Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• synthesized in moderate yields of 24% and 26%, respectively, over three steps from the same two building blocks, the ditosylate 5 and the monobutyl-protected NDI precursor 7 (Scheme 1). The connectivity and conformation of exTTFC7 was observed in the crystal structure obtained from crystals generated through

• slow evaporation of a CH2Cl2/CH3CN solution. The structure of the exTTF unit does not exhibit any significant changes upon incorporation into the crown ether [48]. No intermolecular stacking between the exTTF units was observed in the crystal structure of exTTFC7 (Figure 2a and section 2 in Supporting

• the experiment. The folded structure observed in the crystal structure hints towards a possible “side-on” complex, where the ammonium axle is not threading through the ring of the macrocycle, yet still forms hydrogen bonds to the crown ether [24][25] (see spectroelectrochemical measurements below

Synthesis of novel fluorinated building blocks via halofluorination and related reactions

• Attila Márió Remete,
• Tamás T. Novák,
• Melinda Nonn,
• Matti Haukka,
• Ferenc Fülöp and
• Loránd Kiss

Beilstein J. Org. Chem. 2020, 16, 2562–2575, doi:10.3762/bjoc.16.208

• fine-tuning the reaction conditions of other halofluorination and fluoroselenation reactions are currently being studied in our research group. Crystal structure of (rac)-11b. Crystal structure of the product (rac)-15a. Crystal structure of the product (rac)-15b. Proposed outcome of the

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• S6 in Supporting Information File 1). Movahedin et al. hypothesized that the glycan modulates the conformation of the peptide portion of the Tn-antigen and does not bind directly, noting that in the crystal structure GalNAc is positioned 4 Å away from the side chain of Tyr100, and indicating that any

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• the number of methyl groups [29][49]. On the protein surface, both ligands showed a clear preference for the sterically most accessible dimethyl-lysine residue K34Me2 which is located in a solvent-accessible loop. Binding of cucurbit[7]uril to this residue was confirmed by the co-crystal structure of

• isomerase hPin1 (original data) is shown as an example in Figure 3. On the regulatory N-domain of of the AAA+ ATPase p97 (p97-N), tweezers were found to bind only 6 patches even though this protein domain contains 30 Lys and Arg residues (26 of these are observable in the p97 crystal structure, pdb # 3CF3

Chan–Evans–Lam N1-(het)arylation and N1-alkеnylation of 4-fluoroalkylpyrimidin-2(1H)-ones

• Viktor M. Tkachuk,
• Oleh O. Lukianov,
• Mykhailo V. Vovk,
• Isabelle Gillaizeau and
• Volodymyr A. Sukach

Beilstein J. Org. Chem. 2020, 16, 2304–2313, doi:10.3762/bjoc.16.191

• analogous enamides [57], the facile [2 + 2] photocycloaddition process likely occurred due to favorable orientation of the interacting molecules and close contacts between alkene carbon atoms in the crystal structure. Consequently, the synthesis of product 5c was performed in darkness. N1-Styryl-substituted

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• this software a user uploads a glycan binding protein complexed to a carbohydrate fragment in PDB format. This need not be a co-crystal structure, and can be a modeled structure as well. The application then finds glycans that contain this fragment which are present on the CFG microarray data and

Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 2212–2259, doi:10.3762/bjoc.16.186

• twentieth century when for the first time corannulene was reported by Barth et al. [10] at the University of Michigan (USA) in 1966 (crystal structure 1971) [11]. On the other hand, since the discovery of fullerene (C60) in 1985 [12] by Sir Harry Kroto and the first synthesis of sumanene in 2003 by Sakurai

• not only confirmed by spectroscopic data but also identified by virtue of the single crystal structure. The reason for their unsuccessful results may be the generation of strain in the sumanene molecule from planar aromatic architecture under the experimental reaction conditions. In the quest for

• unable to isolate dioxosumanene 39 under similar reaction conditions in reasonable yield. The structures of these compounds were established by spectroscopy means and also in the case of monosumanene 38, they obtained the single crystal structure which was showing almost a similar bowl depth as for the

Access to highly substituted oxazoles by the reaction of α-azidochalcone with potassium thiocyanate

• Mysore Bhyrappa Harisha,
• Pandi Dhanalakshmi,
• Rajendran Suresh,
• Raju Ranjith Kumar and
• Shanmugam Muthusubramanian

Beilstein J. Org. Chem. 2020, 16, 2108–2118, doi:10.3762/bjoc.16.178

• ) using ethyl acetate/petroleum ether mixture to afford product 4. Examples of biologically active oxazole and aminothiazole scaffolds. Large-scale synthesis of 3i. a) At the start of the reaction, b) after the reaction. ORTEP diagram of compound 5. X-ray crystal structure of 4h. Strategies for the

Isolation and structure determination of a tetrameric sulfonyl dilithio methandiide in solution based on crystal structure analysis and ⁶Li/¹³C NMR spectroscopic data

• Jürgen Vollhardt,
• Hans Jörg Lindner and
• Hans-Joachim Gais

Beilstein J. Org. Chem. 2020, 16, 2057–2063, doi:10.3762/bjoc.16.172

• up to now. Herein, we describe the isolation and determination of the structure of tetrameric dilithio (trimethylsilyl)(phenylsulfonyl) methandiide in solution and in the crystal. The elucidation of the structure of the tetramer is based on crystal structure analysis and 13C/6Li NMR spectroscopic

• in THF solution in fast equilibrium with a further aggregate, which is stable only at low temperatures. Keywords: crystal structure; dilithio sulfonyl methandiide; NMR; solution structure; X-ray analysis; Introduction Functionalized dilithio methandiides I–III (Figure 1) are a fascinating class of

• and sulfonyl-substituted dilithio methandiide 2a [14][15]. The use of n-BuLi, inadvertently containing Li2O, had yielded prismatic crystals of 2a. An X-ray crystal structure analysis had shown a Ci symmetric hexamer, (2a)6·Li2O·(THF)6, the dianionic C atoms of which are each coordinated by two Li

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• Information File 1) of galectin-1, a β-sheet lectin protein that is available in bovine spleen [53] (for a detailed crystal structure see the Protein Data Bank; PDB ID 1SLT). Given the amphiphilic and pH-responsive nature of PEP-1, we investigated both the pH- and concentration-dependent formation of

Controlling the stereochemistry in 2-oxo-aldehyde-derived Ugi adducts through the cinchona alkaloid-promoted electrophilic fluorination

• Yuqing Wang,
• Gaigai Wang,
• Anatoly A. Peshkov,
• Ruwei Yao,
• Muhammad Hasan,
• Manzoor Zaman,
• Chao Liu,
• Stepan Kashtanov,
• Olga P. Pereshivko and
• Vsevolod A. Peshkov

Beilstein J. Org. Chem. 2020, 16, 1963–1973, doi:10.3762/bjoc.16.163

• asymmetric electrophilic fluorination for derivatizing the 2-oxo-aldehyde-derived Ugi adducts. This allowed us to obtain the post-Ugi products fluorinated at the peptidyl position with the enantiomeric excess values in several instances reaching more than 70%. Molecular representation of the X-ray crystal

• structure of (S)-12e (slow enantiomer). Post-transformations of 2-oxo-aldehyde-derived Ugi adducts 8. Synthesis of 2-oxo-aldehyde-derived Ugi adducts. Asymmetric protocols for Passerini three-component reaction (P-3CR). Asymmetric protocols for Ugi four-component reaction (U-4CR) by Houk, Tan and co-workers

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• are listed in Table 1. Firstly, the UDP-Galf native donor substrate was docked into the GlfT2 crystal structure to observe the reference docking score and to predict the Ki value for the native donor substrate. The predicted Ki value of the UDP-Galf is 0.333 µM, however, the experimentally observed Km

Microwave-assisted efficient one-pot synthesis of N²-(tetrazol-5-yl)-6-aryl/heteroaryl-5,6-dihydro-1,3,5-triazine-2,4-diamines

• Moustafa Sherief Moustafa,
• Ramadan Ahmed Mekheimer,
• Saleh Mohammed Al-Mousawi,
• Mohamed Abd-Elmonem,
• Hesham El-Zorba,
• Afaf Mohamed Abdel Hameed,
• Tahany Mahmoud Mohamed and
• Kamal Usef Sadek

Beilstein J. Org. Chem. 2020, 16, 1706–1712, doi:10.3762/bjoc.16.142

• and are uncorrected. X-ray crystallographic structure determinations were performed by using Rigaku Rapid II and Bruker X8 Prospector single crystal X-ray diffractometers. The X-ray crystal structure data can be obtained free of charge from the Cambridge Crystallographic Data Centre via http

Fluorohydration of alkynes via I(I)/I(III) catalysis

• Jessica Neufeld,
• Constantin G. Daniliuc and
• Ryan Gilmour

Beilstein J. Org. Chem. 2020, 16, 1627–1635, doi:10.3762/bjoc.16.135

• Hammett analyses, have identified key determinants that are essential for reaction efficiency. X-ray crystal structure analysis of ketone 2 reveals a dihedral angle of φO=C-C-F = −3.7°. Although the origin of this specificity requires clarification, this fluorohydration reaction constitutes a rare case of

NHC-catalyzed enantioselective synthesis of β-trifluoromethyl-β-hydroxyamides

• Alyn T. Davies,
• Mark D. Greenhalgh,
• Alexandra M. Z. Slawin and
• Andrew D. Smith

Beilstein J. Org. Chem. 2020, 16, 1572–1578, doi:10.3762/bjoc.16.129

• support. dMolecular representation of the X-ray crystal structure of 12. The unit cell of 12 contained two molecules of 12, with only one shown for clarity. Proposed mechanism. Optimization of the NHC-catalyzed formal [2 + 2] cycoaddition.a Supporting Information Supporting Information File 335

Five-component, one-pot synthesis of an electroactive rotaxane comprising a bisferrocene macrocycle

• Natalie Lagesse,
• Luca Pisciottani,
• Maxime Douarre,
• Pascale Godard,
• Brice Kauffmann,
• Vicente Martí-Centelles and
• Nathan D. McClenaghan

Beilstein J. Org. Chem. 2020, 16, 1564–1571, doi:10.3762/bjoc.16.128

• ; found, 501.20295. Crystal structure determination Single crystals of rotaxane 1a (C36H42FeN3O3) were obtained by slow evaporation of a dichloromethane solution. A suitable crystal was mounted on a cryoloop with paratone®-N oil on an AFC11 partial Chi goniometer. The data were collected at 120 K on

One-step route to tricyclic fused 1,2,3,4-tetrahydroisoquinoline systems via the Castagnoli–Cushman protocol

• Aleksandar Pashev,
• Nikola Burdzhiev and
• Elena Stanoeva

Beilstein J. Org. Chem. 2020, 16, 1456–1464, doi:10.3762/bjoc.16.121

• recrystallization. Compounds comprising a benzo[a]quinolizidine ring system. Representative NOE interactions in cis and trans-21–24 (only one enantiomer is shown). X-ray crystal structure of products 25 and 26. Representative NOE interactions in 28 and 29. Reactions between enolizable anhydrides and imines

Ferrocenyl-substituted tetrahydrothiophenes via formal [3 + 2]-cycloaddition reactions of ferrocenyl thioketones with donor–acceptor cyclopropanes

• Grzegorz Mlostoń,
• Mateusz Kowalczyk,
• André U. Augustin,
• Peter G. Jones and
• Daniel B. Werz

Beilstein J. Org. Chem. 2020, 16, 1288–1295, doi:10.3762/bjoc.16.109

• obtained free of charge from the Cambridge Crystallographic Data Centre via http://www.ccdc.cam.ac.uk/structures. Supporting Information File 44: Experimental data for selected compounds 9, details of the crystal structure determination, and the original 1H and 13C NMR spectra for all products

The charge-assisted hydrogen-bonded organic framework (CAHOF) self-assembled from the conjugated acid of tetrakis(4-aminophenyl)methane and 2,6-naphthalenedisulfonate as a new class of recyclable Brønsted acid catalysts

• Svetlana A. Kuznetsova,
• Alexander S. Gak,
• Yulia V. Nelyubina,
• Vladimir A. Larionov,
• Han Li,
• Michael North,
• Vladimir P. Zhereb,
• Alexander F. Smol'yakov,
• Artem O. Dmitrienko,
• Michael G. Medvedev,
• Igor S. Gerasimov,
• Ashot S. Saghyan and
• Yuri N. Belokon

Beilstein J. Org. Chem. 2020, 16, 1124–1134, doi:10.3762/bjoc.16.99

• atoms to engage the ammonium groups of TAPM (see the crystal structure of the F-1a phase). This structure was thermodynamically stable and hinted at a possible activation of water or methanol as nucleophiles by the sulfate anions during the ring opening of epoxides. When the coordinated water was

• frameworks could be tuned by varying the ratio of anion/cation multitopic components and the basicity of the cation component. View of the crystal structure of F-1 (F-1a phase), with representation of atoms by thermal ellipsoids at a 30% probability level. The hydrogen atoms, except for those in NH groups

• and solvate water molecules, were omitted for clarity. Only the labels of symmetry-independent heteroatoms are shown. View of the crystal structure of F-1 (F-1a’ phase), with representation of the atoms via thermal ellipsoids at a 30% probability level. The hydrogen atoms, except for those in NH

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• constant of 16 Hz between the two olefinic protons of the styryl fragment. Further characterization of the new oxazolones was provided by the determination of the crystal structure of oxazolone 2c. A molecular drawing of 2c is shown in Figure 4, where the (Z)-configuration of the exocyclic C=C bond (C7–C8

• )=C bond disappeared and two new signals appeared at around 68–69 ppm (quaternary C) and 51–60 ppm (CH). These facts are consistent with the expected hybridization change from Csp2 to Csp3 after formation of the cyclobutane ring. Determination of the crystal structure of complex 4a, which is shown in

• shorter than the sum of the van der Waals radii (2.67 Å) [51]. This suggest a close interaction between these two atoms, as observed in the crystal structure of 2c (see above). The analysis of other internal bond distances and angles in the coordination sphere of the Pd atom shows that they are similar to

Efficient synthesis of piperazinyl amides of 18β-glycyrrhetinic acid

• Dong Cai,
• ZhiHua Zhang,
• Yufan Meng,
• KaiLi Zhu,
• LiYi Chen,
• ChangXiang Yu,
• ChangWei Yu,
• ZiYi Fu,
• DianShen Yang and
• YiXia Gong

Beilstein J. Org. Chem. 2020, 16, 798–808, doi:10.3762/bjoc.16.73

• -glycyrrhetinic acid derivative 18. The molecular structure of compound 18 in the crystalline state is shown in Figure 3. In this crystal structure, there is an orientational disorder of the m-fluorophenyl moiety due to the rotation of a single bond. Details for the crystal structure determinations are given in

• intermediate 6; b) Possible aminolysis process. Crystal structure of conpound 18. Synthesis of compound 4. Reagents and conditions: (a) Ac2O, NEt3, DMF (cat.), DCM, 25 °C, 1 day; (b) oxalyl chloride, NEt3, DMF (cat.), DCM, 25 °C, 5 h, then piperazine, DCM, NEt3, DMAP, 0/25 °C, 30 min. Synthesis of compound 4

One-pot synthesis of dicyclopenta-fused peropyrene via a fourfold alkyne annulation

• Ji Ma,
• Yubin Fu,
• Junzhi Liu and
• Xinliang Feng

Beilstein J. Org. Chem. 2020, 16, 791–797, doi:10.3762/bjoc.16.72

• 1 were obtained by slow evaporation from a carbon disulfide solution, allowing us to disclose the molecular structure by X-ray crystallography (Figure 2a). As shown in Figure 2a, the crystal structure of 1 clearly displayed a nonplanar conformation, resulting from steric repulsion between the phenyl

• . Hydrogen atoms and solvent molecules are omitted for clarity. (d) Selected bond lengths (from the crystal structure) and calculated NICS(1) values of rings A–I in 1. (e) Clar valence structure representation of 1 with three benzeneoid rings. (a) UV–vis absorption spectra of precursor 5 and 1 in CH2Cl2

Towards triptycene functionalization and triptycene-linked porphyrin arrays

• Gemma M. Locke,
• Keith J. Flanagan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2020, 16, 763–777, doi:10.3762/bjoc.16.70

• molecule in the asymmetric unit with the bridgehead substituents being almost 180° to each other (Figure 2, for labelling see Figure S33 in Supporting Information File 1). Unlike the unsubstituted triptycene 1 crystal structure which exhibits a high degree of C–H···π interactions between the aromatic rings

• for C102H88N4O4Si2Zn, 1552.5636; found, 1552.5616. Crystal structure determinations Crystals were grown following the protocol developed by Hope by dissolving the compound in CH2Cl2 and layering with a MeOH for liquid–liquid diffusion [52]. Single crystal X-ray diffraction data for all compounds were

• (iii) of another triptycene molecule. Hydrogen atoms and minor disorder omitted for clarity (thermal displacement 50%). Single crystal X-ray structure of triptycene-linked zinc-nickel porphyrin dimer 16 showing the conformation within the crystal structure; (a) top-view of zinc porphyrin; (b) top-view

Synthesis of C₇₀-fragment buckybowls bearing alkoxy substituents

• Yumi Yakiyama,
• Shota Hishikawa and
• Hidehiro Sakurai

Beilstein J. Org. Chem. 2020, 16, 681–690, doi:10.3762/bjoc.16.66

• vapour diffusion method using CHCl3/hexane conditions. Figure 2 shows the crystal structure of 5a. The crystal was obtained as a racemic compound containing a pair of two enantiomers defined by bowl chirality [26], as a result of the rapid bowl inversion under the crystallization conditions. 5a formed a

• crystal structure of 5c, two crystallographically independent units were observed (Figure 5a). 5c also contained both of the enantiomers and formed a columnar structure along the b axis with the slipped stack manner, which was composed of only one side of the enantiomer (Figure 5b,c). The columns with the

• succeeded in synthesizing three different alkoxy-substituted C70-fragment buckybowls 5a–c. In particular, 5c was not an intended molecule, but was formed unexpectedly through the rearrangement through the Pd-catalyzed C–H bond activation reaction. The X-ray crystal structure analysis of 5a–c clearly

Synthesis of organic liquid crystals containing selectively fluorinated cyclopropanes

• Zeguo Fang,
• Nawaf Al-Maharik,
• Peer Kirsch,
• Matthias Bremer,
• Alexandra M. Z. Slawin and
• David O’Hagan

Beilstein J. Org. Chem. 2020, 16, 674–680, doi:10.3762/bjoc.16.65

• an essentially isoenergetic conformer is that found in the X-ray crystal structure. The first conformers where the terminal bispirocyclohexane ring lies axial are significantly higher in energy (ΔG = +1.25 kcal/mol−1 and ΔG = +1.19 kcal/mol−1) than the equatorial conformers as illustrated in Figure 3