Annulation of a 1,3-dithiole ring to a sterically hindered o-quinone core. Novel ditopic redox-active ligands

• Sergey V. Norkov,
• Anton V. Cherkasov,
• Andrey S. Shavyrin,
• Maxim V. Arsenyev,
• Viacheslav A. Kuropatov and
• Vladimir K. Cherkasov

Beilstein J. Org. Chem. 2021, 17, 273–282, doi:10.3762/bjoc.17.26

• [52] and CrysAlisPro [53] software packages. The structures were solved by direct methods and were refined by full-matrix least squares on F2 for all data using SHELX [54]. SADABS [55] and CrysAlisPro were used to perform the absorption corrections. All non-hydrogen atoms in 6a–d and 7–9 were found

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• MicroCal ITC data analysis software for Origin 7.0. Top: pelargonidin cation (Flavy) and network of chemical reactions; bottom: corresponding UV–vis spectra of the different states of Flavy. Characterization of Flavy: a) 1H NMR spectrum at pH 7.0 (form A) before and after irradiation; b) 13C NMR spectrum

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• an attempt at resolving this problem by means of the electronic circular dichroism (ECD) technique. We recorded an ECD spectrum of both compounds and compared it with simulated spectra, generated for both possible diastereomers (2-(R) and 2-(S)) using computational chemistry software. Unfortunately

• calculations were performed on a simplified model to provisionally validate this proposed mechanism. The geometry of the intermediate species were optimized with Gaussian 09 software [44], using the B3LYP/LANL2DZ theory level for Zr and B3LYP/6-31G(d,p) for other atoms, with GD3 empirical dispersion correction

• . The optimization was followed by a single-point energy calculation using the larger basis set Def2TZVP with a PCM solvatation model for THF, as implemented in the Gaussian software. Energy values reported are a sum of electronic and zero-point energies. Scheme 8 shows possible pathways for the

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• . The light is normally dispersed by a 300 gr/mm grating onto a fast CCD camera (Andor Newton DU-970N-UV, operating at 1,000 spectra per second using "crop mode"). The whole setup is controlled by the National Instruments LabView software. A variable neutral-density filter was employed to adjust the

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• analysis software and automation in liquid chromatography–mass spectrometry over the past decade made HDXMS an increasingly attractive tool for biochemists. In HDXMS, changes in the mass associated with the isotopic exchange between amide hydrogen atoms and surrounding deuterated solvent are measured. The

• painting. However, even though HDXMS is a very reproducible and straightforward method (albeit the experiment has to be carefully and properly performed), data analysis, even with recent software automation, is the major limitation as the interpretation requires a certain level of expertise. Biophysical

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• aided by the Byonic software. Additional MS1-based glycopeptide identification relying on accurate mass and retention time differences using GlycopeptideGraphMS considerably expanded the set of confidently annotated glycopeptides. For glycopeptide quantification, the performance of LaCyTools was

• automated processing of several IgA glycopeptides. Finally, this study presents a semiautomated workflow for reliable glycoproteomic data analysis by the combination of software packages for MS/MS- and MS1-based glycopeptide identification as well as the integration of analyte quality control and

• /MS-based scoring software tools such as Byonic [14] are frequently used for glycopeptide identification [12]. Recently, software tools were developed that are based on the retention time (RT) characteristics and accurate mass differences of glycopeptide MS1 signals in RPLC–MS [10][15]. These tools

Chiral anion recognition using calix[4]arene-based ureido receptors in a 1,3-alternate conformation

• Tereza Horáčková,
• Jan Budka,
• Vaclav Eigner,
• Wen-Sheng Chung,
• Petra Cuřínová and
• Pavel Lhoták

Beilstein J. Org. Chem. 2020, 16, 2999–3007, doi:10.3762/bjoc.16.249

• isotherms obtained from the complexation-induced chemical shift (CIS) values of urea NH protons or aromatic CH signals (Figure 5) [50][51][52]. The nonlinear curve-fitting of the experimental data was performed using the freely available software Bindfit [53]. The stoichiometry of the complexes was

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• generated with FastTree 2 from the representative sequences [71][72][73]. Relative species abundance and phylogenetic diversity analyses QIIME 2 artefacts were imported into the R software (4.0.2) with the R package qiime2R, and further analyses were conducted in the R package phyloseq [74][75][76]. The

Controlled decomposition of SF₆ by electrochemical reduction

• Sébastien Bouvet,
• Bruce Pégot,
• Stéphane Sengmany,
• Erwan Le Gall,
• Eric Léonel,
• Anne-Marie Goncalves and
• Emmanuel Magnier

Beilstein J. Org. Chem. 2020, 16, 2948–2953, doi:10.3762/bjoc.16.244

• Parstat 2273 potentiostat was also used with its internal «Powersuite» software. For all cyclic voltammetries, the conventional representation of anodic currents is reported as positive values and cathodic currents as negative values. SF6 electrolysis was performed in acetonitrile with a constant

One-pot multicomponent green Hantzsch synthesis of 1,2-dihydropyridine derivatives with antiproliferative activity

• Giovanna Bosica,
• Kaylie Demanuele,
• José M. Padrón and
• Adrián Puerta

Beilstein J. Org. Chem. 2020, 16, 2862–2869, doi:10.3762/bjoc.16.235

• mass spectrometer. The software used was ThermoXcalibur 2.2 SP1.48. The XRF spectroscopy analysis of the catalyst was performed using a Bruker S2 Ranger®. Catalyst preparation The method previously reported by Zhu et al. was used to prepare several supported heteropoly acids (silicotungstic and PW) on

Dirhamnolipid ester – formation of reverse wormlike micelles in a binary (primerless) system

• David Liese,
• Hans Henning Wenk,
• Xin Lu,
• Jochen Kleinen and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2020, 16, 2820–2830, doi:10.3762/bjoc.16.232

• freshly cleaned mica surface (Plano) and waiting for 12 h. The AFM data were analyzed using the Gwyddion-2.53 software. Rheological measurements The rheological data were obtained using an Anton Paar MCR 301 rheometer equipped with a cylindrical geometry (CC27 – measuring unit). The temperature was

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• relevant factors that affect the affinity and selectivity of such ligands. Experimental Equipment NMR data were recorded with a Varian VNMR-S600 spectrometer [600 MHz (1H), 150 MHz (13C)] at 35 °C. NMR spectra were processed with the software ACD/NMR Processor Academic Version 12.01 and are referenced to

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• were determined using the peak fitting utility in ACDLabs Spectrus Processor software (v. 2018.1.1). X-ray diffraction X-ray data for 7a, 2a, 3a, 4a, and 6a were collected at −100 °C using a Bruker APEX-II CCD system equipped with a sealed tube molybdenum source and a graphite monochromator. The

• structures were solved and refined using the SHELXTL software package [26], refinement by full-matrix least squares on F2, scattering factors from [25]. Crystallographic data (excluding structure factors) for the structures in this paper have been deposited with the Cambridge Crystallographic Data Center as

• supplementary publication nos. CCDC #1998565−1998569. Computational chemistry Computational optimization of 8a and 8b structures was performed with Gaussian 9 software. Density functional theory at the B3LYP level, with a 6-311g++ basis set (Co phase) was employed. Reaction of purine (2) and 1 A mixture of 1.2

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

• Yuvixza Lizarme-Salas,
• Alexandra Daryl Ariawan,
• Ranjala Ratnayake,
• Hendrik Luesch,
• Angela Finch and
• Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

• . This was achieved by performing a DFT study in the Gaussian software, using the M06-2X level of theory with the 6-311+G(d,p) basis set, parameters similar to those employed by Linclau and co-workers for their studies of vicinal difluoro systems [22]. A set of starting structures of 2 was generated by

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• of reactions possible, nor open-source software available to implement the parsing of such rules. Representing reaction rules in Linear Code is not easy because of a few ambiguous cases not completely described in the initial Linear Code paper. Subsequent studies, therefore, have developed their own

• . Ideally, succinct, readable, and comprehensible reaction rules sets will be sufficiently standardized, like XML-type representations, so that they will be “interoperable” across multiple modeling software so that models can be “reused,” reproduced, validated, and extended across labs. Toward encouraging

Particle size effect in the mechanically assisted synthesis of β-cyclodextrin mesitylene sulfonate

• Stéphane Menuel,
• Sébastien Saitzek,
• Eric Monflier and
• Frédéric Hapiot

Beilstein J. Org. Chem. 2020, 16, 2598–2606, doi:10.3762/bjoc.16.211

• ). The spherical morphology could be deduced from the Solidicity program incorporated in the ImageJ software [22]. However, further grinding up to 297 min did not lead to further changes in either the morphology or the size of the β-CD particles (Figure 1f). From the SEM images and the inspection with

• the ImageJ software, we also calculated the granulometric composition of the β-CD particles against the grinding time (Figure 2). While a rapid decrease in size was observed over the first 10 min of grinding, a slight variation on the particle size was noticed when the grinding of β-CD was left to

• . From the SEM images and using the ImageJ software, we were able to determine the size of the β-CD particles and the calculated Feret mean diameter (mean value of the Feret diameters over all orientations, i.e., 0–180°) are collected in Table 1. BET analysis The β-CD particle size was also confirmed by

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• software available to assist with the building up of glycosylated biomolecular systems. As opposed to manual preparation, there are glycan-specific tools and toolkits such as doGlycans [27], Glycosylator [28], and online platforms such as GLYCAM-WEB [29] and CHARMM-GUI [30]. In this work, the CHARMM-GUI

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve

• ], glycosidic linkage stereochemistry [14] and torsion [15][16], and most recently, ring conformation [17]. Most of these issues have now been addressed as part of ongoing efforts to provide better software tools for structure determinations of glycoproteins, although the most difficult cases remain hard to

• atomic model will be expected as the final result of the study. Modelling of carbohydrates into 3D maps can be more complex than modelling proteins [33], although recent advances in software are closing the gap [34][35][36]. However, to date it remains true that most model building software is protein

Conformational preferences of fluorine-containing agrochemicals and their implications for lipophilicity prediction

• Daniela Rodrigues Silva,
• Joyce K. Daré and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2020, 16, 2469–2476, doi:10.3762/bjoc.16.200

• involving organofluorine agrochemicals, for example, towards modeling herbicidal activity, and/or for environmental risk assessment. Computational Details The conformational search of agrochemicals I–VII was performed at the ωB97X-D/6-31G(d,p) [16][17] level of theory using the Spartan’18 software [30]. The

• lowest energy minimum conformation of each compound was then reoptimized and the dipole moment determined using a higher level of theory, ωB97X-D/6-311++G(d,p) [16][18], in the Gaussian 09 software [31]. The geometries and dipole moments for compounds 1–11 were calculated at the same level, which has

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visualisation and modelling of glycans. The article also provides details on the standard representation of glycans, and

• . Consequently, unless the interface is rather straightforward and the building dynamic is well-designed, the software would be too difficult to use effectively. The ideal carbohydrate builder pick would also allow liberty for the user in terms of levels of precision since it has to fit every level of complexity

• list of pre-built core N- and O-linked carbohydrate moieties, which are usually present in glycoproteins structures, can be used as a template for further modification. A shortlist of glycan epitopes is also included providing templates for drawing more complex molecules. The software uses the Symbol

Styryl-based new organic chromophores bearing free amino and azomethine groups: synthesis, photophysical, NLO, and thermal properties

• Anka Utama Putra,
• Deniz Çakmaz,
• Nurgül Seferoğlu,
• Alberto Barsella and
• Zeynel Seferoğlu

Beilstein J. Org. Chem. 2020, 16, 2282–2296, doi:10.3762/bjoc.16.189

• Shimadzu 1800 UV–vis spectrophotometer in Britton–Robinson buffer solutions [63] with pH values ranging from 5.5 to 11 at room temperature (25 °C). The pKa values were obtained using the Origin software by recording the curve data. Computational methods The geometries of the dyes in their ground states

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• alignments are usually done by hand with assistance from the scanner software, which usually offers partial alignment algorithms based on background intensities. The spot diameters are also adjusted as some glycans just form smaller spots in comparison to others. Spots where information is not reliable due

• to extraneous factors such as poor printing due to a flaw in the surface, spot overlap/fusion with adjacent spot or presence of dust particles are flagged with a “bad” (or some numeric value) flag, so as to be disregarded in the data processing. The software then provides a results file as an output

• . CarbArrayART: Status: Development (available for testing upon request). Description: CarbArrayART is a software in development for the storage, processing and presentation of microarray data [38][39]. It is based on the GRITS Toolbox (classically used for mass spectrometry data) [40]. Features of CarbArrayART

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• ). Origin 7.0 software, supplied by the manufacturer, was used for data analysis. During the titration of ct-DNA, d: poly(rA)–poly(rU), poly(dAdT)–poly(dAdT), and poly(dGdC)–poly(dGdC) with the compound 4, one aliquot of 2 μL and 27 aliquots of 10 μL of 4 (c = 1.0 × 10−4 M) were injected from rotating

• silicon cantilevers (AC-160TS, Olympus) a NanoDrive controller with an Innova scanning probe microscope (Veeco, Germany, Mannheim) was used. The analysis of the AFM images was carried out by use of the Gwyddion (version 2.19) software. DLS experimental All measurements were carried out using a

• compound 4 (5–100 μM) were prepared and filtered prior to measurement through 0.20 μm nylon filters. The autocorrelation functions of the backscattered light fluctuations were analysed with the DTS 6.20 software from Malvern providing the hydrodynamic diameter (Z-average), polydispersity, and size

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• automated software pipeline which integrates the complementary outputs of Byonic and Proteome Discoverer to allow high-throughput automated quantitative glycoproteomic data analysis. The output of GlypNirO is clearly structured, allowing manual interrogation, and is also appropriate for input into diverse

• acquisition methods [10]. Progress in MS technology in particular has enabled deep and sensitive measurement of highly complex glycoproteomes, generating large amounts of high quality data [11]. With that comes the need for robust and automated workflows for extracting meaningful results. Numerous software

• are few efficient, robust, and automated workflows for glycopeptide quantification. There are several freely available software programs for quantitative label-free glycoproteomics using MS1 or data-dependent acquisition. These include LaCyTools [17], MassyTools [18], and GlycoSpectrumScan [19], which

Muyocopronones A and B: azaphilones from the endophytic fungus Muyocopron laterale

• Ken-ichi Nakashima,
• Junko Tomida,
• Tomoe Tsuboi,
• Yoshiaki Kawamura and
• Makoto Inoue

Beilstein J. Org. Chem. 2020, 16, 2100–2107, doi:10.3762/bjoc.16.177

• –7.62 (m, 10H, phenyl groups of MTPAs). Computational methods Calculation of the ECD spectra were performed using CONFLEX 8, Gaussian 16, and SpecDis software as described previously [13][14]. Geometry optimizations were performed using DFT at the CAM-B3LYP/6-311+G(d,p) level of theory, while TDDFT