Chemical dynamics simulations of the monohydrated OH−(H2O) + CH3I reaction. Atomic-level mechanisms and comparison with experiment

2015 ◽  
Vol 142 (24) ◽  
pp. 244308 ◽  
Author(s):  
Jing Xie ◽  
Rico Otto ◽  
Roland Wester ◽  
William L. Hase
Keyword(s):  
Atomic Level ◽  
Chemical Dynamics ◽  
Comparison With Experiment ◽  
Dynamics Simulations

Comparison of direct dynamics simulations with different electronic structure methods. F− + CH3I with MP2 and DFT/B97-1

2015 ◽  
Vol 17 (4) ◽  
pp. 2589-2597 ◽  
Author(s):  
Rui Sun ◽  
Collin J. Davda ◽  
Jiaxu Zhang ◽  
William L. Hase
Keyword(s):  
Electronic Structure ◽  
Atomic Level ◽  
Chemical Dynamics ◽  
Ion Imaging ◽  
Direct Dynamics ◽  
Electronic Structure Methods ◽  
Dynamics Simulations

In previous work, ion imaging experiments and direct chemical dynamics simulations with DFT/B97-1 were performed to study the atomic-level dynamics of the F− + CH3I → FCH3 + I− SN2 reaction at different collision energies.

scholarly journals A QM/MM Evaluation of the Missing Step in the Reduction Mechanism of HMG-CoA by Human HMG-CoA Reductase

Processes ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 1085
Author(s):  
Paula Mihaljević-Jurič ◽  
Sérgio F. Sousa
Keyword(s):  
Mevalonate Pathway ◽  
Atomic Level ◽  
Amino Acid Residues ◽  
Protonation State ◽  
Primary Target ◽  
Cholesterol Levels ◽  
The Subject ◽  
Electron Reduction ◽  
Dynamics Simulations ◽  
Coa Reductase

Statins are important drugs in the regulation of cholesterol levels in the human body that have as a primary target the enzyme β-hydroxy-β-methylglutaryl-CoA reductase (HMGR). This enzyme plays a crucial role in the mevalonate pathway, catalyzing the four-electron reduction of HMG-CoA to mevalonate. A second reduction step of this reaction mechanism has been the subject of much speculation in the literature, with different conflicting theories persisting to the present day. In this study, the different mechanistic hypotheses were evaluated with atomic-level detail through a combination of molecular dynamics simulations (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The obtained Gibbs free activation and Gibbs free reaction energy (15 kcal mol−1 and −40 kcal mol−1) show that this hydride step takes place with the involvement of a cationic His405 and Lys639, and a neutral Glu98, while Asp715 remains in an anionic state. The results provide an atomic-level portrait of this step, clearly demonstrating the nature and protonation state of the amino acid residues involved, the energetics associated, and the structure and charge of the key participating atoms in the several intermediate states, finally elucidating this missing step.

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 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

scholarly journals Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

2019 ◽  
Vol 21 (1) ◽  
pp. 1-31 ◽  
Author(s):  
Lindong Weng ◽  
Shannon L. Stott ◽  
Mehmet Toner
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Motion ◽  
State Of The Art ◽  
Level Structure ◽  
Cost Effective ◽  
Atomic Level ◽  
Computational Research ◽  
Dynamics Simulations ◽  
Biological Entities

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

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
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