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

• proteomic sample preparation and protease digestion, coupled with depletion of abundant proteins or enrichment of glycopeptides to enable their measurement. There have also been several advances in glycopeptide quantification strategies including chemical labelling, label-free and data-independent

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• µg aliquots using a CentriVap benchtop vacuum concentrator (Labconco, USA). Free N-glycan labelling with APTS: Free-N-glycans from purified antibodies were labelled with 8-aminopyrene-1,3,6-trisulfonic acid (APTS) using the FAST Glycan Kit (SCIEX, USA). Digestion, denaturing and labelling solutions

• supernatant. The supernatant was removed, labelling solution containing an internal standard (DP3) was added, and samples incubated at 60 °C for 20 min in the dark. After incubation, a cleanup solution and acetonitrile were added, followed by separation on a magnetic plate, and removal of supernatant. This

• Reagent Solution (0.07 mg/µL in anhydrous dimethylformamide (DMF, Waters Corp.) was added to the released glycans, and the labelling proceeded at room temperature for 5 min. The reaction mixture was diluted by adding acetonitrile (ACN; final concentration 89.5%) in preparation for HILIC SPE. Purification

Isolation and structure determination of a tetrameric sulfonyl dilithio methandiide in solution based on crystal structure analysis and ⁶Li/¹³C NMR spectroscopic data

• Jürgen Vollhardt,
• Hans Jörg Lindner and
• Hans-Joachim Gais

Beilstein J. Org. Chem. 2020, 16, 2057–2063, doi:10.3762/bjoc.16.172

• Li2 (δ = 1.17 pm) [15][51][52][53]. Essential for the success of the NMR spectroscopic investigation of 2a was the 13C,6Li labelling of the dilithio methandiide. It allowed the detection of the otherwise low intensity signals of the dianionic carbon atoms of the aggregates and the attainment of

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• analogues in complex biological systems such as peptides and proteins, especially in 19F NMR labelling, where fluorinated prolines can serve as spectroscopic probes. Potential areas for the application of fluorinated prolines are numerous, and include the design of molecular recognition systems [101

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

• biological labelling and are known photostable substitutes for fluorescein, giving them applications in cell imaging [20]. Due to the conjugated π-electron system present in BODIPYs they are more electron rich than porphyrins and possess an intense UV–vis absorption at approximately 400 nm, making them ideal

• molecule in the asymmetric unit with the bridgehead substituents being almost 180° to each other (Figure 2, for labelling see Figure S33 in Supporting Information File 1). Unlike the unsubstituted triptycene 1 crystal structure which exhibits a high degree of C–H···π interactions between the aromatic rings

• unit (for labelling see Figure S35 in Supporting Information File 1). In this structure, the two porphyrin residues are held at 74.1(1)° rotation to one another and at a meso–meso distance of 10.823(6) Å, while the bridgehead substituents are held in a linear fashion (≈180°) around the triptycene

Recent advances in Cu-catalyzed C(sp³)–Si and C(sp³)–B bond formation

• Balaram S. Takale,
• Ruchita R. Thakore,
• Elham Etemadi-Davan and
• Bruce H. Lipshutz

Beilstein J. Org. Chem. 2020, 16, 691–737, doi:10.3762/bjoc.16.67

• under mild reaction conditions to yield saturated ketones 410 and 411 in good to excellent yields. Hydrogen isotope labelling showed that water was likely the source of hydrogen since no reaction was observed under anhydrous conditions. By contrast, the addition of either TEMPO and BHT to the reaction

Regioselectively α- and β-alkynylated BODIPY dyes via gold(I)-catalyzed direct C–H functionalization and their photophysical properties

• Takahide Shimada,
• Shigeki Mori,
• Masatoshi Ishida and
• Hiroyuki Furuta

Beilstein J. Org. Chem. 2020, 16, 587–595, doi:10.3762/bjoc.16.53

• -tethered BODIPY derivatives serve as a substrate in the copper-catalyzed azide–alkyne cycloaddition (CuAAC) reaction, which is known as “click” reaction, allowing for a biological tissue labelling [35][36]. In addition, ethynyl-substituted BODIPYs yield unique π-conjugated BODIPY-based macrocycles by

Bipolenins K–N: New sesquiterpenoids from the fungal plant pathogen Bipolaris sorokiniana

• Chin-Soon Phan,
• Hang Li,
• Simon Kessler,
• Peter S. Solomon,
• Andrew M. Piggott and
• Yit-Heng Chooi

Beilstein J. Org. Chem. 2019, 15, 2020–2028, doi:10.3762/bjoc.15.198

• at the nerolidyl cation (Figure 5b) [28][29][30][31]. The biosynthesis of 1–8 and 10–11 are likely to be derived from sativene with a key oxidation at C-15 followed by a Baeyer–Villiger oxidation to break the C-14–C-15 bond (Figure 5c). Based on an isotope labelling study, the γ-butyrolactone moiety

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

• (bs, 12H), 0.96 (d, J = 6.6 Hz, 24H). Figure S61 (Supporting Information File 1). Structures of the compounds used in this study and labelling scheme for NMR spectra. Spectra of complexes [1(LysOMe)2], [1(ArgOMe)2], [1(HisOMe)2]: 1H NMR (a–g) and ROESY (h–j) in methanol at 298 K, 600 MHz (NMR). CD (a

Installation of -SO₂F groups onto primary amides

• Jing Liu,
• Shi-Meng Wang,
• Njud S. Alharbi and
• Hua-Li Qin

Beilstein J. Org. Chem. 2019, 15, 1907–1912, doi:10.3762/bjoc.15.186

• liver [23]. The nucleotide-derived probe 5’-(para-fluorosulfonylbenzoyl)adenosine (5’-FSBA) was used for labelling the second nucleotide binding site, the adenine nucleotide regulatory site [24]. In addition, aryl fluorosulfates have also been widely applied as sustainable alternative to aryl halides in

The cyclopropylcarbinyl route to γ-silyl carbocations

• Xavier Creary

Beilstein J. Org. Chem. 2019, 15, 1769–1780, doi:10.3762/bjoc.15.170

• intermediates in these solvolysis reactions of 1 and 2. Labelling [13][14][15], stable ion [16][17][18][19], and computational studies [19] implicate the involvement of three degenerate cyclopropylcarbinyl cations, 6a, 6b, and 6c, in equilibrium with cyclobutyl cation 7, as well as the homoallylic cation 8

Selenophene-containing heterotriacenes by a C–Se coupling/cyclization reaction

• Pierre-Olivier Schwartz,
• Sebastian Förtsch,
• Astrid Vogt,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2019, 15, 1379–1393, doi:10.3762/bjoc.15.138

• quantum chemical calculated geometry of DTT 1 and general atom labelling for all heterotriacenes 1–4 discussed. Representative electron density of frontier orbitals LUMO, HOMO, and HOMO-1 for heterotriacene DSS 4 (left). Energy of the first S1 (red dot) and second S2 (green dot) electronic transition

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

• rather the compound 8 containing the 3,3-diphenyl-3H-indazole core structure. The crystals were found to be triclinic, P-1 space group with cell constants a = 9.2107(4), b = 10.0413(5), c = 14.4363(6) Å, α = 78.183(2), β = 87.625(2), γ = 71.975(2)°. The structure of 8 and the atom-labelling scheme are

• . Possible compounds with the molecular formula C33H26N2O (structure 7 contains 27 hydrogen atoms). ORTEP view of the molecule 8 showing the atom labelling (ellipsoids are drawn at 50% probability level). Significant intermolecular interactions made by the benzhydryl group (a, upper) and the gem-diphenyl

Extending mechanochemical porphyrin synthesis to bulkier aromatics: tetramesitylporphyrin

• Qiwen Su and
• Tamara D. Hamilton

Beilstein J. Org. Chem. 2019, 15, 1149–1153, doi:10.3762/bjoc.15.111

• 138.4, 137.2, 136.6, 126.7, 116.5, 37.1, 30.9; UV–vis (CHCl3) λ = 414 (Soret band), 513, 543, 590, 648 (Q-bands). A) Porphyrin structure and labelling system. B) Substituents in the ortho-position of the group attached to the methane bridge create steric hindrance around the meso-position, above and

Mechanistic investigations on multiproduct β-himachalene synthase from Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 1008–1019, doi:10.3762/bjoc.15.99

• TSs is largely unknown [12]. In this study, we present the characterisation of a bacterial TS with a reduced selectivity both for substrates and for products together with the challenging investigation of its cyclisation mechanism by labelling experiments. Results and Discussion A bacterial β

• , Supporting Information File 1). The absolute configuration of 1 was determined as the (+)-enantiomer, unanimously by optical rotary power measurement and an isotopic labelling strategy, which involved conversion of stereoselectively deuterated and at the same position 13C-labelled FPPs by the TS to yield

• , Supporting Information File 1). To shed light on the stereochemical course of the 1,3-hydride shift connecting cations D and F, a series of labelling experiments were conducted to determine the origin of the shifting hydrogen (C-1) and its destination (C-10) for 1 (Figure 8). A comparison of the 13C NMR

Stereochemical investigations on the biosynthesis of achiral (Z)-γ-bisabolene in Cryptosporangium arvum

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2019, 15, 789–794, doi:10.3762/bjoc.15.75

• terpinyl cation has been investigated using deuterium labelling, demonstrating different stereochemical courses in the plant Salvia officinalis [8][9] and in the bacterium Streptomyces clavuligerus [10]. Also the highly unusual methylated sesquiterpene sodorifen (4) possesses a mirror plane [11] making any

• labelling experiment hard to interpret and is nevertheless most likely biosynthesised through chiral intermediates [12]. For these cases, it is a particular challenge to uncover the stereochemical information hidden behind the achiral product structure. In this study, we addressed the chiral intermediates

• assigned from HMBC data, labelling experiments with (6-13C)- and (7-13C)FPP [18] were also conducted (Figure S4, Supporting Information File 1). These results characterise the TS from C. arvum as a (Z)-γ-bisabolene synthase (BbS). The achiral, monocyclic sesquiterpene 5 is abundant in many essential oils

Synthesis of the polyketide section of seragamide A and related cyclodepsipeptides via Negishi cross coupling

• Jan Hendrik Lang and
• Thomas Lindel

Beilstein J. Org. Chem. 2019, 15, 577–583, doi:10.3762/bjoc.15.53

• partial structures is driven by an interest in the chemistry of photoreactive amino acids and heterocycles that may find application in photoaffinity labelling. Knowing the binding of a natural product to a biological target at atomic resolution, as it is the case for the cyclodepsipeptide jasplakinolide

• A (1, Scheme 1) [1][2], is an ideal situation for the validation of the chemoselectivity and efficiency of photoaffinity labelling. Recently, it has been determined by cryo-electron microscopy how jasplakinolide A (1) binds to F-actin and alters the actin skeleton in vivo, resulting in pronounced

• -bromoabrine unit of 1 could be replaced by phototryptophan [7], whereas photo β-phenylalanine [8] could replace the β-tyrosine moiety. For photoaffinity labelling studies with seragamides and geodiamolides, D-photophenylalanine could be incorporated. In this paper we describe, as the first step of such an

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• to increased fluorescence quantum yield (74%) in THF solution. The compounds exhibit low cytotoxicity and as such are useful for the cell labelling studies in the future. Keywords: 7-deazapurines; fluorescence; nucleophilic aromatic substitution; purines; push–pull systems; pyrrolo[2,3-d]pyrimidines

• in the cytoplasm. The representative fluorescent image of the labeled MCF-7 cells with compound 9 is shown in Figure 8 (for other examples see Figure S82 in Supporting Information File 1). Based on the recent investigation of metabolic labelling of DNA [30][56] by deaza-7-ethenyl-2'-deoxyguanosine

Volatiles from the hypoxylaceous fungi Hypoxylon griseobrunneum and Hypoxylon macrocarpum

• Jan Rinkel,
• Alexander Babczyk,
• Tao Wang,
• Marc Stadler and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2018, 14, 2974–2990, doi:10.3762/bjoc.14.277

• includes three SAM-dependent methylation steps. A feeding experiment with (methyl-2H3)methionine, the biosynthetic precursor of SAM, resulted in the incorporation of labelling into up to three methyl groups of 24, but not into the fourth methyl group (Figure 5), which is in line with the biosynthetic model

• major peaks originating from 20 shown in red, C) the commercial standard of 23, D) the commercial standard of 20, E) 2,5-dimethyl-p-anisaldehyde (25), F) methyl 2,5-dimethyl-p-anisate (26). Biosynthesis of 24. Feeding of (methyl-2H3)methionine resulted in the incorporation of labelling into up to three

MoO₃ on zeolites MCM-22, MCM-56 and 2D-MFI as catalysts for 1-octene metathesis

• Hynek Balcar,
• Martin Kubů,
• Naděžda Žilková and
• Mariya Shamzhy

Beilstein J. Org. Chem. 2018, 14, 2931–2939, doi:10.3762/bjoc.14.272

• . For catalyst labelling following the mode has been adopted: x MoO3/MCM-22(y), where x = Mo concentration in wt % Mo, y = Si/Al molar ratio. After spreading Mo compounds over the support surface areas (SBET, Sext) as well as void volumes (V) decreased. Similar reduction of these quantities has been

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• , a novel competition assay employing ‘clickable’ active-site-labelling probes was developed. These compounds contain terminal alkyne moieties, which can be exploited for straightforward decoration via copper(I)-catalyzed alkyne–azide cycloaddition (CuAAC), the prototypic click reaction. This

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• ’-azido-2’,5’-dideoxycytidine 2. Earlier, the nucleoside precursor 1 was used for DNA cross-linking and labelling [36]. The unprotected nucleoside 1 was treated with equimolar amounts of carbon tetrabromide and triphenylphosphine and a five-fold excess of sodium azide to obtain the azide derivative 2 (37

Applications of organocatalysed visible-light photoredox reactions for medicinal chemistry

• Michael K. Bogdos,
• Emmanuel Pinard and
• John A. Murphy

Beilstein J. Org. Chem. 2018, 14, 2035–2064, doi:10.3762/bjoc.14.179

• immediately obvious application of this bioconjugation to biochemistry and molecular biology as a tool for protein labelling, it could also be used as a convenient tool for peptide chemists in medicinal chemistry programs for modification of peptides. 2.2 C(sp2)–C(sp2) bond formation Suzuki–Miyaura and

Cationic cobalt-catalyzed [1,3]-rearrangement of N-alkoxycarbonyloxyanilines

• Itaru Nakamura,
• Mao Owada,
• Takeru Jo and
• Masahiro Terada

Beilstein J. Org. Chem. 2018, 14, 1972–1979, doi:10.3762/bjoc.14.172

• labelling experiments indicate that the rearrangement of the alkoxycarbonyloxy group proceeds in [1,3]-manner. In this article, we discuss the overall picture of the cobalt-catalysed [1,3]-rearrangement reaction including details of the reaction conditions and substrate scope. Keywords: anilines; cobalt

• confirmed that the present reaction proceeds in an intramolecular manner. Next, 18-oxygen-labelling experiments were conducted using substrate 1h-18O, of which the oxygen-18 content at the hydroxylamine oxygen atom was 62% [16][17]. The reaction of 1h-18O in the presence of the cationic cobalt catalyst at

A pyridinium/anilinium [2]catenane that operates as an acid–base driven optical switch

• Sarah J. Vella and
• Stephen J. Loeb

Beilstein J. Org. Chem. 2018, 14, 1908–1916, doi:10.3762/bjoc.14.165

• combined and anion exchanged to the triflate salt to yield [2]catenane [8DB24C8][OTf]6. Characterization The 1H NMR spectrum of [2]catenane [8DB24C8]6+ (298 K, CD2Cl2) is shown in Figure 3 and the labelling scheme for the H-atoms is given in Scheme 1. All resonances were assigned based on 2D COSY NMR

• ]catenane containing two identical bis(pyridinium)ethane recognition sites on a large macrocycle and two smaller threaded DB24C8 rings. 1H NMR spectrum of [2]catenane [8DB24C8]6+ (500 MHz, 298 K, CD2Cl2) showing the assigned proton chemical shifts; see Scheme 1 for labelling. a) The [2]catenane [8DB24C8]6

• + can be protonated to yield [8-HDB24C8]7+ in two different co-conformations A and B. b) The partial 1H NMR spectrum (500 MHz, 298 K, CD3CN) of [8-HDB24C8]7+ shows key resonances for both co-conformations A (red) and B (blue). See Scheme 1 for labelling; atoms of co-conformer B are labelled with a prime