Isolation of fungi using the diffusion chamber device FIND technology

• Benjamin Libor,
• Henrik Harms,
• Stefan Kehraus,
• Ekaterina Egereva,
• Max Crüsemann and
• Gabriele M. König

Beilstein J. Org. Chem. 2019, 15, 2191–2203, doi:10.3762/bjoc.15.216

• Waters HPLC system equipped with a 1525µ binary pump, a 2998 PDA detector, Breeze 2 software and a Rheodyne 7725i injection system. A Macherey-Nagel Nucleoshell C18 column (250 mm × 4.6 mm; 5 µm), Nucleodur PolarTec column (250 mm × 4.6 mm; 5 µm), Pyramid C18 column (250 mm × 4.6 mm; 5 µm) and Phenomenex

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• ionization single quadrupole MS (LCMS-2020) controlled by Shimadzu LabSolution software (Version 5.91). Chromatographic purification of products was performed by flash chromatography on silica gel (20–45 µm, Carl Roth) applying pressured air up to 0.8 bar. NMR spectra were recorded on a Bruker Avance III

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

• structures in this paper have been deposited with the Cambridge Crystallographic Data Centre as supplementary publication: 3 CCDC 1912951, 6a CCDC 1912953, 7a CCDC 1912952. Quantum mechanical calculations were done with Gaussian 09 software [22] using B3LYP/6-311+G(2d,p) model chemistry. All energies include

Fluorinated azobenzenes as supramolecular halogen-bonding building blocks

• Esther Nieland,
• Oliver Weingart and
• Bernd M. Schmidt

Beilstein J. Org. Chem. 2019, 15, 2013–2019, doi:10.3762/bjoc.15.197

• ) ρ = 0.001. For visualization, the MoleCoolQt software was used [47]. Top: Vertical electronic absorption spectra of a) A2 and b) A3, calculated using TD-B3LYP/def2-TZVP level of theory with Grimme D3 dispersion corrections and implicit MeCN solvent. Pink line: Z-isomer, purple line: E-isomer. Bottom

Analysis of sesquiterpene hydrocarbons in grape berry exocarp (Vitis vinifera L.) using in vivo-labeling and comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS)

• Philipp P. Könen and
• Matthias Wüst

Beilstein J. Org. Chem. 2019, 15, 1945–1961, doi:10.3762/bjoc.15.190

• ) mode at −70 eV. The ion source temperature was 250 °C and the detector voltage was set to −2236.8 V. Ions in the mass range 35–250 amu were acquired at a rate of 100 spectra s−1. All samples were analyzed in triplicate. Data analysis Data processing was performed using the software ChromSpace (Markes

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• following simulations, a structure of sarco/endoplasmic reticular calcium ATPase (SERCA) protein bound to 8-O-(dodecanoyl-8-O-debutanoyltrilobolide) [DTB] with 3NAL code was obtained from Protein Data Bank [22]. The structure of compound 1 was drawn using MarvinSketch 6.006 software (ChemAxon Ltd.), the

• structure of compound 2 was obtained by editing the DTB structure. First, we computed General Amber Force Field parameters for molecules of compound 1 and 2 in Antechamber software. Charges were calculated by restrained electrostatic potential method (RESP) based on a wave function calculated using quantum

• chemistry at the HF/6-31G*//HF/6-31G* level. Compound 1 molecule was manually docked into the SERCA binding site for thapsigargin using UCSF CHIMERA 1.10.2 (University of California, San Francisco) software by two approaches. In the first one, the molecule was docked so that the spatial orientation of the

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• , respectively. Other parameters include the following: a sweep width of 12 000 Hz, 32 K data points. The data were processed using Varian DOSY software [26]. ECD spectra were recorded on ECD Jasco J-715 spectropolarimeter. 2,8,14,20–Tetraisobutylresorcin[4]arene was obtained according to a literature procedure

Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade

• Hajime Sato,
• Takaaki Mitsuhashi,
• Mami Yamazaki,
• Ikuro Abe and
• Masanobu Uchiyama

Beilstein J. Org. Chem. 2019, 15, 1890–1897, doi:10.3762/bjoc.15.184

• -house software written in C++ (see Supporting Information File 3). Energy diagram and heat map analysis of 5/12/5 tricycle formation (A) IM1–IM4 in quiannulatene biosynthesis. (B) IM1–IM5 in sesterfisherol biosynthesis. An energy diagram, heat map of inherent mobility and structural heat map are shown

• Supporting Information File 423: Coordinates and energies of quiannulatene biosynthesis. Supporting Information File 424: Coordinates and energies of sesterfisherol biosynthesis. Supporting Information File 425: Software for inherent mobility analysis. Supporting Information File 426: How to use in house

• software to calculate inherent atomic mobility. Acknowledgements This work was supported by JSPS KAKENHI (S) (No. 17H06173 (M.U.)), JSPS Grant-in-Aid for Scientific Research on Innovative Areas (No. 17H05430 (M.U.), JP16H06454 (M.Y.), and JP16H06443 (I.A.)). Provision of computational resources (Project

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• complex formation, ∆Hε, in condensed medium (water, Equation 2): Basis set superposition errors (BSSE) were considered by following the counterpoise approach of Boys and Bernardi as implemented in Gaussian 09 package. The PyMOL software was used for creating the molecular graphics images [24]. M062X/6-31G

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• and SPARKY software [40]. For 2D ROESY, if it was possible, the separation between two geminal protons in −CH2− group was used as a reference in distance calculations, otherwise interatomic distances were calculated from the intensity of the cross and diagonal peaks. In both cases calculated distances

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

• Manuel Pedrón,
• Laura Legnani,
• Maria-Assunta Chiacchio,
• Pierluigi Caramella,
• Tomás Tejero and
• Pedro Merino

Beilstein J. Org. Chem. 2019, 15, 1552–1562, doi:10.3762/bjoc.15.158

• . Francis-Prof. Thyagarajan Foundation (San Antonio, TX, USA) is gratefully acknowledged for a donation for software acquisition. M.-A. C. and L. L. thank Universities of Catania and Pavia for partial financial support.

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

• series. Symmetry-related absorption corrections using the program SADABS [33] were applied, and the data were corrected for Lorentz and polarisation effects using Bruker APEX3 software [33]. The structure was solved by program SHELXT [34] (with intrinsic phasing), and the full-matrix least-square

• refinements were carried out using SHELXL-2014 [35] through Olex2 [36] suite of software. The non-hydrogen atoms were refined anisotropically. Molecular graphics were generated using Mercury [37]. Key crystallographic data and refinement details are presented in Table 1. Crystal structure data

Understanding the unexpected effect of frequency on the kinetics of a covalent reaction under ball-milling conditions

• Ana M. Belenguer,
• Adam A. L. Michalchuk,
• Giulio I. Lampronti and
• Jeremy K. M. Sanders

Beilstein J. Org. Chem. 2019, 15, 1226–1235, doi:10.3762/bjoc.15.120

• parameterization and additional model features. Acknowledgements We thank: C. A. Bland for the mechanical and P. Donnelly for the software design of the automation of the grinders for repeat grinding; Richard Nightingale and his team from the mechanical workshop at the Department of Chemistry, University of

Mechanochemical amorphization of chitin: impact of apparatus material on performance and contamination

• Thomas Di Nardo and
• Audrey Moores

Beilstein J. Org. Chem. 2019, 15, 1217–1225, doi:10.3762/bjoc.15.119

• , also at residence times of 50 ms. Deconvolution and peak position were determined using Avantage processing software. IR ATR-IR spectra were recorded using a Perkin-Elmer Spectrum 400 for 16 scans from 4000 cm−1 to 450 cm−1 using approximately 2 mg of sample. ICP ICP analysis was conducted on a Thermo

Phylogenomic analyses and distribution of terpene synthases among Streptomyces

• Lara Martín-Sánchez,
• Kumar Saurabh Singh,
• Mariana Avalos,
• Gilles P. van Wezel,
• Jeroen S. Dickschat and
• Paolina Garbeva

Beilstein J. Org. Chem. 2019, 15, 1181–1193, doi:10.3762/bjoc.15.115

• , aBSREL [64] model was used to infer nonsynonymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding sequence alignment and corresponding phylogeny. The treefix-DTL (duplication-transfer-loss) software, version 1.0.2 [64], was applied to fix the topology of each terpene

Mechanochemical synthesis of hyper-crosslinked polymers: influences on their pore structure and adsorption behaviour for organic vapors

• Sven Grätz,
• Sebastian Zink,
• Hanna Kraffczyk,
• Marcus Rose and
• Lars Borchardt

Beilstein J. Org. Chem. 2019, 15, 1154–1161, doi:10.3762/bjoc.15.112

• utilized and the resulting spectra were treated with ATR-correction by the OPUS 6.5 software. Powder X-ray diffraction (PXRD) patterns were collected in transmission geometry (MYTHEN 1K detector) with a STOE STADI P diffractometer operated at 40 kV and 30 mA with a Ge monochromator using Cu Kα1 radiation

Unexpected polymorphism during a catalyzed mechanochemical Knoevenagel condensation

• Sebastian Haferkamp,
• Andrea Paul,
• Adam A. L. Michalchuk and
• Franziska Emmerling

Beilstein J. Org. Chem. 2019, 15, 1141–1148, doi:10.3762/bjoc.15.110

• component analysis (PCA) and multivariate curve resolution (MCR) with the software The Unscrambler® X Vers. 10.5 (CAMO). Prior to multivariate analysis, Raman spectra were baseline corrected followed by unit vector normalization in the spectral range of 200–2500 cm−1. PCA was conducted with mean centered

Design of a double-decker coordination cage revisited to make new cages and exemplify ligand isomerism

• Sagarika Samantray,
• Sreenivasulu Bandi and
• Dillip K. Chand

Beilstein J. Org. Chem. 2019, 15, 1129–1140, doi:10.3762/bjoc.15.109

• performed using Gaussian 09 software package at the B3LYP/6-31G* level of theory [37]. Since the complex [Pd3(tmeda)3(L1)2]6+ could not be prepared exclusively, we looked into the energetics of the system. The overall Gibbs free energies (∆G) and the enthalpies (∆H) for the formation of the trinuclear

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

Diaminoterephthalate–α-lipoic acid conjugates with fluorinated residues

• Leon Buschbeck,
• Aleksandra Markovic,
• Gunther Wittstock and
• Jens Christoffers

Beilstein J. Org. Chem. 2019, 15, 981–991, doi:10.3762/bjoc.15.96

• were recorded with ESCALAB 250 iX (Thermo Fisher, East Grinsted, UK) using a monochromatized Al Kα excitation (1486.6 eV) and the magnetic lens mode. Data acquisition and spectra processing was performed with the Avantage software v. 5.52. After recording a survey spectrum, high-resolution spectra were

• different regions of the same sample (area scan). The peak-fit analysis used the "smart background" from Avantage software and sum of Gaussian and Lorentzian contributions for each spectral component. The area ratio between S 2p3/2 and S 2p1/2 emissions from each state was fixed to 2:1. The graphs show the

Towards the preparation of synthetic outer membrane vesicle models with micromolar affinity to wheat germ agglutinin using a dialkyl thioglycoside

• Dimitri Fayolle,
• Nathalie Berthet,
• Bastien Doumeche,
• Olivier Renaudet,
• Peter Strazewski and
• Michele Fiore

Beilstein J. Org. Chem. 2019, 15, 937–946, doi:10.3762/bjoc.15.90

• . Micrographs were recorded with an inverted microscope (Zeiss LSM 800) equipped with a 50× objective through the AxioCam software. Micrographs were used without any graphical treatment and the image size was adjusted respecting the x/y pixel proportions Synthesis of compounds 3–8 Compound 3: A stirred solution

• 8C4 were prepared using OpenBabel (version 2.4.1). Docking was performed using autodock vina implemented in the Samson software (version beta 0.7.0, NANO-D Inria, https://www.samson-connect.net). A grid (60 × 60 × 60 Å) including the whole protein was used and 20 poses leading to the lowest energies

Strong hyperconjugative interactions limit solvent and substituent influence on conformational equilibrium: the case of cis-2-halocyclohexylamines

• Camila B. Francisco,
• Cleverton S. Fernandes,
• Ulisses Z. de Melo,
• Roberto Rittner,
• Gisele F. Gauze and
• Ernani A. Basso

Beilstein J. Org. Chem. 2019, 15, 818–829, doi:10.3762/bjoc.15.79

• spectra, with number of points 32k, resulting in a digital resolution of 0.12 Hz/point. The spectral data are available in Supporting Information File 1. Theoretical calculations Theoretical calculations were performed with the software package Gaussian 09 [41]. To determine the lowest energy structures

• function LanL2DZ-ECP was employed for the iodine atom. Solvation calculations were performed in dichloromethane and methanol, with the the implicit model IEF-PCM and the description of the molecular cavity through Bondi’s atomic radii. Molecular Mechanics calculations were performed using the software

• Avogadro 1.2.0 [42], employing the Amber force field GAFF [33]. NBO calculations were performed in the optimized structures in the gas phase (M06-2X/6-311++G(2df,2p)), through the module NBO 5.9 [43] from Gaussian 09. For the PCA, it was used the software R, version 3.5.0 [44], with the graphical interface

New sesquiterpenoids from the South China Sea soft corals Clavularia viridis and Lemnalia flava

• Qihao Wu,
• Yuan Gao,
• Meng-Meng Zhang,
• Li Sheng,
• Jia Li,
• Xu-Wen Li,
• Hong Wang and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2019, 15, 695–702, doi:10.3762/bjoc.15.64

• continuously monitored and the initial rate of hydrolysis was determined by using the early linear region of the enzymatic reaction kinetic curve. The IC50 was calculated with Prism 4 software (Graphpad, San Diego, CA) from the nonlinear curve fitting of the percentage of inhibition (% inhibition) vs the

• 4 software (Graphpad, San Diego, CA) from the nonlinear curve fitting of the percentage of inhibition (% inhibition) versus the inhibitor concentration [I] by using the following equation: % inhibition = 100/(1 + [IC50/[I]]k), where k is the Hill coefficient. Bortezomib was used as a positive

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• overlapping signals J coupling constants were extracted from 2nd order spectra simulations using Bruker TopSpin software (DAISY). The obtained results (see Tables 1–3) showed good coincidence with previously published data for related monosaccharides [15][26][27]. As can be seen from Table 3, J coupling

• standard pulse sequence from the Bruker software. In J-HMBC experiments the delay for the long-range couplings was optimized for 1.5 Hz. All spectra were transformed and analyzed with the Bruker Topspin 3.6 software. Geometry optimization were performed using the ORCA 2.9.1 program [29][30]. RHF

• . Coupling constants were computed using DFT/B3LYP/pcJ-1 [33] approximation and DALTON-2015 software [34]. Only Fermi-contact terms were evaluated. Synthesis of propyl α-D-mannofuranoside (1) To a suspension of D-mannose (400 mg, 2.22 mmol) in n-propanol (4 mL) was added resin IR-120(H+) (475 mg). The

Catalyst-free assembly of giant tris(heteroaryl)methanes: synthesis of novel pharmacophoric triads and model sterically crowded tris(heteroaryl/aryl)methyl cation salts

• Rodrigo Abonia,
• Luisa F. Gutiérrez,
• Braulio Insuasty,
• Jairo Quiroga,
• Kenneth K. Laali,
• Chunqing Zhao,
• Gabriela L. Borosky,
• Samantha M. Horwitz and
• Scott D. Bunge

Beilstein J. Org. Chem. 2019, 15, 642–654, doi:10.3762/bjoc.15.60

• refinement, scaling, and data reduction were carried out using the APEX2 Version 2014.11 software package [72][73]. The data were corrected for absorption using the SCALE program within the APEX2 software suite [72][73]. The structure was solved using SHELXT [74]. This procedure yielded a number of the C, N

• and O atoms. Subsequent Fourier synthesis yielded the remaining atom positions. The hydrogen atoms are fixed in positions of ideal geometry (riding model) and refined within the XSHELL software package [75]. The final refinement of the compound included anisotropic thermal parameters on all non