Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• potential. Additionally, structural analysis revealed that each cation was stabilized by noncovalent interactions, such as π–cation and dipole–cation interactions. A comparison of the transition state structures in the gas phase vs the active site model is shown in Table 2. These findings suggest that the

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

• a synthetic solution to create scents that mimic violet flower oils. First, a similarly smelling but more affordable orris root oil (Iris pallida Lam., fam. Iridaceae) was chosen for structural analysis. Thiemann and Krüger isolated irone (27, Figure 3), whose molecular formula was first falsely

Synthesis, photophysical and electrochemical properties of pyridine, pyrazine and triazine-based (D–π–)₂A fluorescent dyes

• Keiichi Imato,
• Toshiaki Enoki,
• Koji Uenaka and
• Yousuke Ooyama

Beilstein J. Org. Chem. 2019, 15, 1712–1721, doi:10.3762/bjoc.15.167

• dye molecules in the solid state, although we could not prepare single crystals of OUY-2, OUK-2 and OUJ-2 for the X-ray structural analysis. Electrochemical properties The electrochemical properties of OUY-2, OUK-2 and OUJ-2 were investigated by cyclic voltammetry (CV) in DMF containing 0.1 M

Molecular basis for the plasticity of aromatic prenyltransferases in hapalindole biosynthesis

• Takayoshi Awakawa and
• Ikuro Abe

Beilstein J. Org. Chem. 2019, 15, 1545–1551, doi:10.3762/bjoc.15.157

• [13]. More interestingly, the D172A mutation altered the AmbP1 reaction, as it prefers C-3 prenylation even in the presence of Mg2+ ions. There are several X-ray crystal structural analyses of PTases that utilize Mg2+ as a Lewis acid, such as NphB [4], but this is the first structural analysis of the

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

• in AcCN (1 mL, HPLC grade), and injected in 10–20 µL batches. Each fluorometabolite was separated in vials, evaporated and analysed. Structural analysis of the resulting metabolites and remaining starting materials was carried out by NMR characterisation (1H, 19F, 13C, COSY, HSQC and HMBC) and

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

• the indazole ring. The ambiguity was overcome through the X-ray structural analysis of the compound. The single crystals were easily obtained by recrystallisation from CH2Cl2. Crystal structure analysis The X-ray crystal analysis revealed that the product was not the diazonium intermediate 7, but

Homo- and hetero-difunctionalized β-cyclodextrins: Short direct synthesis in gram scale and analysis of regiochemistry

• Gábor Benkovics,
• Mihály Bálint,
• Éva Fenyvesi,
• Erzsébet Varga,
• Szabolcs Béni,
• Konstantina Yannakopoulou and
• Milo Malanga

Beilstein J. Org. Chem. 2019, 15, 710–720, doi:10.3762/bjoc.15.66

• ). Analysis of regiochemistry of homo-difunctionalized β-cyclodextrins by full NMR spectral assignment NMR structural analysis was performed on the ditosyl derivatives, precursors of the corresponding diazido compounds. There are two factors that warrant large signal dispersion in the 1H NMR spectra of

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• unit and possibly positively impact the duplex stability. Here we report on the synthesis of the two 6’F-bc4,3 pyrimidine analogs with the base T and C, their incorporation into DNA, their biophysical properties, as well as a structural analysis by molecular dynamics simulations of hybrid DNA and RNA

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