Chemical Dynamics Simulations on Association and Ensuing Dissociation of a Benzene–Hexafluorobenzene Molecular System

2019 ◽  
Vol 123 (24) ◽  
pp. 5019-5026 ◽  
Author(s):  
Himashree Mahanta ◽  
Daradi Baishya ◽  
Sk. Samir Ahamed ◽  
Amit K. Paul
Keyword(s):  
Molecular System ◽  
Chemical Dynamics ◽  
Dynamics Simulations

Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

Data Reduction Through Increased Data Utilization in Chemical Dynamics Simulations

2017 ◽  
Vol 9 ◽  
pp. 57-66 ◽  
Author(s):  
Misha Ahmadian ◽  
Yu Zhuang ◽  
William L. Hase ◽  
Yong Chen
Keyword(s):  
Data Reduction ◽  
Chemical Dynamics ◽  
Data Utilization ◽  
Dynamics Simulations

The VENUS/NWChem software package. Tight coupling between chemical dynamics simulations and electronic structure theory

2014 ◽  
Vol 185 (3) ◽  
pp. 1074-1080 ◽  
Author(s):  
Upakarasamy Lourderaj ◽  
Rui Sun ◽  
Swapnil C. Kohale ◽  
George L. Barnes ◽  
Wibe A. de Jong ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Software Package ◽  
Electronic Structure Theory ◽  
Structure Theory ◽  
Chemical Dynamics ◽  
Tight Coupling ◽  
Dynamics Simulations

scholarly journals Investigating Tunneling Controlled Chemical Reactions Through Ab-Initio Ring Polymer Molecular Dynamics

2021 ◽  
Author(s):  
Xinyang Li ◽  
Pengfei Huo
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Chemical Reaction ◽  
Quantum Tunneling ◽  
Quantum Dynamics ◽  
Density Functional ◽  
Molecular System ◽  
Ring Polymer ◽  
Ring Polymer Molecular Dynamics ◽  
Dynamics Simulations

<div>We use the ab-initio ring polymer molecular dynamics (RPMD) approach to investigate tunneling controlled reactions in methylhydroxycarbene. Nuclear tunneling effects enable molecules to overcome the barriers which can not be overcome classically. Under low-temperature conditions, intrinsic quantum tunneling effects canfacilitate the chemical reaction in a pathway that is neither favored thermodynamically nor kinetically. This</div><div>behavior is referred to as the tunneling controlled chemical reaction and regarded as the third paradigm of chemical</div><div>reaction controls. In this work, we use the ab-initio RPMD approach to incorporate the tunneling effects in our quantum dynamics simulations. The reaction kinetics of two competitive reaction pathways at various temperatures are investigated with the Kohn-Sham density functional theory (KS-DFT) on-the-fly molecular dynamics simulations and the ring polymer quantization of the nuclei. The reaction rate constants obtained here agree extremely well with the experimentally measured rates. We demonstrate the feasibility of using ab-initio RPMD rate calculations in a realistic molecular system, and provide an interesting and important example for future investigations on reaction mechanisms dominated by quantum tunneling effects.</div>

scholarly journals Recombination and chemical energy accommodation coefficients from chemical dynamics simulations: O/O2 mixtures reacting over a β-cristobalite (001) surface

2011 ◽  
Vol 13 (39) ◽  
pp. 17494 ◽  
Author(s):  
Víctor Morón ◽  
Pablo Gamallo ◽  
Ludovic Martin-Gondre ◽  
Cédric Crespos ◽  
Pascal Larregaray ◽  
...  
Keyword(s):  
Chemical Energy ◽  
Chemical Dynamics ◽  
Energy Accommodation ◽  
Accommodation Coefficients ◽  
Dynamics Simulations
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