Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• (Figure 9A) [39][40]. For cage 1, DFT calculations suggests a population consisting of perhaps two major conformers (C5, C9), with 3–4 minor contributors (298 K, THF) [39][40], but we can control the preference of these conformers by introducing functionality which favors particular amide orientations [39

The effect of neighbouring group participation and possible long range remote group participation in O-glycosylation

• Rituparna Das and
• Balaram Mukhopadhyay

Beilstein J. Org. Chem. 2025, 21, 369–406, doi:10.3762/bjoc.21.27

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

• -(1,1-Dimethyl-1H-benzo[e]indolin-2-yl)-5,6,7-trichloro-1,3-tropolone exhibited high in vitro cytotoxic activity against A431 skin cancer and H1299 lung cancer cell lines. Keywords: cytotoxic activity; fluorescence; o-chloranil; quantum chemical DFT calculations; 1,3-tropolones; X-ray diffraction

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• simulated using Spartan’10 [26] on the PM6 level of theory [27]. Density-functional theory (DFT) calculations were computed utilizing the Gaussian program package, revision C.01 [28]. The geometry of the conformers was optimized on the B3LYP/6-311+G(2d,p) [29][30][31][32] level of theory with tight cutoffs

• on forces and step size. The IEFPCM solvent model [33] was used to simulate the solvent effects of methanol and frequency calculations were used to determine the conformers as minima. Conformers 4.5 kcal/mol above the lowest energy conformer and double conformers were discarded. Time-dependent DFT

• calculations were carried out on the same level of theory. A Boltzmann-averaged spectra were created and compared to the experimental spectrum using SpecDis 1.71 [12]. Chemical structures of compounds 1–6, prototenellin D and pretenellin B [7]. Key 1H-1H COSY, HMBC and ROESY correlations of 1. Comparison of

Oxidation of [3]naphthylenes to cations and dications converts local paratropicity into global diatropicity

• Abel Cárdenas,
• Zexin Jin,
• Yong Ni,
• Jishan Wu,
• Yan Xia,
• Francisco Javier Ramírez and
• Juan Casado

Beilstein J. Org. Chem. 2025, 21, 277–285, doi:10.3762/bjoc.21.20

• , 2000 scans at a resolution better than 4 cm−1 were accumulated to optimize the signal-to-noise ratio. Theoretical methods Quantum chemistry was addressed with the Gaussian 09 suite of programs [28]. DFT calculations were performed at the (U)B3LYP[29][30] level, using the 6-311G* basis set [31]. This

Synthesis and characterizations of highly luminescent 5-isopropoxybenzo[rst]pentaphene

• Islam S. Marae,
• Jingyun Tan,
• Rengo Yoshioka,
• Zakaria Ziadi,
• Eugene Khaskin,
• Serhii Vasylevskyi,
• Ryota Kabe,
• Xiushang Xu and
• Akimitsu Narita

Beilstein J. Org. Chem. 2025, 21, 270–276, doi:10.3762/bjoc.21.19

• optimized by density functional theory (DFT) calculations (Figure S2 in Supporting Information File 1). The optoelectronic properties of BPP-OiPr 3 and BPP-dione 4 were initially investigated by UV–vis absorption spectroscopy in comparison with BPP 2 (Figure 2a). BPP 2 and BPP-OiPr 3 displayed similar and

• (see Table S6 in Supporting Information File 1). BPP-dione 4 exhibited a broad absorption extending to 540 nm with a peak at 305 nm and featureless maxima at 469 and 497 nm, which were in line with the results of time-dependent DFT (TD-DFT) calculations at the M062X/6-311G(d,p) level of theory

• also showed significant differences (Figure S5 in Supporting Information File 1), indicating an intramolecular charge-transfer character both in its ground and excited states [30][31]. DFT calculations were performed to understand the effects of the substituents on the frontier orbitals. As shown in

Effect of substitution position of aryl groups on the thermal back reactivity of aza-diarylethene photoswitches and prediction by density functional theory

• Misato Suganuma,
• Daichi Kitagawa,
• Shota Hamatani and
• Seiya Kobatake

Beilstein J. Org. Chem. 2025, 21, 242–252, doi:10.3762/bjoc.21.16

• effective methods for predicting the thermal back reactivity, density functional theory (DFT) calculations can be considered [51][58][59][60][61][62]. For example, in previous studies on the thermal back reactivity of diarylbenzene that is an analogue of diarylethene, we found that the M06-2X level of

• reproduces the ΔG‡(exp) values in DFT calculations. According to the previous studies on the prediction of the thermal back reactivity of diarylethene and diarylbenzene derivatives using DFT calculations, we performed geometry optimizations and harmonic frequency calculations of the closed-ring isomer and

• transition state (see Tables S7–S14 in Supporting Information File 1). Table 2 shows the differences in ΔG‡ between the theoretical value obtained by DFT calculations and the experimental value, i.e., ΔG‡(calc) − ΔG‡(exp). The B3LYP and M05 functionals underestimated the ΔG‡ value, while the BMK, CAMB3LYP

Dioxazolones as electrophilic amide sources in copper-catalyzed and -mediated transformations

• Seungmin Lee,
• Minsuk Kim,
• Hyewon Han and
• Jongwoo Son

Beilstein J. Org. Chem. 2025, 21, 200–216, doi:10.3762/bjoc.21.12

• theory (DFT) calculations, a proposed reaction mechanism is suggested as shown in Figure 3. Initially, copper acetylide INT-11 is formed by the reaction of acetylene with a copper precatalyst, leading to the formation of an N-acyl nitrene acetylide intermediate INT-12 after the incorporation of

• dioxazolone 7. Subsequently, nitrene insertion of INT-12 into the Cu–C bond, forms INT-13, which then undergoes isomerization and protodemetalation, followed by catalyst regeneration, as suggested by the DFT calculations. Finally, the nucleophilic addition of the amine to the electrophilic intermediate INT-15

• , providing the corresponding products (16g–k). Mechanistically, the reaction begins with the generation of the active copper species 17, successively forming INT-19 and INT-20 (Figure 5). The penta-coordinated copper nitrenoid species INT-20, as suggested by DFT calculations, undergoes reductive elimination

Quantifying the ability of the CF₂H group as a hydrogen bond donor

• Matthew E. Paolella,
• Daniel S. Honeycutt,
• Bradley M. Lipka,
• Jacob M. Goldberg and
• Fang Wang

Beilstein J. Org. Chem. 2025, 21, 189–199, doi:10.3762/bjoc.21.11

• ; titration studies; DFT calculations. Acknowledgements High-Performance Computing at the University of Rhode Island and the Massachusetts Green High-Performance Computing Center (MGHPCC) are gratefully acknowledged. Funding This research was made possible by the use of equipment available through the Rhode

Recent advances in organocatalytic atroposelective reactions

• Henrich Szabados and
• Radovan Šebesta

Beilstein J. Org. Chem. 2025, 21, 55–121, doi:10.3762/bjoc.21.6

• ) annulation of enals with ynamides 8 to afford axially chiral 7-arylindolines 9 was reported [20]. The reaction mechanism, rationalized by DFT calculations, is believed to occur through catalyst C3 activation of the substrate 8, dehydration, and deprotonation with tautomerization leading to the enamine

• transformation relies on the catalysis with azolium precatalyst C12 (Scheme 11a). The reaction also allowed the synthesis of indol-derived bridged biaryls 35 (Scheme 11b). The proposed mechanism, supported by DFT calculations, comprises propargylic substitution towards Int-20 with NHC-derived enolate Int-19

• 196a–k (Scheme 58) [88]. Both organocatalysts showed comparable effectivity in terms of enantioselectivity across. The difference between these catalysts becomes more visible through DFT calculations. In the case of biaryl phosphoric acid C30, stereocontrol is driven by the steric effects of the groups

Synthesis, structure and π-expansion of tris(4,5-dehydro-2,3:6,7-dibenzotropone)

• Yongming Xiong,
• Xue Lin Ma,
• Shilong Su and
• Qian Miao

Beilstein J. Org. Chem. 2025, 21, 1–7, doi:10.3762/bjoc.21.1

• for conformational change is provided by the earlier report that the NMR spectrum of 1 at −80 °C did not display significant broadening [1]. To better understand the two conformers of 1 found in the crystals, density functional theory (DFT) calculations were carried out using the molecular geometries

Non-covalent organocatalyzed enantioselective cyclization reactions of α,β-unsaturated imines

• Sergio Torres-Oya and
• Mercedes Zurro

Beilstein J. Org. Chem. 2024, 20, 3221–3255, doi:10.3762/bjoc.20.268

• -position of the activating group with good yields (52–98%), excellent diastereoselectivities and good enantioselectivities (76–94% ee). Additionally, to understand the mechanism of the reaction, the authors performed DFT calculations. Based on the calculations, once the dienolate is hydrolyzed to the free

• mechanism and the origin of the enantioselectivity, the authors performed DFT calculations, highlighting the importance of the outer phenyl ring of the chiral phosphoric acid on the enantioinduction. To demonstrate the synthetic applicability of the chiral axial derivatives a variety of transformations were

Synthesis of 2H-azirine-2,2-dicarboxylic acids and their derivatives

• Anastasiya V. Agafonova,
• Mikhail S. Novikov and
• Alexander F. Khlebnikov

Beilstein J. Org. Chem. 2024, 20, 3191–3197, doi:10.3762/bjoc.20.264

• not isomerize at room temperature, which is typical for highly sterically congested isoxazoles containing a 3-tert-butyl substituent [26]. The mechanism of such isomerizations of isoxazoles has been previously discussed using DFT calculations [25][26], which revealed the formation of an isoxazole–Fe

Direct trifluoroethylation of carbonyl sulfoxonium ylides using hypervalent iodine compounds

• Radell Echemendía,
• Carlee A. Montgomery,
• Fabio Cuzzucoli,
• Antonio C. B. Burtoloso and
• Graham K. Murphy

Beilstein J. Org. Chem. 2024, 20, 3182–3190, doi:10.3762/bjoc.20.263

• reactants. Finally, DFT calculations provided insights about the mechanism of this transformation, which strongly suggest that an SN2 reaction is operative. Keywords: alkylation; DFT calculations; fluorine chemistry; hypervalent iodine; sulfoxonium ylide; sulphur ylides; Introduction Introducing fluorine

Controlled oligomerization of [1.1.1]propellane through radical polarity matching: selective synthesis of SF₅- and CF₃SF₄-containing [2]staffanes

• Jón Atiba Buldt,
• Wang-Yeuk Kong,
• Yannick Kraemer,
• Masiel M. Belsuzarri,
• Ansh Hiten Patel,
• James C. Fettinger,
• Dean J. Tantillo and
• Cody Ross Pitts

Beilstein J. Org. Chem. 2024, 20, 3134–3143, doi:10.3762/bjoc.20.259

• chloropentafluorosulfanylated [2]staffane (SF5-BCP-BCP-Cl, 2), based on alternating radical polarity matching in the chain-propagation steps (Figure 1, bottom) [45][46][47]. Density functional theory (DFT) calculations provide insight into our observed selectivity, and our hypothesis is bolstered by computation of relative

• established that [1.1.1]propellane participates in radical-chain reactions (i.e., oligomerization) at room temperature in solution to form unsubstituted [n]staffanes. The origin of this innately controlled oligomerization was then investigated through density functional theory (DFT) calculations. The free

Hypervalent iodine-mediated intramolecular alkene halocyclisation

• Charu Bansal,
• Oliver Ruggles,
• Albert C. Rowett and
• Alastair J. J. Lennox

Beilstein J. Org. Chem. 2024, 20, 3113–3133, doi:10.3762/bjoc.20.258

• is then attacked by a nucleophile. The use of chiral iodine catalysts is essential for controlling the stereochemistry of the reaction. The specific arrangement of the catalyst influences the orientation of this nucleophilic attack as supported by density functional theory (DFT) calculations. In 2022

• up to 95% within a short time-frame of 10 minutes. Treatment of N-(2-phenylallyl)benzamides with 10 equivalents of BF3·Et2O, iodobenzene, m-CPBA in dichloromethane (DCM) at 0 °C resulted in the formation of the oxazoline product (Scheme 21). DFT calculations indicated several steps in the mechanism

Advances in the use of metal-free tetrapyrrolic macrocycles as catalysts

• Mandeep K. Chahal

Beilstein J. Org. Chem. 2024, 20, 3085–3112, doi:10.3762/bjoc.20.257

• , with TBAI as a co-catalyst, up to 74% yields (Table 1). The inactivity of porphyrin 18 was attributed to the inaccessibility of the inner core imine due to its planar structure. The mechanism of the epoxide ring-opening reaction was elucidated by DFT calculations, which suggested that the macrocycle

• (Table 5). DFT calculations predicted that the catalytically active species is the adduct of porphyrin and TBACl (18-I), which forms an activated complex (18-II) with the substrate followed by a ring-opening nucleophilic attack of Cl−. The electron-rich nitrogen atom in 18-III further activates

• zero due to too strong association of trifluoroacetate with protonated porphyrin. DFT calculations suggested that the O–O bond in O2 becomes polarized upon binding in {(H4TPP2+)·(TB−)·O2}, which facilitates

Enantioselective regiospecific addition of propargyltrichlorosilane to aldehydes catalyzed by biisoquinoline N,N’-dioxide

• Noble Brako,
• Sreerag Moorkkannur Narayanan,
• Amber Burns,
• Layla Auter,
• Valentino Cesiliano,
• Rajeev Prabhakar and
• Norito Takenaka

Beilstein J. Org. Chem. 2024, 20, 3069–3076, doi:10.3762/bjoc.20.255

• in the absence and presence of N,N-diisopropylethylamine using density functional theory (DFT) calculations (Figure 1). According to the DFT calculations, the free propargyltrichlorosilane (Iprop) can isomerize to allenyltrichlorosilane (Iall) with a prohibitively high barrier of 43.8 kcal/mol

gem-Difluorovinyl and trifluorovinyl Michael acceptors in the synthesis of α,β-unsaturated fluorinated and nonfluorinated amides

• Monika Bilska-Markowska,
• Marcin Kaźmierczak,
• Wojciech Jankowski and
• Marcin Hoffmann

Beilstein J. Org. Chem. 2024, 20, 2946–2953, doi:10.3762/bjoc.20.247

• approximately 150° [42][43][44][45]. These data were consistent with DFT calculations (see Supporting Information File 1). The reaction of the amide 1d with n-BuLi resulted in a surprising outcome. In this case, product 9d and only traces of the expected product 10d were received, as indicated by the 19F NMR

• ]. These findings are in alignment with DFT calculations (see Supporting Information File 1) and corroborate data for compounds 9a–d. We further decided to use tert-BuLi in our research, considering its role as a stronger base and simultaneously as a weak nucleophile. We first performed the reaction with 2

• experimental procedures, DFT calculations, characterization data, and copies of 1H, 13C, 19F NMR and 1H−13C HSQC spectra. Acknowledgements The calculations were performed in the Poznan Supercomputing and Networking Center.

The charge transport properties of dicyanomethylene-functionalised violanthrone derivatives

• Sondos A. J. Almahmoud,
• Joseph Cameron,
• Dylan Wilkinson,
• Michele Cariello,
• Claire Wilson,
• Alan A. Wiles,
• Peter J. Skabara and
• Graeme Cooke

Beilstein J. Org. Chem. 2024, 20, 2921–2930, doi:10.3762/bjoc.20.244

• the Knoevenagel condensation with malononitrile was successfully reported [33]. Theoretical studies Density functional theory (DFT) calculations of two derivatives of compounds 2 and 3, having methoxy groups instead of the longer alkyl chains have been reported in the literature [32], providing

• hindered charge transport. Experimental Computational Density functional theory (DFT) calculations were performed using Gaussian 09 software. Molecular geometries were initially optimised semi-empirically (AM1) and then reoptimised by DFT using the B3LYP method with the 6-311G(d,p) basis set unless stated

Recent advances in transition-metal-free arylation reactions involving hypervalent iodine salts

• Ritu Mamgain,
• Kokila Sakthivel and
• Fateh V. Singh

Beilstein J. Org. Chem. 2024, 20, 2891–2920, doi:10.3762/bjoc.20.243

• aryl sulfides 85 from thiols 84 using diaryliodonium salts 16 in basic conditions (Scheme 34). A multitude of thiols and diaryliodonium salts was examined in the reaction under optimized conditions, yielding exceptional yields [88]. To embrace the chemical process, DFT calculations were performed in

N-Glycosides of indigo, indirubin, and isoindigo: blue, red, and yellow sugars and their cancerostatic activity

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 2840–2869, doi:10.3762/bjoc.20.240

• -β-41a (55%) and E-β-41a (41%) are in accordance with the relative thermodynamic stability of the two geometric isomers. According to DFT calculations, the Z-isomer is slightly energetically favored by 14.88 kJ/mol. The configurations were determined by comparison of chemical shifts of our products

Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines

• Dmitriy Yu. Vandyshev,
• Daria A. Mangusheva,
• Khidmet S. Shikhaliev,
• Kirill A. Scherbakov,
• Oleg N. Burov,
• Alexander D. Zagrebaev,
• Tatiana N. Khmelevskaya,
• Alexey S. Trenin and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236

• 2 and 3, the minimum energy paths (MEPs) of these processes were calculated. Quantum chemical DFT calculations were performed using the B3LYP/6-311++G(d,p) basis set and taking into account solvation effects using the polarizable continuum model (PCM). Interactions of 1 with N-phenylmaleimide (2a

• ). Conclusion Thus, we have proposed an efficient way to construct tetrahydroimidazo[1,2-a]pyrimidines without substituents at the 4 and 5-positions of the imidazole fragment by the reaction of 2-aminoimidazole with N-arylitaconimides and N-substituted maleimides. With the aid of DFT calculations, the most

Copper-catalyzed yne-allylic substitutions: concept and recent developments

• Shuang Yang and
• Xinqiang Fang

Beilstein J. Org. Chem. 2024, 20, 2739–2775, doi:10.3762/bjoc.20.232

• ). Further control experiments and DFT calculations show that during the catalytic process, tertiary amine directly participates as a nucleophilic reagent to give the ammonium salt, which then releases dimethylaminium to provide the final product (Scheme 12). Chiral allylic sulfone compounds can be easily

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• properties of γ-CD (the largest of the three most abundant native CDs), the main experimental methods applied in this study were differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). By coupling these techniques with density functional theory (DFT) calculations we try to shed some