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

• difference in binding constants as well as the isolation of two distinct molecular conformations of phenylalanine HIM 1 (Figure 1), DFT calculations were performed. The details of DFT calculations are shown in Table 1. For DFT calculations, we assigned two HIM macrocycles per LiBArF20 as found in the co

Recent advances in synthetic approaches for bioactive cinnamic acid derivatives

• Betty A. Kustiana,
• Galuh Widiyarti and
• Teni Ernawati

Beilstein J. Org. Chem. 2025, 21, 1031–1086, doi:10.3762/bjoc.21.85

Pd-Catalyzed asymmetric allylic amination with isatin using a P,olefin-type chiral ligand with C–N bond axial chirality

• Natsume Akimoto,
• Kaho Takaya,
• Yoshio Kasashima,
• Kohei Watanabe,
• Yasushi Yoshida and
• Takashi Mino

Beilstein J. Org. Chem. 2025, 21, 1018–1023, doi:10.3762/bjoc.21.83

• allylic amination of acetate 12 with isatin (11a).a Supporting Information Data of thermal racemization of 7, DFT calculations for investigating racemization mechanism of 7, general methods and materials, experimental procedures and characterization data, 1H, 13C and 31P NMR spectra for 9 and 10, 1H, 13C

Recent total synthesis of natural products leveraging a strategy of enamide cyclization

• Chun-Yu Mi,
• Jia-Yuan Zhai and
• Xiao-Ming Zhang

Beilstein J. Org. Chem. 2025, 21, 999–1009, doi:10.3762/bjoc.21.81

• bridge cycle [36][37]. The excellent diastereoselectivity in this radical cyclization was further rationalized by DFT calculations, which suggests an energy discrepancy of the hydrogen atom transfer process from different faces of the resulting α-hydroxyl radical. Final reduction of the ketone and amide

On the photoluminescence in triarylmethyl-centered mono-, di-, and multiradicals

• Daniel Straub,
• Markus Gross,
• Mona E. Arnold,
• Julia Zolg and
• Alexander J. C. Kuehne

Beilstein J. Org. Chem. 2025, 21, 964–998, doi:10.3762/bjoc.21.80

• to break the symmetry. Here, the molecule consists of a pentalchloro phenyl and two tribromophenyl units (PCl-TBr2M) [55], or with two p-bromotetrafluorophenyl rings (PCl-TFBr2M) (see Figure 2d–f) [52]. DFT calculations for these mixed per- and trihalophenylmethyl radicals and their orbitals show a

• = 697 nm with 2% (in cyclohexane) [10]. DFT calculations display that the Cz unit acts as an electron-donor moiety, facilitating a CT excited state with a clear C2 symmetry (see Figure 5b). Similarly, a biscarbazolylanthracenylmethyl radical has been reported; however, the ϕ has been too low to be

• (because of spin selection rules forbidding the direct transition from the quartet to the doublet state). While for TTM and PTM substituted with weak donors such energetically low-lying quartet (Q1) states have been observed in TD-DFT calculations [20][62] and EPR spectroscopy [63], there are no such

Recent advances in controllable/divergent synthesis

• Jilei Cao,
• Leiyang Bai and
• Xuefeng Jiang

Beilstein J. Org. Chem. 2025, 21, 890–914, doi:10.3762/bjoc.21.73

• thiols act as stoichiometric reductants. Mechanistic insights, elucidated through control experiments and DFT calculations, revealed that photoexcitation of diazo imide 41 triggers nitrogen extrusion (ΔG‡ = +10.0 kcal·mol−1), generating the triplet carbene intermediate Int-45. In DCM, this species

• substrates 61. At 10 °C, the catalytic system consisting of NiBr₂(diglyme), oxazoline ligand, (EtO)₃SiH, and K₃PO₄(H₂O) achieved β-selective hydroalkylation. When the temperature was raised to 100 °C, the reaction selectively produced α-branched products. DFT calculations showed that at low temperatures, the

• mechanistic experiments and DFT calculations, the authors proposed a possible mechanism for the reaction: first, DPZ is excited by light to form the excited state DPZ*, which then oxidizes bromide ions through single-electron transfer to generate corresponding radical anions. These radical anions undergo

Unraveling cooperative interactions between complexed ions in dual-host strategy for cesium salt separation

• Zhihua Liu,
• Ya-Zhi Chen,
• Ji Wang,
• Qingling Nie,
• Wei Zhao and
• Biao Wu

Beilstein J. Org. Chem. 2025, 21, 845–853, doi:10.3762/bjoc.21.68

• solution into chloroform and controllable release into acidic solution [32]. Very recently, it was found that the receptor L alone can further extract solid Li2SO4 into DMSO solution [33], where sulfate binding is sufficiently strong to drive the solid–liquid extraction. DFT calculations suggest that an

Substituent effects in N-acetylated phenylazopyrazole photoswitches

• Radek Tovtik,
• Dennis Marzin,
• Pia Weigel,
• Stefano Crespi and
• Nadja A. Simeth

Beilstein J. Org. Chem. 2025, 21, 830–838, doi:10.3762/bjoc.21.66

• often show higher quantum yields and increased thermal half-life of the metastable state. For the half-life, the choice of the heterocycle is crucial, as revealed through density functional theory (DFT) calculations, which showed that a 5-membered ring promotes the stability of the Z isomer [30]. Within

• predicted using quantum chemistry to describe the Z→E isomerization in azobenzenes, namely: rotation, inversion, inversion-assisted rotation, and concerted inversion depending on the structure of the azobenzene [40][41][42][43][44]. For PAPs, Calbo et al. showed by DFT calculations that the inversion

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

• , while density functional theory (DFT) calculations provided insights into their electronic properties, including reactivity and stability. This comprehensive approach, integrating synthesis, biological evaluation, and computational methods, highlights the potential of 4-(1-methylamino)ethylidene-1,5

Development and mechanistic studies of calcium–BINOL phosphate-catalyzed hydrocyanation of hydrazones

• Carola Tortora,
• Christian A. Fischer,
• Sascha Kohlbauer,
• Alexandru Zamfir,
• Gerd M. Ballmann,
• Jürgen Pahl,
• Sjoerd Harder and
• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2025, 21, 755–765, doi:10.3762/bjoc.21.59

• hydrocyanation of hydrazones, catalyzed by a calcium–BINOL phosphate complex, has been studied for the first time both experimentally and computationally with DFT methods. A full catalytic cycle for the enantioselective synthesis of α-hydrazinonitriles is proposed based on insights gained from DFT calculations

• –BINOL phosphate complex as catalyst. Herein, we report the development of the first Ca–BINOL phosphate-catalyzed asymmetric hydrocyanation of hydrazones and the results from DFT calculations to elucidate the mechanism of this transformation. Results and Discussion We first set out to study the

Recent advances in allylation of chiral secondary alkylcopper species

• Minjae Kim,
• Gwanggyun Kim,
• Doyoon Kim,
• Jun Hee Lee and
• Seung Hwan Cho

Beilstein J. Org. Chem. 2025, 21, 639–658, doi:10.3762/bjoc.21.51

• transfer, X-ray crystallographic analysis of the (tert-butyl)(adamantyl)Bpin·Li(THF)2 complex revealed that the B–(adamantyl) bond is shorter than the B–(tert-butyl) bond (1.673 vs 1.692 Å). DFT calculations further illuminated the underlying mechanism by comparing two distinct transition states: TS1

• traditional crotyl addition to acetaldehyde. This methodology represents the first example of highly enantio- and diastereoselective copper-catalyzed allylic substitution that controls vicinal stereogenic centers. DFT calculations revealed that the high enantioselectivity (98:2 er) originates from a face

• copper complex formation and subsequent selective olefin insertion results in the high levels of enantioselectivity (98:2 er) observed experimentally. DFT calculations further elucidated the origin of the high diastereoselectivity (up to 96:4 dr) in the allylic substitution step (Scheme 13b). Analysis of

Photocatalyzed elaboration of antibody-based bioconjugates

• Marine Le Stum,
• Eugénie Romero and
• Gary A. Molander

Beilstein J. Org. Chem. 2025, 21, 616–629, doi:10.3762/bjoc.21.49

• a photoredox reaction, whereas when embedded within the protein, the Ru-based ArM complex promoted histidine modification through an energy-transfer mechanism (Figure 5). Based on DFT calculations, this is permitted by the modification of the energy diagram of the ruthenium complex in the presence

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