to its substrate must be cleaved under environmental conditions found in everyday life, and the substrate should be non-volatile and non-toxic [17]. Typical triggers that may be used for mild chemical reactions are temperature, enzymatic or pH-dependent