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

• interaction. Isotopic labeling experiments demonstrated that also in laboratory cultures roseobacter group bacteria efficiently degrade DMSP into sulfur volatiles [22][23], but also from other sulfur sources including 2,3-dihydroxypropane-1-sulfonic acid (DHPS, Scheme 1C) labeling was efficiently incorporated

• identical to (E)-42. Feeding experiments with isotopically labeled precursors The biosynthesis of sulfur volatiles in C. marinus was investigated in a series of feeding experiments with isotopically labeled precursors. Feeding of (methyl-2H3)methionine resulted in the efficient incorporation of labeling

• incorporation of labeling into two or three of the sulfur atoms in 41 (Figure 3D; also here the signal at m/z = 213 represents inseparable unlabeled 41). In this experiment, the base peak did not change which allowed the localization of labeling specifically in the MeS group of 41. The fact that no

CF₃-substituted carbocations: underexploited intermediates with great potential in modern synthetic chemistry

• Anthony J. Fernandes,
• Armen Panossian,
• Bastien Michelet,
• Agnès Martin-Mingot,
• Frédéric R. Leroux and
• Sébastien Thibaudeau

Beilstein J. Org. Chem. 2021, 17, 343–378, doi:10.3762/bjoc.17.32

• solvolysis reaction of 13f, a mixture of the major product 15f, resulting from solvent substitution, and the minor elimination product 16f was observed. Further, 14C labeling experiments on 13f confirmed that the formation of the ion pair 14fOTs was a reversible process [42]. Later, Liu et al. explored the

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

• spiropentane to form methylenecyclobutane occurred with the cleavage of the C1–C2 bond [94]. Dolbier then used deuterium labeling to study the analogous reaction of 1,1-difluorospiropentane (101) (Scheme 47) [95]. The cleavage of the C1–C2 bond that is proximal to the fluorine resulted in the formation of two

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• . Accordingly, the field has developed to a stage that allows custom-design of RNA probes and tools for specific application. For example, investigations of RNA structures by NMR, EPR, or fluorescence spectroscopy require labeling of the RNA molecules with specific reporter groups [2][4][7][8][9][10]. Likewise

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

• encryption keys that change with time, we combined our expertise in modifying bacteria with synthetic receptors [2] and in message encryption using pattern-generating probes [5]. In our recent work, E. coli-expressing His-OmpC were decorated with fluorescently labeled synthetic receptors [2]. The labeling of

• colors, the individual bacteria were only labeled with a single dye (Figure 2). We hypothesized that incubating the bacteria with a mixture of three artificial receptors, each of which is appended with a distinct dye, should lead to a mixed labeling of each bacterium and to the generation of unique

• emission was recorded 24 hours after bacterial labeling. To encrypt the message, the encryption key is added to the numeric message, which affords the cipher text (Figure 5C). At this point, the message is secured and can be safely sent to a recipient who possesses identical synthetic receptors and

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

• binding site. Here we discuss protein-based solution NMR techniques including classic 1H,15N-HSQC spectra, TROSY variants for large proteins, fast acquisition techniques and specific isotope labeling strategies, as well as the use of 13C-edited spectra and side chain specific spectra for lysine and

• protein. These methods require excess (5–20-fold) ligand together with relatively small protein concentrations (10–50 µM). Further advantages include no size limit for the protein, as well as no need for isotope labeling of the protein, assignment of protein resonances, and elaborate multidimensional NMR

• ligand-detected techniques. 1H,15N-HSQC and 1H,15N-TROSY-HSQC spectra 1H,15N-HSQC NMR spectra are a widely used tool to study the interaction of proteins with natural or synthetic ligands as well as other biomolecules [83]. This spectrum requires 15N-labeling of the protein of interest, which is easily

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

• the mechanochemical approach (the B & B, ball milling for boronic acid conjugation) as bioconjugation strategy for the labeling of biocompatible carbohydrates. Fluorescent labeling is of key importance to follow up the fate of molecules and (nano)materials inside cells and in the human body. In this

• roughly equimolar amount of Dex and 1, in a glucose units/1 molar ratio of 60:1 (assuming an average molecular weight for Dex of 10 kDa). For the labeling in solution, Dex was dissolved in dry dimethyl sulfoxide (DMSO) and PBA-BODIPY (1) was added in roughly equimolar amounts (Scheme 1, route A). The

• and the two ethanol washings were kept separated for further analysis (vide infra). In order to evaluate the outcome of the two approaches in terms of dextran labeling with BODIPY, firstly, the amount of the recovered PBA-BODIPY (1, i.e., nonreacted 1) in each ethanol washing solution was quantified

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• complexed with streptavidin 24 (Figure 6). The resulting complex 25 was then incubated with HGM cells. These are stable cell lines, expressing the self-labeling HaloTag protein and GFP in the outer mitochondrial membrane (Figure 6a) [55]. If the complex 25 indeed reaches the cytosol, the chloroalkane will

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• for peptides can be powerful tools for labeling or inhibition. Finding those binding motifs, especially in water which competes for intermolecular H-bonds, poses an enormous challenge. A dynamic combinatorial library can be a powerful method to overcome this issue. We previously reported artificial

Fluorinated phenylalanines: synthesis and pharmaceutical applications

• Laila F. Awad and
• Mohammed Salah Ayoup

Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91

• yields of 25–35% and with a radiochemical purity of more than 99%. The 18F-labeling of 4-borono-ᴅ,ʟ-phenylalanine (BPA) provided a potential tool for cancer treatment by boron neutron capture therapy [53] (Scheme 16). The syntheses of a variety of clinically relevant radiotracers including protected 4

Synthesis and properties of tetrathiafulvalenes bearing 6-aryl-1,4-dithiafulvenes

• Aya Yoshimura,
• Hitoshi Kimura,
• Kohei Kagawa,
• Mayuka Yoshioka,
• Toshiki Itou,
• Dhananjayan Vasu,
• Takashi Shirahata,
• Hideki Yorimitsu and
• Yohji Misaki

Beilstein J. Org. Chem. 2020, 16, 974–981, doi:10.3762/bjoc.16.86

• of the EBDT sites, b) the succeeding eight-electron oxidations of the non-equivalent EBDT sites, and c) the small ΔE value (0.16 V) of the EBDT sites. Target compounds. An optimized structure of 1a. a) Top view, b) side view, and c) labeling of the 1,3-dithiole rings. Molecular orbitals of 1a. Cyclic

Rhodium-catalyzed reductive carbonylation of aryl iodides to arylaldehydes with syngas

• Zhenghui Liu,
• Peng Wang,
• Zhenzhong Yan,
• Suqing Chen,
• Dongkun Yu,
• Xinhui Zhao and
• Tiancheng Mu

Beilstein J. Org. Chem. 2020, 16, 645–656, doi:10.3762/bjoc.16.61

• corresponding aldehydes 36–42 were isolated with yields of 65−73%. Isotope labeling experiments Isotope labeling experiments were conducted to study the mechanism of the reductive carbonylation of aryl iodide with CO and H2 under our optimized conditions, using 13CO and D2 instead of CO and H2, respectively, as

• both CO and H2 participated in the formation of the formyl group in the product (Scheme 4a–c). Reaction mechanism and role of each component Based on the results from the labeling experiments a reaction mechanism for the reductive carbonylation of aryl iodides was proposed, as shown in Scheme 5 [57

• . Reaction conditions: PhI (1 mmol), RhCl3·3H2O (2.5 mol %), PPh3 (10 mol %), Et3N (1.2 mmol), DMA (2 mL), CO (5 bar), H2 (5 bar), 90 °C, 12 h. Isolated yields of the products are given and the structures were determined by NMR. Detailed information is given in Supporting Information File 1. Isotope-labeling

KOt-Bu-promoted selective ring-opening N-alkylation of 2-oxazolines to access 2-aminoethyl acetates and N-substituted thiazolidinones

• Qiao Lin,
• Shiling Zhang and
• Bin Li

Beilstein J. Org. Chem. 2020, 16, 492–501, doi:10.3762/bjoc.16.44

• -dihydrothiazole (0.5 mmol), benzyl bromides (1.0 mmol), I2 (1.0 mmol) in DMC (2 mL), at 80 °C, under air for 16 h. aWith chloromethyl derivative. Transformation of 2-aminoethyl acetate derivative to 2-(dibenzylamino)ethanol. Control experiments and 18O-labeling experiment. Control experiments with radical

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• decade, numerous interdisciplinary studies have addressed the chemical mechanism of CotB2 catalysis utilizing different detection and analysis methods. Meguro and co-workers [41] established the chemical mechanism for the formation of cyclooctatin using isotope labeling experiments (Scheme 1). Recently

• isotope labeling experiments combined with QM calculations. Intermediate G forms via a 1,5-hydride shift from C6 to C10 to generate a homoallylic cation, and the formation of intermediate H occurs due to cyclization to yield a cyclopropyl ring. Intermediate I forms due to isomeric formation of a

• cyclopropylcarbinyl cation, as shown by isotope labeling [41]. QM calculations support this unusual 1,3-alkyl shift that interconverts H and I [38][39]. Finally, the cyclopropyl ring opens by virtue of a nucleophilic water attack, and cyclooctat-9-en-7-ol is formed. Although gas phase calculations shed light on the

Chemical tuning of photoswitchable azobenzenes: a photopharmacological case study using nicotinic transmission

• Lorenzo Sansalone,
• Jun Zhao,
• Matthew T. Richers and
• Graham C. R. Ellis-Davies

Beilstein J. Org. Chem. 2019, 15, 2812–2821, doi:10.3762/bjoc.15.274

• hydrolyzed succinimides could be useful. Our data (Figure 2 and Figure 3) suggested that t-4FABTA (1) could be used to replace MAHoCh in the labeling of genetically tagged nicotinic acetylcholine receptors on living cells. Thus, we co-transfected the nicotinic acetylcholine receptors α4 subunit with β2E61C

• and health of cells. Next we examined if 1 could serve as a photoswitchable antagonist of nicotinic acetylcholine receptors having α4β2E61C mutant as predicted from previous results [16]. After labeling HEK293 cells as described above, we recorded the currents evoked by puffing the agonist carbachol

• labeling, labeling solutions were checked by UPLC. The external solution was (in mM): 140 NaCl, 2.8 KCl, 2 CaCl2, 2 MgCl2, 10 HEPES, 12 glucose (pH 7.3 with NaOH). Compound 1 (0.05 mM) was dissolved in external solution and sonicated for 5 min. HEK293 cells with green fluorescence were chosen for recording

Fluorinated maleimide-substituted porphyrins and chlorins: synthesis and characterization

• Valentina A. Ol’shevskaya,
• Elena G. Kononova and
• Andrei V. Zaitsev

Beilstein J. Org. Chem. 2019, 15, 2704–2709, doi:10.3762/bjoc.15.263

• heterocycles have also been used as linkers and for labeling biomolecules in chemical biology [43]. Moreover, this synthetic approach provides high yields, selectivity, mild reaction conditions and simple purification methods. It was demonstrated that the CuAAC reaction of porphyrins 3a and 3b with N

Unexpected one-pot formation of the 1H-6a,8a-epiminotricyclopenta[a,c,e][8]annulene system from cyclopentanone, ammonia and dimethyl fumarate. Synthesis of highly strained polycyclic nitroxide and EPR study

• Sergey A. Dobrynin,
• Igor A. Kirilyuk,
• Yuri V. Gatilov,
• Andrey A. Kuzhelev,
• Olesya A. Krumkacheva,
• Matvey V. Fedin,
• Michael K. Bowman and
• Elena G. Bagryanskaya

Beilstein J. Org. Chem. 2019, 15, 2664–2670, doi:10.3762/bjoc.15.259

• effect on the reduction rates of nitroxides than does the introduction of linear alkyl substituents. However, spirocyclic nitroxides may have much longer spin relaxation times at 70–150 K which make them attractive agents for spin labeling [7][8][9]. Sterically hindered nitroxides can be used as spin

Acid-catalyzed rearrangements in arenes: interconversions in the quaterphenyl series

• Sarah L. Skraba-Joiner,
• Carter J. Holt and
• Richard P. Johnson

Beilstein J. Org. Chem. 2019, 15, 2655–2663, doi:10.3762/bjoc.15.258

• explain odd results from Friedel–Crafts reactions [19] and this type of process is sometime referred to as a Baddeley rearrangement. Many examples of alkyl group migration have been described [19]. Phenyl groups migrate easily and degenerate phenyl shifts in biphenyl were confirmed by isotopic labeling

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

• Ronja Driller,
• Daniel Garbe,
• Norbert Mehlmer,
• Monika Fuchs,
• Keren Raz,
• Dan Thomas Major,
• Thomas Brück and
• Bernhard Loll

Beilstein J. Org. Chem. 2019, 15, 2355–2368, doi:10.3762/bjoc.15.228

• date, CotB2 represents the best studied bacterial diterpene synthase. Its reaction mechanism has been addressed by isoptope labeling, targeted mutagenesis and theoretical computations in the gas phase, as well as full enzyme molecular dynamic simulations. By X-ray crystallography different snapshots of

• stereochemical reaction. The cyclization mechanism of CotB2 has been investigated extensively in recent years. By isotope labeling and NMR spectroscopic investigations [35], it has been shown that CotB2 catalyzes the complex regio- and stereospecific cyclization reaction with an unusual carbon–carbon bond

• labeling [34]. Another important step towards a deeper understanding of the cyclization mechanism was the availability of crystal structures (Table 1) revealing structural snapshots along the reaction trajectory commencing with the open, inactive conformation completing with the closed, active conformation

Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp.

• Amit Raj Sharma,
• Enjuro Harunari,
• Tao Zhou,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2327–2332, doi:10.3762/bjoc.15.225

• methyl groups in dinoflagellate compounds are positioned at the carbons derived from the carbonyl carbon of acetate (C1). Precursor labeling studies indicated that the origin of the methyl carbon is not SAM but one carbon fragment derived from the cleavage of another acetate unit (Figure 3C) [15]. The

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

• available for most of the analytes. For this reason, feeding experiments (in vivo labeling) were carried out using the stable isotope-labeled precursors [5,5-2H2]-1-deoxy-ᴅ-xylulose (d2-DOX) and [6,6,6-2H3]-(±)-mevalonolactone (d3-MVL) to clearly identify the volatiles. Based on the recorded mass spectra of

• -copaene, β-copaene, α-cubebene, β-cubebene and the bicyclic δ-cadinene were biosynthesized via (S)-(−)-germacrene D rather than via (R)-(+)-germacrene D as intermediate. Keywords: biosynthesis; deuterium labeling; germacrene; HS-SPME; terpenes; TOF–MS; Introduction The aroma profile of grape berries at

• advantages of multidimensional gas chromatography with those of in vivo labeling. In vivo labeling makes it possible to identify compounds for which authentic standards are not commercially available, which applies to the majority of compounds found in plant foods [18]. We performed feeding experiments on

Functional panchromatic BODIPY dyes with near-infrared absorption: design, synthesis, characterization and use in dye-sensitized solar cells

• Quentin Huaulmé,
• Cyril Aumaitre,
• Outi Vilhelmiina Kontkanen,
• David Beljonne,
• Alexandra Sutter,
• Gilles Ulrich,
• Renaud Demadrille and
• Nicolas Leclerc

Beilstein J. Org. Chem. 2019, 15, 1758–1768, doi:10.3762/bjoc.15.169

• high stability in various media. More importantly, they display a very versatile chemistry, allowing the fine tuning of all their physical and optical properties [14]. They hence have found applications in various fields, such as lasers dyes [15], (bio)-labeling [16][17], photodynamic therapy [18], or

Complexation of a guanidinium-modified calixarene with diverse dyes and investigation of the corresponding photophysical response

• Yu-Ying Wang,
• Yong Kong,
• Zhe Zheng,
• Wen-Chao Geng,
• Zi-Yi Zhao,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2019, 15, 1394–1406, doi:10.3762/bjoc.15.139

• most common high-performance fluorescent reagents routinely used in biological research for labeling and detection. It is characterized by high absorptivity, excellent brightness, a relatively good water solubility and possesses ACQ properties. In our previous work, we have reported the complexation

Self-assembly behaviors of perylene- and naphthalene-crown macrocycle conjugates in aqueous medium

• Xin Shen,
• Bo Li,
• Tiezheng Pan,
• Jianfeng Wu,
• Yangxin Wang,
• Jie Shang,
• Yan Ge,
• Lin Jin and
• Zhenhui Qi

Beilstein J. Org. Chem. 2019, 15, 1203–1209, doi:10.3762/bjoc.15.117

• widely used in the dye industry and have been applied as advanced materials in the fields of fluorescence labeling [58][59], organic semiconducting devices [60][61], and light harvesting [62][63][64][65]. PDI and NDI units have been extensively incorporated into functional supramolecular architectures

Diaminoterephthalate–α-lipoic acid conjugates with fluorinated residues

• Leon Buschbeck,
• Aleksandra Markovic,
• Gunther Wittstock and
• Jens Christoffers

Beilstein J. Org. Chem. 2019, 15, 981–991, doi:10.3762/bjoc.15.96

• similar chemical shifts in binding energies, fragments of larger organic compounds are not easily distinguished. Labeling molecular entities with elements possessing large excitation cross sections like fluorine, chlorine, or bromine [40] represents an approach that can greatly simplify the detection of

• suitability for molecular surface labeling. Conclusion Two bifunctional diaminoterephthalate (DAT) fluorescence dyes have been prepared. One functional unit is α-lipoic acid (ALA) for binding the dye to gold surfaces. The other carries a trifluoromethyl group for facile detection of the surface-bound material