A chiral self-sorting photoresponsive coordination cage based on overcrowded alkenes

• Constantin Stuckhardt,
• Diederik Roke,
• Wojciech Danowski,
• Edwin Otten,
• Sander J. Wezenberg and
• Ben L. Feringa

Beilstein J. Org. Chem. 2019, 15, 2767–2773, doi:10.3762/bjoc.15.268

• crystal of Pd2(stable E-1)4 formed from a racemic mixture of ligand E-1 suitable for X-ray structure determination was grown by vapor diffusion of a 1:1 mixture of benzene and diethyl ether into a solution of the cage in a 1:1 mixture of acetonitrile and chloroform. The crystal structure shows cage

• agreement with the solved X-ray structure (Figure 4). Moreover, the calculations revealed that the homochiral cage Pd2((S,S)-stable E-1)4 (and its enantiomer) are energetically favored by at least 61 kJ mol−1 compared to the other possible diastereomers (Table S1, Supporting Information File 1). Similar

• coordination complexes (SCCs) represent a promising class of compounds which have been used in a variety of molecular systems [1][2][3][4][5][6]. Taking advantage of the vacant cavity inside these complexes, SCCs have been applied in drug delivery [6][7][8], supramolecular catalysis [9][10][11][12], X-ray

Emission solvatochromic, solid-state and aggregation-induced emissive α-pyrones and emission-tuneable 1H-pyridines by Michael addition–cyclocondensation sequences

• Natascha Breuer,
• Irina Gruber,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2019, 15, 2684–2703, doi:10.3762/bjoc.15.262

• -pyridines 5 was further corroborated by a single crystal X-ray structure determination of compound 5a (Figure 1) [35]. In the single crystal the carboxyl ester group is oriented to the N–H and via a hydrogen bond. Solid-state torsional/dihedral angles between the 4- and 6-positioned aryl rings differ

• especially for the 6-positioned phenyl ring with 27° in the X-ray structure and 38° from calculation (for comparison to the DFT calculated ground state structure of 1H-pyridine 5a, see chapter 12.3 in Supporting Information File 1). This is probably due to packing constraints from the involvement of the 6

Synthesis of aryl-substituted thieno[3,2-b]thiophene derivatives and their use for N,S-heterotetracene construction

• Nadezhda S. Demina,
• Nikita A. Kazin,
• Nikolay A. Rasputin,
• Roman A. Irgashev and
• Gennady L. Rusinov

Beilstein J. Org. Chem. 2019, 15, 2678–2683, doi:10.3762/bjoc.15.261

• synthesized in this work. ORTEP diagram for the X-ray structure of compound 7d. Thermal ellipsoids of 50% probability are shown. Synthesis of aryl-substituted TT derivatives 3a–k, product scope, and yields. Synthesis of thieno[3,2-b]thiophen-3(2H)-one 4a–k, product scope, and yields. Synthesis of TTI

Unexpected one-pot formation of the 1H-6a,8a-epiminotricyclopenta[a,c,e][8]annulene system from cyclopentanone, ammonia and dimethyl fumarate. Synthesis of highly strained polycyclic nitroxide and EPR study

• Sergey A. Dobrynin,
• Igor A. Kirilyuk,
• Yuri V. Gatilov,
• Andrey A. Kuzhelev,
• Olesya A. Krumkacheva,
• Matvey V. Fedin,
• Michael K. Bowman and
• Elena G. Bagryanskaya

Beilstein J. Org. Chem. 2019, 15, 2664–2670, doi:10.3762/bjoc.15.259

• -recovery technique with a π-pulse for inversion and a two-pulse ESE sequence for detection. The π-pulse lengths were nominally 20 ns. X-ray structure of compound 1 (one of the two enantiomers present in the crystal). A possible mechanism for the trans-position of the methyne hydrogens in the azepine ring

• : the electrocyclization proceeds via a conrotatory mechanism due to the antisymmetry of the HOMO. Selective formation of a single diastereomer in the 1,3-dipolar cycloaddition reaction. X-ray structure of compound 6 (one of the two enantiomers present in the crystal). A, B) Temperature dependence of

Synthetic terpenoids in the world of fragrances: Iso E Super^® is the showcase

• Alexey Stepanyuk and
• Andreas Kirschning

Beilstein J. Org. Chem. 2019, 15, 2590–2602, doi:10.3762/bjoc.15.252

• discovery of (+)-Iso E Super Plus® (34) as a highly active component (Scheme 6). Fráter et al. confirmed these experiences after isolation of active olfactory compounds of Iso E Super Plus® (34) and Georgywood® (35). Racemic resolution provided a crystalline material that served to obtain an X-ray structure

Self-assembled coordination thioether silver(I) macrocyclic complexes for homogeneous catalysis

• Zhen Cao,
• Aline Lacoudre,
• Cybille Rossy and
• Brigitte Bibal

Beilstein J. Org. Chem. 2019, 15, 2465–2472, doi:10.3762/bjoc.15.239

• three different batches of silver complexes prepared by the same procedure (see Supporting Information File 1, Figure S9). The complex formed with AgNO3 had a different stoichiometry, due to the multidentate nitrate anions. The X-ray structure of 1c appeared as a large (R,S-1)4·(AgNO3)6 complex with

• acetate 70:1) to obtain pyrrole 5. X-ray structures of complex 1a, as two diastereoisomeric macrocycles (R,S-1)2·(AgOTf)2 with ligands assembled in: (a) a head-to-head fashion and, (b) a head-to-tail mode. Hydrogen atoms are omitted for clarity. X-ray structure of complex 1c, as a (R,S-1)4·(AgNO3)6 cage

• with three nitrate anions as coordinating bridges. Hydrogen atoms are omitted for clarity. X-ray structure of complex 1d, as a racemic mixture of (R,R)- and (S,S)-(syn-1)·(PPh3AgOTf)2. Variable temperature 1H NMR of complex 1a in CDCl3 (7 mM) from −30 °C to 60 °C. Synthesis of ligand 1, as its syn

Indium-mediated C-allylation of melibiose

• Christian Denner,
• Manuel Gintner,
• Hanspeter Kählig and
• Walther Schmid

Beilstein J. Org. Chem. 2019, 15, 2458–2464, doi:10.3762/bjoc.15.238

• conversion (98%) was obtained by employing indium as the metal species, a solvent mixture of ethanol/water 4:1 (v/v), at a temperature of 65 °C under vigorous stirring. The resulting epimeric forms were isolated and the stereochemical outcome was determined via X-ray structure analysis of the per-O

Photochromic diarylethene ligands featuring 2-(imidazol-2-yl)pyridine coordination site and their iron(II) complexes

• Andrey G. Lvov,
• Max Mörtel,
• Anton V. Yadykov,
• Frank W. Heinemann,
• Valerii Z. Shirinian and
• Marat M. Khusniyarov

Beilstein J. Org. Chem. 2019, 15, 2428–2437, doi:10.3762/bjoc.15.235

• . Crystals suitable for X-ray structure were obtained in a fritted U-shape tube by the slow diffusion of methanol solutions of in situ-prepared “Fe(H2B(pz)2)2“ and diarylethene 6. Unexpectedly, we have found that the structure of the product depends on the reaction time. Reproducible crystals isolated after

Reversible switching of arylazopyrazole within a metal–organic cage

• Anton I. Hanopolskyi,
• Soumen De,
• Michał J. Białek,
• Yael Diskin-Posner,
• Liat Avram,
• Moran Feller and
• Rafal Klajn

Beilstein J. Org. Chem. 2019, 15, 2398–2407, doi:10.3762/bjoc.15.232

• release of "high-energy" water molecules from the cavity of 2 [50][51]. Determining the X-ray structure was challenging; the difficulty lies in the fact that both the cage and the encapsulated guest dimer exist in the form of two different conformations. Figure 3 shows (E-1)22 that features the main

•  2 above). For example, E-1’s Ha protons at 1.07 ppm correlate with 2’s axial – but not equatorial – acidic imidazole H1 protons (cyan in Figure 2), which is in agreement with the close proximity of these two protons in the X-ray structure (da–1 = 3.68 Å). Conversely, Hc protons only correlate with

• arrangement of the two guest molecules within the X-ray structure is such that the N-bound methyl group (i.e., Hb protons) of one guest lies directly above the phenyl ring of the other guest (see Figure S15, Supporting Information File 1). Specifically, the distance between Hb and the plane of the phenyl ring

Synthesis of acremines A, B and F and studies on the bisacremines

• Nils Winter and
• Dirk Trauner

Beilstein J. Org. Chem. 2019, 15, 2271–2276, doi:10.3762/bjoc.15.219

• 16 (CCDC 1854563) and 17 (CCDC 1854564) are available free from charge on https://www.ccdc.cam.ac.uk/structures/). Supporting Information File 296: Experimental part. Acknowledgements The authors thank Dr. Peter Mayer for X-ray structure analysis. Additionally, we acknowledge the Deutsche

1,2,3,4-Tetrahydro-1,4,5,8-tetraazaanthracene revisited: properties and structural evidence of aromaticity loss

• Arnault Heynderickx,
• Sébastien Nénon,
• Olivier Siri,
• Vladimir Lokshin and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2019, 15, 2059–2068, doi:10.3762/bjoc.15.203

• led to variation of its electron donor/acceptor capability that allowed fine-tuning the absorption properties. The propensity of these compounds and a number of its derivatives to form infinite chains involving >N–H···N= and >N–H···Hal−···N+ atoms is demonstrated by X-ray structure analysis. The DFT

• chemistry also reproduce the distortion, albeit to a smaller extent: 1.07 and 0.2 degrees. The frequency calculation reproduces the experimental IR spectrum reasonably well (Supporting Information File 1, Figure S1). The X-ray structure determination of 6a confirms that the protonation occurs at 5,8

• (Figure 3). At the same time, the geometry optimized structure of 6a exhibits much greater torsion angles of 6.23 and 2.28 degrees. The X-ray structure analysis of 7a confirms that the methylation occurs at the N4 atom to form the respective cation (Figure 4). Examination of the bond distances revealed a

Tautomerism as primary signaling mechanism in metal sensing: the case of amide group

• Vera Deneva,
• Georgi Dobrikov,
• Aurelien Crochet,
• Daniela Nedeltcheva,
• Katharina M. Fromm and
• Liudmil Antonov

Beilstein J. Org. Chem. 2019, 15, 1898–1906, doi:10.3762/bjoc.15.185

• : Theoretically predicted structure of 6K (blue), overlaid with the X-ray structure (red). Right: X-ray structure of 6, #1: x − 1, y, z; #2: x + 1, y, z; H bonds are drawn as blue dashed lines. Left: Absorption spectra of 6 with stepwise addition of Mg(ClO4)2 in acetonitrile (1 – neutral ligand; 7 – complex CMg

A heteroditopic macrocycle as organocatalytic nanoreactor for pyrroloacridinone synthesis in water

• Piyali Sarkar,
• Sayan Sarkar and
• Pradyut Ghosh

Beilstein J. Org. Chem. 2019, 15, 1505–1514, doi:10.3762/bjoc.15.152

• different spectroscopic techniques, 1H NMR, 13C NMR, IR and HRMS. In addition, one of the compounds, 4d, was also examined by single crystal X-ray structure analysis (Figure 5). Mechanistic pathway A probable mechanism is portrayed in Scheme 3 including the role of the BATA-MC nanoreactor. The nanoreactor

Synthesis of pyrrolo[1,2-a]quinolines by formal 1,3-dipolar cycloaddition reactions of quinolinium salts

• Anthony Choi,
• Rebecca M. Morley and
• Iain Coldham

Beilstein J. Org. Chem. 2019, 15, 1480–1484, doi:10.3762/bjoc.15.149

• ). The adducts could be reduced, oxidised, or could undergo Suzuki–Miyaura coupling to give different substituted dihydro- and tetrahydroquinoline derivatives. Single crystal X-ray structure for 7c. Single crystal X-ray structure for 9. Reaction of ketone 1 with electron-deficient alkenes 2. Reactions of

Fluorine-containing substituents: metabolism of the α,α-difluoroethyl thioether motif

• Andrea Rodil,
• Alexandra M. Z. Slawin,
• Nawaf Al-Maharik,
• Ren Tomita and
• David O’Hagan

Beilstein J. Org. Chem. 2019, 15, 1441–1447, doi:10.3762/bjoc.15.144

• of sulfoxide 7 was also confirmed by X-ray structure analysis. The incubation of 4 in C. elegans, and then HPLC purification, was repeated three times all with very similar results. These incubations showed full conversion into the metabolites, and no starting thioether 4 was observed by NMR or HPLC

• Spectrometer, operating in positive and negative mode, from solutions of the analyte in methanol or acetonitrile. The X-ray structure analysis of 7 (CCDC deposition code 1911894) was obtained using a Rigaku XtaLAB P200 diffractometer, using multi-layer mirror monochromed Mo Kα radiation. Structures of

• confirmed by X-ray structure analysis. Putative pathways for (α,α-difluoroethyl)(4-methoxyphenyl)sulfane (4) metabolism. C. elegans incubation of 5. Ratios are the average of three incubations. Incubation (four times) of oxygen ether 14 with C. elegans, gave 4-acetoxyphenol (15) as the major metabolite. On

Selenophene-containing heterotriacenes by a C–Se coupling/cyclization reaction

• Pierre-Olivier Schwartz,
• Sebastian Förtsch,
• Astrid Vogt,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2019, 15, 1379–1393, doi:10.3762/bjoc.15.138

• starting material, but also ring fusion to selenophene was achieved by Cu-catalyzed C–Se cross-coupling reaction [28]. The detailed geometric structure and the packing behaviour in the solid state of triacenes 2–4 have been elucidated by single crystal X-ray structure analysis and X-ray diffraction on

• accordance with data for selenophene compared to thiophene [35]. Single crystal X-ray structure analysis Single crystals of heterotriacenes DTS 2, DST 3, and DSS 4 suitable for X-ray structure analysis were obtained and details of the refinements are summarized in Tables S1-S3 (Supporting Information File 1

• ). X-ray structure analysis of DTT 1 was already published by Brédas et al. [36][37]. Single crystals of DTS 2 and DSS 4 as very thin crystalline needles were obtainned by careful sublimation. Both heterotriacenes crystallized in the monoclinic space group P21/c with 18 molecules in the unit cell (DTS

One-pot activation–alkynylation–cyclization synthesis of 1,5-diacyl-5-hydroxypyrazolines in a consecutive three-component fashion

• Christina Görgen,
• Katharina Boden,
• Guido J. Reiss,
• Walter Frank and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2019, 15, 1360–1370, doi:10.3762/bjoc.15.136

• -hydroxypyrazolines in moderate to good yields. The structures were unambiguously corroborated by comprehensive NMR spectroscopy and X-ray structure analyses of selected derivatives. Keywords: activation; alkynylation; C–C coupling; copper; cyclization; multicomponent reactions; Introduction Pyrazoles [1][2] and

• to spectroscopic assignment the structure of 6a has now been corroborated by an X-ray structure analysis showing infinite chains of molecules 6a formed by intermolecular hydrogen bonding between the pyrazole N1 and the carbonyl O1 (Figure 3) [53]. The first assumption was that the tentative

• additionally corroborated by X-ray structure analysis showing that the assignment of intermediate 5a was not a fully unsaturated pyrazole (Figure 4) [53]. Therefore, we set out to optimize the one-pot synthesis of 1,5-diacyl-5-hydroxypyrazolines by choosing the model reaction of phenylglyoxylic acid (1a

Formation of an unexpected 3,3-diphenyl-3H-indazole through a facile intramolecular [2 + 3] cycloaddition of the diazo intermediate

• Andrew T. King,
• Hugh G. Hiscocks,
• Lidia Matesic,
• Mohan Bhadbhade,
• Roger Bishop and
• Alison T. Ung

Beilstein J. Org. Chem. 2019, 15, 1347–1354, doi:10.3762/bjoc.15.134

• OCH2–H···N interactions. In addition to these, there are Ar–H···H–Ar close contacts, (edge–edge and surrounding inversion centres) arranged as infinite tapes along the a direction. Keywords: Ar-H...H-Ar contact; [2 + 3] cycloaddition; diazo; 3H-indazole; X-ray structure; Introduction The use of

Bambusuril analogs based on alternating glycoluril and xylylene units

• Tomáš Lízal and
• Vladimír Šindelář

Beilstein J. Org. Chem. 2019, 15, 1268–1274, doi:10.3762/bjoc.15.124

• of one glycoluril unit and methine protons of the second glycoluril unit. The monocrystals of 1b suitable for X-ray analysis were obtained upon slow diffusion of diisopropyl ether into the solution of 1b in dichloromethane and benzene. The X-ray structure features Cs symmetry (Figure 5), which is in

Catalytic asymmetric oxo-Diels–Alder reactions with chiral atropisomeric biphenyl diols

• Chi-Tung Yeung,
• Wesley Ting Kwok Chan,
• Wai-Sum Lo,
• Ga-Lai Law and
• Wing-Tak Wong

Beilstein J. Org. Chem. 2019, 15, 955–962, doi:10.3762/bjoc.15.92

• optimization with different substituents are ongoing in our group and further experiments are underway to develop the use of these diols for other catalytic reactions. (a) Single crystal X-ray structure of 3: showing intra- and intermolecular hydrogen bonds (green dashed line). Torsion angles of biphenyl rings

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• has been observed on at least two ThDP-dependent enzymes. Dihydrothiachromine diphosphate (TC) was observed in the X-ray structure of phosphoketolase from Bifidobacterium breve [46], and its hydroxyethyl derivative was identified in the structure of acetolactate synthase from Klebsiella pneumoniae

• whose crystals had been soaked with pyruvate [47]. In a very recent study, we used quantum chemical methodology to investigate the detailed reaction mechanism of benzoylformate decarboxylase (BFDC) [29]. A model of the active site was designed on the basis of the X-ray structure of BFDC in complex with

• in the absence of enzyme. Model C: active site including the crystallographic water In the X-ray structure of unliganded BFDC, there is a crystallographic water molecule that is displaced when a ligand is present [13][49]. In model C, that water molecule is included and is found to bind in the same

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• [43][44] followed by phosphitylation at the 3’-oxygen afforded the phosphoramidite 9. X-ray structure and molecular modeling of the 6’-diF-bc4,3 nucleoside To verify the relative configuration of nucleoside 6, crystals of this compound were subjected to X-ray diffraction analysis. The asymmetric unit

• complementary RNA strand less efficiently as compared to the natural DNA/RNA duplex. This is a promising finding which points to a possible application for both modifications in therapeutic gapmer oligonucleotides. Chemical structure of selected fluorine-modified nucleic acids. X-ray structure of nucleoside 6a

• National Science Foundation (grant-no: 200020_165778). We thank the group of Chemical Crystallography of the University of Bern (Prof. Dr. P. Macci) for the X-ray structure and the Swiss National Science Foundation (R’equip project 206021_128724) for co-funding of the single crystal X-ray diffractometer at

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• upon inserting an additional OMe group. Such a NHO bond is clearly visible in the X-ray structure of 6c (Figure 8). As a result, in solutions of 6c and 7c, NH2+ proton signals are observed separately up to 40 °C (for spectra in CD3CN see also Figures S20–S23 in Supporting Information File 1

Generation of 1,2-oxathiolium ions from (arysulfonyl)- and (arylsulfinyl)allenes in Brønsted acids. NMR and DFT study of these cations and their reactions

• Stanislav V. Lozovskiy,
• Alexander Yu. Ivanov,
• Olesya V. Khoroshilova and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2018, 14, 2897–2906, doi:10.3762/bjoc.14.268

• followed by acetylene–allene rearrangement was used to prepare (arylsulfinyl)allenes 1 according to the literature procedure [24][25]. The latter were in situ oxidized to (arylsulfonyl)allenes 2 (see X-ray structure of 2h in Figure 1). Allenes 1a,b were specially isolated to compare their reactivity with

• equivalent of TfOH to generate the corresponding cations Ba–h. Then, the reaction mixture was cooled down to −35 °C and quenched under very mild and low nucleophilic conditions with frozen aqueous HCl at −60 °C, that finally led quantitatively to butadienes 3a–h (see X-ray structure of 3e in Figure 1). Worth

• ). The exclusive formation of thiochromene 1,1-dioxides 5a–c was obtained by running the reaction of 2a,c,d with 1 equivalent of CF3SO3H at high temperature (reflux in ortho-dichlorobenzene at 144 °C) for 2 h (Scheme 5, see X-ray structure of 5c in Figure 1). It was found by H,H-NOESY and COSY

Synthesis of pyrrolidine-based hamamelitannin analogues as quorum sensing inhibitors in Staphylococcus aureus

• Jakob Bouton,
• Kristof Van Hecke,
• Reuven Rasooly and
• Serge Van Calenbergh

Beilstein J. Org. Chem. 2018, 14, 2822–2828, doi:10.3762/bjoc.14.260

• . Structures of hamamelitannin (1), lead compound 2 and target compounds 3. Molecular X-ray structure of 3a, showing thermal displacement ellipsoids at the 50% probability level. Positional disorder of the chlorophenyl ring and the water solvent molecule are not shown. Proposed strategy for the synthesis of