Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• , and its dynamic nature was comprehensively clarified by thermodynamic analysis. This motivated us to integrate this motif into the polymer system. Further details of the thermodynamic analyses with the actual kinetic parameters are discussed in the original articles [46][47]. To integrate this motif

Homogeneous continuous flow nitration of O-methylisouronium sulfate and its optimization by kinetic modeling

• Jiapeng Guo,
• Weike Su and
• An Su

Beilstein J. Org. Chem. 2024, 20, 2408–2420, doi:10.3762/bjoc.20.205

• systems, and has a promising application. In this work, we constructed a continuous flow microreactor system to determine the kinetic parameters of IO nitration, which allows precise control of temperature and residence time (Figure 1). Due to the high viscosity of the reaction system, a simple and

• and temperatures can be determined. Determination of intrinsic kinetic parameters With and Mc at different conditions determined in Figure 5, was plotted against Mc at different temperatures (Figure 6a–c), and fitting these data into Equation 10 leads to (R2 > 0.99). The values of k0 and n at

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• for inositol dehydrogenases. (b) Comparison of the hygromycin A (red) and hygromycin A-like (orange) biosynthetic gene clusters. A more detailed comparison can be found in Supporting Information File 1, Table S2. Kinetic parameters for Hyg17. Supporting Information Supporting Information File 36

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• in the visible region were evident in their CD spectra. Using the Arrhenius and Eyring formalisms, the kinetic parameters for the thermal racemization of 57 and 58 were obtained. The activation free enthalpy (ΔG‡) for the racemization of 57 (ΔG‡298 K = 24.8 kcal mol−1) was ≈1.5 kcal mol−1 larger than

• column. In 62, unlike 59 and 60, thermally induced racemization was observed and kinetic parameters were obtained (ΔG‡298 K = 25.4 kcal mol−1), which were similar to those reported for 57 and 58 [133]. Photoluminescence properties Most anilino-substituted TCBD molecules exhibit negligible fluorescence in

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• . albus." Kinetic analysis of AvaA7 To measure the kinetic parameters of NADPH or NADH, the reaction mixture (90 µL) containing 10 µM CmaA6, 1.0 mM 3-AAA (7), 2 mM ATP, 5 mM NaNO2, 2.5 mM MgCl2, 20 mM HEPES-NaOH (pH 8.0), 10% glycerol, and 200 mM NaCl was prepared and incubated at 30 °C for 1 h. Then, 5.0

• decrease in absorbance at 435 nm for 3-DAA using a SpectraMax M2 microplate reader (Molecular Devices, San Jose, CA, USA). The kinetic parameters (Vmax, kcat, and Km) were calculated by fitting the substrate concentration [S]–initial velocity (v) plot using the equation v = Vmax × [S] / (Km + [S]). To

• measure the kinetic parameters of 3-DAA, the reaction mixture (90 µL) containing 10 µM CmaA6, 1.0 mM 3-AAA (7), 2 mM ATP, 5 mM NaNO2, 2.5 mM MgCl2, 20 mM HEPES-NaOH (pH 8.0), 10% glycerol, and 200 mM NaCl was prepared and incubated at 30 °C for 1 h. Then, the concentration of 3-DAA (8) in the reaction

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• constants and certain enzyme kinetics parameters via the Haldane relationships. These relationships are discussed in references [10][36] and, in fact, values of K′ have been obtained for a fair number of enzyme-catalyzed reactions by measuring rates of reaction and obtaining the enzyme kinetic parameters

Insight into oral amphiphilic cyclodextrin nanoparticles for colorectal cancer: comprehensive mathematical model of drug release kinetic studies and antitumoral efficacy in 3D spheroid colon tumors

• Sedat Ünal,
• Gamze Varan,
• Juan M. Benito,
• Yeşim Aktaş and
• Erem Bilensoy

Beilstein J. Org. Chem. 2023, 19, 139–157, doi:10.3762/bjoc.19.14

• profiles. Formulation parameters affected the release kinetics of the drug-loaded nanoparticles [31][32]. According to the release kinetic parameters in SGF medium, as seen in Table 1, the highest R2, MSC and lowest AIC values were observed in the Weibull model for 6-O-capro-β-CD and CS-(6-O-capro-β-CD

• first release seen in the SGF medium is dominantly diffusion-related. According to the release kinetic parameters in SIF medium, as seen in Table 1, the highest R2, MSC and lowest AIC values were observed in the Korsmeyer–Peppas model for 6-O-capro-β-CD and poly-β-CD-C6 NPs, and in Korsmeyer–Peppas and

• as a result of the relaxation of the nanoparticle polymer structure [46]. According to the release kinetic parameters in the targeted main release medium, SCof, the highest R2, MSC, and lowest AIC values were observed in the Weibull model for 6-O-capro-β-CD and CS-(6-O-capro-β-CD) formulations, and

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• substrate bonds (Figure 2e) [17]. Apart from the structures, the kinetic preference of either polyP synthesis (NTP usage) or NTP synthesis (polyP degradation) has been described to be a characteristic feature of PPK1 and PPK2(-I), respectively (Figure 2a). This is supported by analysis of the kinetic

• parameters KM and vmax of selected enzymes (Table S6, Supporting Information File 1) [5][10][11][15][19][20][21]. A sequence-based classification of PPKs is in most cases straightforward and unambiguous. Nevertheless, there seem to be exceptions: regarding the amino acid sequence, the PPK1 from Vibrio

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• on the mechanistic details of the HP and IE pathways using computational methods in the gas phase. Gas-phase studies have been crucial in understanding terpene chemistry [10][11][12][13][14][15][16][17][18][19][20][21][22]. This work sheds light on the thermodynamic and kinetic parameters of the

Shift of the reaction equilibrium at high pressure in the continuous synthesis of neuraminic acid

• Jannis A. Reich,
• Miriam Aßmann,
• Kristin Hölting,
• Paul Bubenheim,
• Jürgen Kuballa and
• Andreas Liese

Beilstein J. Org. Chem. 2022, 18, 567–579, doi:10.3762/bjoc.18.59

• can be modelled as a Michaelis–Menten rate expression. The Michaelis–Menten equation was used to fit the reaction rates at different substrate concentrations for different pressures in Figure 8. The resulting kinetic parameters are listed with 95% confidence intervals in Table 3. The influence of

• were kept constant and only the pressure was varied, resulting in the reactions rates shown in Figure 10 (left). By rearranging the rate expression and inserting the previously calculated kinetic parameters, the inhibition constant was calculated (Figure 10 (right)). The change in molar volume

• , and as the mean residence time. The RDT was measured by placing the reactor into an HPLC, replacing the regular separation column. Hereby, the mean residence time of the reactor was calculated to be 66% of the quotient of reactor volume and flow rate. When kinetic parameters were calculated by

Kinetics of enzyme-catalysed desymmetrisation of prochiral substrates: product enantiomeric excess is not always constant

• Peter J. Halling

Beilstein J. Org. Chem. 2021, 17, 873–884, doi:10.3762/bjoc.17.73

• -pong second (ketone amination, diol esterification, desymmetrisation in the second half reaction); ping-pong first (diol ester hydrolysis) and ping-pong both (prochiral diacids). For plausible values of enzyme kinetic parameters, the product enantiomeric excess (ee) can decline substantially as the

• study if and how the product ee declines at high conversion. Keywords: enantiomeric excess; enzyme; kinetic mechanisms; kinetic parameters; prochiral; Introduction There is great interest in using enzymatic catalysis in the synthesis of homochiral molecules. An early approach was to use

• the ultimate equilibrium value of 0, although the timescale for this depends on details of the enzyme kinetics. To understand the range of possible behaviour, progress curves for the conversion and the ee were calculated for a wide variety of possible enzyme kinetic parameters. The calculation used

Diels–Alder reaction of β-fluoro-β-nitrostyrenes with cyclic dienes

• Savva A. Ponomarev,
• Roman V. Larkovich,
• Alexander S. Aldoshin,
• Andrey A. Tabolin,
• Sema L. Ioffe,
• Jonathan Groß,
• Till Opatz and
• Valentine G. Nenajdenko

Beilstein J. Org. Chem. 2021, 17, 283–292, doi:10.3762/bjoc.17.27

• study of reactions of 1h with CPD and CHD. The Diels–Alder reaction of the nitrostyrene 1h with 1-methoxy-1,3-cyclohexadiene. Selected chemical transformations of norbornenes 2 (dr = exo:endo). Kinetic parameters for the reactions of 1h with CPD and CHD. Supporting Information Supporting Information

Mechanochemical amorphization of chitin: impact of apparatus material on performance and contamination

• Thomas Di Nardo and
• Audrey Moores

Beilstein J. Org. Chem. 2019, 15, 1217–1225, doi:10.3762/bjoc.15.119

• , with the specific reaction kinetic parameters [33]. There is, however, an interest in investigating these aspects further. In particular, it would be interesting to track the role of parameters such as ball size and mass on the progress of the reaction. In mechanochemistry, it is accepted that chemical

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

• important parameter as it is used to quantify enzyme specificity, efficiency and proficiency [4][5]. In fact, kcat and kcat/Km should be considered as the two primary steady state kinetic parameters, rather than kcat and Km. A half century ago Cleland stressed that the two fundamental steady state kinetic

• defines 1/kcat and the slope defines 1/kcat/Km. In Cleland’s analysis, the two primary steady state kinetic parameters were kcat and kcat/Km because they were the parameters derived in fitting data displayed on a double reciprocal plot. Today, the emphasis is on interpreting the steady state kinetic

• kcat and kcat/Km, so we consider that the Michaelis constant is a derivative of the two primary steady state kinetic parameters. Although this statement appears as trivial algebra, it is profound because kcat and kcat/Km can reflect different steps in the enzyme pathway as will be described below

Thermophilic phosphoribosyltransferases Thermus thermophilus HB27 in nucleotide synthesis

• Ilja V. Fateev,
• Ekaterina V. Sinitsina,
• Aiguzel U. Bikanasova,
• Maria A. Kostromina,
• Elena S. Tuzova,
• Larisa V. Esipova,
• Tatiana I. Muravyova,
• Alexei L. Kayushin,
• Irina D. Konstantinova and
• Roman S. Esipov

Beilstein J. Org. Chem. 2018, 14, 3098–3105, doi:10.3762/bjoc.14.289

• phosphoribosyltransferase Thermus thermophilus (TthHPRT), investigated its substrate specificity and optimal conditions for catalytic activity, and determined the kinetic parameters of the enzyme. A comparative study of the substrate specificity of TthAPRT and TthHPRT was performed to determine the usability of

• . After optimization of the reaction conditions, kinetic parameters for TthHPRT were determined (Table 2). Based on the Km values, the affinity of 5-phosphoribosyl-α-1-pyrophosphate for the active site is much lower than that of heterocyclic bases. The similar situation we observed for TthAPRT [1

• ). Reaction mixtures were incubated at 70 °C. Substrate and product quantities were determined using HPLC (Waters 1525, column Ascentis Express C18, 2.7 μm, 3.0 × 75 mm, eluent A 0.1% aqeous TFA, eluent B 0.1% TFA / 70% acetonitrile in water, detection at 254 nm, Waters 2489). Kinetic parameters determination

The enzymes of microbial nicotine metabolism

• Paul F. Fitzpatrick

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

• are both reported to have the ability to catalyze this reaction [48]. NicA1 was also reported to catalyze the subsequent oxidation of pseudooxynicotine to 3-succinylpyridine and methylamine, but no kinetic parameters for the two reactions were reported [51]. However, deletion of nicA2 but not of nicA1

One hundred years of benzotropone chemistry

• Arif Dastan,
• Haydar Kilic and
• Nurullah Saracoglu

Beilstein J. Org. Chem. 2018, 14, 1120–1180, doi:10.3762/bjoc.14.98

• the thermal and electron impact-induced decarbonylation reaction of 12 (Scheme 36) [131]. Tajiri’s group reported the resolution and determination of the kinetic parameters of the optically active 2,3-benzotropone(tricarbonyl)iron complex 221 using high-performance liquid chromatography (HPLC) and

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

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

• AcGlyGlyProGlyGlyNH2 [71] and AcGlyProOMe [68] compounds when measured in deuterium oxide. For 1–5, we found the trans/cis ratios ≈ 5 for all five esters when measured in aqueous medium; the kinetic parameters of the amide rotation were also nearly identical (Table 2). We then noticed that the trans/cis ratios

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• chemical approach, in contrast to synthetic biology, might involve the construction of a network of individual reactions that are well-characterized where the key kinetic parameters can all be experimentally verified. We recently showed that a chemical reaction network can be designed using enzymatic

Synthesis and enzymatic ketonization of the 5-(halo)-2-hydroxymuconates and 5-(halo)-2-hydroxy-2,4-pentadienoates

• Tyler M. M. Stack,
• William H. Johnson Jr. and
• Christian P. Whitman

Beilstein J. Org. Chem. 2017, 13, 1022–1031, doi:10.3762/bjoc.13.101

• formation of the α,β-isomer for the 5-fluoro derivative. Kinetic parameters were also obtained for both sets of compounds in the presence of 4-oxalocrotonate tautomerase (4-OT) from Pseudomonas putida mt-2 and Leptothrix cholodnii SP-6. For 5-halo-2-hydroxymuconates, there are no major differences in the

• kinetic parameters for the two enzymes (following the formation of the β,γ-unsaturated ketones). In contrast, the L. cholodnii SP-6 4-OT is ≈10-fold less efficient than the P. putida mt-2 4-OT in the formation of the β,γ-unsaturated ketones and the α,β-isomers from the 5-halo-2-hydroxy-2,4-pentadienoates

• faster conversion of the dienols to the β,γ-unsaturated ketones [14]. Hence, we only examined the ketonization of the dienols to the β,γ-unsaturated ketones (following the loss of the λmax associated with the dienol). The steady-state kinetic parameters for the 4-OT-catalyzed ketonization of 3b–d (to 10b

Automating multistep flow synthesis: approach and challenges in integrating chemistry, machines and logic

• Chinmay A. Shukla and
• Amol A. Kulkarni

Beilstein J. Org. Chem. 2017, 13, 960–987, doi:10.3762/bjoc.13.97

NMR reaction monitoring in flow synthesis

• M. Victoria Gomez and
• Antonio de la Hoz

Beilstein J. Org. Chem. 2017, 13, 285–300, doi:10.3762/bjoc.13.31

• . Determination of the kinetic parameters for a reaction usually requires the measurement of the initial reaction rate for different initial substrate concentrations and temperatures, and fitting of the data to the corresponding reaction rate law. Overall this is a very time-consuming process. However, the use of

• analyze very small volumes. Bearing in mind once again that the detection volume is much smaller than the reaction volume, it is possible to extract information at the onset and during the steady state of the reaction, and to analyze the data to determine the kinetic parameters in a single non-isothermal

• collection of experimental data and therefore, a fast optimization of reaction conditions and determination of kinetic parameters. On the other hand, some limitations and problems are encountered when combining microcoils with flow techniques. The usual limitations of working on flow NMR (i.e., clogging

Self-optimisation and model-based design of experiments for developing a C–H activation flow process

• Alexander Echtermeyer,
• Yehia Amar,
• Jacek Zakrzewski and
• Alexei Lapkin

Beilstein J. Org. Chem. 2017, 13, 150–163, doi:10.3762/bjoc.13.18

• rate constant k3 in Scheme 2. Empirical information provided constraints of process conditions, such as temperature and concentration ranges, whereas initial values of kinetic parameters were estimated based on a DFT model. Further details can be found in Supporting Information File 1. Here we

• used for the model development. The parameter estimation was employed to obtain estimates of the kinetic parameters kj,ref and Ea,j, where j {0, 1, 2, 3} in a two-step procedure using standard solver settings in gPROMS. By applying the initial guesses for the parameters, each experiment was first used

• equation in its re-parametrised form, shown in Equation 4 and Equation 5 [27][28]. This facilitates subsequent parameter estimation by decoupling the kinetic parameters of each reaction. Assuming equilibrium for the three reversible reaction steps in Scheme 2, the 8 kinetic parameters of interest in this

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• exponential function from which k2 can be calculated: Kinetic analysis of reference compound 8a revealed exponential first order kinetic (Figure 4) from which k2 was calculated. Interestingly, the comparison of the kinetic parameters showed a ~10-fold increase of the k2 value from pH 4 to pH 3 and also from

• -3 position. Experiments were performed in triplicate (mean + SD). Kinetic analysis of hydrolysis of reference compound 8a in dependency of different pH values and calculation of kinetic parameters. Curves and k2 values were calculated assuming a pseudo-first-order kinetic as described in Equation 3