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

Homo- and hetero-difunctionalized β-cyclodextrins: Short direct synthesis in gram scale and analysis of regiochemistry

• Gábor Benkovics,
• Mihály Bálint,
• Éva Fenyvesi,
• Erzsébet Varga,
• Szabolcs Béni,
• Konstantina Yannakopoulou and
• Milo Malanga

Beilstein J. Org. Chem. 2019, 15, 710–720, doi:10.3762/bjoc.15.66

• favored. • The monotosylation of 6-monoazido-β-CD (both in pyridine and Cu(II)-mediated in aqueous solution) is a primary-side process that leads to the theoretical three couples of pseudoenantiomers. Schematic representation of β-CD with glucopyranose atom numbering and with alphabetic labeling of the

Cyclopropene derivatives of aminosugars for metabolic glycoengineering

• Jessica Hassenrück and
• Valentin Wittmann

Beilstein J. Org. Chem. 2019, 15, 584–601, doi:10.3762/bjoc.15.54

• reaction kinetics and their labeling intensities after metabolic incorporation. To determine the efficiencies by which the derivatives are metabolized to sialic acids, we synthesized and investigated the corresponding cyclopropane derivatives because cyclopropenes are not stable under the analysis

• acceptance results in the same cell-surface labeling intensity due to its superior reactivity in the DAinv reaction. Based on the high incorporation efficiency of the Cp derivative we synthesized and investigated two new Cp-modified glucosamine and galactosamine derivatives. Both compounds lead to comparable

• cyclopropene derivatives were not stable under these conditions, an observation that has also been made by Ye and co-workers [27]. Therefore, we decided to investigate the corresponding cyclopropane derivatives instead. We expected them to be stable under the DMB labeling conditions and during the preparation

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

• ] have been actively studied for their fluorescent properties. Among others, also azole containing compounds of type E [28] and F [29] have been described. Similarly, to purine derivatives also 7-deazapurines are used in DNA labeling [30]. On the other hand, modified purines have found also applications

• described N(9)-alkylated-2-amino-6-triazolylpurines and 7-deazapurines as cell labeling agents for biological chemistry applications. Conclusion A group of novel and structurally related N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines was obtained, using the corresponding 2,6-diazido

• biocompatible, cell-permeable, not cytotoxic and do not influence cell proliferation. Thus, one can predict that the developed purine and 7-deazapurine derivatives possessing the novel substitution pattern may find their application also in cell labeling in the future besides the potential use as materials in

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

• ]-manner was confirmed by a crossover experiment and oxygen-18 labeling experiments. That is, the reaction of a 1:1 mixture of equally-reactive substrates 1h and 1r under the standard reaction conditions afforded only the products 2h and 2r derived from the starting materials (Scheme 3a). Thus, we

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• , Christiana Albertina University of Kiel, Niemannsweg 11, D-24105 Kiel, Germany Department of Cell and Molecular Biology, Uppsala University, Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala, Sweden 10.3762/bjoc.14.163 Abstract Photoaffinity labeling is frequently employed for the investigation of

• X-ray crystallography, studies in solution add valuable information in molecular recognition studies as they take molecular dynamics as well as solvent effects into consideration. In the latter respect, photoaffinity labeling has evolved as a useful tool for studies under physiological conditions [1

• ][2][3][4]. Photoaffinity labeling requires a ligand equipped with a photolabile group, which can be converted into a highly reactive intermediate upon irradiation with light of an appropriate wavelength. This technique involves incubation of the photolabile ligand with the target protein (receptor

Strong binding and fluorescence sensing of bisphosphonates by guanidinium-modified calix[5]arene

• Jie Gao,
• Zhe Zheng,
• Lin Shi,
• Si-Qi Wu,
• Hongwei Sun and
• Dong-Sheng Guo

Beilstein J. Org. Chem. 2018, 14, 1840–1845, doi:10.3762/bjoc.14.157

• molecules [9]. However, this method will greatly reduce the life of the column [10]. Moreover, the absence of a chromophore in most BPs lead to the employment of derivatization by an UV–vis light-absorbing or fluorescence label for detection [11][12]. However, directly labeling BPs in biological media is

• difficult because many other components can reduce the efficiency of the labeling reaction. Especially in urine, it is extraordinary challenging to achieve labelling of BPs because urine generally contains a large amount of polar compounds such as phosphates, unless these are removed in advance [7]. Ion

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• L−1 after 2 h (Figure 2). Cell death assays Flow cytometry experiments were performed in an attempt to obtain insight into the mechanism of peptide-mediated death of cancer cells. For these proof-of-concept assays, we focused on WT peptide Dec-NH2. We utilized Annexin V labeling FITC (X axis) and

Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133

• measure long distances that are hardly accessible by NMR [9][10]. Furthermore, spin labeling of biopolymers can support NMR studies by paramagnetic relaxation enhancement [11][12]. For nucleic acids, spin labeling is most often achieved by covalent attachment of nitroxides. Unfortunately, the conditions

• distance. The results for all PELDOR measurements are shown in Figure S21 (Supporting Information File 1). The experimental distances are summarized in Table 1 and coincide well with values predicted from modelling. However, although the degree of spin labeling was very high in all cases, large variations

• of hemiacetals. After the annealing procedure, mean spin labeling efficiencies of 96% have been found. Samples of similar quality including TEMPO labeled cytidines are also accessible by postsynthetic modification of convertible nucleotides [8][25][26]. However, the analogous reaction forming TEMPO