The activity of indenylidene derivatives in olefin metathesis catalysts

• Maria Voccia,
• Steven P. Nolan,
• Luigi Cavallo and
• Albert Poater

Beilstein J. Org. Chem. 2018, 14, 2956–2963, doi:10.3762/bjoc.14.275

• in energy for system 2. Overall, for all substituted indenylidenes this concerted transition state I–III is confirmed to be higher in energy. The structural analysis included in Table 2 supports the fact that the substituted indenylidenes display similar characteristics whatever the substituents are

• lengths are given in Å). Catalysts studied by DFT calculations. Precatalyst initiation in olefin metathesis (L = NHC ligand). Precatalyst initiation reaction pathway for catalysts 1–6 (M06/TZVPsdd//BP86/SVPsdd; Gibbs free energies in kcal/mol). Structural analysis for species I–III for catalysts 1–6 (in

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

• which the cationic character of the pyrrolidine nitrogen is removed, were also synthesized. The correct stereochemistry of the synthesized analogues was unequivocally proven via X-ray structural analysis of compound 3a (Figure 2). Biological evaluation The synthesized analogues were tested in a S

Determining the predominant tautomeric structure of iodine-based group-transfer reagents by ¹⁷O NMR spectroscopy

• Nico Santschi,
• Cody Ross Pitts,
• Benson J. Jelier and
• René Verel

Beilstein J. Org. Chem. 2018, 14, 2289–2294, doi:10.3762/bjoc.14.203

• structural analysis. Tautomerism in iodine-based group-transfer reagents probed by 17O NMR spectroscopy (A) and key structures investigated herein (B). Assignment of acyclic (b) and cyclic (a) structures to 5 and 6, respectively, based on computed isotropic shift values (δiso) and experimental 17O NMR

Recent advances in hypervalent iodine(III)-catalyzed functionalization of alkenes

• Xiang Li,
• Pinhong Chen and
• Guosheng Liu

Beilstein J. Org. Chem. 2018, 14, 1813–1825, doi:10.3762/bjoc.14.154

• epoxidation products. Not only terminal styrenes but also internal alkenes were suitable to this reaction, affording the anti-diamination products. The exact mode of stereoinduction with the new catalyst 23 was examined, and the single crystal X-ray structural analysis of 26 revealed that a water molecule

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• maintain helicity (see Structural Analysis below) and effectively interact with the binding pocket. Thus, pending no unexpected enhancement from isosteric substitutions (e.g., pyridylalanine, cyclohexylalanine, etc.), they are likely not ideal positions for further optimization. With regards to the ComD2

• of the chain-length for effective binding, while the tyrosine substitution results suggest that the binding pockets within the ComD2 receptor cannot accommodate polar/electron-rich substituents. Structural analysis of CSP1 analogs Next, we wanted to assess the impact our modifications to the CSP1

• . Interestingly, L13 is predicted to be positioned on the opposite face of the helix, away from the proposed binding interface between CSP1 and ComD1. It is therefore not clear why this residue was found to be important for effective receptor binding. In-depth structural analysis of CSP1 in membrane mimicking

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• concerning the utilisation of 4-(n-octyloxy)aniline, a “traditional” source for mesogenic N-substituted Schiff bases [26][27][28][29]. Following up our contributions in the field of dendritic melamines’ synthesis, structural analysis [30][31][32][33] and electrochemistry [34][35][36], we recently become

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• sophisticated local coupled cluster method. The latter also yields a quantification as well as a visualization of London dispersion, which prove to be valuable tools for understanding the role of dispersion on the docking preferences. Beyond the structural analysis of the electronic ground state (S0), the

Design and biological characterization of novel cell-penetrating peptides preferentially targeting cell nuclei and subnuclear regions

• Anja Gronewold,
• Mareike Horn and
• Ines Neundorf

Beilstein J. Org. Chem. 2018, 14, 1378–1388, doi:10.3762/bjoc.14.116

• –S4 (Supporting Information File 1), all peptides could be successfully synthesized in high purities. First, we performed a structural analysis by diluting all peptides to a concentration of 20 μM in phosphate buffer (pH 7.0), with or without the presence of the secondary structure inducing solvent

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• , Slovakia 10.3762/bjoc.14.115 Abstract The aromatic nucleophilic substitution reaction based synthesis of a three-armed cryptand displaying 2,4,6-triphenyl-1,3,5-triazine units as caps and pyridine rings in the bridges, along with NMR, MS and molecular modelling-based structural analysis of this compound

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

• Ido Azuri,
• Anna Hirsch,
• Anthony M. Reilly,
• Alexandre Tkatchenko,
• Shai Kendler,
• Oded Hod and
• Leeor Kronik

Beilstein J. Org. Chem. 2018, 14, 381–388, doi:10.3762/bjoc.14.26

• peak observed in experiment, for the range of frequencies studied here. Results and Discussion Structural analysis Before discussing vibrational properties, we first ascertain that our computational approach is sufficiently accurate for obtaining reliable structural predictions. Crystallographic

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• using in vitro transcription which limits possible applications for example in structural analysis. Co-transcriptional capping of short RNA fragments For preparation of short, capped RNA with the sequence GpppANn or m7GpppANn (1 ≤ n ≤ 9 nt), bacteriophage T7 gene 4 primase [52] or its active domain [53

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• from the European Regional Development Fund under the Operational Programme Innovative Economy, 2007–2013. This research was supported by NCN (Polish National Center of Science) grants 2013/09/B/NZ3/01389, 2012/05/E/ST2/02180 (TB) and MAESTRO grant-DEC-2012/04/A/ST5/00609 (DT and KW – structural

• analysis). We thank Mr. Marcel Shafikov for his help in recording of fluorescence spectra.

Synthesis and application of trifluoroethoxy-substituted phthalocyanines and subphthalocyanines

• Satoru Mori and
• Norio Shibata

Beilstein J. Org. Chem. 2017, 13, 2273–2296, doi:10.3762/bjoc.13.224

• Pc-subPc. Although Pc-subPc was synthesized via a two-step statistical unsymmetric synthesis, it can be easily purified by silica gel column chromatography due to the aggregation inhibitory effect caused by the trifluoroethoxy group. The structure of Pc-subPc was confirmed by X-ray crystal structural

• analysis, having both a planar structure derived from phthalocyanine and a cone-shaped structure derived from subphthalocyanine (left of Figure 10). In the UV–vis absorption spectrum, Pc-subPc shows an absorption band around 800 nm which is located between the absorption bands of Pc-Pc and subPc-subPc

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

• spectrometry in conjunction with oxidative degradation and deuterium exchange experiments [56]. In spite of the challenge posed by the severely limited availability of natural material for structural analysis, Kishi and co-workers later demonstrated by total synthesis (vide infra) that the Leadlay structure

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• biological materials (BioSAXS) is a complementary tool to protein crystallography and has become an invaluable resource for structural biologists [80]. Although at a much lower resolution than protein crystallography, BioSAXS permits the structural analysis of macromolecules at more physiological conditions

Expression, purification and structural analysis of functional GABA transporter 1 using the baculovirus expression system

• Jing Hu,
• Chris Weise,
• Christoph Böttcher,
• Hua Fan and
• Jian Yin

Beilstein J. Org. Chem. 2017, 13, 874–882, doi:10.3762/bjoc.13.88

• protein, GAT1, is a potential drug target. The exact three-dimensional structure of GAT1 protein could provide more information for pharmaceutical research. The structural analysis of most membrane proteins is challenging since significant protein yields are required and because eukaryotic membrane

• structure on the N-glycans, which is consistent with previous findings [12]. Therefore, the GAT1/GFP protein produced in the baculovirus system can be suitable for further structural analysis with correct folding and more uniform, less complex N-glycans. Purification of the GAT1/GFP fusion protein from

• glycans on the activity of the GAT1 protein, the glycol-engineered insect cells coupled with the baculovirus system may be further applied to produce a GAT1/GFP protein with complex, terminally sialylated N-glycans. Further structural analysis of the GAT1/GFP fusion protein is possible using

Cyclodextrins tethered with oligolactides – green synthesis and structural assessment

• Cristian Peptu,
• Mihaela Balan-Porcarasu,
• Alena Šišková,
• Ľudovít Škultéty and
• Jaroslav Mosnáček

Beilstein J. Org. Chem. 2017, 13, 779–792, doi:10.3762/bjoc.13.77

• amount for γ-CD while for α- and β-CD this ratio is similar. Therefore, the performance of different CDs in L-LA polymerization (in current reaction conditions) is decreasing in the order β-CD > α-CD > γ-CD. The structural analysis aimed the following targets: to determine the substitution degrees for CD

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• procedures as previously described for other CD preparations, hyaluronate was heated in a Teflon-lined autoclave in the presence of glycine, which was found to be key, to 200 °C for 4 h to yield CDs of under 10 nm in size (Scheme 22). Structural analysis of the resultant CDs indicated the presence of

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

Beilstein J. Org. Chem. 2017, 13, 348–371, doi:10.3762/bjoc.13.39

• with the direction of reduction and therefore presumably guiding substrate entry, were initially identified by comparative sequence analysis [64][67], and shown subsequently by structural analysis to occupy positions proximal to the active site [56][57][58][59][60][61][62]. The strongest indicator for

• mutagenesis of the Caffrey motifs [74] and other residues identified as potentially participating in stereocontrol by sequence and/or structural analysis [58][61], failed to produce consistent results, with certain mutations leading to the predicted shift in stereochemistry, others again strengthening wild

• ][84][85], the origin of this stabilization remains unknown. KRs were first suggested to act as epimerases – despite the fact that no other SDR enzyme exhibits this activity – based on structural analysis [57]. This proposal led to the classification of PKS KRs working on C-2 methylated substrates into

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934

• Veronika Ulrich,
• Clara Brieke and
• Max J. Cryle

Beilstein J. Org. Chem. 2016, 12, 2849–2864, doi:10.3762/bjoc.12.284

• turnover assay triplicates and the standard deviation is shown. (b) Structures of the peptides used as substrates for StaF, being Tei7-L/D-Hpg7 (1), Pek7-rac-Hpg7 (2) and Act7-rac-Hpg7 (3); R = CoA or methylamine. Structural analysis of StaF: (A) overall structure of StaF, with the heme moiety depicted

A chiral analog of the bicyclic guanidine TBD: synthesis, structure and Brønsted base catalysis

• Mariano Goldberg,
• Denis Sartakov,
• Jan W. Bats,
• Michael Bolte and
• Michael W. Göbel

Beilstein J. Org. Chem. 2016, 12, 1870–1876, doi:10.3762/bjoc.12.176

• (42%, 48% ee) yielded 26% of material with 95% ee. Assignment of absolute configurations (Scheme 3): Well grown crystals of enantiopure Michael product 30 suitable for X-ray structural analysis could be obtained by a second recrystallization from CH2Cl2/cyclohexane. The 4-bromophenyl residue allowed

Modular synthesis of the pyrimidine core of the manzacidins by divergent Tsuji–Trost coupling

• Sebastian Bretzke,
• Stephan Scheeff,
• Felicitas Vollmeyer,
• Friederike Eberhagen,
• Frank Rominger and
• Dirk Menche

Beilstein J. Org. Chem. 2016, 12, 1111–1121, doi:10.3762/bjoc.12.107

• an X-ray structure of tert-butylsulfinylamine 28 was obtained. Remarkably, these types of substances have not been broadly evaluated by X-ray structural analysis which adds to the importance of this general evaluation. Next, we focused on further homologation towards a suitably functionalized urea

Bi- and trinuclear copper(I) complexes of 1,2,3-triazole-tethered NHC ligands: synthesis, structure, and catalytic properties

• Shaojin Gu,
• Jiehao Du,
• Jingjing Huang,
• Huan Xia,
• Ling Yang,
• Weilin Xu and
• Chunxin Lu

Beilstein J. Org. Chem. 2016, 12, 863–873, doi:10.3762/bjoc.12.85

• SQUEEZE [48]. Further details of the structural analysis are summarized in Table 3. X-ray diffraction structure of copper(II) complex 2 with thermal ellipsoids drawn at 30% probability. The anion and hydrogen atoms are omitted for clarity. Selected bond distances (Å) and angles (°): Cu1-O1 1.931(4), Cu1

Synthesis, structure, and mechanical properties of silica nanocomposite polyrotaxane gels

• Kazuaki Kato,
• Daisuke Matsui,
• Koichi Mayumi and
• Kohzo Ito

Beilstein J. Org. Chem. 2015, 11, 2194–2201, doi:10.3762/bjoc.11.238

• following structural analysis. Small-angle X-ray scattering measurement Synchrotron small-angle X-ray scattering (SAXS) experiments were carried out at the beamline 6A of Photon Factory, HighEnergy Accelerator Research Organization, KEK (Tsukuba, Japan). The wavelength λ of the incident X-ray beam was 1.50

Grubbs–Hoveyda type catalysts bearing a dicationic N-heterocyclic carbene for biphasic olefin metathesis reactions in ionic liquids

• Maximilian Koy,
• Hagen J. Altmann,
• Benjamin Autenrieth,
• Wolfgang Frey and
• Michael R. Buchmeiser

Beilstein J. Org. Chem. 2015, 11, 1632–1638, doi:10.3762/bjoc.11.178

• . Selected bond lengths (pm) for Ru-2 and Ru-1 [21]. ROMP reactions under biphasic conditions.a,b ROMP of M1 under biphasic conditions with recycling.a Supporting Information Supporting Information File 310: Analytical data for Ru-2, the polymers prepared, details on the single crystal X-ray structural

• analysis of Ru-2, results for biphasic RCM. Acknowledgements Financial support provided by the Deutsche Forschungsgemeinschaft (DFG, grant no. BU 2174/8-1) is gratefully acknowledged.