FLUXY: a simple code for computing steady-state metal fluxes at consuming (bio)interfaces, in natural waters

2008 ◽  
Vol 5 (3) ◽  
pp. 204 ◽  
Author(s):  
Zeshi Zhang ◽  
Jacques Buffle ◽  
Konstantin Startchev ◽  
Davide Alemani
Keyword(s):  
Steady State ◽  
Rate Constants ◽  
Natural Waters ◽  
Equilibrium Constants ◽  
Computer Time ◽  
Rate Limiting Step ◽  
Broad Size Distribution ◽  
Metal Flux ◽  
User Friendly ◽  
Rate Limiting

Environmental context. Until now there was no user-friendly code for metal flux computations in natural mixtures of aquatic complexants, which are however essential for prediction of metal bioavailability. The present paper describes the capabilities and limitations of one of the only two such codes presently available, called FLUXY. The results of FLUXY are compared with those of another code, and it is shown that it enables quick computation and is applicable to natural ligands under many environmental conditions. Abstract. The computation of metal fluxes at consuming interfaces like microorganisms or bioanalogical sensors is of great importance in ecotoxicology. The present paper describes the application of a simple code, FLUXY, for the computation of steady-state metal fluxes in the presence of a very large number of complexes, with broadly varying values of equilibrium constants, rate constants and diffusion coefficients. This code includes two major limiting assumptions, namely, (i) the existence of excess of ligand (L) compared with metal (M), and (ii) the fact that in a series of successive MLn complexes, the reaction is the rate-limiting step in flux computation. The domains of rate constants for which these assumptions are valid are tested systematically, and the corresponding errors are evaluated by comparison with the exact results given by another code: MHEDYN. FLUXY is then applied and compared with MHEDYN for case studies typical of aquatic systems, namely (i) a culture medium containing simple ligands; (ii) solutions of fulvic compounds including a broad distribution of complex stability and rate constants; and (iii) suspensions of aggregates with a broad size distribution. It is shown that FLUXY gives good results for cases (i) and (iii). Application to case (ii) (fulvic compounds) is also feasible under conditions that are clearly described. Altogether, FLUXY and MHEDYN are complementary. In particular, FLUXY only computes steady-state fluxes and requires the fulfilment of a few conditions, but when these are met, computations require much less computer time than MHEDYN.

Reactions of 1-substituted 2,4,6-trinitrobenzenes with nucleophiles

1979 ◽  
Vol 44 (5) ◽  
pp. 1453-1459 ◽  
Author(s):  
Jaromír Kaválek ◽  
Ahmad Ashfaq ◽  
Vojeslav Štěrba
Keyword(s):  
Methyl Ether ◽  
Rate Constants ◽  
Equilibrium Constants ◽  
Nucleophilic Aromatic Substitution ◽  
Aromatic Substitution ◽  
Phenyl Ester ◽  
Methyl Derivative ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

Rate constants have been determined of nucleophilic aromatic substitution of 2,4,6-trinitrophenyl methyl ether (Ia), 2,4,6-trinitrophenyl ethanoate (Ic), 2,4,6-trinitrochlorobenzene (Ib), 2,4,6-trinitrodiphenyl ether (Id), 2,4,6-trinitro-4'-bromodiphenyl ether (Ie), 2,3',4,6-tetranitrodiphenyl ether (If) and 2,4,4',6-tetranitrodiphenyl ether (Ig) with methoxide, ethanoate and methyl cyanoethanoate (II) anions in methanol. For the compounds Ia,b rate and equilibrium constants of addition of the anion II(-) at positions 3 and 5 have been measured, too. In reactions of the compounds Ia to Ig with ethanoate anion the first (rate-limiting) step produces the phenyl ester Ic which reacts with a further ethanoate anion to give 2,4,6-trinitrophenol (Ih) and ethanoic anhydride. In reactions of the bromo derivative Ie and, to a still larger extent, compound Id the methyl derivative Ia is formed besides the compound Ih.

Reactions of 1,3-diacylthioureas with methoxide ion and with amines

1987 ◽  
Vol 52 (1) ◽  
pp. 120-131 ◽  
Author(s):  
Jaromír Kaválek ◽  
Josef Jirman ◽  
Vojeslav Štěrba
Keyword(s):  
Carbonyl Group ◽  
Rate Constants ◽  
Dissociation Constants ◽  
Equilibrium Constants ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Order Of Magnitude ◽  
Acetyl Group ◽  
Methoxide Ion ◽  
Rate Limiting

Rate constants of base-catalyzed methanolysis and dissociation constants in methanol have been determined for benzoylthiourea (II), 1,3-diacetylthiourea (III), 1,3-dibenzoylthiourea (IV), and 1-acetyl-3-benzoylthiourea (V). With the diacyl derivatives III and IV, the reaction of methoxide ion with the neutral substrate is accompanied by that of methoxide with the substrate anion (at higher alkoxide concentrations). Above 0.1 mol l-1 CH3O(-), the rate constants are also affected by medium. The rate of the reaction of neutral diacyl derivative is decreased, and that of the reaction of methoxide with the substrate anion is rapidly increased. The dissociation constant of II is higher than that of acetylthiourea (I) by about one order of magnitude, but the attack of methoxide on the carbonyl group of II is about three times slower than that in I. The benzoyl group at the N1 nitrogen exhibits a greater activating influence (in both the rate and the equilibrium constants) on the other NHCOR group than the acetyl group does. With V the ratio of methanolysis rate constants is 9 : 1 in favour of the acetyl group. The reaction of diacetyl derivative III with 1-butanamine has been followed in butanamine buffers. At the lowest butanamine concentrations, the reaction is second order in the amine, and the rate-limiting step is the proton transfer from the intermediate to the second amine molecule. At the highest butanamine concentrations the reaction becomes first order in the amine, and the rate-limiting step changes to the attack of butanamine on the carbonyl group of diacetyl derivative III.

scholarly journals Kinetics and mechanism of action of muscle pyruvate kinase

1978 ◽  
Vol 169 (1) ◽  
pp. 39-54 ◽  
Author(s):  
Leighton G. Dann ◽  
Hubert G. Britton
Keyword(s):  
Steady State ◽  
Dissociation Constant ◽  
Pyruvate Kinase ◽  
Alternative Pathway ◽  
Slow Step ◽  
Velocity Data ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Muscle Pyruvate Kinase ◽  
Rate Limiting

1. The mechanism of rabbit muscle pyruvate kinase was investigated by measurements of fluxes, isotope trapping, steady-state velocity and binding of the substrates. All measurements were made at pH8.5 in Tris/HCl buffer and at 5mm-free Mg2+. 2. Methods of preparing [32P]phosphoenolpyruvate from [32P]Pi in high yield and determining [32P]-phosphoenolpyruvate and [8-14C]ADP are described. 3. The ratio Flux of ATP to ADP/Flux of ATP to phosphoenolpyruvate (measured at equilibrium) increased hyperbolically with ADP concentration from unity to about 2.1 at 2mm-ADP, but was unaffected by phosphoenolpyruvate concentration. Since the ratio is greater than unity, one pathway for the addition of substrates must involve phosphoenolpyruvate adding first to the enzyme in a rate-limiting step. However, the substrates must also add in the alternative order, because of the non-linear increase in the ratio with ADP concentration and because the rate of increase is very much less than that predicted from the steady-state velocity data for an ordered addition. The lack of influence of phosphoenolpyruvate on the ratio is consistent with the rapid addition of ADP in the alternative pathway. At low ADP concentrations the alternative pathway contributes less than 33% to the total reaction. 4. Isotope trapping was observed with [32P]phosphoenolpyruvate, confirming that when phosphoenolpyruvate adds first to the enzyme it is in a rate-limiting step. The release of phosphoenolpyruvate from the ternary complex must also be a slow step. Trapping was not observed with [8-14C]ADP, hence the addition of ADP to the free enzyme must be rapid unless its dissociation constant is very large (>20mm). 5. Binding studies showed that 4mol of [32P]phosphoenolpyruvate binds to 1mol of the enzyme, probably unligated to Mg2+, with a dissociation constant appropriate to the mechanism indicated above. Binding of [8-14C]ADP could not be detected, and hence the binding of ADP occurs by a low-affinity step. The latter is also demanded by the steady-state velocity data. 6. The ratio Flux of phosphoenolpyruvate to ATP/Flux of phosphoenolpyruvate to pyruvate (determined from the incorporation of label into phosphoenolpyruvate from [3-14C]-pyruvate or [γ-32P]ATP during the forward reaction) did not differ significantly from unity. Steady-state velocity data predicted grossly different flux ratios for ordered dissociations of the products, and the results indicate that the dissociation must be rapid and random. The data also exclude a Ping-Pong mechanism. 7. Permissible rate constants for the above mechanism are calculated. The results indicate a high degree of cooperativity in binding, whatever the order of addition of substrate.

scholarly journals Beyond the Active Site: Mechanistic Investigations of the Role of the Secondary Coordination Sphere and Beyond on Multi-Electron Electrocatalytic Reactions and Their Relations Between Kinetics and Thermodynamics

2020 ◽  
Author(s):  
Vincent Wang
Keyword(s):  
Thermodynamic Parameters ◽  
Coordination Sphere ◽  
Active Site ◽  
Rate Constants ◽  
Reduction Reaction ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Secondary Coordination Sphere ◽  
Catalytic Rate ◽  
Rate Limiting

<p>The development of an electrocatalyst with a rapid turnover frequency, low overpotential and long-term stability is highly desired for fuel-forming reactions, such as water splitting and CO<sub>2</sub> reduction. The findings of the scaling relationships between the catalytic rate and thermodynamic parameters over a wide range of electrocatalysts in homogeneous and heterogeneous systems provide useful guidelines and predictions for designing better catalysts for those redox reactions. However, such relationships also suggest that a catalyst with a high catalytic rate is typically associated with a high overpotential for a given reaction. Inspired by enzymes, the introduction of additional interactions through the secondary coordination sphere beyond the active site, such as hydrogen-bonding or electrostatic interactions, have been shown to offer a promising avenue to disrupt these unfavorable relationships. Herein, we further investigate the influence of these cooperative interactions on the faster chemical steps, in addition to the rate-limiting step widely examined before, for molecular electrocatalysts with the structural and electronic modifications designed to facilitate the dioxygen reduction reaction, CO<sub>2</sub> reduction reaction and hydrogen evolving reaction. Based on the electrocatalytic kinetic analysis, the rate constants for faster chemical steps and their correlation with the corresponding thermodynamic parameters are evaluated. The results suggest that the effects of the secondary coordination sphere and beyond on these fuel-forming reactions are not necessarily beneficial for promoting all chemical steps and no apparent relation between rate constants and thermodynamic parameters are found in some cases studied here, which may implicate the design of electrocatalysts in the future. Finally, these analyses demonstrate that the characteristic features for voltammograms and foot-of-the-wave-analysis plots are associated with the specific kinetic phenomenon among these multi-electron electrocatalytic reactions, which provides a useful framework to probe the insights of chemical and electronic modifications on the catalytic steps quantitatively (i.e. kinetic rate constants) and to optimize some of critical steps beyond the rate-limiting step.</p>

scholarly journals NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao Feng ◽  
Evgenii L. Kovrigin ◽  
Carol Beth Post
Keyword(s):  
Kinetic Model ◽  
Molecular Interactions ◽  
Rate Constants ◽  
Nmr Spectra ◽  
Equilibrium Constants ◽  
Software Tool ◽  
Biological Interactions ◽  
Equilibrium Binding ◽  
Accurate Quantitative Analysis ◽  
User Friendly

Abstract The ability of high-resolution NMR spectroscopy to readout the response of molecular interactions at multiple atomic sites presents a unique capability to define thermodynamic equilibrium constants and kinetic rate constants for complex, multiple-step biological interactions. Nonetheless, the extraction of the relevant equilibrium binding and rate constants requires the appropriate analysis of not only a readout that follows the equilibrium concentrations of typical binding titration curves, but also the lineshapes of NMR spectra. To best take advantage of NMR data for characterizing molecular interactions, we developed NmrLineGuru, a software tool with a user-friendly graphical user interface (GUI) to model two-state, three-state, and four-state binding processes. Application of NmrLineGuru is through stand-alone GUIs, with no dependency on other software and no scripted input. NMR spectra can be fitted or simulated starting with user-specified input parameters and a chosen kinetic model. The ability to both simulate and fit NMR spectra provides the user the opportunity to not only determine the binding parameters that best reproduce the measured NMR spectra for the selected kinetic model, but to also query the possibility that alternative models agree with the data. NmrLineGuru is shown to provide an accurate, quantitative analysis of complex molecular interactions.

Regulation of the purine salvage pathway in rat liver

1992 ◽  
Vol 262 (3) ◽  
pp. E344-E352 ◽  
Author(s):  
Y. A. Kim ◽  
M. T. King ◽  
W. E. Teague ◽  
G. A. Rufo ◽  
R. L. Veech ◽  
...  
Keyword(s):  
Rat Liver ◽  
De Novo ◽  
Equilibrium Constants ◽  
Purine Metabolism ◽  
Purine Salvage ◽  
Rate Limiting Step ◽  
Delta G ◽  
Salvage Pathways ◽  
Rate Limiting

The regulation of purine metabolism in rat liver has been examined under conditions that alter the flux through the pathway. Rats were given intraperitoneal injections of ethanol, sodium acetate, or sodium phosphate to attain body water concentrations of approximately 70, 20, and 10 mM, respectively. The livers were freeze-clamped after 30 min, and extracts were made for the analysis of metabolites, cofactors, purine bases, and nucleosides; homogenates were made for the measurement of the activities and kinetic parameters of seven enzymes that participate in purine salvage. The values of the equilibrium constants of nine reactions were determined in vitro and compared with the ratios of the reactants measured in liver. The changes in phosphoribosylpyrophosphate (PRPP), a key intermediate in both the de novo and salvage pathways of purine metabolism, were directly correlated with the changes in ribose 5-phosphate (ribose-5-P); ([PRPP] = 1.7[ribose-5-P] - 7.4 mumol/kg). Ribose-5-P concentrations in turn could be predicted from the liver content of fructose 6-phosphate and glyceraldehyde 3-phosphate by calculation from the known equilibria. The maximum velocities in the tissue of the seven enzymes measured were calculated from the measured substrate values in the liver and with consideration of other effectors of enzyme activity. PRPP synthetase was the least active of the enzymes measured, indicating a possible rate-limiting step. The delta G of the enzyme steps differed from equilibrium values by factors ranging from 4 (nucleoside phosphorylase) to 10(5) (PRPP synthetase and purine transferase reactions). The regulation of purine salvage appeared to depend on the levels of PRPP and ribose-5-P.

scholarly journals Control analysis applied to single enzymes: can an isolated enzyme have a unique rate-limiting step?

1993 ◽  
Vol 294 (1) ◽  
pp. 87-94 ◽  
Author(s):  
G C Brown ◽  
C E Cooper
Keyword(s):  
Rate Constants ◽  
General Assumption ◽  
Control Analysis ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Steady State Rate ◽  
Carbamate Kinase ◽  
State Rate ◽  
Rate Limiting ◽  
Control Coefficients

Control analysis is used to analyse and quantify the concept of a rate-limiting step within an enzyme. The extent to which each rate constant within the enzyme limits the steady-state rate of the enzyme and the levels of enzyme intermediate species are quantified as flux and concentration control coefficients. These coefficients are additive and obey summation theorems. The control coefficients of triose phosphate isomerase, carbamate kinase and lactate dehydrogenase are calculated from literature values of the rate constants. It is shown that, contrary to previous assumption, these enzymes do not have a unique rate-limiting step, but rather flux control is shared by several rate constants and varies with substrate, product and effector concentrations, and with the direction of the reaction. Thus the general assumption that an enzyme will have a unique rate-limiting step is unjustified.

scholarly journals Chorismate synthase. Pre-steady-state kinetics of phosphate release from 5-enolpyruvylshikimate 3-phosphate

1990 ◽  
Vol 265 (3) ◽  
pp. 899-902 ◽  
Author(s):  
T R Hawkes ◽  
T Lewis ◽  
J R Coggins ◽  
D M Mousdale ◽  
D J Lowe ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Steady State ◽  
Lag Phase ◽  
Chorismate Synthase ◽  
Phosphate Release ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Steady State Kinetics ◽  
Rate Limiting ◽  
Kinetics Of

The pre-steady-state kinetics of phosphate formation from 5-enolpyruvylshikimate 3-phosphate catalysed by Escherichia coli chorismate synthase (EC 4.6.1.4) were studied by a rapid-acid-quench technique at 25 degrees C at pH 7.5. No pre-steady-state ‘burst’ or ‘lag’ phase was observed, showing that phosphate is released concomitant with the rate-limiting step of the enzyme. The implications of this result for the mechanism of action of chorismate synthase are discussed.

scholarly journals The Deoxyglucose Method in the Ferret Brain. II. Glucose Utilization Images and Normal Values

1989 ◽  
Vol 9 (1) ◽  
pp. 43-52 ◽  
Author(s):  
C. Redies ◽  
M. Diksic ◽  
Y. L. Yamamoto
Keyword(s):  
Rate Constants ◽  
Glucose Utilization ◽  
Normal Values ◽  
Brain Size ◽  
Experimental Period ◽  
Brain Structures ◽  
Rate Limiting Step ◽  
Rate Limiting ◽  
The Brain ◽  
Deoxyglucose Method

To measure cerebral glucose utilization with the autoradiographic deoxyglucose method, the tracer transfer rate constants and lumped constants must be known. 2-Deoxyglucose (2-DG) and fluorodeoxyglucose (FDG) constants were determined in 18 gray and white matter brain structures of the anesthetized ferret. The ferret is a domestic carnivore particularly suitable for deoxyglucose studies because of its small brain size and low body weight. The average gray matter rate constants for tracer transfer across the blood-brain barrier are similar for 2-DG and FDG in the ferret brain ( K*1 = 0.21 ml/g/min and k*2 = 0.39 min−1). The rate constant for the rate-limiting step of tracer phosphorylation, k*3, is 1.6 times higher for FDG than for 2-DG (0.21 vs. 0.13 min−1). Loss of metabolized tracer is about 1–1.5%/min throughout the ferret brain for both tracers as estimated for a 180 min experimental period. Taking into account this loss, the lumped constant is 0.92 for FDG and 0.68 for 2-DG. Glucose utilization values in the brain of the anesthesized ferret range from 33 μmol/100 g/min in the corpus callosum to 104 μmol/100 g/min in the caudate nucleus. Representative glucose utilization images of coronal sections of the ferret brain are shown. Brain structures are identified on the same slices counterstained with thionin.

The nature of the transition state in diarylmethyl cation – nucleophile combination reactions as probed by secondary α-deuterium isotope effects

2001 ◽  
Vol 79 (12) ◽  
pp. 1887-1897
Author(s):  
Thuy Van Pham ◽  
Robert A McClelland
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Rate Constant ◽  
Rate Constants ◽  
Flash Photolysis ◽  
Isotope Effects ◽  
Equilibrium Constants ◽  
Bond Formation ◽  
Kinetic Isotope ◽  
Rate Limiting

Transition-state structures for the carbocation–nucleophile combination reactions of (4-substituted-4'- methoxydiphenyl)methyl cations with water, chloride, and bromide ions in acetonitrile–water mixtures have been investigated by measuring the secondary α-deuterium kinetic and equilibrium isotope effects. Rate constants in the combination direction were measured with laser flash photolysis. Equilibrium constants were measured for the water reaction by a comparison method in moderately concentrated sulfuric acid solutions, for the bromide reaction via the observation of reversible combination, and for the chloride reaction from the ratio of the combination rate constant and the rate constant for the ionization of the diarylmethyl chloride product. The fraction of bond making in the transition state has been calculated as the ratio log (kinetic isotope effect):log (equilibrium isotope effect). For the water reaction, there is 50–65% bond making in the transition state; this is also true for cations that are many orders of magnitude less reactive. The same conclusions, 50–65% bond formation in the transition state independent of reactivity, have previously been made in correlations of log kw vs. log KR. Thus, two quite different measures of transition structure provide the same result. The kH:kD values for the halide combinations in 100% acetonitrile are within experimental error of unity. This is consistent with suggestions that these reactions are occurring with diffusional encounter as the rate-limiting step. Addition of water has a dramatic retarding effect on the halide reactions, with rate constants decreasing steadily with increased water content. Small inverse kinetic isotope effects are observed (in 20% acetonitrile:80% water) indicating that carbon—halogen bond formation is rate-limiting. Comparison of the kinetic and equilibrium isotope effects shows ~25 and ~40% bond formation in the transition states for the reactions with bromide and chloride, respectively.Key words: carbocation, isotope effect, transition state, halide.

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