Homogeneous Kinetics Research Articles

Single-Molecule Imaging of an in Vitro-Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics

Many studies of RNA folding and catalysis have revealed conformational heterogeneity, metastable folding intermediates, and long-lived states with distinct catalytic activities. We have developed a single-molecule imaging approach for investigating the functional heterogeneity of in vitro-evolved RNA aptamers. Monitoring the association of fluorescently labeled ligands with individual RNA aptamer molecules has allowed us to record binding events over the course of multiple days, thus providing sufficient statistics to quantitatively define the kinetic properties at the single-molecule level. The ligand binding kinetics of the highly optimized RNA aptamer studied here displays a remarkable degree of uniformity and lack of memory. Such homogeneous behavior is quite different from the heterogeneity seen in previous single-molecule studies of naturally derived RNA and protein enzymes. The single-molecule methods we describe may be of use in analyzing the distribution of functional molecules in heterogeneous evolving populations or even in unselected samples of random sequences.

Homogenizing a Nickel-Based Superalloy: Thermodynamic and Kinetic Simulation and Experimental Results

If the chemical inhomogeneity profile is known a priori, kinetic modeling software such as diffusion-controlled transformations (DICTRA) can be used to model the homogenization kinetics of an alloy. In this study, the Scheil module within the Thermo-Calc software was used to predict the as-cast segregation present within the Ni-based superalloy Nimonic 105. The segregation profiles were read into DICTRA to refine the homogenization heat treatment of this alloy. The thermodynamic and kinetic modeling of the computationally predicted heat treatment and microstructure, and subsequent experimental verification on a real casting of Nimonic 105, are presented.

Hetero-/homogeneous combustion of hydrogen/air mixtures over platinum at pressures up to 10 bar

The hetero-/homogeneous combustion of fuel-lean hydrogen/air premixtures over platinum was investigated experimentally and numerically in the pressure range 1 bar ⩽ p ⩽ 10 bar. Experiments were carried out in an optically accessible channel-flow catalytic reactor and included planar laser induced fluorescence (LIF) of the OH radical for the assessment of homogeneous (gas-phase) ignition, and 1-D Raman measurements of major gas-phase species concentrations for the evaluation of the heterogeneous (catalytic) processes. Simulations were performed with a full-elliptic 2-D model that included detailed heterogeneous and homogeneous chemical reaction schemes. The predictions reproduced the measured catalytic hydrogen consumption, the onset of homogeneous ignition at pressures of up to 3 bar and the diminishing gas-phase combustion at p ⩾ 4 bar. The suppression of gaseous combustion at elevated pressures bears the combined effects of the intrinsic homogeneous hydrogen kinetics and of the hetero/homogeneous chemistry coupling via the catalytically produced water over the gaseous induction zone. Transport effects, associated with the large diffusivity of hydrogen, have a smaller impact on the limiting pressure above which gaseous combustion is suppressed. It is shown that for practical reactor geometrical confinements, homogeneous combustion is still largely suppressed at p ⩾ 4 bar even for inlet and wall temperatures as high as 723 and 1250 K, respectively. The lack of appreciable gaseous combustion at elevated pressures is of concern for the reactor thermal management since homogeneous combustion moderates the superadiabatic surface temperatures attained during the heterogeneous combustion of hydrogen.

Parallels between multiple population-period transient spectroscopy and multidimensional coherence spectroscopies

We have recently shown that homogeneous and heterogeneous kinetics can be distinguished by experiments that compare the evolution of the population of a state over two time intervals [E. van Veldhoven et al., ChemPhysChem 8, 1761 (2007)]. This paper elaborates on the analogy between these multiple population-period transient spectroscopy (MUPPETS) experiments and more familiar spectroscopies based on the evolution of coherences. Using a modified inverse-Laplace transform, a standard kinetics decay is re-expressed as a "rate spectrum." A nonexponential decay creates a linewidth in this spectrum. Mechanisms for line broadening in rate spectra are compared to those for line broadening in frequency-domain spectra. Homogeneous and heterogeneous kinetics are defined precisely and are shown to be the counterparts of homogeneous and inhomogeneous line broadenings in frequency-domain spectra. Homogeneous line broadening mechanisms are further divided into equilibrium and nonequilibrium mechanisms, with equilibrium mechanisms more prevalent in frequency spectra and nonequilibrium mechanisms more prevalent in rate spectra. Spectral representations of two-dimensional MUPPETS experiments are developed that are equivalent to two-dimensional coherence spectroscopies. In particular, spectra equivalent to hole-burning and to correlation spectra are defined. Frequency-domain spectra are often modeled as an inhomogeneous distribution of identical homogeneous line shapes. A parallel homogeneous-heterogeneous model for kinetics is defined. Within this model, MUPPETS has sufficient information to completely separate the homogeneous and heterogeneous contributions to a nonexponential decay, even when the homogeneous contribution is nonexponential.

Investigation of Mediated Oxidation of Ascorbic Acid by Ferrocenemethanol Using Large-Amplitude Fourier Transformed ac Voltammetry under Quasi-Reversible Electron-Transfer Conditions at an Indium Tin Oxide Electrode

The ability of the technique of large-amplitude Fourier transformed (FT) ac voltammetry to facilitate the quantitative evaluation of electrode processes involving electron transfer and catalytically coupled chemical reactions has been evaluated. Predictions derived on the basis of detailed simulations imply that the rate of electron transfer is crucial, as confirmed by studies on the ferrocenemethanol (FcMeOH)-mediated electrocatalytic oxidation of ascorbic acid. Thus, at glassy carbon, gold, and boron-doped diamond electrodes, the introduction of the coupled electrocatalytic reaction, while producing significantly enhanced dc currents, does not affect the ac harmonics. This outcome is as expected if the FcMeOH (0/+) process remains fully reversible in the presence of ascorbic acid. In contrast, the ac harmonic components available from FT-ac voltammetry are predicted to be highly sensitive to the homogeneous kinetics when an electrocatalytic reaction is coupled to a quasi-reversible electron-transfer process. The required quasi-reversible scenario is available at an indium tin oxide electrode. Consequently, reversible potential, heterogeneous charge-transfer rate constant, and charge-transfer coefficient values of 0.19 V vs Ag/AgCl, 0.006 cm s (-1) and 0.55, respectively, along with a second-order homogeneous chemical rate constant of 2500 M (-1) s (-1) for the rate-determining step in the catalytic reaction were determined by comparison of simulated responses and experimental voltammograms derived from the dc and first to fourth ac harmonic components generated at an indium tin oxide electrode. The theoretical concepts derived for large-amplitude FT ac voltammetry are believed to be applicable to a wide range of important solution-based mediated electrocatalytic reactions.

Autoignition of Hydrogen and Air Inside a Continuous Flow Reactor With Application to Lean Premixed Combustion

With the need to reduce carbon emissions such as CO2, hydrogen is being examined as potential “clean” fuel for the future. One potential strategy is lean premixed combustion, where the fuel and air are allowed to mix upstream before entering the combustor, which has been proven to curb NOx formation in natural gas fired engines. However, premixing hydrogen and air may increase the risk of autoignition before the combustor, resulting in serious engine damage. A flow reactor was set up to test the ignition delay time of hydrogen and air at temperatures relevant to gas turbine engine operations to determine maximum possible mixing times. The results were then compared to past experimental work and current computer simulations. The current study observed that ignition is very sensitive to the initial conditions. The ignition delay times follow the same general trend as seen in previous flow reactor studies: ignition within hundreds of milliseconds and relatively low activation energy. An experimentally derived correlation by Peschke and Spadaccini (1985, “Determination of Autoignition and Flame Speed Characteristics of Coal Gases Having Medium Heating Values,” Research Project No. 2357-1, Report No. AP-4291) appears to best predict the observed ignition delay times. Homogenous gas phase kinetics simulations do not appear to describe ignition well in these intermediate temperatures. Therefore, at the moment, only the current empirical correlations should be used in predicting ignition delay at engine conditions for use in the design of gas turbine premixers. Additionally, fairly large safety factors should still be considered for any design to reduce any chance of autoignition within the premixer.

Electron Transfer to Sulfides and Disulfides: Substituent Effects, Intrinsic Barriers, and Relationship between Heterogeneous and Homogeneous Electron Transfer Kinetics

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Characterization of the degree of polymerization of xylooligomers produced by flowthrough hydrolysis of pure xylan and corn stover with water

Mechanisms that control xylan removal during pretreatment of lignocellulosic biomass are not well understood. For example, although hemicellulose hydrolysis is virtually always assumed to follow first-order homogeneous kinetics, the increase in xylan removal with flow rate for flowthrough pretreatment systems is inconsistent with the predictions for such models, and better information is needed to understand the causes of such discrepancies. Thus, new methods were developed to follow the fate of xylooligomers with degrees of polymerization of up to 30, a range not possible before, for water-only flowthrough pretreatment of oat spelt xylan and corn stover for temperatures of 200–240 °C. Material balances based on the oligomer release profiles produced by batch and flowthrough operations could be closed, suggesting the methods were quite accurate. However, the results also showed that increasing the flow rate from 0 to 2 and then 25 mL/min affected the size distribution of the xylan oligomers (DP < 30) released from corn stover but not from oat spelt xylan and also increased overall hemicellulose sugar solubilization. One explanation for these difference is that lignin and lignin–xylan compounds in particular play an important role in the hydrolysis of lignocellulosic biomass.

Electron Transfer to Sulfides and Disulfides: Intrinsic Barriers and Relationship between Heterogeneous and Homogeneous Electron‐Transfer Kinetics

The electron-acceptor properties of series of related sulfides and disulfides were investigated in N,N-dimethylformamide with homogeneous (redox catalysis) and/or heterogeneous (cyclic voltammetry and convolution analysis) electrochemical techniques. The electron-transfer rate constants were determined as a function of the reaction free energy and the corresponding intrinsic barriers were determined. The dependence of relevant thermodynamic and kinetic parameters on substituents was assessed. The kinetic data were also analyzed in relation to corresponding data pertaining to reduction of diaryl disulfides. All investigated reductions take place by stepwise dissociative electron transfer (DET) which causes cleavage of the C(alkyl)--S or S--S bond. A generalized picture of how the intrinsic electron-transfer barrier depends on molecular features, ring substituents, and the presence of spacers between the frangible bond and aromatic groups was established. The reduction mechanism was found to undergo a progressive (and now predictable) transition between common stepwise DET and DET proceeding through formation of loose radical anions. The intrinsic barriers were compared with available results for ET to several classes of dissociative- and nondissociative-type acceptors, and this led to verification that the heterogeneous and the homogeneous data correlate as predicted by the Hush theory.

The Role of Homogeneous Chemical Kinetics in the Anomalous Codeposition of Binary Alloys

The role of finite-rate homogeneous chemistry during the electrodeposition of binary alloys is analyzed using a detailed mathematical model. The model accounts for solute reactions and transport within the aqueous boundary layer as well as multistep reactions on the electrode surface. Calculations are carried out for nickel-iron deposition from a sulfate bath, using a previously proposed surface-reaction mechanism that accounts for the observed anomalous codeposition. The common assumption of homogeneous chemical equilibrium is found to produce only modest errors in the computed deposition rates, but it distorts the relative importance of hydrolyzed metal ions. In contrast with previous literature claims, the present calculations show that these ions tend to have a greater role than is predicted by assuming equilibrium. The model also suggests that the precipitation of solid metal hydroxides may be slow, i.e., that substantial supersaturation of the plating solution may occur.

Soluble nanopolymer-based phosphoproteomics for studying protein phosphatase

Protein phosphorylation is a vital reversible post-translational modification that regulates protein–protein interactions, enzymatic activity, subcellular localization, complex formation and protein stability. The emerging field of mass spectrometry-based proteomics allows us to investigate phosphorylation and dephosphorylation on a global scale. In this review, we describe a new strategy based on soluble nanopolymers that have been used to selectively isolate phosphopeptides for mass spectrometric analysis. Functionalized soluble nanopolymers provide a homogeneous environment and linear reaction kinetics for chemical derivatization to isolate phosphopeptides with high specificity. Combined with phosphatase inhibitors and stable isotopic labeling, the approach has the capability of quantitatively measuring phosphorylation and dephosphorylation on individual sites. We provide experimental details for the approach and describe some other complementary techniques that can be used.

Statistical Thermodynamic Description of Homogeneous Dispersive Kinetics

A statistical thermodynamic interpretation of homogeneous dispersive kinetics (which assumes the existence of a pseudo-equilibrium between a distribution of reagent states and a single activated state, which together define the rate-determining step), coupled with a previous "quantum kinetic" description for this same type of system (Skrdla, P. J. J. Phys. Chem. A 2006, 110, 11494), is found to provide new insights into the kinetics of these conversions. In particular, the change in the (apparent) activation energy with conversion time is shown to be a function of the entropy change associated with the ensemble of reagent molecules as they traverse the activation energy barrier. Using these two "orthogonal" stochastic interpretations of dispersive kinetics, a fundamental physical description of the rate parameter beta in the author's model is obtained.

Modelling of microsegregation and homogenization of 6061 extrudable Al-alloy

A simulation of the evolution of the as-cast microstructure during the homogenization heat treatment of A6061 aluminum alloy is presented. The microstructure is dendritic with phase and solute segregation. The alloy microsegregation, which results after casting, was calculated with the Scheil equation by employing computational alloy thermodynamics. The microstructure evolution during homogenization was simulated by employing computational kinetics for the solution of the multicomponent diffusion equations. The composition profiles of the alloying elements and the volume fraction of the secondary phases were calculated as a function of homogenization time. The simulation results were validated qualitatively by comparison with metallographic examinations. During homogenization, the Mg2Si dissolution and the transformations of the Fe-intermetallics were confirmed. It is concluded that the model reproduces the homogenization kinetics reasonably and it is capable for the prediction of the homogenization heat treatment completion times. © 2007 Elsevier B.V. All rights reserved.

Phase-field modeling of coring structure evolution in Pu–Ga alloys

During casting of Pu–Ga alloys, the huge difference in Ga diffusivity in ε (body centered cubic) and δ (face centered cubic) phases results in the formation of coring structures which consist of Ga-rich cores with Ga-poor edges. The elastic interaction among different oriented δ grains, matrix ε and diffusive Ga atoms may lead to a directional diffusion and δ grain growth. A phase-field model for modeling the coring structure evolution and Ga homogenization kinetics in three dimensions is developed. The effects of diffusivity inhomogeneity, internal stresses and cooling rate on the coring structure evolution are studied.

Hydrothermal Dechlorination of a Reclaimed Oil in a Continuous Packed-Bed Reactor

The liquid-phase hydrothermal dechlorination of a reclaimed oil (Cl content = 2280 ppm) derived from waste lubricating oils was investigated at 275–325°C by using a continuous packed-bed reactor. The reaction proceeded readily in aqueous NaOH solutions, especially at higher NaOH concentrations and at higher reaction temperatures. Thus, the chlorine content in the oil decreased to 57 ppm at 325°C when 0.4 mol/L NaOH was used at the weight feed ratio of 1.3 and at the residence time of 8.0 min. However, the reaction did not proceed further even when the concentrated NaOH solutions of more than 0.4 mol/L were used. The rate of the dechlorination could be well described in terms of a homogeneous SN2-type reaction kinetics involving the participation of water molecules and OH– ions. In contrast to the contribution of water molecules to the reaction, that of OH– ions increased at higher NaOH concentrations and at higher reaction temperatures.

Coulometry on the Voltammetric Timescale: Microdisk Potential‐Step Chronoamperometry in Aprotic Solvents Reliably Measures the Number of Electrons Transferred in an Electrode Process Simultaneously with the Diffusion Coefficients of the Electroactive Species

AbstractMicrodisk, single potential‐step chronoamperometry, is applied to a range of organic substrates in the aprotic solvents tetrahydrofuran, propylene carbonate, acetonitrile and the room temperature ionic liquid [C4dmim][N(Tf)2]. Fitting of the chronoamperometric transients was achieved using the Shoup and Szabo method [3]. Accurate values for the diffusion coefficients, D, and the number of electron(s) transferred, n, in the electrode process have been simultaneously and consistently obtained. This method is shown to be generally applicable and reliable for the determination of the number of electrons transferred in faradaic processes uncomplicated by relatively slow coupled homogeneous kinetics. Since the experiment is conducted essentially on typical voltammetric timescales it can be commended as a complementary technique for classical coulometry which is only possible on much longer timescales. The chronoamperometric method is therefore likely to be of greater relevance to the interpretation of voltammetric data.

Nanoparticle Assembly of Ordered Multicomponent Mesostructured Metal Oxides via a Versatile Sol−Gel Process

Multicomponent metal oxides have attracted attention for their potential use in electronic, (photo)catalytic, photovoltaic, and energy storage applications. The ability to simultaneously control the nanoscale structure and composition of such materials using simple and inexpensive routes is important for that potential to be realized. Here we introduce a simple and widely applicable methodology for the synthesis of multicomponent mesostructured metal oxides (MMMOs) from the combination of inexpensive and commercially available polymers with metal alkoxides solubilized in a sol−gel solution consisting of acetic acid, hydrochloric acid, and ethanol (AcHE). MMMOs obtained utilizing the AcHE system have tunable pore structures, a high degree homogeneity, and in certain cases thermal stability above 1000 °C. The ability to easily process these diverse MMMOs in the form of thin films, free-standing membranes, and monoliths provides distinct advantages over previously reported MMO synthesis proceduresespecially when large quantities of material are required, for instance, in heterogeneous catalyst development. Most importantly, we demonstrate that the controlled binding of reactive metal ions with acetic acid in the AcHE solution yields nanometer-sized particles for a diverse collection of inorganic materials with homogeneous condensation kinetics. This allows for the simple synthesis of complicated and novel MMMO compositions (e.g., rare earth and mixed transition metal oxides) via cooperative assembly with amphiphilic block copolymers. The development of such simple and widely applicable methodologies are extremely important for the practical implementation of porous metal oxides.

Kinetic behavior of the reaction between hydroxyl radical and the SV40 minichromosome

Aqueous solutions containing the minichromosomal form of the virus SV40 and the radical scavenger DMSO were subjected to γ-irradiation, and the resulting formation of single-strand breaks (SSB) was quantified. Under the irradiation conditions, most SSBs were produced as a consequence of hydroxyl radical ( OH) reactions. By controlling the competition between DMSO and the viral DNA substrate for OH, we are able to estimate the rate coefficient for the reaction of OH with the SV40 minichromosome. The results cannot be described adequately by homogeneous competition kinetics, but it is possible to describe the rate coefficient for the reaction as a function of the scavenging capacity of the solution. The experimentally determined rate coefficient lies in the range 1×10 9–2×10 9 L mol −1 s −1 at 10 7 s −1, and increases with increasing scavenging capacity.

The enhancement of xylose monomer and xylotriose degradation by inorganic salts in aqueous solutions at 180 °C

The inorganic salts KCl, NaCl, CaCl 2, MgCl 2, and FeCl 3, and especially the latter, significantly increased xylose monomer and xylotriose degradation in water heated to 180 °C with unaccountable losses of xylose amounting to as high as 65% and 78% for xylose and xylotriose, respectively, after 20 min incubation with 0.8% FeCl 3. Furthermore, losses of both xylose and xylotriose were well described by first order homogeneous kinetics, and the rate constants for xylose and xylotriose disappearance increased 6- and 49-fold, respectively, when treated with 0.8% FeCl 3 solution compared to treatment with just pressurized hot water at the same temperature. Although the addition of these inorganic salts produced a significant drop in pH, the degradation rates with salts were much faster than could be accounted for by a pH change. For example, the rate constants for the disappearance of xylose and xylotriose with 0.8% FeCl 3 were 3-fold and 7-fold greater, respectively, than for treatment with very dilute sulfuric acid at the same pH. In addition, xylose losses were greater than could be accounted for by just furfural production, suggesting that other degradation products were also formed, and xylose losses to unidentified compounds increased significantly with the addition of FeCl 3. The unidentified compounds could be formed through aqueous furfural resinification and condensation reactions that are accelerated by FeCl 3, but the actual mechanisms are still not clear.

Scale-up of an electrochemical reactor for treatment of industrial wastewater with an electrochemically generated redox mediator

This paper presents the results of a study on the scale-up, from a batch to a continuous flow unit, of an electrochemical reactor applied for the treatment of textile wastewater. Decolourisation of the wastewater bearing a reactive dye Red Procion H-EXGL proceeded via indirect electro-oxidation, mediated by “active chlorine”. The kinetics of decolourisation in a single-cell reactor under different operating conditions were second order, with the highest apparent rate constant (k = 0.523 l mol−1 s−1) achieved at 40 °C. A low Hatta number (Ha = 0.03) indicated that the reaction occurred totally in the bulk solution, hence homogeneous reaction kinetics were used successively to scale-up a continuous flow electrochemical unit: a once-through filter-press reactor. Its hydrodynamic characteristics were defined by the residence time distribution (E(t)) function using a pulse injection method. The decolourisation efficiency experimentally determined in a continuous flow reactor was further compared with that predicted on the basis of the knowledge of the E(t) of the reactor and the homogeneous phase kinetic expression, obtained from the batch study and corrected for the geometric parameters of the reactors. A complete segregation of the fluid inside the flow reactor was assumed. For different applied flow rates, the experimentally defined conversion of the dye was close to the calculated value.