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

• sphere. The phosphate ligands are in cis-position with respect to each other. The structure of 4 shows similarities to that of a BINOL-derived calcium phosphate complex that also crystallizes with four methanol ligands, creating an octahedral coordination sphere with phosphate ligands in cis-position [52

• ]. As observed earlier [53], cis/trans preferences in octahedral calcium complexes are influenced by small changes in sterics. Further details on the structure of 4 can be found in Supporting Information File 1. Complex 4 appeared to be a well-defined achiral model system for the catalyst combination

• later stages of the catalytic cycle, are less likely to racemize without bond breaking. The barrier to pyramidal inversion has been found to be 15.1 kcal·mol−1. Berry rotation itself proceeds via a tetragonal pyramid as transition-state structure and does therefore not occur here. A second isocyanide

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

• periphery of the FimH form the basis of the higher FimH affinity of the E isomers (as was argued in similar case [15]) (cf. Supporting Information File 1, Figure S25 and Figure S26). A possible allosteric regulation of the CRD structure [55][56], on the other hand, which might be effected by one of the

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

• fluorophore derivatives bind the Pepper aptamer with affinities in the low nanomolar range [12]. Crystal structure analyses revealed that in the ligand binding pocket, a characteristic hydrogen bond is formed between the hydroxy group of the N-hydroxyethyl substituent of HBC and the N7 of G41 [12][13]. We

• . HPLC traces were recorded with UV absorption by 260 nm. Structure-guided approach for engineering the (non-covalent) fluorescent light-up aptamer Pepper into its covalent counterpart [11]. a) Secondary structure of the Pepper aptamer [12]; b) chemical structure of the fluorophore HBC530 [7]; c) three

• -dimensional structure of the Pepper binding site with a bound HBC derivative (pdb code 7EOM). The hydrogen bond between N7 of guanine in position 41 (G41) and the hydroxy group of HBC is highlighted as gray dashed line [12]; d) concept for covalent attachment of HBC fluorophores to the N7 atom of G41 of the

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

• alkyl sulfate ionic groups. The X-ray crystal structure of the C1·Me6CHDA complex is reported. Host C1 is significantly less soluble in water (4 mM) compared to the analogous acyclic CB[n] host M1 which features sulfonate ionic groups (346 mM). Host C1 does not undergo significant self-association

• are acyclic CB[n]-type receptors which have been extensively studied by our lab and others over the past decade [42][43][44][45][46][47][48][49][50][51][52]. Figure 1 shows the chemical structure of the prototypical acyclic CB[n]-type known as M1 [53][54]. M1 features a central glycoluril tetramer

• acyclic CB[n] are not macrocycles, they are preorganized into a C-shaped geometry by virtue of their polycyclic chemical structure and display binding affinities approaching those of macrocyclic CB[n]. M1 and analogues display outstanding biocompatibility and have been used for a number of in vivo

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

• attached to every carbon of an alkyl chain (e.g., II, Figure 4), then a structure results that is conceptually intermediate between alkanes and perfluoroalkanes. Such structures, dubbed “multivicinal fluoroalkanes”, have interesting conformational properties that are dependent upon the stereochemistry [39

• ubiquitous molecules in biology. Their functions permeate every aspect of life, including as essential components of oligonucleotide structure; as principal players in metabolism and energy storage; as motifs for the post-translational modification of proteins; and as partners in myriad supramolecular

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

• serves as a p-channel organic semiconductor [37], whereas perfluoropentacene can be used as an n-channel material [38]. It has been demonstrated that the molecular structure of [7]helicenes was modified by fluorination, thus, the helicenes’ pitch was manipulated by terminal fluorination modes [39][40

• homologue structure, there was a significant contribution from the H–L transition in the α band, presumably because of the difference in the molecular symmetry. Conclusion Octafluorinated phenacenes, F8PIC, F8FUL, and F87PHEN, were conveniently synthesized through the Mallory photoreaction as the key step

Asymmetric synthesis of fluorinated derivatives of aromatic and γ-branched amino acids via a chiral Ni(II) complex

• Maurizio Iannuzzi,
• Thomas Hohmann,
• Michael Dyrks,
• Kilian Haoues,
• Katarzyna Salamon-Krokosz and
• Beate Koksch

Beilstein J. Org. Chem. 2025, 21, 659–669, doi:10.3762/bjoc.21.52

• , which have yet to be described in the context of peptide chemistry. The several CF3 groups employ a strong inductive effect on the aromatic ring structure, making these amino acids highly interesting building blocks for modification of aromatic–aromatic interactions in the context of protein folding

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

• feature at Ep = 1.78 V vs Ag/Ag+ (100 mV/s scan rate; see Figure 3A), and the electrolysis of pyrrolidine 6a under the optimized anodic decarboxylative cyclization conditions (entry 8, Table 1) afforded cyclic hemiaminal 12a (33% NMR yield), whose structure was proved by NMR experiments (Figure 3B). The

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

• such methods are generally reported with a heterogeneous DAR, the group developed a site-specific approach leading to a homogeneous DAR 2, thanks to a photoreactive Fc-binding peptide derivative (pFcBP) containing a photoleucine (pLeu) [46]. By analyzing the X-ray crystal structure of IgG, the

• intermediates can lead to protein denaturation or aggregation [61]. Because photoredox reactions often generate highly reactive species (such as radicals or singlet oxygen), long exposure times could cause unwanted side reactions, including the degradation of 3D structure of the protein or antibody. A short

Semisynthetic derivatives of massarilactone D with cytotoxic and nematicidal activities

• Rémy B. Teponno,
• Sara R. Noumeur and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 607–615, doi:10.3762/bjoc.21.48

• , 4.4 Hz) and H-4 (δH 4.38, dd, J = 4.3, 0.9 Hz, H-4), the trans-2-methyl-2-butenoyl moiety was placed at C-7. The above spectroscopic data combined to the analysis of 2D experiments led to the elucidation of the structure of compound 6 as massarilactone D 7-O-trans-2-methyl-2-butenoyl. The reaction of

• cytotoxic activity of natural products by increasing the hydrophobicity, enhancing cell membrane permeability and binding affinity with intracellular targets [26]. Structure–activity relationships analysis of both hemisynthetic products 2 and 3 revealed a shared conjugated methylene olefinic function that

• , as indicated by structure–activity relationship analysis. Conclusion In the present study, the use of various acylating reagents to modify massarilactone D introduces distinct functional groups, each with unique chemical properties. This approach led to the synthesis of seven previously undescribed

Total synthesis of (±)-simonsol C using dearomatization as key reaction under acidic conditions

• Xiao-Yang Bi,
• Xiao-Shuai Yang,
• Shan-Shan Chen,
• Jia-Jun Sui,
• Zhao-Nan Cai,
• Yong-Ming Chuan and
• Hong-Bo Qin

Beilstein J. Org. Chem. 2025, 21, 601–606, doi:10.3762/bjoc.21.47

• , including insecticidal, antibacterial, anti-inflammatory, analgesic, and neurotrophic activities [3]. In 2013, Wang’s group isolated (±)-simonsol C from star anise, which features a unique 6/5/6 tricyclic benzofuran structure [4]. They found that it exhibits biological activity that promotes neuronal

• oxy-Michael addition from dienone 15. The 6/6/6 tricyclic structure in 15 can be constructed through dearomatization of compound 16, which in turn can be readily synthesized through consecutive alkylation steps starting from magnolol (11). Additionally, using magnolol as the starting material brings

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

• first reacts with the aniline under cobalt(III) catalysis, and the resulting intermediate C then attacks the thionium ion A. Quinolines of general structure II are formed after the loss of methyl sulfide from intermediate D, followed by final cyclization of intermediate E (Scheme 8, path II

• various substitution patterns in the aromatic ring, allowing a high variety of quinolines of general structure I and II. In a related work, quinolines of structure I (Scheme 8) could be obtained by similar reaction pathways. Jadhav et al. proposed a three-component cascade reaction between anilines

• was carried out via copper catalysis or iodine–acid catalysis. Interestingly, when aliphatic amines are employed (R3 = n-Pr, n-Bu, product 8) only the N atoms are incorporated in the structure of the final product, probably because the high temperature favors the elimination of the alkyl group. The

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

• structure of used N-nucleophile various types of a heterocyclic system can be obtained. A large number of examples of reactions with substituted amines have been reported in the literature. Generally, this process includes opening of the furanone ring followed by cyclization to the pyrrolone moiety [6][7][8

• recyclization can be extended for the synthesis of relative isoxazolone 11. In this case the reaction of furanone 1c with hydroxylamine hydrochloride 12 also was carried out in refluxing EtOH for 8 h (Scheme 7). All prepared products 8, 10 and 11 are solid crystalline compounds whose structure was proved by 1H

• units was isolated (Scheme 9). The structure of synthesized compound 13 was unambiguously confirmed by X-ray diffraction. Conclusion In summary, we studied the interaction of 2H-furo[3,2-b]pyran-2-one derivatives with various amines and hydrazines. It was demonstrated that, depending on the nature of

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

• 3aa–ca in good yields (47–69%). On the other hand, the reaction with tetrahydro-4H-pyran-4-one (1d) occurred with a significant decrease in yield, dropping to 11%. The yield is also affected by the number of carbon atoms of the starting cyclic ketone 1. In the case of structure 3ea, which involves 2

• chromatography. Diastereoisomeric ratio (dr) determined by 1H NMR of the crude reaction mixture. Plausible mechanism and X-ray structure of compound 5aca. Optimization of the reaction conditions.a Supporting Information Supporting Information File 14: Detailed experimental procedures, characterization data, and

Cryptophycin unit B analogues

• Thomas Schachtsiek,
• Jona Voss,
• Maren Hamsen,
• Beate Neumann,
• Hans-Georg Stammler and
• Norbert Sewald

Beilstein J. Org. Chem. 2025, 21, 526–532, doi:10.3762/bjoc.21.40

• connected to the homing device by a linker. For covalent attachment of the drug to the linker a suitable functional group is needed such as an amino, hydroxy, carboxy or sulfhydryl group [7]. Since the cryptophycins’ discovery, considerable efforts were made for the establishment of structure–activity

• of, firstly, m-chloro-p-(methylamino) derivative 1 to dissect the structure–activity relationship between the primary (IC50(CCRF-CEM) = 0.58 nM), secondary, and tertiary amine (IC50(CCRF-CEM) = 54 pM) derivatives [20]. Secondly, p-(dimethylamino) derivative 2 was synthesised to investigate the effect

• control of equivalents and pH, or Leuckart–Wallach-like reaction with ammonium formate and Pd/C [25] provided monomethylaniline 7 in 37% and 35% yield, respectively. The absolute structure of monomethylaniline 7 was confirmed by single-crystal X-ray diffraction measurements (Figure 2). Compound 7

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

• photochemical reaction. Its structure was elucidated by NMR spectroscopy and single crystal X-ray diffractometry. The latter revealed no π–π interaction between neighboring ANTH cores. A combination of high photoluminescence quantum yield (PLQY) of 0.85 for 9,10-ANTH(BnF)2, its significantly improved

• ratio was found to be 1.74 (theoretical = 1.75), confirming the composition to be ANTH(BnF)2. Slow evaporation of a CH2Cl2 solution of 9,10-ANTH(BnF)2 at 2 °C afforded off-white plates suitable for X-ray diffraction. The structure shown in Figure 2 (top panel) confirmed the 9,10-substitution pattern

• , whereas 9,10-ANTH(BnF)2 loses vibronic structure in the emission spectrum. This may be the result of different conformations upon relaxation [31]. The HOMO–LUMO gap (Eg) decreases from ANTH (3.28 eV) to 9,10-ANTH(BnF)2 (3.05 eV). A decrease in Eg is regarded as one of the methods for improving the

Unprecedented visible light-initiated topochemical [2 + 2] cycloaddition in a functionalized bimane dye

• Metodej Dvoracek,
• Brendan Twamley,
• Mathias O. Senge and
• Mikhail A. Filatov

Beilstein J. Org. Chem. 2025, 21, 500–509, doi:10.3762/bjoc.21.37

• E. M. Kosower in 1978. In this study, we report the topochemical cycloaddition of diethyl 2,6-dichloro-1,7-dioxo-1H,7H-pyrazolo[1,2-a]pyrazole-3,5-dicarboxylate (Cl2B), initiated by visible light. Crystal structure analysis confirmed that the reactive double bonds are parallel and coplanar, in line

• compounds used thus far is likely due to reliance on their ability to undergo π-stacking interactions, which facilitate face-to-face packing. Therefore, the discovery of a new type of structure capable of undergoing this reaction, as reported here, represents a significant advancement, enabling the

• development of a novel scaffold for topochemically active monomers. Bimanes Bimanes, a class of bicyclic compounds first synthesized by Kosower and Pazhenchevsky in 1978 [16], are based on a 1H,7H-pyrazolo[1,2-a]pyrazole-1,7-dione scaffold. The general structure of a bimane is depicted in Figure 1a. The term

Synthesis of N-acetyl diazocine derivatives via cross-coupling reaction

• Thomas Brandt,
• Pascal Lentes,
• Jeremy Rudtke,
• Michael Hösgen,
• Christian Näther and
• Rainer Herges

Beilstein J. Org. Chem. 2025, 21, 490–499, doi:10.3762/bjoc.21.36

• azobenzenes, spiropyranes and diarylethenes in organic solvents [3][13][15]. There are two strategies of applying diazocines in photopharmacology. The first one exploits the structural similarity of the tricyclic diazocine framework to the tricyclic structure of, e.g., tetrahydrodibenzazocines [16][17] and

• because the design of a photoswitchable agent usually starts with a known, non-switchable drug or a known biological molecule, which is already carefully "optimized" either by pharmaceutical industry or by nature. Hence, there is a high risk that any change in structure will also lead to a reduction in

• substitution. Substituents such as halogen atoms must be introduced into the N-acetyl diazocine structure during the synthesis of the building blocks. In the present work we start from mono- and dihalogenated N-acetyl diazocine 2–4 (Figure 2) and focus on the further derivatization via cross-coupling reactions

Electrochemical synthesis of cyclic biaryl λ³-bromanes from 2,2’-dibromobiphenyls

• Andrejs Savkins and
• Igors Sokolovs

Beilstein J. Org. Chem. 2025, 21, 451–457, doi:10.3762/bjoc.21.32

• extractive workup followed by reversed-phase chromatography and its structure was unambiguously confirmed by X-ray crystallography (Table 1, graphic). Gratifyingly, a two-fold increase in the yield was achieved by a slight reduction of the current density to j = 8 mA·cm−2 (entry 2 vs entry 1 in Table 1). A

• : Representative jp vs v0.5 slope values for oxidation of Martin’s bromane precursor 6 (ref. [17]). D: Plausible reaction mechanism. Optimization of electrochemical oxidation/cyclization conditions.a Supporting Information Crystallographic data for the structure reported in this paper have been deposited with the

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

• exploiting emergent geometric rules and post-assembly modifications; (3) improved screening and collection of detailed structure–activity-relationship (SAR) data for modular systems to allow systematic design, rational and computational development, and identification of novel activity. These developments

• constriction (ground-state destabilization) are also possible [140][168][169][170]. The metals can sometimes participate in redox catalysis [171], and may be stabilized by the cage structure [160][172][173][174]. The organic part of the MOC has also been levied as a hydrogen-bond donor to activate an

• chemistry [200]. “Switchable” metal-organic cages [212] use a stimulus like light to change ligand geometries. This often triggers disassembly since new geometries can lead to new thermodynamic minima, though where geometric changes are tolerated within the original structure the stimuli can trigger guest

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

• compared to the C–C bond by 2.4 kcal/mol further supports the above statement [44]. Next, we have compared the above o-carborane-fused pyrazoles with a series of reference systems with the aim to better understand the electronic structure of the fused heterocycle and its aromaticity (Figure 3). First, the

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

• characterisation of the isolated samples significantly arduous and faulty. Therefore, the syntheses of these important carbohydrates through chemical means became inevitable to elucidate the structure unambiguously and to get hold of their biological implications with minimal doubt [17]. The oligosaccharide

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

• determined. The structure of 2-(3,3-dimethyl-3H-benzo[g]indolin-2-yl)-5,6,7-trichloro-1,3-tropolone was determined by X-ray diffraction analysis. The compounds obtained are capable of switching emission at 420–440 nm and 476–530 nm upon successive exposure to CN− and Hg2+ ions in an acetonitrile solution. 2

• ; Introduction 1,2-Benzoquinones represent unique building blocks for various classes of heterocyclic systems. Their structure depends on the reactivity of the initial heterocycles and 1,2-benzoquinones, as well as on the reaction conditions. In the series of 2-methylquinolines [1], 2-methylquinoxalines [2], 2

• reaction of o-chloranil with benzoannelated derivatives of 2,3,3-trimethylindolenine, a comprehensive evaluation of the structure of the compounds obtained using quantum chemical methods, X-ray diffraction analysis, two-dimensional correlation NMR spectroscopy, as well as investigation of their ionochromic

Synthesis, characterization, antimicrobial, cytotoxic and carbonic anhydrase inhibition activities of multifunctional pyrazolo-1,2-benzothiazine acetamides

• Ayesha Saeed,
• Shahana Ehsan,
• Muhammad Zia-ur-Rehman,
• Erin M. Marshall,
• Sandra Loesgen,
• Abdus Saleem,
• Simone Giovannuzzi and
• Claudiu T. Supuran

Beilstein J. Org. Chem. 2025, 21, 348–357, doi:10.3762/bjoc.21.25

• oxygen atom [50]. Preferential N-alkylation (over O-alkylation) of 1,2-benzothiazine scaffolds has also been carried out by Ahmad and co-workers in 2014 and Szczęśniak-Sięga and companions in 2018 [37][51]. Structure elucidation of all the synthesized derivatives was carried out using 1H, 13C NMR, and

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

• data, they luminesce in DMSO solution when irradiated with light at wavelengths of 352 and 283 nm. Compounds 7a–f are capable of existing as lactim–lactam tautomers due to the presence of an amide fragment in their structure (Scheme 7). At the same time, the 1H and 13C NMR spectra of compounds 7a–f

• phase and visualized under UV light (λ 254 nm). X-ray structure determination X-ray diffraction studies of single crystals of compounds 5a, 5b, 6b, 6c, and 7a were carried out on a Bruker D8 QUEST diffractometer. The cell parameters and experimental data were obtained at 100 K (graphite monochromator

• , λMo Kα = 0.71073 Å, ω and φ scanning in 0.5° steps) at the distributed spectral-analytical center of shared facilities for study of structure, composition and properties of substances and materials of FRC Kazan scientific center of Russian academy of sciences. Crystals of compounds suitable for X-ray