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

• in the reported crystal structure of 1·CH2Cl2 [22]. The side view of compound 1 indicates that two of its carbonyl groups are oriented upwards while the third one points downwards. Compound 1 comprises three [5]helicenoid moieties, each containing three benzene rings and two seven-membered rings. In

• the helicity of the three [5]helicenoid moieties. This crystal structure is essentially the same as that reported by Jones earlier [1]. Figure 2b illustrates the structure of (P,M,P)-1 with the C2 axis, where one carbonyl group points upward, another downward, and the third one faces forwards

• -membered ring, and one seven-membered ring, and the third one containing three benzene rings and two seven-membered rings. The crystal structure of 3·CH2Cl2 reveals that each unit cell contains a pair of enantiomers, (M,P,M)-3 and (P,M,P)-3, co-crystallized with two molecules of CH2Cl2. Here P and M

Efficient synthesis of fluorinated triphenylenes with enhanced arene–perfluoroarene interactions in columnar mesophases

• Yang Chen,
• Jiao He,
• Hang Lin,
• Hai-Feng Wang,
• Ping Hu,
• Bi-Qin Wang,
• Ke-Qing Zhao and
• Bertrand Donnio

Beilstein J. Org. Chem. 2024, 20, 3263–3273, doi:10.3762/bjoc.20.270

• derivatives and the antiparallel stacking mode into columnar structures stabilized by arene–perfluoroarene intermolecular interactions were confirmed by the single-crystal structure of the alkoxy-free side chain analog, i.e., 1,2,4-trifluoro-3-(perfluorophenyl)triphenylene (F). UV–vis absorption and

• analysis (Figures S1–S32, Supporting Information File 1), and all the results agree with the proposed molecular structures. Single-crystal structure of F Suitable single crystals of compound F for X-ray analysis were obtained by slow evaporation of an ethyl acetate/ethanol solution (Figure 2, and

• Supporting Information File 1, Figures S33, S34 and Tables S1–S3). The crystal structure unequivocally confirms that the reaction pattern between 2Li-BP and perfluorobiphenyl, effectively yielded the desired 1,2,4-trifluoro-3-(perfluorophenyl)triphenylene and that the annulation occurred at the expected

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

• procedures, characterization data, NMR spectra, computational details, and X-ray crystallographic experimental details. Supporting Information File 16: LTP X-ray crystal structure of compound 3 (2357079.cif), HTP X-ray crystal structure of compound 3 (2357080.cif) and X-ray crystal structure of compound 2 at

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

• the hydrogen bonding by the primary- or secondary-alcohol groups, as confirmed by theoretical analyses. This structure was consistent with a previously reported X-ray crystal structure analysis of the complex structure comprising α-CD, polyion, and Li+ or Cd2+ [45]. Regarding the small rotaxane

• other synthetic methods: (1) the reaction can proceed on a 100 g scale in a 1 L flask and a 500 mL solution of water, sufficiently indicating the possibility of large-scale material applications; (2) the product contains only head-to-head structured [3]rotaxane, as confirmed by the X-ray crystal

• structure analysis, and is purified by simple precipitation without requiring chromatography; (3) various end-capping agents are available, and well-optimized conditions can ensure a high yield (e.g., 2-methoxyphenyl isocyanate obtains an 85% yield after 3 h of reaction [49]). Owing to such a high-yield

Tailored charge-neutral self-assembled L₂Zn₂ container for taming oxalate

• David Ocklenburg and
• David Van Craen

Beilstein J. Org. Chem. 2024, 20, 3007–3015, doi:10.3762/bjoc.20.250

• well as metalla-bowls [76][77][78][79] resulting in binding constants of log K = 3.60 [76], 4.60 [77], and 3.48 [78] for oxalate binding in methanol. Additionally, a crystal structure of a positively charged copper(II) helicate with encapsulated oxalate was reported in a study with the focus on

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

• charge on this substituent in the hypervalent bond. The long I–X distances (a = 2.758–4.165 Å) are indicative of ionic compounds, with the exception of the cyclic benziodoxolone 2, in which a covalent I–O bond is observed (a = 2.484 Å). We were unable to obtain a crystal structure of the ortho-nitro

• compound 1j. However, a previously reported crystal structure of ylid 3, which also contains an ortho-nitrobenzene substituent, suggests a pseudocyclic structure where the nitro group is coordinating to the iodine centre (a(I–ON) = 2.695 Å) [28], which we propose is likely to be the case in 1j as well. In

• ligand occupies the position trans to the ylid substituent, with the aryl substituent in the equatorial position. Substituents on hypervalent iodine compounds can interconvert via Barry pseudorotation [31] and, interestingly, the crystal structure for compound 1i contains two isomers in its unit cell

The charge transport properties of dicyanomethylene-functionalised violanthrone derivatives

• Sondos A. J. Almahmoud,
• Joseph Cameron,
• Dylan Wilkinson,
• Michele Cariello,
• Claire Wilson,
• Alan A. Wiles,
• Peter J. Skabara and
• Graeme Cooke

Beilstein J. Org. Chem. 2024, 20, 2921–2930, doi:10.3762/bjoc.20.244

• single-crystal X-ray analysis were obtained by slow evaporation of a dichloromethane/isopropanol solution of 3b. The crystal structure of 3b, displayed in Figure 4, shows a very similar twisted conformation of the core of the molecule to that of the related methoxy-substituted structure obtained from

• . Details of the crystal structure of 3b are given in the CIF which can be obtained from the CCDC free of charge CCDC 2128169 from the Cambridge Crystallographic Data Centre [40]. Compound 3c Compound 2c (300 mg, 0.360 mmol) and malononitrile (100 mg, 1.08 mmol) were dissolved in anhydrous chlorobenzene (6

• dihydroxyviolanthrone. Chemical structures of 2b and 3b. Optimised ground state geometries of compounds 2 and 3 calculated using B3LYP/6-311G(d,p) in the gas phase. Views of the crystal structure of 3b (left, shows displacement ellipsoids drawn at 50% probability level, right showing the twisted conformation

Synthesis of pyrrole-fused dibenzoxazepine/dibenzothiazepine/triazolobenzodiazepine derivatives via isocyanide-based multicomponent reactions

• Marzieh Norouzi,
• Mohammad Taghi Nazeri,
• Ahmad Shaabani and
• Behrouz Notash

Beilstein J. Org. Chem. 2024, 20, 2870–2882, doi:10.3762/bjoc.20.241

• studied by X-ray diffraction analysis, and the crystal structure is illustrated in Figure 2 (detailed information can be found in the Supporting Information File 1). The 1H NMR spectrum of product 6f obtained through the I-MCR was investigated and some unexpected chemical shifts were observed at room

• washed with n-hexane and ethyl acetate solvent mixtures (1:3 for 3a and 3d; 2:1 for compounds 5). Representation of distinguished structures of benzodiazepine/benzoxazepine/benzothiazepine with pharmaceutical to electronic applications. The crystal structure of 4h (CCDC 2365305). The DNMR (dynamic

• nuclear magnetic resonance) spectra of compound 6f (DMSO-d6, 300 MHz) at 25–85 °C; spectrum A: 25 °C, spectrum B: 35 °C, spectrum C: 45 °C, spectrum D: 55 °C, spectrum E: 65 °C, spectrum F: 75 °C and spectrum E: 85 °C. The crystal structure of 6a (CCDC2365306). UV–vis absorption for compounds 4a, 6c and

N-Glycosides of indigo, indirubin, and isoindigo: blue, red, and yellow sugars and their cancerostatic activity

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 2840–2869, doi:10.3762/bjoc.20.240

• not visible, E/Z < 2:98). The configurations were determined by comparison of chemical shifts of our products with those of non-glycosylated indirubin, by the presence of an intramolecular hydrogen bond N–H···O and by crystal structure analysis. In fact, the chemical shifts of the H-4 proton signals

• products with those of non-glycosylated thioindirubin and by crystal structure analysis. As mentioned above for the indirubins, the chemical shifts of the H-4 proton signals are strongly influenced by the anisotropic effect of the carbonyl group resulting in a downfield shift in case of the Z-isomers. In

• with those of non-glycosylated indirubin, by the presence of an intramolecular hydrogen bond N–H···O and by crystal structure analysis. As mentioned above for the indirubins and thioindirubins, the chemical shifts of the H-4 proton signals are strongly influenced by the anisotropic effect of the

C–C Coupling in sterically demanding porphyrin environments

• Liam Cribbin,
• Brendan Twamley,
• Nicolae Buga,
• John E. O’ Brien,
• Raphael Bühler,
• Roland A. Fischer and
• Mathias O. Senge

Beilstein J. Org. Chem. 2024, 20, 2784–2798, doi:10.3762/bjoc.20.234

• reactivity, where not previously possible. X-ray crystal structure analysis Despite the many examples in literature of the crystal structure and packing of nonplanar porphyrins [3][6][8][13][52][53], few examples of crystal structure and packing analysis exist for arm-extended porphyrins. One of the few

• interesting crystal packing features were that observed in the structures of compound 27 and borylated porphyrin 46. In the case of porphyrin 27, when crystallized by slow evaporation from CDCl3, a crystal structure with a void diameter of approximately 5.8 Å was obtained (Figure 4). The void was measured

• compared to tightly packed arrangements, similar to nitrobenzene, bis(pinacolato)diboron may be templating the formation of these channels [61]. However, more research is needed to understand the formation of these supramolecular assemblies. X-ray crystal structure analysis of compound 11 As observed in

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

• ]+ calcld for C30H32ClN2O4, 519.2045; found, 519.2051. The X-ray crystal structure of compound 4a (CCDC 2352876). The X-ray crystal structure of compound 7 (CCDC 2352878). Synthesis of tetronic acid derivatives. Synthesis of amide derivatives 3. Synthesis of target tetronic acids 4a. aReaction conditions

• , copies of NMR spectra, X-ray crystallographic data and refinement details. Supporting Information File 142: Analytical data of all compounds 4, 7 and 9. Acknowledgements Crystal structure determination was performed in the Department of Structural Studies of Zelinsky Institute of Organic Chemistry

HFIP as a versatile solvent in resorcin[n]arene synthesis

• Hormoz Khosravi,
• Valeria Stevens and
• Raúl Hernández Sánchez

Beilstein J. Org. Chem. 2024, 20, 2469–2475, doi:10.3762/bjoc.20.211

• translated to the formation of other macrocycles as long as they share a similar reaction mechanism. (a) Control experiment testing deiodination of 2-iodoresorcinol. (b) Molecular crystal structure of chlorinated resorcin[4]arenes 1h and 1i, and carboxylic acid-containing 1s at 100 K. Thermal ellipsoids are

Synthesis and conformational analysis of pyran inter-halide analogues of ᴅ-talose

• Olivier Lessard,
• Mathilde Grosset-Magagne,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2024, 20, 2442–2454, doi:10.3762/bjoc.20.208

• results showed no qualitative difference. Entries marked – are below the 0.50 kcal/mol threshold. Supporting Information Supporting Information File 118: Experimental and analytical data, crystal structure determination and NMR spectra. Funding This work was supported by the Natural Sciences and

Evaluating the halogen bonding strength of a iodoloisoxazolium(III) salt

• Dominik L. Reinhard,
• Anna Schmidt,
• Marc Sons,
• Julian Wolf,
• Elric Engelage and
• Stefan M. Huber

Beilstein J. Org. Chem. 2024, 20, 2401–2407, doi:10.3762/bjoc.20.204

• ) Å, 84% of Σr, and C1–I1···Br1 = 176.08(9)°]. The bond distances indicate that the hydrogen bond is noticeably weaker than the two XBs and thus constitutes merely an assisting interaction. The XB interactions in this crystal structure were compared to the ones in the literature-known co-crystal of

• prototypic iodolium 1BArF with bromide (CCDC: 1145291) [5]. For the latter, such a dimeric binding motif was also found, with I–Br bond lengths of 3.1936(9) Å [83% of Σr] and 3.2299(9) Å [84% of Σr]. It can be concluded that stronger halogen bonding can be found in the crystal structure of iodoloisoxazolium

• 3Cl which resulted from crystallization of the respective cation with the abstracted chloride from the Ritter-type solvolysis of benzhydryl chloride [13]. The crystal structure of 5Br was also obtained directly from the halide-abstraction reaction (see Supporting Information File 1). These three facts

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

• 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

Tandem diazotization/cyclization approach for the synthesis of a fused 1,2,3-triazinone-furazan/furoxan heterocyclic system

• Yuri A. Sidunets,
• Valeriya G. Melekhina and
• Leonid L. Fershtat

Beilstein J. Org. Chem. 2024, 20, 2342–2348, doi:10.3762/bjoc.20.200

• . Supporting Information Supporting Information File 96: Experimental procedures, characterization data of all products, copies of 1H, 13C NMR, 15N spectra of new compounds, DSC curves,X-ray crystallographic data and copies of IR spectra. Acknowledgements The crystal structure determination was performed at

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

• -phenyl-3,5-substituted pyrazoles 148 (Scheme 51) [156]. Efforts to synthesize bridged pyrazoles using fumaryl chloride proved unsuccessful, with only 3,5-substituted pyrazoles isolated. Nonetheless, the crystal structure of such a pyrazole was investigated [157]. In their study, Alizadeh et al. showed

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

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• intermolecular Diels–Alder reactions with 34 or other dienophiles, leading to a diverse array of bisorbicillinoids. Based on the crystal structure of TropB, a homologous enzyme of SorbC, Narayan and co-workers have intensively elucidated that the detailed mechanisms of the oxidative dearomatization catalyzed by

• total synthesis of 3 utilizing an identified Diels–Alderase, MaDA. (A) Chemo-enzymatically synthesized natural products by using the originally identified MaDA. (B) MaDA homologue enzyme MaDA-3: X-ray crystal structure and synthesized natural products by leveraging this enzyme. Proposed biosynthetic

Oxidation of benzylic alcohols to carbonyls using N-heterocyclic stabilized λ³-iodanes

• Thomas J. Kuczmera,
• Pim Puylaert and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2024, 20, 1677–1683, doi:10.3762/bjoc.20.149

• ]. A crystal structure was additionally obtained for tetrazine 1c. Bond lengths and angles were similar to those of known five-membered NHIs [25], including a strong intramolecular interaction between the nitrogen of the tetrazine and the hypervalent iodine atom (I1–N1: 2.44(4) Å; the sum of VdW radii

• on silica. Overview of common non-iodine-based (left) and iodine-based (right) oxidizing reagents for the generation of carbonyls from the corresponding alcohols. NHIs investigated for the oxidation of benzylic alcohols and the crystal structure (ORTEP drawing) of 1c (CCDC 2321313), showing the

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

• cyclised core peptide to exert its effects on the precursor peptide. Furthermore, SAM was shown to be an obligate co-substrate for OlvSA [71]. Crystallographic data of OlvSA is not yet available. The predicted three-dimensional structure displays substantial differences from the crystal structure of LahSB

• cobalamin and the [4Fe-4S] cluster (Figure 10). The structural variation among C-MTs becomes apparent when comparing the crystal structure of TsrM with the predicted structures of PoyB and PoyC. Class C rSAM MTs are enzymes with a HemN-like didomain structure, consisting of an rSAM core domain and a C

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

• and cloned from deep-sea-derived Microbulbifer sp. JAMB-A94 with pH and temperature optima being 7.0 and 55 °C, respectively [26]. The recombinant enzyme was likewise produced using a B. subtilis host. The crystal structure of the catalytic domain was determined to show a β-jelly roll fold with

• structural similarity to two other β-agarases, ZgAgaA and ZgAgaB, from Zobellia galactanivorans, which is a model marine bacterium for the bioconversion of algal biomass [29][107][108][109]. The crystal structure suggested that the thermostability of rAgaA likely derives from the numerous surface salt

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

• (nN→σ*CF anomeric and σCH→σ*CF fluorine gauche effects) on the conformation of different stereoisomers is explored. MAE comparing the geometry parameters (bond length, bond angle, and dihedral angle) obtained from DFT calculations at the CCSD/DGTZVP level. The MAE for the crystal structure compared to

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• the known crystal structure. The extended E-isomer establishes contact through galactoside and the first aryl ring only, while the bent Z-isomer has proper conformation to wrap around the central His53 residue and to establish a more extended interaction with the protein surface. This would be in

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

• KRC, the N-terminal helix αB and the lid region αFG located at the C-terminal of KRC (Figure 2d). Indeed, this lid region exhibits a direct interaction with the DH and DH-KR linker (Figure 2c). However, such interaction was not observed between the N-terminal helix αB and DH in the crystal structure

• rings. The triangles indicate a product having α-substituents. (c) Crystal structure of DH-ER-KR tridomain (PDB ID 8G7W) [24]. DH, KRS, ER, KRC are colored in cyan, pink, yellow, and purple, respectively. The lid of KR catalytic pocket is colored in red. The co-crystallized cofactor is represented as