scholarly journals Conformational evolution following the sequential molecular dehydrogenation of PMDI on a Cu(111) surface

2021 ◽  
Author(s):  
Lacheng Liu ◽  
Alexander Timmer ◽  
Elena KOLODZEISKI ◽  
Hongying Gao ◽  
Harry Mönig ◽  
...  
Keyword(s):  
Chemical Reaction ◽  
Reaction Pathway ◽  
Chemical Processes ◽  
Theoretical Methods

Molecular spatial conformational evolution following the corresponding chemical reaction pathway at surfaces is important to understand and optimize chemical processes. Combining experimental and theoretical methods, the sequential N−H and C−H...

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>

scholarly journals Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data

2020 ◽  
Author(s):  
Timur Gimadiev ◽  
Ramil Nugmanov ◽  
Dinar Batyrshin ◽  
Timur Madzhidov ◽  
Satoshi Maeda ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Chemical Reaction ◽  
Relational Database ◽  
Quantum Chemical ◽  
Reaction Pathway ◽  
Transition States ◽  
Structural Data ◽  
Database Management System ◽  
Pathway Data ◽  
Machine Learning Applications

Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

Metallothermic reduction as an electronically mediated reaction

1998 ◽  
Vol 13 (12) ◽  
pp. 3372-3377 ◽  
Author(s):  
Toru H. Okabe ◽  
Donald R. Sadoway
Keyword(s):  
Mass Transfer ◽  
Electron Transfer ◽  
Electron Transport ◽  
Chemical Reaction ◽  
Reaction Pathway ◽  
Tantalum Powder ◽  
Metallothermic Reduction ◽  
Rate Of Reaction

The commonly held view that metallothermic reduction is strictly a chemical reaction and that the process is rate limited by mass transfer has been found to be incomplete. In a study of the production of tantalum powder by the reaction of K2TaF7 with sodium, it has been shown that there are two dominant kinetic pathways, both involving electron transfer. Furthermore, the overall rate of reaction is limited by electron transport between the reactants. This indicates that metallothermic reduction is an “electronically mediated reaction” (EMR). Experiments found that the location of the tantalum deposit and its morphology are governed by the reaction pathway.

scholarly journals A graph-based network for predicting chemical reaction pathways in solid-state materials synthesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Matthew J. McDermott ◽  
Shyam S. Dwaraknath ◽  
Kristin A. Persson
Keyword(s):  
Solid State ◽  
Chemical Reaction ◽  
Reaction Pathway ◽  
Reaction Network ◽  
Functional Materials ◽  
Reaction Pathways ◽  
Materials Synthesis ◽  
Pathway Prediction ◽  
Solid State Materials ◽  
Cost Paths

AbstractAccelerated inorganic synthesis remains a significant challenge in the search for novel, functional materials. Many of the principles which enable “synthesis by design” in synthetic organic chemistry do not exist in solid-state chemistry, despite the availability of extensive computed/experimental thermochemistry data. In this work, we present a chemical reaction network model for solid-state synthesis constructed from available thermochemistry data and devise a computationally tractable approach for suggesting likely reaction pathways via the application of pathfinding algorithms and linear combination of lowest-cost paths in the network. We demonstrate initial success of the network in predicting complex reaction pathways comparable to those reported in the literature for YMnO3, Y2Mn2O7, Fe2SiS4, and YBa2Cu3O6.5. The reaction network presents opportunities for enabling reaction pathway prediction, rapid iteration between experimental/theoretical results, and ultimately, control of the synthesis of solid-state materials.

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>

scholarly journals Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data

2020 ◽  
Author(s):  
Timur Gimadiev ◽  
Ramil Nugmanov ◽  
Dinar Batyrshin ◽  
Timur Madzhidov ◽  
Satoshi Maeda ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Chemical Reaction ◽  
Relational Database ◽  
Quantum Chemical ◽  
Reaction Pathway ◽  
Transition States ◽  
Structural Data ◽  
Database Management System ◽  
Pathway Data ◽  
Machine Learning Applications

Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

scholarly journals Electrocatalytic oxidation of phenol from wastewater using Ti/SnO2–Sb2O4 electrode: chemical reaction pathway study

2016 ◽  
Vol 23 (19) ◽  
pp. 19735-19743 ◽  
Author(s):  
Mahshid Loloi ◽  
Abbas Rezaee ◽  
Mahmood Aliofkhazraei ◽  
Alireza Sabour Rouhaghdam
Keyword(s):  
Chemical Reaction ◽  
Electrocatalytic Oxidation ◽  
Reaction Pathway ◽  
Oxidation Of Phenol
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