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

Synthesis of 2,2-difluoro-1,3-diketone and 2,2-difluoro-1,3-ketoester derivatives using fluorine gas

• Alexander S. Hampton,
• David R. W. Hodgson,
• Graham McDougald,
• Linhua Wang and
• Graham Sandford

Beilstein J. Org. Chem. 2024, 20, 460–469, doi:10.3762/bjoc.20.41

• ); ref codes IZICEA [47], XOPZEK and XOPZIO [48]) are known. Interestingly, in contrast to the previously described acyclic structures no OH···O(H) hydrogen bonds are present in structure 5e – the molecules are linked by OH···O(NO2) interactions. Discussion Keto–enol tautomer studies have shown that DBM

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• times, compared to their electron-donating counterparts. The mechanism of action involves the Al atom, which is located at the center of the regular octahedron (Scheme 22), forming hydrogen bonds with the carbonyl group, facilitating the electrophilic reaction with indole by lowering the LUMO orbital of

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• , attracts the attention of researchers involved in the study of various types of hydrogen bonds and the problem of superbasicity [7][8]. Indeed, the basicity of quinoline and simple azaarenes is rather low. At the same time, the correct structural organization of azaarenes, where unshared electron pairs are

• 5. As the XRD study of the crystals showed (Figure 3), the molecular and crystal structure of the isolated compound is strongly dominated, on the one hand, by intra- and intermolecular hydrogen bonds with the participation of N, Cl, and O heteroatoms (forming an endless slightly corrugated ribbon

• divergence angle between them of only 1.33°) and are simultaneously connected by two bifurcated hydrogen bonds with the hydroxy groups of dichlororesorcinol. What would be the crystal structure of quinoquinoline 5 free of foreign particles? This is not an easy question to answer, since the superbasic nature

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• , it was already known that the intermolecular hydrogen bonding with solvent molecules may hinder the photoisomerization of indigo derivatives [46]. Nagasawa and co-workers found that the photoisomerization of 9a was inhibited by polar DMF due to formation of weak hydrogen bonds with formyl groups

• used in the synthesis of indigo [4]. a) Intramolecular (a = 2.26 Å) and intermolecular (b = 2.11 Å) hydrogen bonds in indigo, b) crystal packing of indigo in the solid state obtained from the single-crystal X-ray diffraction data, CCDC 796873 [12], c) photos of indigo in the solid state and solutions

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• towards the binding site to observe if it reproduces a pose similar to the starting pose. To describe these unbinding and rebinding processes, analyses of RMSD, binding energy, contacts, and hydrogen bonds were performed. Additionally, after the final pulling step, a short MD run of 500 ns was performed

• restore any native contacts. This suggests that the GAG gets close to the binding site but does not return to a similar conformation as the initial (experimental) pose. A similar trend is observed with hydrogen bonds where the number of H-bonds drops when the ligand is pulled away but never gets fully

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• Hirshfeld surfaces and evidence the strong flatness of the structures (Figures S2B and S3B in Supporting Information File 1). Important contributions of hydrogen bonds (O···H/H···O) can also be found, especially for hdz-NO2. Besides the interaction maps, crystal structures themselves may be used to

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• , interacting with the calixpyrrole macrocycle through hydrogen bonds. The water molecule was bound near the fluoride and was further stabilised through hydrogen bonding to the oxygen atoms in the central part of the receptor. This selective fluoride binding was evidenced with the help of 1H NMR spectroscopy

• complexes, the fragment originating from the porphyrinoid could form hydrogen bonds with a carboxyl group, while the crown ether cavity would allow interaction with the protonated amine group of an amino acid molecule. The choice of macrocycle size could enable the recognition of different biomolecules

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• as chloroform and toluene, in which the forming structures are stabilized by hydrogen bonds. The last few years have seen an increase in works showing the course of various types of reactions in the cavities of hexameric systems (closed spaces) created by R[4]A [8]. Complexes of R[4]A with amines [9

• ], amino alcohols [10], and amino acids [11] have been studied due to their potential applications in supramolecular chemistry, drug delivery, and molecular recognition. The complexation of R[4]A with amines is based on the formation of hydrogen bonds between the hydroxy groups of the resorcinol units and

• (cavity) and the other directional due to hydrogen bonds (hydroxy groups), leads to the formation of these complexes. Results and Discussion The addition of two equivalents of sec-amines to an ethanol solution of R[4]A results in the formation of a crystalline precipitate with limited solubility in non

Non-noble metal-catalyzed cross-dehydrogenation coupling (CDC) involving ether α-C(sp³)–H to construct C–C bonds

• Hui Yu and
• Feng Xu

Beilstein J. Org. Chem. 2023, 19, 1259–1288, doi:10.3762/bjoc.19.94

• and regenerates the tert-butoxyl radical to complete the entire catalytic cycle. The formation of hydrogen bonds between the oxygen of the carbonyl group and the hydrogen of the 2,2,2-trifluoroethanol (TFE) reduces the activation energy of the radical reaction and improves the coupling efficiency. In

Light-responsive rotaxane-based materials: inducing motion in the solid state

• Adrian Saura-Sanmartin

Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64

• UMUMOF-(E)-3 due to the decrease of the number of hydrogen bonds interactions between the counterparts, as determined by solid-state 2H NMR. Interestingly, UMUMOF-(E)-3 was employed as a molecular nanodispenser of para-benzoquinone working through a cyclic operation mode which involved three steps