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

Assessing the possibilities of designing a unified multistep continuous flow synthesis platform

• Mrityunjay K. Sharma,
• Roopashri B. Acharya,
• Chinmay A. Shukla and
• Amol A. Kulkarni

Beilstein J. Org. Chem. 2018, 14, 1917–1936, doi:10.3762/bjoc.14.166

• ]. Flow chemistry gains its benefits from excellent heat and mass transfer rates and rapid mixing which is not possible in the case of conventional synthesis modes [21]. In general, the continuous flow synthesis aims at conducting the reactions at intrinsic kinetics. This helps to have reactors having

• unified platform for multistep synthesis. Such a platform can be integrated with chromatography purification systems, in-line analytical instruments, a mold for tablet making and various commercial instruments. As suggested, a priory information should be known regarding kinetics of various processes

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

• Eric Detmar,
• Valentin Müller,
• Daniel Zell,
• Lutz Ackermann and
• Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

• hydrogen transposition) [42][43]. Inspired by this computational analysis, we experimentally probed the effect of differently substituted cyanation agents 2 on the kinetics of the cobalt(III)-catalyzed C–H cyanation (Scheme 3). Thus, we observed that electron-withdrawing groups significantly facilitated

Recent advances in phosphorescent platinum complexes for organic light-emitting diodes

• Cristina Cebrián and
• Matteo Mauro

Beilstein J. Org. Chem. 2018, 14, 1459–1481, doi:10.3762/bjoc.14.124

• this way, long-lived and low energy lying excited states with triplet (Tn states) character are accessible and can be efficiently populated. The subsequent deactivation from the lowest lying T1 state into the electronic ground state (S0) through radiative channels, T1 → S0, occurs with decay kinetics

Cobalt–metalloid alloys for electrochemical oxidation of 5-hydroxymethylfurfural as an alternative anode reaction in lieu of oxygen evolution during water splitting

• Jonas Weidner,
• Stefan Barwe,
• Kirill Sliozberg,
• Stefan Piontek,
• Justus Masa,
• Ulf-Peter Apfel and
• Wolfgang Schuhmann

Beilstein J. Org. Chem. 2018, 14, 1436–1445, doi:10.3762/bjoc.14.121

• most promising approaches. However, this reaction is energy intensive, especially due to sluggish kinetics and high overpotential of the oxygen evolution reaction (OER) leading to a low energy conversion efficiency [3]. Importantly, the oxygen that is produced as an inevitable byproduct possesses

• optimization of the electrocatalyst could enhance the kinetics of the HMF oxidation and minimize its decomposition even further. Experimental All chemicals were of analytical grade and used without further purification. All aqueous solutions were prepared using ultrapure Milli-Q water (SG Water). KOH was

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

• AFCs have several advantages over PEMFCs such as faster kinetics of the oxygen reduction reaction at the cathode, greater longevity and the possible adaption of less precious metals due to the alkaline electrolyte [6][7]. In direct alkaline alcohol FCs (DAAFCs) electricity is generated by oxidizing

[3 + 2]-Cycloaddition reaction of sydnones with alkynes

• Veronika Hladíková,
• Jiří Váňa and
• Jiří Hanusek

Beilstein J. Org. Chem. 2018, 14, 1317–1348, doi:10.3762/bjoc.14.113

• by Taran et al. [4]. In order to avoid duplication our review is therefore focused in more detail on thermal, photochemical as well as metal-catalyzed reactions of sydnones with alkynes and factors that influence the yield and ratio of both possible regioisomers and also the kinetics and mechanism of

• absence of light. Depending on the temperature, a new reaction pathway involving benzylic group migration, CO2 extrusion and final cycloaddition was proposed (Scheme 4). Kinetics and mechanism of thermal cycloaddition The kinetics and reaction mechanism of the thermal cycloaddition between 4-methyl-3

Acyl-group specificity of AHL synthases involved in quorum-sensing in Roseobacter group bacteria

• Lisa Ziesche,
• Jan Rinkel,
• Jeroen S. Dickschat and
• Stefan Schulz

Beilstein J. Org. Chem. 2018, 14, 1309–1316, doi:10.3762/bjoc.14.112

• different enzyme kinetics for the PCE substrates. In contrast, in the single-substrate incubation experiments (Table 3) an excess of SAM was used, and this may have led to the formation even of products that are disfavored in the competition experiments. Conclusion The results showed that the enzymes

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• maximum stabilization was found for (R,S)-4. For the other diastereomer, see Supporting Information File 1). As it can be seen in Table 2, the computations reproduced the stabilization of the tight conformations relative to their open forms, which is in agreement with the experimentally observed kinetics

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• binding affinity, selectivity, and especially kinetics, Wilson and co-workers conducted a thorough study by synthesizing eight heterocyclic HP polyamides having single and double β-substituted derivatives with their cognate and mutant sequences [79]; two of the representative conjugates 20 and 21 are

• shown in the Figure 6. In conclusion, the authors reported that β-substituted polyamides weakens the binding affinity of these conjugates with cognate DNA and drastically influence the binding kinetics such as association and dissociation rates in a position- and number-dependent manner. The authors, in

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• studies with small molecular phosphodiesters. Keywords: Cleavage; DNA; kinetics; mechanism; RNA; Introduction Nucleic acids are polymeric diesters of phosphoric acid that store and transfer biological information. In biological systems, the diester linkages bridging 3´-O of one nucleoside to the 5´-O of

• phosphorothioates and 3´-arylphosphates are 0.63 and 0.59, respectively [102]. The thio effect, kO/kS, is somewhat greater than in specific base catalysis, ranging from 1.2 to 3.6. Altogether, the effect of non-bridging thiosubstitution on the kinetics of RNA phosphodiesters remains very modest, which makes

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

• NMR (399 MHz, CDCl3) δ 9.44 (d, J = 7.7 Hz, 1H), 6.78 (dt, J = 15.6, 6.8 Hz, 1H), 6.05 (ddq, J = 15.5, 7.8, 1.3 Hz, 1H), 2.33–2.18 (m, 2H), 1.48 (h, J = 7.4 Hz, 2H), 0.90 (t, J = 7.4 Hz, 3H); 13C NMR (101 MHz, CDCl3) δ 194.3, 158.9, 133.3, 34.8, 21.3, 13.8. Michaelis–Menten kinetics of the PeAAOx

Investigating radical cation chain processes in the electrocatalytic Diels–Alder reaction

• Yasushi Imada,
• Yohei Okada and
• Kazuhiro Chiba

Beilstein J. Org. Chem. 2018, 14, 642–647, doi:10.3762/bjoc.14.51

• reaction kinetics. However, the observed induction period indicated that this was not the case and an intermediate(s) was involved in the rate determining step. This mechanism could be rationalized on the basis of a radical cation chain process since the concentrations of both starting trans-anethole (1

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

• "helper oligonucleotides" [28][29]. Kinetics measured without downstream-binding element were two- to seven-fold slower, depending on the sequence context [27]. Overall, the data mentioned above suggest that there is indeed a strong dependence of the templating base and sequence context on the rate of

• group. Either of these steps can be rate-limiting, and we have encountered two-step kinetics with a lag-phase in some reactions involving aminoterminal primers [27]. More often, though, and in all cases involving ribonucleosides at the 3'-terminus of the primer, kinetics characteristic of a single rate

• [28][29][34][40]. Hydrolysis follows pseudo-first order kinetics and is readily measured by 31P NMR spectroscopy [28][32][33][34]. Oxyazabenzotriazolides were indeed found to hydrolyze faster than methylimidazolides, and half-live times of hydrolysis at room temperature for the different nucleotides

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

• K) and high-pressure (even 350 atm). Even though the hydrogenation is performed using either homogeneous or heterogeneous catalysts to enhance chemical kinetics, a number of side reactions reduces the selectivity of the chemical reaction providing also complex and cost-ineffective work-up procedures

Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review

• Fabio Tonin and
• Isabel W. C. E. Arends

Beilstein J. Org. Chem. 2018, 14, 470–483, doi:10.3762/bjoc.14.33

• redox-neutral cascade seems most elegant, but in order to fully understand and push the equilibrium of the reaction, a full biochemical characterization and a deep knowledge of the kinetics and stability of the involved enzymes is required. Other ways to obtain 7-OH epimerization Other chemical routes

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

• thermolytic ONs with thermolabile groups displaying slower or faster removal kinetics than that of fma groups. In particular, the subsequent heat-sensitive groups for phosphate masking were designed with a phosphate or a thiophosphate branched to a propyl or a butyl chain connected to the internucleoside

• slower or faster thermolytic deprotection rates than those of the fma group at 37 °C (t1/2 = 72 h) [60]. Typically, the thermostable groups with deprotection kinetics slower than those of the fma group may be used for the protection of terminal phosphodiesters of the immunomodulatory DNA sequence

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• kinetics and high signal-to-background ratio regardless of the salt concentration. Moreover, it can be applied for the direct detection of dsDNA targets under non-denaturing conditions either directly for short dsDNA sequences [47] or with the assistance of a pair of PNA openers for longer dsDNA targets

• nucleotide polymorphisms (SNP), insertions and deletions [74][75][76]. They have also been used for the detection and quantification of ribosomal RNA in a wash-free FISH [77]. Side-by-side comparison showed that the PNA beacons gave faster hybridization kinetics, a higher signal-to-noise ratio and a much

• probes [108][109]. The slow kinetics of the strand displacement involving highly stable PNA–DNA hybrids can be a major limitation of all the PNA-based strand displacement probes. Strand exchange can be facilitated by heating or increasing the salt concentration, where Mg2+ is more effective than Na+ [107

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• demonstrates the potential of base–base FRET in short time-scale kinetics investigations [82]. Conclusion Base–base FRET has a great potential as a detailed structure and dynamics tool in biomolecular sciences. It serves as an interesting complement to FRET pairs based on external fluorophores enabling higher

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• ) characterization of single molecule binding would be studied at large excess (10 to 50-fold) of DNA/RNA over ligand; b) ligand aggregation within DNA/RNA would be studied at excess of ligand over DNA/RNA; c) kinetics of binding would be studied at different temperatures and instrument response times; d

• binding events shown in Figure 2 are usually detectable and can be subjected to detailed analysis). The incubation time prior to the collection of the spectrum depends on the kinetics of binding, determined previously by other methods (UV–vis or fluorimetric titration). After each addition, the buffer

A Brønsted base-promoted diastereoselective dimerization of azlactones

• Danielle L. J. Pinheiro,
• Gabriel M. F. Batista,
• Pedro P. de Castro,
• Leonã S. Flores,
• Gustavo F. S. Andrade and
• Giovanni W. Amarante

Beilstein J. Org. Chem. 2017, 13, 2663–2670, doi:10.3762/bjoc.13.264

• analogue of streptopyrrolidine was accomplished in 65% overall yield. Keywords: azlactones; dimerization; diasteoreselective synthesis; kinetics; streptopyrrolidine analogue; Findings Azlactones have been acknowledged as a common nucleophilic reagent to introduce a quaternary carbon stereocenter in the α

• into this kind of transformation, we carried out some kinetics experiments. Taking into account the dimerization kinetic studies suggested by Mazurkiewicz et al. and experiments by NMR spectroscopy, we report here kinetic studies revealing mechanistic features on the dimerization reaction catalyzed by

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

• regeneration of the CuIIBr2/TPMA complex. To investigate the kinetics of the electrochemical catalytic process, the dependence of the ratio (catalytic current)/(reduction peak current in the absence of QC-Br5) – for the peak at −0.3 V, on the square root of different QC-Br5 concentration was analyzed (Figures

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

• abundant in the unfolded protein states [91]. Hydrolytic stability in peptides Finally, we tested hydrolytic stability in esterified peptides 8b, 9b and 10b by observing hydrolysis of the ester using 19F NMR in buffered deuterium oxide (pH 7). We expected pseudo-first order kinetics as for the hydrolysis

• of esters 1–5 at pH 11. Nonetheless, for the peptide esters 8b, 9b and 10b, the experimental decay (Figure 7) of the ester concentration resembled pseudo-zero order kinetics, which was also observed for another amino acid ester hydrolysis not shown here. Both fittings to the zero (Equations 6 and 7

• decoupling) spectra at 298 K by integration. The kinetics was measured in 1H and/or 19F{1H} z-cross-relaxation experiments at either 310 K (for deuterium oxide samples) or 298 K (for benzene samples). The Jαβ-coupling values were obtained by visual inspection of the α-CH resonances in the 1H NMR spectra, and

The effect of milling frequency on a mechanochemical organic reaction monitored by in situ Raman spectroscopy

• Patrick A. Julien,
• Ivani Malvestiti and
• Tomislav Friščić

Beilstein J. Org. Chem. 2017, 13, 2160–2168, doi:10.3762/bjoc.13.216

• reactivity on small variations in milling frequency. In particular, in situ measurements revealed the establishment of two different regimes of reaction kinetics at different frequencies, providing tentative insight into processes of mechanical activation in organic mechanochemical synthesis. Keywords

• mechanochemical synthesis of a MOF from ZnO and imidazole in the presence of a small amount of N,N-dimethylformamide [41]. This study revealed reaction kinetics consistent with a 2nd order reaction rate law, rationalized through a “pseudo-fluid” reaction model in which the rate-determining factor is the frequency

• particular frequency are mutually consistent when milling at 30 Hz, 27.5 Hz, 22.5 Hz and 20 Hz. At 25 Hz, however, the behavior of the reaction for each of the triplicate measurements was highly erratic and generally irreproducible. Overall, there is a clear difference in the kinetics of product formation

Solid-state studies and antioxidant properties of the γ-cyclodextrin·fisetin inclusion compound

• Joana M. Pais,
• Maria João Barroca,
• Maria Paula M. Marques,
• Filipe A. Almeida Paz and
• Susana S. Braga

Beilstein J. Org. Chem. 2017, 13, 2138–2145, doi:10.3762/bjoc.13.212

• corresponding hydrazine (pale yellow in color), a reaction which can be monitored by UV–vis spectroscopy. As the kinetics of the reaction varies from sample to sample, the stabilization time for a complete reduction of the DPPH· free radical was determined. For all samples studied, the steady-state