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

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

Synthesis and biological profile of 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines, a novel class of acyl-ACP thioesterase inhibitors

• Jens Frackenpohl,
• David M. Barber,
• Guido Bojack,
• Birgit Bollenbach-Wahl,
• Ralf Braun,
• Rahel Getachew,
• Sabine Hohmann,
• Kwang-Yoon Ko,
• Karoline Kurowski,
• Bernd Laber,
• Rebecca L. Mattison,
• Thomas Müller,
• Anna M. Reingruber,
• Dirk Schmutzler and
• Andrea Svejda

Beilstein J. Org. Chem. 2024, 20, 540–551, doi:10.3762/bjoc.20.46

• pI50 values were calculated from plots of inhibition values vs test compound concentration using Model 205 of the ID Business Solutions Ltd Xlfit software suite. The FAT A binding fluorescent tracer was synthesized from (2S,4S)-4-[(2,6-difluorophenyl)methoxymethyl]-4-ethyl-2-methyl-N-(prop-2

Pseudallenes A and B, new sulfur-containing ovalicin sesquiterpenoid derivatives with antimicrobial activity from the deep-sea cold seep sediment-derived fungus Pseudallescheria boydii CS-793

• Zhen Ying,
• Xiao-Ming Li,
• Sui-Qun Yang,
• Hong-Lei Li,
• Xin Li,
• Bin-Gui Wang and
• Ling-Hong Meng

Beilstein J. Org. Chem. 2024, 20, 470–478, doi:10.3762/bjoc.20.42

• by Chromeleon software (version 6.80). LC–MS were obtained with a Bruker maXis plus Q-TOF. Column chromatography was carried out using commercially available silica gel (200–300 mesh, Qingdao Haiyang Chemical Co.), Lobar LiChroprep RP-18 (40–63 μm, Merck), and Sephadex LH-20 (Pharmacia). Thin-layer

• structures were solved by direct methods using the SHELXTL software package [18][19]. All non-hydrogen atoms were refined anisotropically. The H atoms were located by geometrical calculations, and their positions and thermal parameters were fixed during the structure refinement. The absolute structures were

Facile approach to N,O,S-heteropentacycles via condensation of sterically crowded 3H-phenoxazin-3-one with ortho-substituted anilines

• Eugeny Ivakhnenko,
• Vasily Malay,
• Pavel Knyazev,
• Nikita Merezhko,
• Nadezhda Makarova,
• Oleg Demidov,
• Gennady Borodkin,
• Andrey Starikov and
• Vladimir Minkin

Beilstein J. Org. Chem. 2024, 20, 336–345, doi:10.3762/bjoc.20.34

• reflexes as well as the determination and refinement of unit cell parameters were performed by using the specialized CrysAlisPro 1.171.38.41 software suite [28]. The structures were solved by using the SHELXT program [29]. Structural refinement was performed with the SHELXL program [30]. Molecular graphics

• were rendered and prepared for publication with the Olex2 version 1.3.0 software suite [31]. The complete X-ray diffraction datasets were deposited in the Cambridge Crystallographic Data Center (CCDC numbers 2292841, 2292840, 2292847, 2308520, and 2292848, Tables S2–S9, Supporting Information File 1

Discovery of unguisin J, a new cyclic peptide from Aspergillus heteromorphus CBS 117.55, and phylogeny-based bioinformatic analysis of UngA NRPS domains

• Sharmila Neupane,
• Marcelo Rodrigues de Amorim and
• Elizabeth Skellam

Beilstein J. Org. Chem. 2024, 20, 321–330, doi:10.3762/bjoc.20.32

• TF 1.8.1 software. Fungal growth and extraction A. heteromorphus CBS 117.55 was cultivated in 2 Erlenmeyer flasks (500 mL), each containing 90 g of rice and 150 mL of H2O [16]. The medium was autoclaved at 121 °C for 20 min. After sterilization, the medium was inoculated with the spore solution of A

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• overlay of streptavidin-Alexa Fluor 647 (Molecular Probes) at 1 µg/mL. The microarray slides were scanned with GenePix 4300A scanner instrument (50% laser power at PMT 350), and the image analysis (quantitation) was performed with GenePix® Pro 7 software. The results can be found in Supporting Information

• reference (streptavidin only) and subtracting a blank injection (running buffer – zero analyte concentration). Data evaluation and curve fitting was performed using the provided BIACORE X100 evaluation software (version 2.0). Measurements were at least done in duplicate. Then, to perform competition

• using the free software “data entry”. The IC50 was calculated using https://www.aatbio.com/tools/ic50-calculator. X-ray crystallography All consumables for crystallization and crystal handling were purchased at Molecular Dimensions, Calibre Scientific, Rotherham, UK, unless stated otherwise. CMA1

Synthesis of the 3’-O-sulfated TF antigen with a TEG-N₃ linker for glycodendrimersomes preparation to study lectin binding

• Mark Reihill,
• Hanyue Ma,
• Dennis Bengtsson and
• Stefan Oscarson

Beilstein J. Org. Chem. 2024, 20, 173–180, doi:10.3762/bjoc.20.17

• reported to one decimal point unless an additional digit was required to distinguish overlapping peaks. Software for data processing: MestReNova, version 11.0.0–17609 (MestReLab Research S.L.). High-resolution mass spectrometry (HRMS) data were recorded on a Waters Micromass LCT LC–TOF instrument using

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• , and gHMBC experiments. The spectra were processed with the MestreNova software. The mass spectra were recorded with a Finnigan LCQ Deca (driving current: 6 kV, collision gas: argon, capillary temperature: 200 °C, support gas: nitrogen) and an Orbitrap mass spectrometer Thermo Fisher Exactive (driving

• current: 3.5 kV, capillary temperature: 300 °C, capillary voltage: 45 V, injection rate: 5 μL/min, scanning range: 150−750 m/z, and resolution: ultra-high) and processed with the software Xcalibur. The CHNS analysis data were determined in-house with a HEKAtech EuroEA combustion analyzer. The melting

Optimizing reaction conditions for the light-driven hydrogen evolution in a loop photoreactor

• Pengcheng Li,
• Daniel Kowalczyk,
• Johannes Liessem,
• Mohamed M. Elnagar,
• Dariusz Mitoraj,
• Radim Beranek and
• Dirk Ziegenbalg

Beilstein J. Org. Chem. 2024, 20, 74–91, doi:10.3762/bjoc.20.9

• -DHC s/n: LS-2001019) and an Avantes spectrometer (AvaSpec-Mini2048CL) was used to measure the absorbance with AvaSoft software. An example of the whole absorption measurement setup using 1cm light-path cuvette and the cuvette holder setup is shown in Supporting Information File 1, Figure S7

• variable (response). Design-Expert® software (10.0.5.0 Stat-Ease, Inc.) was used to perform the DOE analysis. To avoid random experimental values from a range of chosen values of the parameters when using the software, the values for the independent variables were chosen manually based on the technical

• variables, yi,pred is the predicted response, yi,exp is the experimental data, is the arithmetic mean of the experimental data, and e−i is a deletion residual computed by fitting a model without the ith run then predicting the ith observation with the resulting model used in the Design-Expert® software

Multi-redox indenofluorene chromophores incorporating dithiafulvene donor and ene/enediyne acceptor units

• Christina Schøttler,
• Kasper Lund-Rasmussen,
• Line Broløs,
• Philip Vinterberg,
• Ema Bazikova,
• Viktor B. R. Pedersen and
• Mogens Brøndsted Nielsen

Beilstein J. Org. Chem. 2024, 20, 59–73, doi:10.3762/bjoc.20.8

• obtained using an Autolab PGSTAT12 instrument and Nova 1.11 software with a scan rate of 0.1 V/s for the CVs. A silver wire immersed in a 0.1 M Bu4NPF6 solution in CH2Cl2 separated from the analyte solution by a frit was used as the reference electrode, a Pt wire was used as the counter electrode, and a