Conformational effects on iodide binding: a comparative study of flexible and rigid carbazole macrocyclic analogs

• Guang-Wei Zhang,
• Yong Zhang,
• Le Shi,
• Chuang Gao,
• Hong-Yu Li and
• Lei Xue

Beilstein J. Org. Chem. 2025, 21, 2369–2375, doi:10.3762/bjoc.21.181

• (Figure S3) in Supporting Information File 1. WDG exhibited poor solubility, which hindered the direct acquisition of its single crystal structure for characterization. However, after Boc (tert-butyloxycarbonyl) protection, a single crystal structure (CCDC Number: 2339028) of the modified compound was

Insoluble methylene-bridged glycoluril dimers as sequestrants for dyes

• Suvenika Perera,
• Peter Y. Zavalij and
• Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 2302–2314, doi:10.3762/bjoc.21.176

• methyl substituents (H2). Fortunately, the X-ray crystal structures of G2W1 and G2W3 reported below shed further light on their poor performance as solid state sequestrants. X-ray crystal structure of G2W1 and G2W3 Eventually, we were able to grow single crystals of G2W3 (CCDC 2466611) and solve their

• H2O and TFA are also seen in the crystal structure. At one C=O portal, an H2O molecule engages in H-bonding interactions with one C=O group (O···O: 2.948 Å, H···O: 2.149 Å, O–H···O angle: 163.603˚) and one OMe (O···O: 2.963 Å, H···O: 2.169 Å, O–H···O angle: 159.887°) group. The other C=O portal

Research towards selective inhibition of the CLK3 kinase

• Vinay Kumar Singh,
• Frédéric Justaud,
• Dabbugoddu Brahmaiah,
• Nangunoori Sampath Kumar,
• Blandine Baratte,
• Thomas Robert,
• Stéphane Bach,
• Chada Raji Reddy,
• Nicolas Levoin and
• René L. Grée

Beilstein J. Org. Chem. 2025, 21, 2250–2259, doi:10.3762/bjoc.21.172

• ). Second, molecular docking using DYRK1A crystal structure was used to understand the unexpected binding on the DYRK kinases (Figure 6). Surprisingly, another lysine (K175) is also located near the acidic group of VS-77 (at 3.2 Å between the carbonyl carbon atom and nitrogen from amine). This residue is

A m-quaterphenyl probe for absolute configurational assignments of primary and secondary amines

• Yuka Takeuchi,
• Mutsumi Kobayashi,
• Yuuka Gotoh,
• Mari Ikeda,
• Yoichi Habata,
• Tomohiko Shirai and
• Shunsuke Kuwahara

Beilstein J. Org. Chem. 2025, 21, 2211–2219, doi:10.3762/bjoc.21.168

• based on B3LYP/6-31G* level. Four major conformers of (S)-3f based on B3LYP/6-31G* level. The distribution of conformers of (S)-3a–h against dihedral angles ϕ (C6–C1–C1'–C6') calculated by B3LYP/6-31G*. Crystal structure of (S)-2b. Four conformers exist in the unit cell. Hydrogen atoms are omitted for

• were recorded on a Jeol ECP400 spectrometer (400 MHz) and a Bruker AVANCE II spectrometer (400 MHz). All NMR spectroscopic data of CDCl3 solutions are reported in ppm (δ) downfield from TMS. UV and CD spectra were recorded on JASCO V-650 and JASCO J-820 spectrometers, respectively. X-ray single-crystal

• structure analysis was performed on a Bruker SMART diffractometer equipped with a CCD area detector at 120 K. Silica gel 60 F254 precoated plates on glass from Merck Ltd. were used for thin-layer chromatography (TLC). General procedure for the synthesis of conjugates 2a–h (S)-2-[2,10-Bis(4-methoxyphenyl

Solar thermal fuels: azobenzene as a cyclic photon–heat transduction platform

• Jie Yan,
• Shaodong Sun,
• Minghao Wang and
• Si Wu

Beilstein J. Org. Chem. 2025, 21, 2036–2047, doi:10.3762/bjoc.21.159

• azobenzene polymer solar thermal fuels: (a) Photoisomerization and thermally induced reverse isomerization of diacetylene monomers. The inset depicts the crystal structure of diacetylene monomer (n = 6, X = N–H) with dashed lines indicating intermolecular hydrogen bonds. Figure 4a was used with permission of

Synthesis of N-doped chiral macrocycles by regioselective palladium-catalyzed arylation

• Shuhai Qiu and
• Junzhi Liu

Beilstein J. Org. Chem. 2025, 21, 1917–1923, doi:10.3762/bjoc.21.149

• characterized by NMR spectroscopy, mass spectrometry, and X-ray crystallography. Single crystals suitable for X-ray diffraction measurements of compounds 3a, MC2, and MC3 were successfully obtained to reveal their molecular structures. In the crystal structure of 3a (Figure 2a), the two pyrene units are nearly

• , theoretical calculations were performed to evaluate the energy barriers of isomerization. As shown in Figure S3 (Supporting Information File 1), the configuration observed in the crystal structure has the lower energy by 24.0 kcal mol−1 than that of the isomeric structure with two pyrene units at the same

Preparation of spirocyclic oxindoles by cyclisation of an oxime to a nitrone and dipolar cycloaddition

• Beth L. Ritchie,
• Alexandra Longcake and
• Iain Coldham

Beilstein J. Org. Chem. 2025, 21, 1890–1896, doi:10.3762/bjoc.21.146

• , 52.7, 39.4, 26.8; HRESIMS (m/z): [M + H]+ calcd for C18H21N2O6, 361.1400, found: 361.1404. Representative oxindole alkaloids. Orientation for the cycloaddition (left) and the crystal structure of the major stereoisomer 5a (right) with the anisotropic displacement parameters drawn at 50% (oxygen – red

Unique halogen–π association detected in single crystals of C–N atropisomeric N-(2-halophenyl)quinolin-2-one derivatives and the thione analogue

• Mai Uchibori,
• Nanami Murate,
• Kanako Shima,
• Tatsunori Sakagami,
• Ko Kanehisa,
• Gary James Richards,
• Akiko Hori and
• Osamu Kitagawa

Beilstein J. Org. Chem. 2025, 21, 1748–1756, doi:10.3762/bjoc.21.138

• detected in the crystals of (P)-1a and (P)-1b. Angles (θ, α) and distances (d) in racemate rac-1a,b and (P)-1a,b. Crystal structure of racemic quinoline-2-thione rac-2a. Synthesis of N-(2-halophenyl)quinolin-2-ones 1a,b and quinoline-2-thione 2a. Supporting Information Crystallographic data for compounds

3,3'-Linked BINOL macrocycles: optimized synthesis of crown ethers featuring one or two BINOL units

• Somayyeh Kheirjou,
• Jan Riebe,
• Maike Thiele,
• Christoph Wölper and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2025, 21, 1719–1729, doi:10.3762/bjoc.21.134

• compounds, as well as the crystal structure data for Me-M16. CCDC-2427523 contains the supplementary crystallographic data for this paper. This data can be obtained free of charge from The Cambridge Crystallographic Data Centre via https://www.ccdc.cam.ac.uk/data_request/cif. Supporting Information File 3

Structural analysis of stereoselective galactose pyruvylation toward the synthesis of bacterial capsular polysaccharides

• Tsun-Yi Chiang,
• Mei-Huei Lin,
• Chun-Wei Chang,
• Jinq-Chyi Lee and
• Cheng-Chung Wang

Beilstein J. Org. Chem. 2025, 21, 1671–1677, doi:10.3762/bjoc.21.131

• In conclusion, we could successfully synthesize the pure R-isomer of pyruvated galactose, simultaneously avoiding anomeric epimerization. The crystal structure of pyruvylated galactose, potentially stabilized by hydrogen bonding, provided direct evidence confirming the diastereochemistry of the

• ), 1.15 EPS (2) and Rhizobium leguminosarum bv. viciae VF39 EPS (3). (a) Oak Ridge Thermal Ellipsoid Plot view of the X-ray crystal structure of pyruvylated galactose 6. (b) Hydrogen-bonding in the crystal structure of pyruvylated galactose 6. Synthesis of trisaccharide precursor 14. Optimization of

Synthesis of an aza[5]helicene-incorporated macrocyclic heteroarene via oxidation of an o-phenylene-pyrrole-thiophene icosamer

• Yusuke Matsuo,
• Aoi Nakagawa,
• Shu Seki and
• Takayuki Tanaka

Beilstein J. Org. Chem. 2025, 21, 1561–1567, doi:10.3762/bjoc.21.119

• and nanobelt. (b) Cyclo[4]helicenylene and cyclo(oxa[5]helicenylene-biphenylene). (c) Intramolecular oxidative coupling of cyclic o-phenylene-pyrrole-thiophene dodecamers. X-ray crystal structure of 4. Thermal ellipsoids are scaled to 50% probability level. Solvent molecules and hydrogen atoms except

• for NHs are omitted for clarity. 1H NMR spectra of 5 in DMSO-d6 (a) at room temperature and (b) at 100 °C. (a) X-ray crystal structure of 5; (left) top view, (right) side view. Thermal ellipsoids are scaled to 50% probability level. Solvent molecules and hydrogen atoms except for NHs are omitted for

Ambident reactivity of enolizable 5-mercapto-1H-tetrazoles in trapping reactions with in situ-generated thiocarbonyl S-methanides derived from sterically crowded cycloaliphatic thioketones

• Grzegorz Mlostoń,
• Małgorzata Celeda,
• Marcin Palusiak,
• Heinz Heimgartner,
• Marta Denel-Bobrowska and
• Agnieszka B. Olejniczak

Beilstein J. Org. Chem. 2025, 21, 1508–1519, doi:10.3762/bjoc.21.113

• , the quality of the X-ray measurements and structure determination meets all high standards for reliable data. The same applies to the crystal data of 10i, even though its crystal structure contains four independent molecules per unit cell. These molecules exhibit slight differences in their geometry

• . Supporting Information File 40: General information and experimental data of all isolated products, procedure for determination of biological activity, details of the crystal structure determination, and copies of 1H and 13C NMR spectra for all products. Acknowledgements The authors thank Prof. Zbigniew J

A multicomponent reaction-initiated synthesis of imidazopyridine-fused isoquinolinones

• Ashutosh Nath,
• John Mark Awad and
• Wei Zhang

Beilstein J. Org. Chem. 2025, 21, 1161–1169, doi:10.3762/bjoc.21.92

• chromatography with 30:70 EtOAc/hexanes. Product structures were confirmed by 1H and 13C NMR analysis and X-ray crystal structure analysis of 8a. Density functional theory (DFT) calculations DFT computations were conducted utilizing Gaussian 16W with the B3LYP functional and the 6-31G(d,p) basis set [21][22

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

• with relevant position numbering. Crystals obtained for 2 were analysed by X-ray crystallographic studies and confirmed the NMR-based structure assignment. The crystal structure of 2 is shown as a thermal ellipsoid plot below (Figure 3). With a simplified approach for the synthesis of aminated

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

• pattern of assembly between HIM and metal cation in 2:1 ratio. While association with sodium leads to a polymer-like network, the lithium crystal structure was limited to dimeric assemblies of HIM. In the lithium-coordinating complex, the oxygen–lithium–oxygen bond angle is approximately 98.83

• projecting outward denoted by an asterisk. Furthermore, the resulting crystal structure reveals that 1 is also a distorted planar macrocyclic system consisting of the amino acids carbonyl oxygens facing inside the ring. All three benzyl groups are located above a single plane (more figures are provided in

• Supporting Information File 1, Figure S1). In addition, the crystal structure also demonstrates that the three iodine atoms, three carbonyl carbon atoms and six oxygen atoms circumscribe a small bowl-like cavity within the macrocycle. With the consideration of all primary and secondary bonds, the small

On the photoluminescence in triarylmethyl-centered mono-, di-, and multiradicals

• Daniel Straub,
• Markus Gross,
• Mona E. Arnold,
• Julia Zolg and
• Alexander J. C. Kuehne

Beilstein J. Org. Chem. 2025, 21, 964–998, doi:10.3762/bjoc.21.80

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

• ) Crystal structure of B4aH (hydrogen atoms are omitted for clarity), and (c) the stacking structure of the crystal of B4aH (the blue dotted lines represent hydrogen bonds). (a) The structures of host and guests, (b) 1H NMR spectra (298 K, 400 MHz, CD3CN) of B4aH upon titration with C62− (c(B4aH) = 1 mM

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

• -pairing) could be enhanced along with the charge of the anion and its binding affinity with L (from Cl– to CO32–, and PO43–). Notably, for the first time, direct ion-pairing between receptor-complexed phosphate and 18-crown-6 complexed cesium was observed in the single crystal structure, facilitating

• interaction in nonpolar solvent could be stronger than that in polar solvent [45][46][47][48]. The ion-dipole interaction between complexed Cs+ cation and receptor–sulfate complex was first identified by single crystal structure analysis (Figure 2). The overall stoichiometry of L, 18-crown-6, Cs+, and SO42

• understand cooperative interactions between complexed ions, we tried to grow the crystal structure of studied salts. Fortunately, single crystals of Cs2CO3 and Cs3PO4 complexes were obtained by slow vapor diffusion from acetonitrile and diethyl ether. Notably, clearly stronger ion-dipole interactions of

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

• situ generation of the calcium complex, as known from, e.g., Posner's well-defined colloidal calcium phosphates [60]. Crystal structure of the calcium diphenyl phosphate complex 4. Hydrogen atoms are omitted for clarity. Selected bond lengths (in Å) and angle: Ca1–O4 2.2510(13), Ca1–O6 2.4004(14), Ca1

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

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

• spectroscopic characterization of C1 along with determination of its inherent aqueous solubility and self-association properties. Next, we present the X-ray crystal structure of C1 as its C1·Me6CHDA complex. Subsequently, we describe a qualitative investigation of C1·guest and M1·guest complexation by 1H NMR

• hydrophobic region of the guest which changes the orientation of Ha with respect to the magnetically shielding region [54][63][64]. X-ray crystal structure of C1 We were fortunate to obtain single crystals of the C1·Me6CHDA complex and solved the crystal structure by X-ray diffraction (CCDC 2411723). Figure 5

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

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

• Supporting Information File 2: General information, characterization data, NMR spectra and crystallographic data of synthesized compounds. Acknowledgements Crystal structure determination was performed in the Department of Structural Studies of Zelinsky Institute of Organic Chemistry, Moscow.

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

• purification, the 1H NMR of Cl2B showed 6% of an impurity, possibly the anti-isomer. Further purification of Cl2B reduced the impurity content to less than 3%. Topochemical photocycloaddition Upon examining the crystal structure of our first sample of Cl2B, Cl2B (A), we observed that the compound had undergone

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

• steric clash is thought to contribute to the increased cage axial twist and reduced cavity height observed in the crystal structure [39]. Thus the cages have “micro-flexibility” of the sort that can finetune enzyme-like transition-state binding, and perhaps even satisfy Sanders, who has lamented the lack