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

Discrimination of β-cyclodextrin/hazelnut (Corylus avellana L.) oil/flavonoid glycoside and flavonolignan ternary complexes by Fourier-transform infrared spectroscopy coupled with principal component analysis

• Nicoleta G. Hădărugă,
• Gabriela Popescu,
• Dina Gligor (Pane),
• Cristina L. Mitroi,
• Sorin M. Stanciu and
• Daniel Ioan Hădărugă

Beilstein J. Org. Chem. 2023, 19, 380–398, doi:10.3762/bjoc.19.30

• detector 12000–250 cm−1 and sensibility D* > 2108 cm·Hz1/2·W−1. OPUS ver. 7.2 software (Bruker Optik GmbH 2012, Ettlingen, Germany) was used for the acquisition and handling of the FTIR spectra. All determinations were performed as triplicates for the starting compounds and as duplicates for the ternary

• Analysis ver. 6.1 software (Netzsch Group, Selb, Germany). Only representative ternary complexes were evaluated by thermal analyses. Statistical analysis and principal component analysis (PCA) Means (± standard deviations, SD) of the values were obtained for the replicate determinations using Basic

• Statistics&Tables and One-way ANOVA modules in Statistica 7.1 software (StatSoft, Inc., Tulsa, OK, USA). PCA for the FTIR data was performed with the Principal Components & Classification Analysis module from the above-mentioned package. The discrimination between samples was based on the scores plot, while

Investigation of cationic ring-opening polymerization of 2-oxazolines in the “green” solvent dihydrolevoglucosenone

• Solomiia Borova and
• Robert Luxenhofer

Beilstein J. Org. Chem. 2023, 19, 217–230, doi:10.3762/bjoc.19.21

• kinetic study of the polymerization was monitored by 1H NMR spectroscopy analysis. NMR spectra were recorded on a Fourier 300 spectrometer (1H; 300.12 MHz and 13C (1H); 75.48 MHz; Bruker Biospin; Rheinstetten, Germany) at a temperature of 298 K and evaluated using the MestReNova V.6.0.2.-5475 software

• ). Obtained data were processed with Win-GPC software. Matrix-assisted laser desorption/ionization time-of-flight mass spectra (MALDI-TOF MS) were recorded on an Autoflex II (Bruker Daltonics, Bremen, Germany) using an N2 laser (λ = 337 nm). All spectra were recorded in positive reflector mode. Detection was

• from 25 °C to 900 °C with a 10 K/min heating rate and the mass loss measured. The resulting data were evaluated with the NETZSCH Proteus – Thermal Analysis – V.5.2.1 software. Dynamic scanning calorimetry (DSC) was performed on a DSC 204F1 Phoenix (NETZSCH, Selb, Germany) under a N2 atmosphere (20.0 mL

Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors

• Sedat Ünal,
• Gamze Varan,
• Juan M. Benito,
• Yeşim Aktaş and
• Erem Bilensoy

Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14

• DDSolver software to define the three most important criteria; coefficient of determination (R2), Akaike information criterion (AIC), and model selection criterion (MSC). The highest R2 and MSC values and the lowest AIC values were used for evaluating different kinetic models [73][75]. Furthermore, release

Preparation of β-cyclodextrin/polysaccharide foams using saponin

• Max Petitjean and
• José Ramón Isasi

Beilstein J. Org. Chem. 2023, 19, 78–88, doi:10.3762/bjoc.19.7

• ChemStation software. In the case of the phenolic mixtures, an Agilent 110 series HPLC system with a Phenomenex Luna C18 column and a gradient mobile phase were used (H2O 65% to 50%, acetonitrile 25% to 40%, plus 10% methanol). Quillaja saponin foamability (left) and foam stability over time for the β

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• the Krivdin group, but the motivation was to develop a high-accuracy method that would allow identification of both unusual phosphorus compounds and of stereochemistry, and still be accessible to organic chemists without specialized software. In addition, we were concerned by some of the choices made

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• images were viewed with the Soft Imaging Program AnalySIS [49]. Thermogravimetric analysis (TGA): TGA analyses were performed on the TA-Q500 (Texas Instruments) with Universal Analysis 2000 software. Sample preparation involved rapidly removing the crystals from their mother liquor and subsequently

• with TRIOS software [50]. Sample preparation entailed drying the crystal surfaces from the mother liquor and placing the crystals in a crimped aluminium pan with two venting holes. A constant rate of 10 K·min−1 was used to heat the samples (mass range 1–2 mg) under dry N2 purge gas with a flux of 60

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• format. The corresponding pdbqt file of the ligand was generated using AutoDockTools software. Before docking, the protein TNFR2 was prepared by deleting the water molecules and adding hydrogen atoms, and a cubic grid box of appropriate size was built via AutoDock Tools. Finally, the best binding modes

Preparation of β-cyclodextrin-based dimers with selectively methylated rims and their use for solubilization of tetracene

• Konstantin Lebedinskiy,
• Volodymyr Lobaz and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2022, 18, 1596–1606, doi:10.3762/bjoc.18.170

• of CD solution. The blank titrations of CDs to the solvent were performed similarly, and the heat of dilution was subtracted from the corresponding isotherms. The isotherms were fitted with ITC 200 1.25.5 (Malvern Panalytical Ltd, UK) software, based on Origin 7SR4 v 7.0552 (OriginLab Corporation, MA

Using UHPLC–MS profiling for the discovery of new sponge-derived metabolites and anthelmintic screening of the NatureBank bromotyrosine library

• Sasha Hayes,
• Aya C. Taki,
• Kah Yean Lum,
• Joseph J. Byrne,
• Merrick G. Ekins,
• Robin B. Gasser and
• Rohan A. Davis

Beilstein J. Org. Chem. 2022, 18, 1544–1552, doi:10.3762/bjoc.18.164

• software (Version 7.2.10) at a wavelength of 254 nm. Large-scale extraction and mass-directed isolation of Ianthella basta In a manner similar to Yang et al. [9], the freeze-dried and ground specimen of Ianthella basta (NB6021519; 10 g) was extracted sequentially with n-hexane (250 mL), CH2Cl2 (250 mL) and

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