Dicarboxylate recognition based on ultracycle hosts through cooperative hydrogen bonding and anion–π interactions

• Wen-Hui Mi,
• Teng-Yu Huang,
• Xu-Dong Wang,
• Yu-Fei Ao,
• Qi-Qiang Wang and
• De-Xian Wang

Beilstein J. Org. Chem. 2025, 21, 884–889, doi:10.3762/bjoc.21.72

• ) solution of the compound at 4 °C, enabling structural analysis of the ultracycle. As illustrated in Figure 1, the backbone of B4aH adopts a Z-like shape with a flexible conformation. The two oxacalix[2]arene[2]triazine subcavities are positioned along the short axis in a staggered face-to-face arrangement

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

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

• -phenacenes for clarifying the different solid-fluorescence behavior between the parent and fluorinated phenacenes. Although we have extensively examined crystallization of F8-phenacenes, no single crystal suitable for an X-ray diffraction analysis was obtained. The crystalline structural analysis is still

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

• researchers identified high-affinity binding sites for the ligand within the Fc domain. This structural analysis allowed precise determination of amino acid residue positions and orientations. Upon photoirradiation, the pLeu within the pFcBP generated a carbene from the diazirine moiety. This transformation

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

• organic cages allows structural analysis in a way not possible for assemblies [38][39][41][42][43][44]. Due to their enhanced stability over imine assemblies, our amide-linked cages are amenable to complex processing (the cages remain unchanged in connectivity across changing solvents and temperature) 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

• structural analysis were obtained by crystallization from MeOH (5a), EtOH (5b), or DMFA (6b, 6c, and 7a). Single crystals of a suitable size were glued to the top of a glass fiber in a random orientation. The preliminary unit cell parameters were determined using three runs at different ω angle positions

Synthesis, structure and π-expansion of tris(4,5-dehydro-2,3:6,7-dibenzotropone)

• Yongming Xiong,
• Xue Lin Ma,
• Shilong Su and
• Qian Miao

Beilstein J. Org. Chem. 2025, 21, 1–7, doi:10.3762/bjoc.21.1

• Abstract The polycyclic skeleton of tris(4,5-dehydro-2,3:6,7-dibenzotropone) is a key structural fragment in carbon schwarzites, a theoretical form of negatively curved carbon allotrope. This report presents a new synthesis of this compound using a Ni-mediated Yamamoto coupling reaction and structural

• analysis of it with X-ray crystallography. Interestingly, it is observed that tris(4,5-dehydro-2,3:6,7-dibenzotropone) crystallized from its solution in hexane resulting in colorless and yellow crystal polymorphs, where it adopts conformations of approximate Cs and C2 symmetry, respectively. Furthermore

Controlled oligomerization of [1.1.1]propellane through radical polarity matching: selective synthesis of SF₅- and CF₃SF₄-containing [2]staffanes

• Jón Atiba Buldt,
• Wang-Yeuk Kong,
• Yannick Kraemer,
• Masiel M. Belsuzarri,
• Ansh Hiten Patel,
• James C. Fettinger,
• Dean J. Tantillo and
• Cody Ross Pitts

Beilstein J. Org. Chem. 2024, 20, 3134–3143, doi:10.3762/bjoc.20.259

• for the first time created an opportunity for structural analysis. We previously reported and contextualized single-crystal X-ray diffraction (SC-XRD) data on 2 [36]; thus, we proceeded to grow crystals of 3 suitable for X-ray analysis through slow evaporation of ethyl acetate. To our surprise, an

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

• synthetic study, the structural analysis of the obtained (poly)rotaxanes was performed to evaluate the fundamental relationship between the axle length and the number and directions of the CD wheels. The directions of the CDs on the PEG-based polyrotaxane framework were analyzed by scanning tunneling

• position of the wheel on the axle component. Meanwhile, the ICD evaluation based on the chirality of CD is a powerful tool for analyzing the inclusion behavior, which is also used for structural analysis. In 2006, Tian and co-workers reported the structural control of the rotaxane framework by subjecting a

Structure and thermal stability of phosphorus-iodonium ylids

• Andrew Greener,
• Stephen P. Argent,
• Coby J. Clarke and
• Miriam L. O’Duill

Beilstein J. Org. Chem. 2024, 20, 2931–2939, doi:10.3762/bjoc.20.245

• and potential decomposition pathways will enable the future design and development of new reagents. Keywords: hypervalent iodine; reagent development; structural analysis; thermal stability; thermogravimetric analysis; Introduction Hypervalent iodine(III) reagents have experienced a renaissance in

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

• , providing practical guidelines for carbohydrate structural analysis, spanning from the purification to the structural analysis of polysaccharides. MD simulations: Once the 3D glycan structure is built, taking into account the energetically favourable conformations of each constituent disaccharide unit, and

Multicomponent syntheses of pyrazoles via (3 + 2)-cyclocondensation and (3 + 2)-cycloaddition key steps

• Ignaz Betcke,
• Alissa C. Götzinger,
• Maryna M. Kornet and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2024, 20, 2024–2077, doi:10.3762/bjoc.20.178

• methyl esters 144. Subsequently, these esters are converted to various 3-hydroxypyrazoles 143 with hydrazine salts by microwave-assisted cyclization (Scheme 49) [152]. The method tolerates a large number of functional groups. In addition, X-ray structural analysis proved that the products are aromatic 3

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• surfactants. Structural analysis and site-directed mutagenesis identified residues important for the catalytic activity of ChSase B6 [60]. In addition, a novel laminarinase, MaLamNA, was characterized and expressed in Pichia pastoris from the same bacterium. It functioned exclusively towards the substrate

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• 7.450 (E-INS-i option), Neighbor-Joining trees were built by Geneious Tree Builder using Jukes-Cantor distance model. Sequence logo visualization was conducted by WebLogo 3. Protein structural analysis was conducted by PyMOL. (a) Domain compositions and the products of α-, β-, γ- and δ-modules in cis-AT

Two-fold addition reaction of silylene to C₆₀: structural and electronic properties of a bis-adduct

• Masahiro Kako,
• Masato Kai,
• Masanori Yasui,
• Michio Yamada,
• Yutaka Maeda and
• Takeshi Akasaka

Beilstein J. Org. Chem. 2024, 20, 1179–1188, doi:10.3762/bjoc.20.100

• 3e showed rough agreement with the corresponding values of 3 obtained using the X-ray structural analysis (Table 1 and Table S1 in Supporting Information File 1). As shown in Figure 7, few differences in relative energies are apparent among 3e, 3trans-1, 3trans-2, 3trans-3, and 3trans-4, although

Synthesis and properties of 6-alkynyl-5-aryluracils

• Ruben Manuel Figueira de Abreu,
• Till Brockmann,
• Alexander Villinger,
• Peter Ehlers and
• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 898–911, doi:10.3762/bjoc.20.80

• molecules within and between a layer with two molecules at the top and the bottom of the unit cell. b) Determined from X-ray structural analysis at 123 K. Element color: carbon (grey), hydrogen (white), oxygen (red) and nitrogen (blue). The thermal ellipsoids are drawn at the 50% probability level. UV–vis

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• melon [18], yet not much else is known about binding specificities exhibited by lectins derived from melons. In particular, existing research in this area often lacks a comprehensive characterization that includes both functional and structural analysis of these lectins. Here, we introduce a novel

Aldiminium and 1,2,3-triazolium dithiocarboxylate zwitterions derived from cyclic (alkyl)(amino) and mesoionic carbenes

• Nedra Touj,
• François Mazars,
• Guillermo Zaragoza and
• Lionel Delaude

Beilstein J. Org. Chem. 2023, 19, 1947–1956, doi:10.3762/bjoc.19.145

• on 13C NMR spectroscopy (see below). We suspect that deleterious hydrophilic effects caused the subsequent decomposition of the CAAC·CS2 and MIC·CS2 zwitterions when an aqueous work-up was applied. Structural analysis Several analytical techniques were employed to characterize the nine aldiminium and

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

• ][24][25][26]. The structural analysis of GAGs improves the understanding of their biological functions and helps in the development of structure–activity relationships for these important biopolymers [27][28]. Although the composition of the individual saccharide components of GAGs is simple, the

• structural analysis of GAGs is extremely difficult due to their complex pattern of modification such as epimerization and sulfation [29]. In addition, GAGs’ high flexibility and periodicity render these molecules profoundly challenging to analyze using experimental techniques only [30][31]. Thus

Controlling the reactivity of La@C₈₂ by reduction: reaction of the La@C₈₂ anion with alkyl halide with high regioselectivity

• Yutaka Maeda,
• Saeka Akita,
• Mitsuaki Suzuki,
• Michio Yamada,
• Takeshi Akasaka,
• Kaoru Kobayashi and
• Shigeru Nagase

Beilstein J. Org. Chem. 2023, 19, 1858–1866, doi:10.3762/bjoc.19.138

• afforded the corresponding single-bonded adducts 2–5 with high regioselectivity. One-electron reduction of La@C2v-C82 increased its reactivity during thermal reaction relative to that of neutral La@C2v-C82. Structural analysis of the two major products indicated that the characteristic absorption features

Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect

• Ken-ichi Nakashima,
• Naohito Abe,
• Masayoshi Oyama,
• Hiroko Murata and
• Makoto Inoue

Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117

• between the two glucopyranose moieties was confirmed by the HMBC correlation of H-1′′/C-2′ and the H2BC correlation of H-1′/C-2′, giving the relative structure of 4 shown in Figure 1. Although 1D NMR and HRESIMS data for probreynin I (4) were reported in a Chinese patent in 2019 [13], no structural

• analysis based on 2D NMR spectroscopy has previously been described. He et al. reported that epibreynin D, which bears the same aglycone moiety as compounds 2 and 7, exhibits anti-inflammatory effects in mice and rat models [12]. To investigate the anti-inflammatory effects of the sulfur-containing

Selective construction of dispiro[indoline-3,2'-quinoline-3',3''-indoline] and dispiro[indoline-3,2'-pyrrole-3',3''-indoline] via three-component reaction

• Ziying Xiao,
• Fengshun Xu,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2023, 19, 1234–1242, doi:10.3762/bjoc.19.91

• the three-component reaction. To our surprise, instead of the above mentioned dispiro[indoline-3,2'-quinoline-3',3''-indolines] 3a–m, the novel dispiro[indoline-3,2'-pyrrole-3',3''-indoline] derivatives 4a–i were obtained in high yields. The results are summarized in Table 3. The structural analysis

Synthesis of imidazo[4,5-e][1,3]thiazino[2,3-c][1,2,4]triazines via a base-induced rearrangement of functionalized imidazo[4,5-e]thiazolo[2,3-c][1,2,4]triazines

• Dmitry B. Vinogradov,
• Alexei N. Izmest’ev,
• Angelina N. Kravchenko,
• Yuri A. Strelenko and
• Galina A. Gazieva

Beilstein J. Org. Chem. 2023, 19, 1047–1054, doi:10.3762/bjoc.19.80

• –spin interaction constants of other doublets (2JCH = 1.3–1.5 Hz) indicate the position of the carboxyl (for 4a, red) or carbonyl (for 5a, blue) groups through two bonds relative to the olefinic proton. The structure of compound 5a was additionally confirmed by X-ray structural analysis data (Figure 5

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• and DSC results for each sample are available (Section 5, pp. S15 and S16 in Supporting Information File 1). Single crystal X-ray structural analysis The crystal structures of β-CD·BES, β-CD·PRO and γ-CD·PRO were solved by isomorphous replacement using as trial models the rigid host atom frameworks of

Synthesis, optical and electrochemical properties of (D–π)₂-type and (D–π)₂Ph-type fluorescent dyes

• Kosuke Takemura,
• Kazuki Ohira,
• Taiki Higashino,
• Keiichi Imato and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2022, 18, 1047–1054, doi:10.3762/bjoc.18.106

• , compared with those in toluene. The Φfl-solid (0.24) of OTT-2 is higher than that (Φfl-solid = 0.15) of OTK-2, while the Φfl-solid of OTK-2 and OTT-2 are lower than those in toluene. Although single crystals of OTK-2 and OTT-2 with sufficient size for X-ray structural analysis were not obtained, the