Thiazolidinones: novel insights from microwave synthesis, computational studies, and potentially bioactive hybrids

• Luan A. Martinho,
• Victor H. J. G. Praciano,
• Guilherme D. R. Matos,
• Claudia C. Gatto and
• Carlos Kleber Z. Andrade

Beilstein J. Org. Chem. 2025, 21, 2618–2636, doi:10.3762/bjoc.21.203

Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA

• Grant D. Walby,
• Brandon R. Tessier,
• Tristan L. Mabee,
• Jennah M. Hoke,
• Hallie M. Bleam,
• Angelina Giglio-Tos,
• Emily E. Harding,
• Vladislavs Baskevics,
• Martins Katkevics,
• Eriks Rozners and
• James A. MacKay

Beilstein J. Org. Chem. 2025, 21, 2513–2523, doi:10.3762/bjoc.21.193

• UV melting and ITC, Db2 showed especially poor affinity for the U–A base pair in HRP1. To help explain experimental binding results, we turned to computational molecular dynamics modeling using HRP1 and PNA1–3 as a model based on the PNA–dhRNA triplex provided by previous NMR studies [41] (for

• phenyl group out of the plane of the isoorotamide is required. Such distortion likely causes a disruption in triplex stability. Together, the UV melting data and computational modeling offer several lessons for future monomer design. First, despite the success of past nucleobases that incorporate a

• calorimetry.c Supporting Information Supporting Information File 20: General synthetic details and procedures, characterization data for synthetic intermediates, biophysical assays, and computational details. Acknowledgements We thank Ilze Kumpina for help with the ITC data analysis. Funding This work was

Synthesis of the tetracyclic skeleton of Aspidosperma alkaloids via PET-initiated cationic radical-derived interrupted [2 + 2]/retro-Mannich reaction

• Ru-Dong Liu,
• Jian-Yu Long,
• Zhi-Lin Song,
• Zhen Yang and
• Zhong-Chao Zhang

Beilstein J. Org. Chem. 2025, 21, 2470–2478, doi:10.3762/bjoc.21.189

• construction of the tetracyclic core of Aspidosperma alkaloids. Our method involves an Ir-catalyzed PET reaction of K for the stereoselective formation of the cis-configured BC bicyclic core with an all-carbon quaternary center [25][26]. Computational studies suggest that the observed tandem PET reaction of K

• 62% and 58%, respectively. Computational study The synthesis of (±)-aspidospermidine (1) and (±)-limaspermidine (2) showcased the effectiveness of our strategy for constructing complex monoterpene indole alkaloids [26]. In this work, we turned our attention to investigating the mechanistic

• synthesis; d) naturally occurring Aspidosperma alkaloids; e) ring strain energy of cyclopentene, bicyclo[3.2.0]heptane, cycloheptane, cyclobutene, bicyclo[2.2.0]hexane and cyclohexane. Computational study. a) Energy profiles from IN1 to IN3 and spin density of TS2 (isovalue = 0.004), solvated (SMD) Gibbs

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

• , we turned to computational studies to elucidate the driving force of this pyranoside-into-furanoside isomerisation. The DFT B3LYP-D3 approach was employed for this task with additional validation of its results at DLPNO-CCSD(T) level for the lowest energy conformers. The results demonstrate that the

• 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

• employed. CPCM model [35] with the default parameters for methylene chloride was used to account for bulk solvent effects. Such choice of computational parameters for protected carbohydrate molecules was validated in our previous investigation [36]. The defgrid3 option was used throughout the calculations

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

• computational schematic (Figures S16 and S17 in Supporting Information File 1), the anions are positioned within the macrocycle cavity, exhibiting close contacts to hydrogen atoms on the bridging benzene rings, peripheral substituted phenyl groups, and carbazole moieties. These spatial interactions suggest a

Adaptive experimentation and optimization in organic chemistry

• Artur M. Schweidtmann and
• Philippe Schwaller

Beilstein J. Org. Chem. 2025, 21, 2367–2368, doi:10.3762/bjoc.21.180

• human–AI synergy emerges repeatedly. The computational design of asymmetric catalysts by Ferrer et al. demonstrates how AI can accelerate discovery while relying on chemical principles to guide the search space [14]. The most successful approaches combine the rapid exploration capabilities of AI with

Recent advances in Norrish–Yang cyclization and dicarbonyl photoredox reactions for natural product synthesis

• Peng-Xi Luo,
• Jin-Xuan Yang,
• Shao-Min Fu and
• Bo Liu

Beilstein J. Org. Chem. 2025, 21, 2315–2333, doi:10.3762/bjoc.21.177

• , enabling the total synthesis of 13 via in situ intramolecular lactonization as a key step. Computational and experimental studies reveal that the regio- and stereoselectivity of the Norrish−Yang cyclization are governed by the influence of the methyl group at C10: (1) In terms of regioselectivity, the 1,3

A chiral LC–MS strategy for stereochemical assignment of natural products sharing a 3-methylpent-4-en-2-ol moiety in their terminal structures

• Rei Suo,
• Raku Irie,
• Hinako Nakayama,
• Yuta Ishimaru,
• Yuya Akama,
• Masato Oikawa and
• Shiro Itoi

Beilstein J. Org. Chem. 2025, 21, 2243–2249, doi:10.3762/bjoc.21.171

• A terminal 3-methylpent-4-en-2-ol (MPO) moiety is a common structural feature in various polyketide natural products. Stereochemical assignments of this moiety have mainly relied on computational analyses of NMR, ECD, and specific rotation data. However, none of these approaches can be applied to

• typically determined using NMR-based techniques, such as coupling constant analysis and NOE experiments, sometimes with the aid of computational chemistry [3][4][5][6][7]. In contrast, absolute configuration remains more challenging to determine, as it frequently requires chemical degradation or

• analysis, and computational methods have been widely used. For example, the absolute configuration of chaetomugilin B [19] was determined by X-ray crystallography, while that of capsulactone (1) was established through density functional theory (DFT)-based simulations of NMR chemical shifts and electronic

A m-quaterphenyl probe for absolute configurational assignments of primary and secondary amines

• Yuka Takeuchi,
• Mutsumi Kobayashi,
• Yuuka Gotoh,
• Mari Ikeda,
• Yoichi Habata,
• Tomohiko Shirai and
• Shunsuke Kuwahara

Beilstein J. Org. Chem. 2025, 21, 2211–2219, doi:10.3762/bjoc.21.168

• Supporting Information File 1). In the quaternary ammonium salts (S)-3f, the populations of the M conformers were greater than those of the P conformers (Figure 4). These computational results were consistent with the signs of the experimentally observed CD Cotton effects. From the conformational analyses

C2 to C6 biobased carbonyl platforms for fine chemistry

• Jingjing Jiang,
• Muhammad Noman Haider Tariq,
• Florence Popowycz,
• Yanlong Gu and
• Yves Queneau

Beilstein J. Org. Chem. 2025, 21, 2103–2172, doi:10.3762/bjoc.21.165

• temperatures between 180–240 ºC in a maximum yield of about 30–40% (Scheme 14) [72][73]. Dihydroxyacetone (DHA) The formose process is the conversion of formaldehyde to glycolaldehyde and 1,3-dihydroxy-2-propanone (dihydroxyacetone, DHA). A computational protein-directed evolution allowed to create "formolase

Solar thermal fuels: azobenzene as a cyclic photon–heat transduction platform

• Jie Yan,
• Shaodong Sun,
• Minghao Wang and
• Si Wu

Beilstein J. Org. Chem. 2025, 21, 2036–2047, doi:10.3762/bjoc.21.159

• ]. Since Olmsted’s pioneering exploration of azobenzene compounds as solar thermal fuels in 1983 [42], significant breakthroughs have been achieved through interdisciplinary integration of organic synthesis, functional materials engineering, photophysical mechanism analysis, and computational chemistry. So

• transition behavior, achieving high gravimetric energy densities (300–400 J/g) with long-term storage stability (Figure 6d). Grossman and Durgun proposed methods for incorporating azobenzenes into macrocyclic structures [82]. Their computational models indicated that the molecular rings connecting the

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

• synthetic organic chemists. We report a computational study on the mechanism of diazabicyclo[2.2.1]heptenes to address long standing mechanistic questions. Indeed, the mechanism of these reactions has been disputed for over six decades. We employed non-adiabatic molecular dynamics (NAMD) simulations

• ][68][69][70][71][72][73][74][75][76][77][78] mechanisms of cyclic azoalkenes have been studied with experimental and computational techniques for more than six decades, in solution [51][55][59][60][61][64][67][69][70][73][74][75][76][78][79], gas phase [50][55][62][64][65], and solid state [60][63

• observation aligns with previous computational studies on the photodenitrogenation of DBH. The black dots represent the hopping points, the geometries where the trajectory crosses from S1 to S0. Figure 4 shows that the first σCN bond breaks on the S1 surface, while the second σCN bond breaks after relaxation

Photochemical reduction of acylimidazolium salts

• Michael Jakob,
• Nick Bechler,
• Hassan Abdelwahab,
• Fabian Weber,
• Janos Wasternack,
• Leonardo Kleebauer,
• Jan P. Götze and
• Matthew N. Hopkinson

Beilstein J. Org. Chem. 2025, 21, 1973–1983, doi:10.3762/bjoc.21.153

• , however, did not reveal any significant change in the absorption profile. To gain further insight, time-dependent density functional theory (TD-DFT) calculations were carried out (for details of the computational studies, see Supporting Information File 1). In line with the UV–vis studies, comparison of

• : Experimental procedures, characterization data of all isolated products, details of UV–vis, time-course and computational studies as well as copies of NMR spectra for novel compounds. Acknowledgements We thank Prof. Dr. Beate Koksch and the AG Koksch (FU Berlin) for supervisory assistance and helpful

Chiral phosphoric acid-catalyzed asymmetric synthesis of helically chiral, planarly chiral and inherently chiral molecules

• Wei Liu and
• Xiaoyu Yang

Beilstein J. Org. Chem. 2025, 21, 1864–1889, doi:10.3762/bjoc.21.145

• derivatizations. Based on experimental and computational studies, the origin of helical chirality in this method was elucidated. We proposed that the asymmetric Povarov reaction would generate a pair of diastereomeric tetrahydroquinoline derivatives displaying helical conformation, with a modest energetic barrier

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

• development of liquid crystals, ion carriers, and other technologies dependent on precise molecular properties. Computational Details The fluorinated cyclopropanes shown in Figure 1 were optimized using density functional theory (DFT) at the B3LYP-GD3BJ/6-311++G(d,p) level [20][21][22], which includes

• dispersion corrections to improve the modeling of nonbonding interactions [23]. The same computational protocol was applied to cyclopropane, methane, and methyl fluoride, used as reference molecules in the isodesmic reactions. This methodology has proven reliable for predicting the energetics and properties

On the aromaticity and photophysics of 1-arylbenzo[a]imidazo[5,1,2-cd]indolizines as bicolor fluorescent molecules for barium tagging in the study of double-beta decay of ¹³⁶Xe

• Eric Iván Velazco-Cabral,
• Fernando Auria-Luna,
• Juan Molina-Canteras,
• Miguel A. Vázquez,
• Iván Rivilla and
• Fernando P. Cossío

Beilstein J. Org. Chem. 2025, 21, 1627–1638, doi:10.3762/bjoc.21.126

• Abstract In this paper, the behavior of a bicolor fluorescent indicator for the detection of barium cations formed by double-beta decay of 136Xe is analyzed by means of computational tools. Both DFT and TDDFT permit to understand the origin of the bicolor fluorescent signal emitted by 1-arylbenzo[a]imidazo

• corresponding double bonds (C=C, C=N). We computed the HOMA values associated with the total, peripheral and modular patterns using the standard parameters and a more recent set based on computational parameters that take into account antiaromaticity, denoted as HOMAc [23]. According to our results, formal

• efficiency of crown ethers as components in cation-selective fluorescent probes has been extensively explored [7][30], to the best of our knowledge no previous computational DFT studies on the selectivity of crown ethers of different sizes with Ba2+ have been reported. Therefore, we explored (Scheme 2A) the

Transition-state aromaticity and its relationship with reactivity in pericyclic reactions

• Israel Fernández

Beilstein J. Org. Chem. 2025, 21, 1613–1626, doi:10.3762/bjoc.21.125

• aromatic character in their transition states, this increased aromaticity does not necessarily correlate with lower activation barriers. State-of-the-art computational methods on reactivity, such as the combined activation strain model (ASM)–energy decomposition analysis (EDA) method, reveal that factors

• other than aromaticity govern the barrier heights of these pericyclic reactions. Keywords: activation barrier; activation strain model; aromaticity; computational chemistry; transition state; Introduction Aromaticity is arguably one of the most fundamental and extensively studied concepts in chemistry

Synthesis of optically active folded cyclic dimers and trimers

• Ena Kumamoto,
• Kana Ogawa,
• Kazunori Okamoto and
• Yasuhiro Morisaki

Beilstein J. Org. Chem. 2025, 21, 1603–1612, doi:10.3762/bjoc.21.124

• S1 states of (A) (Sp)-6 and (B) (Sp)-7 (TD-MN15/6-31G(d)). Synthesis of cyclic dimer (Sp)-6 and trimer (Sp)-7. Supporting Information Supporting Information File 26: Statement of computational methods, NMR and HRMS spectra, PL decay curves, glum charts, calculated ECD spectra, and cartesian

Thermodynamic equilibrium between locally excited and charge transfer states in perylene–phenothiazine dyads

• Issei Fukunaga,
• Shunsuke Kobashi,
• Yuki Nagai,
• Hiroki Horita,
• Hiromitsu Maeda and
• Yoichi Kobayashi

Beilstein J. Org. Chem. 2025, 21, 1577–1586, doi:10.3762/bjoc.21.121

• : Experimental and computational details, synthesis and characterization of compounds, additional spectroscopic results, and theoretical calculations. Acknowledgements The authors acknowledge Dr. Tatsuo Nakagawa, UNISOKU Co., Ltd., for nanosecond transient absorption measurements Funding This work was supported

Azobenzene protonation as a tool for temperature sensing

• Antti Siiskonen,
• Sami Vesamäki and
• Arri Priimagi

Beilstein J. Org. Chem. 2025, 21, 1528–1534, doi:10.3762/bjoc.21.115

• and solvent polarity, we demonstrate that the degree of protonation, and thus solution color, is highly temperature-dependent, changing from pale yellow to deep red as temperature decreases. We also present mechanistic insights and compare our experimental findings with computational results. Results

• performed to study these interactions at the molecular level. Better understanding on the protonation process emerges from combining computational findings with experimental data, as discussed in the following section. Discussion Upon protonation, azobenzene and the conjugate base of the acid form either an

• polar aprotic solvent such as DCE, we assume the formation of CIP, as supported by computational results. This discussion focuses on compound 3, which showed most promising characteristics for temperature sensing, including a larger red-shift upon protonation and a broader sensing range. DFT

Advances in nitrogen-containing helicenes: synthesis, chiroptical properties, and optoelectronic applications

• Meng Qiu,
• Jing Du,
• Nai-Te Yao,
• Xin-Yue Wang and
• Han-Yuan Gong

Beilstein J. Org. Chem. 2025, 21, 1422–1453, doi:10.3762/bjoc.21.106

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

• computational quantum chemistry calculations. As seen from Table S2 in Supporting Information File 1, the deprotonation of the tautomeric proton requests substantially more energy, while the deprotonation of the phenyl OH group leads to a single E− tautomer. This fact is confirmed by a simple experiment. As

• part should be considered with care. They originate from computational quantum chemistry calculations in toluene and their aim is not to suggest definite compounds, but to show directions of structural modifications that can solve one of the problems with the switching of compounds originating from 1

• –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

High-pressure activation for the solvent- and catalyst-free syntheses of heterocycles, pharmaceuticals and esters

• Kelsey Plasse,
• Valerie Wright,
• Guoshu Xie,
• R. Bernadett Vlocskó,
• Alexander Lazarev and
• Béla Török

Beilstein J. Org. Chem. 2025, 21, 1374–1387, doi:10.3762/bjoc.21.102

• -products. A computational study accompanies the experimental data to interpret the outcome of the reactions. Keywords: acetaminophen; acetylsalicylic acid; benzimidazoles; catalyst-free synthesis; cyclization; esters; high hydrostatic pressure; pyrazoles; Introduction Non-traditional activation methods

• broad agreement that a decrease in the activation volume (ΔV‡) and reaction volume (ΔV) is the driving force for these reactions [14][15][16]. A recent computational analysis of high pressure reactions by the extreme pressure polarizable continuum model (XP-PCM) improved the theoretical understanding of

• impact ionization (EI, 70 eV) mode using a 30m long DB-5 type column (J&W Scientific). Computational details To determine the reaction volume (ΔV), the volumes of the starting materials and products were calculated separately using the Gaussian 09 program suite [48]. Geometry optimizations were performed

Oxetanes: formation, reactivity and total syntheses of natural products

• Peter Gabko,
• Martin Kalník and
• Maroš Bella

Beilstein J. Org. Chem. 2025, 21, 1324–1373, doi:10.3762/bjoc.21.101

• epimerisation to obtain diastereoenriched spirocycles, utilising t-BuOK/t-BuOH for the anti-diastereomer 163 and LDA/PivOH at −78 °C for the syn-diastereomer 162 (dr >10:1 in both protocols). Mechanistic and computational studies suggested the following series of steps: excitation of 159 via energy transfer

• challenging amines. The combination of simple reaction conditions and excellent chemoselectivity makes this protocol very robust and suitable for both the academia and industry. Kinetic and computational experiments support an SN1 mechanism via loss of sulphur dioxide and oxetane carbocation formation. Two

Enhancing chemical synthesis planning: automated quantum mechanics-based regioselectivity prediction for C–H activation with directing groups

• Julius Seumer,
• Nicolai Ree and
• Jan H. Jensen

Beilstein J. Org. Chem. 2025, 21, 1171–1182, doi:10.3762/bjoc.21.94

• molecular architectures in pharmaceuticals, polymers, and agrochemicals. Despite advancements in directing group (DG) methodologies and computational approaches, predicting accurate regioselectivity in C–H activation poses significant difficulties due to the diversity and complexity of organic compounds

• . This study introduces a novel quantum mechanics-based computational workflow tailored for the regioselective prediction of C–H activation in the presence of DGs. Utilizing (semi-empirical) quantum calculations hierarchically, the workflow efficiently predicts outcomes by considering concerted

• computational cost. Validation against a comprehensive dataset reveals that the workflow achieves high accuracy, significantly surpassing traditional models in both speed and predictive capability. This development promises substantial advancements in the design of new synthetic routes, offering rapid and