Melifoliox B, a novel phloroglucin derivative isolated from Melicope barbigera (Rutaceae) and synthesis of new oxidation products from melifoliones A and B

• Horst Weber,
• Kim-Thao Tran-Cong,
• Bernhard Mayer,
• Guido J. Reiss,
• Iryna S. Konovalova,
• Marc S. Appelhans,
• Kenneth R. Wood and
• Claus M. Passreiter

Beilstein J. Org. Chem. 2026, 22, 535–546, doi:10.3762/bjoc.22.39

• and data acquisition. Data collection was therefore applied with seriously elongated exposure time. The crystal structure was successfully solved using methods as implemented in the SHELXT program [16], followed by refinement with SHELXL [17]. The refined asymmetric unit was found to contain about

Synthesis of a HDAC inhibitor–nanogold probe for cryo-EM visualization in class I HDAC co-repressor complexes

• Wiktoria A. Pytel,
• John W. R. Schwabe and
• James T. Hodgkinson

Beilstein J. Org. Chem. 2026, 22, 480–485, doi:10.3762/bjoc.22.35

• , like other benzamide HDAC inhibitors, exhibits slow on/off binding kinetics, hence once bound to the HDAC within the complex it should not readily dissociate [16]. A crystal structure of HDAC2 bound to an analogue of CI-994 (PDB: 4LY1) revealed that the acetamide moiety is oriented outside the HDAC

Structural reassignment of compound 968, an allosteric glutaminase inhibitor

• Lindsey A. Albertelli,
• Sainabou Jallow,
• Chun Li and
• Scott M. Ulrich

Beilstein J. Org. Chem. 2026, 22, 455–460, doi:10.3762/bjoc.22.33

• synthesized using the published cyclocondensation reaction (middle), and the isomeric benzo[c]acridine compound purchased from ChemDiv. B) Dose–response curves of the three compounds against the glutaminase isoform GAC. C) ORTEP diagram of the X-ray crystal structure of the material synthesized according to

Synthesis and anti-cancer activity of naphthalimide–organylselanyl conjugates

• Rajkumar Ravi and
• Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2026, 22, 416–435, doi:10.3762/bjoc.22.29

• 7 was obtained by slow evaporation of a chloroform–methanol mixture (1:3 v/v). Single-crystal X-ray diffraction analysis revealed that compound 7 crystallises in the triclinic crystal system with the space group . The crystal structure of compound 7 is shown in Figure 2a. It shows a typical V-shaped

• carbonyl oxygen surface promotes hydrogen-bond formation. The binding site interactions of compounds 7 and 8 with the tyrosine kinase were further validated by comparison with the crystal structure of 1M17 with co-crystallised ligand erlotinib (Figure 9c), showing that both compounds form similar active

• . Comparison with the crystal structure of 4HJO co-crystallised ligand erlotinib (Figure 10c) further confirmed that the synthesised ligands exhibit a similar interaction pattern within the inactive tyrosine kinase domain of the EGFR. The compounds 7 and 8 possess well-defined structural features comprising

Cone p-aminocalix[4]arenes enriched with ‘clickable’ alkyne or azide functionalities

• Ilia Korniltsev,
• Vasily Bazhenov,
• Alexander Gorbunov,
• Dmitry Cheshkov,
• Stanislav Bezzubov,
• Vladimir Kovalev and
• Ivan Vatsouro

Beilstein J. Org. Chem. 2026, 22, 399–415, doi:10.3762/bjoc.22.28

• Supporting Information File 18: Synthesis details, copies of 1H and 13C NMR spectra of novel compounds, details of X-ray diffraction measurements and crystal structure data. Supporting Information File 19: Crystallographic information file for compound 16. Supporting Information File 20: Crystallographic

Spirobarbiturates with a pyrrolizidine moiety: synthesis, structure and biological evaluation

• Arthur A. Puzyrkov,
• Andrew S. Drachuk,
• Ekaterina A. Popova,
• Alexander V. Stepakov and
• Vitali M. Boitsov

Beilstein J. Org. Chem. 2026, 22, 274–288, doi:10.3762/bjoc.22.20

• the hydrogen atom of the maleimide methyl group and the carbonyl oxygen of an adjacent maleimide ring. The crystal structure of compound 4b exists as a solvate. The oxygen atom of a water molecule forms a hydrogen bond with the amide hydrogen of the barbiturate fragment (N–H···O–H = 2.783 Å), while

• ), including O···H–N hydrogen bonds between barbiturate rings and O···H–Ph contacts involving maleimide carbonyl oxygens and phenyl ring hydrogens. The crystal structure of adduct 4c includes a molecule of dichloromethane. Due to the disorder of the dichloromethane molecule, the exact distances of the

• results obtained, docking simulations were performed for the possible interaction of spiro-adducts with actin, as the most widespread and highly conserved cellular protein. Since the initial determination of the G-actin crystal structure in complex with DNase I, many actin structures have been registered

Configuration–packing synergy enabling integrated crystalline-state RTP and amorphous-state TADF

• Ruiyan Wang and
• Yunan Wu

Beilstein J. Org. Chem. 2026, 22, 224–236, doi:10.3762/bjoc.22.16

• obtained through the method of slow solvent evaporation, which allows for the formation of high-quality crystals suitable for detailed structural analysis. The crystal structure of 1 was thoroughly characterized using single-crystal X-ray diffraction (CCDC 2492630). This technique provides precise three

• -dimensional information about the atomic arrangement within the crystal lattice. As depicted in Figure 1a, the crystal structure reveals that the dihedral angle between the phthalimide moiety and the bridging phenyl ring is 50.71°, while the angle between the bridging phenyl ring and the carbazole unit is

• , an in-depth analysis was conducted on both the molecular structure and the packing arrangement in single crystals of 1. As depicted in Figure 6a, the crystal structure of 1 reveals the presence of significant π–π interactions between adjacent molecules. These interactions are crucial for stabilizing

Improved synthesis and physicochemical characterization of the selective serotonin 2A receptor agonist 25CN-NBOH

• Adrian G. Rossebø,
• Hannah G. Kolberg,
• Anders E. Tønder,
• Louise Kjaerulff,
• Poul Erik Hansen,
• Karla A. Frydenvang,
• Jesper Østergaard and
• Jesper L. Kristensen

Beilstein J. Org. Chem. 2026, 22, 175–184, doi:10.3762/bjoc.22.11

• solid form Crystals of 1·HCl were grown from an ethanolic solution, and the crystal structure was determined by single-crystal X-ray diffraction (SCXRD, Figure 2). As seen in Figure 2a, 1·HCl adopts a twisted U shape and is involved in three hydrogen bonds. Therein, the ammonium N atom interacts with

• ). Notably, the crystal structure shows that there are no water molecules of crystallization present, nor are any other solvent molecules incorporated into the crystal packing. When comparing the diffractogram obtained by SCXRD (Figure 3, green) with that obtained by X-ray powder diffraction (XRPD) of 1·HCl

• -NBOH (1), providing easier access to this compound. When the hydrochloride salt 1·HCl was precipitated and recrystallized from ethanol, a single and stable, nonhygroscopic polymorph with a well-defined melting point formed. A crystal structure determined by SCXRD confirmed the structural assignment

Highly electrophilic, gem- and spiro-activated trichloromethylnitrocyclopropanes: synthesis and structure

• Ilia A. Pilipenko,
• Mikhail V. Grigoriev,
• Olga Yu. Ozerova,
• Igor A. Litvinov,
• Darya V. Spiridonova,
• Aleksander V. Vasilyev and
• Sergey V. Makarenko

Beilstein J. Org. Chem. 2026, 22, 123–130, doi:10.3762/bjoc.22.5

• cyclopropane 2 under various conditions. Supporting Information The crystallographic data of the structure are deposited in the Cambridge Crystal Structure Data Bank (CCDC 2: 2237758; CCDC 3: 2481941; CCDC 9a: 2450586; CCDC 9b: 2450587). Statistics on the collection of X-ray diffraction data and refinement of

Sustainable electrochemical synthesis of aliphatic nitro-NNO-azoxy compounds employing ammonium dinitramide and their in vitro evaluation as potential nitric oxide donors and fungicides

• Alexander S. Budnikov,
• Nikita E. Leonov,
• Michael S. Klenov,
• Andrey A. Kulikov,
• Igor B. Krylov,
• Timofey A. Kudryashev,
• Aleksandr M. Churakov,
• Alexander O. Terent’ev and
• Vladimir A. Tartakovsky

Beilstein J. Org. Chem. 2025, 21, 2739–2754, doi:10.3762/bjoc.21.211

• all compounds, XRD of 2c, computational details, and copies of 1H, 13C, 14N, 1H,13C HSQC, and 1H,13C HMBC NMR spectra. Supporting Information File 5: Crystallographic information for compound 2c. Supporting Information File 6: CheckCIF report for the data of 2c. Acknowledgements Crystal structure

Competitive cyclization of ethyl trifluoroacetoacetate and methyl ketones with 1,3-diamino-2-propanol into hydrogenated oxazolo- and pyrimido-condensed pyridones

• Svetlana O. Kushch,
• Marina V. Goryaeva,
• Yanina V. Burgart,
• Marina A. Ezhikova,
• Mikhail I. Kodess,
• Pavel A. Slepukhin,
• Alexandrina S. Volobueva,
• Vladimir V. Zarubaev and
• Victor I. Saloutin

Beilstein J. Org. Chem. 2025, 21, 2716–2729, doi:10.3762/bjoc.21.209

• -equatorial position and is in the trans-position toward the Bu group. The single crystal structure of the bicycle 5ctc is ordered by intermolecular hydrogen bonds between the hydroxy group and the amino group as well as between the amino group and fluorine of the CF3 substituent of the neighboring molecule

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