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

• the double bond to the carbonyl in a relative re-si approach, generating intermediate I, which undergoes a tautomerization to recover the aromatic pyrazole ring. The increased yield observed in some cases with SQ-1 may be attributed to the formation of additional hydrogen bonds that enhance

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

• groups play a role by increasing the number of hydrogen bonds (C–H···O, 3.18(5)–3.62(6) Å) The intermolecular distances between the C–H groups and the chlorine atoms in Cl2B (A) are C13A–H13···Cl1A, 3.69(5), and C18A–H18C···Cl2A, 3.69(3) Å, indicating further molecular attraction [22]. A previously

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

• coordinative bonds on one side and hydrogen bonds on the other. Surprisingly, when the crystals were manually ground for 5 min before irradiation, the conversion to dimer 1.2 remarkably increased to 88% in only 4 h of UV irradiation time. Overall, the role of manual grinding was not only to increase 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

• ]. Chemists thus turned toward scaffolds that were easier to access [36][111]. Self-assembled containers, capsules, nanoreactors In the 1990s, Rebek popularized “softball”/”tennis ball” reactors [112][113][114]. These “capsules” [115][116][117] are two or more molecules that self-assemble via hydrogen bonds

• the cage framework to polarize adjacent aryl–hydrogen bonds in the ligands by enough to coordinate and activate substrates (Figure 5E) [190]. Here, the use of bulky counteranions reinforces the cationic cage interior, which is enhanced further by use of lower polarity solvents, and the pKa of confined

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

• region of the DNA double helix, leading to the formation of a reversible covalent bond [9][10][11][12]. In this process, the oxygen functional groups at the C8 and C18 positions of the core scaffold interact with the DNA bases through multipoint hydrogen bonds (HBs), allowing recognition of approximately

Hydrogen-bonded macrocycle-mediated dimerization for orthogonal supramolecular polymerization

• Wentao Yu,
• Zhiyao Yang,
• Chengkan Yu,
• Xiaowei Li and
• Lihua Yuan

Beilstein J. Org. Chem. 2025, 21, 179–188, doi:10.3762/bjoc.21.10

• aromatic amide macrocycles [36][37][38][39][40][41][42], a class of cyclic compounds comprising a number of aromatic residues with consecutive intramolecular hydrogen bonds and amide linkages, stand out as versatile host molecules as their cavity size, peripheral side chains, and recognition sites are

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

• the azodicarboxylate as crucial to forming hydrogen bonds with the organocatalyst. Benzylation of this nitrogen or substitution of just one of the carboxylate groups led to no product being observed. A series of naphthylindoles 71 was tested for potential biological activity and showed promising

• with key hydrogen bonds between substrates, organocatalyst, and HFIP. Sheng et al. utilized the BINOL-derived organocatalyst C34 in the reaction of benzylindoles 148 and 2-indolylmethanols 149 leading to the bisindoles 150 (Scheme 44) [72]. Very good yields and good to high enantioselectivities were

• racemization process of 161 was observed at 70 °C, and the experimentally determined rotational barrier of 30.5 kcal/mol was observed at 100 °C in toluene. Control experiments gave insights into the potential importance of hydrogen bonds on the nitrogen atoms of the isoindolinone ring in 160 and one indole

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

• , commonly referred to as sulfa drugs. These include top seller drugs, e.g., antimicrobials, anti-inflammatories, antihypertensives, and antitumor agents [24][25][26]. Particularly, the sulfonamide motif can act as a bioisostere of carboxylic acids, establishing a set of hydrogen bonds similar to those

Synthesis of extended fluorinated tripeptides based on the tetrahydropyridazine scaffold

• Thierry Milcent,
• Pascal Retailleau,
• Benoit Crousse and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2024, 20, 3174–3181, doi:10.3762/bjoc.20.262

• phenylalanine) indicate that they are not involved in hydrogen bonds. Furthermore, the 2D 1H-1H NOE NMR spectra and the chemical shifts of the NH protons of compounds 8f’, 8e, and 8e’ did not show any significant differences compared to 8f. Overall, the ability of the new fluorinated β-analogs of

Advances in the use of metal-free tetrapyrrolic macrocycles as catalysts

• Mandeep K. Chahal

Beilstein J. Org. Chem. 2024, 20, 3085–3112, doi:10.3762/bjoc.20.257

• adopts a 1,3-alternate conformation and binds simultaneously to the epoxide O-atom and iodide anion via (NH···O and NH···I) hydrogen-bonding interactions. The TBA countercation is bound to the O-atom of the epoxide ring with hydrogen bonds and is situated away from the I− anion. This crucial transition

• ) via NH+···O2 hydrogen bonds initiated the ORR, whereas an increase in the HTB concentration inhibited the ORR by blocking NH+ binding sites for O2. Further, the role of the proton source on ORR was confirmed by testing a stronger acid, TFA: in this case, the O2 reduction rate is decreased to almost

Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• nature of the rotaxane framework, CD-based polyrotaxane is known to form an aggregation structure by the formation of hydrogen bonds among the CD units [89][90][91][92][93]. Owing to the inclusion structure on the polyrotaxane, it is likely to form a hexagonal packing-type crystalline structure, which is

Photoluminescence color-tuning with polymer-dispersed fluorescent films containing two fluorinated diphenylacetylene-type fluorophores

• Kazuki Kobayashi,
• Shigeyuki Yamada,
• Motohiro Yasui and
• Tsutomu Konno

Beilstein J. Org. Chem. 2024, 20, 2682–2690, doi:10.3762/bjoc.20.225

• short-axis direction of the electron-deficient aromatic ring significantly retards the internal conversion via the formation of H···F hydrogen bonds, leading to a marked blue fluorescence in the crystalline state (Figure 1b) [17][18][19][20]. Recently, the introduction of N,N-disubstituted amino groups

• . Judging from the fact that compounds 1a and 1c form a tight molecular packing via intermolecular H···F hydrogen bonds which suppress non-radiative deactivation in the crystalline state [20][21], we speculated that the polymer dispersion state had lost the intermolecular interactions, which accelerated the

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• intramolecular hydrogen bonds between themselves, with water molecules in aqueous solution, or with guest molecules that fit into host’s cavity [20]. The primary hydroxy groups in the nonhydrated γ-CD (located in the upper/narrow rim; O6 side of the truncated cone) can be coordinated (arranged) in two ways

• (Figure 1): (1) facing inward into the cavity, which creates a belt of hydrogen bonds (the so-called “head–tail” arrangement, “closed” conformation). Notably, in this way, the size of the cavity vestibule is significantly reduced and in the second way (2) they are directed outside the cavity, thus

• enlarging the aperture (“open” configuration). In the “open” configuration, the primary hydroxy groups are not involved in the intramolecular hydrogen-bonding interactions with neighboring OH groups. Relatively weak hydrogen bonds are formed between the secondary hydroxy groups at the wider/lower rim of the

Base-promoted cascade recyclization of allomaltol derivatives containing an amide fragment into substituted 3-(1-hydroxyethylidene)tetronic acids

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

Beilstein J. Org. Chem. 2024, 20, 2585–2591, doi:10.3762/bjoc.20.217

• compound 4t with a cyclohexylamine moiety the final product contains 20% of Z-isomer. At the same time, the considered products are differed by disposition of double and hydrogen bonds in the tetronic acid moiety. So, in the case of hydrazide derivatives the additional nitrogen atom participates in the

• fragments and hydrogen bonds leads to the alteration in chemical behavior. Based on the aforementioned stability of tetronic acids 4 toward action of MeOH we supposed that various derivatives at the hydroxyethylidene group can be synthesized. For example, interaction of compound 4a with hydrazine in

• refluxing EtOH allowed us to obtain substituted enehydrazine 7 (Scheme 5a). The similar condensation with amine 8 led to enamine derivative 9 (Scheme 5b). Based on the data of X-ray analysis compound 7 has the same configuration of double and hydrogen bonds as in the case of starting tetronic acids 4

Synthesis, electrochemical properties, and antioxidant activity of sterically hindered catechols with 1,3,4-oxadiazole, 1,2,4-triazole, thiazole or pyridine fragments

• Daria A. Burmistrova,
• Andrey Galustyan,
• Nadezhda P. Pomortseva,
• Kristina D. Pashaeva,
• Maxim V. Arsenyev,
• Oleg P. Demidov,
• Mikhail A. Kiskin,
• Andrey I. Poddel’sky,
• Nadezhda T. Berberova and
• Ivan V. Smolyaninov

Beilstein J. Org. Chem. 2024, 20, 2378–2391, doi:10.3762/bjoc.20.202

• corresponding thiones. The yield of reaction products ranges from 42 to 80%. The crystal structures of catechols with 3-nitropyridine or 1,3,4-oxadiazole-2(3H)-thione moieties were established by single-crystal X-ray analysis. The possibility of forming intra- and intermolecular hydrogen bonds has been

• of neighboring molecules [57][58][59][60][61]. The intra- and intermolecular interactions in crystals 5, 6·0.5CH3CN, and 8 lead to different complex structural motifs in crystals of these compounds. Two intramolecular hydrogen bonds (Figure 1) are observed in the crystal structure of 5: between OH

• heterocycle moiety. The formation of intramolecular hydrogen bonds between the OH group and the pyridine ring facilitates the electrooxidation process (1.,0 V) (Supporting Information File 1, Figure S21) for catechol thioether 5. The second oxidation peak is shifted to the anodic region due to the influence

Factors influencing the performance of organocatalysts immobilised on solid supports: A review

• Zsuzsanna Fehér,
• Dóra Richter,
• Gyula Dargó and
• József Kupai

Beilstein J. Org. Chem. 2024, 20, 2129–2142, doi:10.3762/bjoc.20.183

• binding with an electron-withdrawing group. This acidity can result in stronger hydrogen bonds between the substrate and the catalyst C30, which contains a bis(trifluoromethyl)phenyl-modified squaramide moiety. This stronger interaction potentially enhances the catalyst–substrate interaction, allowing for

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• refinement. Among them, PROCHEK [98] is an open-source program that permits to check the quality of the protein structure by analysing the Ramachandran plots, the planarity of peptide bonds, the bad non-bonded interactions, the distortions of the geometry around the Cα atoms, the energies of hydrogen bonds

• molecular docking method specifically designed to accommodate carbohydrate-like compounds, employing a genetic algorithm that allows for ligand and receptor side-chain flexibility. Designed specifically for protein–carbohydrate interactions, SLICK includes terms that consider CH–π interactions, hydrogen

• bonds, smoothed van der Waals interactions, and electrostatic interactions. The SLICK scoring function, tailored for carbohydrates, enhances the accuracy of predicting binding modes and free binding energies. Compared to other programs such as AutoDock and FlexX (see below), BALLDock/SLICK demonstrates

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• , albeit with a slow but continuous deterioration of catalytic activity. Preliminary molecular docking and molecular dynamics simulation studies revealed that Thr40 and Ser105 residues played a crucial role in catalyzing the GBB reaction, forming hydrogen bonds with 2-aminopyridine substrate, increasing

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• its β-helical structure; reversion of the N-methylation led to complete conformation loss. The methylated asparagine residues at positions 16, 22, and 28 form an intramolecular chain of hydrogen bonds along the outside of the β-helix. Hydrogen atoms from the amide methyl group form hydrogen bonds with

• the oxygen of the neighbouring N-methylated asparagine amino acid side chain. This chain of hydrogen bonds stabilises the β-helical structure of polytheonamide B [110]. PoyE acts independently of the dehydratase and epimerase activities of other maturases in the cluster, but the MT is more efficient

Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines

• Ana Flávia Candida Silva,
• Francisco A. Martins and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2024, 20, 1572–1579, doi:10.3762/bjoc.20.140

• -fluoroalkylamines and the respective cations [6]. Intramolecular hydrogen bonds involving either the carboxy or hydroxy group of 4R- and 4S-hydroxyproline have been identified as key factors in stabilizing the favored conformations in the gas phase. Therein, the contribution of a gauche effect due to electron

A comparison of structure, bonding and non-covalent interactions of aryl halide and diarylhalonium halogen-bond donors

• Nicole Javaly,
• Theresa M. McCormick and
• David R. Stuart

Beilstein J. Org. Chem. 2024, 20, 1428–1435, doi:10.3762/bjoc.20.125

• diarylhalonium salts in halogen-bonding catalysis [13][14][15][16][17][18][19]. Crabtree has outlined the similarity in molecular orbitals (MO) formed in halogen bonds and hypervalent bonds (and hydrogen bonds) [20]. Recently, we [21], and Legault and Huber [22], independently investigated the connection between

Mild and efficient synthesis and base-promoted rearrangement of novel isoxazolo[4,5-b]pyridines

• Vladislav V. Nikol’skiy,
• Mikhail E. Minyaev,
• Maxim A. Bastrakov and
• Alexey M. Starosotnikov

Beilstein J. Org. Chem. 2024, 20, 1069–1075, doi:10.3762/bjoc.20.94

• molecule is not shown), 13c (top right), and 13d (bottom) with thermal ellipsoids set at a 50% probability level. Intermolecular hydrogen bonds are drawn with dashed lines. Methods for the synthesis of isoxazolo[4,5-b]pyridines: (A) annulation of an isoxazole fragment to a pyridine ring; (B) annulation of

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• -stacking distances (≈3.2 Å) are observed between the 5b units. For 6b, this is likely due to the included solvent (ethylene glycol) that hydrogen bonds to the quinoxalinedione. Moving forward, 2b stands out as a promising candidate for future solid-state characterization and device fabrication studies

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• ]. Actually, the presence of solutes consisting of water and proteins improves the stability of conformation 2. This stabilization is explained partly by the formation of hydrogen bonds between water molecules and PASE. Conformation 2 increases the number of sites where hydrogen bonds can form with water

• PBA-linked molecule is used, the relative energy of conformation II to that of conformation I can be better suited using our strategy. This stabilization is explained partly by the formation of hydrogen bonds between water molecules and PASE. As in the case of PASE, the chain portion of the PBA-linked

• molecule turns upward, increasing the number of sites that can form hydrogen bonds with water molecules in conformation II. Therefore, the formation of hydrogen bonds can stabilize conformation II relatively more strongly than conformation I. The hydration effect also improves the stability of conformation

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

• mainly driven by intramolecular hydrogen bonds. The methoxyphenyl-pyridine-methoxyphenyl moiety, developed by Petitjean et al. [19], demonstrates conformational switching upon the addition of acid in aqueous media (Figure 2). The neutral tweezers adopt a "U"-shaped conformation with both arms pointing in

• attached functional arms. The formation of new hydrogen bonds between -OMe groups and protonated pyridine stabilizes a "W"-shaped open conformation. The conformation switch can be easily followed by NMR spectroscopy in solution. Remarkably, the water-soluble tweezers 1, when functionalized with hydrophobic

• conformational switching is di(hydroxyphenyl)pyrimidine which was developed by Osakada et al. [25] (Figure 5). By default, this moiety adopts a U-shaped conformation stabilized by OH···N hydrogen bonds. In this conformation, tweezers 4 with two 9-ethynylanthryl arms form a 1:1 complex with 2,4,7