First-principles Kinetic Model Research Articles

Kinetic Model of Acid Gas Induced Defect Propagation in Zeolitic Imidazolate Frameworks

Understanding the degradation of nanoporous materials under exposure to common acid gas contaminants (e.g., SO2, CO2, NO2, and H2S) is essential to elongate their lifetime and thus enable their practical applications in separations and catalysis. Previous theoretical investigations have focused on the formation of isolated point defects, which are insufficient to provide direct insights into the long-term evolution of the bulk properties of materials such as zeolitic imidazolate frameworks (ZIFs) under sustained acid gas exposure. To bridge this divide in both length and time scales, we developed a first-principles lattice-based kinetic model to simulate the defect propagation and bulk material breakdown in ZIFs. This model closely reproduces the experimentally measured macroscopic evolution of the time-dependent bulk materials proprieties and also yields important new insights regarding the autocatalytic nature of ZIF degradation and the spatial distribution of defects. Our results suggest new experimental directions to identify nascent defect clusters in degraded ZIFs and avenues to mitigate degradation under challenging conditions of acid gas exposure.

Iron cycle tuned by thiosulfate in Fenton reactions: Kinetic modelling and mechanisms

The widespread application of Fenton reaction have been limited by the rapid precipitation of Fe(III) and the slow Fe(III) reduction. This work presents a strategy to address these concerns by adding metal-free reducing agent thiosulfate (S2O32−). Compared to the classical Fenton reaction at pH 3.0, S2O32− significantly accelerated the degradation of sulfamethoxazole (SMX) over a wide pH range of 3.0–7.0. The enhancement of SMX degradation was attributed to the complexation and reduction role of S2O32−, preventing the precipitation of iron ions and accelerating the reduction of Fe(III). A first-principles kinetic model was established and revealed that the interaction of S2O32− and Fe(III) was a fast equilibrium reaction, affecting the oxidation kinetics of SMX. Both HO• and Fe(IV) were found to be involved in the SMX degradation. Compared to HO•, Fe(IV) is much more selective, and thus SMX degradation was less affected by water matrices, maintaining high efficiency in real water samples. Transformation products analysis demonstrated that (i) sulfonamide bond (S-N or C-S bonds) cleavage, (ii) hydroxylation and (iii) nitrosubstitution and deamination were the major transformation pathway. This study could improve our understanding the role of S2O32− in Fe(III)/H2O2 system and provide a novel promising Fenton-like reaction for wastewater treatment.

Collision-induced dissociation of Na+-tagged ketohexoses: experimental and computational studies on fructose.

Collision-induced dissociation tandem mass spectrometry (CID-MSn) and computational investigation at the MP2/6-311+G(d,p) level of theory have been employed to study Na+-tagged fructose, an example of a ketohexose featuring four cyclic isomers: α-fructofuranose (αFruf), β-fructofuranose (βFruf), α-fructopyranose (αFrup), and β-fructopyranose (βFrup). The four isomers can be separated by high-performance liquid chromatography (HPLC) and they show different mass spectra, indicating that CID-MSn can distinguish the different fructose forms. Based on a simulation using a micro-kinetic model, we have obtained an overview of the mechanisms for the different dissociation pathways. It has been demonstrated that the preference for the C-C cleavage over the competing isomerization of linear fructose is the main reason for the previously reported differences between the CID-MS spectra of aldohexoses and ketohexoses. In addition, the kinetic modeling helped to confirm the assignment of the different measured mass spectra to the different fructose isomers. The previously reported assignment based on the peak intensities in the HPLC chromatogram had left some open questions as the preference for the dehydration channels did not always follow trends previously observed for aldohexoses. Setting up the kinetic model further enabled us to directly compare the computational and experimental results, which indicated that the model can reproduce most trends in the differences between the dissociation pathways of the four cyclic fructose isomers.

Room Temperature Hydrolysis of Benzamidines and Benzamidiniums in Weakly Basic Water.

Benzamidinium compounds have found widespread use in both medicinal and supramolecular chemistry. In this work, we show that benzamidiniums hydrolyze at room temperature in aqueous base to give the corresponding primary amide. This reaction has a half-life of 300 days for unsubstituted benzamidinium at pH 9, but is relatively rapid at higher pH's (e.g., t1/2 = 6 days at pH 11 and 15 h at pH 13). Quantum chemistry combined with first-principles kinetic modeling can reproduce these trends and explain them in terms of the dominant pathway being initiated by attack of HO- on benzamidine. Incorporation of the amidinium motif into a hydrogen bonded framework offers a substantial protective effect against hydrolysis.

Training set design for machine learning techniques applied to the approximation of computationally intensive first-principles kinetic models

We propose a design procedure for the generation of the training set for Machine Learning algorithms with a specific focus on the approximation of computationally-intensive first-principles kinetic models in catalysis. The procedure is based on the function topology and behavior, by means of the calculation of the discrete gradient, and on the relative importance of the independent variables. We apply the proposed methodology to the tabulation and regression of mean-field and kinetic Monte Carlo models aiming at their coupling with reactor simulations. Our tests – in the context both of mean-field kinetics and kinetic Monte Carlo simulations – show that the procedure is able to design a dataset that requires between 60 and 80% fewer data points to achieve the same approximation accuracy than the one obtained with an evenly distributed grid. This strong reduction in the number of points results in a significant computational gain and a concomitant boost of the approximation efficiency. The Machine Learning algorithms trained with the results of the procedure are then included in both macroscopic reactor models and computational fluid dynamics (CFD) simulations. First, a Plug Flow Reactor is employed to carry out a direct comparison with the solution of the full first-principles kinetic model. The results show an excellent agreement within 0.2% between the models. Then, the CFD simulation of complex tridimensional geometry is carried out by using a tabulated kMC model for CO oxidation on Ruthenium oxide, thus providing a showcase of the capability of the approach in making possible the multiscale simulation of complex chemical reactors.

Kinetic theory of transport driven current in centrally fuelled plasmas

When a steady-state cylindrical plasma discharge is centrally fuelled, the collisionless radial electron flux is canonically coupled to an axial current. The identification and analysis of this transport driven current, previously reported in collisionless simulations [W. J. Nunan and J. M. Dawson, Phys. Rev. Lett. 73, 1628 (1994)], are addressed analytically and extended to the collisional regime by means of first-principles kinetic models. Collisionless radial transport is described with the standard quasilinear model and collisional velocity anisotropy relaxation with the Landau kinetic equation. When trapped particle corrections are taken into account, the solution of this kinetic model provides the analytical expression for the transport driven current in a centrally fuelled steady-state tokamak as a function of the thermonuclear power and discharge parameters. For ITER type discharges, with central fuelling, a current of about one mega-ampere is predicted by this first-principles analytical kinetic model.

Oxidation of Microcystin-LR via Activation of Peroxymonosulfate Using Ascorbic Acid: Kinetic Modeling and Toxicity Assessment.

Advanced oxidation processes (AOPs) have been widely used for the destruction of organic contaminants in the aqueous phase. In this study, we introduce an AOP on activated peroxymonosulfate (PMS) by using ascorbic acid (H2A) to generate sulfate radicals (SO4•-). Sulfate radicals, hydroxyl radicals (HO•), and ascorbyl radicals (A•-) were found using electron spin resonance (ESR). But we found A•- is negligible in the degradation of microcystin-LR (MCLR) due to its low reactivity. We developed a first-principles kinetic model to simulate the MCLR degradation and predict the radical concentrations. The MCLR degradation rate decreased with increasing pH. The scavenging effect of natural organic matter (NOM) on SO4•- was relatively small compared to that for HO•. Considering both energy consumption and MCLR removal, the optimal H2A and PMS doses for H2A/PMS process were determined at 1.0 × 10-6 M and 1.6 × 10-5 M, respectively. In addition, we determined the toxicity using the protein phosphatase 2A (PP2A) test and the results showed that MCLR was readily detoxified and its oxidation byproducts were not hepatotoxic. Overall, our work provides a new type of AOP and a promising, efficient, and environmental-friendly method for removing microcystins in algae-laden water.

Quantitative First-Principles Kinetic Modeling of the Aza-Michael Addition to Acrylates in Polar Aprotic Solvents.

This work presents a detailed computational study and kinetic analysis of the aza-Michael addition of primary and secondary amines to acrylates in an aprotic solvent. Accurate rate coefficients for all elementary steps in the various competing mechanisms are calculated using an ONIOM-based approach in which the full system is calculated with M06-2X/6-311+G(d,p) and the core system with CBS-QB3 corrected for solvation using COSMO-RS. Diffusional contributions are taken into account using the coupled encounter pair model with diffusion coefficients calculated based on molecular dynamics simulations. The calculated thermodynamic and kinetic parameters for all forward and reverse elementary reactions are fed to a microkinetic model giving excellent agreement with experimental data obtained using GC analysis. Rate analysis reveals that for primary and secondary amines, the aza-Michael addition to ethyl acrylate occurs preferentially according to a 1,2-addition mechanism, consisting of the pseudoequilibrated formation of a zwitterion followed by a rate controlling amine assisted proton transfer toward the singly substituted product. The alternative 1,4-addition becomes competitive if substituents are present on the amine or double bond of the acrylate. Primary amines react faster than secondary amines due to increased solvation of the zwitterionic intermediate and less sterically hindered proton transfer.

Pyramidal Structure Formation at the Interface between III/V Semiconductors and Silicon

An enhancement of computer performance following Moore’s law requires the miniaturization of semiconductor devices. Presently, their dimensions reach the nanoscale. Interfaces between materials become increasingly important as the volume is reduced. It is shown here how a pyramidal interface structure is formed irrespective of the conditions applied during the growth of two semiconductors. This drastically changes the common view of interfaces, which were assumed to be either atomically abrupt or interdiffused. Especially in semiconductor heteroepitaxy, a simple surface segregation of one atomic species is often assumed. It is proven by first-principles computations and kinetic modeling that the atom mobility during growth and the chemical environment at the interface are the decisive factors in the formation of the actual structure. Gallium phosphide grown on silicon was chosen as representative, nearly unstrained material combination to study the fundamental parameters influencing the interface morpholo...

Perfluorooctanoic Acid Degradation Using UV-Persulfate Process: Modeling of the Degradation and Chlorate Formation.

In this study, we investigated the destruction and by-product formation of perfluorooctanoic acid (PFOA) using ultraviolet light and persulfate (UV-PS). Additionally, we developed a first-principles kinetic model to simulate both PFOA destruction and by-product and chlorate (ClO3(-)) formation in ultrapure water (UW), surface water (SW), and wastewater (WW). PFOA degradation was significantly suppressed in the presence of chloride and carbonate species and did not occur until all the chloride was converted to ClO3(-) in UW and for low DOC concentrations in SW. The model was able to simulate the PS decay, pH changes, radical concentrations, and ClO3(-) formation for UW and SW. However, our model was unable to simulate PFOA degradation well in WW, possibly from PS activation by NOM, which in turn produced sulfate radicals.

Methane Oxidation over PdO(101) Revealed by First-Principles Kinetic Modeling.

The catalytic oxidation of methane to carbon dioxide and water over PdO(101) is investigated with first-principles based microkinetic modeling. Extensive exploration of the reaction landscape allows for determination of preferred pathways at different reaction conditions. The predicted kinetic behavior is in good agreement with a range of experimental findings including reaction orders in methane, water, and oxygen as well as apparent activation energies. The results consolidate the role of the PdO(101) surface in the activity of PdO catalysts and offer starting points for computational design of materials with improved catalytic activity. Moreover, the study demonstrates the predictive power of first-principles based kinetic modeling for oxide surfaces when hybrid functionals are applied in conjugation with kinetic models that go beyond the mean-field approximation.

Simulation of the scrape-off layer region of tokamak devices

Understanding the key processes occurring in the tokamak scrape-off layer (SOL) is becoming of the outmost importance while we enter the ITER era and we move towards the conception of future fusion reactors. By controlling the heat exhaust, by playing an important role in determining the overall plasma confinement, and by regulating the impurity level in tokamak core, the dynamics of the fusion fuel in the SOL is, in fact, related to some of the most crucial issues that the fusion program is facing today. Because of the limited diagnostic access and in view of predicting the SOL dynamics in future devices, simulations are becoming crucial to address the physics of this region. The present paper, which summarizes the lecture on SOL simulations that was given during the 7th ITER international school (August 25–29, 2014, Aix-en-Provence, France), provides a brief overview of the simulation approaches to the SOL dynamics. First, disentangling the complexity of the system, the key physics processes occurring in the SOL are described. Then, the different simulation approaches to the SOL dynamics are presented, from first-principles kinetic and fluid models, to the phenomenological analysis.

Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.

Computer-based first-principles kinetic modeling of degradation pathways and byproduct fates in aqueous-phase advanced oxidation processes.

In this study, a computer-based first-principles kinetic model is developed to predict the degradation mechanisms and fates of intermediates and byproducts produced during aqueous-phase advanced oxidation processes (AOPs) for various organic compounds. The model contains a rule-based pathway generator to generate the reaction pathways, a reaction rate constant estimator to estimate the reaction rate constant for each reaction generated, a mechanistic reduction module to reduce the generated mechanisms, an ordinary differential equations generator and solver to solve the generated mechanisms and calculate the concentration profiles for all species, and a toxicity estimator to estimate the toxicity of major species and calculate time-dependent profiles of relative toxicity (i.e., concentration of species divided by toxicity value). We predict concentration profiles of acetone and trichloroethylene and their intermediates and byproducts in photolysis with hydrogen peroxide (i.e., UV/H2O2) and validate with experimental observations. The predicted concentration profiles for both parent compounds are consistent with experimental data. The calculated profiles of 96-h green algae chronic toxicity show that the overall toxicity decreases during the degradation process. These generated mechanisms also provide detailed and quantitative insights into the pathways for the formation and consumption of important intermediates and byproducts produced during AOPs. Our approach is sufficiently general to be applied to a wide range of contaminants.

ChemInform Abstract: First Principles Kinetic Modeling in Heterogeneous Catalysis: An Industrial Perspective on Best Practice, Gaps and Needs

AbstractReview: 154 refs.

First-principles kinetic modeling in heterogeneous catalysis: an industrial perspective on best-practice, gaps and needs

Electronic structure calculations have emerged as a key contributor in modern heterogeneous catalysis research, though their application in chemical reaction engineering remains largely limited to academia. This perspective aims at encouraging the judicious use of first-principles kinetic models in industrial settings based on a critical discussion of present-day best practices, identifying existing gaps, and defining where further progress is needed.

Accurate coverage-dependence incorporated into first-principles kinetic models: Catalytic NO oxidation on Pt (1 1 1)

The coverage of surface adsorbates influences both the number and types of sites available for catalytic reactions at a heterogeneous surface, but accounting for adsorbate–adsorbate interactions and understanding their implications on observed rates remain challenges for simulation. Here, we demonstrate the use of a density functional theory (DFT)-parameterized cluster expansion (CE) to incorporate accurate adsorbate–adsorbate interactions into a surface kinetic model. The distributions of adsorbates and reaction sites at a metal surface as a function of reaction conditions are obtained through Grand Canonical Monte Carlo simulations on the CE Hamiltonian. Reaction rates at those sites are obtained from the CE through a DFT-parameterized Brønsted–Evans–Polyani (BEP) relationship. The approach provides ready access both to steady-state rates and rate derivatives and further provides insight into the microscopic factors that influence observed rate behavior. We demonstrate the approach for steady-state O2 dissociation at an O-covered Pt (111) surface—a model for catalytic NO oxidation at this surface—and recover apparent activation energies and rate orders consistent with experiment.

Reactivity of Aqueous Phase Hydroxyl Radical with Halogenated Carboxylate Anions: Experimental and Theoretical Studies

With concerns about emerging contaminants increasing, advanced oxidation processes have become attractive technologies because of potential mineralization of these contaminants via radical involved reactions that are induced by highly reactive hydroxyl radical. Considering the expensive and time-consuming experimental studies of degradation intermediates and byproduct, there is a need to develop a first-principles computer-based kinetic model that predict reaction pathways and associated reaction rate constants. In this study, we measured temperature-dependent hydroxyl radical reaction rate constants for a series of haloacetate ions and obtained their Arrhenius kinetic parameters. We found a linear correlation between these reaction rate constants and theoretically calculated aqueous-phase free energies of activation. To understand the quantitative effects on entropy of solvation due to solvent water molecules, we calculate each portion of the entropic energies that contribute to the overall aqueous phase entropy of activation; cavity formation is a dominant portion. For the series of reactions of hydroxyl radical with carboxylate ions, the increase in the entropy of activation during the solvation process is approximately 10-15 cal mol(-1)K(-1) because of interactions with solvent water molecules and the transition state. Finally, charge distribution analysis for the aqueous-phase reactions of hydroxyl radical with acetate/haloacetate ions reveals that in the aqueous phase, the degree of polarizability at the transition state is less substantial than those that are in the gaseous phase resulting in a high charge density. In the presence of electronegative halogenated functional groups, the transition state is less polarized and hydrogen bonding interactions are expected to be weaker.

Ab Initio Kinetic Modeling of Living Anionic and Zwitterionic Chain Polymerization Mechanisms

A scale-bridging study of first-principles calculations and kinetic modeling has been carried out to investigate anionic and zwitterionic chain polymerizations. On the example of the industrially r...

First-Principles Analysis of the Activity of Transition and Noble Metals in the Direct Utilization of Hydrocarbon Fuels at Solid Oxide Fuel Cell Operating Conditions

The direct on-cell use of hydrocarbon fuels in solid oxide fuel cells (SOFCs) involves many thermochemical and electrochemical reactions that occur on anode electrocatalysts, both at and away from the three-phase boundary. We have used first-principles density functional theory calculations and kinetic modeling to investigate relevant reactions associated with the direct utilization of methane on different electrocatalysts at SOFC operating conditions. The investigated reactions are steam and dry reforming of methane, electrochemical oxidation of and CO, and direct electrochemical oxidation of methane. These studies allowed us to compare the relative activity of different metals and to identify those metals that offer optimal performance. Our analysis shows that under relevant operating conditions, there exists a family of metals (mainly Ni, Co, Rh, Ru, and Ir) that offer maximum activity for all relevant reactions. The findings suggest that a fairly simple anode design including only one material in combination with yttria-stabilized zirconia performing multiple reactions should offer close to optimal performance. While we outline our results for methane in detail, we also comment on the direct utilization of other hydrocarbons.