Synthesis of (Z)-3-[amino(phenyl)methylidene]-1,3-dihydro-2H-indol-2-ones using an Eschenmoser coupling reaction

• Lukáš Marek,
• Lukáš Kolman,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2021, 17, 527–539, doi:10.3762/bjoc.17.47

• ) and 39.6 ppm (13C). High-resolution mass spectra were recorded on a MALDI LTQ Orbitrap XL equipped with a nitrogen UV laser (337 nm, 60 Hz, 8–20 μJ) in the positive ion mode. For the CID experiment using the linear trap quadrupole (LTQ) helium was used as the collision gas and 2,5-dihydroxybenzoic

A new and efficient methodology for olefin epoxidation catalyzed by supported cobalt nanoparticles

• Lucía Rossi-Fernández,
• Viviana Dorn and
• Gabriel Radivoy

Beilstein J. Org. Chem. 2021, 17, 519–526, doi:10.3762/bjoc.17.46

• 548 spectrometer, using Mg Kα radiation at 250 W and 20 mA. The resolution spectra were taken at 50 eV of pass energy, giving an absolute resolution of ±0.5 eV. The operation base pressure was kept in 10−10 Torr range. The adventitious C 1s binding energy was taken as a charge reference and fixed at

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41

• phosphonodepsidipeptides 28 were prepared and investigated as VanX inhibitors. The racemic N-Cbz 1-aminoethylphosphonic acid (29) was separated by chemical resolution with quinine, affording the (S)-N-Cbz-1-aminoethylphosphonic acid ((S)-29), which was transformed to the corresponding phosphonochloridate and further

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• intrinsically disordered proteins remains unclear. 6 Fluoroprolines in crystal structures of proteins Several high-resolution crystal structures have been reported for proteins containing fluoroprolines. In a study of enhanced green fluorescent protein from Aquorea victoria, fluoroprolines were incorporated at

Regioselective chemoenzymatic syntheses of ferulate conjugates as chromogenic substrates for feruloyl esterases

• Olga Gherbovet,
• Fernando Ferreira,
• Apolline Clément,
• Mélanie Ragon,
• Julien Durand,
• Sophie Bozonnet,
• Michael J. O'Donohue and
• Régis Fauré

Beilstein J. Org. Chem. 2021, 17, 325–333, doi:10.3762/bjoc.17.30

• (t), doublet of doublets (dd), doublet of doublets of doublets (ddd), broad (br), and quadruplet of triplets (qt) as abbreviations. Analyses and assignments were made using 1D (1H, 13C, and J-modulated spin–echo (Jmod)) and 2D NMR experiments (COSY and HSQC). High-resolution mass spectrometry (HRMS

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• ) and 19F nuclei in native tryptophan, and 5-FTrp-labelled bromodomain protein Brd4 against a panel of ligands (Figure 4) [34]. 1H NMR was found to be 6–20 times less responsive than fluorine with regards to chemical shift perturbations. Indeed, the high resolution observed in the fluorine spectra

• in the analysis of the dissociation constants due to the higher spectrum resolution and greater chemical environment sensitivity of the 19F nuclei when compared to that offered by the 15N. Due to the fact that different regions of a protein give rise to unique NMR resonances, protein-observed

• their functional architecture. Such an approach typically includes the use of a variety of high-resolution proteomic tools, cryo-electron microscopy and X-ray crystallography to achieve full molecular characterization at the atomic level. However, macromolecules such as DNA/RNA and proteins are not

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

• hydrogenation of difluorocyclopropenes [73][79]. Enzymatic hydrolysis or esterification: The first example of the enzymatic resolution of gem-difluorocyclopropanes was reported by Itoh et al. [80]. The prochiral diacetate of cis-1,2-bis-(hydroxymethyl)-3,3-difluorocyclopropane was converted into the

Facile preparation and conversion of 4,4,4-trifluorobut-2-yn-1-ones to aromatic and heteroaromatic compounds

• Takashi Yamazaki,
• Yoh Nakajima,
• Minato Iida and
• Tomoko Kawasaki-Takasuka

Beilstein J. Org. Chem. 2021, 17, 132–138, doi:10.3762/bjoc.17.14

• . The crude mixture proved to be substantially pure, and thus 2c and 2d afforded appropriate analytical data, including NMR (1H, 13C, and 19F), IR, as well as high-resolution MS data. This process allowed us to obtain the required ynones 2 as long as the residue R was aromatic, while with an aliphatic

Circularly polarized luminescent systems fabricated by Tröger's base derivatives through two different strategies

• Cheng Qian,
• Yuan Chen,
• Qian Zhao,
• Ming Cheng,
• Chen Lin,
• Juli Jiang and
• Leyong Wang

Beilstein J. Org. Chem. 2021, 17, 52–57, doi:10.3762/bjoc.17.6

• -gel was about three times higher than the glum values of R2N-TBPP and S2N-TBPP enantiomers. Interestingly, the CPL handedness of the rac-TBPP/DGG co-gel could be adjusted effectively by changing their stoichiometric ratios. Keywords: circularly polarized luminescence; chiral resolution; co-gelation

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• proteins and other biological molecules, all of which have their own biological role and chemical interactions. Characterisation methods that can be employed to study PPIs can be divided into four categories: atomic resolution methods, mass spectrometry methods, biophysical methods, and computational

• methods. These methods are summarised in Figure 1. Atomic resolution methods focus on the structure determination of protein complexes and elucidating the PPIs at a near-atomic resolution. Such methods include X-ray crystallography [12], nuclear magnetic resonance (NMR) [13], and cryogenic electron

• a lower resolution of protein structures and size requirements of the proteins under investigation. Nonetheless, resolution and size barriers are continuously being broken, with resolutions of up to 1.15 Å (human apoferritin, EMD-11668, PDB: 7a6a [17]) and structures as small as 25 kDa (Bacillus

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• digest from affinity-purified immunoglobulins G and A was analyzed on a nano-reversed-phase liquid chromatography–tandem mass spectrometry platform with a high-resolution mass analyzer and higher-energy collisional dissociation fragmentation. Initial glycopeptide identification based on MS/MS data was

• -centered glycoproteomics aims at the characterization of macroheterogeneity and microheterogeneity of protein glycosylation [6]. Reversed-phase liquid chromatography coupled to high-resolution tandem mass spectrometry (RPLC–MS/MS) is a standard analytical method in the field of glycoproteomics [7]. The

• mode. The resolution was set to 120,000. The target for automatic gain control (AGC) was set to 400,000. The maximum injection time was 50 ms. An intensity threshold of 20,000 was applied. For MS/MS analysis, charge states 2–7 were included for stepped higher-energy C-trap dissociation (HCD) with a

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• intensity, lifetime or excitation/emission maxima. The fluorescence turn-on response offers a bright signal against a dark background, which maximizes spatial resolution than the fluorescence turn-off signal [19]. A shift in the absorption/emission spectrum is also advantageous as the changes in ratio of

Regioselective synthesis of heterocyclic N-sulfonyl amidines from heteroaromatic thioamides and sulfonyl azides

• Vladimir Ilkin,
• Vera Berseneva,
• Tetyana Beryozkina,
• Tatiana Glukhareva,
• Lidia Dianova,
• Wim Dehaen,
• Eugenia Seliverstova and
• Vasiliy Bakulev

Beilstein J. Org. Chem. 2020, 16, 2937–2947, doi:10.3762/bjoc.16.243

• synthesis of complexes of bis(sulfonyl amidines) 3aj–an with metals is in progress. 1H and 13C NMR spectra including 2D HMBC and HSQC experiments of compounds 3a–an, as well as high-resolution mass spectra are consistent with the proposed structures. Carbon signals of the amidine groups of compounds 3

Ultrasound-assisted Strecker synthesis of novel 2-(hetero)aryl-2-(arylamino)acetonitrile derivatives

• Emese Gal,
• Luiza Gaina,
• Hermina Petkes,
• Alexandra Pop,
• Castelia Cristea,
• Gabriel Barta,
• Dan Cristian Vodnar and
• Luminiţa Silaghi-Dumitrescu

Beilstein J. Org. Chem. 2020, 16, 2929–2936, doi:10.3762/bjoc.16.242

• confirmed the molecular weight of the new compounds, while high-resolution 1H and 13C NMR spectroscopy afforded the complete characterization of the molecular skeleton. In the 1H NMR spectra of compounds 2c, 2e–l a vicinal coupling constant between the protons in the >CH–NH– unit (3J ≈ 7.5–8.7 Hz) was

Synthesis of imidazo[1,5-a]pyridines via cyclocondensation of 2-(aminomethyl)pyridines with electrophilically activated nitroalkanes

• Dmitrii A. Aksenov,
• Nikolai A. Arutiunov,
• Vladimir V. Maliuga,
• Alexander V. Aksenov and
• Michael Rubin

Beilstein J. Org. Chem. 2020, 16, 2903–2910, doi:10.3762/bjoc.16.239

• DMSO-d6, using TMS as an internal standard. High-resolution mass spectra were obtained using a Bruker Maxis spectrometer (electrospray ionization, MeCN solution, using HCO2Na/HCO2H for calibration). Melting points were measured with a Stuart smp30 apparatus. All reactions were performed in oven-dried

A novel and robust heterogeneous Cu catalyst using modified lignosulfonate as support for the synthesis of nitrogen-containing heterocycles

• Bingbing Lai,
• Meng Ye,
• Ping Liu,
• Minghao Li,
• Rongxian Bai and
• Yanlong Gu

Beilstein J. Org. Chem. 2020, 16, 2888–2902, doi:10.3762/bjoc.16.238

• further utilized to analyze the chemical states of the elements on the surface of the catalyst (Figure 5). The wide survey spectrum of LS-FAS-Cu showed that all of the essential elements could be detected. In the high-resolution spectrum of C 1s, the peak at 284.9 eV was ascribed to C–C, and the peak at

Ring-closing metathesis of prochiral oxaenediynes to racemic 4-alkenyl-2-alkynyl-3,6-dihydro-2H-pyrans

• Viola Kolaříková,
• Markéta Rybáčková,
• Martin Svoboda and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2020, 16, 2757–2768, doi:10.3762/bjoc.16.226

• , 372.1570; found, 372.1571. Computational details DFT calculations were performed using the Gaussian 16 program suite [43]. For visualizations, the GaussView 6 interface program was used [44]. Due to economy, the pure M06L functional [45], def2-SV(P) basis set [46], and resolution of identity approximation

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• the bacteria was obtained by incubating them with the DNA-based receptors (Figure 1) and washing off the excess of unbound receptors. The super resolution fluorescent images revealed that the bacterial membrane was densely covered [2]. Although this approach was used to label bacteria with different

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• obtained through nucleophilic substitution reactions between BImNs (N = 4, 10, 12, 14) and 3. All synthesized compounds were characterized by NMR spectroscopy and high-resolution mass spectrometry. Self-assembly properties of PBImNs in aqueous buffer The self-assembly properties of the four PBImN

• spectrofluorometer. Images were taken under a 365 nm UV lamp. DLS and zeta potential measurements were carried out using a Malvern Zetasizer NanoZS. A Horiba Jobin Yvon Fluorocube instrument fitted with a 340 nm diode laser excitation source (with a temporal resolution of 70 ps) was used for the time-resolved

A heterobimetallic tetrahedron from a linear platinum(II)-bis(acetylide) metalloligand

• Matthias Hardy,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2020, 16, 2701–2708, doi:10.3762/bjoc.16.220

• , correlation of the proton. Low- and high-resolution electrospray ionization mass spectrometry (ESIMS) spectra were recorded on a Bruker Daltonic LTQ Orbitrap XL. The UV–vis spectrum was recorded on a Specord 200 spectrometer (Analytik Jena AG) at ambient temperature. 4-Ethynylaniline (1) [50], trans-[Pt(PBu3

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

• Yuvixza Lizarme-Salas,
• Alexandra Daryl Ariawan,
• Ranjala Ratnayake,
• Hendrik Luesch,
• Angela Finch and
• Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

• geometry of 2 might be favoured in AChE but not in BACE-1. These possibilities all remain speculative in the absence of high-resolution structural data of the enzyme–ligand complexes. Conclusion A threo-difluorinated piperine analog (2) was successfully synthesised through a stepwise route. The

Synthesis and characterization of S,N-heterotetracenes

• Astrid Vogt,
• Florian Henne,
• Christoph Wetzel,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2020, 16, 2636–2644, doi:10.3762/bjoc.16.214

• -heterotetracenes and -hexacene were clearly identified, fully characterized, and their structures confirmed by 1H and 13C NMR spectroscopy and high-resolution mass spectrometry (HRMS) via matrix-assisted laser desorption/ionization (MALDI) (Supporting Information File 1, Figures S1–S5). In the 1H NMR spectra, the

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• mass spectrum also shows the characteristic losses of up to at least three tentacle residues from both the [M + Na]+ and [M + K]+ molecular ions [44][45][46]. In contrast to the MALDI mass spectrum, the high-resolution ESI-(+) mass spectrum of TBTQ-(OAcG)6 (see Figure S11 and Table S2) exhibits a sole

• loss of the entire tentacle as an C9H14N3O5· radical (244 u) from the [M + Na]+ ion followed by H atom transfer. Again, accurate mass measurements were not obtained. As another surprise, the high-resolution ESI-(−) mass spectrum of TBTQ-(OG)6 (see Figure S15 and Table S4, Supporting Information File 1

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• solve. Chiefly among these is the scenario where the experimentally resolved electron density map provides evidence of glycosylation, without enough resolution to derive definite and comprehensive details about the structural composition of the oligosaccharides (Figure 1). Glycan microheterogeneity and

• of glycoprotein structures have been solved using MX [24][25]. The biggest bottleneck in MX is the formation of crystals of the target macromolecule or complex. The quality of the crystal directly determines the resolution – a measure of the detail in the electron density map. Homogenous samples at

• map. Unfortunately, this problematic situation happens frequently, especially in view of the fact that the median resolution for glycoproteins (2.4 Å) is lower than that of non-glycosylated – potentially including fully deglycosylated – proteins (2.0 Å) [41]. To date, only one publicly available model

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• Peter Bayer Anja Matena Christine Beuck Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany 10.3762/bjoc.16.203 Abstract As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the

• multivalent ligands, like multi-armed GCP ligands with flexible scaffolds or nanoparticles, have been published yet. NMR spectroscopy is the ideal method to gain structural information and identify residues involved in ligand binding because it delivers single-residue resolution. It is also suitable to