Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• training set for scaling, gave the best fit for these 10 compounds (MAD/RMSD = 5.3/7.0 ppm). Use only of our different training set gave a significantly worse fit (MAD/RMSD = 9.1/11.0 ppm), showing that Jensen’s point that choice of functional resembles data fitting [8] can also be applied to choice of

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

• kcat/Km. Keywords: computer simulation; data fitting; enzyme catalysis; induced-fit; Michaelis constant; specificity constant; Review When Henri, Michaelis and Menten derived the equation for steady state enzyme turnover, they chose to define the rate in terms of Vmax and the substrate dissociation

• one figure to represent both methods (Figure 3A). However, as summarized in Table 1, the error estimates vary depending on the method used. As seen previously with equation-based data fitting, using the model to define kcat/Km directly is more precise than computing kcat/Km from individual estimates

• of kcat and Km. It should also be noted that either method of fitting data by simulation is more accurate than the corresponding equation-based data fitting. This is because we are fitting the entire data set using only two parameters rather than fourteen. Using extraneous parameters introduces

C–C Bond formation catalyzed by natural gelatin and collagen proteins

• Dennis Kühbeck,
• Basab Bijayi Dhar,
• Eva-Maria Schön,
• Carlos Cativiela,
• Vicente Gotor-Fernández and
• David Díaz Díaz

Beilstein J. Org. Chem. 2013, 9, 1111–1118, doi:10.3762/bjoc.9.123

• reached 100% yield, data fitting was made according to the variation of ln[(Ct − C∞)/(C∞ − C0)] with time, where Ct is the concentration at a given time t; C∞ the final concentration (at infinite time) and C0 the initial concentration (at t = zero time). For reaction conversions close to 100%, plots of ln

Thermodynamic and kinetic stabilization of divanadate in the monovanadate/divanadate equilibrium using a Zn-cyclene derivative: Towards a simple ATP synthase model

• Hanno Sell,
• Anika Gehl,
• Frank D. Sönnichsen and
• Rainer Herges

Beilstein J. Org. Chem. 2012, 8, 81–89, doi:10.3762/bjoc.8.8

• spectrum (tmix = 1 ms) of a solution containing 1.5 mM Na3VO4, 3 mM Zn-benzylcyclene and 100 mM EPPS (pH = 7.9). Stoichiometry and formation constants of the complex species in the proton/vanadium/Zn benzylcyclene system. Supporting Information Supporting Information File 28: 51V NMR spectra and data

• fitting results. Acknowledgements We would like to thank the Deutsche Forschungsgemeinschaft (DFG) for funding via SFB 677 (Function by Switching).

Kinetic studies and predictions on the hydrolysis and aminolysis of esters of 2-S-phosphorylacetates

• Milena Trmčić and
• David R. W. Hodgson

Beilstein J. Org. Chem. 2010, 6, 732–741, doi:10.3762/bjoc.6.87

• -nitrophenyl ester 7 (R = mNP) at 25 °C. Squares correspond to data for p-nitrophenyl ester 7 (R = pNP); circles correspond to data for m-nitrophenyl ester 7 (R = mNP). The dashed line corresponds to data fitting for p-nitrophenyl ester 7 (R = pNP) and the solid line corresponds to data fitting for m

• -nitrophenyl ester 7 (R = mNP). The dashed black line corresponds to data fitting for the hydrolysis of p-nitrophenyl ester 7 (R = pNP) and the solid black line corresponds to data fitting for the hydrolysis of m-nitrophenyl ester 7 (R = mNP) (Figure 1). The dashed red line corresponds to data fitting for the

• combined aminolysis and hydrolysis of p-nitrophenyl ester 7 (R = pNP); solid red line corresponds to data fitting for the combined aminolysis and hydrolysis of m-nitrophenyl ester 7 (R = mNP). Predicted concentration-time profile for the reaction between starting concentrations of 0.05 M p-nitrophenyl