Experimental and DFT studies on the regioselective methanolysis of 5-azido-9-oxabicyclo[6.1.0]nonan-4-yl 4-nitrobenzoate isomers

• İlknur Polat,
• Selçuk Eşsiz and
• Emine Salamci

Beilstein J. Org. Chem. 2026, 22, 547–556, doi:10.3762/bjoc.22.40

• formation mechanisms of the products yielded from the methanolysis of isomeric epoxides 9, we performed a series of density functional theory (DFT) computations using the software Gaussian 16 [26]. For this, geometry optimizations and harmonic vibrational frequency computations for the structures considered

• ++(d,p) [29][30][31], and SMD [32] model (methanol (ε = 32.613)) were employed. Initial geometries were pre-optimized using MM2 (ChemDraw 3D) prior to DFT optimization to account for conformational flexibility. The 3D molecular structures were visualized using the open-source software cheMVP.exe. DFT

Melifoliox B, a novel phloroglucin derivative isolated from Melicope barbigera (Rutaceae) and synthesis of new oxidation products from melifoliones A and B

• Horst Weber,
• Kim-Thao Tran-Cong,
• Bernhard Mayer,
• Guido J. Reiss,
• Iryna S. Konovalova,
• Marc S. Appelhans,
• Kenneth R. Wood and
• Claus M. Passreiter

Beilstein J. Org. Chem. 2026, 22, 535–546, doi:10.3762/bjoc.22.39

• during crystallization, was identified within solvent-accessible voids in the crystal lattice. Due to its high level of disorder, the DMF molecule was removed computationally using the SQUEEZE routine implemented in the PLATON software package [18]. The final structural model clearly establishes the

Structural reassignment of compound 968, an allosteric glutaminase inhibitor

• Lindsey A. Albertelli,
• Sainabou Jallow,
• Chun Li and
• Scott M. Ulrich

Beilstein J. Org. Chem. 2026, 22, 455–460, doi:10.3762/bjoc.22.33

• Bruker Smart Breeze CCD diffractometer (Mo sealed X-ray tube, Kα = 0.71073 Å). All diffractometer manipulations, including data collection, integration and scaling were carried out using the Bruker APEXII software. The structure was solved using SHELXS [33] and was refined using SHELXL [34]. Olex2 was

Synthesis and anti-cancer activity of naphthalimide–organylselanyl conjugates

• Rajkumar Ravi and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2026, 22, 416–435, doi:10.3762/bjoc.22.29

• viability, one-way ANOVA was performed using GraphPad Prism software [64], as shown in Figure 8, comparing the control group to each test concentration of the compound 7 (Figure 8a) and compound 8 (Figure 8b). The results showed no significant differences between the control and 6.12 µM concentrations

Spirobarbiturates with a pyrrolizidine moiety: synthesis, structure and biological evaluation

• Arthur A. Puzyrkov,
• Andrew S. Drachuk,
• Ekaterina A. Popova,
• Alexander V. Stepakov and
• Vitali M. Boitsov

Beilstein J. Org. Chem. 2026, 22, 274–288, doi:10.3762/bjoc.22.20

• using the free online software SwissADME (http://www.swissadme.ch/). The molecular descriptors were calculated according to Lipinski’s rule of five. This rule was formulated by Ch.A. Lipinski based on the observation that most orally administered drugs are relatively small and moderately lipophilic

• and nucleotide, DNaze I-binding). The structure of the 8DNH protein was retrieved from the protein data bank and the Molegro Virtual Docker 6.0 software was used to prepare it for the docking study [66][67]. The pose organizer and the ligand energy inspector tool were used to examine the docking

Conformational analysis of difluoromethylornithine: factors influencing its gas-phase and bioactive conformations

• Matheus P. Freitas

Beilstein J. Org. Chem. 2026, 22, 237–243, doi:10.3762/bjoc.22.17

• optimized geometries correspond to true minima. These calculations were performed using the Gaussian 16 program [32]. The optimized structures were then subjected to single-point energy calculations at the DLPNO-CCSD(T)/CBS level [33][34] with the ORCA software package [35] to obtain accurate conformational

Configuration–packing synergy enabling integrated crystalline-state RTP and amorphous-state TADF

• Ruiyan Wang and
• Yunan Wu

Beilstein J. Org. Chem. 2026, 22, 224–236, doi:10.3762/bjoc.22.16

• influencing the electronic properties and excited-state dynamics of 1. Building on the crystallographic data, quantum-chemical calculations were performed using the Gaussian 09 software at the B3LYP level of theory. The calculations revealed that the highest occupied molecular orbital (HOMO) is primarily

• Bruker SMART 1000 CCD system and structures were solved using Olex software. UV–vis absorption spectra of dilute solutions were measured on a Hitachi U-3900 UV–vis spectrophotometer with the corresponding solvent as the blank. Solution-state photoluminescence spectra were recorded on a Shimadzu RF-5301PC

Improved synthesis and physicochemical characterization of the selective serotonin 2A receptor agonist 25CN-NBOH

• Adrian G. Rossebø,
• Hannah G. Kolberg,
• Anders E. Tønder,
• Louise Kjaerulff,
• Poul Erik Hansen,
• Karla A. Frydenvang,
• Jesper Østergaard and
• Jesper L. Kristensen

Beilstein J. Org. Chem. 2026, 22, 175–184, doi:10.3762/bjoc.22.11

• diffraction studies was mounted and immersed in a stream of nitrogen gas (T = 100(1) K). Diffraction data were collected using Mo Kα radiation (λ = 0.71073 Å) with multilayer optics on a Bruker D8 Venture diffractometer. Data collection and cell refinement were performed using the Bruker Apex4 Suite software

• . The samples were measured in reflectance mode in the range of 5–35° 2θ with a step size of 0.013° 2θ and a counting time of 358 s/step. Data was collected using the X’Pert Data Collector software (Version 2.2.4, PANalytical). TGA and DSC The water content was assessed by TGA using a Discovery TGA (TA

• punctured aluminium lids. The samples were heated from 40–300 °C at 10 °C/min, and the melting point was determined as the onset temperature of the peak. The melting point was determined in triplicate. Data was collected and analyzed using the Trios software (V5.1.1 and V5.8.1, TA Instruments). Solubility

Highly electrophilic, gem- and spiro-activated trichloromethylnitrocyclopropanes: synthesis and structure

• Ilia A. Pilipenko,
• Mikhail V. Grigoriev,
• Olga Yu. Ozerova,
• Igor A. Litvinov,
• Darya V. Spiridonova,
• Aleksander V. Vasilyev and
• Sergey V. Makarenko

Beilstein J. Org. Chem. 2026, 22, 123–130, doi:10.3762/bjoc.22.5

• (Rigaku OD, 2021) software package. All of the structures were solved by direct methods using the SHELXT program [48] and refined by the full-matrix least squares method over F2 using the SHELXL program [49]. All of the calculations were performed in the WinGX software package [49], the calculation of the

Synthesis of new tetra- and pentacyclic, methylenedioxy- and ethylenedioxy-substituted derivatives of the dibenzo[c,f][1,2]thiazepine ring system

• Gábor Berecz,
• András Dancsó,
• Mária Tóthné Lauritz,
• Loránd Kiss,
• Gyula Simig and
• Balázs Volk

Beilstein J. Org. Chem. 2025, 21, 2645–2656, doi:10.3762/bjoc.21.205

• . The pulse programs were taken from the Bruker software library (TopSpin 3.5) and full 1H and 13C assignments were achieved with widely accepted strategies. 1H assignments were accomplished using general knowledge of chemical shift dispersion with the aid of the 1H–1H coupling pattern. CDCl3 or DMSO-d6

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