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Search for "calculations" in Full Text gives 869 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.

Data accessibility in the chemical sciences: an analysis of recent practice in organic chemistry journals

  • Sally Bloodworth,
  • Cerys Willoughby and
  • Simon J. Coles

Beilstein J. Org. Chem. 2025, 21, 864–876, doi:10.3762/bjoc.21.70

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  • data, but only 47 shared any primary data at all (Figure 3a). Of these, most (39) shared ‘MODEL’ data derived from in silico modelling – i.e., Cartesian coordinates associated with modelled structures in thermochemical calculations or binding studies (Figure 3b). 72% of these coordinates were given in
  • whether authors can select from alternative licenses or create a tailored license for their data. Reuse_3, ‘are code scripts necessary to reproduce findings available?’. For data that had been generated through software processing, algorithms or other calculations performed on primary data, only one paper
  • shared any code. Statistical outcomes shared in one Excel file reported only values, with no calculations. Discussion We frame our discussion (below) according to the four research questions posed in our introduction to this work and provide specific recommendations for strategies towards improved
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Published 02 May 2025

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

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  • 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
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Published 29 Apr 2025

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

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  • 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
  • activation enthalpy ΔH‡ and ΔS‡. In particular, NAc-PAP-CN showed a negative ΔS‡ = −30.0 ± 2.0 J/(mol·K), while NAc-PAP-OMe showed a relatively similar value (−39.0 ± 4.0 J/(mol·K)), hinting towards the same mechanism of relaxation operating for both compounds. Comparing these values to the calculations for
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Published 25 Apr 2025

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

Graphical Abstract
  • , 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
  • ), electronegativity (χ), hardness (η), and softness (S). The calculations were based on established formulas, as described in literature [49]. Natural products and synthetic medicinal compounds containing a 2-pyrrolidinone subunit. The molecular structure of 5a, showing the atom-labelling scheme and displacement
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Published 24 Apr 2025

Synthesis and photoinduced switching properties of C7-heteroatom containing push–pull norbornadiene derivatives

  • Daniel Krappmann and
  • Andreas Hirsch

Beilstein J. Org. Chem. 2025, 21, 807–816, doi:10.3762/bjoc.21.64

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  • various positions of the NBD scaffold were envisioned, although such modifications have primarily been investigated theoretically thus far [25][26][27][28]. Recently, high-throughput calculations were conducted to screen a wide array of hetero-substituted NBD species. These studies predominantly
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Published 22 Apr 2025

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

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  • 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
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Published 14 Apr 2025

Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

  • Leon M. Friedrich and
  • Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

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  • . Supporting Information File 1). The calculations were performed with two conformers of FimH, the open and the closed gate conformation, PDB 1KLF [45] and PDB 1UWF [46], respectively. These protein structures differ in the relative orientation of the so-called tyrosine gate, which is formed by Tyr48 and
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Published 08 Apr 2025

Photochemically assisted synthesis of phenacenes fluorinated at the terminal benzene rings and their electronic spectra

  • Yuuki Ishii,
  • Minoru Yamaji,
  • Fumito Tani,
  • Kenta Goto,
  • Yoshihiro Kubozono and
  • Hideki Okamoto

Beilstein J. Org. Chem. 2025, 21, 670–679, doi:10.3762/bjoc.21.53

Graphical Abstract
  • recognized for fluorinated oligoacene systems [30][34][36]. The theoretical calculations suggest that, in the ground state, the polarization of the phenacene molecules inverted upon the introduction of fluorine atoms. As seen from electrostatic potential (ESP) mapping (Figure 5b), the phenacene cores are
  • , and their electronic spectral features were investigated. They displayed UV–vis and fluorescence spectra which were seemingly the same as those of the parent phenacene molecules in the solution phase although theoretical calculations predicted the MO energy levels of F8-phenacenes markedly lowered by
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Published 24 Mar 2025

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

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  • 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
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Published 20 Mar 2025

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

Graphical Abstract
  • 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
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Published 18 Mar 2025

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

Graphical Abstract
  • (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
  • rational design, which depend on systematic access to incrementally varied experimental datasets, which are not always available for metastable systems. Further, without many-electron metals to model [208][376], high-throughput calculations of organic cages are facile [366][377][378][379][380][381][382
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Published 24 Feb 2025

Unraveling aromaticity: the dual worlds of pyrazole, pyrazoline, and 3D carborane

  • Zahra Noori,
  • Miquel Solà,
  • Clara Viñas,
  • Francesc Teixidor and
  • Jordi Poater

Beilstein J. Org. Chem. 2025, 21, 412–420, doi:10.3762/bjoc.21.29

Graphical Abstract
  • calculations were performed with the Gaussian 16 package [64] by means of the B3LYP [65][66][67] hybrid density functional and the 6-311++G(d,p) basis set [68]. The geometry optimizations were carried out without symmetry constraints (Table S2 in Supporting Information File 1). Analytical Hessians were
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Published 21 Feb 2025

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

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Published 17 Feb 2025

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

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  • leads to new 2-(benzo[e(g)]indolin-2-yl)-5,6,7-trichloro-1,3-tropolones and 2-(benzo[e(g)]indolin-2-yl)-4,5,6,7-tetrachloro-1,3-tropolones. Based on the results of PBE0/6-311+G(d,p) calculations, the structural and energetic characteristics of the tautomeric forms of the obtained 1,3-tropolones were
  • -(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
  • large Stokes shift values (Table 2, Figure 5). This is consistent with the above conclusion about the existence of tautomeric equilibrium 7,8 (OH)–7,8 (NH) in solutions based on NMR data and DFT quantum chemical calculations (Scheme 2). The emission with a larger Stokes shift appears to correspond to
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Published 17 Feb 2025

Synthesis of new condensed naphthoquinone, pyran and pyrimidine furancarboxylates

  • Kirill A. Gomonov,
  • Vasilii V. Pelipko,
  • Igor A. Litvinov,
  • Ilya A. Pilipenko,
  • Anna M. Stepanova,
  • Nikolai A. Lapatin,
  • Ruslan I. Baichurin and
  • Sergei V. Makarenko

Beilstein J. Org. Chem. 2025, 21, 340–347, doi:10.3762/bjoc.21.24

Graphical Abstract
  • method according to the SHELXT-2014/5 program [34] and refined by the full-matrix least-square on F2 according to the SHELXL-2018/3 program [35]. All calculations were performed using the WingX-2020.1 software package [36]. Structure 6c was refined using OLEX2-1.5 software package [37]. Non-hydrogen
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Published 12 Feb 2025

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

Graphical Abstract
  • 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
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Published 11 Feb 2025

Red light excitation: illuminating photocatalysis in a new spectrum

  • Lucas Fortier,
  • Corentin Lefebvre and
  • Norbert Hoffmann

Beilstein J. Org. Chem. 2025, 21, 296–326, doi:10.3762/bjoc.21.22

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  • of these compounds in the field of photocatalysis [49]. The study has included a detailed mechanistic investigation to differentiate between competing single-electron transfer and energy transfer pathways. Through both experimental measurements and theoretical calculations, the authors have
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Published 07 Feb 2025

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

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  • shift (NICS) calculations and anisotropy of the current induced density (ACID) plots, as they evidenced the presence of a perimetral diatropic global ring current upon oxidation. Keywords: ACID; aromaticity; force constants; NICS; spectroscopy; Introduction Since the discovery of conjugated polymers
  • vibrational Raman spectroscopies, normal mode and force field calculations, and magnetic-based analysis to gain comprehensive understanding of the electronic and molecular structures of the oxidized forms of these aromatic/antiaromatic molecular amalgams, aiming to discover the driving forces that govern the
  • has been used here to calculate complete sets of stretching force constants associated to the individual CC bonds of 1 and 2, hereafter designated as k[ν(CC)] (see Supporting Information File 1 for details of these calculations). They account for bond strengths, hence allowing a direct comparison
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Published 05 Feb 2025

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

Graphical Abstract
  • 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
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Published 04 Feb 2025

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

Graphical Abstract
  • analysis of the thermal back reaction revealed activation parameters, highlighting how the substitution position of the aryl group affects the thermal stability. Additionally, density functional theory calculations identified M06 and MPW1PW91 as the most accurate functionals for predicting the thermal back
  • 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
  • calculations can be a powerful tool for molecular design. In this work, we newly synthesize various aza-diarylethene derivatives N3, N4, and I1–I4 with different substitution positions of the aryl group, and investigate their photochromic behaviors and thermal back reactivities as the data set for the
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Published 31 Jan 2025

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

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  • 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
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Published 22 Jan 2025

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

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  • systems significantly enhances its hydrogen bond donation ability, a result consistent with theoretical calculations. We anticipate that this chemistry will be valuable for designing functional molecules for chemical biology and medicinal chemistry applications. Keywords: bioisostere; difluoromethyl
  • . We expect this information to be useful for the rational application of the CF2H group in drug development and molecular design. Previous quantum mechanical calculations revealed that the CF2H···O binding energy (ΔE) ranges from 1.0 kcal/mol to 5.5 kcal/mol [14][15][18][21]. In addition, as measured
  • ; 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
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Published 20 Jan 2025

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

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  • ) 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
  • results in one case, providing high cytotoxicity toward the MCF-7 cancer cell line. The stable axial chirality of the products 71 and 73 was confirmed by calculations of the rotational barriers ranging from 30.2 to 46.3 kcal/mol. Kinetic resolution by amino group protection of biaryls (R,S)-74a–r with
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Published 09 Jan 2025

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

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  • 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
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Published 02 Jan 2025

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

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  • -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
  • calculations also revealed that due to kinetic control the activation of the C2 carbon of the dienolate is preferred vs the C4 atom, therefore only one regioisomer is observed. Additionally, the asymmetric IEDADA reaction could be performed at a higher scale (1 mmol) leading to the synthesis of the
  • 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
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Published 10 Dec 2024
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