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

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

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