Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• better identification of the modified peptides by search algorithms and second, if labeled with stable isotopes, it allows for quantification of the modified probe–peptide conjugates. Inspired by tandem mass spectrometry tags (TMT-tags) Makarov et al. have developed a ‘clickable’ 2,6-dimethylpiperidine

• commonly used proteases [109]. Multiple modifications to the peptide sequence and linker structure were consecutively introduced by the Cravatt lab including the ‘light’ and ‘heavy’ derivatives containing stable isotopes enabling the quantification and direct comparison between the conditions [80]. The

• the shortened version described in the previous paragraph (Figure 13) [112][113][114][115]. As an interesting feature, the DADPS-linker with dibromo substitution takes advantage of the naturally occurring stable isotopes 79Br and 81Br in almost stoichiometric ratio. The predictable isotopic pattern

New triazinephosphonate dopants for Nafion proton exchange membranes (PEM)

• Fátima C. Teixeira,
• António P. S. Teixeira and
• C. M. Rangel

Beilstein J. Org. Chem. 2024, 20, 1623–1634, doi:10.3762/bjoc.20.145

• for 35Cl and 37Cl isotopes, respectively, with an approximately 3/4 and 1/4 proportion. The symmetry of the obtained compound TP1 gives simple NMR spectra, with the 31P NMR spectrum showing a singlet signal (Figure 2) and the signal at 169.5 ppm, on the 13C NMR spectrum, confirming the presence of a

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

• glutamate decarboxylase, and incubated with BaeJ-KS2. Substrate binding was demonstrated through 13C NMR analysis of the products against the background of various control experiments. Keywords: bacillaene; biosynthesis; enzyme mechanisms; isotopes; trans-AT polyketide synthases; Introduction Polyketides

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

• , for example, the adiabatic potential energy surface, defined as the Born–Oppenheimer surface, is invariant for substitution between isotopes of carbon. This is an example of the weak perturbation. In substitutions where the mass effect can be regarded as the predominant effect, it is safe to assume

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

• ; isotopes; substrate analogs; terpenes; Introduction The musty odorant 2-methylisoborneol (1, Scheme 1) has first been obtained through synthesis from camphor [1] and has subsequently been discovered as a natural product in streptomycetes [2][3]. The volatile compound was later also found in various other

Radical ligand transfer: a general strategy for radical functionalization

• David T. Nemoto Jr,
• Kang-Jie Bian,
• Shih-Chieh Kao and
• Julian G. West

Beilstein J. Org. Chem. 2023, 19, 1225–1233, doi:10.3762/bjoc.19.90

• important medical radioisotope used for positron emission tomography (PET) [43]. Optimized conditions of both isotopes included fast reaction times of under two hours; in the case of the 18F radioisotope, reactions were carried out in 10 minutes and resulted in moderate to high yields, demonstrating the

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

• calculations; enzyme mechanisms; isotopes; terpenes; Introduction Patchouli oil, the essential oil of the shrub Pogostemon cablin, has a pleasant woody odour and is of high economic value for the perfumery and cosmetics industries. It is mainly composed of sesquiterpenes with patchoulol as the main compound

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

• mechanisms; isotopes; site-directed mutagenesis; terpenes; Introduction Terpenoids now span more than 90,000 known compounds, which makes them by far the largest class of natural products [1]. Despite this fact, all compounds are made from only two C5 building blocks, dimethylallyl diphosphate (DMAPP) and

Identification of volatiles from six marine Celeribacter strains

• Anuj Kumar Chhalodia,
• Jan Rinkel,
• Dorota Konvalinkova,
• Jörn Petersen and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 420–430, doi:10.3762/bjoc.17.38

• Celeribacter strains are capable of methionine and DMSP degradation to widespread sulfur volatiles, but the analysis of trace compounds in natural samples must be taken with care. Keywords: GC–MS; isotopes; Roseobacter; sulfur metabolism; volatiles; Introduction Bacteria from the roseobacter group belong to

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

• cut-offs for mass accuracy, isotopic pattern matching, and the signal-to-noise ratio of an analyte. Finally, the integrated areas of all charge states passing the quality criteria were summed for each glycopeptide composition, the area was corrected for missing isotopes, and total area normalization

• pattern). LaCyTools provides information on the mass accuracy and isotopic pattern and integrates the isotopes of selected features in summed MS spectra within user-defined RT windows. Here, it is crucial to select appropriate RT windows and isotopes of interest before starting the analysis to prevent the

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

• investigation of the electron impact mass spectrometry (EIMS) fragmentation reactions of these sesterterpene hydrocarbons. Keywords: isotopes; mass spectrometry; reaction mechanisms; sesterterpenes; Streptomyces mobaraensis; Introduction The sestermobaraenes A–F (1–6) and sestermobaraol (7) are a series of

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• isotopes for positron emission tomography (PET) due to their suitable half-life (t1/2 = 110 min) and low positron energy, which allows the production of high-resolution images [23]. Therefore, radiopharmaceuticals that contain fluorine substituents are in high demand. Fluorine enhances important properties

Palladium-catalyzed Sonogashira coupling reactions in γ-valerolactone-based ionic liquids

• László Orha,
• József M. Tukacs,
• László Kollár and
• László T. Mika

Beilstein J. Org. Chem. 2019, 15, 2907–2913, doi:10.3762/bjoc.15.284

• Laszlo Orha Jozsef M. Tukacs Laszlo Kollar Laszlo T. Mika Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics Műegyetem rkp. 3, Budapest, H-1111, Hungary Institute of Isotopes, Konkoly-Thege Miklós str. 29-33. Budapest, H-1121, Hungary

Analysis of sesquiterpene hydrocarbons in grape berry exocarp (Vitis vinifera L.) using in vivo-labeling and comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS)

• Philipp P. Könen and
• Matthias Wüst

Beilstein J. Org. Chem. 2019, 15, 1945–1961, doi:10.3762/bjoc.15.190

• ], while [6,6,6-2H3]-(±)-mevalonolactone (d3-MVL) was purchased from C/D/N Isotopes Inc. (Pointe-Claire, Quebec, Canada). Retention indices were calculated using a C7–C30 saturated alkanes standard solution obtained from Sigma-Aldrich (St. Louis, MO, U.S.A.). The analytical standard (+)-valencene (purity

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

• potential was also exploited in the preparation of sesquiterpene isotopomers, which provided insights into their EIMS fragmentation mechanisms. Keywords: enzyme mechanisms; isotopes; mass spectrometry; promiscuity; terpenes; Introduction The organic chemist usually prefers to work with pure compounds

Syntheses and chemical properties of β-nicotinamide riboside and its analogues and derivatives

• Mikhail V. Makarov and
• Marie E. Migaud

Beilstein J. Org. Chem. 2019, 15, 401–430, doi:10.3762/bjoc.15.36

Novel solid-phase strategy for the synthesis of ligand-targeted fluorescent-labelled chelating peptide conjugates as a theranostic tool for cancer

• Sagnik Sengupta,
• Mena Asha Krishnan,
• Premansh Dudhe,
• Ramesh B. Reddy,
• Bishnubasu Giri,
• Sudeshna Chattopadhyay and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2018, 14, 2665–2679, doi:10.3762/bjoc.14.244

• imaging (MRI) are exploited and each modality has its own strengths and weaknesses [3]. However, imaging studies using fluorescent probes [4] or radioactive isotopes [5][6] offers real-time, non-invasive, high-resolution images, during the examination of pathological diseased state. Prostate specific

Dynamic light scattering studies of the effects of salts on the diffusivity of cationic and anionic cavitands

• Anthony Wishard and
• Bruce C. Gibb

Beilstein J. Org. Chem. 2018, 14, 2212–2219, doi:10.3762/bjoc.14.195

• . Deuterated solvents were purchased from Cambridge Isotopes and used without further purification. Hosts 1 and 2 were synthesized by the procedures reported previously [15][16][31]. All 1H NMR spectra were collected on a Bruker 500 MHz spectrometer at 25 °C. Spectral processing was performed using Mnova

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• , partly because it is performed at much higher concentrations (millimolar, rather than micromolar analytes), and partly because it provides site-specific information without labeling. Labeling of an analyte as small as a mononucleotide with something other than isotopes was considered problematic, as it

¹⁵N-Labelling and structure determination of adamantylated azolo-azines in solution

• Sergey L. Deev,
• Alexander S. Paramonov,
• Tatyana S. Shestakova,
• Igor A. Khalymbadzha,
• Oleg N. Chupakhin,
• Julia O. Subbotina,
• Oleg S. Eltsov,
• Pavel A. Slepukhin,
• Vladimir L. Rusinov,
• Alexander S. Arseniev and
• Zakhar O. Shenkarev

Beilstein J. Org. Chem. 2017, 13, 2535–2548, doi:10.3762/bjoc.13.250

• mass spectrometry. In addition, ≈50% excess of the 15N isotopes in compounds 15a*-15N2 and 15b*-15N2 after reaction was confirmed by 13C NMR spectroscopy. In this case, the C1' signals of the labelled and unlabelled components demonstrated approximately equal integral intensities (Figure S24 in

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• background in spectroscopic observations of biological samples. This feature is especially beneficial for NMR applications because the sole stable fluorine isotope (19F) has the third largest magnetogyric ratio among the nuclei measured by NMR (after 3H and 1H hydrogen isotopes); as a result, 19F NMR

Curcuminoid–BF₂ complexes: Synthesis, fluorescence and optimization of BF₂ group cleavage

• Henning Weiss,
• Jeannine Reichel,
• Helmar Görls,
• Kilian Rolf Anton Schneider,
• Mathias Micheel,
• Michael Pröhl,
• Michael Gottschaldt,
• Benjamin Dietzek and
• Wolfgang Weigand

Beilstein J. Org. Chem. 2017, 13, 2264–2272, doi:10.3762/bjoc.13.223

• around −140 ppm, while 11B{1H} NMR signals appear as up to 3 ppm broad singlets at about +0.9 ppm. No coupling between 19F and 11B nuclei was observed because of the high quadrupole moment of the 11B nucleus. Due to the high relative mass difference between both naturally occurring boron isotopes

Recent highlights in biosynthesis research using stable isotopes

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2015, 11, 2493–2508, doi:10.3762/bjoc.11.271

• understanding of biosynthesis. As demonstrated in this article, the usage of isotopes is not at all old-fashioned, but continues to give important insights into biosynthetic pathways of secondary metabolites. This review with 85 cited references is structured by separate discussions of compounds from different

• a special emphasis on mechanistic surprises. Keywords: biosynthesis; enzyme mechanisms; isotopes; labeling experiments; natural products; Introduction This year may be seen as the 80th anniversary of using isotopes in biosynthetical and biochemical research. Since the first experiments performed

• by Schoenheimer and Rittenberg in 1935 using deuterated fatty acids and sterols to follow their fate in a living organism [1], a lot of new synthetic and analytical methods for the detection of isotopes have been developed that today allow for nearly unlimited applications in biosynthesis research

Easy access to heterobimetallic complexes for medical imaging applications via microwave-enhanced cycloaddition

• Nicolas Desbois,
• Sandrine Pacquelet,
• Adrien Dubois,
• Clément Michelin and
• Claude P. Gros

Beilstein J. Org. Chem. 2015, 11, 2202–2208, doi:10.3762/bjoc.11.239

• future use of radioactive isotopes possessing short life times (e.g. Cu2+ and In3+). Microwave irradiation, known to accelerate the polarization of the starting materials to promote the reactions, was investigated. A mixture of azidocorrole 8a, Gd propargyl DOTA 10a, CuI, DIPEA and DMF were irradiated in

Redox active dendronized polystyrenes equipped with peripheral triarylamines

• Toshiki Nokami,
• Naoki Musya,
• Tatsuya Morofuji,
• Keiji Takeda,
• Masahiro Takumi,
• Akihiro Shimizu and
• Jun-ichi Yoshida

Beilstein J. Org. Chem. 2014, 10, 3097–3103, doi:10.3762/bjoc.10.326

• derived from the initiator at the end of the polystyrene. The broader peaks seem to be attributable to two isotopes of the bromo groups (79 and 81 Da), and the small peak separation 101–103 Da is consistent with the molecular weight of styrene monomer (104 Da). The MS analysis indicated that 6 reacted