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Search for "computational" in Full Text gives 604 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Molecular tweezer–peptide conjugates disrupt the protein–protein interaction between survivin and histone H3 essential in mitosis
Beilstein J. Org. Chem. 2026, 22, 557–567, doi:10.3762/bjoc.22.41
- by computational modeling (MD and QM/MM simulations) as well as structural biology (NMR/X-ray). Following our powerful concept of reinforcing natural peptide–protein interactions by tweezer conjugation [9][10], we envisaged to attach molecular tweezers to the histone H3 terminus at a distance which
Concept-driven strategies in target-oriented synthesis
Beilstein J. Org. Chem. 2026, 22, 451–454, doi:10.3762/bjoc.22.32
- computational methodology are poised to enhance both accuracy and efficiency, thereby opening new opportunities across various branches of chemical and data sciences. However, while these achievements exemplify the collaborative spirit of scientific inquiry, it is essential to recognize that the primary focus
Synthesis and anti-cancer activity of naphthalimide–organylselanyl conjugates
Beilstein J. Org. Chem. 2026, 22, 416–435, doi:10.3762/bjoc.22.29
- solid state structure of the compound 7. All the above-mentioned non-bonded interaction distances are shorter than the sum of the van der Waals radii of the respective elements in contact [55]. Computational analysis To further evaluate the energy-minimised structures useful for molecular
- . X-ray data Table 3 shows the X-ray data of compound 7. In addition, a packing diagram of compound 7 in the crystal can be found in Figure S20 in Supporting Information File 1. Computational details All computational calculations were carried out using the Gaussian 16 (g16) program [76]. Geometry
Electrosynthetic access to unsymmetrical oxaza[8]helicenes with high chiral stability and strong circularly polarized luminescence (CPL)
Beilstein J. Org. Chem. 2026, 22, 372–382, doi:10.3762/bjoc.22.25
- : Cartesian coordinates of DFT calculations. Acknowledgements We acknowledge the technical staff of the Comprehensive Analysis Center at SANKEN, The University of Osaka. Computations were performed at the Research Center for Computational Science, Okazaki, Japan (Project: 25-IMS-C280). Funding This work was
Recent advances in the cleavage of non-activated amides
Beilstein J. Org. Chem. 2026, 22, 352–369, doi:10.3762/bjoc.22.23
- lower reactivity than the twisted N-Boc-N-phenylbenzamide (177) but was more reactive than N,N-dialkylamides 3, 4, 168, 169, and 170. Computational analysis also revealed that the intramolecular nucleophilic attack of intermediate AF through transition state AG constitutes the rate-determining step
Arene activation via π-bond localization: concepts and opportunities
Beilstein J. Org. Chem. 2026, 22, 257–273, doi:10.3762/bjoc.22.19
- process. Subsequent computational studies, however, refined this mechanistic understanding, revealing that reductive elimination proceeds through coupling of the C(3) terminus of the η1-allyl fragment with the para-carbon of the η3-benzyl ligand (Scheme 6A, right) [75]. Together, these insights
- introduced by Cheong and Altman in 2020 (Figure 10A) [83]. In this study, the authors explored an intramolecular, decarboxylative C–H functionalization of benzylic electrophiles, uncovering a decisive role of the base in governing site selectivity. Computational and mechanistic analyses revealed that only
- [80]. Computational investigations of this latter transformation identified an η3-allylnaphthalene–η1-allenyl palladium complex as the key to achieving ortho-selectivity (Figure 10B) [85][86]. Building on these insights, the Bao group employed malonates as alkylating agents in reactions with
Screwing the helical chirality through terminal peri-functionalization
Beilstein J. Org. Chem. 2026, 22, 205–212, doi:10.3762/bjoc.22.14
- enantioselectivity. Notably, [6]helicene 3k was also readily produced, via kinetic resolution (Scheme 1). Computational studies suggested that hydrogen bonding and π interactions between the reactants and catalyst L1 controlled the stereochemical output of the products 3. The catalyst proximate both reactants to
Improved synthesis and physicochemical characterization of the selective serotonin 2A receptor agonist 25CN-NBOH
Beilstein J. Org. Chem. 2026, 22, 175–184, doi:10.3762/bjoc.22.11
- and 0.1% phosphoric acid in the ratios 35:65 and 25:75, v/v for the distribution coefficient and stability experiments, respectively. The ChemStation software (Version B.04.03, Agilent Technologies) was used for instrument control and data collection. Computational chemistry DFT calculations were
Symmetrical D–π–A–π–D indanone dyes: a new design for nonlinear optics and cyanide detection
Beilstein J. Org. Chem. 2026, 22, 131–142, doi:10.3762/bjoc.22.6
- extinction coefficient Also, dyes exhibit positive solvatochromism, consistent with their ICT characteristics. Moreover, synthesized symmetric dyes containing D–π–A–π–D systems were analyzed using experimental and computational methods for second-order nonlinear optical properties. NLO measurements conducted
Sustainable electrochemical synthesis of aliphatic nitro-NNO-azoxy compounds employing ammonium dinitramide and their in vitro evaluation as potential nitric oxide donors and fungicides
Beilstein J. Org. Chem. 2025, 21, 2739–2754, doi:10.3762/bjoc.21.211
- spectroscopy using 1,1,2,2-tetrachloroethane as an internal standard. Computational details: DFT computations were performed for 1 atm. and 298.15 K in Orca 6.1.0 package [93]. Results were visualized in Chemcraft 1.8 program. For conformationally flexible structures, generation of conformational ensembles was
- all compounds, XRD of 2c, computational details, and copies of 1H, 13C, 14N, 1H,13C HSQC, and 1H,13C HMBC NMR spectra. Supporting Information File 5: Crystallographic information for compound 2c. Supporting Information File 6: CheckCIF report for the data of 2c. Acknowledgements Crystal structure
Mechanistic insights into hydroxy(tosyloxy)iodobenzene-mediated ditosyloxylation of chalcones: a DFT study
Beilstein J. Org. Chem. 2025, 21, 2703–2715, doi:10.3762/bjoc.21.208
- )3/CH3OH, PhI(OCOCH3)2/CH3OH and PhI(OH)OTs/CH3OH in polar nucleophilic solvents [24][25][26][27][28]. A number of experimental and computational studies have explored the reaction pathway for these oxidative rearrangement reactions under metal-free conditions with the use of hypervalent iodine(III
- computationally. The results obtained for chalcones are in qualitative agreement with results reported for substituted styrenes [31]. Computational Methodology Quantum chemical calculations were carried out using Gaussian 09 package [37]. The hybrid exchange-correlation functional B3LYP-D3 (including dispersion
Thiazolidinones: novel insights from microwave synthesis, computational studies, and potentially bioactive hybrids
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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