Advancements in hydrochlorination of alkenes

• Daniel S. Müller

Beilstein J. Org. Chem. 2024, 20, 787–814, doi:10.3762/bjoc.20.72

• the higher-substituted carbon atom to furnish intermediate species C. The irreversibility of the hydride addition and the regioselectivity thereof were supported by a deuterium labelling study with PhSiD3. The next steps involve homolytic cleavage of the cobalt–carbon bond to yield a carbon-centered

Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• Zhiyong Yin Jeroen S. Dickschat Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany 10.3762/bjoc.20.67 Abstract An isotopic labelling method was developed to investigate substrate binding by ketosynthases, exemplified by the

• , to investigate the function of the KS domain BaeJ-KS2 the synthesis of 13C-labelled (S)-11 as a mimic of the intermediate bound to the ACP of module 3 was performed. It was planned to introduce the 13C-labelling from (5-13C)glutamate into the γ-aminobutyrate portion of (S)-11. For this purpose, the

• have established a new method based on stable isotope (13C) labelling to investigate the KS domain substrate specificity that makes use of simple 13C NMR analysis of protein preparations obtained by a buffer exchange after enzyme incubations with substrate surrogates (SNAC esters), and its application

Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs

• Binbin Gu,
• Lin-Fu Liang and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104

• unpleasant off-flavour [19][20]. The biosynthesis of 1 has been extensively studied. The initial hypothesis that 1 could be a degraded sesquiterpene [3] was not confirmed through isotopic labelling experiments that rather pointed to a methylated monoterpene [10][21]. Based on these experiments a biosynthetic

Pyridine C(sp²)–H bond functionalization under transition-metal and rare earth metal catalysis

• Haritha Sindhe,
• Malladi Mounika Reddy,
• Karthikeyan Rajkumar,
• Akshay Kamble,
• Amardeep Singh,
• Anand Kumar and
• Satyasheel Sharma

Beilstein J. Org. Chem. 2023, 19, 820–863, doi:10.3762/bjoc.19.62

• containing bioactive molecules (Scheme 10). To attain enantioselectivity a chiral phosphine oxide (43)-ligated Ni–Al bimetallic catalyst was used that was critical in improving the reactivity and controlling the selectivity of the reaction. Further, based on deuterium labelling experiments, KIE studies, and

• with various tethered alkenes, such as 1,1-disubstituted alkenes, styrene, diene, trisubstituted alkene and enamines. To get insights into the mechanism the authors conducted additional experiments including deuterium labelling reactions and proposed the mechanism depicted in Scheme 37b. Initially, the

pH-Responsive fluorescent supramolecular nanoparticles based on tetraphenylethylene-labelled chitosan and a six-fold carboxylated tribenzotriquinacene

• Nan Yang,
• Yi-Yan Zhu,
• Wei-Xiu Lin,
• Yi-Long Lu and
• Wen-Rong Xu

Beilstein J. Org. Chem. 2023, 19, 635–645, doi:10.3762/bjoc.19.45

• synthesized a new chitosan bioconjugate CS-TPE with varying amounts of TPE labelling. It can self-assemble into fluorescent polymeric nanoparticles in an aqueous solution at pH 5.3, either alone or as a guest by electrostatic interaction with the TBTQ-C6 host. These nanoparticles were disassembled upon

• bioconjugates with different degrees of fluorescence labelling were synthesized as guests by controlling the feed ratios (Rf) of 4-(1,2,2-triphenylvinyl)benzaldehyde (TPE-CHO) [23] to 2 mol %, 10 mol %, and 20 mol %, respectively. They were obtained with chitosan and TPE-CHO through an aldimine condensation

• of these peaks confirmed that the TPE units were successfully labelled in the CS chain. The degree of fluorescence labelling (DL) of TPE attached to the CS chain was estimated by comparing the integrated areas of Har and H2 in the 1H NMR spectra (Figure 1) [24]. Accordingly, the DL at Rf = 2, 10 and

Group 13 exchange and transborylation in catalysis

• Dominic R. Willcox and
• Stephen P. Thomas

Beilstein J. Org. Chem. 2023, 19, 325–348, doi:10.3762/bjoc.19.28

• [58]. The alkyne 1 and dialkylborane reacted to give an alkenylborane 2. Transborylation with HBpin gave the alkenyl boronic ester 3 and regenerated the catalyst, HBR2. Isotopic labelling (H10Bpin) confirmed B–C(sp2)/B–H transborylation proceeded by σ-bond metathesis, and not ligand exchange. Using

• H-B-9-BBN, followed by B‒O/B‒H transborylation with HBpin to give the Bpin-enolate 52 and regenerate H-B-9-BBN (Scheme 12). Isotopic labelling with DBpin and H10Bpin supported this proposal. Fontaine reported that boric acid could be used as a precatalyst for the BH3-catalysed hydroboration of

• isotopic labelling and proposed to proceed by hydroboration of the allene 62 by the borane catalyst (H-B-9-BBN or 10-phenyl-9-borabicyclo[3.3.2]decane [Ph-BBD]) followed by rapid isomerisation from the (Z)-63 to (E)-allylborane 64 which underwent allylation of the ketone 65 to give an allylic borinic ester

Synthesis of the biologically important dideuterium-labelled adenosine triphosphate analogue ApppI(d₂)

• Petri A. Turhanen

Beilstein J. Org. Chem. 2022, 18, 1466–1470, doi:10.3762/bjoc.18.153

• spectrometry. Keywords: ApppI; ATP; deuterium labelling; HPCCC; mevalonate pathway; NMR; synthesis; Introduction It has become clear and evident that phosphonate chemistry plays a crucial role in drug research and development [1][2][3][4]. There are several phosphonate-containing compounds under research or

The enzyme mechanism of patchoulol synthase

• Houchao Xu,
• Bernd Goldfuss,
• Gregor Schnakenburg and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2022, 18, 13–24, doi:10.3762/bjoc.18.2

• Chemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany 10.3762/bjoc.18.2 Abstract Different mechanisms for the cyclisation of farnesyl pyrophosphate to patchoulol by the patchoulol synthase are discussed in the literature. They are based on isotopic labelling experiments, but the

• results from these experiments are contradictory. The present work reports on a reinvestigation of patchoulol biosynthesis by isotopic labelling experiments and computational chemistry. The results are in favour of a pathway through the neutral intermediates germacrene A and α-bulnesene that are both

• ), seychellene (11) and pogostol (12) as further side products [8]. The biosynthetic mechanism of the formation of compound 3 was investigated by several groups through isotopic labelling experiments. In 1987, Croteau et al. have suggested a pathway through 1,10-cyclisation of FPP to the (E,E)-germacradienyl

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• of biomolecules [35][36][37]. The approaches by Buchwald and Pentelute are suitable for selective, bioorthogonal labelling of cysteine- [38][39][40] and lysine-containing [41][42] peptides and proteins using stochiometric amounts of pre-formed Pd(II)-aryl complexes. They can further be applied for

• part in the destruction complex for β-catenin labelling in the canonical Wnt signalling. Loss-of-function mutations in this pathway lead to a dysregulated signal transduction causing cancer [75][76]. All-hydrocarbon stapled peptides comprising amino acids 467 to 481 of the axin CBD had been studied in

Synthesis of new bile acid-fused tetrazoles using the Schmidt reaction

• Dušan Đ. Škorić,
• Olivera R. Klisurić,
• Dimitar S. Jakimov,
• Marija N. Sakač and
• János J. Csanádi

Beilstein J. Org. Chem. 2021, 17, 2611–2620, doi:10.3762/bjoc.17.174

• molecular structures of compounds 13 and 14, with labelling of nonhydrogen atoms. Hydrogen atoms are drawn as spheres of arbitrary radii. Dose dependence of the cytotoxicity of tested compounds on treated cell lines. All compounds were tested in the concentration range 0.1–100 μM. A) Cytotoxicity of

Targeting active site residues and structural anchoring positions in terpene synthases

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 2441–2449, doi:10.3762/bjoc.17.161

• of cross peaks in blue and in red refers to the hydrogens in Scheme 1 of same colour. Determination of the enantiomeric composition of 8 and 9 obtained from GGPP with SmTS1 enzyme variants through enantioselective labelling with (R)- and (S)-(1-13C,1-2H)GGPP. Compound 8 is obtained with different

On the application of 3d metals for C–H activation toward bioactive compounds: The key step for the synthesis of silver bullets

• Renato L. Carvalho,
• Amanda S. de Miranda,
• Mateus P. Nunes,
• Roberto S. Gomes,
• Guilherme A. M. Jardim and
• Eufrânio N. da Silva Júnior

Beilstein J. Org. Chem. 2021, 17, 1849–1938, doi:10.3762/bjoc.17.126

• co-workers described the deuteration of several pharmaceuticals via an Fe-catalyzed C–H activation protocol (Scheme 29A and B) [161]. The site selectivity of the bulky iron catalyst was orthogonal to conventional iridium catalysts used in deuterium labelling experiments, allowing the

A new glance at the chemosphere of macroalgal–bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry

• Marine Vallet,
• Filip Kaftan,
• Veit Grabe,
• Fatemeh Ghaderiardakani,
• Simona Fenizia,
• Aleš Svatoš,
• Georg Pohnert and
• Thomas Wichard

Beilstein J. Org. Chem. 2021, 17, 1313–1322, doi:10.3762/bjoc.17.91

• combined LDI-MS imaging mass spectrometry and cLSM using a non-specific fluorescence labelling probe to visualise the bacterial cells living in symbiosis with U. mutabilis. Following a one-month incubation in clean cuvette slides placed in Petri dishes filled with medium, axenic and bacteria-inoculated U

Breakdown of 3-(allylsulfonio)propanoates in bacteria from the Roseobacter group yields garlic oil constituents

• Anuj Kumar Chhalodia and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 569–580, doi:10.3762/bjoc.17.51

• labelling into dimethyl disulfide (DMDS), the oxidative dimerization product from MeSH, showing the activity of the demethylation pathway in these bacteria. However, knockout of the dmdA gene in R. pomeroyi still gave a low incorporation of labelling into DMDS, suggesting the presence of another gene

• responsible for the demethylation activity [28]. Also the labelling from (34S)DMSP was efficiently incorporated into DMDS and dimethyl trisulfide (DMTS) [29]. Our previous investigations have also demonstrated that synthetic, i.e., non-natural DMSP analogues such as 3-(ethylmethyl)sulfoniopropanoate (EMSP), 3

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

• labelling 19F NMR offers an attractive option for investigating the interactions between proteins and other biomolecules such as nucleic acids. Many of the advantages of 19F NMR have already been discussed but it is worth highlighting that it is a particularly useful technique to study large proteins that

• this technique is that the natural amino acid translation process incorporates the specific fluorinated analogue in all the locations where the original amino acid was present, resulting in a “global” labelling of the protein. This can result in a variety of unwanted side effects, including, in some

• -phase peptide synthesis (SPPS) methods (15 and 16, Figure 1). A second well-established methodology for the 19F isotopic labelling of protein and peptides involves the post-translational chemical conjugation of an 19F probe to specific amino acids present within the protein, typically cysteine and

On the mass spectrometric fragmentations of the bacterial sesterterpenes sestermobaraenes A–C

• Anwei Hou and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2020, 16, 2807–2819, doi:10.3762/bjoc.16.231

• Anwei Hou Jeroen S. Dickschat Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53127 Bonn, Germany 10.3762/bjoc.16.231 Abstract A 13C-labelling was introduced into each individual carbon of the recently discovered sestermobaraenes by the

• reaction proceeds in reverse order of a thermal reaction promoted by the thermal conditions of the gaschromatographic analysis) [14]. The fragmentation reactions of structurally simple compounds such as fatty acid methyl esters have been well investigated by isotopic labelling experiments [15][16] and the

• knowledge allows for structural predictions based on GC–MS data [17]. The deuterium labelling technique was also applied to other compound classes such as alkylbenzenes and ketones [18][19][20][21]. For terpenes, structural proposals can only be made based on the mass spectra for structurally less

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• phenylboronic acid (PBA)-functionalized boron dipyrromethene (BODIPY) applying the ball milling approach. The ball milling formation of boron esters between PBA BODIPY and dextran proved to be more efficient in terms of reaction time, amount of reactants, and labelling degree compared to the corresponding

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• molecules were dyes used for the DNA/RNA labelling or even monitoring or influencing DNA/RNA function [3][4]. However, due to the complexity of DNA-coded or RNA-coded processes, also including epigenetics, there is permanent need for novel dyes, differing in selectivity, colour, or method of monitoring [5

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