Synthesis of 1-indolyl-3,5,8-substituted γ-carbolines: one-pot solvent-free protocol and biological evaluation

• Premansh Dudhe,
• Mena Asha Krishnan,
• Kratika Yadav,
• Diptendu Roy,
• Krishnan Venkatasubbaiah,
• Biswarup Pathak and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2021, 17, 1453–1463, doi:10.3762/bjoc.17.101

• Software, San Diego, CA). HeLa cell uptake study of γ-carboline 3ac A live-cell imaging experiment was performed with HeLa cells. The HeLa cells were placed in a 4-well confocal dish (cell count ≈ 100 cells per well) and incubated for 48 h at 37 °C under 5% CO2. After 3 h of incubation with carboline

Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV

• Santiago Ramos-Carreño,
• Ivone Giffard-Mena,
• Jose N. Zamudio-Ocadiz,
• Alfredo Nuñez-Rivera,
• Ricardo Valencia-Yañez,
• Jaime Ruiz-Garcia,
• Maria Teresa Viana and
• Ruben D. Cadena-Nava

Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95

• electron microscope equipped with a digital camera operated at 200 keV. The size of the VLPs was measured using the ImageJ (U.S. NIH) software from digital recorded TEM images. Shrimp and rearing conditions. P. vannamei postlarvae (PL) were grown in 2,500 L circular tanks containing seawater (34 ppt

• concentration range of the standard curve was 3.9 × 109 to 3.9 × 104 copies/ng. The ABI StepOnePlus v2.0 sequence detection system software (Applied Biosystems, USA) was used. Amplification reactions included all shrimp were analyzed (alive, dying and dead) from each experimental group. The viral load of WSSV

• with the antiviral therapy was evaluated through the survival and mean lethal time (LT50) [52]. A Log-Rank (Mantel–Cox) test was used to analyze the Kaplan–Meier survival curves generated with the GraphPad Prism version 5.01 software (San Diego California USA). In all cases, a value of p < 0.05 was

Photoinduced post-modification of graphitic carbon nitride-embedded hydrogels: synthesis of 'hydrophobic hydrogels' and pore substructuring

• Cansu Esen and
• Baris Kumru

Beilstein J. Org. Chem. 2021, 17, 1323–1334, doi:10.3762/bjoc.17.92

• contact angle measurement was performed using a Krüss contact angle measuring system G10 and recorded via Krüss official software. The sample with ideally flat surface is placed in front of a camera which records the water drop on the surface and estimates the angle between water droplet and surface. This

A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

• Marine Vallet,
• Filip Kaftan,
• Veit Grabe,
• Fatemeh Ghaderiardakani,
• Simona Fenizia,
• Aleš Svatoš,
• Georg Pohnert and
• Thomas Wichard

Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91

• shot−1) within the laser frequency of 60 Hz. MS spectra were acquired in a mass range from m/z 100 to m/z 1000 with a resolving power of 280000. Pseudo ion intensity maps of selected m/z values were generated using the Mirion V3 software package with an m/z width of 0.01 u. In the profiling mode, the

• acquired in MSI mode were collected with Xcalibur software version 2.8 SP1 Build 2806 (Thermo Fisher Scientific, Germany) while the acquisition of spatial scans, pre-defined in the x- and y-direction as rectangular sample regions, was controlled by the MCP (Master Control Program, TransMIT GmbH, Giessen

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• device. Data were collected by using omega and phi scans and were corrected for Lorentz and polarization effects by using the APEX software suite [60][61][62][63]. Using Olex2, the structure was solved with the XS or XT structure

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• . Emission spectra: Varian Cary Eclipse spectrophotometer in quartz cells (10 mm × 4 mm) at 20 °C. NMR spectra: Jeol ECZ 500 (1H: 500 MHz, 13C: 125 MHz) at 25 °C; processed with MestReNova software and referenced to the solvent [δ(DMSO-d5): 1H = 2.50 ppm, 13C: δ = 39.5 ppm, δ(CHCl3): 1H = 7.26 ppm, 13C: δ

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• macrophages were 100% positive for Cy5. Additionally, using QuPath analysis software, we determined the Cy5 MFI for each image. Interestingly, we found that the LNP A-1 and the LNP G-3 had higher MFI values in all the donors assessed compared to the Tat and T7 counterparts (Figure 4C). Further, we found that

• Concentration and size of LNPs with and without peptides were additionally confirmed using the NanoSight NS300 device (Malvern Panalytical, UK) with the NTA software (Version 3.44, Malvern Panalytical, UK). Samples were run at a 1:1000 dilution, with three technical replicates per sample. A blue 488 nm laser

• Zeiss AxioCam 503 color camera (Carl Zeiss Microscopy GmbH, Germany). Images were processed using ZEN blue software (Version 2.3, Carl Zeiss Microscopy GmbH, Germany) and merged using ImageJ Version 1.53a (Wayne Rasband, NIH, USA). To assess uptake of the LNPs in primary macrophages, samples were washed

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• ], Tellurium [39], or other modelling software supporting this format. Glycan structures can be imported or exported as GlycoCT [40], and exported as Linear Code [41] or IUPAC condensed linear formats. Sets of structures can be downloaded as CSV or GlycoCT. A key function of Glycologue is the ability to

• improve upon. Nevertheless, we have shown that the knockouts are able to reproduce the distinct species-specific features and disease states arising from congenital defects of ganglioside biosynthesis. Kinetic models based on the networks described here can be generated in modelling software, using the

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

• Kenji Morokuma,
• Shuntaro Tsukamoto,
• Kyosuke Mori,
• Kei Miyako,
• Ryuichi Sakai,
• Raku Irie and
• Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

• (Figure 10), is therefore, of interest [5], and the synthesis is also underway in our laboratory. Experimental Procedures for all chemical syntheses are described in Supporting Information File 1. Molecular modeling The CONFLEX calculations were performed using BARISTA software (Version 1.2.2.22, Conflex

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• , methanol, water. Solvation effects were considered using the SMD [40] model in terms of Linear Response scheme [41]. The analysis of charge transfer during S0→S1 transition was carried out by using the Multiwfn software [36]. The NBO analysis and MESP calculations were performed using the B3LYP/6-31G(d

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