Halogen-bonding-induced diverse aggregation of 4,5-diiodo-1,2,3-triazolium salts with different anions

• Xingyu Xu,
• Shiqing Huang,
• Zengyu Zhang,
• Lei Cao and
• Xiaoyu Yan

Beilstein J. Org. Chem. 2020, 16, 78–87, doi:10.3762/bjoc.16.10

• diffraction data for 2-OAc, 2-TFA, 2-BF4.0.5bpy, 2-I.1.5I2 and 2-I.3.5I2 were collected at 150 K while 2-BF4 was collected at 298 K. All the data were collected 0.5 degree per step and using the ω scan mode. Frames were integrated using the Bruker SAINT [47] software. Semi-empirical absorption correction was

Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• File 1. ECD theoretical calculations TDDFT-ECD was used to perform theoretical ECD calculations. Conformational searches for the investigated compounds were first performed with a MMFF94S force field and an energy window of 10 kcal/mol using Omega2 software [54][55]. Each resulting conformer was then

• subjected to geometrical optimization and vibrational frequency calculation at the B3LYP/6-31+G* level of theory using the Gaussian 09 software [56]. Based on the optimized geometries, TDDFT calculations were finally carried out at the B3LYP/6-311+G* level of theory, and the first 50 excitation states were

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• General information Conformational search was performed with MacroModel version 12.1 in the Maestro 11.7 software package [32][33]. All DFT-based calculations were performed with the Gaussian 16 Rev B.01 program [34]. A part of these computations were conducted using a Fujitsu PRIMERGY CX400 multi-node

• server (Information Technology Center of Nagoya University). Molecular structures were visualized using Maestro 11.7 software package. DP4+ analysis was performed with the Excel spreadsheet [25] made by Sarotti et al. Cartesian coordinates of the structures described in this paper are included in

Chemical tuning of photoswitchable azobenzenes: a photopharmacological case study using nicotinic transmission

• Lorenzo Sansalone,
• Jun Zhao,
• Matthew T. Richers and
• Graham C. R. Ellis-Davies

Beilstein J. Org. Chem. 2019, 15, 2812–2821, doi:10.3762/bjoc.15.274

• (530 nm, 3 mW) or 1 s violet light (405 nm, 10 mW). Data were analyzed in Patchmaster software (Heka). The amplitudes of currents were calculated as the difference of the peak and baseline. All data were present as the mean ± SEM. One-way ANOVA was used to determine whether there are any statistically

Nanangenines: drimane sesquiterpenoids as the dominant metabolite cohort of a novel Australian fungus, Aspergillus nanangensis

• Heather J. Lacey,
• Cameron L. M. Gilchrist,
• Andrew Crombie,
• John A. Kalaitzis,
• Daniel Vuong,
• Peter J. Rutledge,
• Peter Turner,
• John I. Pitt,
• Ernest Lacey,
• Yit-Heng Chooi and
• Andrew M. Piggott

Beilstein J. Org. Chem. 2019, 15, 2631–2643, doi:10.3762/bjoc.15.256

• recorded at 25 °C, processed using Bruker Topspin 3.5 software and referenced to residual non-deuterated solvent signals (DMSO-d6: δH 2.49, δC 39.5 ppm). Collection and cultivation A. nanangensis MST-FP2251 was isolated by serial dilution of an aqueous suspension of soil collected in Nanango, Queensland

A toolbox of molecular photoswitches to modulate the CXCR3 chemokine receptor with light

• Xavier Gómez-Santacana,
• Sabrina M. de Munnik,
• Tamara A. M. Mocking,
• Niels J. Hauwert,
• Shanliang Sun,
• Prashanna Vijayachandran,
• Iwan J. P. de Esch,
• Henry F. Vischer,
• Maikel Wijtmans and
• Rob Leurs

Beilstein J. Org. Chem. 2019, 15, 2509–2523, doi:10.3762/bjoc.15.244

• similar to those observed in the biaryl series. To reinforce this hypothesis, molecular alignments were performed with Molecular Operating Environment (MOE) software [26] in which 1e was used as a model for full agonism (Figure 2). Its 3D structure was superposed with both the trans and cis-isomers of

Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• Avance III HD 300 NMR spectrometer. Samples were prepared at 10 mM concentration and 1:3 host–guest ratio in CDCl3/CD3CN (4:3, v:v) mixture. DFT calculations were performed by Spartan’ 16 and Gaussian 09 (D01) software packages. More detailed information of the experiments and parametrization can be

Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

• Eric W. Webb,
• Jonathan P. Moerdyk,
• Kyndra B. Sluiter,
• Benjamin J. Pollock,
• Amy L. Speelman,
• Eugene J. Lynch,
• William F. Polik and
• Jason G. Gillmore

Beilstein J. Org. Chem. 2019, 15, 2473–2485, doi:10.3762/bjoc.15.240

• the Gaussian 03 software package [25], implemented through the WebMO [26] graphical user interface on the Curie cluster [27] in the Hope College Computational Science & Modeling Laboratory on a single node (a single 2.60 GHz AMD Opteron-252 processor with 8 GB RAM and 250 GB HD). Calculations of bond

• node (dual Intel X5650 CPU, with 6 cores running at 2.66 GHz) using the Gaussian 09 [30] software package implemented through the WebMO [26] graphical user interface. Restricted open-shell Hartree-Fock (ROHF) theory [31] with the Becke 3, Lee, Yang, and Parr (B3LYP) hybrid functional [32][33][34] was

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• taken both in analog integration (200 exposures, 100 ms exposure time) and in photon counting (1000–10000 exposures, 20–30 ms exposure time). The decays were collected over emission spectral ranges of 20 nm. HPD-TA 9.3 software from Hamamatsu was used for data acquisition and analysis. The overall time

Sugar-derived oxazolone pseudotetrapeptide as γ-turn inducer and anion-selective transporter

• Sachin S. Burade,
• Sushil V. Pawar,
• Tanmoy Saha,
• Navanath Kumbhar,
• Amol S. Kotmale,
• Manzoor Ahmad,
• Pinaki Talukdar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2019, 15, 2419–2427, doi:10.3762/bjoc.15.234

• thus supported the presence of γ-turn helical type conformation of 2a. Molecular modeling studies In order to corroborate our results, obtained from the NMR studies, the molecular modeling study was performed using Spartan’14 software [29][30]. The initial geometry of 2a, generated from the NOESY study

Perspective isomorphs – a new classification of molecular structures based on artistic and chemical concepts

• Jannis Neumann,
• Ansgar Schnurr and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2019, 15, 2319–2326, doi:10.3762/bjoc.15.224

• virtual observer in the process of analysis. Although this might appear as an artificial construct the contact of the investigated molecules with another entity with nanometer dimensions can be regarded as a congruent event. Although current software packages do not allow the automated classification of

Small anion-assisted electrochemical potential splitting in a new series of bistriarylamine derivatives: organic mixed valency across a urea bridge and zwitterionization

• Keishiro Tahara,
• Tetsufumi Nakakita,
• Alyona A. Starikova,
• Takashi Ikeda,
• Masaaki Abe and
• Jun-ichi Kikuchi

Beilstein J. Org. Chem. 2019, 15, 2277–2286, doi:10.3762/bjoc.15.220

• performed using the Gaussian09 software [63]. The three-parameterized Becke–Lee–Yang–Parr (B3LYP) hybrid exchange-correlation functional [64] was selected using the 6-31G(d) basis set for 1a and 1b with a restricted method and using the 6-311++G(d,p) basis set for the MV species with an unrestricted method

Aggregation-induced emission effect on turn-off fluorescent switching of a photochromic diarylethene

• Luna Kono,
• Yuma Nakagawa,
• Ayako Fujimoto,
• Ryo Nishimura,
• Yohei Hattori,
• Toshiki Mutai,
• Nobuhiro Yasuda,
• Kenichi Koizumi,
• Satoshi Yokojima,
• Shinichiro Nakamura and
• Kingo Uchida

Beilstein J. Org. Chem. 2019, 15, 2204–2212, doi:10.3762/bjoc.15.217

• mm quartz cell, which was then placed in the integral sphere. The quantum yield was calculated using an installed software. The solid-state absorption spectrum was obtained by Kubelka–Munk conversion of a diffractive reflectance spectrum of the above mixture measured on a JASCO FP-6600

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