Tri(n-butyl)phosphine-promoted domino reaction for the efficient construction of spiro[cyclohexane-1,3'-indolines] and spiro[indoline-3,2'-furan-3',3''-indolines]

• Hui Zheng,
• Ying Han,
• Jing Sun and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2022, 18, 669–679, doi:10.3762/bjoc.18.68

• (thiophen-2-yl)penta-1,4-dien-3-one was also successfully employed in the reaction. The major isomers of the corresponding spiro compounds 3x and 3y were predominately produced in moderate yields. In order to determine the relative configuration of the spiro compounds, the single crystal structures of the

• to give selectively spiro[indoline-3,2'-furan-3',3''-indolines] in satisfactory yields. The relative configuration of the complex spirooxindoles was confirmed by determination of several single crystal structures. Also, plausible reaction mechanisms have been proposed. This reaction has the

A Se···O bonding catalysis approach to the synthesis of calix[4]pyrroles

• Qingzhe Tong,
• Zhiguo Zhao and
• Yao Wang

Beilstein J. Org. Chem. 2022, 18, 325–330, doi:10.3762/bjoc.18.36

• range of typical reactions [24], thus providing a new platform for organic synthesis. The phenomenon of chalcogen bonding was initially observed in the crystal structures of small organic molecules as well as proteins [25]. The application of this type of bonding interactions has achieved significant

Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase

• Peterson de Andrade,
• Sanaz Ahmadipour and
• Robert A. Field

Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24

• [4]. For instance, hydrophobic pockets in the glycerol- and acetamide-binding subsites have been reported for neuraminidases [10][37] as well as for TcTS, which has a more spacious and hydrophobic active site around C9 of sialic acid [16]. Nonetheless, a simple comparison from the crystal structures

Efficient synthesis of polyfunctionalized carbazoles and pyrrolo[3,4-c]carbazoles via domino Diels–Alder reaction

• Ren-Jie Fang,
• Chen Yan,
• Jing Sun,
• Ying Han and
• Chao-Guo Yan

Beilstein J. Org. Chem. 2021, 17, 2425–2432, doi:10.3762/bjoc.17.159

• of p-toluenesulfonic acid. The structures of both products were fully characterized by various spectroscopy methods and confirmed by determination of their single crystal structures (Figure 2 and Figure 3). From Figure 2, it can be seen that the phenyl group and the adjacent p-chlorobenzoyl group are

Synthesis and antimicrobial activity of 1H-1,2,3-triazole and carboxylate analogues of metronidazole

• Satya Kumar Avula,
• Syed Raza Shah,
• Khdija Al-Hosni,
• Muhammad U. Anwar,
• Rene Csuk,
• Biswanath Das and
• Ahmed Al-Harrasi

Beilstein J. Org. Chem. 2021, 17, 2377–2384, doi:10.3762/bjoc.17.154

• . Crystal structure of compound 3. Colour codes: carbon = grey, mitrogen = blue, oxygen = red, hydrogen = white. Crystal structure of 1H-1,2,3-triazole compound 5c: Colour codes: carbon = grey, nitrogen = blue, oxygen = red, fluorine = yellow, hydrogen = white. Crystal structures of compound 7b. Colour

Co-crystallization of an organic solid and a tetraaryladamantane at room temperature

• Fabian Rami,
• Jan Nowak,
• Felix Krupp,
• Wolfgang Frey and
• Clemens Richert

Beilstein J. Org. Chem. 2021, 17, 1476–1480, doi:10.3762/bjoc.17.103

• as guest molecules. Here we report the co-crystal structures of phenol, which is solid at room temperature, with both 1,3,5,7-tetrakis(2,4-dimethoxyphenyl)adamantane (TDA) and 1,3,5,7-tetrakis(2,4-diethoxyphenyl)adamantane (TEO). The co-crystals were obtained from solutions in dichloromethane by slow

• (2,4-diethoxyphenyl)adamantane (TEO), and 1,3,5,7-tetrakis(2-bromo-4-methoxyphenyl)adamantane (TBro). The X-ray crystal structures of over 100 EnOCs have been reported thus far [13][14][15][16], including structures with chiral guests that allow for the determination of the absolute [17] or relative

• configuration [18]. One limitation of the EnOC method was that the guest compound to be encapsulated had to be a liquid, so that it could act as solvent for the TAA, which would rapidly crystallize upon cooling of a hot, saturated solution. Here we report two co-crystal structures of TAAs with phenol, obtained

Structural effects of meso-halogenation on porphyrins

• Keith J. Flanagan,
• Maximilian Paradiz Dominguez,
• Zoi Melissari,
• Hans-Georg Eckhardt,
• René M. Williams,
• Dáire Gibbons,
• Caroline Prior,
• Gemma M. Locke,
• Alina Meindl,
• Aoife A. Ryan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2021, 17, 1149–1170, doi:10.3762/bjoc.17.88

• CSD. In this study we have used the Hirshfeld fingerprint plots together with normal-coordinate structural decomposition and determined crystal structures to elucidate the conformation, present intermolecular interactions, and compare respective contacts within the crystalline architectures

• structures, the features are generally similar to each other. DFT calculations and NSD analysis The limited availability of meso-halogenic porphyrin crystal structures in the CSD makes it difficult to study a complete series. While we can develop certain trends based on the current data sets, the gaps

• data in the supporting information for completion. However, we were able to extract atom coordinates and NSD data which can be compared to the existing crystal structures (Supporting Information File 1, Figures S72–S74 and S75–S129) [28][45]. Series 1 In series 1 (Figure 22) the conformations of the

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• in nuclease stability, even relative to PS-modified duplexes [91]. Crystal structures of PS2-modified RNA duplexes were determined to be isomorphous to their native RNA counterpart, causing no perturbation in the ribose sugar conformation, nor the torsion angles of the backbone [92]. More

Synthesis of (Z)-3-[amino(phenyl)methylidene]-1,3-dihydro-2H-indol-2-ones using an Eschenmoser coupling reaction

• Lukáš Marek,
• Lukáš Kolman,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2021, 17, 527–539, doi:10.3762/bjoc.17.47

• solid state by X-ray diffraction. The important role of the intramolecular hydrogen bond fixing the (Z)-configuration has also been observed in the crystal structures of other 3-aminomethylidene derivatives containing a primary or secondary nitrogen [14][49][50][51][52]. The (Z)-configuration of the

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• intrinsically disordered proteins remains unclear. 6 Fluoroprolines in crystal structures of proteins Several high-resolution crystal structures have been reported for proteins containing fluoroprolines. In a study of enhanced green fluorescent protein from Aquorea victoria, fluoroprolines were incorporated at

• (position 76) [120]. Both S-Flp and R-Flp were incorporated into the mutant. The resulting protein variant showed an elevated stability in the reduced, and a lowered stability in the oxidized form of the protein. Crystal structures of the proteins containing Pro, S-Flp and R-Flp at position 76 demonstrated

• their high similarity (Figure 12D). The variants containing Pro and R-Flp did not show a clearly defined pucker, whereas the variant with S-Flp was found in a single C4-endo-pucker conformation. Overall, the crystal structures illustrate that the pucker preference observed in small molecules (Figure 6

Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• -regioisomers (152–156 and 143.4 ppm for 1-methyl-5H-tetrazole) [31]. The de-tert-butylation selectivity observed for compound 11b can be explained by the higher stability of the t-Bu cation versus the Me cation. Crystal structures The mesoionic compounds 8a, 10, 11a, and salt 9 were characterized by single

• show no hydrogen bonds in their crystal structures and only van der Waals interactions take place between the molecules. The bistetrazolium salt 9 (bromide salt of mesoionic compound 10) crystallizes in the trigonal space group , with 18 formula units in the unit cell. The asymmetric unit includes one

Au(III) complexes with tetradentate-cyclam-based ligands

• Ann Christin Reiersølmoen,
• Thomas N. Solvi and
• Anne Fiksdahl

Beilstein J. Org. Chem. 2021, 17, 186–192, doi:10.3762/bjoc.17.18

• -tetraazacyclotetradecane), cyclen (1,4,7,10-tetraazacyclododecane)), ethylenediamine and triethylenetetraamine derivatives. Studies of Au(III)-cyclam modified complexes have been limited to arylated [16] or polymer-bound cyclams for selective uptake of Au(III) from water [17] as well as X-ray crystal structures [18][19

Tuning the solid-state emission of liquid crystalline nitro-cyanostilbene by halogen bonding

• Subrata Nath,
• Alexander Kappelt,
• Matthias Spengler,
• Bibhisan Roy,
• Jens Voskuhl and
• Michael Giese

Beilstein J. Org. Chem. 2021, 17, 124–131, doi:10.3762/bjoc.17.13

• group is a suitable halogen bond acceptor, which interacts with polarised iodobenzene components in three different geometries – symmetrical, unsymmetrical or sidewise. Many other crystal structures support these findings and suggest the suitability of this synthon for the construction of supramolecular

Synthesis, crystal structures and properties of carbazole-based [6]helicenes fused with an azine ring

• Daria I. Tonkoglazova,
• Anna V. Gulevskaya,
• Konstantin A. Chistyakov and
• Olga I. Askalepova

Beilstein J. Org. Chem. 2021, 17, 11–21, doi:10.3762/bjoc.17.2

• steps of the method are electrophile-induced 6-endo-dig cyclizations of ortho-alkynylated biaryls. The overall yields of helicenes in five stages of the synthesis exceed 30%. The single-crystal X-ray diffraction analysis revealed the non-planar crystal structures of the synthesized helicenes responsible

Construction of pillar[4]arene[1]quinone–1,10-dibromodecane pseudorotaxanes in solution and in the solid state

• Xinru Sheng,
• Errui Li and
• Feihe Huang

Beilstein J. Org. Chem. 2020, 16, 2954–2959, doi:10.3762/bjoc.16.245

• pseudorotaxanes to construct rotaxanes, which will broaden the range of potential applications of pillararene derivatives for the manufacture of sophisticated supramolecular architectures and functional supramolecular systems. Crystal structures of the [3]pseudorotaxane composed of H and G in the solid state

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

• connection to the crown ether core, and in NDIC7, a more flexible ethylenediamine linker is used. Crown ether synthesis and crystal structures With respect to the synthesis of previously reported TTFC8 and exTTFC8 [35][37], we synthesized the novel 21-crown-7 analogs following a similar synthetic route

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

• be detected by its luminescence [77][78][79]. Overall, while crystal structures provide fantastic insight into molecular interactions of such supramolecular ligands, they do not necessarily reflect the binding situation in solution. Furthermore, to our knowledge no protein co-crystal structures with

• (SEC-MALS), and have provided detailed insight into the binding mechanism of these supramolecular ligands. In general, the binding sites showing the largest perturbations in the NMR titrations largely agree with the sites observed in the crystal structures. Occasional discrepancies, where an additional

• in the crystal structures, which enable a greater diversity of non-covalent interactions with the protein and even different binding modes on the same lysine side chain. With increasing ring size, the calixarenes promote ligand-induced ordered multimerization of proteins. Cyt c for example is

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

• the microarray along with glycan ligand length parameters. GlyMDB then retrieves the protein crystal structures for those PDB ids with protein matching the sample and glycans in the PDB structure. It allows you to view the structure in the browser to see how the glycan binds to the protein. GlyMDB

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

• )6 and (2a)6·Li2O·(THF)6 with functionalized sulfonyl dilithio methandiides Besides the crystal structures of (2a)4·(THF)6 and (2a)6·Li2O·(THF)6 those of the sulfonyl dilithio methandiides IIIa (FG1 = SO2Ph, FG2 = P(S)Ph2) [36] and IIIb ((FG1 = SO2Ph, FG2 = P(NSiMe3)Ph2) [43] have been determined

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

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

• ]. The estimated structure was supported by crystal structures of similar structural compounds [23]. Figure 2b suggests that the steric hindrance around the C30 ester group of intermediate 6 has a remarkable influence on the aminolysis reaction. The mechanism of the aminolysis reaction revealed that a

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

• dependent on the temperature as shown in Table 1. It is assumed that the ring-rotation process, which generated the regioisomer did not occurred in case of 4a because of two larger methoxy groups than the methylenedioxy group. Crystal structures of 5a–c Single crystals of 5a–c were successfully obtained by

Regioselectively α- and β-alkynylated BODIPY dyes via gold(I)-catalyzed direct C–H functionalization and their photophysical properties

• Takahide Shimada,
• Shigeki Mori,
• Masatoshi Ishida and
• Hiroyuki Furuta

Beilstein J. Org. Chem. 2020, 16, 587–595, doi:10.3762/bjoc.16.53

• : triisopropylsilyl group; Mes: 2,4,6-trimethylphenyl group. Top and front views of the crystal structures of (a) 4a and (b) 6b with 50% thermal ellipsoid probabilities. The isopropyl groups on the silicon atom are omitted in the front view for clarity. Partial 1H NMR spectra of (a) 1a, (b) 3a, (c) 4a, (d) 5a, and (e

Synthesis and circularly polarized luminescence properties of BINOL-derived bisbenzofuro[2,3-b:3’,2’-e]pyridines (BBZFPys)

• Ryo Takishima,
• Yuji Nishii,
• Tomoaki Hinoue,
• Yoshitane Imai and
• Masahiro Miura

Beilstein J. Org. Chem. 2020, 16, 325–336, doi:10.3762/bjoc.16.32

• characteristics in the solid state. The crystal structures of the coupling products were also evaluated by single crystal X-ray analysis and the well-ordered intermolecular stacking arrangements appeared to be responsible for the enhanced CPL. Keywords: BINOL; C–H activation; circularly polarized luminescence

• and 4c were likely to assist the formation of well-ordered aggregates, being consistent with the observation of the red-shifted luminescence discussed above. Crystal structures of 4b and 4c The molecular structures of 4b and 4c were unambiguously determined by single crystal X-ray diffraction analysis

• stacking distance of around 3.45 Å. It is noteworthy that both 4b and 4c pile up while minimizing the steric repulsion between the tert-butyl groups which occupy “staggered” orientations in their crystal structures (Figure 5c and 5d). Unfortunately, the crystal structure of 4a was not determined after

Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors

• Man-Man Wang,
• Hao Huang,
• Lei Shu,
• Jian-Min Liu,
• Jian-Qiu Zhang,
• Yi-Le Yan and
• Da-Yong Zhang

Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25

• docking study was conducted with the method reported previously [10][19][32][33][34]. Crystal structures of Arabidopsis thaliana HPPD (PDB ID: 1TFZ) with the native ligand, named DAS869 were downloaded from the Protein Data Bank. The docking was carried out using Discovery Studio 4.0. During the docking

• binding modes of compound I39 and I40 in a target enzyme (AtHPPD). The key residues in the active site are shown in blue sticks, the FeII is shown as a dark blue sphere, and compound I39 and I40 is shown in gray sticks. Crystal structures of I18 and III4. Simulated binding mode of mesotrione (A), compound