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

• carbon atom), and the lowest DG strength if the other two priorities are unambiguous. Figure 2 and Table 1 show examples of the results from running the program with “CCCN(C)C(=O)c1ccc(C(=O)c2ccccc2)cc1” as the input SMILES string. The sites marked with red indicate the predicted reaction sites. The

Synthetic approach to borrelidin fragments: focus on key intermediates

• Yudhi Dwi Kurniawan,
• Zetryana Puteri Tachrim,
• Teni Ernawati,
• Faris Hermawan,
• Ima Nurasiyah and
• Muhammad Alfin Sulmantara

Beilstein J. Org. Chem. 2025, 21, 1135–1160, doi:10.3762/bjoc.21.91

• , successfully processing up to 15 g of starting material. Compound 93 was reduced to its corresponding aldehyde using DIBAL-H, followed by Horner–Wadsworth–Emmons (HWE) olefination with (EtO)2P(O)CH2COSEt, resulting in the unsaturated thioester 95. Reapplying the 1,4-addition reaction conditions to 95 produced

• 70% overall yield across three steps, with a dr exceeding 98:2. The reaction continued with the reduction of thioester 98 to aldehyde 99, followed by HWE olefination with (EtO)2P(O)CH2COMe, yielding compound 100 in 92% yield (Scheme 16). The stereocontrol achieved by the catalysts was again

• acetal in the presence of Hoveyda–Grubbs’ second-generation catalyst, affording aldehyde 112 in 75% yield as the E-isomer after a careful acidic workup. Finally, HWE olefination of aldehyde 112 with (EtO)2P(O)CHBrCN completed the synthesis of fragment 62b of borrelidin. Minnaard and Madduri emphasized

Investigations of amination reactions on an antimalarial 1,2,4-triazolo[4,3-a]pyrazine scaffold

• Henry S. T. Smith,
• Ben Giuliani,
• Kanchana Wijesekera,
• Kah Yean Lum,
• Sandra Duffy,
• Aaron Lock,
• Jonathan M. White,
• Vicky M. Avery and
• Rohan A. Davis

Beilstein J. Org. Chem. 2025, 21, 1126–1134, doi:10.3762/bjoc.21.90

• purified by the Davis group [8]. In vitro antiplasmodial image-based assay Plasmodium falciparum 3D7 were cultured in RPMI1640 (Life Technologies, Camarillo, CA, USA) supplemented with 2.5 mg/mL Albumax II, 5% AB human serum, 25 mM HEPES, and 0.37 mM hypoxanthine. Human red blood cells (RBC) (O+) were

Gold extraction at the molecular level using α- and β-cyclodextrins

• Susana Santos Braga

Beilstein J. Org. Chem. 2025, 21, 1116–1125, doi:10.3762/bjoc.21.89

• cations, the geometry is different from that observed in {α-CD·[K(OH2)6]+[AuBr4]−}n, because coordination of Rb+ and Cs+ takes place both at OH groups and at the O atoms of the glucopyranosyl ring in the CD tori (Figure 2, right). This strong coordination, in cooperation with the geometrically favourable

• (left) and the 2:1 (right) complexes, showing the positions of K+ cations and Au(CN)2− anions as well as the relative dispositions of the α-CD tori. Adapted with permission from [49], Liu, W.; Jones, L. O.; Wu, H.; Stern, C. L.; Sponenburg, R. A.; Schatz, G. C.; Stoddart, J. F. Supramolecular gold

• . C skyblue, O red, Br brown, Au yellow. (c) Schematic illustration of the mechanism leading to precipitation (named “supramolecular polymerisation” by the authors) after adding various additives to the solution of β-CD and [AuBr4]− anions. Reproduced from [51] (© 2023 H. Wu et al., published by

Supramolecular assembly of hypervalent iodine macrocycles and alkali metals

• Krishna Pandey,
• Lucas X. Orton,
• Grayson Venus,
• Waseem A. Hussain,
• Toby Woods,
• Lichang Wang and
• Kyle N. Plunkett

Beilstein J. Org. Chem. 2025, 21, 1095–1103, doi:10.3762/bjoc.21.87

• bonding is characterized as those interactions that involve intermolecular hypervalent connections with lengths shorter than the sum of the van der Waals radii between a heavy p-block element and an electron-pair donor (typically O, N, S, or halogen) [15]. Secondary I···O interactions have been found to

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

• methodologies based on the functional groups of cinnamic acid reported in the last five years: modifying the carboxyl group can involve several pathways, such as O/N-acylation, oxidative acylation, alkenyl/alkynyl carboxylation, and other reactions. Altering the double bond can be approached through double-bond

• these derivatives, this study aims to offer direct synthetic guidance and important insights into the rational design of novel cinnamate molecules with promising potential as future drug candidates. The reaction mechanisms will be discussed briefly. 2 Carboxyl group functionalization 2.1 O/N-acylations

• 2.1.1 Stoichiometric reagents: Anhydride formation is one reliable method to activate the carboxylic group of cinnamic acid. For instance, in 2020, Longobardo and DellaGreca utilized isobutyl chloroformate in water to construct an O-protected amide derivative 2 of hydroxycinnamic acid 1 with an

Biobased carbon dots as photoreductants – an investigation by using triarylsulfonium salts

• Valentina Benazzi,
• Arianna Bini,
• Ilaria Bertuol,
• Mariangela Novello,
• Federica Baldi,
• Matteo Hoch,
• Alvise Perosa and
• Stefano Protti

Beilstein J. Org. Chem. 2025, 21, 1024–1030, doi:10.3762/bjoc.21.84

• carbon nanomaterials category in view of their stability, water affinity/dispersibility, and low toxicity [1][2][3][4]. Such nanomaterials significantly absorb in the 280–350 nm region due to a wide range of π–π* (C=C) and n–π* (C=O) transitions in both the core and on the surface of the particles. CDs

• * transition of the sp2 C=C conjugated system), 265–280 nm (in turn ascribed to the n–π* transition of the C=O group on the surface), and 350–360 nm (due to the n–π* transition of defects states). The spectra of both doped and undoped CDs obtained from citric acid are mainly comparable (see Figure 1), with a

Studies on the syntheses of β-carboline alkaloids brevicarine and brevicolline

• Benedek Batizi,
• Patrik Pollák,
• András Dancsó,
• Péter Keglevich,
• Gyula Simig,
• Balázs Volk and
• Mátyás Milen

Beilstein J. Org. Chem. 2025, 21, 955–963, doi:10.3762/bjoc.21.79

• Pharmaceuticals Plc., Directorate of Drug Substance Development, P. O. Box 100, Keresztúri út 30-38, H-1475 Budapest, Hungary Department of Organic Chemistry, Faculty of Pharmacy, Semmelweis University, Hőgyes Endre utca 7, H-1092 Budapest, Hungary Center for Pharmacology and Drug Research & Development

Harnessing tethered nitreniums for diastereoselective amino-sulfonoxylation of alkenes

• Shyam Sathyamoorthi,
• Appasaheb K. Nirpal,
• Dnyaneshwar A. Gorve and
• Steven P. Kelley

Beilstein J. Org. Chem. 2025, 21, 947–954, doi:10.3762/bjoc.21.78

• regioselective, diastereoselective, and metal-free protocol for alkene amino-hydroxylation, which compared favorably to prior art in this area [25][26][27][28][29][30][31][32]. Naturally, we wondered if other O-nucleophiles were competent in the ring-opening of the aziridinium intermediate. Indeed, almost all

Study of tribenzo[b,d,f]azepine as donor in D–A photocatalysts

• Katy Medrano-Uribe,
• Jorge Humbrías-Martín and
• Luca Dell’Amico

Beilstein J. Org. Chem. 2025, 21, 935–944, doi:10.3762/bjoc.21.76

• computational study to design new PCs to be employed in atom transfer radical polymerization (O-ATRP) [17]. Notably, the sulfur-based structure 2 showed excellent performance for this transformation. One year later, the same research group reported its use in a reversible addition-fragmentation chain-transfer

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

• involving the Ugi reaction between arylglyoxals 1, benzylamines 2, o-azidobenzoic acid (3), and cyclohexyl isocyanide (4a), followed by a triphenylphosphine-promoted tandem Staudinger/aza-Wittig cyclization (Scheme 1a) [33]. The overall strategy was enabled by the presence of an azide group in the

• trifluoromethyl and nitro groups. Furthermore, substrates 15m–o derived from aliphatic amines, also performed well, furnishing pyrazolodiazepines 16m–o in up to 89% yield. The structure of 16m, a representative compound of this series, was confirmed through single-crystal X-ray diffraction (scXRD) analysis

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

• , thereby offering unprecedented control over chemo-, regio-, and stereoselectivity parameters in catalytic manifolds. In 2015, the Jiang group developed a palladium-catalyzed regioselective three-component C1 insertion reaction (Scheme 1) [19]. In this reaction, an o-iodoaniline 1, phenylacetylene, and

• carbon monoxide were used as starting materials, and two natural product frameworks of phenanthridone and acridone alkaloids could be selectively obtained by controlling ligands. The reaction of o-iodoaniline with in situ-generated arynes under CO atmosphere under ligand-free conditions selectively

• intermediates Int-53 or Int-53'. Reductive elimination of Int-53 or Int-53' regenerates Pd(0) and produces intermediate 55. With the assistance of the base K2CO3, the ten-membered silacycle 55 undergoes rapid ring contraction via cleavage of two Si–O bonds and formation of one Si–O bond, leading to 56 and Int

Cu–Bpin-mediated dimerization of 4,4-dichloro-2-butenoic acid derivatives enables the synthesis of densely functionalized cyclopropanes

• Patricia Gómez-Roibás,
• Andrea Chaves-Pouso and
• Martín Fañanás-Mastral

Beilstein J. Org. Chem. 2025, 21, 877–883, doi:10.3762/bjoc.21.71

• species A which is in equilibrium with the Cu–O enolate B [11]. In the presence of excess of LiOt-Bu, a salt metathesis reaction between this base and intermediate B generates lithium enolate C and LCuOt-Bu to close the copper catalytic cycle. The formation of a lithium enolate is consistent with the

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

• carbonyl (C=O) groups, as well as direct ion-pairing interactions between 18-crown-6-complexed Cs+ and hexaurea-bound PO43−. Single-crystal structural analysis corroborates these interactions, shedding light on the underlying mechanisms and providing valuable guidance for the rational design of advanced

• , only two examples provide clear evidence of cooperative interactions based on single crystal structures [28][29], where the 18-crown-6 complexed K+ cation forms ion-dipole interactions with the carbonyl (C=O) or nitro (NO2) groups of the anion-bound receptors (KF and K2CO3). Recently, we demonstrated

• interactions between K+ and C=O moieties [31], similar to these seen in the single crystal structures of KF and K2CO3 complexes. These provide a promising opportunity that can be used to identify the cooperative interaction underpinning complexed ions in dual-host strategy-based extraction. To do this, the

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

• -hybridized carbon atom directly bonded to the nitrogen atom of the secondary amino group of compound 5a. In the structure of each pyrrolidine-2,3-dione derivative 3a–e, there is an α,β-unsaturated ketone moiety in which the π systems of the C=C and C=O bonds could overlap each other to yield an extended

• a dihedral angle of 49.86(10) 86.22(11)° with the phenyl rings C6–C11 and C18–C23, respectively. The angle between both phenyl rings is 70.76(11)°. The stereochemistry around the double bond is Z, allowing an intramolecular N–H···O hydrogen bond between one of the carbonyl oxygen atoms and the amino

• group (Table S2 in Supporting Information File 1). The N and C atoms of the 1-methylamino)ethylidene group are coplanar with the pyrrolidine ring (max. deviation of 0.074(2) Å for atom C17). The molecules form inversion dimers through N–H···O hydrogen bonding. Despite the presence of aromatic rings, no

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

• . Starting with 1-((bromoethynyl)sulfonyl)-4-methylbenzene, which was previously prepared and characterized [40][41], Diels–Alder reaction with either cyclopentadiene, furan or Boc-protected pyrrol, resulted in the NBD precursors C-NBD1, O-NBD1 and N-NBD1, respectively [31][42]. With these precursors in hand

• the corresponding boronic acid in a degassed toluene/H2O mixture (4:1, v/v) which was heated to 80 °C for 18 h (for detailed information see Supporting Information File 1). Using the described procedure, the oxygen containing derivatives O-NBD2 and nitrogen substituted N-NBD2 were successfully

• . Photoswitching The photoswitching of the NBDs to corresponding QCs was monitored by UV–vis and 1H NMR spectroscopy. With increasing electronegativity of the bridge-atom, a slight bathochromic shift in the absorption spectra of the parent NBD precursors O-NBD1 and N-NBD1 was found (Figure 2a and 2c). For the

Regioselective formal hydrocyanation of allenes: synthesis of β,γ-unsaturated nitriles with α-all-carbon quaternary centers

• Seeun Lim,
• Teresa Kim and
• Yunmi Lee

Beilstein J. Org. Chem. 2025, 21, 800–806, doi:10.3762/bjoc.21.63

• , ethyl, phenethyl, and allyl groups, also underwent smooth cyanation, resulting in α-quaternary nitriles 3f–i in yields of 85–94%. Furthermore, aryl-substituted allenes 1j–o, incorporating electron-donating or electron-withdrawing substituents such as methyl, fluoro, chloro, bromo, trifluoromethyl, or

• methoxy groups on the phenyl ring, were compatible with the reaction, producing nitriles 3j–o in 88–93% yields. In particular, thienyl-substituted allene 1p was efficiently transformed into the desired nitrile 3p. We further demonstrated the versatility of this protocol using 1,1,3-trisubstituted allenes

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

• that when the reaction was carried out in the presence of TEMPO as a radical scavenger, a side product, TEMPO-P(O)R2, was formed (it was confirmed using high-resolution mass spectrometry). The results revealed that the reaction proceeded in a radical pathway (Scheme 1). Based on the cyclic voltammetry

• derivatives of glycine with diarylphosphine oxide (R2P(O)–H) for the synthesis of 1-aminoalkylphosphine oxides without the use of any transition metal catalyst or external oxidant. In this conversion, 1-aminoalkylphosphine oxides were formed in an undivided cell using a carbon electrode as the anode and

• nickel as the cathode in the presence of tetrabutylammonium bromide (TBAB) at the constant current of 6 mA. The electrodes used in the reaction are all in plate form. The presence of TBAB causes the resulting bromide anion to oxidize to bromine radical and react with R2P(O)–H to produce a radical

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

• that silicon is bound via the carbonyl oxygen in 12, as also shown by DFT computations. This is further corroborated by observation of a 13C NMR signal at 146 ppm for an sp2 carbon in the backbone of the product, which fits better for a C=N than a C=O bond. Recovery of the catalyst resting state 7 is

• -state structure, two bonds (Ca–O and Si–C) are broken, while a Si–O bond is simultaneously formed, in a concerted step implying a cyclic flow of six electrons in a five-membered ring. The isocyanide Ca–N–C bond angle in TS 11-12 lies between that of 7 and 9. While the replacement step is slow, and hence

• (product O=C(C1=CC=C(Br)C=C1)NNC(C#N)CC2=CC=CC=C2, 2’’) contain the supplementary crystallographic data for this paper. These data are provided free of charge by The Cambridge Crystallographic Data Centre via http://www.ccdc.ac.uk/data request/cif. Supporting Information File 32: Synthetic procedures, 1H

Copper-catalyzed domino cyclization of anilines and cyclobutanone oxime: a scalable and versatile route to spirotetrahydroquinoline derivatives

• Qingqing Jiang,
• Xinyi Lei,
• Pan Gao and
• Yu Yuan

Beilstein J. Org. Chem. 2025, 21, 749–754, doi:10.3762/bjoc.21.58

• to be compatible substrates, affording cyclo-O/S-containing STHQ derivatives 3ab and 3ac in good yields. Additionally, ester-functionalized cyclobutanones exhibited smooth reactivity with aniline, enabling the synthesis of substituted STHQ motifs 3ad and 3ae in satisfactory yields. Notably, when

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

• conjugated to the 3- and the 6-position of a methyl mannoside scaffold (Figure 1, 1 (6βGlc3αMan)) [24]. Orthogonal photoswitching of the two glycoantennas is guaranteed by (i) ortho-fluorination of one azobenzene moiety and (ii) S-azobenzene versus O-azobenzene conjugation, resulting in significantly shifted

• 3-O-(mannosyloxyazobenzene)-6-thio-mannoside 11 was employed, which was prepared according to a known procedure applied for the synthesis of the heterobivalent glycocluster 6βGlc3αMan 1 (cf. Supporting Information File 1, Scheme S1). The cross-coupling of thiol 11 with the azobenzene

• α-ᴅ-mannopyranosyloxyazobenzene mannosides 6βGlc 3 and 6αMan 4 were prepared first (Scheme 2A). The synthesis of the β-ᴅ-glucopyranosyl mannoside 6βGlc 3 started from the literature-known S,O-acetylated mannoside 13 [35], which was chemoselectively deprotected at the 6-position employing DTT (1,4

Acyclic cucurbit[n]uril bearing alkyl sulfate ionic groups

• Christian Akakpo,
• Peter Y. Zavalij and
• Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 717–726, doi:10.3762/bjoc.21.55

• , two aromatic o-xylylene walls, and four sulfonates as solubilizing ionic groups. In accord with these structural features, M1 binds a variety of hydrophobic and cationic guest molecules by the hydrophobic effect, π–π interactions, and electrostatic (ion–dipole and ion–ion) interactions. Although

• ][66][67]. Previously, we have studied the influence of the length of the O(CH2)nSO3Na sidearm (n = 0, 2, 3, 4) and found that the M0 host – where the hydrophobic linker (CH2)n was completely removed – displayed higher binding affinity than M1 which we attributed to the location of the ionic group

• closer to the ureidyl C=O portals [68][69]. However, a close examination of the structures of M0 and M1 show that the ionic group for M1 is a sulfonate and for M0 is a sulfate. Accordingly, M1 and M0 differ in two ways: a) different (CH2)n linker length and b) different ionic group (sulfonate versus

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

• fluorine atoms into the structure. The C–F bond has certain fundamental characteristics that enable it to serve as an effective conformational tool (Figure 1) [2][3][4]. First, the C–F bond is quite short at only ≈1.35 Å (cf. ≈1.09 Å for C–H, or ≈1.43 Å for C–O). The short length of the C–F bond, and the

• happens if fluorine is introduced onto one of the carbons that is directly attached to oxygen (Figure 6). This makes possible a hyperconjugative interaction between a lone pair on oxygen and the σ* orbital of the C–F bond (I, Figure 6) [76]. This interaction biases the rotational profile about the O–C(F

• pendant aryl moiety, is better for target-binding and hence 41 is a ≈10-fold more potent inhibitor of BACE-1 than 40. Several further examples of cyclic ethers will be examined in section 5 (sugars). The anomeric effect applies in acyclic ethers, too. Consider the non-fluorinated scaffold, Ph–O–CH3 (42

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

• napthalene-1,5-dicarboxaldehyde was protected as an acetal, was prepared through a 5-step reaction sequence. Phosphonium salt 5 [39] and the partly protected o-phthalaldehyde 6 [47] were obtained by previously reported procedures. The reaction of phosphonium salt 5 with aldehyde 6 in the presence of KOH and

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

• significance of this transformation lies in its unique ability to efficiently create a stereogenic center while forming new carbon–carbon or carbon–heteroatom bonds (e.g., C–N, C–O, and C–S) with excellent selectivities. The field of metal-catalyzed allylic substitution has evolved significantly since its