Computational design for enantioselective CO₂ capture: asymmetric frustrated Lewis pairs in epoxide transformations

• Maxime Ferrer,
• Iñigo Iribarren,
• Tim Renningholtz,
• Ibon Alkorta and
• Cristina Trujillo

Beilstein J. Org. Chem. 2024, 20, 2668–2681, doi:10.3762/bjoc.20.224

• free energy correction at double-zeta. The kinetics of some reactions were calculated, applying the transition state theory [40]. Within this theory, the rate constant of an elementary reaction with the free energy barrier ΔG‡ is given by Equation 1, where k is the rate constant in s−1, kB is the

• File 1). Notably, the CO2 capture exhibits a lower activation barrier compared to the capture of epoxide (+10.0 kcal·mol−1 vs +30.0 kcal·mol−1). Using transition state theory [40] as expressed in Equation 1, the rate constants were calculated for binding to either molecule at 273.0 K, resulting in k1

• mechanism leading to the (S) product presents an asymmetric TS, 1.2 kcal·mol−1 higher in energy than that of the (R) mechanism. Thus, the asymmetric catalyst enables to generate an enantiomeric excess of 95% with the (R) product being the most abundant product. Surprisingly, a transition state connecting

Machine learning-guided strategies for reaction conditions design and optimization

• Lung-Yi Chen and
• Yi-Pei Li

Beilstein J. Org. Chem. 2024, 20, 2476–2492, doi:10.3762/bjoc.20.212

• extensive effort. This involves complex parameter optimization, meticulous validation against experimental data, and careful consideration of diverse reaction conditions and possible reaction mechanisms [28][29]. Although some studies employ transition-state (TS) theory to simulate activation energies and

Hypervalent iodine-mediated cyclization of bishomoallylamides to prolinols

• Smaher E. Butt,
• Konrad Kepski,
• Jean-Marc Sotiropoulos and
• Wesley J. Moran

Beilstein J. Org. Chem. 2024, 20, 2455–2460, doi:10.3762/bjoc.20.209

• that the transition state was stabilized by 4.1 kcal·mol−1 by an extra molecule of trifluoroacetic acid. A similar stabilizing interaction was not identified in this case with 3a, despite significant effort, but it cannot be ruled out. The cyclization of 9 was shown to be possible by attack of the

Asymmetric organocatalytic synthesis of chiral homoallylic amines

• Nikolay S. Kondratyev and
• Andrei V. Malkov

Beilstein J. Org. Chem. 2024, 20, 2349–2377, doi:10.3762/bjoc.20.201

• attributed to the chair-like transition state where the organoboron reagent 1 exchanges one isopropoxy group for one of the BINOL 3 oxygen atoms, whereas the free OH group of the BINOL forms a hydrogen bond to the carbonyl of substrate 2. The flanking phenyl groups on the BINOL facilitate recognition between

• -Fmoc-aryl- and -alkylimines, catalysed by a chiral disulfonimide 45 (Scheme 10). Since allyltrimethylsilane (46) belongs to the type 2 allylation reagents [33], the nucleophilic addition proceeds via an open transition state (Figure 1). Two possible mechanistic pathways were proposed, where the Fmoc

• , in the COBI–imine complex 74 it appears at 8.41 ppm, while in the imine TfOH salt 75 it shows at 9.24 ppm. This detailed NMR investigation sparked further interest in the structure of the transition state of this reaction. An analysis of the potential energy profiles of the two hypothetical pathways

Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis

• Stefan P. Schmid,
• Leon Schlosser,
• Frank Glorius and
• Kjell Jorner

Beilstein J. Org. Chem. 2024, 20, 2280–2304, doi:10.3762/bjoc.20.196

• [92] and a phase-transfer catalysed oxidative amination reaction [93]. In the latter, NCI descriptors were both used to simplify previously existing MLR models and also led to a hypothesis of key NCIs in the transition state. Whereas these descriptors require the selection of a suitable probe model

• [96] investigated a bromocyclization catalysed by a chiral phosphoric acid (CPA) and a DABCOnium brominating reagent (Figure 6). The authors calculated transition state conformer ensembles for several flexible DABCOnium systems and performed energy decomposition analysis to separate the interactions

• develop a comprehensive model, finding that imine parameters govern the defining transition state and hence the preferred enantiomer. In a focused modelling, two separate models are constructed, one for all E- and Z-imines, respectively, finding substrate–catalyst matching is important for E- and Z-imines

Synthesis and reactivity of the di(9-anthryl)methyl radical

• Tomohiko Nishiuchi,
• Kazuma Takahashi,
• Yuta Makihara and
• Takashi Kubo

Beilstein J. Org. Chem. 2024, 20, 2254–2260, doi:10.3762/bjoc.20.193

• small about 1.18 kcal mol−1 (Supporting Information File 1, Figure S2). To investigate the activation barrier of this equilibrium, potential energy curve by changing the dihedral angle θ of one anthryl group was calculated. The transition state was calculated with the dihedral angle θ = 30.6° and the

Metal-free double azide addition to strained alkynes of an octadehydrodibenzo[12]annulene derivative with electron-withdrawing substituents

• Naoki Takeda,
• Shuichi Akasaka,
• Susumu Kawauchi and
• Tsuyoshi Michinobu

Beilstein J. Org. Chem. 2024, 20, 2234–2241, doi:10.3762/bjoc.20.191

• (PCM) solvent (Figure 4). The reaction initially started with the addition of benzyl azide to one of the internal alkynes of 5. Although the benzyl group is situated on the interior side of DBA, a more energetically unstable transition state (in-ts) is generated. However, the resulting monoadduct (in

• the experimental observation that no monotriazoles were obtained. During the second azide addition, the orientation of benzyl azide is once more controlled. The benzyl group positioned on the inner side results in a thermodynamically less stable transition state (in-in-ts) compared to that on the

• was taken into account by the polarizable continuum model using the integral equation formalism (IEFPCM) [25] for DFT calculations. The optimized molecular structures were verified by vibrational analysis; equilibrium structures did not have imaginary frequencies and transition-state structures had

Regioselective alkylation of a versatile indazole: Electrophile scope and mechanistic insights from density functional theory calculations

• Pengcheng Lu,
• Luis Juarez,
• Paul A. Wiget,
• Weihe Zhang,
• Krishnan Raman and
• Pravin L. Kotian

Beilstein J. Org. Chem. 2024, 20, 1940–1954, doi:10.3762/bjoc.20.170

• indazole and the deprotonated indazole was only −0.2 kcal/mol (Figure 11). Again, no preorganized intermediates were found. The NCIs were consistent with the parent system. The hydrogen bond between the H on the electrophilic methyl group and an ester oxygen was found in the transition state leading to the

• N1 product, was conserved (18-N1-OMe, Figure 11), in a total of 4 NCIs. The only relevant NCIs in 18-N2-OMe were between an aryl hydrogen, N1 and an ester oxygen, the result of which is ΔΔG‡ = 2.0 kcal/mol favoring the N1 transition state 18-N1-OMe among the NCIs found. To further probe whether the

• stabilization, nucleophilicity would dictate regioselectivity outcomes. This also implies that the favorable NCIs and chelation are stronger driving forces towards transition-state energy partitioning than nucleophilicity alone. These results suggest chelation is a highly plausible driving force for

Divergent role of PIDA and PIFA in the AlX₃ (X = Cl, Br) halogenation of 2-naphthol: a mechanistic study

• Kevin A. Juárez-Ornelas,
• Manuel Solís-Hernández,
• Pedro Navarro-Santos,
• J. Oscar C. Jiménez-Halla and
• César R. Solorio-Alvarado

Beilstein J. Org. Chem. 2024, 20, 1580–1589, doi:10.3762/bjoc.20.141

• , and transition-state structures were optimized by density functional theory (DFT) calculations employing the software Gaussian 16 [34]. Although the B3LYP functional could be suitable for these calculations, e.g., for tracing reaction pathways, nitrations, halogenations, or FC acylations in solution

• ) must exhibit only positive harmonic frequencies, whereas each energy maximum (transition state) exhibited only one negative frequency. From these last calculations, zero-point energy, thermal, and entropy corrections were obtained, which were added to the electronic energy to express the calculated

• rise to the chlorinating species I-2–Cl in equilibrium with I-3–Cl. At this point, 2-naphthol reacts, leading to the formation of the ion pair I-4–Cl via chlorine atom transfer, which then yields the adduct I-5–Cl trough transition state TS2–Cl. Then, the release of the second equivalent of the TFAO

Benzylic C(sp³)–H fluorination

• Alexander P. Atkins,
• Alice C. Dean and
• Alastair J. J. Lennox

Beilstein J. Org. Chem. 2024, 20, 1527–1547, doi:10.3762/bjoc.20.137

• intramolecular fluorine-atom-transfer (FAT) from an N-fluorinated amide to a pendant carbon-based radical formed from an iron catalyst (Figure 15) [55][56]. This concept of fluorine transfer through a 6-membered transition state was shown to work efficiently from primary, as well as secondary, benzylic radicals

Synthetic applications of the Cannizzaro reaction

• Bhaskar Chatterjee,
• Dhananjoy Mondal and
• Smritilekha Bera

Beilstein J. Org. Chem. 2024, 20, 1376–1395, doi:10.3762/bjoc.20.120

• of a hydride ion from a tetracoordinated intermediate (B), which is formed upon hydroxide addition to the aldehyde (A). The primary pathway of the reaction entails the rate-determining step of hydride ion transfer via either a linear or bent transition state (C) to a second molecule of aldehyde

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• barrier through the chair–chair transition state of 28.1 kcal mol−1 and an overall ΔG from 2 to 10a/10b, which have the same predicted energy, of −2.0 kcal mol−1 (Figure 3B). The relative free energy barrier through the chair–boat transition state was calculated to be 36.9 kcal mol−1, but would require a

• , Supporting Information File 1). The lowest transition state for a Cope rearrangement, a chair–chair structure at 29.3 kcal mol−1, originates from a DD (down–down orientations of the methyl groups on the 10-membered ring) conformer that is 3.2 kcal mol−1 higher in free energy than the most dominant conformer

• previously reported [10]. A biosynthetically related analog is similarly proposed to undergo oxy-Cope rearrangement to yield 13a/13b. (B) Results of DFT calculations indicate that the Cope rearrangement of 2 is more favorable via a chair–chair transition state than a chair–boat transition state. (C) Results

Sustainable tandem acylation/Diels–Alder reaction toward versatile tricyclic epoxyisoindole-7-carboxylic acids in renewable green solvents

• Ayhan Yıldırım

Beilstein J. Org. Chem. 2024, 20, 1308–1319, doi:10.3762/bjoc.20.114

• study indicates that the retro-IMDAF reaction does not occur under the reaction conditions developed. As seen in Figure 4b, the different sigma bond lengths formed in the exo transition state (calculations which were performed in Gaussian 16 Rev B.01 (Gaussian, Inc., Wallingford, CT, USA)) [135

• ] indicate that the IMDAF reaction proceeds through an asynchronous process (the same is true for the endo transition state). Accordingly, the length of the σ bond formed near the amide functional group was calculated to be 2.012 Å, while the length of the bond formed on the far side was calculated to be

• 2.160 Å. These bond lengths support path I, which is a more valid pathway in the reaction mechanism. As can be seen in Figure 4, the energies of both the exo transition state and the exo product are lower than those of the endo, which also supports the experimental results. Conclusion Vegetable oils

Two-fold addition reaction of silylene to C₆₀: structural and electronic properties of a bis-adduct

• Masahiro Kako,
• Masato Kai,
• Masanori Yasui,
• Michio Yamada,
• Yutaka Maeda and
• Takeshi Akasaka

Beilstein J. Org. Chem. 2024, 20, 1179–1188, doi:10.3762/bjoc.20.100

• the transition state was ascribed to the donor–acceptor interactions between the HOMO of the silylene and the LUMO of ethylene, and vice versa [42]. For 2a, the LUMO is largely distributed at the e' bonds, followed by the cis-2 and trans-3 bonds (Figure 8). These results suggest that the formation of

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• cytosine deamination involves a nucleophilic attack at the C4 position by a Zn2+-activated water molecule [40][41][42], it was proposed to employ transition state analogues and mimetics of the tetrahedral intermediate formed as inhibitors of these enzymes [43][44][45][46][47]. More than 30 compounds have

Novel route to enhance the thermo-optical performance of bicyclic diene photoswitches for solar thermal batteries

• Akanksha Ashok Sangolkar,
• Rama Krishna Kadiyam and
• Ravinder Pawar

Beilstein J. Org. Chem. 2024, 20, 1053–1068, doi:10.3762/bjoc.20.93

• -transition state bifurcation (PTSB) of the PES [39][40]. Consequently, the reaction tends to produce two different products from a single TS. Thus, the reaction resembles a peculiar ambimodal reaction that can produce multiple products from a single TS structure [41]. Owing to the formation of two singlet

• photoswitching cycle. The dissociation of two newly formed σ-bonds during the thermal back isomerization proceeds in a highly asynchronous mechanism. Initially, only one of the two newly formed σ-bonds is dissociated leading to the formation of singlet biradicals in the transition state (TS) structure. Therefore

Enantioselective synthesis of β-aryl-γ-lactam derivatives via Heck–Matsuda desymmetrization of N-protected 2,5-dihydro-1H-pyrroles

• Arnaldo G. de Oliveira Jr.,
• Martí F. Wang,
• Rafaela C. Carmona,
• Danilo M. Lustosa,
• Sergei A. Gorbatov and
• Carlos R. D. Correia

Beilstein J. Org. Chem. 2024, 20, 940–949, doi:10.3762/bjoc.20.84

• upward, therefore creating an asymmetric center with absolute configuration (R), in accordance with experimental results. A rationalization for the transition state that would lead to the observed outcome is depicted in Figure 2. Conclusion The palladium-catalyzed Heck–Matsuda desymmetrization of N

Synthesis and properties of 6-alkynyl-5-aryluracils

• Ruben Manuel Figueira de Abreu,
• Till Brockmann,
• Alexander Villinger,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 898–911, doi:10.3762/bjoc.20.80

• compounds show a very similar absorption band, indicating that the first transition state (S0 → S1) does not seem to be affected by the substitution pattern. Furthermore, all compounds show broadened absorption bands and no major differences in the first absorption band were observed. The greatest

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• synthetic intermediate of 2 to spiroviolene. By taking advantage of the DFT transition state analysis of the hydroboration reaction of a key intermediate, as well as NOE correlation analysis of the resultant product, Snyder and co-workers have reassigned the right structure of spiroviolene to 1. However

Skeletal rearrangement of 6,8-dioxabicyclo[3.2.1]octan-4-ols promoted by thionyl chloride or Appel conditions

• Martyn Jevric,
• Julian Klepp,
• Johannes Puschnig,
• Oscar Lamb,
• Christopher J. Sumby and
• Ben W. Greatrex

Beilstein J. Org. Chem. 2024, 20, 823–829, doi:10.3762/bjoc.20.74

• work, which suggests a stepwise migration of oxygen from C5 to C4, followed by addition of the halogen nucleophile. Furthermore, if the halogen was involved in the transition state via the σ* orbital (avoiding intermediate 27), the opposite configuration would result at C2 in the products. The single

Evaluation of the enantioselectivity of new chiral ligands based on imidazolidin-4-one derivatives

• Jan Bartáček,
• Karel Chlumský,
• Jan Mrkvička,
• Lucie Paloušová,
• Miloš Sedlák and
• Pavel Drabina

Beilstein J. Org. Chem. 2024, 20, 684–691, doi:10.3762/bjoc.20.62

• effective transition state includes the electrophile positioned in the equatorial site (strongly coordinated) and the nucleophile in the perpendicular site (weakly coordinated) [19]. The most favourable orientation of aldehyde should be out of the ligand’s molecular parts, thus forming E-configuration at

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• mechanism to a <1st-order dependence on catalyst, which could indicate a competing alcohol or H-bonding driven mechanism. In CD3OD, first-order-catalyst dependence is maintained. The entropy of activation reveals an organized transition state (−42.1 cal/mol·K) which would be consistent with the mechanism in

• involvement in proton transfer at the transition state [78]. In systems where protodemetalation is rate determining, a metal-carbon bonded intermediate is allegedly characterized, as in the case of a related palladium-catalyzed hydroamination [47], and a propargylamide cyclization [44]. In our studies, the

• less than half complete at the transition state [79]. In foundational work on alkene hydration by Evans and Kirby, a general acid-catalyzed mechanism is concluded, and small isotope effects are observed despite H–O bond breaking in the transition state [80]. In an excellent study by Borhan and co

Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters

• Carlos R. Azpilcueta-Nicolas and
• Jean-Philip Lumb

Beilstein J. Org. Chem. 2024, 20, 346–378, doi:10.3762/bjoc.20.35

• undergo addition to the heterocyclic radical acceptor 19 through a ternary transition state 20 involving hydrogen bonding interactions with the chiral phosphate co-catalyst. Notably, a follow-up report revealed that the radical addition is reversible, and that the selectivity determining step involves the

Unveiling the regioselectivity of rhodium(I)-catalyzed [2 + 2 + 2] cycloaddition reactions for open-cage C₇₀ production

• Cristina Castanyer,
• Anna Pla-Quintana,
• Anna Roglans,
• Albert Artigas and
• Miquel Solà

Beilstein J. Org. Chem. 2024, 20, 272–279, doi:10.3762/bjoc.20.28

• experimental findings discussed earlier. Once INT 1 is formed, for the rest of the process, the TOF determining transition state (TDTS) of the process is α/β-TS 2 and the TOF determining intermediate (TDI) is INT 2 and the energetic span (δG) is 16.2 kcal·mol−1 for the α-attack and 17.0 kcal·mol−1 for the β

Tandem Hock and Friedel–Crafts reactions allowing an expedient synthesis of a cyclolignan-type scaffold

• Viktoria A. Ikonnikova,
• Cristina Cheibas,
• Oscar Gayraud,
• Alexandra E. Bosnidou,
• Nicolas Casaretto,
• Gilles Frison and
• Bastien Nay

Beilstein J. Org. Chem. 2024, 20, 162–169, doi:10.3762/bjoc.20.15

• alternative mechanism, we envisionned a possible interconversion of 7 and 7’ through a [1,5]-sigmatropic rearrangement resulting in a hydrogen and cation shift towards 7’ (Scheme 4). To test this hypothesis, this rearrangement was computed at the DFT level. A cyclic transition state (TS) was found between

• oxocarbenium 7 and 7’ which exists as a stabilized form including an intramolecular stabilizing interaction between the carbocation and the ester carbonyl group. However, in close agreement with Hess and Baldwin’s values found for the rearrangement of cis-1,3-pentadiene [24], this transition state was high in