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

• metallation deprotonation mechanisms mediated by common catalysts like Pd(OAc)2. Our methodology not only identifies potential activation sites but also addresses the limitations of existing models by including a broader range of directing groups and reaction conditions while maintaining moderate

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

• ) reported a carboxyl group activation of cinnamic acid (7) by applying pivalic anhydride in a single step to afford the corresponding amide 8 in excellent yield (Scheme 3B) [35]. Moreover, pivalic anhydride is easier to handle than its chloride counterpart. Wang and co-workers (2022) utilized 5-nitro-4,6

• could be recycled by adding POCl3 and KSCN, thus promoting the reagent’s sustainability by reducing waste. Carboxyl group activation can also be achieved by using triazine-based reagents. For example, Saberi and Salimiyan (2019) applied 2,4,6-trichloro-1,3,5-triazine (TCT) to perform amidation of

• cinnamic acid (7) and N,N’-dimethylformamide (DMF)-mediated by POCl3 via acid chloride 36 formation (Scheme 20) [52]. On top of the carboxyl activation approaches demonstrated above, O/N-acylation could also be achieved by employing an electrophilic alkylating agent by exploiting the nucleophilicity of the

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

• Education, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan Soft Molecular Activation Research Center, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan Institute for

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

• first report by Stork in the 1950s [1][2][3]. Compared with enols, enamines benefit from the lone pair of electrons on the nitrogen atom, which enhances the nucleophilicity of the alkene, enabling it to react with a broad range of electrophiles. This activation mode of carbonyl compounds has been so

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

• , hinting at the type of non-radiative decay pathways in these molecules [63]. For medium strong donors the Gibbs energy of activation ΔGCT‡ for crossing over into the CT state is low, and emission can occur from here with high ϕ (see point 2 in Figure 9). For strong donors, ΔGCT‡ is close to 0 allowing

Silver(I) triflate-catalyzed post-Ugi synthesis of pyrazolodiazepines

• Muhammad Hasan,
• Anatoly A. Peshkov,
• Syed Anis Ali Shah,
• Andrey Belyaev,
• Chang-Keun Lim,
• Shunyi Wang and
• Vsevolod A. Peshkov

Beilstein J. Org. Chem. 2025, 21, 915–925, doi:10.3762/bjoc.21.74

• ) [46]. In 2019, Li, Yang, Van der Eycken and co-workers reported a modification of this strategy relying on thermal activation instead of cationic gold catalysis [47]. The approach worked particularly well with substrates featuring terminal alkynes. Inspired by these developments and taking into

• heteroannulation leading to the pyrazolo[1,5-a][1,4]diazepine scaffold. Our initial choice was to investigate the use of silver(I) triflate (AgOTf) as a catalyst in toluene, given its previously demonstrated efficiency in various transformations involving the activation of triple bonds towards nucleophilic attack

• . The first step, the Ugi-4CR, introduces molecular diversity, while the second step, an efficient silver(I)-catalyzed heteroannulation, facilitates the formation of the pyrazolodiazepine core via alkyne activation towards the nucleophilic attack by the pyrazole nitrogen. This strategy expands the array

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

• pathway bifurcated based on the steric demands of Si–C-bond activation. The methyl-substituted ligand (S)-8H-binaphthyl phosphoramidite L4, featuring a spacious cavity, favored sterically encumbered Si–C(sp3)-bond activation, selectively delivering axially chiral (S)-1-silacyclohexenyl arenes 17 with high

• enantiocontrol. Conversely, the bulky tert-butyl-decorated (R)-spirophosphoramidite L5 imposed a confined cavity, steering selectivity toward Si–C(sp2)-bond activation and predominantly afforded the regioisomeric (S)-2-silacyclohexenylarenes 18. In 2025, Gong and co-workers reported a visible-light-mediated

• species Int-44. This reactive intermediate then engages with a Ti(IV)-enolate complex through radical recombination, ultimately delivering 2-aza-bicyclo[3.1.1]heptene (BCHepe) while regenerating the Ti(III) catalyst to complete the catalytic cycle. (2) Scandium-catalyzed pathway: Activation of the donor

Light-enabled intramolecular [2 + 2] cycloaddition via photoactivation of simple alkenylboronic esters

• Lewis McGhie,
• Hannah M. Kortman,
• Jenna Rumpf,
• Peter H. Seeberger and
• John J. Molloy

Beilstein J. Org. Chem. 2025, 21, 854–863, doi:10.3762/bjoc.21.69

• facilitated landmark organic transformations, such as the venerable Paternò–Büchi [6][7][8], Norrish–Yang [9][10][11], and enone–alkene cycloadditions [12][13][14], that proceed via the generation of a singlet or triplet diradical through the activation of an unsaturated bond [2][14]. While these seminal

• contributions have enabled the efficient activation of carbonyl and alkene moieties, the inability of most organic molecules to efficiently absorb photons at longer wavelengths often preclude their use in direct excitation strategies, requiring unique experimental set ups and light sources that are

• activation of polyboronated alkenes [51] and β-borylstyrenes [43][48], was ineffective and no reactivity was observed. Implementing a higher energy iridium sensitizer (≈60 kcal/mol) was also unsuccessful (Table 1, entry 2), however, employing thioxanthone (65 kcal/mol) demonstrated efficient activation of

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

• triplet state [48], appear to play a role. Specifically, the rotation mechanism does not explain the low activation entropy observed in azobenzene systems [49] sparking new discussions on the possibility of alternative isomerization pathways [34]. Recently, Reimann et al. computationally showed that the

• involvement of a triplet state mechanism, which crosses the transition state for the Z→E relaxation, could explain the low values of the activation entropy. The same authors also showed experimental evidence for this proposal by an external heavy atom effect on Z→E isomerization. To understand the thermal Z→E

• 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

Recent advances in the electrochemical synthesis of organophosphorus compounds

• Babak Kaboudin,
• Milad Behroozi,
• Sepideh Sadighi and
• Fatemeh Asgharzadeh

Beilstein J. Org. Chem. 2025, 21, 770–797, doi:10.3762/bjoc.21.61

• or ketones. They used nickel foam as both anode and cathode electrodes in an undivided cell under air at room temperature. The reaction was carried out in the presence of KI as an electrolyte, a key additive, and acetone as a solvent. HI increases the reaction yield due to the activation of the

New advances in asymmetric organocatalysis II

• Radovan Šebesta

Beilstein J. Org. Chem. 2025, 21, 766–769, doi:10.3762/bjoc.21.60

• Radovan Sebesta Department of Organic Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, Slovakia 10.3762/bjoc.21.60 Keywords: asymmetric organocatalysis; covalent activation; noncovalent activation; Organocatalysis is

• ]. Kowalczyk and co-workers showed how asymmetric organocatalysis can benefit from mechanochemical activation. They established that Michael additions of thiomalonates to enones, catalyzed by cinchona-derived primary amines, is efficient and enantioselective under ball-milling conditions [24]. Kondratyev and

• organocatalytic cycloaddition reactions of unsaturated imines. A broad variety of activation modes, as well as catalyst structures, was covered and found to be useful in affording a diverse array of chiral N-heterocycles [27]. In my group, we recently became interested in atroposelective catalytic syntheses

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

• and TMSCN (8). Model complex 4 initially reacts with TMSCN to give MeOTMS and HCN. Even under methanol-free conditions, an excess of TMSCN is therefore needed to achieve complete conversion (Table 1), which hints at a mechanism of catalyst activation through reaction of the metal complex with the

• the R-product from E-hydrazone is slightly lower in energy (Table 3). However, the activation barrier for the rate-limiting step is 0.4 kcal·mol−1 lower for the pathway shown in Figure 2 and that yields the S-product from the Z-hydrazone. As the activation barrier to thermal E/Z-isomerization is more

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

• 3αMan 5, first order reactions were assumed with the rate constants k5, k7, and k6 (Figure 2C). In order to determine the half-lifes τ1/2 and activation energies Ea of the photoswitching units comprised in the homobivalent glycocluster 6αMan3αMan 2, the decay of the metastable ZZ isomer to the

• k7 obtained with a first-order exponential decay fit (Table 2 and Supporting Information File 1, Figures S7, S9, and S11). The half-lifes τ1/2 and the activation energies Ea of thermal relaxation were calculated based on the determined rate constants. The kinetics show that thermal relaxation of the

• ), resulting half-lifes (τ1/2) and activation energies (Ea) for the thermal ZZ to EE isomerization of glycoclusters 1 [24] and 2 and thermal Z to E isomerization of the glycoantennas 3, 4, and 5 at 37 °C. The top-ranked results of the molecular modeling study of the various isomers of the ligands 6βGlc3αMan 1

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• -fluoroamide gauche effect has frequently been exploited is N-acylpyrrolidines, a structural motif found within many bioactive molecules (e.g., the fibroblast activation protein (FAP) inhibitors 111 and 112, Figure 12) [188][189][190][191][192]. When fluorinated analogues of N-acylpyrrolidines are prepared

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

• configurationally stable organoboron compounds was recently developed by Morken and co-workers, which employs only catalytic amounts of copper [47][48]. Their strategy uses chiral secondary organoboron compounds 20 as precursors to generate chiral alkylcopper species through a carefully controlled activation and

• transmetalation sequence (Scheme 6). For secondary boronic esters, Morken and co-workers conducted a systematic investigation to develop an efficient activation strategy [47]. Computational studies using DFT revealed an important relationship between the length of the boron–carbon bonds and the corresponding

• electronegativity, reaching 1.648 Å in the reactive alkoxytrialkyl complex D and 1.659 Å in the tetraalkyl "ate" complex E. The B–C bond lengths in amido- and alkyl-substituted boronic ester complexes B and C fell between these extremes, suggesting an intermediate level of activation. These findings prompted

Entry to 2-aminoprolines via electrochemical decarboxylative amidation of N‑acetylamino malonic acid monoesters

• Olesja Koleda,
• Janis Sadauskis,
• Darja Antonenko,
• Edvards Janis Treijs,
• Raivis Davis Steberis and
• Edgars Suna

Beilstein J. Org. Chem. 2025, 21, 630–638, doi:10.3762/bjoc.21.50

• -disubstituted piperidine-containing amino acid subunits. Likewise, a cyano-substituted cyclic aminal is a core structural unit of the fibroblast activation protein inhibitor 5 [3] (Figure 1). The widespread use of non-proteinogenic cyclic amino acids in drug discovery justifies both the design of new analogs

Formaldehyde surrogates in multicomponent reactions

• Cecilia I. Attorresi,
• Javier A. Ramírez and
• Bernhard Westermann

Beilstein J. Org. Chem. 2025, 21, 564–595, doi:10.3762/bjoc.21.45

• products (products 2 to 5, Scheme 4). In other cases, under acidic and thermal conditions, DMSO can undergo a Pummerer-type process in which, upon activation of the sulfoxide oxygen, a reactive methyl(methylene)sulfonium ion (MMS) is formed (Scheme 5) that acts as an active electrophile. Depending on the

• ). Additionally, the Tiwari group developed a metal-free protocol using only K2S2O8 as an oxidant for the activation of DMSO to MMS (Scheme 8, path II) [38]. Under these conditions, an alternative mechanism arises in which the imine intermediate B, formed as previously stated through reaction between the aniline

• , methyl aryl ketones, and DMSO under iron(III) catalysis and using K2S2O8 for its activation [39]. The proposed mechanism is very close to those described above, with the methyl aryl ketone taking part of the reaction in place of the styrene component in the Povarov cyclization. In this case, the imine

Asymmetric synthesis of β-amino cyanoesters with contiguous tetrasubstituted carbon centers by halogen-bonding catalysis with chiral halonium salt

• Yasushi Yoshida,
• Maho Aono,
• Takashi Mino and
• Masami Sakamoto

Beilstein J. Org. Chem. 2025, 21, 547–555, doi:10.3762/bjoc.21.43

• , Japan; Grant-in-Aid for Early-Career Scientists (No. 22K14674) and Scientific Research (C) (No. 24K08424) from the Japan Society for the Promotion of Science; and the Leading Research Promotion Program “Soft Molecular Activation” of Chiba University, Japan.

Vinylogous functionalization of 4-alkylidene-5-aminopyrazoles with methyl trifluoropyruvates

• Judit Hostalet-Romero,
• Laura Carceller-Ferrer,
• Gonzalo Blay,
• Amparo Sanz-Marco,
• José R. Pedro and
• Carlos Vila

Beilstein J. Org. Chem. 2025, 21, 533–540, doi:10.3762/bjoc.21.41

• . Considering the high diastereoselectivity observed both in the presence and absence of the squaramide catalyst, we propose a plausible mechanism (Scheme 3) that involves hydrogen bonding activation of the methyl trifluoropyruvate by the NH₂ group of the aminopyrazole. This interaction directs the attack of

• electrophile activation. In certain reactions, we isolated compound A, the hydrate of methyl trifluoropyruvate. We hypothesized that preventing the formation of this byproduct could improve the reaction yield by using molecular sieves (entries 17 and 18, Table 1). However, when molecular sieves were added, the

Deep-blue emitting 9,10-bis(perfluorobenzyl)anthracene

• Long K. San,
• Sebastian Balser,
• Brian J. Reeves,
• Tyler T. Clikeman,
• Yu-Sheng Chen,
• Steven H. Strauss and
• Olga V. Boltalina

Beilstein J. Org. Chem. 2025, 21, 515–525, doi:10.3762/bjoc.21.39

• used to achieve higher yields [27]. Even in the absence of a transition-metal-based photosensitizer, a recent study showed that perfluoroalkylation using perfluoroalkyl iodides (RFI) could be carried out by activation of the RF–I bonds by formation of electron donor–electron acceptor complexes with an

• reactions) Dry Mg turnings (excess) were added to an oven-dried 100 mL Schlenk flask and mechanically activated via stirring and heating. After 1 h, dry THF (20 mL) and 9,10-ANTH(Br)2 (84 mg, 0.25 mmol) were added. Several activation methods were tried (ultra sonic bath, careful heating, addition of I2

Photomechanochemistry: harnessing mechanical forces to enhance photochemical reactions

• Francesco Mele,
• Ana M. Constantin,
• Andrea Porcheddu,
• Raimondo Maggi,
• Giovanni Maestri,
• Nicola Della Ca’ and
• Luca Capaldo

Beilstein J. Org. Chem. 2025, 21, 458–472, doi:10.3762/bjoc.21.33

• transfer [13][14][15]. Regardless of the mechanistic details of the activation manifold, all photochemical reactions obey two laws: the Grotthuss–Draper and the Einstein–Stark laws [16]. The Grotthuss–Draper law dictates that only absorbed light can induce photochemical transformations within a system. In

• mechanochemistry holds potential for unique opportunities for substrate activation while adopting an environmentally benign emerging technology (Figure 2, top). For example, it is well known that molecules in the solid state (or in very high concentration) often exhibit photophysical behaviors distinct from those

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

• any charge generation requires that an equal and opposite charge be generated elsewhere, the unifying concept for polarization is that of “cooperative [4] bifunctionality”: providing opposing functionalities able to stabilize opposite charges: dual activation (e.g., the simultaneous activation of

• , therefore, that for redistribution penalties to be lessened, the equal and opposite stabilization must be granted to that same space. This is the basis of bifunctional/dual activation, as shown in Figure 1. Since very few reported supramolecular cavity designs provide bifunctional activation, cavity

• hydrophobic hosts [37]. Directed polarization, the basis for organocatalysis, is rare in cavity catalysis. Now, I believe the field of supramolecular catalysis to be on the cusp of putting these two elements – “organization and polarization” or “confinement and dual activation” – together with greater

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

• temperature or the activation entropy, hydrogen bonding, solvent [24], nature of the leaving groups and the promoter used [25]. The mechanism of glycosylation reactions has long been categorised mostly as dissociative SN1 reactions proceeding through stabilised oxocarbenium ions with the role of counterions

• levulinoyl protecting group, the 4,4-(ethylenedithio)pentanoyl group 28 [99]. Wong and co-workers illustrated the selective activation (Scheme 5) of C-2 levulinoyl-protected thiotolyl glycopyranosyl donor 29 for the synthesis of the disaccharide fragment 31 of fucosyl ganglioside GM1 [100]. Pivalate

• ) and 2-naphthylmethoxymethyl (NAPOM) derivatives [141][142]. Activation of the thiophenyl glycoside donors 78, protected by the alkoxymethyl groups at the C-2 position by a combination of NIS and In(OTf)3, followed by the nucleophilic attack of the acceptor glycoside 79 produced 1,2-trans glycosides

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

• acetone, allowing the pre-activation of the ruthenium complex with the successive release of an N-heterocyclic carbene ligand and a chlorine atom, which are replaced by two acetone molecules to form compound 2. Simultaneously, excitation of the osmium(II) complex in the red region (660 nm) decreases its

• , thereupon highlighting potential for broad applications in photoredox catalysis on an industrial scale. In this context, T. Rovis et al. have studied a C–N cross-coupling Buchwald–Hartwig-like reaction using dual nickel and osmium catalysis under red-light activation, addressing common challenges such as

Three-component reactions of conjugated dienes, CH acids and formaldehyde under diffusion mixing conditions

• Dmitry E. Shybanov,
• Maxim E. Kukushkin,
• Eugene V. Babaev,
• Nikolai V. Zyk and
• Elena K. Beloglazkina

Beilstein J. Org. Chem. 2025, 21, 262–269, doi:10.3762/bjoc.21.18

• [4][5][6] and polymerization processes of unstable methylidene adducts [7][8][9], instead of the desired formation of a monocrotonic product. Therefore, heating [6][10][11][12][13][14] or Lewis acid activation [15][16][17][18] have often been used in the literature for successful multicomponent