Reaction Rate Theory Research Articles

Nucleation Rate Theory for Coordination Number: Elucidating Water-Mediated Formation of a Zigzag Na2SO4 Morphology.

Predicting and controlling nanostructure formation during nucleation can pave the way to synthesizing novel energy materials via crystallization. However, such control over nucleation and crystallization remains challenging due to an inadequate understanding of critical factors that govern evolving atomistic structures and dynamics. Herein, we utilize coordination number as a reaction coordinate and rate theory to investigate how sodium sulfate, commonly known as a phase-change energy material, nucleates in a supersaturated aqueous solution. In conjunction with ab initio and force field-based molecular dynamics simulation, the rate theoretical analysis reveals that sodium sulfate from an initially dissolved metastable state transits to a heterogeneous mixture of prenucleated clusters and finally to a large cylindrical zigzag morphology. Measurements of Raman spectra and their ab initio modeling confirm that this nucleated morphology contains a few waters for every sulfate. Rate processes such as solvent exchange and desolvation exhibit high sensitivity to the evolving prenucleation/nucleation structures, providing a means to distinguish between critical nucleation precursors. Desolvation and forming the first-shell interionic coordination structure via monomer-by-monomer addition around sulfates are found to explain the formation of large nuclei. Thus, a detailed understanding of the step-by-step structure formation across scales has been achieved. This can be leveraged to predict nucleation-related structures and dynamics and potentially control the synthesis of novel phase-change materials for energy applications.

Proton-transfer spectroscopy beyond the normal-mode scenario.

A stochastic theory is developed to predict the spectral signature of proton-transfer processes and is applied to infrared spectra computed from ab initio molecular-dynamics simulations of a single H5O2 + cation. By constraining the oxygen atoms to a fixed distance, this system serves as a tunable model for general proton-transfer processes with variable barrier height. Three spectral contributions at distinct frequencies are identified and analytically predicted: the quasi-harmonic motion around the most probable configuration, amenable to normal-mode analysis, the contribution due to transfer paths when the proton moves over the barrier, and a shoulder for low frequencies stemming from the stochastic transfer-waiting-time distribution; the latter two contributions are not captured by normal-mode analysis but exclusively reported on the proton-transfer kinetics. In accordance with reaction rate theory, the transfer-waiting-contribution frequency depends inversely exponentially on the barrier height, whereas the transfer-path-contribution frequency is rather insensitive to the barrier height.

In-situ microstructure observation of oxidized SiC layer in surrogate TRISO fuel particles under krypton ion irradiation

In accidental scenarios of high temperature gas-cooled reactors, both oxidation of and irradiation to the SiC layer in tri-structural-isotropic (TRISO) fuel particles can change the microstructure and integrity of the fuel elements. In the present study, microstructure and defect evolution in the oxidized SiC layer of surrogate TRISO fuel particles under 1.2 MeV krypton ion irradiation was observed by in-situ transmission electron microscopy. The SiC layers oxidized in water vapor at 1200 °C were irradiated azt room temperature and 800 °C and at damage levels of 0.28–11.2 dpa, respectively. SiC and SiO2 were found to still be in their crystal structures at the damage level of 11.2 dpa at 800 °C, while SiC was observed to have been amorphized at only 0.56 dpa irradiation at room temperature. The defect number density at 800 °C was an order of magnitude lower than that in the sample irradiated at room temperature. Also, crystalline SiO2 had higher radiation resistance compared to SiC. A defect reaction rate theory was utilized to understand the fundamental defect evolution process and irradiation resistance difference.

Impact of the size and degree of branching of alkanes on the rate rules approach: The case of isomerizations

The accurate and high-throughput generation of kinetic data for combustion detailed chemical kinetic models remains a challenge given the large size of these models. For large organic molecules, the majority of kinetic data of the kinetic models are estimated using quantitative structure activity relationships within reaction classes and reaction rate rules approaches. In this work, we question the limits of the rate rule approach for the isomerization reaction classes, using electronic structure calculations and reaction rate theories. Systematic calculations were performed to investigate the effect of the size and the degree of branching of alkyl radicals on the rate coefficients and their consequences on the rate rule approach. Our computed kinetic data show that when the size of alkyl group is increased, the rate coefficients remains close to each other. This allows the use of methyl as representative models of larger alkyl groups to investigate the influence of increasing the degree of branching. The computed rate coefficients for 1,3- and 1,4-H-atom shifts show that the increase of the branching level, with spectator methyl groups in the transition state cyclic structure can strongly increase the rate coefficients, up to several orders of magnitude. Consequently, a single rate rule is not feasible for any degree of branching of a reaction belonging to the same isomerization reaction class. As variation in rate coefficients are important, this would lead to an explosion of the number rate rules as a function of branching in 5-, 6-, and 7-membered cyclic transition states. A new approach is demonstrated and proposed where model transition states are tabulated, and methyl groups are assumed as alkyl groups and all combinations of substitutions in the model TSs, for a given reaction class, are included in a table with associated ab initio rate coefficients. The automation of the construction of such tables is possible and could be an interesting high-throughput / high-accuracy alternative to on-the-fly ab initio calculations of kinetic parameters.

Theoretical Study of the Thermal Decomposition of Urea Derivatives.

An extensive theoretical study of the thermal decomposition of alkyl- and phenylureas, which are widely used in the pesticides, pharmaceuticals, and materials industries, has been carried out using electronic structure calculations and reaction rate theories. Enthalpies of formation and bond dissociation energies (BDE) of 11 urea derivatives have been calculated using different levels of theory (CBS-QB3, CCSD(T)/CBS//M06-2X/6-311++G(3df,2pd), and CBS-QM062X) according to the size of the system. Potential energy surfaces for the unimolecular decomposition pathways of these urea derivatives were also systematically computed for the first time. Several pericyclic reactions can be envisaged, as a function of the size and the nature of the N substituents, and all of these pathways were explored. Our calculations show that these compounds are solely decomposed by four-center pericyclic reactions, yielding substituted isocyanates and amines, and that initial bond fissions are not competitive. Based on the set of urea derivatives studied, a new reaction rate rule for their thermal decomposition was defined and involves the nature of the transferred H atom (primary or secondary/alkyl or benzyl) and the nature of the N-atom acceptor (primary, secondary, or tertiary). This new reaction rate rule allows us to determine the product branching ratios in the thermal decomposition of a given urea derivative and its total rate of decomposition. Applications on urea derivatives used in the chemical industry are presented and illustrate the usefulness of this new rate rule that allows to predict the previously unknown thermal decomposition kinetics of a large number of these compounds.

Cosh gradient systems and tilting

We review a class of gradient systems with dissipation potentials of hyperbolic-cosine type. We show how such dissipation potentials emerge in large deviations of jump processes, multi-scale limits of diffusion processes, and more. We show how the exponential nature of the cosh derives from the exponential scaling of large deviations and arises implicitly in cell problems in multi-scale limits.We discuss in-depth the role of tilting of gradient systems. Certain classes of gradient systems are tilt-independent, which means that changing the driving functional does not lead to changes of the dissipation potential. Such tilt-independence separates the driving functional from the dissipation potential, guarantees a clear modelling interpretation, and gives rise to strong notions of gradient-system convergence.We show that although in general many gradient systems are tilt-independent, certain cosh-type systems are not. We also show that this is inevitable, by studying in detail the classical example of the Kramers high-activation-energy limit, in which a diffusion converges to a jump process and the Wasserstein gradient system converges to a cosh-type system. We show and explain how the tilt-independence of the pre-limit system is lost in the limit system. This same lack of independence can be recognized in classical theories of chemical reaction rates in the chemical-engineering literature.We illustrate a similar lack of tilt-independence in a discrete setting. For a class of ‘two-terminal’ fast subnetworks, we give a complete characterization of the dependence on the tilting, which strongly resembles the classical theory of equivalent electrical networks.

Theoretical Study on the Kinetics of the Rubisco Carboxylase Reaction by a Model Based on Quantum Chemistry and Absolute Reaction Rate Theory.

The rate of the Rubisco carboxylase reaction is evaluated by statistical mechanics and hybrid density functional theory (DFT). The Rubisco molecular model given by Kannappan et al. was modified and used in the present calculation. The activation energies of CO2 addition reaction, H2O addition reaction, C2–C3 bond scission, and C2 protonation are estimated. We calculated the turnover number (TON) for each of the four reaction steps based on a revised absolute reaction rate theory, which became applicable to soft matter reactions. The molecular parameters used in TON calculations were obtained by DFT calculations. The TON of the total Rubisco reaction was finally evaluated using rate equations. The calculation in a vacuum gave the total TON to be around 5 × 10–5, which was much lower than the experimental value. The DFT calculation in water solvent gave the total TON to be around 0.1, which agreed reasonably well with experimentally reported values (∼2.71). The rate-limiting process was the scission reaction. The present calculation showed that both the phosphate groups in the substrate accelerate each reaction step. The present calculation showed that a more comprehensive molecular model including enolization and quantum chemical methods is necessary to make a more precise reaction model including the irreversibility of some reactions.

A general theory for temperature dependence in biology

At present, there is no simple, first principles-based, and general model for quantitatively describing the full range of observed biological temperature responses. Here we derive a general theory for temperature dependence in biology based on Eyring-Evans-Polanyi's theory for chemical reaction rates. Assuming only that the conformational entropy of molecules changes with temperature, we derive a theory for the temperature dependence of enzyme reaction rates which takes the form of an exponential function modified by a power law and that describes the characteristic asymmetric curved temperature response. Based on a few additional principles, our model can be used to predict the temperature response above the enzyme level, thus spanning quantum to classical scales. Our theory provides an analytical description for the shape of temperature response curves and demonstrates its generality by showing the convergence of all temperature dependence responses onto universal relationships-a universal data collapse-under appropriate normalization and by identifying a general optimal temperature, around 25 ∘C, characterizing all temperature response curves. The model provides a good fit to empirical data for a wide variety of biological rates, times, and steady-state quantities, from molecular to ecological scales and across multiple taxonomic groups (from viruses to mammals). This theory provides a simple framework to understand and predict the impact of temperature on biological quantities based on the first principles of thermodynamics, bridging quantum to classical scales.

Nonequilibrium reaction rate theory: Formulation and implementation within the hierarchical equations of motion approach.

The study of chemical reactions in environments under nonequilibrium conditions has been of interest recently in a variety of contexts, including current-induced reactions in molecular junctions and scanning tunneling microscopy experiments. In this work, we outline a fully quantum mechanical, numerically exact approach to describe chemical reaction rates in such nonequilibrium situations. The approach is based on an extension of the flux correlation function formalism to nonequilibrium conditions and uses a mixed real and imaginary time hierarchical equations of motion approach for the calculation of rate constants. As a specific example, we investigate current-induced intramolecular proton transfer reactions in a molecular junction for different applied bias voltages and molecule-lead coupling strengths.

Reaction between propionaldehyde and hydroxyperoxy radical in the atmosphere: A reaction route for the sink of propionaldehyde and the formation of formic acid

Understanding the chemical transformations of volatile organic compounds is particularly important for atmospheric modeling and elucidating their effects on atmospheric environment, where the key parameters are reaction mechanism and kinetics. Here, we report that the reaction mechanism and kinetics of propionaldehyde with hydroxyperoxy radical by using quantum chemical methods and reaction rate theory. In particular, we use our very recently developed dual-level strategy to obtain the high-pressure limit rate constants of the reaction of propionaldehyde (CH3CH2CHO) with hydroxyperoxy radical (HO2). We find that the enthalpy of activation at 0 K is only −1.86 kcal/mol in the CH3CH2CHO + HO2 reaction. The present results also uncover that the CH3CH2CHO + HO2 reaction depends on temperature and pressure and its high-pressure limit rate constant has negative temperature dependency with the value of 7.76 × 10−13 to 3.06 × 10−14 cm3 molecules−1 s −1 at 190–350 K. Moreover, the present findings also show that the reaction of propionaldehyde with hydroxyperoxy radical can make great contribution to the sink of propionaldehyde below 260 K and 1 atm when OH concentration is less than 8.4 × 104 molecules cm−3 at night and can not be ignored at 0–10 km altitude. We also find a potential route for the formation of formic acid by the reaction of propionaldehyde with hydroxyperoxy radical.

Thermodynamic stability of microheterogenic states in Fe – Mn – C melts

Possibility of existence of microheterogeneous states in Fe – Mn – C melts was analyzed carried out according to the concepts of chemical thermodynamics. Microheterogeneous state of a chemically inhomogeneous Fe – Mn – C melt was understood as presence of dispersed Fe – C particles in it, which are suspended in Mn – C environment and separated from it by interface. Hypothesis of microheterogeneous state of Fe – Mn – C melts is supported by numerous experimental data on their thermodynamic and physical properties. Identification of anomalies in temperature dependences of physical properties of Fe – Mn – C melts made it possible to determine temperature values above which the melt superheating treatment (MST) leads to destruction of microheterogeneity, i.e., the liquid – liquid structure transition (LLT) in the melt. LLT is understood by authors as a structural transition “microheterogeneous melt – homogeneous solution” and this is expressed in destruction of microheterogeneous state when the melt is heated to a temperature determined for each composition (MST). This paper describes a method for theoretical determination of temperature range where microheterogeneous state of the Fe – Mn – C melt is thermodynamically stable. Thermodynamic stability of dispersed Fe – C particles in the Mn – C medium was estimated according to the equations proposed by Kaptay for a regular solution. It was assumed that interface between the melt of dispersed Fe – C particles with sizes from 2 to 34 nm, distributed in the Mn – C dispersion medium and separated from it by an interface with increased carbon content. This result of the assessment is consistent with the data on size of the structural units of a viscous flow obtained earlier within framework of the theory of absolute reaction rates.

Implementation of an guided inquiry learning model in the reaction rate theory to improve the student creative thinking skills

This study aims to analyze the implementation of guided inquiry learning, student activities, students' creative thinking skills, and student responses after the guided inquiry model implementation on the reaction rate theory. The investigation uses a quantitative descriptive method with a one-group pretest-posttest design. The data collection method used the observation method, and the tests were tested using the normality test, Paired Sample T-Test, and n-gain. The subjects of this study were the eleventh-grade student at SMAN 7 Kediri, East Java, Indonesia. It shows that guided inquiry learning to improve creative thinking skills has been carried out well. Students use 16% of the time at meeting 1 and 15% at meeting 2 to practice fluency. 23% and 26% at meetings 1 and 2 to practice flexibility, and 11% of meeting time 1 and 8% of meeting 2 is used to practice elaboration. The students' creative thinking skills increased from before and after applying guided inquiry. There were 8 students categorized as quite creative and 24 others less creative before the learning was carried out. After learning, as many as 11 students were categorized as creative, and 21 others were very creative.

Quantum-Chemical Kinetic Study of the Unimolecular Decomposition Reactions of 1-Bromo-3-Chloropropane

The pressure and temperature dependence of the thermal decomposition of 1-bromo-3-chloropropane has been theoretically investigated. The reaction takes place majorly through the elimination of HBr. Molecular properties of 1-bromo-3-chloropropane and transition states were derived from MN15/6-311++G(3df,3pd) and G4 quantum-chemical calculations. The resulting rate constants obtained from the unimolecular reaction rate theory for the high- and low-pressure limits of reaction BrCH2CH2CH2Cl → CH2CHCH2Cl + HBr at 400-1000 K were k∞ = 6.1 × 1013 exp(-57.2 kcal mol-1/RT) s-1 and k0 = [BrCH2CH2CH2Cl] 1.45 × 10-1 (T/1000 K)-7.9 exp(-55.9 kcal mol-1/RT) cm3 molecule-1 s-1. A value of -26.3 ± 1.0 kcal mol-1 for the standard enthalpy of formation of 1-bromo-3-chloropropane at 298 K was derived.

Comment on "Microhydration of Biomolecules: Revealing the Native Structures by Cold Ion IR Spectroscopy".

This Viewpoint presents a re-examination of the conclusions of a study reported in The Journal of Physical Chemistry Letters (Saparbaev, et al. 2021, 12, 907) that compared the structure of microsolvated ions formed by electrospray ionization to those formed in the gas-phase via a previously published cryogenic ion trap approach. We conducted additional experiments that clearly show that most of the observed differences in the IR spectra can be accounted for by considering the different spectroscopic action schemes used to obtain them. In particular, the presence of the D2-tag induces shifts in some of the N-H and O-H peaks which need to be carefully considered before comparing spectra. Once these spectral effects are taken into account, we show that both clustering approaches yield similar cluster structures for the small GlyH+(H2O)n species. Using unimolecular reaction rate theory, we also show that for the small complexes considered here, only the gas-phase equilibrium distribution of conformers should be expected in both experimental approaches. In addition, the barrier heights necessary to kinetically trap high-energy conformers at 298 K is explored using a series of model polyalanine chains.

A constitutive framework for steady-state creep in coarse-grained zirconium alloys under irradiation

ABSTRACT A constitutive framework for steady-state creep in polycrystalline zirconium alloys under neutron irradiation is elaborated. The framework combines a two-scale description with internal variables. The structure of the local constitutive laws within individual grains follows from a thermodynamical formulation accounting for freely migrating defects nucleated by radiation and for deformation produced by dislocation glide and climb, while the structure of the overall constitutive relations for the polycrystalline aggregate follows from homogenisation. The resulting description is thermodynamically consistent and conforms to the generalised standard material model. A special class of constitutive laws is generated using convex dissipation potentials reproducing the mean-field reaction rate theory. The relations are nonlinear and reflect an inherent coupling between irradiation creep and growth; however, they admit partial linearisation even for moderate stress levels. Some implications for mechanistic creep models of common use are discussed.

Reaction Rate Theory-Based Mathematical Approximation for the Amount of Time it Takes For Cellular Respiration to Occur

Abstract The venerable process of cellular respiration is essential for cells to produce energy from glucose molecules, in order to carry out cellular work. The process is responsible for producing molecules of ATP, a molecule which is thermodynamically coupled with other biochemical and biophysical processes in order to provide energy for such processes to occur. While the process of cellular respiration is essential to biology, one cycle of the process occurs only in a matter of milliseconds, and so, it would be impractical to measure the time it takes for the process to occur through conventional means. Therefore, using concepts from reaction rate theory, particularly Marcus Theory of electron transfer, Michaelis-Menten kinetics for enzymatic catalysis, and the hard-sphere model of collision theory, I formulate and propose a mathematical approximation for the amount of time it takes for cellular respiration to occur. Through this heuristic approach, quantitatively knowing the amount of time it takes for one cycle of cellular respiration to occur could potentially have future applications in biological research.

Thermal decomposition mechanism and kinetics of perfluorooctanoic acid (PFOA) and other perfluorinated carboxylic acids: a theoretical study.

Perfluorinated carboxylic acids (PFCAs), particularly perfluorooctanoic acid (PFOA), are broadly used for chemical synthesis and as surfactants, but they pose a serious threat to humans and wildlife because of toxicity concerns, environmental stability, and tendency to bioaccumulate. PFCA waste is commercially treated in incinerators, however, their exact degradation mechanisms are still unknown. In the present work, we report the decomposition mechanism and kinetics of straight-chain PFCAs using quantum chemistry and reaction rate theory calculations. Degradation mechanisms and associated kinetic parameters are determined for the complete series of straight-chain PFCAs from perfluorononanoic acid (C8F17COOH, C9) to fluoroformic acid (FCOOH, C1). Our results show that PFCA decomposition follows an analogous mechanism to perfluorinated sulfonic acids, where HF elimination from the acid head group produces a three membered ring intermediate, in this case a perfluorinated α-lactone. These perfluorinated α-lactones are short-lived intermediates that readily degrade into perfluorinated acyl fluorides and CO, thus shortening the perfluorinated chain by one C atom. Because perfluorinated acyl fluorides are known to hydrolyse to PFCAs, repeated cycles of carboxylic acid decomposition followed by acyl fluoride hydrolysis provides a mechanism for the complete mineralization of PFCAs to HF, CO, CO2, COF2, and CF2 during thermal decomposition in the presence of water vapor. These results provide a theoretical basis for future detailed chemical kinetic studies of incineration reactors and will assist in their design and optimisation so as to more efficiently decompose PFCAs and related waste.

Robust Simulations of Nanoscale Phase Change Memory: Dynamics and Retention.

A robust simulation framework was developed for nanoscale phase change memory (PCM) cells. Starting from the reaction rate theory, the dynamic nucleation was simulated to capture the evolution of the cluster population. To accommodate the non-uniform critical sizes of nuclei due to the non-isothermal conditions during PCM cell programming, an improved crystallization model was proposed that goes beyond the classical nucleation and growth model. With the above, the incubation period in which the cluster distributions reached their equilibrium was captured beyond the capability of simulations with a steady-state nucleation rate. The implications of the developed simulation method are discussed regarding PCM fast SET programming and retention. This work provides the possibility for further improvement of PCM and integration with CMOS technology.

금-은 폐광산 광미의 수은 열적감량 특성

This study conducted thermal desorption experiments for the remediation of mercury-contaminated soils with a mercury concentration of 26.39 mg-Hg/kg from gold-silver mine tailings. The thermal desorption experiments were performed in a muffle furnace at a pressure of 1 atm in the temperature range from 300 to 700℃. In addition, indirect thermal treatment experiments were conducted by adding 20 g of homogeneous samples into the crucible for 1 to 30 min. The mercury concentrations of the residual samples were analyzed using EPA method 7471a. Based on the results of the analysis of mercury concentration in the thermal treatment, the thermal desorption characteristics of mercury contaminated tailings were analyzed using reaction rate theory. The reaction rate constants (k) were calculated from 1.3 × 10^-3 to 1.9 × 10^-2 sec^-1 with a change in the temperature conditions. The results revealed that k increased with increasing temperature. In addition, the calculated pre-exponential factor and activation energy were 0.118 sec^-1 and 2.76 kcal/gmol, respectively. Furthermore, the thermal treatment conditions required to achieve the 4 mg-Hg/kg criteria for Hg content were approximately 1,451 s at 300℃ and 992 s at 400℃.

Dynamical Models of Chemical Exchange in Nuclear Magnetic Resonance Spectroscopy.

Chemical exchange line-broadening is an important phenomenon in nuclear magnetic resonance (NMR) spectroscopy, in which a nuclear spin experiences more than one magnetic environment as a result of chemical or conformational changes of a molecule. The dynamic process of chemical exchange strongly affects the sensitivity and resolution of NMR experiments, and increasingly provides a powerful probe of the inter-conversion between chemical and conformational states of proteins, nucleic acids, and other biological macromolecules. A simple and often used theoretical description of chemical exchange in NMR spectroscopy is based on an idealized two-state jump model (the random-phase or telegraph signal). However, chemical exchange can also be represented as a barrier-crossing event that can be modeled using chemical reaction rate theory. The time scale of crossing is determined by the barrier height, the temperature, and the dissipation modeled as collisional or frictional damping. This tutorial explores the connection between the NMR theory of chemical exchange line-broadening and strong-collision models for chemical kinetics in statistical mechanics. Theoretical modeling and numerical simulation are used to map the rate of barrier-crossing dynamics of a particle on a potential energy surface to the chemical exchange relaxation rate constant. By developing explicit models for the exchange dynamics, the tutorial aims to elucidate the underlying dynamical processes that give rise to the rich phenomenology of chemical exchange observed in NMR spectroscopy. Software for generating and analyzing the numerical simulations is provided in the form of Python and Fortran source codes.