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

• nowadays mass spectrometric hardware and bioinformatic software tools. Review Principles of chemical proteomics workflows The linker connects the affinity or reporter tag to the probe–protein conjugate to offer several principally different analytical pathways (Figure 3) [53][54]. Although chemical

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

O,S,Se-containing Biginelli products based on cyclic β-ketosulfone and their postfunctionalization

• Kateryna V. Dil and
• Vitalii A. Palchykov

Beilstein J. Org. Chem. 2024, 20, 2143–2151, doi:10.3762/bjoc.20.184

• derivatives 3–7 using SwissADME (http://www.swissadme.ch) [44], ProTox 3.0 (https://tox-new.charite.de) [45], and MolPredictX (https://www.molpredictx.ufpb.br) [46] free online software. Considering ADMET [47] and other crucial properties, we found that all compounds (except for the nitro derivative 2e) do

• , see Supporting Information File 1 (Table S1). To visualize the lead-likeness of compounds 2a–r, 3–7, we utilized the free online software LLAMA (https://llama.leeds.ac.uk) [53], which showed that 70% of the products (16 of 23) fall within the specific lead-like space (Figure 2). We then used the free

• online software ProTox 3.0 for computational toxicity assessment of the products as their LD50 values. The tested compounds mainly belong to the 4th class of acute oral toxicity with 300 < LD50 ≤ 2000 mg/kg. In addition, we used MolPredictX (https://www.molpredictx.ufpb.br) [46] to evaluate potential

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

• web servers and downloadable software, which can help researchers in designing the workflow to study a glycan–protein system, are also reported. Computational tools to study glycans in the free state Since the first molecular dynamics simulations performed in the late 1980s on oligomannose type

• web services and software to build 2D and 3D models of carbohydrate structures is reported here. Notably, despite the existence of several encoding formats for glycans (Figure 3), significant efforts have been made in the years to enable a simple and standardised glycan representation, which would

• allow manual drawing and sketching of carbohydrates, as reviewed by Lal et al. [47]. Here, we list free tools useful not only for sketching and drawing but also for building the glycan structure of interest (last accessed date: May 2024) [47][48]. 1. doGlycans [49]: Free desktop software package in the

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

• place during light and X-ray exposure. Frames of 500 ms were taken, and the 2D diffraction patterns were radially averaged and integrated to obtain 1D data. The solvent background was subtracted and frames were averaged using the ScÅtter software [48]. The number of frames averaged was varied to strike

• averaged and integrated to obtain 1D data. The container background was subtracted and sets of three frames were averaged using the ScÅtter software [48]. In-situ light irradiation was achieved using the custom-made setup at beamline B21, using a fibre-coupled pE-4000 (coolLED) focussed onto the sample

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

• (Avantes IC-DB26-RM), which allows the proprietary software AvaSoft from Avantes to control the internal shutter of the light source via a PC. With this configuration, starting a single measurement in AvaSoft sends a TTL signal to the light source that opens the shutter, which is followed by the

• measurement altering the kinetics of isomerization, a known problem for similar setups [24]. The power readings from the thermal power sensor were recorded by using Thorlabs’ Optical Power Monitor (OPM) software. The resulting data showed some fluctuations depending on environment temperature and air movement

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

• 10 mV, over a frequency range of 65 kHz to 5 Hz. The bulk resistance (Rb) of the membranes were calculated using the ZView software (Version 2.6b, Scribner Associates). A Binder KBF 115 climatic chamber was used to perform the measurements at a temperature of 60 °C and different relative humidity (RH

pKalculator: A pK_a predictor for C–H bonds

• Rasmus M. Borup,
• Nicolai Ree and
• Jan H. Jensen

Beilstein J. Org. Chem. 2024, 20, 1614–1622, doi:10.3762/bjoc.20.144

• database only contains an image of each molecule, we employ the “Deep Learning for Chemical Image Recognition” software (DECIMER v. 2.0), developed by Rajan and co-workers [8][9][10]. While DECIMER converts molecular images into SMILES, manual intervention is required to ensure the SMILES string correctly

Supramolecular assemblies of amphiphilic donor–acceptor Stenhouse adducts as macroscopic soft scaffolds

• Ka-Lung Hung,
• Leong-Hung Cheung,
• Yikun Ren,
• Ming-Hin Chau,
• Yan-Yi Lam,
• Takashi Kajitani and
• Franco King-Chi Leung

Beilstein J. Org. Chem. 2024, 20, 1590–1603, doi:10.3762/bjoc.20.142

• were anisotropic, and the models used by Wyatt software are fitted to spherical objects. To determine the CAC of DA6, DA7, and DA11, the scattering intensity of solutions of DA6 (1.0 × 10−4–0.5 mM), DA7 (1.0 × 10−4–0.5 mM), and DA11 (1.0 × 10–4–0.1 mM) was recorded at 20 °C. This scattering rate was

• wavelength of the X-ray beam (Cu Kα irradiation, 1.54 Å). The sample-to-detector distance was ≈100 mm. The obtained diffraction patterns were integrated along the Debye–Scherrer ring to afford 1D intensity data using the Rigaku 2DP software. Attachment of hBM-MSCs onto DAn scaffold surface The preparation of

Divergent role of PIDA and PIFA in the AlX₃ (X = Cl, Br) halogenation of 2-naphthol: a mechanistic study

• Kevin A. Juárez-Ornelas,
• Manuel Solís-Hernández,
• Pedro Navarro-Santos,
• J. Oscar C. Jiménez-Halla and
• César R. Solorio-Alvarado

Beilstein J. Org. Chem. 2024, 20, 1580–1589, doi:10.3762/bjoc.20.141

• , and transition-state structures were optimized by density functional theory (DFT) calculations employing the software Gaussian 16 [34]. Although the B3LYP functional could be suitable for these calculations, e.g., for tracing reaction pathways, nitrations, halogenations, or FC acylations in solution

Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines

• Ana Flávia Candida Silva,
• Francisco A. Martins and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2024, 20, 1572–1579, doi:10.3762/bjoc.20.140

• Gaussian 16 package of software [24]. a) Pseudoequatorial and pseudoaxial conformations of pyrrolidine. b) Cis- and trans-isomers of 3-fluoropyrrolidine. Flat representations of 2,3-, 3,4-, and 2,4-difluoropyrrolidines. The potential effects resulting from the addition of a second 1,2- or 1,3-fluorine atom

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

• ). rnaSPAdes was used to assemble the raw reads using the default settings [15]. This software package was chosen primarily for its speed (≈1.5 h per transcriptome), which was essential for this large analysis effort. Our custom HMM was used to search for potential precursor peptides using an E-value inclusion

Tetrabutylammonium iodide-catalyzed oxidative α-azidation of β-ketocarbonyl compounds using sodium azide

• Christopher Mairhofer,
• David Naderer and
• Mario Waser

Beilstein J. Org. Chem. 2024, 20, 1510–1517, doi:10.3762/bjoc.20.135

• Research Center “RERI uasb”. All NMR spectra were referenced on the solvent residual peak (CDCl3: δ = 7.26 ppm for 1H NMR, δ = 77.16 ppm for 13C NMR,19F NMR unreferenced). IR spectra were recorded on a Bruker Alpha II FTIR spectrometer with diamond ATR-module using the OPUS software package. HRMS spectra

Towards an asymmetric β-selective addition of azlactones to allenoates

• Behzad Nasiri,
• Ghaffar Pasdar,
• Paul Zebrowski,
• Katharina Röser,
• David Naderer and
• Mario Waser

Beilstein J. Org. Chem. 2024, 20, 1504–1509, doi:10.3762/bjoc.20.134

• Thermo Fisher Scientific LTQ Orbitrap XL spectrometer with an Ion Max API source and analyses were made in the positive ionization mode if not otherwise stated. Infrared (IR) spectra were recorded on a Bruker Alpha II FTIR spectrometer with diamond ATR-module using the OPUS software package and are

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• were performed by repeating the same protocol, but injecting the ligand into buffer solution. The supplied software Origin 7 or MicroCal PEAQ-ITC was used to fit the experimental data to a theoretical titration curve allowing the determination of affinity (i.e., dissociation constant, Kd), binding

Diameter-selective extraction of single-walled carbon nanotubes by interlocking with Cu-tethered square nanobrackets

• Guoqing Cheng and
• Naoki Komatsu

Beilstein J. Org. Chem. 2024, 20, 1298–1307, doi:10.3762/bjoc.20.113

• measurements and analyzed with mMass [29] software. 1H and 13C NMR spectra were recorded on JNM-ECS 400 spectrometer using the sample solutions in chloroform-d (CDCl3). Raman spectra were recorded on LabRam HR800 (Horiba Ltd.) and take the average of more than ten different spots for the final curve. UV–Vis

• Cu-nanobrackets@SWNTs complexes were computed with the GFN2-xTB method by using the xtb software [16][17]. (a) MALDI-TOF mass spectrum of Cu-nanobrackets 1b, where the inset shows the isotope peaks of [1b]+ comparing with the simulated ones; (b) absorption spectra of the nanobracket 4b and Cu

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• 1–3 mg of sample in a 100 μL platinum pan (under nitrogen). The data was analyzed on Universal Analysis 2000 4.4A software. Synthetic procedures to access dicyanopyrazinoquinoxalines (DCPQs) 1a–6a Pyrazino[2,3-b]quinoxaline-2,3-dicarbonitrile (1a) To a 50 mL round-bottom flask was added DDQ (0.581 g

Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• scientists. The Privateer software is a validation and analysis tool that provides access to a number of metrics and links to external experimental resources, allowing users to evaluate structures using carbohydrate-specific methods. Here, we present the Privateer database, a free resource that aims to

• in the past has been plagued with software related problems from incorrect libraries to incomplete support [4]. Carbohydrates are mobile, highly branched additions to the comparatively rigid protein framework; in macromolecular crystallography, this causes heterogeneity throughout the crystal lattice

• new resources, including services and databases [9][10][11][12][13], and standalone software [14][15][16][17][18]. Among these, the Privateer software package has been a key tool for glycoprotein and protein–carbohydrate complex validation: Privateer analyses the conformational plausibility of each

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

• nnlA gene, including those described here, were identified by sequence similarity searches and their predicted amino acid sequences were used to infer phylogenetic relationships. An alignment of 11 amino acid sequences with 28 to 87% identity was prepared using MUSCLE software (ver. 5.1) [48] and

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

• library preparation with a Ligation Sequencing Kit (SQK-LSK 109), following the 1D genomic DNA by ligation protocol. The library was applied to a MinION flowcell (FLO MIN106 R9.41revD) operated by the MinKNOW (20.06.9) software, and then processed by Guppy basecaller (4.0.11) in the high accuracy mode. As

A laterally-fused N-heterocyclic carbene framework from polysubstituted aminoimidazo[5,1-b]oxazol-6-ium salts

• Andrew D. Gillie,
• Matthew G. Wakeling,
• Bethan L. Greene,
• Louise Male and
• Paul W. Davies

Beilstein J. Org. Chem. 2024, 20, 621–627, doi:10.3762/bjoc.20.54

• method and Sambvca V.2.0 software (Scheme 2) [29]. Although a similar value to that reported for IPrAuCl (%Vbur = 45.4%) [30] the steric map shows a very different steric environment on either side of the ligand. The AImOxIr(CO)2Cl complex 15 was targeted in order to assess the electronic effects of the

Introduction of a human- and keyboard-friendly N-glycan nomenclature

• Friedrich Altmann,
• Johannes Helm,
• Martin Pabst and
• Johannes Stadlmann

Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53

• definition of positional isomers. The combination with elements of the condensed IUPAC code allows to describe even rather complex structural elements. Thus, this “proglycan” coding could be the missing link between drawn structures and software-oriented representations of N-glycan structures. On top, it may

• depictions and related software has lately been portrayed in a quite enjoyable review [15]. A number of computer-readable formats has been developed of which GlycoCT [16] and WURCS [17] are currently the options of choice. None of these software friendly options is even remotely suitable for labeling of

• software thus often essentially neglects the overinterpretation problem and suggests a particular structure, where actually a range of isomers is possible as recently elaborated for the H5N4F1 composition [26]. A few more prominent alphanumerical codes were developed and shall be described and compared in

Chemical and biosynthetic potential of Penicillium shentong XL-F41

• Ran Zou,
• Xin Li,
• Xiaochen Chen,
• Yue-Wei Guo and
• Baofu Xu

Beilstein J. Org. Chem. 2024, 20, 597–606, doi:10.3762/bjoc.20.52

• version of antiSMASH 7.0 [25] software for the analysis of the Penicillium shentong XL-F41 genome, we identified 46 BGCs. These include 13 NRPS-like fragments, 6 NRPS, 13 type I PKS, 2 PKS/NRPS hybrids, 1 NI-siderophore, 2 NRP-metallophore/NRPS hybrids, 1 fungal RiPP with POP or UstH peptidase types, 1

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• . In addition, NAD+ and NADP cofactors were also tested in reactions with myo-inositol. NAD+ and NADP were purchased from Research Products International. Results were analyzed using GraphPad Prism version 9.5.1 for Windows, GraphPad Software, Boston, Massachusetts USA, https://www.graphpad.com

• determining the slope of the reaction from 0 to 5 min. Results were analyzed using Microsoft Excel and GraphPad Prism version 9.5.1 for Windows, GraphPad Software, Boston, Massachusetts USA, https://www.graphpad.com. SSN network generation and genome mining The sequence similarity network was generated using

Synthesis of photo- and ionochromic N-acylated 2-(aminomethylene)benzo[b]thiophene-3(2Н)-ones with a terminal phenanthroline group

• Vladimir P. Rybalkin,
• Sofiya Yu. Zmeeva,
• Lidiya L. Popova,
• Irina V. Dubonosova,
• Olga Yu. Karlutova,
• Oleg P. Demidov,
• Alexander D. Dubonosov and
• Vladimir A. Bren

Beilstein J. Org. Chem. 2024, 20, 552–560, doi:10.3762/bjoc.20.47

• dedicated CrysAlisPro software suite [34]. The structure was solved with the ShelXT program [35] and refined with the ShelXL program [36], and the graphics were rendered using the Olex2 software suite [37]. The complete X-ray structural dataset for compound 2a was deposited with the Cambridge