Investigations of amination reactions on an antimalarial 1,2,4-triazolo[4,3-a]pyrazine scaffold

• Henry S. T. Smith,
• Ben Giuliani,
• Kanchana Wijesekera,
• Kah Yean Lum,
• Sandra Duffy,
• Aaron Lock,
• Jonathan M. White,
• Vicky M. Avery and
• Rohan A. Davis

Beilstein J. Org. Chem. 2025, 21, 1126–1134, doi:10.3762/bjoc.21.90

• MHz NMR spectrometer equipped with a cryoprobe. MestreNova™ version 14.3.3 software was used for NMR data analysis. The 1H and 13C NMR chemical shifts were referenced to solvent peaks for (CD3)2SO (δH 2.50, δC 39.52). LRESIMS data was recorded on a Thermo Scientific (Waltham, MA, USA) UltiMate™ 3000

• using an Opera PhenixPlus™ High Content Screening System (PerkinElmer, Waltham, MA, USA). Images were analysed using the Harmony software (PerkinElmer, Waltham, MA, USA). In vitro cytotoxicity assay Human embryonic kidney (HEK293) cells were maintained in DMEM (Life Technologies, Camarillo, CA, USA

Supramolecular assembly of hypervalent iodine macrocycles and alkali metals

• Krishna Pandey,
• Lucas X. Orton,
• Grayson Venus,
• Waseem A. Hussain,
• Toby Woods,
• Lichang Wang and
• Kyle N. Plunkett

Beilstein J. Org. Chem. 2025, 21, 1095–1103, doi:10.3762/bjoc.21.87

• , selected from the BindFit software (http://app.supramolecular.org/bindfit/). Lithium complex 2 (red) overlaid with lithium complex 3 (blue). In lithium complex 2, one benzyl ring is pointing outside highlighted by the red-colored asterisk. Binding energies and binding constants for HIM 1 with LiBArF20 and

Data accessibility in the chemical sciences: an analysis of recent practice in organic chemistry journals

• Sally Bloodworth,
• Cerys Willoughby and
• Simon J. Coles

Beilstein J. Org. Chem. 2025, 21, 864–876, doi:10.3762/bjoc.21.70

• , acquisition and processing parameters), and metadata (spectrometer specifications, acquisition and processing software, and sample information). Two of the ACS journals, J. Org. Chem. and Organometallics, give instructions for preparing data files of Cartesian coordinates from computational studies, requiring

• ’ is a file extension for JCAMP-DX, the IUPAC standard file format for spectral data [39]. FIDs are accessible from the MNOVA and JDX files, but access requires additional software. No primary mass spectrometry data were shared. Are data deposited in an open repository? (Find_1) Two thirds of shared

• ), International Chemical Identifiers (InChIs) and InChIKeys are widely supported in software handling chemical information such as databases, inventories, laboratory information management systems (LIMS) and electronic lab notebooks (ELNs). Systematic naming of organic compounds using International Union of Pure

4-(1-Methylamino)ethylidene-1,5-disubstituted pyrrolidine-2,3-diones: synthesis, anti-inflammatory effect and in silico approaches

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Luc Van Meervelt,
• Do Thi Thao and
• Nguyen Minh Thong

Beilstein J. Org. Chem. 2025, 21, 817–829, doi:10.3762/bjoc.21.65

• . The docking algorithm used was the Triangle Matcher placement method, which generates initial poses by aligning ligand atoms to complementary receptor atoms. Molecular docking simulations were performed using the MOE software suite [46] to evaluate the binding activities of the newly synthesized

• compounds and the reference drug dexamethasone (DEX) against the iNOS enzyme. The interactions between the ligands and the target enzyme were further visualized and analyzed using Discovery Studio software [47]. Density functional theory (DFT) method: The molecular structures of the tested compounds were

• optimized at the M062X/6-31+G(d) level of theory using Gaussian 16 software [48]. The reactivity, stability, and electronic properties of molecules determined by key parameters such as frontier molecular orbital energies (EHOMO and ELUMO), energy gap (ΔEL-H), ionization energy (IE), electron affinity (EA

Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• Tyr137 flanking the carbohydrate binding site of FimH [47]. First, Glide [48] as part of the Maestro interface of the Schrödinger software package [49] was used to calculate docking scores (Table 3). More negative docking scores correlate with higher FimH affinity. In a second step, the best docking

Acyclic cucurbit[n]uril bearing alkyl sulfate ionic groups

• Christian Akakpo,
• Peter Y. Zavalij and
• Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 717–726, doi:10.3762/bjoc.21.55

• Figure 6a was integrated and then plotted as ΔH versus molar ratio in Figure 7b. The ΔH versus molar ratio data was then fitted to the single-set-of-sites binding model in the PEAQ ITC data analysis software which delivered Ka = (6.49 ± 0.10) × 105 M−1 and ΔH = −7.82 ± 0.02 kcal mol−1 for the C1·CHDA

• requires that the Ka and ΔH values for the host·competitor complexes have been previously determined and used as known inputs to the competitive binding model in the PEAQ data analysis software. To maximize the heat evolved in the competitive ITC titrations, the host·competitor and host·tight guest

• ) and fitted to the competitive binding model in the PEAQ ITC data analysis software to determine Ka = (2.47 ± 0.06) × 108 M−1 and ΔH = −12.43 ± 0.02 kcal mol−1 for the C1·Me6PXDA complex. The Ka and ΔH values for the remaining C1·guest and M1·guest complexes were determined by analogous direct or

Asymmetric synthesis of fluorinated derivatives of aromatic and γ-branched amino acids via a chiral Ni(II) complex

• Maurizio Iannuzzi,
• Thomas Hohmann,
• Michael Dyrks,
• Kilian Haoues,
• Katarzyna Salamon-Krokosz and
• Beate Koksch

Beilstein J. Org. Chem. 2025, 21, 659–669, doi:10.3762/bjoc.21.52

• ) was used. MeCN/MeOH/H2O mixture with 50 mM formic acid and 25 mM diethylamine was used as eluent. A flow rate of 0.5 mL/min was applied and the detection of the respective compounds occurred at 280 nm. Data analysis was carried out with the EZChrom ELITE software (version 3.3.2 SP2, Agilent). Ni(II

Semisynthetic derivatives of massarilactone D with cytotoxic and nematicidal activities

• Rémy B. Teponno,
• Sara R. Noumeur and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 607–615, doi:10.3762/bjoc.21.48

• Agilent 1100 series preparative HPLC system [ChemStation software (Rev. B.04.03 SP1); binary pump system; column: Kinetex 5u RP C18, dimensions 250 × 21.20 mm; mobile phase: ACN + 0.05% trifluoroacetic acid (TFA) and water + 0.05% TFA; flow rate: 20 mL/min; diode array UV detector; 226 fraction collector

• software (Rev. B.04.03 SP1); binary pump system; column: Kinetex 5u RP C18, dimensions 250 × 21.20 mm; mobile phase: ACN + 0.05% trifluoroacetic acid (TFA) and water + 0.05% TFA; flow rate 20 mL/min; diode array UV detector; 226 fraction collector. A gradient from 47 to 72% solvent B in 50 min was used

Deep-blue emitting 9,10-bis(perfluorobenzyl)anthracene

• Long K. San,
• Sebastian Balser,
• Brian J. Reeves,
• Tyler T. Clikeman,
• Yu-Sheng Chen,
• Steven H. Strauss and
• Olga V. Boltalina

Beilstein J. Org. Chem. 2025, 21, 515–525, doi:10.3762/bjoc.21.39

• software (APEX II) was employed [38], and Bruker SHELXTL software [39] was used for structure solution, refinement, and graphics. Crystal data for 9,10-ANTH(BnF)2: C28H8F14, M = 610.34, orthorhombic, a = 11.5338(4) Å, b = 24.6701(9) Å, c = 8.0275(3) Å, α = 90°, β = 90°, γ = 90°, V = 2284.15 Å3, T = 100(2

Unraveling aromaticity: the dual worlds of pyrazole, pyrazoline, and 3D carborane

• Zahra Noori,
• Miquel Solà,
• Clara Viñas,
• Francesc Teixidor and
• Jordi Poater

Beilstein J. Org. Chem. 2025, 21, 412–420, doi:10.3762/bjoc.21.29

• , the energy decomposition analysis has been performed at the ZORA-BLYP-D3(BJ)/TZ2P level of theory with AMS software [81][82][83][84]. Series o-carborane-fused pyrazoles under analysis. Bond lengths (in Å) of systems under analysis (top row) and reference systems (second and third rows) from the fusion

Synthesis, structure, ionochromic and cytotoxic properties of new 2-(indolin-2-yl)-1,3-tropolones

• Yurii A. Sayapin,
• Eugeny A. Gusakov,
• Inna O. Tupaeva,
• Alexander D. Dubonosov,
• Igor V. Dorogan,
• Valery V. Tkachev,
• Anna S. Goncharova,
• Gennady V. Shilov,
• Natalia S. Kuznetsova,
• Svetlana Y. Filippova,
• Tatyana A. Krasnikova,
• Yanis A. Boumber,
• Alexey Y. Maksimov,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2025, 21, 358–368, doi:10.3762/bjoc.21.26

• ://www.ccdc.cam.ac.uk/data_request/cif. Computational methods Quantum chemical calculations were performed using the Gaussian 09 software package [34] with hybrid functional PBE0 [35][36] and 6-311+G (d,p) basis set. Solvent effects were modeled by using polarizable continuum model (PCM) [37] within the integral

• Tukey’s post hoc test of significance. IC50 values were determined in the RStudio development environment using the DRC software package [40]. Structural characteristics of (NH) and (OH) tautomeric forms of compounds 7 and 8 in the gas phase according to PBE0/6-311+G(d,p) calculations. Bond lengths are

Synthesis of new condensed naphthoquinone, pyran and pyrimidine furancarboxylates

• Kirill A. Gomonov,
• Vasilii V. Pelipko,
• Igor A. Litvinov,
• Ilya A. Pilipenko,
• Anna M. Stepanova,
• Nikolai A. Lapatin,
• Ruslan I. Baichurin and
• Sergei V. Makarenko

Beilstein J. Org. Chem. 2025, 21, 340–347, doi:10.3762/bjoc.21.24

• with 12 frames per run (φ-scan technique). Data collection and indexing, determination and refinement of unit cell parameters were carried out using the APEX2 software package [32]. Absorption correction was carried out according to the SADABS program [33]. The structures were solved by the direct

• method according to the SHELXT-2014/5 program [34] and refined by the full-matrix least-square on F2 according to the SHELXL-2018/3 program [35]. All calculations were performed using the WingX-2020.1 software package [36]. Structure 6c was refined using OLEX2-1.5 software package [37]. Non-hydrogen

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• the samples and the control group was assessed through a two-tailed Student's t-test. The level of statistical significance was set at p < 0.05. The examination was conducted utilizing GraphPad Prism 9® (GraphPad Software, San Diego, CA, USA). Computational details The distribution of conformers was

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

• system comprised of a flow chemistry synthesis platform, a reagent delivery system, a packed bed reactor, process-analytical tools, and an integrated software control system that automates end-to-end process operations and monitoring. The system has been used to demonstrate the synthesis of at least ten

• automated experiments. The optimum conditions for the formation of the monoarylated product 1 (Figure 5b) identified in a microfluidics system were successfully translated to a mesofluidics system on a 50-fold scale to afford 26.9 g of the product 1. LeyLab, a modular software system developed by

• Bédard et al. [62] to mitigate some of the challenges in traditional organic synthesis by the integration of hardware, software, and analytics. Comprising an array of modular components, including units for heating, cooling, LED light exposure, and packed bed reactors, it provides a flexible platform for

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

• GAMESS [36] and has also contributed to Gaussian software packages, in this work the G09 ES64L-G09RevE.01 version [37] of the latter was used. Aromatic stabilization energy across a series of small aromatics (upper); graphical depiction of the BFC/FIC acidity quandry (lower). Clar–Loschmidt graphs

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

• to the genetic code) [58]. Hundreds of known nonribosomal codes and their corresponding BBs can be extracted from natural products that have been characterized over the past several decades, generating a dataset to train NRP prediction algorithms (Figure 3b) [49][59][60]. A software suite called

• ]. Type I PKs are also constructed in a modular assembly line biosynthetic logic and may be amenable to chemical structure metagenomic approaches described herein [82]. In fact, the software suite antiSMASH can already predict the substrate specificity of individual polyketide synthase (PKS) modules, i.e

The charge transport properties of dicyanomethylene-functionalised violanthrone derivatives

• Sondos A. J. Almahmoud,
• Joseph Cameron,
• Dylan Wilkinson,
• Michele Cariello,
• Claire Wilson,
• Alan A. Wiles,
• Peter J. Skabara and
• Graeme Cooke

Beilstein J. Org. Chem. 2024, 20, 2921–2930, doi:10.3762/bjoc.20.244

• hindered charge transport. Experimental Computational Density functional theory (DFT) calculations were performed using Gaussian 09 software. Molecular geometries were initially optimised semi-empirically (AM1) and then reoptimised by DFT using the B3LYP method with the 6-311G(d,p) basis set unless stated

Interaction of a pyrene derivative with cationic [60]fullerene in phospholipid membranes and its effects on photodynamic actions

• Hayato Takagi,
• Çetin Çelik,
• Ryosuke Fukuda,
• Qi Guo,
• Tomohiro Higashino,
• Hiroshi Imahori,
• Yoko Yamakoshi and
• Tatsuya Murakami

Beilstein J. Org. Chem. 2024, 20, 2732–2738, doi:10.3762/bjoc.20.231

• free PyBA. Data analysis, including calculation of the phase transition temperature, was performed using the MicroCal PEAQ-DSC Software. UV–vis absorption measurement UV–vis spectra of DMPC liposomes (1 mM DMPC) with or without catC60 or C60 were measured in PBS(–) using a UV-3600 Plus absorption

Computational design for enantioselective CO₂ capture: asymmetric frustrated Lewis pairs in epoxide transformations

• Maxime Ferrer,
• Iñigo Iribarren,
• Tim Renningholtz,
• Ibon Alkorta and
• Cristina Trujillo

Beilstein J. Org. Chem. 2024, 20, 2668–2681, doi:10.3762/bjoc.20.224

• with the Gaussian16 quantum chemical software package [29], using the B3LYP density functional [30][31] along with the Grimme dispersion correction including Becke and Johnson damping D3(BJ) [32][33][34] and the def2-TZVP basis set [35]. Harmonic frequencies were computed at the optimisation level to

Transition-metal-free decarbonylation–oxidation of 3-arylbenzofuran-2(3H)-ones: access to 2-hydroxybenzophenones

• Bhaskar B. Dhotare,
• Seema V. Kanojia,
• Chahna K. Sakhiya,
• Amey Wadawale and
• Dibakar Goswami

Beilstein J. Org. Chem. 2024, 20, 2655–2667, doi:10.3762/bjoc.20.223

• over anhydrous Na2SO4. FTIR spectra were recorded as films with a Bruker Tensor II spectrophotometer. The 1H and 13C NMR spectra were recorded with a Varian 500 MHz NMR spectrometer, and were processed using Bruker TOPSPIN software. Melting points (mp) were measured on a Büchi B-540 apparatus. X-ray

The scent gland composition of the Mangshan pit viper, Protobothrops mangshanensis

• Jonas Holste,
• Paul Weldon,
• Donald Boyer and
• Stefan Schulz

Beilstein J. Org. Chem. 2024, 20, 2644–2654, doi:10.3762/bjoc.20.222

• column (30 m × 0.25 mm, 0.25 µm film thickness) with helium as the carrier gas. The eluted compounds were applied to a ZnSe disk rotating at 4 mm/min at −40 °C. The resulting IR spectra were processed using GRAMS/AI 9.2 software (Thermo Fisher Scientific). High-resolution mass spectrometry data were

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• G09 package. The PyMOL software was used to create molecular graphics images [32]. Chemical structure of γ-CD (A); M062X/6-31G(d,p) optimized conformers of nonhydrated γ-CD in two projections – side view (B) and top view from O6 side of the truncated cone (C). The "closed" conformation is with

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

• different length scales can be probed to identify how the individual fibres form and then entangle to form the gel network. In addition to showing the shape of the self-assembled structures, with the aid of software tools such as ImageJ [13], features such as the fibre width, fibre length, and pore sizes

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

• ]. Moreover, predicting reaction conditions can help optimize the synthetic route [183] by providing the necessary information for each synthetic step. Coley et al. [12] integrated ASKCOS [184], an automated CASP software, with the self-driving lab [185] and demonstrated the synthesis of 15 small molecules

• optimization platforms have been developed [188][189][190][191], which integrate software optimization algorithms with hardware automation for experiments, enabling large-scale experimentation and data collection. Among these, BO [192] is the most classic and widely used algorithm, which leverages kernel

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