Rational design of boron-dipyrromethene (BODIPY) reporter dyes for cucurbit[7]uril

• Mohammad A. Alnajjar,
• Jürgen Bartelmeß,
• Robert Hein,
• Pichandi Ashokkumar,
• Mohamed Nilam,
• Werner M. Nau,
• Knut Rurack and
• Andreas Hennig

Beilstein J. Org. Chem. 2018, 14, 1961–1971, doi:10.3762/bjoc.14.171

• materials science, but its use in supramolecular chemistry is so far very rare [60][61][62][63][64]. It can be applied to investigate translational and rotational diffusion of supramolecules as well as exchange kinetics. To demonstrate the compatibility of the new BODIPY dyes with FCS, we have determined

• the diffusion coefficient of the 2•CB7 complex in comparison to the free 2 dye. FCS autocorrelation curves (Figure 6) were analysed to obtain the diffusion times tdiff of 2 and the 2•CB7 complex and then converted into diffusion coefficients D using the reported standard rhodamine 6G (D = 2.80 × 10−6

• in 10 mM citrate buffer in 30% (v/v) ACN in water, pH 3.1. FCS autocorrelation curves obtained with 10 nM 2 in the absence (red fitted line) and presence (blue fitted line) of 100 µM CB7 at pH 1.5 in 30% (v/v) ACN in water. The fitted diffusion times for the free dye and the complex were 54.1 and

Synthesis and characterization of π–extended “earring” subporphyrins

• Haiyan Guan,
• Mingbo Zhou,
• Bangshao Yin,
• Ling Xu and
• Jianxin Song

Beilstein J. Org. Chem. 2018, 14, 1956–1960, doi:10.3762/bjoc.14.170

• the metal does not change the antiaromatic pathways in 3. Fortunately we obtained single crystals of 3Pd from its CH2Cl2/CDCl3/MeOH solution via vapor diffusion. All of the bond lengths were carefully measured based on the diffraction results (Figure 4). We found that despite all peripheral C–C bond

Synthesis and photophysical studies of a multivalent photoreactive Ru^II-calix[4]arene complex bearing RGD-containing cyclopentapeptides

• Sofia Kajouj,
• Lionel Marcelis,
• Alice Mattiuzzi,
• Adrien Grassin,
• Damien Dufour,
• Pierre Van Antwerpen,
• Didier Boturyn,
• Eric Defrancq,
• Mathieu Surin,
• Julien De Winter,
• Pascal Gerbaux,
• Ivan Jabin and
• Cécile Moucheron

Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150

• excited state lifetime of conjugate 9 as function of the concentration of guanosine monophosphate (GMP, Figure 4). Stern–Volmer analyses indicate that a dynamic quenching is occurring, with a quenching rate close to the diffusion limit (kQ = 5.6 108 M−1s−1 in intensity and kQ = 5.3 108 M−1s−1 in lifetime

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• compounds D-N

  NH, 4, 5, 7–9 (2.5 or 5 mM in DMSO-d6 at 298 K on 500 MHz timescale) were acquired by means of the ledbpgp2s pulse sequence. The diffusion time (Δ) ranged from 150 to 220 ms and the gradient pulse length (δ) ranged from 1.7 to 1.9 ms. The size of the raw data set was 32 × 16 k. The gradient

Two new 2-alkylquinolones, inhibitory to the fish skin ulcer pathogen Tenacibaculum maritimum, produced by a rhizobacterium of the genus Burkholderia sp.

• Dandan Li,
• Naoya Oku,
• Atsumi Hasada,
• Masafumi Shimizu and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2018, 14, 1446–1451, doi:10.3762/bjoc.14.122

• evaluated by a paper-disc agar diffusion method described in our previous study [40]. Flexibacter maritimus medium (0.5% peptone and 0.05% yeast extract in sea water) solidified with 10% agar was used to test against T. maritimum. Structures of compounds 1–8. Key COSY (bold line) and HMBC (arrow

Spectroelectrochemical studies on the effect of cations in the alkaline glycerol oxidation reaction over carbon nanotube-supported Pd nanoparticles

• Dennis Hiltrop,
• Steffen Cychy,
• Karina Elumeeva,
• Wolfgang Schuhmann and
• Martin Muhler

Beilstein J. Org. Chem. 2018, 14, 1428–1435, doi:10.3762/bjoc.14.120

• substantial local pH drop and cannot be fully compensated by OH− diffusion from the bulk into the thin layer. This pH drop further complicates the identification of products, because the product selectivity may change as a function of pH as demonstrated by Wang et al. [13] on a Pd disk electrode for ethylene

Polysubstituted ferrocenes as tunable redox mediators

• Sven D. Waniek,
• Jan Klett,
• Christoph Förster and
• Katja Heinze

Beilstein J. Org. Chem. 2018, 14, 1004–1015, doi:10.3762/bjoc.14.86

• of 1.1 V and 1.4 V, respectively, probably due to a fast diffusion of 3 and 4 to the anode in the beam path (Figure 4, Figures S11–S14, Supporting Information File 1). In addition, precipitation of some poorly soluble [4][X] also occurs. During oxidation to the respective ferrocenium cations, the C=O

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• supported by the above mentioned guest–host interactions. Therefore, cholesterol is always found in the cavity of the β-CD dimer, its size and shape prohibiting its diffusion in the crystal. Molecular dynamics The crystallographically determined atomic coordinates of the CHL/β-CD complex (host/guest

Nanoreactors for green catalysis

• M. Teresa De Martino,
• Loai K. E. A. Abdelmohsen,
• Floris P. J. T. Rutjes and
• Jan C. M. van Hest

Beilstein J. Org. Chem. 2018, 14, 716–733, doi:10.3762/bjoc.14.61

• formation of temperature gradients when using high temperatures, which leads to an increase in reactant diffusion and a consequent hampering of mass transfer [53]. Furthermore, the catalytic sites in heterogeneous catalysis are often not as well-defined as in homogeneous catalysis. Therefore, homogeneous

• permeability of the cross-linked membrane allowed for substrate/product diffusion, but at basic pH the membrane collapsed and prevented any transport of small molecules. Two different activity tests were performed: 1) GOx and Myo were both entrapped inside the polymersome lumen; 2) GOx and Myo were

• the diffusion through the membrane was not possible. Moreover, the crosslinking enabled stabilization of the enzymes, which remained active also after 10 days. Polymersome nanoreactors have also been used to perform many types of non-enzymatic catalytic reactions, such as the proline-catalyzed

Biocatalytic synthesis of the Green Note trans-2-hexenal in a continuous-flow microreactor

• Morten M. C. H. van Schie,
• Tiago Pedroso de Almeida,
• Gabriele Laudadio,
• Florian Tieves,
• Elena Fernández-Fueyo,
• Timothy Noël,
• Isabel W. C. E. Arends and
• Frank Hollmann

Beilstein J. Org. Chem. 2018, 14, 697–703, doi:10.3762/bjoc.14.58

• an oxidation reaction dissolved O2 is consumed rapidly and diffusion of O2 into the reaction medium can easily become overall rate-limiting. The O2 diffusion rate into the reaction medium directly correlates with the interfacial area between aqueous medium and the gas phase. Large interfacial surface

An alternative to hydrogenation processes. Electrocatalytic hydrogenation of benzophenone

• Cristina Mozo Mulero,
• Alfonso Sáez,
• Jesús Iniesta and
• Vicente Montiel

Beilstein J. Org. Chem. 2018, 14, 537–546, doi:10.3762/bjoc.14.40

• analysis (TGA). Cathodes were prepared using Pd electrocatalytic loadings (LPd) of 0.2 and 0.02 mg cm−2. The anode consisted of hydrogen gas diffusion for the electrooxidation of hydrogen gas, and a 117 Nafion exchange membrane acted as a cationic polymer electrolyte membrane. Benzophenone solution was

• electrocatalytic hydrogenation of benzophenone has not been accomplished using a PEMER yet. This work aims at exploring the electrocatalytic hydrogenation of benzophenone over palladium nanoparticles supported on carbon black based electrode using a PEMER. A nanoparticulate platinum gas diffusion electrode is used

• , however, Pd accessible surface area per weight unit turns out to be enhanced for the lowest electrocatalytic loading, indicating a benzophenone accessibility to the Pd nanoparticulate electrocatalysts. Hydrogen gas evolution reaction in the cathode compartment can be reused to feed a gas diffusion

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• increases cell permeation [33]. The uptake was proportional to the number of SATE groups and probably proceeded through a passive diffusion mechanism [34]. Furthermore, it was shown that SATE-protected phosphates were selectively demasked in cell extracts [35][36][37]. SATE thionophosphotriester ONs were

• reactions, lowering the yield of active ON and inducing toxicity. Moreover, the diffusion of light resulting from long UV irradiation decreases temporal and spatial resolution for experiments in cells. Finally, because light has poor tissue diffusion, the photocaging approach may be restricted to in vitro

Synthesis and biological evaluation of RGD and isoDGR peptidomimetic-α-amanitin conjugates for tumor-targeting

• Lizeth Bodero,
• Paula López Rivas,
• Barbara Korsak,
• Torsten Hechler,
• Andreas Pahl,
• Christoph Müller,
• Daniela Arosio,
• Luca Pignataro,
• Cesare Gennari and
• Umberto Piarulli

Beilstein J. Org. Chem. 2018, 14, 407–415, doi:10.3762/bjoc.14.29

• , unfavorable pharmacokinetics (low tissue diffusion and low accumulation rate) and possible elicitation of immune response [6]. By conjugation to a specific cell-membrane-receptor ligand, the toxin can be delivered at the tumor site and internalized through receptor-mediated endocytosis. In 2013, Reshetnyak

CF₃SO₂X (X = Na, Cl) as reagents for trifluoromethylation, trifluoromethylsulfenyl-, -sulfinyl- and -sulfonylation. Part 1: Use of CF₃SO₂Na

• Hélène Guyon,
• Hélène Chachignon and
• Dominique Cahard

Beilstein J. Org. Chem. 2017, 13, 2764–2799, doi:10.3762/bjoc.13.272

• in good yields from a variety of di- and trisubstituted alkenes (Scheme 17). Labelling and IR experiments were conducted to investigate the reaction mechanism as well as kinetic studies that revealed the reaction rate dependence on O2 diffusion. A case of intramolecular oxytrifluoromethylation of

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• the presence of a very small population of objects having an average diameter of 450 ± 150 nm. However, their concentration was so low that the relevant diffusion signal was very poor in quality. Therefore, the result found must be considered only merely indicative. However, this apparent failure is

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• pyrenyl–thymine 2 was confirmed by single-crystal X-ray analysis. Crystal structure Crystals of 2 suitable for X-ray diffraction analysis were obtained by slow diffusion of pentane into a chloroform solution of 2. The oak ridge thermal-ellipsoid plot (ORTEP) with the atom labelling scheme is shown in

Synthesis of naturally-derived macromolecules through simplified electrochemically mediated ATRP

• Paweł Chmielarz,
• Tomasz Pacześniak,
• Katarzyna Rydel-Ciszek,
• Izabela Zaborniak,
• Paulina Biedka and
• Andrzej Sobkowiak

Beilstein J. Org. Chem. 2017, 13, 2466–2472, doi:10.3762/bjoc.13.243

• V) and reverse anodic peak (–0.2 V) increases linearly with correlation coefficients 0.999 and 0.996 for the corresponding regression lines (Figure S6, Supporting Information File 1). The high linearity indicates that the processes are controlled by the rate of diffusion of the electroactive

Herpetopanone, a diterpene from Herpetosiphon aurantiacus discovered by isotope labeling

• Xinli Pan,
• Nicole Domin,
• Sebastian Schieferdecker,
• Hirokazu Kage,
• Martin Roth and
• Markus Nett

Beilstein J. Org. Chem. 2017, 13, 2458–2465, doi:10.3762/bjoc.13.242

• an agar diffusion assay against a standard selection of Gram-positive and Gram-negative bacteria as well as some fungi. However, the compound was inactive at all tested concentrations. A literature search revealed that 1 is the first microbial terpene possessing an octahydro-1H-indene backbone

• 250 × 10 mm, 5 μm; Macherey-Nagel) using a gradient from 10% (v/v) MeOH in H2O (+ 0.1% trifluoroacetic acid) to 100% (v/v) MeOH over 30 min. The purity of the isolated herpetopanone determined by HPLC was >95% at all wavelengths (compared to sum of total peak areas). Agar diffusion assay The assay was

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

• the same effect, albeit to a lower extent. Predictably, the C-terminal charge has a decreasing effect as the length of the peptide increases. An independent refinement of these conclusions can be found in diffusion measurements conducted by 1H DOSY (diffusion ordered spectroscopy). We previously

• applied a simple set of equations for estimation of the diffusion coefficients of an oligomeric hydrophobic polyproline-II helix [71]. Here, we combined these equations in order to derive Equation 5, which describes diffusion as a function of molecular weight assuming pure deuterium oxide solution at 298

• K. This equation considers molecules to be rigid spheres, as it is based on the Stokes–Einstein relationship. The ‘coil’ state significantly contributes to the conformational flexibility, which results in a diffusion deceleration [88]. We used the simple criterion of the difference between the

Exploring mechanochemistry to turn organic bio-relevant molecules into metal-organic frameworks: a short review

• Vânia André,
• Sílvia Quaresma,
• João Luís Ferreira da Silva and
• M. Teresa Duarte

Beilstein J. Org. Chem. 2017, 13, 2416–2427, doi:10.3762/bjoc.13.239

• steps: i) the synthesis of the framework and ii) the encapsulation of the small molecule by soaking and diffusion methods under mild conditions [96]. However, there are some one-pot syntheses reported for the encapsulation of small molecules into ZIF-8. Liédana et al. disclosed the in situ encapsulation

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• lower content of copper compounds in the reaction mixture. This strongly indicates that during mechanochemical reactions with milling balls containing copper(0), the catalytic process is mostly happening on the surface of milling balls, and diffusion of copper ions to reaction mixture is minute. This

• transformation of reactants to products. Thus, we propose that the catalytic reaction for the method 2c is most likely occurring on the surface of brass milling balls, with minute diffusion of the copper ions to the reaction mixture. During the milling reactions, copper(0) and copper(I) catalysts do not oxidize

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

• (sharp singlet) could be assigned to BF4− as the most common hydrolysis byproduct by comparison with HBF4 in DMSO-d6. X-ray crystallography Compounds 2f, 2g and 2h were also characterized by X-ray diffraction methods. Crystals suitable for analysis were grown by slow diffusion of n-hexane into CH2Cl2

Main group mechanochemistry

• Agota A. Gečiauskaitė and
• Felipe García

Beilstein J. Org. Chem. 2017, 13, 2068–2077, doi:10.3762/bjoc.13.204

• obtained in small-scale via salt metathesis reactions due to poor starting material (SrI2 and K[Cp′]) solubility in ether solution. LAG provides a high yielding synthetic methodology circumventing the scalability issues associated with the inefficient diffusion of reactants in large-scale solution-based

Solid-state mechanochemical ω-functionalization of poly(ethylene glycol)

• Michael Y. Malca,
• Pierre-Olivier Ferko,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2017, 13, 1963–1968, doi:10.3762/bjoc.13.191

• leading to unwanted chain lengthening during the derivatization process. Under mechanochemical conditions, diffusion limitation may favor the reactivity of small molecule reagents over the intermolecular reaction between two polymers to afford the kinetically-favorable end-products, in contrast to solvent

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• diffusion within the particular EO sample and its interaction with the dialysis membrane as it passes through its pores. Similar profiles characterize the release of MO and MR from PAA and adamantyl substituted PAA (Figure 12(ii) and 12(iii), respectively,) and a similar interpretation applies. However, the

• membrane diffusion apparatus (Figure S37, Supporting Information File 1) in which a 3.5 kDa molecular weight cut-off dialysis membrane (Spectr/Por 3) of surface area 7.0 cm2 separated 5.0 cm3 of the dye containing solution (made up in Na2HPO4/KH2PO4 buffer at pH 7.0 and I = 0.10 mol dm−3 with MR, MO or EO