A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

• Heidi-Kristin Walter,
• Bettina Olshausen,
• Ute Schepers and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2017, 13, 127–137, doi:10.3762/bjoc.13.16

Versatile synthesis of end-reactive polyrotaxanes applicable to fabrication of supramolecular biomaterials

• Atsushi Tamura,
• Asato Tonegawa,
• Yoshinori Arisaka and
• Nobuhiko Yui

Beilstein J. Org. Chem. 2016, 12, 2883–2892, doi:10.3762/bjoc.12.287

• -catalyzed click reactions are performed. Additionally, fluorescence labeling of the PRX and intracellular fluorescence imaging were performed as an example application. Results and Discussion Synthesis of azide-terminated PRXs using bis(2-amino-3-phenylpropyl) poly(ethylene glycol) and 4-substituted benzoic

Chemical probes for competitive profiling of the quorum sensing signal synthase PqsD of Pseudomonas aeruginosa

• Michaela Prothiwa,
• Dávid Szamosvári,
• Sandra Glasmacher and
• Thomas Böttcher

Beilstein J. Org. Chem. 2016, 12, 2784–2792, doi:10.3762/bjoc.12.277

• amide probes UA1–3 and the α,β-unsaturated ketone UK1 only resulted in very weak or no labeling, all three α-chloroacetamide probes CA1–3 gave a strong fluorescent signal in the gel (Figure 3A). In order to investigate the selectivity of the probes, we constructed a PqsD C112A mutant, where the active

• site cysteine was replaced by alanine. The purified mutant PqsD C112A exhibited only low background labeling for some probes but not comparable to labelling of the wild type protein by CA1–3, indicating that the probes were selectively targeting the active site (Figure 3A). Concentration series with a

• , variations in the probe structure had little impact on labeling intensity and specificity. Although each α-chloroacetamide probe had one closely related α,β-unsaturated acetamide counterpart, only the reactive group but not the structure of the probe or its side groups determined active-site labeling. These

Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts

• Lukas J. Patalag and
• Daniel B. Werz

Beilstein J. Org. Chem. 2016, 12, 2739–2747, doi:10.3762/bjoc.12.270

• , but spectroscopically different fluorescent probes we believe that these fatty acids might find interest as useful candidates to study the sensitive hydrophobic area of membranes in terms of domain formation or as labeling agents in general. Experimental General. All solvents for column chromatography

Synthesis, dynamic NMR characterization and XRD studies of novel N,N’-substituted piperazines for bioorthogonal labeling

• Constantin Mamat,
• Marc Pretze,
• Matthew Gott and
• Martin Köckerling

Beilstein J. Org. Chem. 2016, 12, 2478–2489, doi:10.3762/bjoc.12.242

• (1)°, V = 1325.74(4) Å3, Z = 4, Dobs = 1.304 g/cm3) were obtained from a saturated ethyl acetate solution. The rotational conformation of these compounds was also verified by XRD. As proof of concept for future labeling purposes, both nitropiperazines were reacted with [18F]F–. To test the

• applicability of these compounds as possible 18F-building blocks, two biomolecules were modified and chosen for conjugation either using the Huisgen-click reaction or the traceless Staudinger ligation. Keywords: building blocks; coalescence; dynamic NMR; labeling; Staudinger ligation; Introduction The

• development of new building blocks for specific and bioorthogonal labeling of biologically active compounds is of high importance. Depending on their size and composition, building blocks can influence (bio-)chemical parameters such as the lipophilicity (log P) affecting the solubility and the biological

Enantioconvergent catalysis

• Justin T. Mohr,
• Jared T. Moore and
• Brian M. Stoltz

Beilstein J. Org. Chem. 2016, 12, 2038–2045, doi:10.3762/bjoc.12.192

• . Deuterium labeling experiments have shown that the hydrogenation reaction occurs only on the chiral keto tautomer, and therefore the catalyst selects one enantiomer of the substrate when the reduction takes place. Enantioconvergent methods are not limited to carbon stereocenters. An exceptional example of

• ]. The observed product arises from hydrolysis of each enantiomer of epoxide at the S-configured carbon atom. Isotopic labeling studies with 18OH2 not only confirmed this mechanistic hypothesis, but also facilitated kinetic studies to determine relative rate constants for each of the four reaction

Synthesis and characterization of fluorinated azadipyrromethene complexes as acceptors for organic photovoltaics

• Forrest S. Etheridge,
• Roshan J. Fernando,
• Sandra Pejić,
• Matthias Zeller and
• Geneviève Sauvé

Beilstein J. Org. Chem. 2016, 12, 1925–1938, doi:10.3762/bjoc.12.182

• materials. Only Zn(L2)2 produced crystals suitable for analysis. Figure 9 shows the ORTEP drawing of Zn(L2)2 with 50% ellipsoids and a partial labeling scheme for clarity. The crystal structure confirms the identity of the complex and gives an idea of the interactions in the complex. Like Zn(ADP)2, the

• evaporator. The devices were characterized using a Oriel Sol2A solar simulator and a Keithley 2400 SourceMeter. The active area of each solar cell is 0.20 cm2. a) Azadipyrromethene ligand labeling positioning; b and c) chelates; d) estimated HOMO/LUMO energy levels [9]. Chemical structures of the fluorinated

• level and a partial labeling scheme. The hydrogen atoms, and dichloromethane solvate were omitted for clarity. ORTEP drawing of Zn(L2)2 with ellipsoids drawn at the 50% probability level and a partial labeling scheme. The hydrogen atoms, and dichloromethane solvate were omitted for clarity. a) Shows the

Potent triazine-based dehydrocondensing reagents substituted by an amido group

• Munetaka Kunishima,
• Daiki Kato,
• Nobu Kimura,
• Masanori Kitamura,
• Kohei Yamada and
• Kazuhito Hioki

Beilstein J. Org. Chem. 2016, 12, 1897–1903, doi:10.3762/bjoc.12.179

• ], a crown-ether-based cyclotransferase [8], membrane fusion of small unilamellar vesicles to form giant unilamellar vesicles [9], modular methods for the affinity labeling of targeting proteins [10][11][12], and reaction acceleration on micelle interfaces [13][14]. Thus, various types of molecular

Rearrangements of organic peroxides and related processes

• Ivan A. Yaremenko,
• Vera A. Vil’,
• Dmitry V. Demchuk and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2016, 12, 1647–1748, doi:10.3762/bjoc.12.162

Experimental and theoretical insights in the alkene–arene intramolecular π-stacking interaction

• Valeria Corne,
• Ariel M. Sarotti,
• Carmen Ramirez de Arellano,
• Rolando A. Spanevello and
• Alejandra G. Suárez

Beilstein J. Org. Chem. 2016, 12, 1616–1623, doi:10.3762/bjoc.12.158

• (in kcal/mol) computed for 6d and 6b (in grey). X-ray thermal ellipsoid plot of 6a (50% probability level) showing the labeling scheme (hydrogen and carbon labels have been omitted for clarity). Synthesis of acrylates 6a,b. Complexes between methyl acrylate (7) and representative anisole derivatives

Dinuclear thiazolylidene copper complex as highly active catalyst for azid–alkyne cycloadditions

• Anne L. Schöffler,
• Ata Makarem,
• Frank Rominger and
• Bernd F. Straub

Beilstein J. Org. Chem. 2016, 12, 1566–1572, doi:10.3762/bjoc.12.151

• of the mandatory role of dinuclear copper complexes as catalyst intermediates has vastly improved (Scheme 1) [33][34][35][36][37]. In 2013, the Fokin group provided evidence for the dicopper pathway of CuAAC reactions by a series of kinetic and isotopic labeling studies [34]. In 2015, the Bertrand

Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• –imidazole polyamides; sequence specificity: DNA; triplex-forming oligonucleotides; Introduction The recognition and detection of specific sequences in native genomic double-stranded DNA (dsDNA) is of significant importance for the development of efficient gene therapies and in vivo gene labeling [1][2][3

• . demonstrated the fluorescent labeling of proteins directly in living cells by copper-free "click chemistry" [29]. Alkyne or azide groups can be inserted into both TFO and MGB using enzymatic or chemical methods during matrix or solid-phase synthesis [2][30][31] or post-synthetically using described conjugation

• fluorescent probes via their labeling by commercial and "home-made" fluorescent dyes bearing azide groups. It was noted that yields of alkyne-modified MGBs were higher (50–83%) compared to those of azide modified MGBs (≈40%). The other variant for insertion of terminal azide or alkyne groups into the

Conjugate addition–enantioselective protonation reactions

• James P. Phelan and
• Jonathan A. Ellman

Beilstein J. Org. Chem. 2016, 12, 1203–1228, doi:10.3762/bjoc.12.116

• mechanism of their reaction through a combination of DFT calculations, deuterium labeling studies, and control experiments (Scheme 13) [34]. The authors proposed that after migratory insertion of the rhodium–aryl bond across the acrylate, 58 undergoes β-hydride elimination of the enamide proton to generate

• rhodium catalyst binding to the benzoxazole nitrogen 68. Deuterium labeling studies were performed on the system and based on their results a mechanism was proposed in which the stereodetermining step is a rhodium-hydride transfer instead of protonation of an oxo-π-allylrhodium species (Scheme 17

Synthesis of a deuterated probe for the confocal Raman microscopy imaging of squalenoyl nanomedicines

• Eric Buchy,
• Branko Vukosavljevic,
• Maike Windbergs,
• Dunja Sobot,
• Camille Dejean,
• Simona Mura,
• Patrick Couvreur and
• Didier Desmaële

Beilstein J. Org. Chem. 2016, 12, 1127–1135, doi:10.3762/bjoc.12.109

• fulfill this task, radioactive labeling or fluorescent probes have been thoroughly used. For example, the subcellular localization of the 3H-radiolabeled GemSQ conjugate has been evaluated by micro-autoradiography coupled to confocal imaging of fluorescently labeled cellular structures [21]. A dual

• radioactive labeling 3H,14C has been taken into profit to study the pharmacokinetics, the biodistribution and the metabolism of squalenoyl adenosine nanoparticles [22]. Nevertheless, the synthesis of labeled compounds is chemically challenging, expensive and submitted to drastic regulation rules. In addition

Strecker degradation of amino acids promoted by a camphor-derived sulfonamide

• M. Fernanda N. N. Carvalho,
• M. João Ferreira,
• Ana S. O. Knittel,
• Maria da Conceição Oliveira,
• João Costa Pessoa,
• Rudolf Herrmann and
• Gabriele Wagner

Beilstein J. Org. Chem. 2016, 12, 732–744, doi:10.3762/bjoc.12.73

• spectrum of 2 (see Supporting Information File 1, Figure S1), shows that the reaction occurs at position 3 of the camphor skeleton (Scheme 1, for labeling). In addition, the observation of partially overlapping IR bands (νCN, 1676, 1641 cm−1) indicate distinct imine groups in agreement with the signals

• Molden [42]. Camphor and some camphor derivatives. ESI mass spectrum of 2 (positive ion mode). 1H NMR spectrum of 2 in CD3CN at T = −20 °C. 13C NMR spectrum of 2 in CD3CN at T = −20 °C. Optimized structure of 2 ((S)-3A isomer) with labeling scheme. NOESY spectrum (detail) showing the cross peak between

Biosynthesis of α-pyrones

• Till F. Schäberle

Beilstein J. Org. Chem. 2016, 12, 571–588, doi:10.3762/bjoc.12.56

• antibiotically active compounds 36 [83] and 34 [84]. The resulting labeling pattern clearly showed that the central α-pyrone ring of the molecule was not the result of a usual intramolecular reaction. Rather, an interconnection of two independent chains should form the central ring structure. In addition further

New synthetic strategies for xanthene-dye-appended cyclodextrins

• Milo Malanga,
• Andras Darcsi,
• Mihaly Balint,
• Gabor Benkovics,
• Tamas Sohajda and
• Szabolcs Beni

Beilstein J. Org. Chem. 2016, 12, 537–548, doi:10.3762/bjoc.12.53

• fluorophores for labeling in order to assess if these versatile molecules cross biological barriers (e.g., cell membrane, blood–brain barrier) and to follow their distribution in living matter [3]. Among the fluorescent dyes, the group of fluorophores based on xanthene scaffolds is one of the most popular. Two

• of this evergreen class of dyes is still an ongoing process [5][6]. Fluorescein is the most widely used fluorescent probe in biological applications and in particular for covalently labeling proteins. Rhodamine derivatives are robust dyes that find application as fluorophores for microscopy, in cell

• derivatives. This method can not only be applied to CDs, but may represent a new general approach for the modification of xanthene dye in water, thus affording amide or ester derivatives. When a fluorophore is used for the labeling of a single-isomer CD, the resulting molecule is rarely the fully substituted

Cupreines and cupreidines: an established class of bifunctional cinchona organocatalysts

• Laura A. Bryant,
• Rossana Fanelli and
• Alexander J. A. Cobb

Beilstein J. Org. Chem. 2016, 12, 429–443, doi:10.3762/bjoc.12.46

• organocatalyst with comparable results. More recently, Johnson and co-worker used the o-toluoyl derived organocatalyst CPD-33 to effect a dynamic kinetic asymmetric transformation of racemic β-bromo-α-keto esters 32 (Scheme 9a) [35]. The mechanism, deduced from deuterium labeling studies, proposes that one of

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• to geometrical changes of a bridged ion resulting from the isotopic substitution. They concluded that it cannot be assumed that a large Δ resulting from isotopic labeling guarantees rapid equilibration between two unlabeled structures. While the cases described below are focused on reaction pathways

• rearranged product. In addition, the dynamics calculations indicated that the 1,2-methyl (C17) shift that forms the abietadiene precursor should occur specifically to one face of the carbocation carbon (C15), a prediction that could be tested through substrate labeling. If only trajectories that lead to the

Diastereoselective synthesis of new O-alkylated and C-branched inositols and their corresponding fluoro analogues

• Charlotte Collet,
• Françoise Chrétien,
• Yves Chapleur and
• Sandrine Lamandé-Langle

Beilstein J. Org. Chem. 2016, 12, 353–361, doi:10.3762/bjoc.12.39

• of this hydroxy group is mandatory for labeling with [18F]-fluoride with regard to a PET application. Therefore the acetylation of myo-26 and scyllo-26 using the transacetylization protocol [52] gave the fully acetylated products myo-27 and scyllo-27 in 56% and 52% isolated yields, respectively. The

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

• Jan Rinkel Jeroen S. Dickschat Kekulé-Institute of Organic Chemistry and Biochemistry, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany 10.3762/bjoc.11.271 Abstract The long and successful history of isotopic labeling experiments within natural products research has both changed and deepened our

• 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

• . The basic principle of labeling an organic molecule in a way that is incognito for metabolism, but easy to follow for the researcher still remains the same. The first application of this idea probably was the investigation on fatty acid degradation by Knoop in 1904, even long before isotopes were

Copper-catalyzed stereoselective conjugate addition of alkylboranes to alkynoates

• Takamichi Wakamatsu,
• Kazunori Nagao,
• Hirohisa Ohmiya and
• Masaya Sawamura

Beilstein J. Org. Chem. 2015, 11, 2444–2450, doi:10.3762/bjoc.11.265

• selectivity. Possible mechanism. Isomerization of the alkenylcopper intermediates. Conjugate addition of alkylborane 2a to alkynoate 3a. Synthesis of five membered carbocycle. Deuterium-labeling experiment. Ligand effects. Copper-catalyzed conjugate addition of alkylboranes 2 to alkynoates 3.a Supporting

Preparation of Pickering emulsions through interfacial adsorption by soft cyclodextrin nanogels

• Shintaro Kawano,
• Toshiyuki Kida,
• Mitsuru Akashi,
• Hirofumi Sato,
• Motohiro Shizuma and
• Daisuke Ono

Beilstein J. Org. Chem. 2015, 11, 2355–2364, doi:10.3762/bjoc.11.257

• hydrophilic DM-β-CD and lipophilic benzene parts, may be affected by their hydrophilic and lipophilic balance of the nanogels. Identification of the CD nanogel assembly at the interface Adsorption of a CD nanogel at the oil–water interface in the emulsion phase was identified using a fluorescent dye-labeling

• particle morphology. Dilute solutions were prepared and deposited onto a copper grid covered by a carbon membrane at ambient temperature. The electronic contrast of the specimen was enhanced by labeling with ammonium molybdate. Surface tension The surface tension of the aqueous solution was measured using

Conformational equilibrium in supramolecular chemistry: Dibutyltriuret case

• Karina Mroczyńska,
• Małgorzata Kaczorowska,
• Erkki Kolehmainen,
• Ireneusz Grubecki,
• Marek Pietrzak and
• Borys Ośmiałowski

Beilstein J. Org. Chem. 2015, 11, 2105–2116, doi:10.3762/bjoc.11.227

• File 1, Figure S2). In Table 2 the correlation coefficients, linearity range (l.r. in °), slope (a) and intercept (b) of the fitted linear functions are collected. Figure 7 shows the signal labeling. The signals were assigned as follows: a) 1d by integration (the most populated form – see computational

Consequences of the electronic tuning of latent ruthenium-based olefin metathesis catalysts on their reactivity

• Karolina Żukowska,
• Eva Pump,
• Aleksandra E. Pazio,
• Krzysztof Woźniak,
• Luigi Cavallo and
• Christian Slugovc

Beilstein J. Org. Chem. 2015, 11, 1458–1468, doi:10.3762/bjoc.11.158

• , 775, 732, 699, 680, 644, 591, 578, 535, 419 cm−1; HRMS (ESI) (m/z): [M − 2Cl + H]+ calcd, 578.1745; found, 578.1732. Selected ruthenium-based complexes. ADPs (atomic displacement parameters) and atoms labeling of the first molecule in the asymmetric part for 14 (left) and 15 (right). Thermal