Synthesis and physical properties of tunable aryl alkyl ionic liquids based on 1-aryl-4,5-dimethylimidazolium cations

• Stefan Fritsch and
• Thomas Strassner

Beilstein J. Org. Chem. 2024, 20, 1278–1285, doi:10.3762/bjoc.20.110

• blocked at the C2 position [33]. The use of a substituent at the C2 position was found to have a strong influence on the properties of these ionic liquids due to changes in the hydrogen-bonding network. Here, we investigate the properties of TAAILs based on the 1-aryl-4,5-dimethylimidazolium cation. It is

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• Molecular Biodiscovery, Massey University Research Fund (MURF 2015, 7003 and RM20734), Kiwi Innovation Network (KiwiNet), Massey Ventures Ltd (MU002391) and the School of Natural Sciences, Massey University.

Spin and charge interactions between nanographene host and ferrocene

• Akira Suzuki,
• Yuya Miyake,
• Ryoga Shibata and
• Kazuyuki Takai

Beilstein J. Org. Chem. 2024, 20, 1011–1019, doi:10.3762/bjoc.20.89

• three-dimensional disordered network of nanographite domains, each of which is a loose stack of 3–4 nanographene sheets with a mean in-plane size of 2–3 nm. ACFs have huge specific surface areas (about 2000 m2/g [24][25]) due to the presence of nanopores of ca. 1 nm in diameter between the nanographite

• as charge transfer and electromagnetic shielding. This is well consistent with the observed partial cationization of the guest molecules for FeCp2-ACFs-150 in XPS due to nanopore structure of the nanographene network in ACFs. The host–guest interaction between guest FeCp2 and host ACFs is most

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• undecylprodigiosin (21) is always triggered in the dying zone of the mycelial network of Streptomyces coelicolor M145 prior to morphological differentiation, right after an initial round of cell death [98]. They hypothesized that under certain circumstances, production of antiproliferative agents could play a role

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• efficiency can be attributed to the reduced kcat and increased KM for scyllo-inositol over myo-inositol. We also found that the catalytic efficiency for NAD+ was 452.4 ± 54.49 M−1 s−1 (Table 1 and Figure 2f). Sequence similarity network We generated a sequence similarity network (SSN) for the protein family

• determining the slope of the reaction from 0 to 5 min. Results were analyzed using Microsoft Excel and GraphPad Prism version 9.5.1 for Windows, GraphPad Software, Boston, Massachusetts USA, https://www.graphpad.com. SSN network generation and genome mining The sequence similarity network was generated using

• sequences and the UniRef50 function was used along with an E-value cut off of 1 × 10−55 and node network with 80% ID. Clusters with a single node were removed for simplicity. This produced an SSN with 28,698 nodes. A second SSN was generated for the IolG cluster from the PF01408 SSN. The Uniprot IDs for all

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• , the magnitude of the activation barrier is expected to be close to that in PASE. This is expected to be the case since a protein weakly bound to the carbon graphitic network can be supplemented onto graphene only by linkers as PASE, which has often been observed experimentally [1]. This type of

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• not correspond to alkylgold buildup. In protic solvents perhaps the strength of the H-bonding network controls the rate of reaction [82]. • Stronger donor ligands that would enhance protodeauration do not increase the rate of reaction. • Rates correlate most significantly with nucleophile effects

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• hollow open interconnected network of CdS nanoparticles emerged as the optimal catalyst structure. This structure was found to promote the reaction between indole and p-chlorobenzaldehyde in solvent-free conditions after 5 hours at a catalyst loading of 3 mol %. Several aromatic aldehydes were also

Additive-controlled chemoselective inter-/intramolecular hydroamination via electrochemical PCET process

• Kazuhiro Okamoto,
• Naoki Shida and
• Mahito Atobe

Beilstein J. Org. Chem. 2024, 20, 264–271, doi:10.3762/bjoc.20.27

• phenoxide in PhOH, the PhOH molecule is included in the hydrogen bond network along with the tetrabutylammonium cation (Bu4N+) to form a large aggregate. The hydrogen bonding between the amide and phosphate base in the small aggregates was stronger than in the large aggregates, which significantly enhanced

• 1. Detailed CV analysis indicated that the size of the hydrogen bond complex determined the selectivity, and HFIP played a crucial role in expanding the hydrogen bond network. These results provide fundamental insights beneficial for the design of PCET-based redox reaction systems under

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• been proposed as a very promising sequencing approach. However, its use as a generic analytical tool relies on the development of recognition techniques that can analyse complex vibrational fingerprints for a large number of monomers. In this study, we used a Bayesian deep neural network model to

• intelligence in combination with spectroscopy-augmented mass spectrometry for carbohydrates sequencing and glycomics applications. Keywords: Bayesian neural network; deep learning; glycomics; IR; spectroscopy; Introduction DNA and protein sequencing technologies that aim at determining the structure of a

• probabilistic deep neural network (Bayesian deep neural networks [12]) to support automated monosaccharide recognition for carbohydrate sequencing. We obtained a highly performing algorithm that we called "GlAIcomics", specifically trained on carbohydrates. Methodology Data production Our carbohydrate analysis

Effects of the aldehyde-derived ring substituent on the properties of two new bioinspired trimethoxybenzoylhydrazones: methyl vs nitro groups

• Dayanne Martins,
• Roberta Lamosa,
• Talis Uelisson da Silva,
• Carolina B. P. Ligiero,
• Sérgio de Paula Machado,
• Daphne S. Cukierman and
• Nicolás A. Rey

Beilstein J. Org. Chem. 2023, 19, 1713–1727, doi:10.3762/bjoc.19.125

• water molecules in the network (calcd.: 9.47% for C18H20O5N2·2H2O, MW = 380.39 g mol−1). On the other hand, hdz-NO2 did not show any mass loss below 250 °C, indicating the absence of solvation molecules in the sample (C17H17O7N3, MW = 375.34 g mol−1). Single crystals of both compounds, as monohydrates

A series of perylene diimide cathode interlayer materials for green solvent processing in conventional organic photovoltaics

• Kathryn M. Wolfe,
• Shahidul Alam,
• Eva German,
• Fahad N. Alduayji,
• Maryam Alqurashi,
• Frédéric Laquai and
• Gregory C. Welch

Beilstein J. Org. Chem. 2023, 19, 1620–1629, doi:10.3762/bjoc.19.119

• (EQE corrected). Here, the short circuit current is JSC; the open circuit voltage is VOC; the fill factor is FF, and the power conversion efficiency is η. Supporting Information Supporting Information File 14: Experimental part. Funding This work was supported by the NSERC Green Electronics Network

Photoredox catalysis harvesting multiple photon or electrochemical energies

• Mattia Lepori,
• Simon Schmid and
• Joshua P. Barham

Beilstein J. Org. Chem. 2023, 19, 1055–1145, doi:10.3762/bjoc.19.81

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• with T, pH, pMg, and I [21]. 3.11. Comparisons with values from the literature, network calculations, and the use of other methods A standard part of reporting any measurement is to make a comparison of the value(s) obtained in the current study with previously reported values of the measured quantity

• network or thermodynamic cycle calculations. It is recommended that the use of this approach be considered and, if the necessary data are present in the literature, that the thermodynamic pathway calculations be performed. Details regarding thermodynamic network calculations for biochemical substances are

Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B

• Adwoa P. Nartey,
• Aboagye K. Dofuor,
• Kofi B. A. Owusu,
• Anil S. Camas,
• Hai Deng,
• Marcel Jaspars and
• Kwaku Kyeremeh

Beilstein J. Org. Chem. 2022, 18, 1763–1771, doi:10.3762/bjoc.18.185

• to confirm the presence of the cyclic ester and the possible absolute stereochemistry around C-39 (δC 71.6) of the fatty acid chain we first of all consulted the global natural products social molecular networking (GNPS) [19][20][21]. The GNPS network data (Figure 6) provided the opportunity to

Synthetic study toward tridachiapyrone B

• Morgan Cormier,
• Florian Hernvann and
• Michaël De Paolis

Beilstein J. Org. Chem. 2022, 18, 1741–1748, doi:10.3762/bjoc.18.183

• helpful discussions. Funding MC thanks Ministère de la Recherche et de l’Education Nationale for a Ph.D. fellowship. This work has been partially supported by CNRS, Normandie University, INSA Rouen, Labex SynOrg (ANR-11-LABX-0029) and Région Normandie (CRUNCh network).

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• ). An example of a deep learning architecture is the artificial neural network inspired by the human brain architecture. It consists of artificial neurons processing information organized in different layers and connected by synapses [73]. These advanced algorithms often provide higher accuracy in their

• prediction but are no longer interpretable as a result of their high level of abstraction [73]. NeuRiPP, for instance, utilizes a parallel convolutional neural network to predict novel RiPP precursor genes independent of their RiPP family. The neural network is trained on a RiPP precursor training set that

• annotations into numeric vectors using a shallow two-layer neural network, an approach adopted from natural language processing [41][72]. These high-dimensional vectors are then used as input for a second two-layer neural network trained on a set of BGC and non-BGC sequences to predict NP BGCs. In the last

Using UHPLC–MS profiling for the discovery of new sponge-derived metabolites and anthelmintic screening of the NatureBank bromotyrosine library

• Sasha Hayes,
• Aya C. Taki,
• Kah Yean Lum,
• Joseph J. Byrne,
• Merrick G. Ekins,
• Robin B. Gasser and
• Rohan A. Davis

Beilstein J. Org. Chem. 2022, 18, 1544–1552, doi:10.3762/bjoc.18.164

• , fragmentation of the mitochondrial tubular network, chromosome misalignment, and cell cycle arrest in mitosis in LNCaP prostate cancer cells [38]. The bastadin structure class is well-documented within the literature for their cytotoxic activity [37][39][40][41], with both bastadins 4 and 8 exhibiting in vitro

An alternative C–P cross-coupling route for the synthesis of novel V-shaped aryldiphosphonic acids

• Stephen J. I. Shearan,
• Enrico Andreoli and
• Marco Taddei

Beilstein J. Org. Chem. 2022, 18, 1518–1523, doi:10.3762/bjoc.18.160

• construction of metal phosphonate frameworks, two main considerations were made when selecting these substrates with regards to rigidity and geometry (Figure S1, Supporting Information File 1). In the compounds considered here, rigidity is ensured by the network of sp2-hybridized carbon atoms, or aromatic

Microelectrode arrays, electrosynthesis, and the optimization of signaling on an inert, stable surface

• Kendra Drayton-White,
• Siyue Liu,
• Yu-Chia Chang,
• Sakashi Uppal and
• Kevin D. Moeller

Beilstein J. Org. Chem. 2022, 18, 1488–1498, doi:10.3762/bjoc.18.156

• other block is used to provide a site for cross-linking the polymer in order to render the surface more stable once it is coated onto an array (the cinnamate block is used to make a polymer network through photochemical cross-linking). The use of the borate ester surface provides a tunable surface that

• detection methods in the subsequent binding studies. The polymer network is not permeable to molecules tethered to its surface or proteins in solution. The synthetic problem was solved by using the electrodes in an array to generate chemical reagents and catalysts and then confining those reagents and

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• of the obtained TAAD derivatives were performed, and the formation of boron chelates and host–guest complexes having an unusual intramolecular H-bonded network was showcased in this work. Results and Discussion Synthesis of 3N-TAADs, 2N,1O-TAADs and 1N,2O-TAADs Our strategy to construct TAAD

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• , amongst many other uses, provided the background for fragment-based drug design [2][3]. – An ever-increasing computer processing speed leading to an ever-growing list of software-based approaches to try to help in various aspects of drugs discovery. The neural network-based software AlphaFold [4], which

Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• fluorescent 9-fluorenone (3) via β-scission (Scheme 1b). To highlight the importance of the polymer network in the transduction of the mechanical stimulus to the mechanophore, the authors demonstrated that ball milling monomeric BMPF-OH at 30 Hz for 3 h only generated traces of 3 (1% after isolation

• Sons. Copyright © 2019 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim. (a) Mechanochemical activation of anthracene–endoperoxide mechanophore incorporated in the cross-linked polyacrylate polymer 1 by cryomilling in a mixer mill. (b) Mechanochemical activation of a polymer network matrix, bis(9

Mechanochemical bottom-up synthesis of phosphorus-linked, heptazine-based carbon nitrides using sodium phosphide

• Blaine G. Fiss,
• Georgia Douglas,
• Michael Ferguson,
• Jorge Becerra,
• Jesus Valdez,
• Trong-On Do,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2022, 18, 1203–1209, doi:10.3762/bjoc.18.125

• previous work [38] of substituting bridging nitrogen atoms for phosphorus in previously reported heptazine-based graphitic carbon nitrides. We adapted the ab initio predicted structures for a network of corrugated sheets [46] (Figure 4a and 4b) and planar sheets (Figure 4c) [47]. Additionally, we modelled

• a chlorine terminated monomeric unit based on an experimentally resolved, nitrogen-bridged, paddlewheel structure (Figure 4d) [48]. Calculations resulted in a single chemical environment for the phosphorus atoms in the three model structures. The corrugated and planar network structures have