A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

2018 ◽  
Author(s):  
Yasemin Basdogan ◽  
John Keith
Keyword(s):  
Reaction Mechanism ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Optimization Procedure ◽  
Cost Effective ◽  
Chemical Reaction Mechanisms ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

2018 ◽  
Author(s):  
Yasemin Basdogan ◽  
John Keith
Keyword(s):  
Reaction Mechanism ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Optimization Procedure ◽  
Cost Effective ◽  
Chemical Reaction Mechanisms ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

Determination of Complex Reaction Mechanisms

2006 ◽  
Author(s):  
John Ross ◽  
Igor Schreiber ◽  
Marcel O. Vlad
Keyword(s):  
Reaction Mechanism ◽  
Reaction Mechanisms ◽  
Reaction Pathway ◽  
Chemical Species ◽  
Rate Coefficients ◽  
Chemical System ◽  
Evolutionary Development ◽  
Complex Reaction ◽  
Oscillatory Reactions

In a chemical system with many chemical species several questions can be asked: what species react with other species: in what temporal order: and with what results? These questions have been asked for over one hundred years about simple and complex chemical systems, and the answers constitute the macroscopic reaction mechanism. In Determination of Complex Reaction Mechanisms authors John Ross, Igor Schreiber, and Marcel Vlad present several systematic approaches for obtaining information on the causal connectivity of chemical species, on correlations of chemical species, on the reaction pathway, and on the reaction mechanism. Basic pulse theory is demonstrated and tested in an experiment on glycolysis. In a second approach, measurements on time series of concentrations are used to construct correlation functions and a theory is developed which shows that from these functions information may be inferred on the reaction pathway, the reaction mechanism, and the centers of control in that mechanism. A third approach is based on application of genetic algorithm methods to the study of the evolutionary development of a reaction mechanism, to the attainment given goals in a mechanism, and to the determination of a reaction mechanism and rate coefficients by comparison with experiment. Responses of non-linear systems to pulses or other perturbations are analyzed, and mechanisms of oscillatory reactions are presented in detail. The concluding chapters give an introduction to bioinformatics and statistical methods for determining reaction mechanisms.

scholarly journals Experimental validation of the reaction mechanism models of dechlorination and [Zn] reclaiming in the roasting steelmaking zinc-rich dust process

2020 ◽  
Vol 39 (1) ◽  
pp. 107-116
Author(s):  
Hongyang Wang ◽  
Kai Dong ◽  
Rong Zhu
Keyword(s):  
Reaction Mechanism ◽  
Dust Particle ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Experimental Validation ◽  
Step Process ◽  
Mass Percent ◽  
Mechanism Model ◽  
Air Atmosphere ◽  
Almost All

AbstractThe reaction mechanism models of dechlorination and [Zn] reclaiming in the roasting steelmaking zincrich dust process are studied. The dust collected from a steelwork contains 63.8% zinc and 3.18% chlorine (mass percent), of which, almost all zinc elements exist in ZnO and ZnCl2 forms, and all the chlorine elements are stored in ZnCl2. When the dust is roasted at above 732∘C in an air atmosphere, the ZnCl2 in the steelmaking zinc-rich dust is volatilized into steam and then oxidized into ZnO. Finding the position where the chemical reaction occurs is the key to determining the reaction mechanisms of dechlorination and [Zn] reclaiming. In this study, two groups of thermal experiments are designed and executed for roasting in different atmosphere environments and at different roasting temperatures. Based on the experiment results, the mechanism model is discussed and built, and the reaction of dechlorination and [Zn] reclaiming is shown to be a multi-step process. Because O2 from the air cannot transmit into the dust particle interior or dust bed effectively, the chemical reaction of [Zn] reclaiming occurs in the external gas environment outside of the dust, where the [Zn] recalcining reaction should be limited by the dynamics of new nucleation of ZnO solids.

scholarly journals Machine Learning Guided Approach for Studying Solvation Environments

2019 ◽  
Author(s):  
Yasemin Basdogan ◽  
Mitchell C. Groenenboom ◽  
Ethan Henderson ◽  
Sandip De ◽  
Susan Rempe ◽  
...  
Keyword(s):  
A Priori ◽  
Optimization Procedure ◽  
Low Energy ◽  
Free Energies ◽  
Continuum Approach ◽  
Explicit Solvent ◽  
Linear Dimensionality Reduction ◽  
Solvent Molecules ◽  
Dynamics Simulations ◽  
Solvation Free Energies

<div><div><div><p>Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics based cluster-continuum approach for calculating single ion solvation free energies. This approach uses a global optimization procedure to identify low energy molecular clusters with different numbers of explicit solvent molecules and then employs the Smooth Overlap for Atomic Positions (SOAP) kernel to quantify the similarity between different low energy solute environments. From these data, we use sketch-map, a non-linear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies with errors within five percent of experimental measurements for most cases.</p></div></div></div>

Models and Explanations: Understanding Chemical Reaction Mechanisms

2000 ◽  
Author(s):  
Barry K. Carpenter
Keyword(s):  
Internal Rotation ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Second Law Of Thermodynamics ◽  
The Other ◽  
Second Law ◽  
Original Design ◽  
Mechanical Analogy ◽  
Boston College ◽  
Chemical Reaction Mechanisms

In 1997, Ross Kelly and his coworkers at Boston College reported their results from an experiment with an intriguing premise (Kelly et al., 1997; see also Kelly et al., 1998). They had synthesized the molecule shown in figure 12.1. It was designed to be a “molecular ratchet,” so named because it appeared that it should undergo internal rotation about the A—B bond more readily in one direction than the other. The reason for thinking this might occur was that the benzophenanthrene moiety—the “pawl” of the ratchet—was anticipated to be helical. Thus, in some sense, this might be an inverse ratchet where the asymmetry dictating the sense of rotation would reside in the pawl rather than in the “teeth” on the “wheel” (the triptycene unit) as it does in a normal mechanical ratchet. Kelly and coworkers designed an elegant experiment to determine whether their molecular ratchet was functioning as anticipated, and they were (presumably) disappointed to find that it was not—internal rotation about the A—B bond occurred at equal rates in each direction. In 1998 Davis pointed out that occurrence of the desired behavior of the molecular ratchet would have constituted a violation of the second law of thermodynamics (Davis, 1998). With hindsight, I think most chemists would agree that Davis’s critique is unassailable, although the appeal of the mechanical analogy was so strong that I imagine those same chemists would also understand if Kelly et al. had overlooked the thermodynamic consequences of their proposal in the original design of the experiment. But now comes the interesting question: Suppose Kelly et al. had been fully aware that their experiment, if successful, would undermine the second law of thermodynamics, should they have conducted it anyway? Davis, in his critique writes: . . .Some would argue that this experiment was misconceived. To challenge the Second Law may be seen as scientific heresy (a nice irony, considering the Jesuit origins of Boston College), and the theoretical arguments against molecular ratchets and trapdoors are well developed. . . .

scholarly journals Reduced chemical reaction mechanisms for simulating sodium emissions by solid-fuel combustion

2020 ◽  
Vol 1-4 ◽  
pp. 100009
Author(s):  
Kaidi Wan ◽  
Luc Vervisch ◽  
Zhenxun Gao ◽  
Pascale Domingo ◽  
Chongwen Jiang ◽  
...  
Keyword(s):  
Chemical Reaction ◽  
Solid Fuel ◽  
Reaction Mechanisms ◽  
Fuel Combustion ◽  
Solid Fuel Combustion ◽  
Chemical Reaction Mechanisms
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