New standards for collecting and fitting steady state kinetic data

• Kenneth A. Johnson

Beilstein J. Org. Chem. 2019, 15, 16–29, doi:10.3762/bjoc.15.2

• content of the data and the desired steady state parameters. One could fit the data using all five rate constants, then calculate the steady state kinetic parameters from Equation 2. It is well known that steady state kinetics cannot define intrinsic rate constants; a corollary of that statement is that

• measured directly compared to values calculated from the ratio of kcat and Km (see Table 1). Analysis of full progress curve kinetics provides the most accurate estimates. Given the experimental constraints of limited substrate concentrations and the same number of data points collected, it is better to

• equilibrium titration [14]. Other methods, such as rapid gel filtration and filter binding assays are limited by the rate of ligand dissociation relative to the time required to perform the separation. Alternatively, the kinetics of a pre-steady state burst of product formation can be used to estimate the

Degenerative xanthate transfer to olefins under visible-light photocatalysis

• Atsushi Kaga,
• Xiangyang Wu,
• Joel Yi Jie Lim,
• Hirohito Hayashi,
• Yunpeng Lu,
• Edwin K. L. Yeow and
• Shunsuke Chiba

Beilstein J. Org. Chem. 2018, 14, 3047–3058, doi:10.3762/bjoc.14.283

• degenerative transfer of xanthates to olefins is enabled by the iridium-based photocatalyst [Ir{dF(CF3)ppy}2(dtbbpy)](PF6) under blue LED light irradiation. Detailed mechanistic investigations through kinetics and photophysical studies revealed that the process operates under a radical chain mechanism, which

Organometallic vs organic photoredox catalysts for photocuring reactions in the visible region

• Aude-Héloise Bonardi,
• Frédéric Dumur,
• Guillaume Noirbent,
• Jacques Lalevée and
• Didier Gigmes

Beilstein J. Org. Chem. 2018, 14, 3025–3046, doi:10.3762/bjoc.14.282

• in a monomer blend. In the case of photopolymerization, a photoinitiating system (PIs) is required to convert light in initiating species. Many factors affect the photopolymerization kinetics. However, the PIs is the most important key factor and that’s why enhancing its properties have drawn many

The influence of the cationic carbenes on the initiation kinetics of ruthenium-based metathesis catalysts; a DFT study

• Magdalena Jawiczuk,
• Angelika Janaszkiewicz and
• Bartosz Trzaskowski

Beilstein J. Org. Chem. 2018, 14, 2872–2880, doi:10.3762/bjoc.14.266

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• thermodynamic profiles as measured via isothermal titration calorimetry (ITC) [55]. Despite its low molecular weight, 13 showed tight-binding kinetics and was able to reduce production of HHQ, as well as PQS. Furthermore, it was capable of attenuating biofilm production [54]. All the information gathered via

Pathoblockers or antivirulence drugs as a new option for the treatment of bacterial infections

• Matthew B. Calvert,
• Varsha R. Jumde and
• Alexander Titz

Beilstein J. Org. Chem. 2018, 14, 2607–2617, doi:10.3762/bjoc.14.239

• these compounds showed superior thermodynamics and kinetics of binding to LecB compared to mannose, resulting in a prolonged receptor residence time of several minutes [48]. In a complementary approach, glycomimetic C-glycoside 17 was obtained, aiming at improved metabolic stability and selectivity [49

Synthesis of aryl sulfides via radical–radical cross coupling of electron-rich arenes using visible light photoredox catalysis

• Amrita Das,
• Mitasree Maity,
• Simon Malcherek,
• Burkhard König and
• Julia Rehbein

Beilstein J. Org. Chem. 2018, 14, 2520–2528, doi:10.3762/bjoc.14.228

• the first 20 ns and has a life-time of around 4 µs. The presence of TMB led to a slower decay kinetics at wavelength where both fluorescence of that catalyst and the transient 1,3,5-TMB•+ occur, for instance at 447 nm kdecay,I/kdecay,A = 1.4. Based on the above experimental results, spectroscopic

Comparative cell biological study of in vitro antitumor and antimetastatic activity on melanoma cells of GnRH-III-containing conjugates modified with short-chain fatty acids

• Eszter Lajkó,
• Sarah Spring,
• Rózsa Hegedüs,
• Beáta Biri-Kovács,
• Sven Ingebrandt,
• Gábor Mező and
• László Kőhidai

Beilstein J. Org. Chem. 2018, 14, 2495–2509, doi:10.3762/bjoc.14.226

• effects of conjugates could be due to their different internalization kinetics, or different mechanism of their action (e.g., induction of apoptosis or inhibition of cell cycle) rather than in case of the long-term activities. This could mean that once the acylated conjugates are internalized into the

• cells (Table 4). Since the conjugates had no or minor apoptotic effect, the cell cycle kinetics of the cells treated with GnRH-III-based conjugates was also investigated to reveal the mechanism of growth inhibition of these conjugates. The distribution of the control and treated cells in the different

The enzymes of microbial nicotine metabolism

• Paul F. Fitzpatrick

Beilstein J. Org. Chem. 2018, 14, 2295–2307, doi:10.3762/bjoc.14.204

• molybdopterin enzymes such as xanthine dehydrogenase and Pno as a member of the trimethylamine dehydrogenase family of flavoproteins [72]. Consistent with this identification, purified Pno contains FMN and a 4Fe/4S center. Preliminary kinetics have been reported for both enzymes. 6-LHNO activity has been

A general and atom-efficient continuous-flow approach to prepare amines, amides and imines via reactive N-chloramines

• Katherine E. Jolley,
• Michael R. Chapman and
• A. John Blacker

Beilstein J. Org. Chem. 2018, 14, 2220–2228, doi:10.3762/bjoc.14.196

• provide a tres for optimal conversion. This was achieved according to reaction kinetics and hydrophobicity of the amine, which affects its partition between phases. Herein, we report improvements to this process and the use of N-alkyl-N-chloramine in subsequent continuous-flow reactions (Figure 1). These

Revisiting ring-degenerate rearrangements of 1-substituted-4-imino-1,2,3-triazoles

• James T. Fletcher,
• Matthew D. Hanson,
• Joseph A. Christensen and
• Eric M. Villa

Beilstein J. Org. Chem. 2018, 14, 2098–2105, doi:10.3762/bjoc.14.184

• colorimetric indicator byproduct encouraged its use in a reaction kinetics investigation, where both electronic and steric properties of the amine reactant were shown to influence rearrangement rates. Having demonstrated its utility in studying this reaction using a high-throughput assay, it is proposed that 1

Synthesis and supramolecular self-assembly of glutamic acid-based squaramides

• Juan V. Alegre-Requena,
• Marleen Häring,
• Isaac G. Sonsona,
• Alex Abramov,
• Eugenia Marqués-López,
• Raquel P. Herrera and
• David Díaz Díaz

Beilstein J. Org. Chem. 2018, 14, 2065–2073, doi:10.3762/bjoc.14.180

• concentrations and gel-to-sol transition temperatures were also determined for each case. In addition, the superior squaramide diester gelator was compared with an analogue triazole-based gelator in terms of critical gelation concentration, gelation kinetics and thermal phase transition. Keywords: glutamic acid

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