Статті в журналах: "Computational Reaction Kinetics"

1

Christophorov, L. N. "Indirect Evidences of Conformational Regulation in Protein Reactions: How Much Can Be Learnt?" Ukrainian Journal of Physics 57, no. 7 (July 30, 2012): 746. http://dx.doi.org/10.15407/ujpe57.7.746.

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Almost all reactions of proteins manifest deviations from the simple behaviour prescribed by standard (bio)chemical kinetics. This is caused by the extraordinary structural lability of protein macromolecules which is often not less important for the reaction efficiency than the properties of the active center. Unveiling the mechanisms of structural regulation encounters serious difficulties because of their hidden character, as either modern experiments or computational methods still fall short of monitoring simultaneously the reaction events and concomitant conformational changes, so that one has to decipher the reaction kinetics only. Nevertheless, it is possible to come to reliable conclusions on the mode of operation of proteins and the character of their structural relaxation with the help of a convenient and computationally accessible approach expounded in the present paper.

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2

König, Matthias. "cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK." F1000Research 5 (July 18, 2016): 1736. http://dx.doi.org/10.12688/f1000research.9211.1.

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Kinetic data of biochemical reactions are essential for the creation of kinetic models of biochemical networks. One of the main resources of such information is SABIO-RK, a curated database for kinetic data of biochemical reactions and their related information. Despite the importance for computational modelling there has been no simple solution to visualize the kinetic data from SABIO-RK. In this work, I present cy3sabiork, an app for querying and visualization of kinetic data from SABIO-RK in Cytoscape. The kinetic information is accessible via a combination of graph structure and annotations of nodes, with provided information consisting of: (I) reaction details, enzyme and organism; (II) kinetic law, formula, parameters; (III) experimental conditions; (IV) publication; (V) additional annotations. cy3sabiork creates an intuitive visualization of kinetic entries in form of a species-reaction-kinetics graph, which reflects the reaction-centered approach of SABIO-RK. Kinetic entries can be imported in SBML format from either the SABIO-RK web interface or via web service queries. The app allows for easy comparison of kinetic data, visual inspection of the elements involved in the kinetic record and simple access to the annotation information of the kinetic record. I applied cy3sabiork in the computational modelling of galactose metabolism in the human liver.

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3

Menshutina, Natalia V., Igor V. Lebedev, Evgeniy A. Lebedev, Ratmir R. Dashkin, Mikhail V. Shishanov, and Maxim L. Burdeyniy. "STUDY AND MODELING 4,4'-DIAMINODIPHENYLMETHANE SYNTHESIS." IZVESTIYA VYSSHIKH UCHEBNYKH ZAVEDENII KHIMIYA KHIMICHESKAYA TEKHNOLOGIYA 64, no. 4 (April 11, 2021): 100–103. http://dx.doi.org/10.6060/ivkkt.20216404.6314.

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The presented work is devoted to reactions of obtaining 4,4´-diaminodiphenylmethane in the presence of a catalyst. The work describes the importance of studying 4,4´-diaminodiphenylmethane obtaining process and possibility of cellular automata approach in modelling chemical reactions. Cellular automata model which allows to predict the kinetic curves of the studied 4,4´-diaminodiphenylmethane-obtaining reaction. Model reflects two processes that are observed in the system under study - the movement of reagents under the stirring and the reaction in the presence of a catalyst. The suggested model does not use complex calculations for operation and can be implemented using high-performance parallel computing, which will speed up calculations and reduce the requirements for computing resources. The developed model was used to carry out computational experiments under various conditions. Since the model contains a number of empirical parameters, first computational experiments were carried out, which made it possible to establish the relationship between the model parameters and real values. Then, computational experiments were carried out to predict the kinetic curves of the studied reactions and were compared with the corresponding experimental data. The suggested model is suitable for predicting 4,4´-diaminodiphenylmethane-obtaining reaction kinetics. Also, model can be the part of complex multiscale modeling from the molecule level to the level of the entire apparatus.

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4

Rosero Chicaíza, David Camilo, and Bibian A. Hoyos. "Reaction kinetic parameters for a distributed model of transport and reaction in Pd/Rh/CeZrO three-way catalytic converters." DYNA 86, no. 210 (July 1, 2019): 216–23. http://dx.doi.org/10.15446/dyna.v86n210.78596.

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This paper presents a two-dimensional distributed model for the transport and reaction of combustion gases in channels of three-way catalytic converters, considering a detailed reaction kinetics with 16 chemical reactions in palladium and rhodium catalysts, and taking into account diffusive effects within the coating, to obtain a new set of reaction kinetic parameters that do not depend on the thickness of the coating. The model was solved using a finite volume method with a first order upwind scheme and simulations were conducted using computational fluid dynamics. The model with the new distributed reaction kinetic parameters, produced an excellent agreement with the experimental data of concentration at the end of the channels. Also, the model reproduced the most important concentration changes for the gas components in the specified temperature range and allowed simulations with excess oxygen and different thicknesses.

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5

Menshutina, Natalia, Igor Lebedev, Evgeniy Lebedev, Andrey Kolnoochenko, Alexander Troyankin, Ratmir Dashkin, Michael Shishanov, Pavel Flegontov, and Maxim Burdeyniy. "Complex Modelling and Design of Catalytic Reactors Using Multiscale Approach—Part 2: Catalytic Reactions Modelling with Cellular Automata Approach." Computation 8, no. 4 (October 10, 2020): 87. http://dx.doi.org/10.3390/computation8040087.

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The presented work is devoted to reactions of obtaining 4,4’-Diaminodiphenylmethane (MDA) in the presence of a catalyst model. The work describes the importance of studying the MDA obtaining process and the possibility of the cellular automata (CA) approach in the modelling of chemical reactions. The work suggests a CA-model that makes it possible to predict the kinetic curves of the studied MDA-obtaining reaction. The developed model was used to carry out computational experiments under the following different conditions—aniline:formaldehyde:catalyst ratios, stirrer speed, and reaction temperature. The results of computational experiments were compared with the corresponding experimental data. The suggested model was shown to be suitable for predicting MDA-obtaining reaction kinetics. The proposed CA model can be used with the CFD model, suggested in Part 1, allowing the implementation of complex multiscale modeling of a flow catalytic reactor from the molecule level to the level of the entire apparatus.

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6

Ke, Wei, Guang-Jin Chen, and Daoyi Chen. "Methane–propane hydrate formation and memory effect study with a reaction kinetics model." Progress in Reaction Kinetics and Mechanism 45 (January 2020): 146867832090162. http://dx.doi.org/10.1177/1468678320901622.

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Although natural gas hydrates and hydrate exploration have been extensively studied for decades, the reaction kinetics and nucleation mechanism of hydrate formation is not fully understood. In its early stage, gas hydrate formation can be assumed to be an autocatalytic kinetic reaction with nucleation and initial growth. In this work, a reaction kinetics model has been established to form structure II methane–propane hydrate in an isochoric reactor. The computational model consists of six pseudo-elementary reactions for three dynamic processes: (1) gas dissolution into the bulk liquid, (2) a slow buildup of hydrate precursors for nucleation onset, and (3) rapid and autocatalytic hydrate growth after onset. The model was programmed using FORTRAN, with initiating parameters and rate constants that were derived or obtained from data fitted using experimental results. The simulations indicate that the length of nucleation induction is determined largely by an accumulation of oligomeric hydrate precursors up to a threshold value. The slow accumulation of precursors is the rate-limiting step for the overall hydrate formation, and its conversion into hydrate particles is critical for the rapid, autocatalytic reaction. By applying this model, the memory effect for hydrate nucleation was studied by assigning varied initial amounts of precursor or hydrate species in the simulations. The presence of pre-existing precursors or hydrate particles could facilitate the nucleation stage with a reduced induction time, and without affecting hydrate growth. The computational model with the performed simulations provides insight into the reaction kinetics and nucleation mechanism of hydrate formation.

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7

Yen, Shih-Wei, Wei-Hsin Chen, Jo-Shu Chang, Chun-Fong Eng, Salman Raza Naqvi, and Pau Loke Show. "Torrefaction Thermogravimetric Analysis and Kinetics of Sorghum Distilled Residue for Sustainable Fuel Production." Sustainability 13, no. 8 (April 11, 2021): 4246. http://dx.doi.org/10.3390/su13084246.

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This study investigated the kinetics of isothermal torrefaction of sorghum distilled residue (SDR), the main byproduct of the sorghum liquor-making process. The samples chosen were torrefied isothermally at five different temperatures under a nitrogen atmosphere in a thermogravimetric analyzer. Afterward, two different kinetic methods, the traditional model-free approach, and a two-step parallel reaction (TPR) kinetic model, were used to obtain the torrefaction kinetics of SDR. With the acquired 92–97% fit quality, which is the degree of similarity between calculated and real torrefaction curves, the traditional method approached using the Arrhenius equation showed a poor ability on kinetics prediction, whereas the TPR kinetic model optimized by the particle swarm optimization (PSO) algorithm showed that all the fit qualities are as high as 99%. The results suggest that PSO can simulate the actual torrefaction kinetics more accurately than the traditional kinetics approach. Moreover, the PSO method can be further employed for simulating the weight changes of reaction intermediates throughout the process. This computational method could be used as a powerful tool for industrial design and optimization in the biochar manufacturing process.

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8

Huang, Sijia, Kangmin Kim, Grant M. Musgrave, Marcus Sharp, Jasmine Sinha, Jeffrey W. Stansbury, Charles B. Musgrave, and Christopher N. Bowman. "Determining Michael acceptor reactivity from kinetic, mechanistic, and computational analysis for the base-catalyzed thiol-Michael reaction." Polymer Chemistry 12, no. 25 (2021): 3619–28. http://dx.doi.org/10.1039/d1py00363a.

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9

Varela, J. A., S. A. Vázquez, and E. Martínez-Núñez. "An automated method to find reaction mechanisms and solve the kinetics in organometallic catalysis." Chemical Science 8, no. 5 (2017): 3843–51. http://dx.doi.org/10.1039/c7sc00549k.

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A novel computational method based on a procedure combining accelerated direct dynamics with an efficient geometry-based post-processing algorithm is proposed for use in discovering reaction mechanisms and solving the kinetics of transition metal-catalyzed reactions.

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10

Gajewska, Magdalena, and Katarzyna Skrzypiec. "Kinetics of nitrogen removal processes in constructed wetlands." E3S Web of Conferences 26 (2018): 00001. http://dx.doi.org/10.1051/e3sconf/20182600001.

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The aim of this paper is to present a state-of-the-art review of the kinetics of nitrogen removal in constructed wetlands. Biological processes of nitrogen removal from wastewater can be described using equations and kinetic models. Hence, these kinetic models which have been developed and evaluated allow for predicting the removal of nitrogen in treatment wetlands. One of the most important, first order removal model, which is still applied, was analysed and its rate coefficients and factors were compared. This study also demonstrates the validity of Monod and multiple Monod kinetics, commonly seen today. Finally, a computational example of the reaction kinetics of nitrogen removal was also included in the study.

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11

Lording, William J., Alan D. Payne, Tory N. Cayzer, Michael S. Sherburn, and Michael N. Paddon-Row. "A Combined Computational–Experimental Study of the Kinetics of Intramolecular Diels–Alder Reactions in a Series of 1,3,8-Nonatrienes." Australian Journal of Chemistry 68, no. 2 (2015): 230. http://dx.doi.org/10.1071/ch14430.

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Activation enthalpies for a series of five 1,3,8-nonatriene intramolecular Diels–Alder (IMDA) reactions involving substrates 1–5 have been determined experimentally and Singleton’s natural abundance method has been employed to determine kinetic isotope effects in the IMDA reaction of fumarate 3. The activation enthalpies for the IMDA reactions of the systems possessing a –CH2OCH2– diene/dienophile tether are significantly smaller than their counterparts possessing the –CH2OC(=O)– tether. The experimental activation enthalpies have been used to benchmark computed values from four model chemistries, namely two density functional theory functionals, B3LYP and M06-2X, and two generally very accurate composite ab initio wave function methods, CBS-QB3 and G4(MP2). G4(MP2) outperformed the computationally more expensive CBS-QB3 method, but the vastly cheaper M06-2X/6-31G(d)//B3LYP/6-31G(d) method was sufficiently accurate to be the recommended method of choice for calculating activation parameters. Experimental 2H kinetic isotope effects for the IMDA reaction of fumarate 3 confirmed the computational predictions that this Diels–Alder reaction is concerted but asynchronous.

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12

Park, Jongmin, Hyo Seok Kim, Won Bo Lee, and Myung-June Park. "Trends and Outlook of Computational Chemistry and Microkinetic Modeling for Catalytic Synthesis of Methanol and DME." Catalysts 10, no. 6 (June 11, 2020): 655. http://dx.doi.org/10.3390/catal10060655.

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The first-principle modeling of heterogeneous catalysts is a revolutionarily approach, as the electronic structure of a catalyst is closely related to its reactivity on the surface with reactant molecules. In the past, detailed reaction mechanisms could not be understood, however, computational chemistry has made it possible to analyze a specific elementary reaction of a reaction system. Microkinetic modeling is a powerful tool for investigating elementary reactions and reaction mechanisms for kinetics. Using a microkinetic model, the dominant pathways and rate-determining steps can be elucidated among the competitive reactions, and the effects of operating conditions on the reaction mechanisms can be determined. Therefore, the combination of computational chemistry and microkinetic modeling can significantly improve computational catalysis research. In this study, we reviewed the trends and outlook of this combination technique as applied to the catalytic synthesis of methanol (MeOH) and dimethyl ether (DME), whose detailed mechanisms are still controversial. Although the scope is limited to the catalytic synthesis of limited species, this study is expected to provide a foundation for future works in the field of catalysis research based on computational catalysis.

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13

Dias Vicentini, Eduardo, Ana P. de Lima Batista, and Antonio G. Sampaio de Oliveira-Filho. "Computational mechanistic investigation of the Fe + CO2 → FeO + CO reaction." Physical Chemistry Chemical Physics 22, no. 29 (2020): 16943–48. http://dx.doi.org/10.1039/d0cp00479k.

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14

Li, Han-Jung, Hui-Lung Chen, Jee-Gong Chang, Hsin-Tsung Chen, Shiuan-Yau Wu, and Shin-Pon Ju. "Computational Study on Reaction Mechanisms and Kinetics of Diazocarbene Radical Reaction with NO." Journal of Physical Chemistry A 114, no. 18 (May 13, 2010): 5894–901. http://dx.doi.org/10.1021/jp1008016.

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15

Ilyin, Daniil V., William A. Goddard, Julius J. Oppenheim, and Tao Cheng. "First-principles–based reaction kinetics from reactive molecular dynamics simulations: Application to hydrogen peroxide decomposition." Proceedings of the National Academy of Sciences 116, no. 37 (September 21, 2018): 18202–8. http://dx.doi.org/10.1073/pnas.1701383115.

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This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over ∼10-nm spatial scales for ∼1 ns, which is prohibitively impractical with QM. Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the reactive molecular dynamics (RMD). We focus here on showing that it is practical to extract from such RMD the reaction mechanisms and kinetics information needed to describe the reactions analytically. This analytic description can then be used to incorporate the correct reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of ∼10 nm to micrometers to millimeters to meters using analytic approaches of computational fluid dynamics and/or continuum chemical dynamics. In the paper we lay out the strategy to extract the mechanisms and rate parameters automatically without the necessity of knowing any details of the chemistry. We consider this to be a proof of concept. We refer to the process as RMD2Kin (reactive molecular dynamics to kinetics) for the general approach and as ReaxMD2Kin (ReaxFF molecular dynamics to kinetics) for QM-ReaxFF–based reaction kinetics.

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16

Wacławek, Stanisław. "Do We Still Need a Laboratory to Study Advanced Oxidation Processes? A Review of the Modelling of Radical Reactions used for Water Treatment." Ecological Chemistry and Engineering S 28, no. 1 (March 1, 2021): 11–28. http://dx.doi.org/10.2478/eces-2021-0002.

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Abstract Environmental pollution due to humankind’s often irresponsible actions has become a serious concern in the last few decades. Numerous contaminants are anthropogenically produced and are being transformed in ecological systems, which creates pollutants with unknown chemical properties and toxicity. Such chemical pathways are usually examined in the laboratory, where hours are often needed to perform proper kinetic experiments and analytical procedures. Due to increased computing power, it becomes easier to use quantum chemistry computation approaches (QCC) for predicting reaction pathways, kinetics, and regioselectivity. This review paper presents QCC for describing the oxidative degradation of contaminants by advanced oxidation processes (AOP, i.e., techniques utilizing •OH for degradation of pollutants). Regioselectivity was discussed based on the Acid Blue 129 compound. Moreover, the forecasting of the mechanism of hydroxyl radical reaction with organic pollutants and the techniques of prediction of degradation kinetics was discussed. The reactions of •OH in various aqueous systems (explicit and implicit solvation) with water matrix constituents were reviewed. For example, possible singlet oxygen formation routes in the AOP systems were proposed. Furthermore, quantum chemical computation was shown to be an excellent tool for solving the controversies present in the field of environmental chemistry, such as the Fenton reaction debate [main species were determined to be: •OH < pH = 2.2 < oxoiron(IV)]. An ongoing discussion on such processes concerning similar reactions, e.g., associated with sulphate radical-based advanced oxidation processes (SR-AOP), could, in the future, be enriched by similar means. It can be concluded that, with the rapid growth of computational power, QCC can replace most of the experimental investigations related to the pollutant’s remediation in the future; at the same time, experiments could be pushed aside for quality assessment only.

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17

Yu, Chunkan, Felipe Minuzzi, and Ulrich Maas. "Numerical Simulation of Turbulent Flames based on a Hybrid RANS/Transported-PDF Method and REDIM Method." Eurasian Chemico-Technological Journal 20, no. 1 (March 31, 2018): 23. http://dx.doi.org/10.18321/ectj705.

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A hybrid RANS/Transported-PDF model for the simulation of turbulent reacting flows based on automatically reduced mechanisms for the chemical kinetics (reaction-diffusion manifold, REDIM) is presented in this work. For modelling of turbulent reacting flows, chemistry is a key problem and affects largely the accuracy. The PDF method has been widely used since the chemical source term is in a closed form, without any modelling. Despite of this advantage of PDF method, detailed chemical kinetics is not desired due to its heavy computational effort. From this aspect, the detailed chemical kinetics is simplified by the reaction-diffusion manifold (REDIM) method. The hybrid RANS/Transported-PDF model based on REDIM reduced kinetics is applied to simulate the Sandia piloted Flame E, which has a moderate degree of local extinction. The numerical results are validated through comparison with experimental data and show good qualitative and quantitative agreements.

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18

Simka, H., M. Hierlemann, M. Utz, and K. F. Jensen. "Computational Chemistry Predictions of Kinetics and Major Reaction Pathways for Germane Gas‐Phase Reactions." Journal of The Electrochemical Society 143, no. 8 (August 1, 1996): 2646–54. http://dx.doi.org/10.1149/1.1837063.

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19

Raymond, K. W., and Y. Pocker. "Bistability and the ordered bimolecular mechanism." Biochemistry and Cell Biology 69, no. 9 (September 1, 1991): 661–64. http://dx.doi.org/10.1139/o91-098.

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An equation describing the instantaneous velocity of an ordered bimolecular enzymatic reaction that exhibits inhibition by substrate and product was derived. Using kinetic constant values for horse liver alcohol dehydrogenase, the velocity expression was applied to an open-reaction system. The calculated steady-state surfaces displayed regions of bistability, which further substantiates the link between substrate inhibition and multiple steady states. This general computational approach may be applied to any system that can be described by an instantaneous velocity equation.Key words: bistability, steady state, enzyme kinetics.

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20

Benjamin, Ilan. "Chemical Reaction Dynamics at Liquid Interfaces: A Computational Approach." Progress in Reaction Kinetics and Mechanism 27, no. 2 (June 2002): 87–126. http://dx.doi.org/10.3184/007967402103165360.

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Recent advances in experimental and theoretical studies of liquid interfaces provide remarkable evidence for the unique properties of these systems. In this review we examine how these properties affect the thermodynamics and kinetics of chemical reactions which take place at the liquid/vapor interface and at the liquid/liquid interface. We demonstrate how the rapidly varying density and viscosity, the marked changes in polarity and the surface roughness manifest themselves in isomerization, electron transfer and photodissociation reactions.

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21

Huang, Xue Zheng, and Hai Ling Chen. "Development of the Simulation Software on the Complex Reaction Kinetics." Advanced Materials Research 634-638 (January 2013): 7–10. http://dx.doi.org/10.4028/www.scientific.net/amr.634-638.7.

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The design idea and design flow of the simulation software on the complex reaction kinetics are introduced in this article. Firstly, the total framework of the software was determined by the goal and function of the software; Secondly, the manuscript was written, the multimedia material was made and the computational programs were designed, the examples of making multimedia material by Photoshop and Flash are introduced, moreover, the thinking and method of program is introduced; Finally, The material such as text, images, sounds, animation is integrated by Authorware. The simulation software has friendly interface and simple operation, it can be used as a computational tool in studying chemical kinetics, in addition, the software can be assisted in the teaching such as physical chemistry and reaction engineering.

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22

Berkemeier, Thomas, Matteo Krüger, Aryeh Feinberg, Marcel Müller, Ulrich Pöschl, and Ulrich K. Krieger. "Accelerating models for multiphase chemical kinetics through machine learning with polynomial chaos expansion and neural networks." Geoscientific Model Development 16, no. 7 (April 14, 2023): 2037–54. http://dx.doi.org/10.5194/gmd-16-2037-2023.

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Abstract. The heterogeneous chemistry of atmospheric aerosols involves multiphase chemical kinetics that can be described by kinetic multi-layer models (KMs) that explicitly resolve mass transport and chemical reactions. However, KMs are computationally too expensive to be used as sub-modules in large-scale atmospheric models, and the computational costs also limit their utility in inverse-modeling approaches commonly used to infer aerosol kinetic parameters from laboratory studies. In this study, we show how machine learning methods can generate inexpensive surrogate models for the kinetic multi-layer model of aerosol surface and bulk chemistry (KM-SUB) to predict reaction times in multiphase chemical systems. We apply and compare two common and openly available methods for the generation of surrogate models, polynomial chaos expansion (PCE) with UQLab and neural networks (NNs) through the Python package Keras. We show that the PCE method is well suited to determining global sensitivity indices of the KMs, and we demonstrate how inverse-modeling applications can be enabled or accelerated with NN-suggested sampling. These qualities make them suitable supporting tools for laboratory work in the interpretation of data and the design of future experiments. Overall, the KM surrogate models investigated in this study are fast, accurate, and robust, which suggests their applicability as sub-modules in large-scale atmospheric models.

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23

Nissen, Anna, Zhouyuan Zhu, Anthony Kovscek, Louis Castanier, and Margot Gerritsen. "Upscaling Kinetics for Field-Scale In-Situ-Combustion Simulation." SPE Reservoir Evaluation & Engineering 18, no. 02 (April 23, 2015): 158–70. http://dx.doi.org/10.2118/174093-pa.

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Summary We demonstrate the effectiveness of a non-Arrhenius kinetic upscaling approach for in-situ-combustion processes, first discussed by Kovscek et al. (2013). Arrhenius reaction terms are replaced with equivalent source terms that are determined by a work flow integrating both laboratory experiments and high-fidelity numerical simulations. The new formulation alleviates both stiffness and grid dependencies of the traditional Arrhenius approach. Consequently, the computational efficiency and robustness of simulations are improved significantly. In this paper, we thoroughly investigate the performance of the non-Arrhenius upscaling method compared with Arrhenius kinetics. We investigate robustness by considering grid effects and sensitivity to heterogeneity. Performance improvements of the new kinetic upscaling approach compared with traditional Arrhenius kinetics are demonstrated through numerical experiments in one and two dimensions for both homogeneous- and heterogeneous-permeability fields.

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Cerri, G., V. Michelassi, S. Monacchia, and S. Pica. "Kinetic combustion neural modelling integrated into computational fluid dynamics." Proceedings of the Institution of Mechanical Engineers, Part A: Journal of Power and Energy 217, no. 2 (January 1, 2003): 185–92. http://dx.doi.org/10.1243/09576500360611218.

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The attempt to replace traditional chemical kinetics model calculations with new ones based on neural networks (NNs) has been successfully carried out. The paper deals with the methodology that has been followed to replace traditional model calculations with neural models (NMs) for methane/air combustion. The reacting flowfield has been described with account taken of the detailed chemical reaction mechanism. Convective and turbulent diffusive transport of species has been taken into consideration by means of a well-known finite volume computational fluid dynamics (CFD) code. Two versions of such a mechanism have been developed. The first one is based on traditional differential equations representing the species production rates. Such equations are integrated over the time intervals related to the cell volumes and local volumetric flows. The second version is based on neural models which can extract and store knowledge from the data presented to them. The neural model capability of connecting output to input quantities by means of the stored knowledge leads to very fast calculations. A reduced combustion mechanism involving 20 species and 68 reactions has been developed both for the traditional calculation and for the neural model calculations. It can be concluded that calculations using chemical kinetics neural models show a 42 times shorter CPU time than that of the traditional procedures, with a comparable solution accuracy of the combustion flowfields.

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Yang, Shu, San Kiang, Parham Farzan, and Marianthi Ierapetritou. "Optimization of Reaction Selectivity Using CFD-Based Compartmental Modeling and Surrogate-Based Optimization." Processes 7, no. 1 (December 29, 2018): 9. http://dx.doi.org/10.3390/pr7010009.

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Mixing is considered as a critical process parameter (CPP) during process development due to its significant influence on reaction selectivity and process safety. Nevertheless, mixing issues are difficult to identify and solve owing to their complexity and dependence on knowledge of kinetics and hydrodynamics. In this paper, we proposed an optimization methodology using Computational Fluid Dynamics (CFD) based compartmental modelling to improve mixing and reaction selectivity. More importantly, we have demonstrated that through the implementation of surrogate-based optimization, the proposed methodology can be used as a computationally non-intensive way for rapid process development of reaction unit operations. For illustration purpose, reaction selectivity of a process with Bourne competitive reaction network is discussed. Results demonstrate that we can improve reaction selectivity by dynamically controlling rates and locations of feeding in the reactor. The proposed methodology incorporates mechanistic understanding of the reaction kinetics together with an efficient optimization algorithm to determine the optimal process operation and thus can serve as a tool for quality-by-design (QbD) during product development stage.

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Xue, Jingwen, Fangfang Ma, Jonas Elm, Jingwen Chen, and Hong-Bin Xie. "Atmospheric oxidation mechanism and kinetics of indole initiated by ●OH and ●Cl: a computational study." Atmospheric Chemistry and Physics 22, no. 17 (September 7, 2022): 11543–55. http://dx.doi.org/10.5194/acp-22-11543-2022.

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Abstract. The atmospheric chemistry of organic nitrogen compounds (ONCs) is of great importance for understanding the formation of carcinogenic nitrosamines, and ONC oxidation products might influence atmospheric aerosol particle formation and growth. Indole is a polyfunctional heterocyclic secondary amine with a global emission quantity almost equivalent to that of trimethylamine, the amine with the highest atmospheric emission. However, the atmospheric chemistry of indole remains unclear. Herein, the reactions of indole with ⚫OH and ⚫Cl, and subsequent reactions of resulting indole radicals with O2 under 200 ppt NO and 50 ppt HO2⚫ conditions, were investigated by a combination of quantum chemical calculations and kinetics modeling. The results indicate that ⚫OH addition is the dominant pathway for the reaction of ⚫OH with indole. However, both ⚫Cl addition and H abstraction are feasible for the corresponding reaction with ⚫Cl. All favorably formed indole radicals further react with O2 to produce peroxy radicals, which mainly react with NO and HO2⚫ to form organonitrates, alkoxy radicals and hydroperoxide products. Therefore, the oxidation mechanism of indole is distinct from that of previously reported amines, which primarily form highly oxidized multifunctional compounds, imines or carcinogenic nitrosamines. In addition, the peroxy radicals from the ⚫OH reaction can form N-(2-formylphenyl)formamide (C8H7NO2), for the first time providing evidence for the chemical identity of the C8H7NO2 mass peak observed in the ⚫OH + indole experiments. More importantly, this study is the first to demonstrate that despite forming radicals by abstracting an H atom at the N site, carcinogenic nitrosamines were not produced in the indole oxidation reaction.

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27

Akanni, Olatokunbo O., Hisham A. Nasr-El-Din, and Deepak Gusain. "A Computational Navier-Stokes Fluid-Dynamics-Simulation Study of Wormhole Propagation in Carbonate-Matrix Acidizing and Analysis of Factors Influencing the Dissolution Process." SPE Journal 22, no. 06 (October 4, 2017): 2049–66. http://dx.doi.org/10.2118/187962-pa.

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Summary This study demonstrates the application of an alternative numerical-simulation approach to effectively describe the flow field in a two-scale carbonate-matrix-acidizing model. The modified model accurately captures the dissolution regimes that occur during carbonate-matrix acidizing. Sensitivity tests were performed on the model to compare the output with experimental observations and previous two-scale models in the literature. A nonlinear reaction-kinetics model for alternative acidizing fluids is also introduced. In this work, the fluid-field flow is described by the Navier-Stokes momentum approach instead of Darcy's law or the Darcy-Brinkman approach used in previous two-scale models. The present model is implemented by means of a commercial computational-fluid-dynamics (CFD) package to solve the momentum, mass-conservation, and species-transport equations in Darcy scale. The software is combined with functions and routines written in the C programming language to solve the porosity-evolution equation, update the pore-scale parameters at every timestep in the simulation, and couple the Darcy and pore scales. The output from the model simulations is consistent with experimental observations, and the results from the sensitivity tests performed are in agreement with previously developed two-scale models with the Darcy approach. The simulations at very-high injection rates with this model require less computational time than models developed with the Darcy approach. The results from this model show that the optimal injection rate obtained in laboratory coreflood experiments cannot be directly translated for field applications because of the effect of flow geometry and medium dimensions on the wormholing process. The influence of the reaction order on the optimal injection rate and pore volumes (PVs) of acid required to reach breakthrough is also demonstrated by simulations run to test the applicability of the model for acids with nonlinear kinetics in reaction with calcite. The new model is computationally less expensive than previous models with the Darcy-Brinkman approach, and simulations at very-high injection rates with this model require less computational time than Darcy-based models. Furthermore, the possibility of extending the two-scale model for acid/calcite reactions with more-complex chemistry is shown by means of the introduction of nonlinear kinetics in the reaction equation.

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28

Moghazy, Yasmen M., Nagwa MM Hamada, Magda F. Fathalla, Yasser R. Elmarassi, Ezzat A. Hamed, and Mohamed A. El-Atawy. "Understanding the reaction mechanism of the regioselective piperidinolysis of aryl 1-(2,4-dinitronaphthyl) ethers in DMSO: Kinetic and DFT studies." Progress in Reaction Kinetics and Mechanism 46 (January 2021): 146867832110274. http://dx.doi.org/10.1177/14686783211027446.

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Reactions of aryl 1-(2,4-dinitronaphthyl) ethers with piperidine in dimethyl sulfoxide at 25oC resulted in substitution of the aryloxy group at the ipso carbon atom. The reaction was measured spectrophotochemically and the kinetic studies suggested that the titled reaction is accurately third order. The mechanism is began by fast nucleophilic attack of piperidine on C1 to form zwitterion intermediate (I) followed by deprotonation of zwitterion intermediate (I) to the Meisenheimer ion (II) in a slow step, that is, SB catalysis. The regular variation of activation parameters suggested that the reaction proceeded through a common mechanism. The Hammett equation using reaction constant σo values and Brønsted coefficient value showed that the reaction is poorly dependent on aryloxy substituent and the reaction was significantly associative and Meisenheimer intermediate-like. The mechanism of piperidinolysis has been theoretically investigated using density functional theory method using B3LYP/6-311G(d,p) computational level. The combination between experimental and computational studies predicts what mechanism is followed either through uncatalyzed or catalyzed reaction pathways, that is, SB and SB-GA. The global parameters of the reactants, the proposed activated complexes, and the local Fukui function analysis explained that C1 carbon atom is the most electrophilic center of ether. Also, kinetics and theoretical calculation of activation energies indicated that the mechanism of the piperidinolysis passed through a two-step mechanism and the proton transfer process was the rate determining step.

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29

Poley, Isabela M., and Leandro S. Oliveira. "CFD Modeling and Simulation of Transesterification Reactions of Vegetable Oils with an Alcohol in Baffled Stirred Tank Reactors." Applied Mechanics and Materials 390 (August 2013): 86–90. http://dx.doi.org/10.4028/www.scientific.net/amm.390.86.

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Alcohol and triglycerides do not form a single phase mixture and thus there is a poor surface contact between them causing transesterification to proceed relatively slow. Introduction of stirring improves the surface contact and consequently the reaction rates and biodiesel yields. Thus, in industrial processes, transesterification is usually carried out in stirred tank reactors. Investigating how this type of reactor works is necessary for successful design, operation and optimization. Experimental methods for investigating flow-fields and chemical reactions are expensive and time demanding and cannot meet this challenge accurately. An alternate way is to model and simulate stirred tanks by computational fluid dynamics (CFD). Thus, in this work, a CFD simulation of transesterification was performed, with reaction rates being evaluated by solving a set of differential equations describing the reaction kinetics. The concentrations profiles for the expected components were in accordance with the kinetic model, and the mass fraction patterns showed efficient mixture.

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30

Xu, Z. F., and M. C. Lin. "Kinetics and mechanism for the CH2O + NO2 reaction: A computational study." International Journal of Chemical Kinetics 35, no. 5 (2003): 184–90. http://dx.doi.org/10.1002/kin.10115.

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31

Gaidamauskaitė, E., and R. Baronas. "A Comparison of Finite Difference Schemes for Computational Modelling of Biosensors." Nonlinear Analysis: Modelling and Control 12, no. 3 (July 25, 2007): 359–69. http://dx.doi.org/10.15388/na.2007.12.3.14697.

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This paper presents a one-dimensional-in-space mathematical model of an amperometric biosensor. The model is based on the reaction-diffusion equations containing a non-linear term related to Michaelis-Menten kinetics of the enzymatic reactions. The stated problem is solved numerically by applying the finite difference method. Several types of finite difference schemes are used. The numerical results for the schemes and couple mathematical software packages are compared and verified against known analytical solutions. Calculation results are compared in terms of the precision and computation time.

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32

Lakin, Matthew R., Simon Youssef, Luca Cardelli, and Andrew Phillips. "Abstractions for DNA circuit design." Journal of The Royal Society Interface 9, no. 68 (July 20, 2011): 470–86. http://dx.doi.org/10.1098/rsif.2011.0343.

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DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations.

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33

SHIH, ANGELA, CALINA CIOBANU, and FU-MING TAO. "THEORETICAL MECHANISMS AND KINETICS FOR THE REACTION OF DIMETHYL SULFIDE AND OZONE IN WATER VAPOR." Journal of Theoretical and Computational Chemistry 04, no. 04 (December 2005): 1101–17. http://dx.doi.org/10.1142/s0219633605001982.

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The reaction mechanisms and kinetics for DMS + O 3 ⇒ DMSO + O 2 in water vapor are studied using density functional theory. A series of reaction pathways are determined with molecular clusters containing the reacting species and up to three water molecules. The results show that the energy barrier, defined as the energy difference between the reactant complex and the transition state, decreases progressively as each water molecule is added to the reacting system. A decreasing energy barrier is attributed to favorable electrostatic interactions between the reacting species and water at the transition state and at the more polar product. Rate constants for the second-order reactions, involving different combinations of hydrated reactants up to three water molecules, are calculated using transition state theory with Eckart tunneling corrections. Effective rate constants for DMS + O 3 ⇒ DMSO + O 2 are obtained using the calculated second-order rate constants and the concentrations of hydrated reactants present in saturated water vapor. The results show that the rate of reaction for DMS + O 3 ⇒ DMSO + O 2 increases dramatically in the presence of water vapor, by up to seven orders of magnitude for reactions involving three water molecules. The study implies that the gas-phase reaction of DMS with ozone is significant in the troposphere and can greatly influence the global climate.

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Ai, Jiali, Chi Zhai, and Wei Sun. "Study on the Formation of Complex Chemical Waveforms by Different Computational Methods." Processes 8, no. 4 (March 27, 2020): 393. http://dx.doi.org/10.3390/pr8040393.

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Chemical wave is a special phenomenon that presents periodic patterns in space-time domain, and the Belousov–Zhabotinsky (B-Z) reaction is the first well-known reaction-diffusion system that exhibits organized patterns out of a homogeneous environment. In this paper, the B-Z reaction kinetics is described by the Oregonator model, and formation and evolution of chemical waves are simulated based on this model. Two different simulation methods, partial differential equations (PDEs) and cellular automata (CA) are implemented to simulate the formation of chemical waveform patterns, i.e., target wave and spiral wave on a two-dimensional plane. For the PDEs method, reaction caused changes of molecules at different location are considered, as well as diffusion driven by local concentration difference. Specifically, a PDE model of the B-Z reaction is first established based on the B-Z reaction kinetics and mass transfer theory, and it is solved by a nine-point finite difference (FD) method to simulate the formation of chemical waves. The CA method is based on system theory, and interaction relations with the cells nearest neighbors are mainly concerned. By comparing these two different simulation strategies, mechanisms that cause the formation of complex chemical waves are explored, which provides a reference for the subsequent research on complex systems.

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35

Zhang, Yunju, Bing He, and Yuxi Sun. "Computational study on the mechanisms and kinetics of the CH2CCl + O2 reaction." Canadian Journal of Chemistry 98, no. 8 (August 2020): 395–402. http://dx.doi.org/10.1139/cjc-2019-0293.

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The potential energy surface for the CH2CCl + O2 reaction has been investigated by using the CCSD(T)/cc-pVTZ//B3LYP/6-311++G(d,p) method. Two type reaction mechanisms have been located. The H-abstraction of CH2CCl by O2 generates CHCCl + HO2 surmounting a 20.86 kcal/mol barrier. The addition between O2 and CH2CCl proceeds to an intermediate CH2CClO2 (IM1t and IM1c) without a barrier, which can further dissociate or isomerize to various products with the complicated processes. The temperature and pressure dependence rate constants for the CH2CCl + O2 reaction were computed by means of multi-channel RRKM-TST theory. Moreover, TDDFT calculations imply that IM1t, IM1c, IM2, IM4, IM5t, and IM5c will photolyze under the sunlight.

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36

Baiano, Carmen, Jacopo Lupi, Nicola Tasinato, Cristina Puzzarini, and Vincenzo Barone. "The Role of State-of-the-Art Quantum-Chemical Calculations in Astrochemistry: Formation Route and Spectroscopy of Ethanimine as a Paradigmatic Case." Molecules 25, no. 12 (June 22, 2020): 2873. http://dx.doi.org/10.3390/molecules25122873.

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The gas-phase formation and spectroscopic characteristics of ethanimine have been re-investigated as a paradigmatic case illustrating the accuracy of state-of-the-art quantum-chemical (QC) methodologies in the field of astrochemistry. According to our computations, the reaction between the amidogen, NH, and ethyl, C2H5, radicals is very fast, close to the gas-kinetics limit. Although the main reaction channel under conditions typical of the interstellar medium leads to methanimine and the methyl radical, the predicted amount of the two E,Z stereoisomers of ethanimine is around 10%. State-of-the-art QC and kinetic models lead to a [E−CH3CHNH]/[Z−CH3CHNH] ratio of ca. 1.4, slightly higher than the previous computations, but still far from the value determined from astronomical observations (ca. 3). An accurate computational characterization of the molecular structure, energetics, and spectroscopic properties of the E and Z isomers of ethanimine combined with millimeter-wave measurements up to 300 GHz, allows for predicting the rotational spectrum of both isomers up to 500 GHz, thus opening the way toward new astronomical observations.

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37

Eikerling, Michael, and Xinwei Zhu. "(Keynote) Deciphering Electrocatalytic Reactions with Theory and Computation: The Case of CO2 Reduction." ECS Meeting Abstracts MA2022-01, no. 49 (July 7, 2022): 2076. http://dx.doi.org/10.1149/ma2022-01492076mtgabs.

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The interfacial region between metal surface and aqueous electrolyte is of central importance for electrochemical reactions. The need to understand the properties of this electrochemical double layer (EDL) region drives extensive research.1,2 A foremost goal of research in electrocatalysis is the development of a theoretical-computational framework. The fundamental task for such a framework is to unravel the complex interplay of electronic structure effects of the catalyst material, potential-induced variations of the chemisorption state, local reaction conditions on the electrolyte side, and electrochemical kinetics of reactions of interest. A recently developed theoretical approach revealed the non-monotonic charging behaviour of a Pt electrode3 and it was thereafter used to decipher the oxygen reduction reaction.4 In the present work, we adapt this approach to study how the local reaction environment dictates the mechanism and kinetics of reduction to CO at an Ag electrode. Our hierarchical model accounts for the multistep reaction kinetics of surface reactions, local chemical equilibria (involving CO2, HCO3 -, CO3 2-, OH-, H+), the specific surface charging state at a given electrode potential, solvent polarization and ion density variations, and reactant/product transport. It integrates interface and pore-level models to account for this interplay. The combined approach rationalizes the impact of the considered effects on the kinetics of the reaction, manifested experimentally in changes of the effective Tafel slope as a function of electrode potential. Lateral interactions between chemisorbed species are seen to contribute to the decrease of the CO current density at high electrode potentials, in addition to mass transport effects, surface charging effects and pH increase. We will conclude with a discussion of the parameters that allow tuning the local reaction environment and thus the electrocatalytic activity and selectivity of the electrocatalyst. 1O.M. Magnussen and A. Gross, Toward an Atomic-Scale Understanding of Electrochemical Interface Structure and Dynamics, J. Am. Chem. Soc. 141, 4777–4790 (2019). 2M.J. Eslamibidgoli and M.H. Eikerling, Approaching the Self-consistency Challenge of Electrocatalysis with Theory and Computation, Current Opinion in Electrochemistry 9, 189-197 (2018). 3J. Huang, A. Malek, J. Zhang and M.H. Eikerling, Non-monotonic Surface Charging Behavior of Platinum: A Paradigm Change, J. Phys. Chem. C 120, 13587-13595 (2016). 4J. Huang, J. Zhang and M. Eikerling, Unifying Theoretical Framework for Deciphering the Oxygen Reduction Reaction on Platinum, Phys. Chem. Chem. Phys. 20, 11776-11786 (2018).

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38

He, Bo, Wan Sheng Nie, Song Jiang Feng, and Guo Qiang Li. "A Modified Implicit Iterative Difference Algorithm for Stiff Chemical Kinetic Equations in Complex Combustion System." Advanced Materials Research 295-297 (July 2011): 2333–40. http://dx.doi.org/10.4028/www.scientific.net/amr.295-297.2333.

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The splitting-operator method has been widely used in the numerical simulation of complex combustion system with its high computation efficiency. The main difficult encountered in the method is how to integrate the stiff chemical kinetics ordinary differential equation (ODE) efficiently and accurately in each grid node of flow field. Although several ODE software packages such as LSODE and VODE have very predominant performance in integrating stiff and non-stiff case, it couldn’t ensure the positivity of mass fraction in integrating stiff chemical kinetic ODE. A detail liquid rocket hypergolic bipropellant combination of Monomethylhydrazine (MMH)/Red Fuming Nitric Acid (RFNA) chemical mechanism consisting of 550 elementary reactions among 83 species was constituted basing on several relevant literatures firstly. And then a modified implicit iterative difference algorithm with variable time steps was developed to tackle the problem of mass fraction non-positive. The results from the integration of MMH /nitrogen tetroxide (NTO) chemical kinetic ODE indicate that the algorithm is always retain stability and positive value of mass fraction. The time step length would also be automatically adjusted at different chemical reaction time in the algorithm to keep its computational efficiency.

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39

Stack, Andrew G., and Paul R. C. Kent. "Geochemical reaction mechanism discovery from molecular simulation." Environmental Chemistry 12, no. 1 (2015): 20. http://dx.doi.org/10.1071/en14045.

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Environmental context Computational simulations are providing an increasingly useful way to isolate specific geochemical and environmental reactions and to test how important they are to the overall rate. In this review, we summarise a few ways that one can simulate a reaction and discuss each technique’s overall strengths and weaknesses. Selected case studies illustrate how these techniques have helped to improve our understanding for geochemical and environmental problems. Abstract Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. Some common methods are summarised that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and their strengths and weaknesses are also discussed. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The effect that molecular simulation has had on our understanding of geochemical reactivity is highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.

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40

Makul, Natt. "Towards Computational CO2 Capture and Storage Models." Global Environmental Engineers 8 (December 25, 2021): 55–69. http://dx.doi.org/10.15377/2410-3624.2021.08.5.

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This review is aimed to increase knowledge on computational CO2 capture and storage models that are gradually evolving in the design and development to act as more effective carbon capture agents with acceptable toxicity and costs and complementary adjuncts to experiments for comprehending amino-CO2 reaction mechanisms. Also, the review discussed experimental research of degradation reactions of aqueous organic amines, measurements, kinetics and forecasts of amine pKₐ values and amine-CO2 equilibria. Also, the researcher comprehensively discussed the computational simulation of mechanisms of carbon capture reactions. In the contexts of experimental and computational studies, the comparative advantages of bicarbonate, carbamic acid, termolecular and zwitterion are described. Computational approaches shall gradually evolve in the design and development to act as more effective carbon capture agents with acceptable toxicity and costs and complementary adjuncts to experiments for comprehending amino-CO2 reaction mechanisms. Some of the main research findings indicate that advancements in quantum computing might help in simulating larger complex molecules such as CO2. Moreover, the simulations might discover new catalysts for CO2 capture that are more efficient and cheaper than present models. CO2 capture and storage (CCS) could minimize the CO2 emission volume by 14%. The first stride in CCS is capturing CO2. It accounts for 70% -80% of this technology total costs. Virtually, 50% of the costs to operate the post-combustion capture (PCC) plants are related to steam costs. It is thus important to acquire the best possible data to avoid unnecessary costs and overdesigns.

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41

Lee, Chen-Chi, Mei-Ya Lin, Yu-Huan Lu, and Hsin-Tsung Chen. "Computational Study of the Kinetics and Mechanisms for the HCO + O3 Reaction." Journal of Physical Chemistry A 118, no. 19 (May 2014): 3395–401. http://dx.doi.org/10.1021/jp4127013.

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42

Vijayendran, Ravi A., Frances S. Ligler, and Deborah E. Leckband. "A Computational Reaction−Diffusion Model for the Analysis of Transport-Limited Kinetics." Analytical Chemistry 71, no. 23 (December 1999): 5405–12. http://dx.doi.org/10.1021/ac990672b.

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43

Chen, Hui-Lung, Ruei-Ching Jian, and Chiitang Tsai. "Reaction mechanisms and kinetics for diazomethyl radical with NO: A computational study." Chemical Physics Letters 497, no. 4-6 (September 2010): 153–58. http://dx.doi.org/10.1016/j.cplett.2010.08.004.

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44

Frei, Reto, Jonathan P. Blitz, Vladimir M. Gun’ko, Bradley E. Frost, and Victor S. Sergeev. "Kinetics and Computational Studies of an Aminosilane Reaction with a Silsesquioxane Silanol." Journal of Physical Chemistry A 113, no. 24 (June 18, 2009): 6612–19. http://dx.doi.org/10.1021/jp9002998.

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45

Zavala-Oseguera, Claudia, Annia Galano, and Gabriel Merino. "Computational Study on the Kinetics and Mechanism of the Carbaryl + OH Reaction." Journal of Physical Chemistry A 118, no. 36 (August 27, 2014): 7776–81. http://dx.doi.org/10.1021/jp507244s.

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46

Cimas, Alvaro, José A. Gámez, Otilia Mó, Manuel Yáñez, and Jean-Yves Salpin. "Computational study on the kinetics of the reaction between Ca2+ and urea." Chemical Physics Letters 456, no. 4-6 (May 2008): 156–61. http://dx.doi.org/10.1016/j.cplett.2008.03.042.

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47

Berry, R. J., and Paul Marshall. "A computational study of the reaction kinetics of methyl radicals with trifluorohalomethanes." International Journal of Chemical Kinetics 30, no. 3 (1998): 179–84. http://dx.doi.org/10.1002/(sici)1097-4601(1998)30:3<179::aid-kin2>3.0.co;2-p.

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48

Planas, Ferran, Michael J. McLeish, and Fahmi Himo. "Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis." Beilstein Journal of Organic Chemistry 15 (January 16, 2019): 145–59. http://dx.doi.org/10.3762/bjoc.15.15.

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Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon–carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate. Given that the cofactor can adopt up to seven states on an enzyme, identifying the factors affecting the stability of the pre-reactant states is important for the overall understanding of the kinetics and mechanism of the individual reactions. In this paper we use density functional theory calculations to systematically study the different cofactor states in terms of energies and geometries. Benzoylformate decarboxylase (BFDC), which is a well characterized chiral catalyst, serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as inhibitor). Overall, the calculations reveal that the relative stabilities of the cofactor states are greatly affected by the presence and identity of the bound ligands. A surprising finding is that benzoylformate binding, while favoring ylide formation, provided even greater stabilization to a catalytically inactive tricyclic state. Conversely, the inhibitor binding greatly destabilized the ylide formation. Together, these observations have significant implications for the reaction kinetics of the ThDP-dependent enzymes, and, potentially, for the use of unnatural substrates in such reactions.

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Jafarzadeh, Siavash, Ziguang Chen, and Florin Bobaru. "Computational modeling of pitting corrosion." Corrosion Reviews 37, no. 5 (September 25, 2019): 419–39. http://dx.doi.org/10.1515/corrrev-2019-0049.

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AbstractPitting corrosion damage is a major problem affecting material strength and may result in difficult to predict catastrophic failure of metallic material systems and structures. Computational models have been developed to study and predict the evolution of pitting corrosion with the goal of, in conjunction with experiments, providing insight into pitting processes and their consequences in terms of material reliability. This paper presents a critical review of the computational models for pitting corrosion. Based on the anodic reaction (dissolution) kinetics at the corrosion front, transport kinetics of ions in the electrolyte inside the pits, and time evolution of the damage (pit growth), these models can be classified into two categories: (1) non-autonomous models that solve a classical transport equation and, separately, solve for the evolution of the pit boundary; and (2) autonomous models like cellular automata, peridynamics, and phase-field models which address the transport, dissolution, and autonomous pit growth in a unified framework. We compare these models with one another and comment on the advantages and disadvantages of each of them. We especially focus on peridynamic and phase-filed models of pitting corrosion. We conclude the paper with a discussion of open areas for future developments.

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50

Horenko, Illia, Sönke Lorenz, Christof Schütte, and Wilhelm Huisinga. "Adaptive approach for nonlinear sensitivity analysis of reaction kinetics." Journal of Computational Chemistry 26, no. 9 (2005): 941–48. http://dx.doi.org/10.1002/jcc.20234.

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