Set Of Kinetic Data Research Articles

Data Formats for Elementary Gas-Phase Kinetics: Part 2. Unique Representations of Reactions

A method of extending the IUPAC International Chemical Identifier (InChI) to describe and identify elementary reactions in a standard computer-readable notation is developed. Denoted InChI-ER, the method is based on the existing InChI formalism, with certain refinements for the better identification of molecular entities as proposed in Part 1 published previously in this journal. Using this base notation, an identifier for elementary reactions on a molecular level is created by adding additional layers in a conceptually similar and extensible manner. Two of the layers describe the atoms involved in the transition state and the connectivity changes that occur during the reaction. Additional layers classify the reactions on the basis of the connectivity changes, providing chemical information useful in organizing and searching kinetic data sets found in databases or used in detailed kinetic modeling. Important aspects of the method are that the proposed layers are optional, that they do not interfere with existing InChI specifications, and that they retain extensibility should further refinements be desired in the future.

The assembly dynamics of the cytolytic pore toxin ClyA.

Pore-forming toxins are protein assemblies used by many organisms to disrupt the membranes of target cells. They are expressed as soluble monomers that assemble spontaneously into multimeric pores. However, owing to their complexity, the assembly processes have not been resolved in detail for any pore-forming toxin. To determine the assembly mechanism for the ring-shaped, homododecameric pore of the bacterial cytolytic toxin ClyA, we collected a diverse set of kinetic data using single-molecule spectroscopy and complementary techniques on timescales from milliseconds to hours, and from picomolar to micromolar ClyA concentrations. The entire range of experimental results can be explained quantitatively by a surprisingly simple mechanism. First, addition of the detergent n-dodecyl-β-D-maltopyranoside to the soluble monomers triggers the formation of assembly-competent toxin subunits, accompanied by the transient formation of a molten-globule-like intermediate. Then, all sterically compatible oligomers contribute to assembly, which greatly enhances the efficiency of pore formation compared with simple monomer addition.

Elementary Kinetic Numerical Simulation of Ni/YSZ SOFC Anode Performance Considering Sulfur Poisoning

An elementary kinetic model is developed and applied to explore the influence of sulfur poisoning on the behavior of solid oxide fuel cell (SOFC) anodes. A detailed multi-step reaction mechanism of sulfur formation and oxidation at Ni/YSZ anodes together with channel gas-flow, porous-media transport and elementary charge-transfer chemistry is established for SOFCs operating on H2/H2O mixtures with trace amounts of hydrogen sulfide (H2S). A thermodynamic and kinetic data set is compiled from various literature sources. The derived chemical model, validated against sulfur chemisorption isobars taken from literature, is used to analyze performance drops of SOFCs working under typical fuel cell operating conditions. Electrochemical results show that at relatively low H2S concentrations SOFC button-cell performance can be interpreted using chemical sulfur formation. However, when the concentration is sufficiently high, the inclusion of second stage degradation and triple-phase boundary reconstruction is necessary to describe the performance decrease. Additionally, it is shown that the sulfur surface coverage increases with increasing current density. In order to shed more light on advanced fundamental understanding of cell poisoning, sensitive analyses toward total anode resistance and sulfur coverage for different operating conditions were performed.

The effect of chain size on the modeling of second sphere effects in biomimetic complexes

In this paper, we describe a new method for the systematic synthesis of catalytic dinuclear Zn(II) hydrolases incorporating second coordination sphere effects by using a polyamidoamine dendrimer as a secondary chain model. Six complexes bearing different dendrimer generations were studied in the hydrolysis of 2-hydroxypropyl-4-nitrophenyl-phosphate (HPNP) and sets of kinetic data were compared in order to better understand the effect of the chain model on the reactivity. The results indicate that a chain of 4000gmol−1 is sufficient to represent the second sphere effect in our model. Although the activation entropy ΔS‡ was significantly increased, the kcat value was not increased, due to unfavorable changes in ΔH‡. The dinuclear catalytic center remained intact, acting through the same mechanism, which opens new possibilities for the rational functionalization at this chain length to further increase the complex activity.

Kinetic study of steam gasification of two mineralogically different lignite chars: An active site/intermediate model

A new active site/intermediate model (ASIM) is formulated in terms of a simplified calcium-catalyzed mechanism of char gasification to characterize a conversion-dependent maximum in reaction rate. In a limited case, the model is retrogressed to a common volumetric model (VM). Two sets of kinetic data were experimentally gathered by steam gasification of two lignite chars in a fixed bed reactor with negligible mass diffusion limitation. The gasification behaviors of two chars were, respectively, representative of catalyzed and uncatalyzed gasification as a result of the influences of different mineral components in them. It was found that ASIM intimately fit the kinetic profiles over the entire range of conversion for both catalyzed and uncatalyzed char gasification, demonstrating the good adaptability to varying chars. The model could determine the activation energies for the formation of the total carbon-containing gases and of two individual gases (CO and CO2) from the oxygenated intermediate. Moreover, for the case of catalyzed gasification, ASIM reasonably predicted the formation, growth and decline of the intermediate with carbon conversion as well as the change in the intermediate concentration with gasification temperature. For the case of uncatalyzed gasification, the model portrayed essentially a linear decline in the intermediate concentration with increasing carbon conversion, similar to VM.

Kinetics of Water Vapor Adsorption on Single-Layer Molecular Sieve 3A: Experiments and Modeling

The objective of the current work was to shorten the gap for fundamental adsorption kinetic data required for the development of advanced adsorption unit-operation models to be incorporated into an overall plant-level model for spent nuclear fuel reprocessing. The kinetics of water-vapor adsorption on molecular sieve 3A was investigated at 25–80 °C and water dew points from −69 to 17 °C. Water uptake curves were fitted with three kinetic models including the linear-driving-force model, the shrinking-core model, and the Langmuir kinetic model. The results suggest that the water-vapor adsorption on molecular sieve 3A under the investigated experimental conditions was controlled by both external film resistance and internal macropore resistance. The contribution of the external film resistance varied from 25% to 50% of the total mass-transfer resistance depending on the adsorption temperature. It was also found that the Langmuir kinetic model fitted individual sets of kinetic data very well, but the Langmuir adsorption constant obtained from curve fitting decreased with increasing adsorption temperature and with increasing water vapor pressure. This result indicates a significant surface heterogeneity of molecular sieve 3A and also implicitly verifies that the Langmuir isotherm model is unable to represent isotherms of water adsorption on molecular sieve 3A.

Sorption kinetics: Obtaining a pseudo-second order rate equation based on a mass balance approach

Various formulations of pseudo second-order rate equations have been widely used in elucidating the rate constants of a wide variety of sorption systems. In this paper, it is shown that a new formulation can be obtained by making use of the mass balance equation of a single stage batch-type system. Two linear forms of the equation were then used to analyze different sets of kinetic data. It is shown that the adequacy of kinetic models should not be linked solely to linear correlation coefficients.

Kinetic fluorescence quenching of CdS quantum dots in the presence of Cu(II): Chemometrics-assisted resolving of the kinetic data and quantitative analysis of Cu(II)

In this work, the kinetic fluorescence behavior of CdS quantum dots (QDs) in the presence of Cu(II) was investigated. In contrast to some other transition metal ions such as Ag(I), Ni(II), and Hg(II), a gradual red-shift in the emission spectrum of CdS QDs was observed for Cu(II) during the reaction course. More investigations revealed the existence of two chemical components in the recorded kinetic data in the presence of Cu(II). Multivariate curve resolution-alternating least squares (MCR-ALS) method was applied in order to extract pure emission spectra and time-dependent profiles of these two components at different concentrations of Cu(II). The results obtained from resolving the data by MCR-ALS got some information about the mechanism of the interaction between CdS QDs and Cu(II) ions which were in good agreement with those reported in the literature. Moreover, the multivariate method of analysis, partial least-squares (PLS) method, was used to develop a multivariate calibration model for quantitative analysis of Cu(II) using the entire kinetic data sets. The calibration and validation sets were created ranging from 0.02 to 1μM of Cu(II) and were successfully calibrated and predicted by the PLS model. This method allowed a sensitive determination of Cu(II) ions with a detection limit of 13nM based on three times of the standard deviation corresponding to PLS regression.

Predicting the Concentration of Verotoxin-Producing Escherichia coli Bacteria during Processing and Storage of Fermented Raw-Meat Sausages

A model to predict the population density of verotoxigenic Escherichia coli (VTEC) throughout the elaboration and storage of fermented raw-meat sausages (FRMS) was developed. Probabilistic and kinetic measurement data sets collected from publicly available resources were completed with new measurements when required and used to quantify the dependence of VTEC growth and inactivation on the temperature, pH, water activity (aw), and concentration of lactic acid. Predictions were compared with observations in VTEC-contaminated FRMS manufactured in a pilot plant. Slight differences in the reduction of VTEC were predicted according to the fermentation temperature, 24 or 34°C, with greater inactivation at the highest temperature. The greatest reduction was observed during storage at high temperatures. A population decrease greater than 6 decimal logarithmic units was observed after 66 days of storage at 25°C, while a reduction of only ca. 1 logarithmic unit was detected at 12°C. The performance of our model and other modeling approaches was evaluated throughout the processing of dry and semidry FRMS. The greatest inactivation of VTEC was predicted in dry FRMS with long drying periods, while the smallest reduction was predicted in semidry FMRS with short drying periods. The model is implemented in a computing tool, E. coli SafeFerment (EcSF), freely available from http://www.ifr.ac.uk/safety/EcoliSafeFerment. EcSF integrates growth, probability of growth, and thermal and nonthermal inactivation models to predict the VTEC concentration throughout FRMS manufacturing and storage under constant or fluctuating environmental conditions.

Experiment and Modeling Studies on Absorption of CO2 by Dilute Ammonia in Rotating Packed Bed

This study presented experimental data of packed bed and rotating packed bed adsorption of carbon dioxide by dilute aqueous ammonia solutions. The heights of transfer units of packed bed were found to be 0.35 to 1.96 m; while the heights of a transfer unit of the rotating packed bed were in the range 0.08 to 0.40 m. Predictive models of the two processes were developed (model details and implications discussed elsewhere) based on the same set of thermodynamic and kinetic data for carbon dioxide into dilute aqueous ammonia solutions and existing mass transfer correlations for packed bed and rotating packed bed. The average absolute deviations between model predictions and experiments were found to be 9.4% for rotating packed bed data and 12% pack bed data.

Detailed Kinetic Analysis and Modeling of Steam Gasification of Char from Ca-Loaded Lignite

A kinetic model of steam gasification of Ca-loaded lignite char has been proposed through the analysis of 41 sets of kinetic data obtained by thermogravimetry with different combinations of Ca concentration, temperature, and partial pressures of hydrogen and steam. The model quantitatively describes the change with time of the char conversion over its entire range by assuming progress of non-catalytic gasification and two different types of Ca-catalyzed gasification (Type-1 and Type-2) in parallel, all of which obey Langmuir–Hinshelwood mechanisms. The model attributes the catalysts for Type-1 and Type-2 to nanosized Ca-based particles and Ca species dispersed in an atomic scale, respectively. The initial concentration of Type-2 catalyst is saturated at a total Ca concentration over 1.0 wt %, while that of Type-1 increased in a linear manner with the total Ca concentration. The catalysis of Type-1 catalyst is more significant but diminished more quickly than that of the Type-2 one. Consequently, there was an optimum initial Ca concentration in the char around 2.0 wt % in terms of the time required for 99% char conversion. This trend is clearly different from that predicted from previous models that simply assumed loading saturation levels (LSLs). The kinetic model predicts characteristics of the steam gasification of the Ca-loaded char in an atmospheric bubbling fluidized bed at 800 °C. The characteristic time for the char gasification, which is given by the amount of in-bed char at steady state per feeding rate of the char (mc/Fc), is reduced by virtue of Ca by a factor of 7–8.

Fischer–Tropsch synthesis: Kinetics and water effect study over 25%Co/Al2O3 catalysts

The kinetics of Fischer–Tropsch synthesis (FTS) over a 25%Co/Al2O3 catalyst was studied using a 1-L continuously stirred tank reactor (CSTR) under the conditions of 205–230°C, 1.4–2.5MPa, H2/CO=1.0–2.5 and 3–16NL/g-cat/h (XCO=7–54%). Thirty-one sets of kinetic data collected at 220°C with a low extent of deactivation were used for kinetic parameter regression. The CAER empirical kinetic model (rFT=kPCOaPH2b/(1+mPH2O/PH2)) was employed to study the kinetic effect of water. A positive kinetic water effect was first evidenced using the kinetic approach, consistent with the results of the effect of co-fed water on cobalt FTS in this work and the literature (e.g. Loegdberg et al., 2011 [21]) for Co/Al2O3 catalysts. The current kinetic results are based on kinetic data taken following an initial catalyst induction period, where the CO conversion had stabilized. These data are different from our earlier investigations where reversible oxidation of small cobalt crystallites and/or catalyst support effects likely impacted the cobalt site densities, resulting in a negative water effect. Thus, in this study, we decoupled the effect of reversible oxidation from the kinetics, so that the effect of water on stable (i.e., presumably larger) metallic cobalt particles could be assessed.In this study, an additional eleven classical FT kinetic models for Co catalysts were tested using the kinetic data. Five of them were also found to adequately describe the kinetic data, including two mechanistic models developed based on carbide mechanisms. The CAER model containing a water effect term and the mechanistic model of Botes et al. (2009) [31] yielded comparable reaction orders for the partial pressures of H2 and CO, resulted in a better fit of the kinetic data.

Resolving the Distribution–Metabolism Interplay of Eight OATP Substrates in the Standard Clearance Assay with Suspended Human Cryopreserved Hepatocytes

Uptake transporters may act to elevate the intrahepatic exposure of drugs, impacting the route and rate of elimination, as well as the drug-drug interaction potential. We have here extended the assessment of metabolic drug stability in a standard human hepatocyte incubation to allow for elucidation of the distribution-metabolism interplay established for substrates of drug transporters. Cellular concentration-time profiles were obtained from incubations of eight known OATP substrates at 1 μM, each for two different 10-donor batches of suspended cryopreserved human hepatocytes. The kinetic data sets were analyzed using a mechanistic mathematical model that allowed for separate estimation of active uptake, bidirectional diffusion, metabolism and nonspecific extracellular and intracellular binding. The range of intrinsic clearances attributed to active uptake, diffusion and metabolism of the test set spanned more than 2 orders of magnitude each, with median values of 18, 5.3, and 0.5 μL/min/10(6) cells, respectively. This is to be compared with the values for the apparent clearance from the incubations, which only spanned 1 order of magnitude with a median of 2.6 μL/min/10(6) cells. The parameter estimates of the two pooled 10-donor hepatocyte batches investigated displayed only small differences in contrast to the variability associated with use of cells from individual donors reported in the literature. The active contribution to the total cellular uptake ranged from 55% (glyburide) to 96% (rosuvastatin), with an unbound intra-to-extracellular concentration ratio at steady state of 2.1 and 17, respectively. Principal component analysis showed that the parameter estimates of the investigated compounds were largely influenced by lipophilicity. Active cellular uptake in hepatocytes was furthermore correlated to pure OATP1B1-mediated uptake as measured in a transfected cell system. The presented approach enables the assessment of the key pathways regulating hepatic disposition of transporter and enzyme substrates from one single, reproducible and generally accessible human in vitro system.

Determinants of phosphorus mobilization during hemodialysis

Our recent work proposed a pseudo one-compartment model for describing intradialysis and postdialysis rebound kinetics of phosphorus. In this model, phosphorus is removed directly from a central distribution volume with the rate of phosphorus mobilization from a second, very large compartment proportional to the phosphorus mobilization clearance. Here, we evaluated factors of phosphorus mobilization clearance and postdialysis central distribution volume from 774 patients in the HEMO Study. Phosphorus mobilization clearance and postdialysis central distribution volume were 87 (65, 116) ml/min, median (interquartile range), and 9.4 (7.2, 12.0) liter, respectively. The phosphorus mobilization clearance was significantly higher for male patients than for female patients. Both the phosphorus mobilization clearance and the postdialysis central distribution volume were significantly associated with postdialysis body weight but negatively with the predialysis serum phosphorus concentration. The postdialysis central distribution volume was also significantly associated with age. Overall, the postdialysis central distribution volume was 13.6% of the postdialysis body weight. Thus, the phosphorus mobilization clearance during hemodialysis is higher when predialysis serum phosphorus concentration is low and higher in male patients than in female patients. The central distribution volume of phosphorus is a space approximating the extracellular fluid volume.

A new regulatory principle for in vivo biochemistry: Pleiotropic low affinity regulation by the adenine nucleotides – Illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

Enzymology tends to focus on highly specific effects of substrates, allosteric modifiers, and products occurring at low concentrations, because these are most informative about the enzyme’s catalytic mechanism. We hypothesized that at relatively high in vivo concentrations, important molecular monitors of the state of living cells, such as ATP, affect multiple enzymes of the former and that these interactions have gone unnoticed in enzymology.We test this hypothesis in terms of the effect that ATP, ADP, and AMP might have on the major free-energy delivering pathway of the yeast Saccharomyces cerevisiae. Assaying cell-free extracts, we collected a comprehensive set of quantitative kinetic data concerning the enzymes of the glycolytic and the ethanol fermentation pathways. We determined systematically the extent to which the enzyme activities depend on the concentrations of the adenine nucleotides. We found that the effects of the adenine nucleotides on enzymes catalysing reactions in which they are not directly involved as substrate or product, are substantial. This includes effects on the Michaelis–Menten constants, adding new perspective on these, 100years after their introduction.

A sectional approach for biomass: Modelling the pyrolysis of cellulose

We present the adaptation of the sectional model approach to the pyrolysis of cellulose, (C6H10O5)n. Cellulose is the major component of lignocellulosic biomass. Due to its longitudinal structure, cellulose is characterised by one-dimensional chains composed of a varying number of cellobiose molecules, C12H22O11. Fragments of those chains with similar mass are grouped into size classes (BINs) determined by characteristic numbers of cellobiose units. During the pyrolysis of cellulose, reaction temperatures of more than 500K (depending on the heating rate) initiate bond dissociation between cellobiose units. We have developed a new reaction scheme for the pyrolysis of cellulose based on literature models. However, we present the sectional approach as a new concept for modelling the degradation of cellulose. We propose a kinetic data set of A = 2.2 ∙ 1013 s−1 and EA = 225.9 kJ/mol for the dissociation of a single glycosidic bond. Additionally, our model includes the cellobiose devolatilisation to glucose or tars (levoglucosan) including primary gaseous products, the formation of char and water, and secondary gas-phase reactions. Our reactor simulations of cellulose pyrolysis at constant heating rates of 1, 10, 15, and 150 K/min show good agreement with two different experimental data sets.

Kinetics of hydrogen oxidation on Rh/Al2O3 catalysts studied in a stagnation-flow reactor

A newly established stagnation flow reactor with analysis of spatially resolved concentrations profiles is presented as useful tool for the investigation of heterogeneously catalyzed gas-phase reactions. The simplicity of this laboratory-scale reactor enables detailed modeling of the diffusive and convective transport within the one-dimensional gas-phase boundary-layer coupled with elementary-step homogeneous and heterogeneous reaction mechanisms. This set-up is applied to study the kinetics of hydrogen oxidation over Rh/Al2O3. By combining experimental and modeling results for a wide range of temperature and fuel/oxygen ratios, a thermodynamically consistent set of kinetic data for a 12-step surface reaction mechanism is derived. The applicability of the mechanism is further tested by the model prediction of experimentally derived ignition temperatures in a stagnation flow reactor and oxygen conversion in H2-rich hydrogen oxidation in an annular flow reactor at varying flow rate and temperature.

Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment

We carried out free-energy calculations and transient kinetic experiments for the insertion of the right (dC) and wrong (dA) nucleotides by wild-type (WT) and six mutant variants of human DNA polymerase β (Pol β). Since the mutated residues in the point mutants, I174S, I260Q, M282L, H285D, E288K, and K289M, were not located in the Pol β catalytic site, we assumed that the WT and its point mutants share the same dianionic phosphorane transition-state structure of the triphosphate moiety of deoxyribonucleotide 5'-triphosphate (dNTP) substrate. On the basis of this assumption, we have formulated a thermodynamic cycle for calculating relative dNTP insertion efficiencies, Ω = (k(pol)/K(D))(mut)/(k(pol)/K(D))(WT) using free-energy perturbation (FEP) and linear interaction energy (LIE) methods. Kinetic studies on five of the mutants have been published previously using different experimental conditions, e.g., primer-template sequences. We have performed a presteady kinetic analysis for the six mutants for comparison with wild-type Pol β using the same conditions, including the same primer/template DNA sequence proximal to the dNTP insertion site used for X-ray crystallographic studies. This consistent set of kinetic and structural data allowed us to eliminate the DNA sequence from the list of factors that can adversely affect calculated Ω values. The calculations using the FEP free energies scaled by 0.5 yielded 0.9 and 1.1 standard deviations from the experimental log Ω values for the insertion of the right and wrong dNTP, respectively. We examined a hybrid FEP/LIE method in which the FEP van der Waals term for the interaction of the mutated amino acid residue with its surrounding environment was replaced by the corresponding van der Waals term calculated using the LIE method, resulting in improved 0.4 and 1.0 standard deviations from the experimental log Ω values. These scaled FEP and FEP/LIE methods were also used to predict log Ω for R283A and R283L Pol β mutants.

Statistical interpretation of medical data of patients with alcohol abuse

Abstract An attempt is made to assess a set of biochemical, kinetic and anthropometric data for patients suffering from alcohol abuse (alcoholics) and healthy patients (non-alcoholics). The main goal is to identify the data set structure, finding groups of similarity among the clinical parameters or among the patients. Multivariate statistical methods (cluster analysis and principal components analysis) were used to assess the data collection. Several significant patterns of related parameters were found to be representative of the role of the liver function, kinetic and anthropometric indicators (conditionally named “liver function factor”, “ethanol metabolism factor”, “body weight factor”, and “acetaldehyde metabolic factor”). An effort is made to connect the role of kinetic parameters for acetaldehyde metabolism with biochemical, ethanol kinetic and anthropometric data in parallel.

Pharmacokinetics and pharmacodynamics – is there anything new?

Pharmacokinetics and pharmacodynamics – is there anything new?