Synthesis and characterization of a isothiouronium-calix[4]arene derivative: self-assembly and anticancer activity

• Giuseppe Granata,
• Loredana Ferreri,
• Claudia Giovanna Leotta,
• Giovanni Mario Pitari and
• Grazia Maria Letizia Consoli

Beilstein J. Org. Chem. 2025, 21, 2535–2541, doi:10.3762/bjoc.21.195

• 10.4.1 (GraphPad Software, Inc., San Diego, CA). Selectivity index determination: The selectivity index of compound 3 was calculated as the ratio of the IC50 in the cancer cell line to the IC50 in the non-malignant cell line, according to the following formula 1H NMR (left) and 13C NMR (right) spectra

The intramolecular stabilizing effects of O-benzoyl substituents as a driving force of the acid-promoted pyranoside-into-furanoside rearrangement

• Alexey G. Gerbst,
• Sofya P. Nikogosova,
• Darya A. Rastrepaeva,
• Dmitry A. Argunov,
• Vadim B. Krylov and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2025, 21, 2456–2464, doi:10.3762/bjoc.21.187

• in this case, a computational study was carried out. Herein, we report the obtained results. Computational Details All the calculations were performed using the ORCA 5.0.4 software package [32]. DFT B3LYP functional with the third order Grimme’s correction (D3) [33] and def2-TZVP [34] basis set were

The high potential of methyl laurate as a recyclable competitor to conventional toxic solvents in [3 + 2] cycloaddition reactions

• Ayhan Yıldırım and
• Mustafa Göker

Beilstein J. Org. Chem. 2025, 21, 2389–2415, doi:10.3762/bjoc.21.184

• , tumorigenic, irritant, or reproductive properties (Table 2). According to the toxicity risk assessments for solvents in this table, determined using the OSIRIS PropertyExplorer software, sulfolane appears to be a safe solvent and its use is recommended for certain purposes in some studies [89]. However, the

• cylinder chart in Figure 7. Indeed, a significant proportion of the experimentally measured Green Chemistry parameters for methyl laurate are consistent with the predictions of various software or web platforms, and in some cases, even demonstrate that certain toxicity parameters of methyl laurate are more

Conformational effects on iodide binding: a comparative study of flexible and rigid carbazole macrocyclic analogs

• Guang-Wei Zhang,
• Yong Zhang,
• Le Shi,
• Chuang Gao,
• Hong-Yu Li and
• Lei Xue

Beilstein J. Org. Chem. 2025, 21, 2369–2375, doi:10.3762/bjoc.21.181

• . This further corroborates the decisive role of the macrocyclic architecture in the anion recognition process. Quantum chemical calculations were performed with the ORCA 5.0.3 software [29]. The geometry optimization was performed by using B3LYP with the def2-SVP basis set. As illustrated in the

Thiadiazino-indole, thiadiazino-carbazole and benzothiadiazino-carbazole dioxides: synthesis, physicochemical and early ADME characterization of representatives of new tri-, tetra- and pentacyclic ring systems and their intermediates

• Gyöngyvér Pusztai,
• László Poszávácz,
• Anna Vincze,
• András Marton,
• Ahmed Qasim Abdulhussein,
• Judit Halász,
• András Dancsó,
• Gyula Simig,
• György Tibor Balogh and
• Balázs Volk

Beilstein J. Org. Chem. 2025, 21, 2220–2233, doi:10.3762/bjoc.21.169

• . When correlating clogP and logk in Figure 5, the fitted line showed a moderate linear correlation (R2 = 0.673). According to the plot, the partition coefficients of the outliers (E)-7a, 3e, and 10b seemed to be overestimated by the Percepta software [36]. The lipophilicity of hydrazone (E)-7a was

• . Each function used a scan time of 0.5 s. Data were acquired in the continuum mode. Instrument mass accuracy calibration was verified using sodium formate. The system was controlled with a MassLynx v4.2 SCN996 software. 8-Hydrazino-2,4-dimethyl-2H-1,2,3-benzothiadiazine 1,1-dioxide (5a). To a mixture of

Understanding the origin of stereoselectivity in the photochemical denitrogenation of 2,3-diazabicyclo[2.2.1]heptene and its derivatives with non-adiabatic molecular dynamics

• Leticia A. Gomes and
• Steven A. Lopez

Beilstein J. Org. Chem. 2025, 21, 2007–2020, doi:10.3762/bjoc.21.156

• TD-DFT calculations were performed using the range-separated hybrid density functional ωB97X-D [89] with the aug-cc-pVTZ [90][104] basis set. All single reference methods were run using the Gaussian 16 software [105]. Multiconfigurational methods The multiconfigurational calculations were performed

Synthesis, biological and electrochemical evaluation of glycidyl esters of phosphorus acids as potential anticancer drugs

• Almaz A. Zagidullin,
• Emil R. Bulatov,
• Mikhail N. Khrizanforov,
• Damir R. Davletshin,
• Elvina M. Gilyazova,
• Ivan A. Strelkov and
• Vasily A. Miluykov

Beilstein J. Org. Chem. 2025, 21, 1909–1916, doi:10.3762/bjoc.21.148

• measured at 590 nm using an Infinite M200 microplate reader (Tecan, Switzerland). Cell viability was calculated relative to the untreated control (set at 100%). Data were processed and analyzed using GraphPad Prism 10 software. Electrochemistry. Linear sweep voltammograms were recorded using a BASi Epsilon

• Eclipse potentiostat (USA). The device includes a measuring unit, a DellOptiplex 320 personal computer with Epsilon-EC-USB-V200 software. As supporting electrolyte 0.1 M Et4NBF4 was used. A glassy carbon electrode modified with carbon paste (surface area 1 mm2) served as the working electrode. Ag/AgCl

Thermodynamics and polarity-driven properties of fluorinated cyclopropanes

• Matheus P. Freitas

Beilstein J. Org. Chem. 2025, 21, 1742–1747, doi:10.3762/bjoc.21.137

• unoccupied orbitals (antibonding and Rydberg), offering insights into the contributions of non-Lewis electron delocalization and its interplay with Lewis-type bonding in the total electronic energy. All calculations were performed using the Gaussian 16 software suite [26]. Quantum theory of atoms in

Facile synthesis of hydantoin/1,2,4-oxadiazoline spiro-compounds via 1,3-dipolar cycloaddition of nitrile oxides to 5-iminohydantoins

• Juliana V. Petrova,
• Varvara T. Tkachenko,
• Victor A. Tafeenko,
• Anna S. Pestretsova,
• Vadim S. Pokrovsky,
• Maxim E. Kukushkin and
• Elena K. Beloglazkina

Beilstein J. Org. Chem. 2025, 21, 1552–1560, doi:10.3762/bjoc.21.118

• reader and Skanlt 6.1 RE software for a microplate reader, both from Thermo Scientific (Waltham, MA, USA). In vitro experiments were performed in triplicate. Graphpad prism version 9.0 was used to determine the IC50. IC50 data are presented as mean ± standard deviation (SD) (Figure 3b) [20][22

Wittig reaction of cyclobisbiphenylenecarbonyl

• Taito Moribe,
• Junichiro Hirano,
• Hideaki Takano,
• Hiroshi Shinokubo and
• Norihito Fukui

Beilstein J. Org. Chem. 2025, 21, 1454–1461, doi:10.3762/bjoc.21.107

• . The racemization dynamics of 5 was investigated by DFT calculations at the B3LYP/6-31G(d) level of theory, employing the Gaussian 16 software package and the global reaction route mapping (GRRM17) [23] program (Figure 4). The interconversion between figure-eight conformation (M,M)-B and bathtub

Tautomerism and switching in 7-hydroxy-8-(azophenyl)quinoline and similar compounds

• Lidia Zaharieva,
• Vera Deneva,
• Fadhil S. Kamounah,
• Nikolay Vassilev,
• Ivan Angelov,
• Michael Pittelkow and
• Liudmil Antonov

Beilstein J. Org. Chem. 2025, 21, 1404–1421, doi:10.3762/bjoc.21.105

• –1000 nm. The spectra were recorded with the specialized software SpectraSuite (Ocean Optics, Inc., Dunedin, USA). Computational quantum chemistry calculations: Quantum-chemical calculations in the ground state were performed using the Gaussian 16 C.01 program suite [93]. All structures (in both ground

Reactions of acryl thioamides with iminoiodinanes as a one-step synthesis of N-sulfonyl-2,3-dihydro-1,2-thiazoles

• Vladimir G. Ilkin,
• Pavel S. Silaichev,
• Valeriy O. Filimonov,
• Tetyana V. Beryozkina,
• Margarita D. Likhacheva,
• Pavel A. Slepukhin,
• Wim Dehaen and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2025, 21, 1397–1403, doi:10.3762/bjoc.21.104

• irradiation, graphite monochromator, ω-scanning in 1° increments at T = 295(2) K). An empirical correction for absorption has been introduced. Using the Olex2 [23] software shell, the structure was solved using the SHELXT program and refined using the SHELXL [24][25] program with a full-matrix F2 MNC for non

N-Salicyl-amino acid derivatives with antiparasitic activity from Pseudomonas sp. UIAU-6B

• Joy E. Rajakulendran,
• Emmanuel Tope Oluwabusola,
• Michela Cerone,
• Terry K. Smith,
• Olusoji O. Adebisi,
• Adefolalu Adedotun,
• Gagan Preet,
• Sylvia Soldatou,
• Hai Deng,
• Rainer Ebel and
• Marcel Jaspars

Beilstein J. Org. Chem. 2025, 21, 1388–1396, doi:10.3762/bjoc.21.103

• Compact Data Analyst (Bruker software) to provide accurate and high-resolution mass per charge of molecular ions in the sample and generate molecular formulae using a Bruker Smart Formula manually. Microbial isolation and identification The Pseudomonas sp. UIAU-6B strain was isolated from a sediment

• cell line are given below), after which the Alamar Blue cell viability reporter was added and the fluorescence recorded using an FLx 800 plate reader (BioTek) with excitation wavelength 535/540 nm and emission wavelength at 590/610 nm using Gen5 Reader Control 2.0 Software (BioTek). EC50 values were

• determined using a 4-parameter non-linear logistic regression equation using GraFit 5.0 (Erithacus Software) [3]. The bloodstream form of T. brucei stain Lister 427 was maintained in HMI-9 growth medium (IMDB medium supplemented with 10% (v/v) foetal bovine serum (FBS), 20% (v/v) Serum Plus, 0.05 mM

A multicomponent reaction-initiated synthesis of imidazopyridine-fused isoquinolinones

• Ashutosh Nath,
• John Mark Awad and
• Wei Zhang

Beilstein J. Org. Chem. 2025, 21, 1161–1169, doi:10.3762/bjoc.21.92

• calculated using the Gaussian 16 software (Figure 3) [21]. The N-acylated compound 6a has a baseline relative energy of 0 kJ/mol, while the transition state of the Diels–Alder (TS-DA) reaction presents the highest energy barrier at 1.221 kJ/mol. The DA adduct shows a little lower energy at 1.001 kJ/mol

Investigations of amination reactions on an antimalarial 1,2,4-triazolo[4,3-a]pyrazine scaffold

• Henry S. T. Smith,
• Ben Giuliani,
• Kanchana Wijesekera,
• Kah Yean Lum,
• Sandra Duffy,
• Aaron Lock,
• Jonathan M. White,
• Vicky M. Avery and
• Rohan A. Davis

Beilstein J. Org. Chem. 2025, 21, 1126–1134, doi:10.3762/bjoc.21.90

• MHz NMR spectrometer equipped with a cryoprobe. MestreNova™ version 14.3.3 software was used for NMR data analysis. The 1H and 13C NMR chemical shifts were referenced to solvent peaks for (CD3)2SO (δH 2.50, δC 39.52). LRESIMS data was recorded on a Thermo Scientific (Waltham, MA, USA) UltiMate™ 3000

• using an Opera PhenixPlus™ High Content Screening System (PerkinElmer, Waltham, MA, USA). Images were analysed using the Harmony software (PerkinElmer, Waltham, MA, USA). In vitro cytotoxicity assay Human embryonic kidney (HEK293) cells were maintained in DMEM (Life Technologies, Camarillo, CA, USA

Supramolecular assembly of hypervalent iodine macrocycles and alkali metals

• Krishna Pandey,
• Lucas X. Orton,
• Grayson Venus,
• Waseem A. Hussain,
• Toby Woods,
• Lichang Wang and
• Kyle N. Plunkett

Beilstein J. Org. Chem. 2025, 21, 1095–1103, doi:10.3762/bjoc.21.87

• , selected from the BindFit software (http://app.supramolecular.org/bindfit/). Lithium complex 2 (red) overlaid with lithium complex 3 (blue). In lithium complex 2, one benzyl ring is pointing outside highlighted by the red-colored asterisk. Binding energies and binding constants for HIM 1 with LiBArF20 and

Data accessibility in the chemical sciences: an analysis of recent practice in organic chemistry journals

• Sally Bloodworth,
• Cerys Willoughby and
• Simon J. Coles

Beilstein J. Org. Chem. 2025, 21, 864–876, doi:10.3762/bjoc.21.70

• , acquisition and processing parameters), and metadata (spectrometer specifications, acquisition and processing software, and sample information). Two of the ACS journals, J. Org. Chem. and Organometallics, give instructions for preparing data files of Cartesian coordinates from computational studies, requiring

• ’ is a file extension for JCAMP-DX, the IUPAC standard file format for spectral data [39]. FIDs are accessible from the MNOVA and JDX files, but access requires additional software. No primary mass spectrometry data were shared. Are data deposited in an open repository? (Find_1) Two thirds of shared

• ), International Chemical Identifiers (InChIs) and InChIKeys are widely supported in software handling chemical information such as databases, inventories, laboratory information management systems (LIMS) and electronic lab notebooks (ELNs). Systematic naming of organic compounds using International Union of Pure

4-(1-Methylamino)ethylidene-1,5-disubstituted pyrrolidine-2,3-diones: synthesis, anti-inflammatory effect and in silico approaches

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Luc Van Meervelt,
• Do Thi Thao and
• Nguyen Minh Thong

Beilstein J. Org. Chem. 2025, 21, 817–829, doi:10.3762/bjoc.21.65

• . The docking algorithm used was the Triangle Matcher placement method, which generates initial poses by aligning ligand atoms to complementary receptor atoms. Molecular docking simulations were performed using the MOE software suite [46] to evaluate the binding activities of the newly synthesized

• compounds and the reference drug dexamethasone (DEX) against the iNOS enzyme. The interactions between the ligands and the target enzyme were further visualized and analyzed using Discovery Studio software [47]. Density functional theory (DFT) method: The molecular structures of the tested compounds were

• optimized at the M062X/6-31+G(d) level of theory using Gaussian 16 software [48]. The reactivity, stability, and electronic properties of molecules determined by key parameters such as frontier molecular orbital energies (EHOMO and ELUMO), energy gap (ΔEL-H), ionization energy (IE), electron affinity (EA

Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• Tyr137 flanking the carbohydrate binding site of FimH [47]. First, Glide [48] as part of the Maestro interface of the Schrödinger software package [49] was used to calculate docking scores (Table 3). More negative docking scores correlate with higher FimH affinity. In a second step, the best docking

Acyclic cucurbit[n]uril bearing alkyl sulfate ionic groups

• Christian Akakpo,
• Peter Y. Zavalij and
• Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 717–726, doi:10.3762/bjoc.21.55

• Figure 6a was integrated and then plotted as ΔH versus molar ratio in Figure 7b. The ΔH versus molar ratio data was then fitted to the single-set-of-sites binding model in the PEAQ ITC data analysis software which delivered Ka = (6.49 ± 0.10) × 105 M−1 and ΔH = −7.82 ± 0.02 kcal mol−1 for the C1·CHDA

• requires that the Ka and ΔH values for the host·competitor complexes have been previously determined and used as known inputs to the competitive binding model in the PEAQ data analysis software. To maximize the heat evolved in the competitive ITC titrations, the host·competitor and host·tight guest

• ) and fitted to the competitive binding model in the PEAQ ITC data analysis software to determine Ka = (2.47 ± 0.06) × 108 M−1 and ΔH = −12.43 ± 0.02 kcal mol−1 for the C1·Me6PXDA complex. The Ka and ΔH values for the remaining C1·guest and M1·guest complexes were determined by analogous direct or

Asymmetric synthesis of fluorinated derivatives of aromatic and γ-branched amino acids via a chiral Ni(II) complex

• Maurizio Iannuzzi,
• Thomas Hohmann,
• Michael Dyrks,
• Kilian Haoues,
• Katarzyna Salamon-Krokosz and
• Beate Koksch

Beilstein J. Org. Chem. 2025, 21, 659–669, doi:10.3762/bjoc.21.52

• ) was used. MeCN/MeOH/H2O mixture with 50 mM formic acid and 25 mM diethylamine was used as eluent. A flow rate of 0.5 mL/min was applied and the detection of the respective compounds occurred at 280 nm. Data analysis was carried out with the EZChrom ELITE software (version 3.3.2 SP2, Agilent). Ni(II

Semisynthetic derivatives of massarilactone D with cytotoxic and nematicidal activities

• Rémy B. Teponno,
• Sara R. Noumeur and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 607–615, doi:10.3762/bjoc.21.48

• Agilent 1100 series preparative HPLC system [ChemStation software (Rev. B.04.03 SP1); binary pump system; column: Kinetex 5u RP C18, dimensions 250 × 21.20 mm; mobile phase: ACN + 0.05% trifluoroacetic acid (TFA) and water + 0.05% TFA; flow rate: 20 mL/min; diode array UV detector; 226 fraction collector

• software (Rev. B.04.03 SP1); binary pump system; column: Kinetex 5u RP C18, dimensions 250 × 21.20 mm; mobile phase: ACN + 0.05% trifluoroacetic acid (TFA) and water + 0.05% TFA; flow rate 20 mL/min; diode array UV detector; 226 fraction collector. A gradient from 47 to 72% solvent B in 50 min was used

Deep-blue emitting 9,10-bis(perfluorobenzyl)anthracene

• Long K. San,
• Sebastian Balser,
• Brian J. Reeves,
• Tyler T. Clikeman,
• Yu-Sheng Chen,
• Steven H. Strauss and
• Olga V. Boltalina

Beilstein J. Org. Chem. 2025, 21, 515–525, doi:10.3762/bjoc.21.39

• software (APEX II) was employed [38], and Bruker SHELXTL software [39] was used for structure solution, refinement, and graphics. Crystal data for 9,10-ANTH(BnF)2: C28H8F14, M = 610.34, orthorhombic, a = 11.5338(4) Å, b = 24.6701(9) Å, c = 8.0275(3) Å, α = 90°, β = 90°, γ = 90°, V = 2284.15 Å3, T = 100(2

Unraveling aromaticity: the dual worlds of pyrazole, pyrazoline, and 3D carborane

• Zahra Noori,
• Miquel Solà,
• Clara Viñas,
• Francesc Teixidor and
• Jordi Poater

Beilstein J. Org. Chem. 2025, 21, 412–420, doi:10.3762/bjoc.21.29

• , the energy decomposition analysis has been performed at the ZORA-BLYP-D3(BJ)/TZ2P level of theory with AMS software [81][82][83][84]. Series o-carborane-fused pyrazoles under analysis. Bond lengths (in Å) of systems under analysis (top row) and reference systems (second and third rows) from the fusion

Synthesis, structure, ionochromic and cytotoxic properties of new 2-(indolin-2-yl)-1,3-tropolones

• Yurii A. Sayapin,
• Eugeny A. Gusakov,
• Inna O. Tupaeva,
• Alexander D. Dubonosov,
• Igor V. Dorogan,
• Valery V. Tkachev,
• Anna S. Goncharova,
• Gennady V. Shilov,
• Natalia S. Kuznetsova,
• Svetlana Y. Filippova,
• Tatyana A. Krasnikova,
• Yanis A. Boumber,
• Alexey Y. Maksimov,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2025, 21, 358–368, doi:10.3762/bjoc.21.26

• ://www.ccdc.cam.ac.uk/data_request/cif. Computational methods Quantum chemical calculations were performed using the Gaussian 09 software package [34] with hybrid functional PBE0 [35][36] and 6-311+G (d,p) basis set. Solvent effects were modeled by using polarizable continuum model (PCM) [37] within the integral

• Tukey’s post hoc test of significance. IC50 values were determined in the RStudio development environment using the DRC software package [40]. Structural characteristics of (NH) and (OH) tautomeric forms of compounds 7 and 8 in the gas phase according to PBE0/6-311+G(d,p) calculations. Bond lengths are