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

• utilized effectively to maximize experimental outcomes. (iv) Enhanced experimental control on the process to deliver constant product quality to meet desired specifications and standards. (v) By providing instantaneous feedback, real-time analysis accelerates the optimization process, reducing the

• Analysis (MOCCA) package, designed for integration into both automated and manual workflows. MOCCA offers a range of benefits, including automated management of internal standards for precise relative quantification, reliable peak assignments, accelerated sample processing, and efficient deconvolution of

Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

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

• ]. While some important efforts have been made to establish uniform data reporting standards [42][43], they are getting picked up by the community rather slowly. With data from experiments conducted by different scientists under varying conditions and adhering to various standards, reproducibility remains

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

• were taken from the databases Chemistry WebBook by the National Institute of Standards and Technology (NIST) (https://webbook.nist.gov/) at 1 bar and 25 °C, PubChem by the National Center for Biotechnology and Information (https://pubchem.ncbi.nlm.nih.gov/), and GESTIS-Stoffdatenbank by Institut für

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

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

• found in Diaporthe cameroonensis [143]. No biological activities were determined for these compounds (Figure 7). A number of sulfate conjugates have been synthesized and used as standards for mass-spectrometric or HPLC analyses [134][141][144]. In this course it turned out that 3-O-sulfates of

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

• various pocket descriptors on a large scale. Fpocket 1.0 outperforms industry standards by detecting a high percentage of pockets within the best-ranked ones and offers a fast, open-source solution for protein pocket detection (https://github.com/Discngine/fpocket). 3. GRID [115]: It is a computational

A fiber-optic spectroscopic setup for isomerization quantum yield determination

• Anouk Volker,
• Jorn D. Steen and
• Stefano Crespi

Beilstein J. Org. Chem. 2024, 20, 1684–1692, doi:10.3762/bjoc.20.150

• photon flux, i.e., the number of photons impinging a unit area of the sample in a unit of time [10]. Potassium ferrioxalate [39][40] is one of the most used actinometers while also some azobenzene derivatives have been reported as reaction quantum yield standards [11][22]. Although new chemical

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

• mass spectra were used to generate a GNPS network using the following parameters: 0.2 Da precursor ion mass tolerance, 0.5 Da fragment ion tolerance, and a minimum of 8 matched fragment ions. Marfey’s analysis To determine the stereochemistry of the new molecules, Marfey’s analysis was used. Standards

• resuspended in 200 µL of MeOH. The sample was injected (6 µL) onto UPLC-MS using the same conditions and instrument as the amino acids standards. To normalize the retention time, 1 µM of fluorescein was added to the standard and peptide samples before injection onto the UPLC-MS. The retention time for the

Cofactor-independent C–C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis

• Jinmin Gao,
• Liyuan Li,
• Shijie Shen,
• Guomin Ai,
• Bin Wang,
• Fang Guo,
• Tongjian Yang,
• Hui Han,
• Zhengren Xu,
• Guohui Pan and
• Keqiang Fan

Beilstein J. Org. Chem. 2024, 20, 1198–1206, doi:10.3762/bjoc.20.102

• reaction mixtures of AlpG, AlpJ, Flu17, and JadG. (a) standards of prejadomycin (9), CR1 (8), dehydrorabelomycin (1), and jadomycin A (6); (b) 9 + AlpG + NADPH + FAD; (c) 9 + JadH + NADPH + FAD; (d) 9 + AlpG + AlpJ + NADPH + FAD; (e) 1 + AlpJ + Fre + NADPH + FAD; (f) 8 + AlpJ; (g) 8 + Flu17; (h) 8 + JadG

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• column with 100 mM tricine with 100 mM NaCl at pH 7.5 as the mobile phase. Protein size exclusion chromatography standards (BioRad) were used to determine molecular masses. Nitramine degradation assays LC–MS analysis was performed using an Agilent 1260 LC stack equipped with a Zorbax RX-C18 column (5 μm

• buffer is 100 mM tricine 100 mM NaCl buffer at pH 7.5. Dashed grey lines represent elution volumes of molecular mass standards. Theoretical molecular weights are as follows Vs NnlA: 21,869 Da; Mr NnlA: 20638 Da; Pd NnlA: 18,473 Da; Ms NnlA : 18,239 Da; and Ps NnlA: 19,042 Da. UV–vis absorption spectra of

Discovery and biosynthesis of bacterial drimane-type sesquiterpenoids from Streptomyces clavuligerus

• Dongxu Zhang,
• Wenyu Du,
• Xingming Pan,
• Xiaoxu Lin,
• Fang-Ru Li,
• Qingling Wang,
• Qian Yang,
• Hui-Min Xu and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2024, 20, 815–822, doi:10.3762/bjoc.20.73

• . (b) HPLC chromatograms comparing standards with metabolites extracted from S. clavuligerus cultured in YMS and XTM media. Biosynthesis of drimenol congeners. (a) The cav BGC. (b) Proposed biosynthetic pathway for drimenol congeners 2–4. (c) HPLC analysis of metabolites from genetically engineered

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• standards (CD3OD: δH 3.31, δC 49.0). LC–MS experiments and ESI–TOF MS/MS analyses were performed with an amaZon SL-NPC (Bruker Daltonics) or LCMS-2020 (Shimadzu) spectrometer coupled with a Shimadzu HPLC system equipped with an LC-20AD intelligent pump. GC–MS experiments were performed with a Shimadzu

• filter, and then injected into an LC–MS system, Cosmosil 5C18-MS-II (2 mm ID × 100 mm, Nacalai Tesque) (oven 40 °C; flowrate 0.2 mL/min) using a gradient of MeCN/H2O (1:9 to 6:4) containing 0.1% formic acid for 45 minutes. The standards were processed in the same manner. Whole genome analysis of

• triplicate, according to the Clinical Laboratory Standards Institute testing standard, in 96-well plate microbroth dilution assays. Compounds were tested against Gram-negative bacteria (Escherichia coli JW5503, Bukholderia multivorans NBRC 102086 and Bukholderia plantarii NBRC 104884) and Gram-positive

Synthesis and biological profile of 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines, a novel class of acyl-ACP thioesterase inhibitors

• Jens Frackenpohl,
• David M. Barber,
• Guido Bojack,
• Birgit Bollenbach-Wahl,
• Ralf Braun,
• Rahel Getachew,
• Sabine Hohmann,
• Kwang-Yoon Ko,
• Karoline Kurowski,
• Bernd Laber,
• Rebecca L. Mattison,
• Thomas Müller,
• Anna M. Reingruber,
• Dirk Schmutzler and
• Andrea Svejda

Beilstein J. Org. Chem. 2024, 20, 540–551, doi:10.3762/bjoc.20.46

• ) and broad-leaved signal grass (BRAPP). We used 1 and 5 as standards to assess the potential of the new lead structures. Both standards showed sufficient crop selectivity only at the lower application rate of 50 g/ha. [1,3]Thiazolo[4,5-b]pyridine 5 showed good control of all tested warm-season weeds

• (ALOMY_R, also known as slender foxtail or black twitch) and ryegrass (LOLSS_R). Remarkably, 2,3-dihydro[1,3]thiazolo[4,5-b]pyridine 7b turned out to be superior to market standards (i.e., 1 and 2 in wheat) in terms of overall efficacy and resistance breaking potential. Halogen-free target compound 7c also

• internal standards cinmethylin (1) and methiozolin (2) against selected resistant and nonresistant monocotyledon weeds in wheat at application rates of 200 and 50 g/ha in advanced greenhouse trials, e.g., LOLSS_R and ALOMY_R (replicates: 10 plants per pot). Preemergence efficacy of 2,3-dihydro[1,3]thiazolo

Comparison of glycosyl donors: a supramer approach

• Anna V. Orlova,
• Nelly N. Malysheva,
• Maria V. Panova,
• Nikita M. Podvalnyy,
• Michael G. Medvedev and
• Leonid O. Kononov

Beilstein J. Org. Chem. 2024, 20, 181–192, doi:10.3762/bjoc.20.18

• maintained with an accuracy of ±0.2 °C. After the instrument was warmed up for at least 1 h (as experience suggests, after this period the temperature within the instrument remains stable for at least 8–10 h of continuous work) the instrument readings were verified against the quartz standards (α = +21.267

• measurement of the quartz standards (to monitor the instrument stability). Each measurement at a particular concentration was repeated 10 times, then averaged and plotted against concentration. The standard deviations were calculated by using the Student’s distribution (95% probability) and did not exceed 1

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• each monosaccharide unit is measured, and subsequently identified by comparison with a library of reference spectra of synthetic monosaccharide standards. In the early days of MS–IR spectroscopy, ca. one hour was necessary to record the IR fingerprint of a single molecule and the identification was

• ultimately be included in the algorithm for an optimal coverage of complex carbohydrates. (a) Fingerprint of an unknown monosaccharide. (b) Labelled reference spectra of monosaccharide standards. Typical experimental MS–IR spectra of the four categories of monosaccharides included in the first dataset. Blue

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

• community working on the analysis of EL that require the preparation of standards for analytical purposes. The analysis and quantification of ether lipids is a very important field of research and development that was previously reviewed [47][48]. In this review, we focus on synthesis methodologies applied

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

• Robert N. Goldberg Robert T. Giessmann Peter J. Halling Carsten Kettner Hans V. Westerhoff Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, USA Institute for Globally Distributed Open Research and Education (IGDORE), Berlin

• general discussion of various aspects of these equilibrium measurements as well as STRENDA (Standards for Reporting Enzymology Data) recommendations regarding the measurements and the reporting of results. Keywords: enzyme-catalyzed reactions; equilibrium constant; standards; thermodynamics; Perspective

• 1. Introduction and motivation for recommendations The aim of the STRENDA (Standards for Reporting Enzymology Data) Commission [1] is to establish standards for reporting the results of measurements related to enzymology with the aim to improve the quality and the findability, accessibility

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• standards. The enzymes screened included two Golgi types (GMIIb and AMAN-2) and two lysosomal types (LManII and JBMan) (Table 1). As for the Golgi-type mannosidases, AMAN-2 is a more relevant enzyme because its amino acid sequence and the 3D structure of its active site are almost identical to those of

Investigation of cationic ring-opening polymerization of 2-oxazolines in the “green” solvent dihydrolevoglucosenone

• Solomiia Borova and
• Robert Luxenhofer

Beilstein J. Org. Chem. 2023, 19, 217–230, doi:10.3762/bjoc.19.21

• K. HFIP was supplemented with 3 g/L potassium triflate, and the flow rate was adjusted to 0.50 mL/min. Calibration was performed using PEG standards with molar masses ranging from 0.1–1,000 kg/mol. Before every measurement, samples were filtered through 0.2 µm PTFE filters, Roth (Karlsruhe, Germany

• typically set from 1000 m/z to 7000 m/z. After parameter optimization, the instrument was calibrated with PEG standards depending on the m/z range of the individual sample. Samples were prepared with sinapinic acid (3,5-dimethoxy-4-hydroxycinnamic acid, SA) as matrices using the dried-droplet spotting

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• based on tentative GC–MS assignments, often even without comparison to authentic standards, which results in a lot of information of questionable relevance. The large number of such papers published today makes it more and more difficult to find the relevant information in the literature. With this work

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• (O)CH3 27.4 [49]/28.61; (iPrO)2P(O)H 4.2 [43]/4.54; PMe3 −62 [44]/−61.58 [50]). We have also included chemical shifts in more polar solvents (i.e., DMSO and methanol) when those were the only reported values. The chemical shifts of two commonly used reference standards for 31P NMR calculations

Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B

• Adwoa P. Nartey,
• Aboagye K. Dofuor,
• Kofi B. A. Owusu,
• Anil S. Camas,
• Hai Deng,
• Marcel Jaspars and
• Kwaku Kyeremeh

Beilstein J. Org. Chem. 2022, 18, 1763–1771, doi:10.3762/bjoc.18.185

• advanced Marfey’s method [16][17][18] involving the complete hydrolysis of compound 1 followed by derivatization of the resultant amino acid residues with N-α-(2,4-dinitro-5-fluorophenyl)-ʟ-alanine amide (ʟ-FDAA). Similar derivatization reactions between ʟ-FDAA and authentic amino acid standards, followed

• promising antimicrobial properties in comparison to the laboratory standards ampicillin and amphotericin B. Compound 1 produced interesting biological activity against the Gram-negative bacteria Shigella sonnei, Shigella flexneri and the multidrug resistant Gram-positive Staphylococcus aureus with IC50 of

Synthesis of the biologically important dideuterium-labelled adenosine triphosphate analogue ApppI(d₂)

• Petri A. Turhanen

Beilstein J. Org. Chem. 2022, 18, 1466–1470, doi:10.3762/bjoc.18.153

• available, and in fact only few papers describe corresponding synthetic methods [19][20][21][22]. It is well known that labelled compounds (such as those with 2H and 13C labels) can be used as internal standards for the quantitative measurements of the equal compound without label, e.g., straight from the

The stereochemical course of 2-methylisoborneol biosynthesis

• Binbin Gu,
• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 818–824, doi:10.3762/bjoc.18.82

• Supporting Information File 1). All compounds were identified from their EI mass spectra and retention indices in comparison to synthetic standards [29]. The substrate (R)-2-Me-LPP gave high yields of compound 1 (62% of total enzyme products in GC), besides 2-methylenebornane (10, 21%) and small amounts of 2

Sesquiterpenes from the soil-derived fungus Trichoderma citrinoviride PSU-SPSF346

• Wiriya Yaosanit,
• Vatcharin Rukachaisirikul,
• Souwalak Phongpaichit,
• Sita Preedanon and
• Jariya Sakayaroj

Beilstein J. Org. Chem. 2022, 18, 479–485, doi:10.3762/bjoc.18.50

• , 321.1309; found, 321.1320. Antimicrobial assay Antimicrobial activity was evaluated according to the Clinical and Laboratory Standards Institute [16]. Vancomycin was used as a positive control for S. aureus and methicillin-resistant S. aureus and exhibited MIC values of 0.25 and 1.0 μg/mL, respectively