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

All-carbon [3 + 2] cycloaddition in natural product synthesis

• Zhuo Wang and
• Junyang Liu

Beilstein J. Org. Chem. 2020, 16, 3015–3031, doi:10.3762/bjoc.16.251

• -membered carbocycles. These reactions have been applied successfully in the synthesis of complex natural products. In 2011, Curran and co-workers reported the synthesis of meloscine (158) featuring a tandem radical cyclization of a divinylcyclopropane [70] (Scheme 13A). Slow addition of tributylstannane

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

• compound 1e and the product of its rearrangement to 5-(4-nitrophenyl)aminotriazole 1j [54], when the reaction was carried out in n-butanol at 105 °C (Table 2). Therefore, we can conclude that compound 3t was the product of a tandem reaction involving first the rearrangement of thioamide 1e to 1j followed

One-pot multicomponent green Hantzsch synthesis of 1,2-dihydropyridine derivatives with antiproliferative activity

• Giovanna Bosica,
• Kaylie Demanuele,
• José M. Padrón and
• Adrián Puerta

Beilstein J. Org. Chem. 2020, 16, 2862–2869, doi:10.3762/bjoc.16.235

• ® SMP11 melting point apparatus. Reactions were monitored by TLC and GC. Mass spectra were measured via a Thermo Scientific GC/MS DSQ II device, which contained a column: EC-5 30 m × 0.25 mm i.d. × 0.25 µm or using the direct-infusion method using a Waters® ACQUITY® TQD system with a tandem quadrupole

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

• reactions of substrates containing three or more multiple bonds attracted special attention due to the applications in tandem metathesis processes [9][10] or stereodiscriminating enantioselective ring-closing metathetic reactions [11][12][13]. Apart from metathesis, enynes are also interesting substrates

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

• -dibromothiophene 6 and Pd(dppf)Cl2 as catalyst to give the corresponding dibromide 7 in a yield of 70%. Organozinc species 6 was obtained from 2,3-dibromothiophene by lithiation with n-BuLi and reaction with zink dichloride. Annulation to TIPS-protected SN4-Hex 8 was achieved in 87% yield by a tandem Buchwald

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• supports the mechanically interlocked structure for NDIRot in analogy to similar structures investigated by tandem mass spectrometry earlier [35][40]. Cyclic voltammograms of NDIRot show two reversible reductions E1/2red1 and E1/2red2 independent of the used solvent (pure DCE or DCE/CH3CN 1:1, Figure S11

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• between MUC1 and antibodies has received much attention, and the specificity of this interaction is of interest in improving the performance of these biomarker assays [12][13]. The extracellular domain of MUC1 contains a variable number of tandem repeats (VNTR). The VNTR region is comprised of a repeating

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

• used to counteract the need for complementary analytic techniques. One of the examples of this is tandem mass spectrometry, where the glycan fragmentation is controlled to obtain the identification of the glycosylation sites and a complete description of the glycan structure compositions, including

Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 2212–2259, doi:10.3762/bjoc.16.186

• catalyst 15 to yield the trimerized products 12 (syn) and 13 (anti) in respectable yields (Scheme 2). The alkene-bridge exchange of 12 (syn) was accomplished by tandem ring-opening and ring-closing metathesis (ROM–RCM) in the presence of Grubbs’ first generation (G-I) catalyst to generate a C3-symmetric

• hexahydrosumanene 17 which on subsequent aromatization using DDQ furnished the desired molecule sumanene (2) in good yield. To their surprise, tandem metathesis for achieving compound 17 from 13 (anti) was fruitless may be because of the endothermic reaction by 37.4 kcal/mol as compared to the exothermic (51.4 kcal

• % yield. Next, the methyl substituents were introduced at the position of the carbonyl groups of 23 to generate the methyl-substituted olefin derivative 25 via alkenyl phosphates 24 by means of three-fold cross-coupling reaction with methylmagnesium iodide in THF. Finally, during the tandem ROM–RCM, they

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• diseased states [8]. The current state-of-the art technology for the characterisation, identification, and quantification of the glycome or glycoproteome is liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) [9]. Popular and powerful glycoproteomic workflows typically involve standard

Metal-free synthesis of phosphinoylchroman-4-ones via a radical phosphinoylation–cyclization cascade mediated by K₂S₂O₈

• Qiang Liu,
• Weibang Lu,
• Guanqun Xie and
• Xiaoxia Wang

Beilstein J. Org. Chem. 2020, 16, 1974–1982, doi:10.3762/bjoc.16.164

• motifs were conveniently synthesized from readily available diphenylphosphine oxides and alkenyl aldehydes via a metal-free tandem phosphinoylation/cyclization protocol. The reaction utilizes K2S2O8 as oxidant and proceeds in DMSO/H2O at environmentally benign conditions with a broad substrate scope and

• under metal-free conditions and uses cheap K2S2O8 as oxidant with easy handling and a broad substrate scope. The reaction proceeds through a radical phosphinoylation–cyclization via a tandem C–P and C–C-bond formation. Biologically active compounds featuring the chroman-4-one framework. X-ray structure

Facile synthesis of 7-alkyl-1,2,3,4-tetrahydro-1,8-naphthyridines as arginine mimetics using a Horner–Wadsworth–Emmons-based approach

• Rhys A. Lippa,
• John A. Murphy and
• Tim N. Barrett

Beilstein J. Org. Chem. 2020, 16, 1617–1626, doi:10.3762/bjoc.16.134

• purification by chromatography on silica. This, combined with the formation of phosphoramidate 13 in 94% yield, represented a marked improvement to the initial one-pot diphosphorylation (Scheme 7). Contrary to reports using 2-methylquinolines, tandem phosphorylation and olefination was not possible [15]. When

• phosphoramidate protecting group, which was superior to the more commonly applied Boc protecting group which was unstable to the lithiation. This synthetic route replaces traditional Wittig and tandem alkylation/reduction methodologies, which suffer from complications arising from troublesome byproducts and

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

Photocatalyzed syntheses of phenanthrenes and their aza-analogues. A review

• Alessandra Del Tito,
• Havall Othman Abdulla,
• Davide Ravelli,
• Stefano Protti and
• Maurizio Fagnoni

Beilstein J. Org. Chem. 2020, 16, 1476–1488, doi:10.3762/bjoc.16.123

• biaryls 5.1a–d in up to excellent yields at room temperature by using α-bromoesters as radical precursors and [fac-Ir(ppy)3] as the photoredox catalyst [49]. A similar photocatalyzed tandem insertion/cyclization approach based on isocyanides and amino acid/peptide-derived Katritzky salts as precursors of

• starting from alkylhydrazines [66]. However, a heteroatom-based radical may be used for the addition onto isonitriles as well. One such example dealt with the photoredox tandem phosphonylation/cyclization of diphenylphosphine oxides with 2-arylphenylisonitriles. Here, the sequential formation of C–P and C

• sulfonyl radical, prone to start a tandem sulfonylation/annulation of vinyl azides [84]. Recently, the phenanthridine core was assembled through a radical cascade triggered by the trifluoromethylthiolation of N-(o-cyanobiaryl)acrylamides. The process occurred under visible-light irradiation (6 W blue LED

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel–Hauser amides, and magnesium alkoxides

• Mateo Berton,
• Kevin Sheehan,
• Andrea Adamo and
• D. Tyler McQuade

Beilstein J. Org. Chem. 2020, 16, 1343–1356, doi:10.3762/bjoc.16.115

• combined with a solution-phase reagent, including: (1) copper(I) oxide to produce N-heterocyclic carbene–Cu(I) complexes for use as catalysts [13]; (2) proline to perform proline-based catalytic reactions [14]; (3) zinc powder to produce organozinc halides in tandem with Negishi couplings [15]; (4) zinc

Synthesis and anticancer activity of bis(2-arylimidazo[1,2-a]pyridin-3-yl) selenides and diselenides: the copper-catalyzed tandem C–H selenation of 2-arylimidazo[1,2-a]pyridine with selenium

• Mio Matsumura,
• Tsutomu Takahashi,
• Hikari Yamauchi,
• Shunsuke Sakuma,
• Yukako Hayashi,
• Tadashi Hyodo,
• Tohru Obata,
• Kentaro Yamaguchi,
• Yasuyuki Fujiwara and
• Shuji Yasuike

Beilstein J. Org. Chem. 2020, 16, 1075–1083, doi:10.3762/bjoc.16.94

• selenium source in the presence of a transition metal catalyst, such as Cu or Ni [27][28][29][30][31][32]. In 2011, Zhou et al. reported the pioneering Cu-catalyzed C–H selenation of 2-arylimidazopyridine with diphenyl diselenide in the presence of CuI (10 mol %) [29]. Tandem reactions involving the

• studies in the synthesis of organoselenium compounds containing imidazo[1,2-a]pyridine rings [27][28][29][30][31][32][33][34], the synthesis of bis(2-arylimidazo[1,2-a]pyridin-3-yl) selenides and diselenides by the Cu-catalyzed tandem C–H selenation of 2-arylimidazo[1,2-a]pyridines with Se powder is

Bipyrrole boomerangs via Pd-mediated tandem cyclization–oxygenation. Controlling reaction selectivity and electronic properties

• Liliia Moshniaha,
• Marika Żyła-Karwowska,
• Joanna Cybińska,
• Piotr J. Chmielewski,
• Ludovic Favereau and
• Marcin Stępień

Beilstein J. Org. Chem. 2020, 16, 895–903, doi:10.3762/bjoc.16.81

• Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) UMR 6226, F-35000 Rennes, France 10.3762/bjoc.16.81 Abstract Boomerang-shaped bipyrroles containing donor–acceptor units were obtained through a tandem palladium-mediated reaction consisting of a cyclization step, involving double C–H bond

• obtained by tandem cyclodehydrogenations of oligoaryl precursors [1][2][3]. This general strategy is attractive because it does not require prefunctionalization of coupling sites and because it provides rapid access to complex π systems. Such cyclodehydrogenations can be performed using diverse oxidants [4

• stoichiometric oxidant. The scope of such Pd(II)-induced couplings was further developed into tandem processes involving consecutive cyclization of substituents (dcTTEE) and oxygenation of pyrrolic α-positions to form lactams cNDA1O and cNMI1O. The mechanism of those transformations was subsequently explored

Combining enyne metathesis with long-established organic transformations: a powerful strategy for the sustainable synthesis of bioactive molecules

• Valerian Dragutan,
• Ileana Dragutan,
• Albert Demonceau and
• Lionel Delaude

Beilstein J. Org. Chem. 2020, 16, 738–755, doi:10.3762/bjoc.16.68

• to build the desired 1,3-dienic units. The advantageous association of this approach with name reactions like Grignard, Wittig, Diels–Alder, Suzuki–Miyaura, Heck cross-coupling, etc. is illustrated. Examples unveil the generality of such tandem reactions in providing not only the intricate structures

• of known, in vivo effective substances but also for designing chemically modified analogs as valid alternatives for further therapeutic agents. Keywords: bioactive compounds; enyne metathesis; ring-closing metathesis; ruthenium catalysts; tandem reactions; Introduction Alkene and alkyne metathesis

• dihydroartemisinic acid (DHAA) [64][65]. Also, high efficient and recyclable catalytic systems based on metal-organic frameworks (MOFs) have also been reported for the tandem hemisynthesis of artemisinin [66]. In a remarkable work, this antimalarial drug was obtained by a new route involving enyne metathesis as the

Cascade trifluoromethylthiolation and cyclization of N-[(3-aryl)propioloyl]indoles

• Ming-Xi Bi,
• Shuai Liu,
• Yangen Huang,
• Xiu-Hua Xu and
• Feng-Ling Qing

Beilstein J. Org. Chem. 2020, 16, 657–662, doi:10.3762/bjoc.16.62

• esters with AgSCF3 for the synthesis of trifluoromethylthiolated coumarins (Scheme 1b) [28]. In 2016, Liu exploited the tandem trifluoromethylthiolation/cyclization of N-arylpropiolamides to construct the SCF3-substituted spiro[4,5]trienones (Scheme 1c) [29]. In the same year, Zhang and Chen disclosed

• the transformation of arylpropynones to SCF3-substituted indenones through the tandem trifluoromethylthiolation/cyclization processes (Scheme 1d) [30]. As part of our continuing research interest in radical trifluoromethylthiolation reactions [33][34][35][36][37][38], herein we disclose a cascade

A systematic review on silica-, carbon-, and magnetic materials-supported copper species as efficient heterogeneous nanocatalysts in “click” reactions

• Pezhman Shiri and
• Jasem Aboonajmi

Beilstein J. Org. Chem. 2020, 16, 551–586, doi:10.3762/bjoc.16.52

• nanomagnetic catalyst for “click” reactions and tandem syntheses of 1,2,3-triazoles substituted at the 1- and 4-position in water [98]. The synthetic approach to 131 is shown in Scheme 28. First, magnetic CuFe2O4 nanoparticles 126 were treated with (3-chloropropyl)triethoxysilane in dry toluene to produce the

Controlling alkyne reactivity by means of a copper-catalyzed radical reaction system for the synthesis of functionalized quaternary carbons

• Goki Hirata,
• Yu Yamane,
• Naoya Tsubaki,
• Reina Hara and
• Takashi Nishikata

Beilstein J. Org. Chem. 2020, 16, 502–508, doi:10.3762/bjoc.16.45

• reaction of 3 equivalents of terminal alkyne 1 (aryl substituted alkyne) and an α-bromocarbonyl compound 2 (tertiary alkyl radical precursor) undergoes tandem alkyl radical addition/Sonogashira coupling to produce 1,3-enyne compound 3 possessing a quaternary carbon in the presence of a copper catalyst

• . Moreover, the reaction of α-bromocarbonyl compound 2 and an alkyne 4 possessing a carboxamide moiety undergoes tandem alkyl radical addition/C–H coupling to produce indolinone derivative 5. Keywords: copper catalyst; 1,3-enyne; functionalized quaternary carbon; indolinone; tandem alkyl radical addition

• addition (ATRA) [21] (Scheme 1, i–iii). Therefore, we postulated that if we could control the reactivities of the alkynyl–Cu and ATRA adducts, a tandem tertiary alkylation followed by an alkynylation could occur to produce a 1,3-enyne possessing a quaternary carbon center with good regio- and

Copper-promoted/copper-catalyzed trifluoromethylselenolation reactions

• Clément Ghiazza and
• Anis Tlili

Beilstein J. Org. Chem. 2020, 16, 305–316, doi:10.3762/bjoc.16.30

• heteroaromatic species. More recently, the same group reported the synthesis of 2-trifluoromethylselenylated benzofused heterocycles (Scheme 7) [24]. This tandem process consisted in a first Pd-catalyzed cyclization of 2-(2,2-dibromovinyl)phenols/-thiophenols/-anilines, leading to the corresponding 2-brominated

• tandem formation of C–Se and Se–fluoroalkyl bonds have emerged in the last five years. In 2014, Hor and Weng reported the trifluoromethylselenolation of (hetero)aryl iodides and alkyl bromides with the Ruppert–Prakash reagent, TMSCF3, elemental selenium, potassium fluoride, and silver carbonate under

Copper-catalyzed enantioselective conjugate addition of organometallic reagents to challenging Michael acceptors

• Delphine Pichon,
• Jennifer Morvan,
• Christophe Crévisy and
• Marc Mauduit

Beilstein J. Org. Chem. 2020, 16, 212–232, doi:10.3762/bjoc.16.24

• –86%) and yield (44–63%) remained decent. The efficiency of TolBINAP (L3)/CuI was also demonstrated in the ECA of Grignard reagents to the 4-chloro-α,β-unsaturated thioester 22 [31]. Interestingly, the presence of the internal chloro leaving group allowed a powerful tandem conjugate addition–enolate

• conversion and the racemic 1,4-product. Additionally, amide substrates featuring a bis(para-methoxybenzyl) moiety could be converted into relevant β-alkyl-substituted chiral amines, ubiquitous in numerous pharmaceutical ingredients, such as 52, a direct precursor of a drug candidate. Moreover, tandem ECA

• vicinal dialkyl arrays via Cu ECA of Grignard reagents to γ-substituted α,β-unsaturated thioesters. 1,6-Cu ECA of MeMgBr to α,β,γ,δ-bisunsaturated thioesters: an iterative approach to deoxypropionate units. Tandem Cu ECA/intramolecular enolate trapping involving 4-chloro-α,β-unsaturated thioester 22. Cu

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• pyrophosphate synthase, and GFPP geranylfarnesyl pyrophosphate. Mechanisms for type I, type II, and type II/type I tandem terpene cyclases. a) Tail-to-head class I germacrene A (13) cyclase. b) Head-to-tail type II brasilicardin (14) cyclase. c) Type II ent-copalyl diphosphate (15) synthase and type I ent