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

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions

• Matthias R. Steiner,
• Max Schmallegger,
• Larissa Donner,
• Johann A. Hlina,
• Christoph Marschner,
• Judith Baumgartner and
• Christian Slugovc

Beilstein J. Org. Chem. 2024, 20, 41–51, doi:10.3762/bjoc.20.6

• displayed in Scheme 1. All simulations were performed with COPASI, an open-source software [48]. The second-order rate constants were obtained by fitting the experimental time traces until a fully consistent data set, being valid for all experimental conditions, was established. For X-ray structure analyses

NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform

• Luc Patiny,
• Hamed Musallam,
• Alejandro Bolaños,
• Michaël Zasso,
• Julien Wist,
• Metin Karayilan,
• Eva Ziegler,
• Johannes C. Liermann and
• Nils E. Schlörer

Beilstein J. Org. Chem. 2024, 20, 25–31, doi:10.3762/bjoc.20.4

• ), Cleveland, Ohio 44106, United States, Department of Chemistry, Johannes Gutenberg University Mainz, 55099 Mainz, Germany 10.3762/bjoc.20.4 Abstract NMRium is the first web-based software that allows displaying, processing, interpretation, and teaching of 1D and 2D NMR data in a user-friendly interface. It

• (oftentimes commercial) software, which imposes additional preconditions that cannot easily be overcome in many institutions [12][13]. Many tasks that required locally installed software before can now be easily performed using web applications (e.g., cloud office services), making the web browser a powerful

• platform for specialized data handling applications. This trend has not been withheld from science: With the advent of web tools for the online representation and manipulation of scientific data [14][15][16][17] and the development of software for spectroscopy visualization [18][19][20][21][22][23][24][25

Thienothiophene-based organic light-emitting diode: synthesis, photophysical properties and application

• Recep Isci and
• Turan Ozturk

Beilstein J. Org. Chem. 2023, 19, 1849–1857, doi:10.3762/bjoc.19.137

• . The high thermal stability is profitable for the preparation of stable and durable OLED devices. Computational chemistry Ground-state geometry optimization of DMB-TT-TPA (8) was performed using density functional theory (DFT) calculations with the Gaussian 16 software at the B3LYP/6-31G (d,p) level

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

• Alessandro L. Alves,
• Simone V. Bernardino,
• Carlos H. Stadtlober,
• Edivandro Girotto,
• Giliandro Farias,
• Rodney M. do Nascimento,
• Sergio F. Curcio,
• Thiago Cazati,
• Marta E. R. Dotto,
• Juliana Eccher,
• Leonardo N. Furini,
• Hugo Gallardo,
• Harald Bock and
• Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

• a monochromator and a multichannel bases photomultiplier (Hamamatsu R3809U-50). Lifetimes were obtained by fitting the fluorescence decay curves with exponential functions using FluoFit® software and the plots of weighted residuals and reduced chi-square were used to determine the best fits during

• , using the Orca 5.0.3 [40] software package within B3LYP/Def2-TZVP(-f) level of theory [41][42][43][44][45]. Dispersion effects were included using Grimme’s D3 correction with Becke-Johnson (BJ) damping [45][46]. The evaluation of the four-center integrals was accelerated with the RIJCOSX algorithm [47

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• were used to calculate the percentage decrease in concentration of the compound with respect to the first reading and data were processed using the OriginPro 21 software. X-ray diffraction Single crystals of hdz-CH3 and hdz-NO2 suitable for X-ray diffraction were obtained from the slow evaporation of

• the syntheses’ mother liquors. They were analyzed in a D8-Venture Bruker diffractometer equipped with Mo Κα X-ray source at 293 K. Diffraction images were collected with a Photon III area detector and the frames were integrated with the Bruker SAINT software using a narrow-frame algorithm [51

• ]. Absorption correction was conducted with the multi-scan method in SADABAS software (APEX3 system) [52]. The structures were solved with directed methods in ShelxS [53] and refined with full-matrix least-square in ShelxL [53], implemented in WinGX [54] and ShelxLE [55] platforms. Non-hydrogen atoms were

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• procedure: Optimization of the R[4]A and sec-amine geometries was performed with the GFN2-xTB method using the ALPB solvent model with the “veryTight” accuracy using the xTB software package [29]. Complex assembly search (aISS) was performed using the “dock” function with “tight” optimization of the

Organic thermally activated delayed fluorescence material with strained benzoguanidine donor

• Alexander C. Brannan,
• Elvie F. P. Beaumont,
• Nguyen Le Phuoc,
• George F. S. Whitehead,
• Mikko Linnolahti and
• Alexander S. Romanov

Beilstein J. Org. Chem. 2023, 19, 1289–1298, doi:10.3762/bjoc.19.95

• measurements were performed at ambient temperature under an inert N2 atmosphere in THF containing the complex under study (0.14 mM) and the supporting electrolyte [n-Bu4N][PF6] (0.13 mM). Data were recorded with Autolab NOVA software (v. 1.11). Thermogravimetric analysis was performed by the Microanalysis

• to ride on their parent atoms with C–H = 0.95–1.00 Å, and Uiso = 1.2–1.5 Ueq (parent atom). All calculations were performed using the SHELXL software and Olex2 graphical user interface [22][23]. 4BGIPN (monoclinic P21), CCDC number 2243340, C60H32N14, monoclinic, space group P21 (no. 4), a = 17.4217

Retraction: One-pot odourless synthesis of thioesters via in situ generation of thiobenzoic acids using benzoic anhydrides and thiourea

• Mohammad Abbasi and
• Reza Khalifeh

Beilstein J. Org. Chem. 2023, 19, 1170–1170, doi:10.3762/bjoc.19.85

• ; thiourea; This article was retracted due to the improper manipulation of NMR spectra with the help of software to obscure peaks corresponding to impurities and solvent.

Two new lanostanoid glycosides isolated from a Kenyan polypore Fomitopsis carnea

• Winnie Chemutai Sum,
• Sherif S. Ebada,
• Didsanutda Gonkhom,
• Cony Decock,
• Rémy Bertrand Teponno,
• Josphat Clement Matasyoh and
• Marc Stadler

Beilstein J. Org. Chem. 2023, 19, 1161–1169, doi:10.3762/bjoc.19.84

• min, 5% B to 100% B within 19.5 min and at 100% B for 5 min. The flow rate was maintained at 0.6 mL/min and UV–vis detection made at 200–600 nm. The calculation of the compounds’ molecular formulas was performed using the Smart Formula algorithm of the Compass DataAnalysis software (Bruker Daltonics

The effect of dark states on the intersystem crossing and thermally activated delayed fluorescence of naphthalimide-phenothiazine dyads

• Liyuan Cao,
• Xi Liu,
• Xue Zhang,
• Jianzhang Zhao,
• Fabiao Yu and
• Yan Wan

Beilstein J. Org. Chem. 2023, 19, 1028–1046, doi:10.3762/bjoc.19.79

• spectrograph and to the detector. The sample was contained in a 1 mm quartz cuvette mounted on a movable stage, in order to avoid photodecomposition. The data were subdivided in two different time intervals and fitted using the Glotaran-Application 1.5.1 and Surface Xplorer software. The number of kinetic

• photolysis spectrometer (Edinburgh Instruments, Ltd., U.K.). The data (kinetic decay traces and the transient difference absorption spectra) were analyzed with the L900 software. All samples were deaerated with N2 for ca. 15 min before measurement and excited with a nanosecond pulsed laser (OPO nanosecond

CO₂ complexation with cyclodextrins

• Cecilie Høgfeldt Jessen,
• Jesper Bendix,
• Theis Brock Nannestad,
• Heloisa Bordallo,
• Martin Jæger Pedersen,
• Christian Marcus Pedersen and
• Mikael Bols

Beilstein J. Org. Chem. 2023, 19, 1021–1027, doi:10.3762/bjoc.19.78

• -brilliance IμS radiation source (λ = 0.71073 Å), a multilayer X-ray mirror and a PHOTON 100 CMOS detector, and an Oxford Cryosystems low temperature device. The instrument was controlled with the APEX3 software package using SAINT (Bruker; Bruker AXS, Inc. SAINT, Version 7.68A; Bruker AXS: Madison, WI, 2009

Five new sesquiterpenoids from agarwood of Aquilaria sinensis

• Hong Zhou,
• Xu-Yang Li,
• Hong-Bin Fang,
• He-Zhong Jiang and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 998–1007, doi:10.3762/bjoc.19.75

• ε) 200 (2.82) nm; HRESIMS (m/z): [M + Na]+ calcd for C15H26O2Na, 261.1825; found, 261.1825; 1H and 13C NMR data, see Table 3. Calculations of NMR spectra Using density functional theory (DFT) and B3LYP/6-31G(d,p) [28] levels in the Gaussian 09 software package [29], the obtained minimum energy

• conformation of the force field was optimized. DFT was used to calculate the gauge-independent atomic orbital [30] for 1H and 13C NMR chemical shifts using the PCM solvent model in Gaussian 09 software [29]. The NMR chemical shift was corrected by the isotope shift of TMS [31]. The calculated 13C NMR chemical

• shift was analyzed by regression with the experimental one. Boltzmann weighing of the predicted chemical shift of each isomer and the DP4+ parameters were calculated using the Excel file provided by Ariel M. Sarotti [32]. Calculations of ECD spectra Using the Spartan'14 software package (Wavefunction

Light-responsive rotaxane-based materials: inducing motion in the solid state

• Adrian Saura-Sanmartin

Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64

• : (i) FAIR open data from X-ray structures and Mercury® 2020.1 Software (Cambridge Crystallographic Data Center) to create Figures 1b (CCDC number 1943103), 3b (CCDC number 2018646) and 4 (CCDC numbers 2090727 and 2090729); (ii) chemical structures employing ChemBioDraw® Ultra 12.0 (CambridgeSoft

A fluorescent probe for detection of Hg²⁺ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene

• Xiaoqian Chen,
• Naqin Yang,
• Yue Ma,
• Xinan Yang and
• Peihua Ma

Beilstein J. Org. Chem. 2023, 19, 864–872, doi:10.3762/bjoc.19.63

• unwanted data point, the data was analyzed using the independent model Launch Nano analysis software. 1H NMR spectroscopy The host–guest interaction between G and TMeQ[6] and the interaction mode between G@TMeQ[6] fluorescent probe and Hg2+ ion were studied by 1H NMR titration spectroscopy. All 1H NMR

Non-peptide compounds from Kronopolites svenhedini (Verhoeff) and their antitumor and iNOS inhibitory activities

• Yuan-Nan Yuan,
• Jin-Qiang Li,
• Hong-Bin Fang,
• Shao-Jun Xing,
• Yong-Ming Yan and
• Yong-Xian Cheng

Beilstein J. Org. Chem. 2023, 19, 789–799, doi:10.3762/bjoc.19.59

• field (MMFF94) and DFT/TDDFT calculations, were performed for model compounds (3R,4R)-1, (3S,4S)-1, (2S,2″R)-4, (2S,2″S)-4, (2R,2″S)-4, and (2R,2″R)-4 using the Spartan'14 software package and the Gaussian 09 program package. The ECD calculations of the predominant conformers (80%) were conducted using

• (Pierce, USA) and analysis system (Bio-Rad, CA, USA) were used to visualize and detect the bands. Immunoblot densitometric analysis results were processed using ImageJ software (NIH, USA). Structures of compounds 1–9. Key 1H–1H COSY, HMBC, and ROESY correlations of compounds 1–4, 7, and 8. Calculated and

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• measured on a Varian Cary 100 Bio spectrometer. Fluorescence spectra were recorded on a Varian Cary Eclipse fluorimeter. CD spectra were recorded on JASCO J815 spectrophotometer. Absolute quantum yields (Φf) were determined using software implemented with the instrument by the Integrating sphere SC-30 of

• calorimetry (ITC) titrations were performed on a Malvern PEAQ-ITC microcalorimeter (MicroCal, Inc.,Northampton, MA, USA). MicroCal PEAQ-ITC analysis software, supplied by the manufacturer, was used for data analysis. Polynucleotides were purchased as noted: calf thymus (ct)-DNA, poly dAdT–poly dAdT, poly dGdC

• determine the heats of dilution of the ligand and the enzyme. The resulting data were analyzed by using MicroCal PEAQ-ITC analysis software, supplied by the manufacturer, according to the model based on a single set of identical binding sites to estimate the binding constants (Ka) and the enthalpy of