Naphthalimide-phenothiazine dyads: effect of conformational flexibility and matching of the energy of the charge-transfer state and the localized triplet excited state on the thermally activated delayed fluorescence

• Kaiyue Ye,
• Liyuan Cao,
• Davita M. E. van Raamsdonk,
• Zhijia Wang,
• Jianzhang Zhao,
• Daniel Escudero and
• Denis Jacquemin

Beilstein J. Org. Chem. 2022, 18, 1435–1453, doi:10.3762/bjoc.18.149

• recorded on a LP920 laser flash 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 in collinear configuration of the pump and

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• , amongst many other uses, provided the background for fragment-based drug design [2][3]. – An ever-increasing computer processing speed leading to an ever-growing list of software-based approaches to try to help in various aspects of drugs discovery. The neural network-based software AlphaFold [4], which

• compounds [65][66][67][68]. But past such filters, the many software designed in the last 30 years to predict which chemicals will be active on a given target, still feature a “large room for improvement” [69]. Concerning ligand-based virtual screening also known as hit expansion, this is a really useful

Cyclodextrin-based Schiff base pro-fragrances: Synthesis and release studies

• Attila Palágyi,
• Jindřich Jindřich,
• Juraj Dian and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2022, 18, 1346–1354, doi:10.3762/bjoc.18.140

• nonlinear regression method (Levenberg–Marquardt algorithm) using both mono- and double-exponential functions (Microcal Origin software). In most cases, the double-exponentials described the observed behavior much better (see Supporting Information File 1, Figures S1–S11). Experimental data were fitted with

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• are typically underestimated by orders of magnitude and not accessible to many researchers. A conceivable alternative approach would be the use of docking software such as Autodock Vina [24][25]. However, these docking methods typically have been developed to dock ligands that are not too large and

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• compound for calculation of ABTS-reducing activity (in %). Computational ECD calculation of compound 1 Merck molecular force field (MMFF) and DFT as well as TDDFT calculations were carried out with the Spartan 14 software (Wavefunction Inc.) and the Gaussian 16 program [41], respectively. Conformers within

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• . X-ray crystallographic analysis. Compound 2 was crystallized from MeCN at 4 °C. The crystallographic data for compound 2 was collected on a Bruker D8 Venture diffractometer using Cu Kα radiation (λ = 1.54178 Å). The collected data integration and reduction were processed with SAINT V8.37A software

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• Series ESIMS spectrometer connected to an analytical Kinetex C18 column (250 mm × 4.6 mm, 5 µm; Phenomenex, Torrance, CA, USA) was utilized. The Agilent 7820A GC system equipped with a 5977B mass selective detector system was controlled by qualitative navigator version B.08.00 software. Preparative HPLC

• based on the Boltzmann populations of each conformer in the associated Gibbs free energy (Supporting Information File 1, Figure S45). The ECD spectra were Boltzmann-weighted and generated using SpecDis software (Version 1.71) [23] with a σ/γ value of 0.30 eV. The chemical shift values were calculated

Substituent effect on TADF properties of 2-modified 4,6-bis(3,6-di-tert-butyl-9-carbazolyl)-5-methylpyrimidines

• Irina Fiodorova,
• Tomas Serevičius,
• Rokas Skaisgiris,
• Saulius Juršėnas and
• Sigitas Tumkevicius

Beilstein J. Org. Chem. 2022, 18, 497–507, doi:10.3762/bjoc.18.52

• 49 ms integration time. Solid-state samples were mounted in a closed cycle He cryostat (Cryo Industries 204 N) for PL measurements in oxygen-free conditions. Quantum chemical calculations were carried out by using density functional theory at the B3LYP/6-31G(d) level as implemented in a software

Comparative study of thermally activated delayed fluorescent properties of donor–acceptor and donor–acceptor–donor architectures based on phenoxazine and dibenzo[a,j]phenazine

• Saika Izumi,
• Prasannamani Govindharaj,
• Anna Drewniak,
• Paola Zimmermann Crocomo,
• Satoshi Minakata,
• Leonardo Evaristo de Sousa,
• Piotr de Silva,
• Przemyslaw Data and
• Youhei Takeda

Beilstein J. Org. Chem. 2022, 18, 459–468, doi:10.3762/bjoc.18.48

• . The photophysics of both molecules was analyzed using a unified approach for photophysical rate calculations that employs the nuclear ensemble method as implemented in the NEMO software [21][22] interfaced with the QChem 5.0 program suite [23]. A total of 500 geometries were sampled for each molecule

Four bioactive new steroids from the soft coral Lobophytum pauciflorum collected in South China Sea

• Di Zhang,
• Zhe Wang,
• Xiao Han,
• Xiao-Lei Li,
• Zhong-Yu Lu,
• Bei-Bei Dou,
• Wen-Ze Zhang,
• Xu-Li Tang,
• Ping-Lin Li and
• Guo-Qiang Li

Beilstein J. Org. Chem. 2022, 18, 374–380, doi:10.3762/bjoc.18.42

• counted by using the Image-Pro Plus software. Structures of compounds 1–7. 1H,1H-COSY and selected key HMBC correlations of 1–4. Selected NOESY correlations of compounds 1–4. X-ray crystallographic analysis of compounds 1–3. Effects of compound 1 on the anti-inflammation of zebrafish internodes

Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase

• Peterson de Andrade,
• Sanaz Ahmadipour and
• Robert A. Field

Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24

• lactose and with 40 μL buffer. The data from three independent experiments were analysed with GraphPad Prism software version 4.0 (San Diego, CA, USA). Inhibition percentages were calculated according to the equation: % I = 100 [1 (Vi/V0)], where Vi is the velocity in the presence of inhibitor and V0 is

Efficient and regioselective synthesis of dihydroxy-substituted 2-aminocyclooctane-1-carboxylic acid and its bicyclic derivatives

• İlknur Polat,
• Selçuk Eşsiz,
• Uğur Bozkaya and
• Emine Salamci

Beilstein J. Org. Chem. 2022, 18, 77–85, doi:10.3762/bjoc.18.7

• , which is a typical transesterification reaction. To explain the formation of lactone 10, we performed a series of DFT computations using the Gaussian 16 software [29]. For this purpose, we performed geometry optimizations using the B3LYP functional [30][31][32][33]. Vibrational frequencies were computed

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• for support in the synthetic work. Funding The project was supported in part by a Bielefeld University Ph.D. fellowship to H.G. and by Deutsche Forschungsgemeinschaft (SE609/16-1). The DFT calculations were carried out using hardware and software resources of the Supercomputing and Networking Center

The ethoxycarbonyl group as both activating and protective group in N-acyl-Pictet–Spengler reactions using methoxystyrenes. A short approach to racemic 1-benzyltetrahydroisoquinoline alkaloids

• Marco Keller,
• Karl Sauvageot-Witzku,
• Franz Geisslinger,
• Nicole Urban,
• Michael Schaefer,
• Karin Bartel and
• Franz Bracher

Beilstein J. Org. Chem. 2021, 17, 2716–2725, doi:10.3762/bjoc.17.183

• ). Multiplicity is defined as s = singlet, d = doublet, t = triplet, q = quartet, p = pentet, m = multiplet. NMR spectra were analyzed with NMR software MestReNova, version 14.2.0-26256 (Mestrelab Research S.L.). High-resolution mass spectra were performed by the LMU Mass Spectrometry Service applying a Thermo

• dispensed into black pigmented, clear-bottom 384-well plates (Greiner, Germany). Then, plates were mounted on the FLIPR, fluo-4 was excited by LED array and emitted light was imaged through a 515 nm long pass filter with a Zyla 5.5 camera (Andor, Belfast, UK) under control of the Micromanager software

• intensities in each single well was calculated with ImageJ software, corrected for the respective background signals and normalized to the initial fluorescence intensities (F/F0). Concentration–response curves were generated by fitting the data to a four-parameter Hill equation (Emin, Emax, EC50/IC50, and

In-depth characterization of self-healing polymers based on π–π interactions

• Josefine Meurer,
• Julian Hniopek,
• Johannes Ahner,
• Michael Schmitt,
• Jürgen Popp,
• Stefan Zechel,
• Kalina Peneva and
• Martin D. Hager

Beilstein J. Org. Chem. 2021, 17, 2496–2504, doi:10.3762/bjoc.17.166

• - software was used. The temperature sweeps (DMTA) and frequency sweeps (FS) were measured with a plate-plate setup (D-PP15-SN0). The sample was heated to 150 °C and the sample gap was set to 1 mm. For the DMTA, the samples were cooled to 25 °C and heated up to 200 °C with a heating rate of 2 °C/min under a

Exfoliated black phosphorous-mediated CuAAC chemistry for organic and macromolecular synthesis under white LED and near-IR irradiation

• Azra Kocaarslan,
• Zafer Eroglu,
• Önder Metin and
• Yusuf Yagci

Beilstein J. Org. Chem. 2021, 17, 2477–2487, doi:10.3762/bjoc.17.164

• detector was calibrated with polystyrene standards having narrow molecular-weight distributions. The data were analyzed using Eco-SEC analysis software. A Hitachi HT7700 (TEM) with EXALENS (120 kV) working at a high-resolution (HR) mode was used to obtain transmission electron microscopy (TEM) images, high

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• equipped with a diode array detector was used for analysis and purification. The computational study was performed using MacroModel implemented in the Maestro 12.3 software package [27] and the Gaussian16, Revision C.01 program [28]. A part of these computations was conducted using the SuperComputer System

• , Institute for Chemical Research, Kyoto University. Molecular structures were visualized using Maestro 12.3 software package. ECD spectra were visualized using GaussView 6.0.16 and Microsoft Excel 2019. Microorganism Actinomadura sp. AKA43 was isolated from a sea water sample collected from Sagami Bay at a

Volatile emission and biosynthesis in endophytic fungi colonizing black poplar leaves

• Christin Walther,
• Pamela Baumann,
• Katrin Luck,
• Beate Rothe,
• Peter H. W. Biedermann,
• Jonathan Gershenzon,
• Tobias G. Köllner and
• Sybille B. Unsicker

Beilstein J. Org. Chem. 2021, 17, 1698–1711, doi:10.3762/bjoc.17.118

• . Identification and heterologous expression of terpene synthase genes To identify putative terpene synthases, a TBLASTN analysis with Aspergillus terreus aristolochene synthase (pdb 20A6) as query and the de novo transcriptome of Cladosporium sp. as a template was performed using the software BioEdit 7.0.9.0 [88

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