Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• biological activity methodology, computational details, and NMR/HRMS spectra of the final products. Acknowledgements Rodrigo Razo (RSRH) thanks to the Laboratorio Nacional de Supercómputo (LNS, Puebla) for the computer time, and Dr. Zeferino Gómez-Sandoval of the University of Colima for the software

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• cost. Another open source resource with immediate applicability to target identification and validation is the Open Worm Movement Database [115]. This is an open platform for analysing and sharing worm behavioural data, such as that obtained from worm tracking software. For example, the researcher can

• how they have been applied to anthelmintic discovery. We concentrate on those where the software source code and/or hardware design is made clearly and openly available. Methods, applications, and location of source code/design are summarised in Table 3. Open tools for phenotypic screening of motility

• software (Automated WormScan) has recently been published [118]. The Lifespan Machine also uses a scanner to acquire images, and has the ability to monitor thousands of worms simultaneously and determine mortality time for individual worms on plates [120]. WormAssay is a combination of a video camera and

Development of fluorinated benzils and bisbenzils as room-temperature phosphorescent molecules

• Shigeyuki Yamada,
• Takuya Higashida,
• Yizhou Wang,
• Masato Morita,
• Takuya Hosokai,
• Kaveendra Maduwantha,
• Kaveenga Rasika Koswattage and
• Tsutomu Konno

Beilstein J. Org. Chem. 2020, 16, 1154–1162, doi:10.3762/bjoc.16.102

• -deficient fluorinated aromatic ring. To confirm the electron-withdrawing effect of this fluorinated aromatic ring, the electronic charge at the adjacent C≡C bond was calculated by density functional theory (DFT) using the Gaussian 16 (Revision B.01) software package [35]. As typical examples, the molecular

Synthesis and properties of quinazoline-based versatile exciplex-forming compounds

• Rasa Keruckiene,
• Simona Vekteryte,
• Ervinas Urbonas,
• Matas Guzauskas,
• Eigirdas Skuodis,
• Dmytro Volyniuk and
• Juozas V. Grazulevicius

Beilstein J. Org. Chem. 2020, 16, 1142–1153, doi:10.3762/bjoc.16.101

• with the Gaussian software [26]. Firstly, the equilibrium conformer search at the ground state was performed by using the MMFF (molecular mechanics force fields) method, and this geometry was used for further optimization. The vertical singlet and triplet energy values were calculated by using the

• energy values at the corresponding excited-state geometry. The time-dependent DFT (TD-DFT) calculations were carried out with the Gaussian 16 software package and molecular orbitals were visualized by using Gaussview. Photoelectron emission spectroscopy measurement was performed according to the

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• isotropic displacement parameter equal to 1.2–1.5 times the equivalent isotropic displacement parameter of its parent atom. For structure solving and refinement the SHELX-97 [70], and Bruker APEX3 software package [71] were used. The structures were refined to Fo2, and all reflections were used in the least

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• (10''-NH); HRESITOFMS (m/z): [M − H]− calcd for C36H36N5O7, 650.2615; found, 650.2614. Computational procedure General information Conformational search was performed with MacroModel implemented in the Maestro 11.7 software package [46][47]. All DFT-based calculations were performed with the Gaussian

• 16 Rev B.01 program [48]. A part of these computations was conducted using the SuperComputer System, Institute for Chemical Research, Kyoto University. Molecular structures were visualized using the Maestro 11.7 software package. DP4+ analysis was performed with the Excel spreadsheet made by Sarotti

Aryl-substituted acridanes as hosts for TADF-based OLEDs

• Naveen Masimukku,
• Dalius Gudeika,
• Oleksandr Bezvikonnyi,
• Ihor Syvorotka,
• Rasa Keruckiene,
• Dmytro Volyniuk and
• Juozas V. Grazulevicius

Beilstein J. Org. Chem. 2020, 16, 989–1000, doi:10.3762/bjoc.16.88

• ] and Gaussview 6 software. The ionization potential measurements of the solid samples were performed by the photoelectron emission method in air [36]. Cyclic voltammetry (CV) measurements of the liquid samples were carried out as described earlier [37]. Charge drift mobility measurements for the

Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates

• Phil M. Pithan,
• Sören Steup and
• Heiko Ihmels

Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82

• : 125 MHz) at 25 °C, or with a Varian VNMR-S 600 (1H: 600 MHz, 13C: 150 MHz) at 25 °C. The spectra were processed with the software ACD/NMR Processor Academic Edition (version: 12.02) or MestReNova (version: 12.0.1) and referenced to the respective solvent (DMSO-d6: δH = 2.50, δC = 39.5; CDCl3: δH

• no more changes were observed in the absorption spectra. All spectrometric titrations were performed at least two times to ensure reproducibility. In general, the absorption spectra were determined in a range between 200 nm and 800 nm and subsequently smoothed with the Origin software function

Efficient synthesis of piperazinyl amides of 18β-glycyrrhetinic acid

• Dong Cai,
• ZhiHua Zhang,
• Yufan Meng,
• KaiLi Zhu,
• LiYi Chen,
• ChangXiang Yu,
• ChangWei Yu,
• ZiYi Fu,
• DianShen Yang and
• YiXia Gong

Beilstein J. Org. Chem. 2020, 16, 798–808, doi:10.3762/bjoc.16.73

• using conventional or microwave methods had no effect on the conversion of intermediate 6 to compound 8. To explain the stable structure of the intermediate 6 (Figure 2a), energy minimization by MM2 was performed using the ChemBio3D Ultra 14.0 (CambridgeSoft Corporation, 2014) software force field [22

Towards triptycene functionalization and triptycene-linked porphyrin arrays

• Gemma M. Locke,
• Keith J. Flanagan and
• Mathias O. Senge

Beilstein J. Org. Chem. 2020, 16, 763–777, doi:10.3762/bjoc.16.70

• corrected for Lorentz and polarization effects by using the APEX software suite [53][54][55]. Using Olex2, the structures were solved with the XT structure solution program, using the intrinsic phasing solution method and refined against |F2| with XL using least-squares minimization [56][57]. Hydrogen atoms

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• application [66]. Data collection [67] in combination with self-leaning software related to artificial intelligence (A.I.) drives their use in applications with more efficiency in large workflows. Such tools can recognize failures in industrial processes just by collection of data in a big database where data

Six-fold C–H borylation of hexa-peri-hexabenzocoronene

• Mai Nagase,
• Kenta Kato,
• Akiko Yagi,
• Yasutomo Segawa and
• Kenichiro Itami

Beilstein J. Org. Chem. 2020, 16, 391–397, doi:10.3762/bjoc.16.37

• ) [24] and refined by full-matrix least-squares techniques against F2 (SHELXL-2018/3) [25] by using Olex2 software package [26]. The intensities were corrected for Lorentz and polarization effects. Non-hydrogen atoms were refined anisotropically, and hydrogen atoms were placed using AFIX instructions

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• consideration, are shown in Table 2 and were calculated using Gaussian 09 software program package [77]. The BDE difference between the two compounds is about 10 kcal/mol, while that in their adiabatic excitation energies is 3.9 kcal/mol. Since Δ0 − D0 is higher for 12 than 11 someone would expect 12 to be more

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• (δC 33.1 for 2 vs 28.3 for 1), a decisive evidence was acquired from spin system simulations using the software ‘nmrpeak’ [19], which gave the best match to the experimentally obtained 1H NMR spectrum with the setting of 3JH8,H9 = 15.6 Hz and 3JH7,H8 = 9.5 Hz (Figure 3). Thus, the C8 geometry was

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• inertia analysis was carried out by calculation of the lowest energy conformation of compounds 3–39 and block buster drugs. The conformation calculation was performed using the built-in AMMP molecular mechanics algorithm with default parameters of the VEGA ZZ molecular modelling software package v.3.0.1

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