Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• nucleophilic aromatic substitution of 4-fluorobenzaldehyde with 2-(methylamino)ethanol, 3-methylamino-1-propanol or 2-[2-(methylamino)ethoxy]ethan-1-ol in the presence of potassium carbonate to afford benzaldehyde derivatives 1, 2, and 3 in excellent yields. Next, the piperidine-induced condensation with 4

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

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

• largely depends on the choice of the nucleophilic organometallic species (Scheme 2). For example, the asymmetric copper-catalyzed allylic alkylation utilizing organometallic species 5 bearing a primary carbon–metal bond predominantly constructs the stereogenic center derived from electrophiles. The

Sequential two-step, one-pot microwave-assisted Urech synthesis of 5-monosubstituted hydantoins from L-amino acids in water

• Wei-Jin Chang,
• Sook Yee Liew,
• Thomas Kurz and
• Siow-Ping Tan

Beilstein J. Org. Chem. 2025, 21, 596–600, doi:10.3762/bjoc.21.46

• conversion of the thioether-containing methionine to hydantoin (H2j) was obtained with a moderate yield of 59%. Lastly, no hydantoin product was observed by 1H NMR when cysteine was subject to the one-pot procedure, possibly due to disulfide formation of the highly nucleophilic thiol group of the cysteine

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

• decompose into DMS (dimethyl sulfide), which then can act as a nucleophile in several MCRs (Scheme 4) [19][20][21][22]. In this context, DMSO can be used as a source of the methylsulfanyl (-SCH3) group after DMS follows a nucleophilic addition or substitution, allowing one to obtain different types of

• nucleophilic species present in the reaction medium, MMS can act as a methylene source. Under hydrolysis conditions, it can be a source of formaldehyde (Scheme 5a), but with other nucleophiles, after nucleophilic addition, the sulfide group can work as a leaving group, allowing for a sequential domino process

• conversion of DMSO to MMS, a wide range of 4-arylquinolines can be synthesized (Scheme 8, path I) [24]. In this reaction, the persulfate ion generates the thionium ion (MMS), which is trapped by a nucleophilic aniline. The loss of methyl sulfide generates an imine intermediate B, which, in turn, reacts with

Study of the interaction of 2H-furo[3,2-b]pyran-2-ones with nitrogen-containing nucleophiles

• Constantine V. Milyutin,
• Andrey N. Komogortsev and
• Boris V. Lichitsky

Beilstein J. Org. Chem. 2025, 21, 556–563, doi:10.3762/bjoc.21.44

• subsequent opening of the furanone ring and proton transfer results in final compounds 8, 10 and 11. The synthetic application of obtained pyrazolones 8 was demonstrated by its further derivatization. The interaction with electrophilic agents is determined by the presence of several nucleophilic centers in

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

• exchange from tetrafluoroborate to the halonium moiety to form chiral ion pair II. Attack of the chiral nucleophilic intermediate II to imine 7 leads to intermediate III. The latter is protonated by in the situ-formed potassium bicarbonate to form the desired product 17, together with the regenerated

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

• diastereoselectivity (up to 7:1). Keywords: alcohols; diastereoselectivity; nitrogen heterocycles; pyrazoles; vinylogous reaction; Introduction Vinylogy refers to the transmission of electronic effects through a conjugated π-system, enabling the extension of a functional group's nucleophilic or electrophilic

• biologically active compounds, particularly antibacterial and antifungal agents [13][14]. This class of functionalized nitrogen heterocycles is notable for its synthetic versatility, because it shows different nucleophilic positions, making regioselectivity a synthetic challenge. Numerous studies have reported

• functionalize 5-aminopyrazoles. Biologically active compounds featuring a trifluoromethyl carbinol motif. Nucleophilic sites of 5-aminopyrazoles and 4-alkenyl-5-aminopyrazoles. Stereoselective synthesis of trifluoromethyl carbinols through an vinylogous addition reaction of 4-alkenyl-5-aminopyrazoles to alkyl

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

• phosphodiesters by 105–107 by electrophilic activation of ester and nucleophilic activation of water or peroxide at the metal ion [101][102]. The takeaway message is that polarization is most effective when it is bifunctional. In enzymes, there is never just a nucleophile – there is always a metal, “oxyanion hole

• generated large electrostatic effects by functionalizing the capsule exteriors with charged groups (Figure 4D) [136][137]. Observed rate accelerations for capsule-promoted nucleophilic substitution reactions demonstrate significant enthalpic stabilization of the transition state attributable due to the

• nucleophile and electrophile in a glycosylation reaction [105]. (D) An externally charged cavitand promotes charge-stabilized nucleophilic substitution reactions of hydrophobically encapsulated substrates [136][137]. (A) Metal-organic cages and key modes in catalysis. (B) Charged metals or ligands can result

Identification and removal of a cryptic impurity in pomalidomide-PEG based PROTAC

• Bingnan Wang,
• Yong Lu and
• Chuo Chen

Beilstein J. Org. Chem. 2025, 21, 407–411, doi:10.3762/bjoc.21.28

• drug”) class of PROTAC molecules with a PEG linker is frequently used to promote targeted protein degradation. The standard protocol for their synthesis involves nucleophilic aromatic substitution of 4-fluorothalidomide with a PEG-amine. We report herein the identification of a commonly ignored

• impurity generated in this process. Nucleophilic acyl substitution competes with aromatic substitution to displace glutarimide and gives a byproduct that can co-elute with the desired product on HPLC throughout the remainder of the synthesis. Scavenging with taurine is a convenient way to minimize this

• contamination. Keywords: glutarimide; IMiD; impurity; nucleophilic acyl substitution; PROTAC; Introduction Targeted protein degradation capitalizing on the concept of chemically induced dimerization has emerged as a new therapeutic approach recently [1]. In particular, the modularity of proteolysis targeting

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

• glycosylation. Conventional glycosylation involves the ‘nucleophilic substitution’ of the leaving group at the sp3 anomeric centre of the donor moiety with a suitable carbohydrate or non-carbohydrate-based aglycon with the help of an electrophilic promoter to form the equatorial glycoside 7 or the axial

• directions away from the central oxocarbenium ion intermediate in the limiting dissociative process involving diastereomeric ion pairs. Destabilisation and greater reactivity of the oxocarbenium intermediate causes the nucleophilic acceptor moiety to attack in a concerted process following a classical SN2

• the anomeric carbon forming an electron-deficient bicyclic acyloxonium ion intermediate 11 which blocks the α-face of the glycosyl ring, inducing the attack of the nucleophilic acceptor 12 to approach from the opposite face to form the 1,2-trans glycoside 13 primarily. Various protecting groups for

Molecular diversity of the reactions of MBH carbonates of isatins and various nucleophiles

• Zi-Ying Xiao,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2025, 21, 286–295, doi:10.3762/bjoc.21.21

• Zi-Ying Xiao Jing Sun Chao-Guo Yan College of Chemistry & Chemical Engineering, Yangzhou University, Yangzhou 225002, China 10.3762/bjoc.21.21 Abstract In this paper, the nucleophilic substitution reactions of various N- and P-containing nucleophiles to MBH carbonates of isatins were investigated

• have made them to become valuable building blocks in organic synthesis. Nucleophilic additions or spiroannulation of the highly reactive carbonyl group at the C-3 position of isatins have various fascinating applications in organic synthesis, which allowed transformation of isatins into various

• synthetic methodologies and in continuation of our aim to develop domino reactions based on MBH carbonates of isatins for efficient construction of diverse polycyclic spiroindolinones [42][43][44][45][46][47][48][49][50][51][52], herein, we wish to report the nucleophilic substitution reactions of various N

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

• role in most cases is to generate highly reactive species in situ from the nucleophilic reaction component. This can subsequently interact with other reaction components to form target products. Compared to the crotonic condensation products of other aliphatic and aromatic aldehydes, methylidene

Streamlined modular synthesis of saframycin substructure via copper-catalyzed three-component assembly and gold-promoted 6-endo cyclization

• Asahi Kanno,
• Ryo Tanifuji,
• Satoshi Yoshida,
• Sota Sato,
• Saori Maki-Yonekura,
• Kiyofumi Takaba,
• Jungmin Kang,
• Kensuke Tono,
• Koji Yonekura and
• Hiroki Oguri

Beilstein J. Org. Chem. 2025, 21, 226–233, doi:10.3762/bjoc.21.14

• antitumor activity, triggered by DNA alkylation [6][7][8]. The aminonitrile/hemiaminal at C21 generates an iminium cation while releasing a cyanide or a hydroxy group under physiological conditions. This iminium cation facilitates nucleophilic attack by guanine residues in the minor groove of the GC-rich

• reaction involves an in situ generation of the iminium cation A followed by isomerization to the thermodynamically more stable iminium cation B. Subsequent nucleophilic attack of a copper acetylide enabled regioselective C–C bond formation at the C11 position. After removal of the cyclic acetal, the

• , was obtained in one-pot, presumably via generation of the aminonitrile 17 and subsequent nucleophilic attack of the phenolic hydroxy group to form the five-membered ring. Our efforts to optimize this one-pot sequence led to the best results, affording 11 in 73% isolated yield, when acetone cyanohydrin

Heteroannulations of cyanoacetamide-based MCR scaffolds utilizing formamide

• Marios Zingiridis,
• Danae Papachristodoulou,
• Despoina Menegaki,
• Konstantinos G. Froudas and
• Constantinos G. Neochoritis

Beilstein J. Org. Chem. 2025, 21, 217–225, doi:10.3762/bjoc.21.13

• the desired thienopyrimidones 5a–e, quinolinopyrimidones 6a–e and indolopyrimidones 7a–e, respectively, as reported in the literature [42][44]. In accordance with the reported mechanism, after the initial formylation of the amino group at position 2, an intramolecular nucleophilic attack by the NH

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

• electrophiles in various nucleophilic transformations due to their susceptibility to rapid decomposition into the corresponding isocyanates (Scheme 1a) [2][3]. They have attracted increasing interest as electrophilic amide sources in amidation using transition-metal catalysts such as ruthenium, rhodium, and

• 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

Recent advances in electrochemical copper catalysis for modern organic synthesis

• Yemin Kim and
• Won Jun Jang

Beilstein J. Org. Chem. 2025, 21, 155–178, doi:10.3762/bjoc.21.9

• standard Cu-catalyzed electrochemical protocol. Based on mechanistic studies, the proposed mechanism is shown in Figure 9. First, hydroquinone 34 is oxidized at the anode to generate a quinone intermediate 38. Meanwhile, the chiral copper catalyst reacts with the Schiff base 33, generating a nucleophilic

• standard conditions. Subsequently, radical-polar coupling between electrophilic Ni-bound α-carbonyl radical intermediate 45 and remaining nucleophilic Cu-enolate 44 provides a chiral product 42 containing vicinal quaternary stereocenters with high stereoselectivity, and all three possible stereoisomers of

• an alkene to generate a radical intermediate, followed by oxidation, which enables radical-polar crossover (RPC) and the subsequent nucleophilic attack of the cationic intermediate [67]. Alternatively, the initial radical intermediate can be trapped by a transition-metal catalyst, followed by a cross

Cu(OTf)₂-catalyzed multicomponent reactions

• Sara Colombo,
• Camilla Loro,
• Egle M. Beccalli,
• Gianluigi Broggini and
• Marta Papis

Beilstein J. Org. Chem. 2025, 21, 122–145, doi:10.3762/bjoc.21.7

• to multiple C–C bonds generates extended carbon radicals capable of giving further functionalization. Regarding the ionic mechanism, the key step generally comprises the complexation with the unsaturated substrate leading to activation of the alkenyl/alkynyl moiety towards a nucleophilic attack. In

• some cases, activation of a carbonyl group by the copper catalyst to facilitate nucleophilic attack has also been reported. Moreover, both activations can be operative simultaneously. Since copper shows affinity either for multiple C–C bonds or polar functional groups, it seems the ideal tool for this

• (Scheme 16) [33]. The reaction, which occurs with formation of C–C, C–N and C–O bonds, involves a nucleophilic addition of the activated alkyne XIV to the in situ-generated iminium ion XV, followed by cyclization to form a quinoxalin-2-one intermediate XVI. A subsequent 5-endo-dig cyclization involving

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

• intermediate Int-9. As the assumed rate-determining step the intramolecular nucleophilic addition takes place, followed by further cyclization and finally, release of the organocatalyst to form the axially chiral product 9. Various aryl-substituted indolines 9 were obtained in good yields and high enantiomeric

• enantioselectivity during the nucleophilic addition, and the subsequent aromatization completes central-to-axial chirality conversion delivering products 68. Dynamic kinetic resolution of naphthylindoles 69 was performed by reaction with bulky electrophiles such as azodicarboxylates 70 or o-hydroxybenzyl alcohols 72

• . The proposed reaction pathway follows hydrogen bonding with alkynylnaphthylamine and later nucleophilic addition of the allene intermediate. The synthesis on the preparative scale provided product 183 with almost no deterioration in yield or enantioselectivity (90%, 91% ee). This product could then be

Emerging trends in the optimization of organic synthesis through high-throughput tools and machine learning

• Pablo Quijano Velasco,
• Kedar Hippalgaonkar and
• Balamurugan Ramalingam

Beilstein J. Org. Chem. 2025, 21, 10–38, doi:10.3762/bjoc.21.3

• , photoredox-catalytic, and nucleophilic aromatic substitution reactions, as well as in the two-step synthesis of cyclobutanone. The molecules synthesized under the optimal conditions are presented in Figure 6b, employing the stable noisy optimization by branch and fit (SNOBFIT) algorithm. SNOBFIT offers a

Synthesis, characterization, and photophysical properties of novel 9‑phenyl-9-phosphafluorene oxide derivatives

• Shuxian Qiu,
• Duan Dong,
• Jiahui Li,
• Huiting Wen,
• Jinpeng Li,
• Yu Yang,
• Shengxian Zhai and
• Xingyuan Gao

Beilstein J. Org. Chem. 2024, 20, 3299–3305, doi:10.3762/bjoc.20.274

• available 2-bromo-4-fluoro-1-nitrobenzene, featuring a noble-metal-free system, mild reaction conditions, and a good yield, especially for the final Cs2CO3-facilitated nucleophilic substitution (77–91% yield). The characterization data obtained from IR and NMR spectroscopy (1H, 13C, 19F, and 31P) as well as

• hand, we turned our attention to the synthesis of PhFlOP-based compounds through a Cs2CO3-facilitated nucleophilic substitution with substituted carbazoles as the nucleophiles (Scheme 2). For example, tert-butyl, bromo, carbazolyl, or phenyl substituents were introduced into the carbazoles. To our

Reactivity of hypervalent iodine(III) reagents bearing a benzylamine with sulfenate salts

• Beatriz Dedeiras,
• Catarina S. Caldeira,
• José C. Cunha,
• Clara S. B. Gomes and
• M. Manuel B. Marques

Beilstein J. Org. Chem. 2024, 20, 3281–3289, doi:10.3762/bjoc.20.272

• in electrophilic transfer reactions, with emphasis on umpolung reactivity of usually nucleophilic functional groups. Thus constituting a powerful synthetic tool, opening room for new synthetic disconnections [10]. Within the benziodoxol(on)e class, a range of HIRs featuring nitrogen-containing groups

• reaction (Table 1, entry 1) [4]. In the presence of potassium carbonate, only starting material 4a was detected. A stronger base to generate the nucleophilic intermediate was tested, and sulfonamide 5aa was detected in trace amounts (Table 1, entry 2). Considering the low solubility of the hypervalent

Efficient synthesis of fluorinated triphenylenes with enhanced arene–perfluoroarene interactions in columnar mesophases

• Yang Chen,
• Jiao He,
• Hang Lin,
• Hai-Feng Wang,
• Ping Hu,
• Bi-Qin Wang,
• Ke-Qing Zhao and
• Bertrand Donnio

Beilstein J. Org. Chem. 2024, 20, 3263–3273, doi:10.3762/bjoc.20.270

• chains and derived from the classical triphenylene core self-assembling in columnar mesophases based on this paradigm. These mesogenic compounds were simply obtained in good yields by the nucleophilic substitution (SNFAr) of various types of commercially available fluoroarenes with the electrophilic

• subsequent second annulation, yielding a new series of extended polyaromatic mesomorphic compounds, i.e., 1,1',3,3',4,4'-hexafluoro-6,6',7,7',10,10',11,11'-octaalkoxy-2,2'-bitriphenylene (Gnm) which were found to display a Colrec mesophase. The specific nucleophilic substitution patterns of the Fn

• red-shift of the emission peak. Keywords: arene–perfluoroarene interaction; decafluorobiphenyl; fluorinated triphenylene; fluoroarene nucleophilic substitution; organolithium; Introduction Non-covalent arene–fluoroarene intermolecular interactions [1][2] are drawing increasing attention due to their

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

• hydrogen bonding with the protonated tertiary amine. Then, a Michael addition of malononitrile to the azadiene takes place to obtain exclusively the (S)-intermediate A. Subsequently an intramolecular nucleophilic addition of the nitrile leads to the intermediate B, which undergoes tautomerization to

• -derived azadiene by H-bonding. This dual activation promotes a stereoselective addition of 3-chlorooxindole to the azadiene leading to intermediate A. The latter is also activated by the chiral guanidine and undergoes an intramolecular nucleophilic substitution which delivers the product 19b with the

• the nitrogen atoms. Then, the azlactone enolate undergoes a nucleophilic attack on its Si-face via Mannich reaction with the 2-benzothiazolimine leading to intermediate A which evolves toward its resonance form B, responsible of the intramolecular attack of the negatively charged nitrogen to the

Synthesis of 2H-azirine-2,2-dicarboxylic acids and their derivatives

• Anastasiya V. Agafonova,
• Mikhail S. Novikov and
• Alexander F. Khlebnikov

Beilstein J. Org. Chem. 2024, 20, 3191–3197, doi:10.3762/bjoc.20.264

• derivatives [1]. In particular, the catalytic isomerization of 5-chloroisoxazoles allows the generation of azirine-2-carbonyl chlorides, which can be easily converted into a variety of azirine-2-carboxylic acid derivatives by reactions with nucleophilic reagents. Using this approach, numerous 2-(1H-pyrazol-1