scholarly journals A hydrated ion model of [UO2]2+ in water: Structure, dynamics, and spectroscopy from classical molecular dynamics

2016 ◽  
Vol 145 (22) ◽  
pp. 224502 ◽  
Author(s):  
Sergio Pérez-Conesa ◽  
Francisco Torrico ◽  
José M. Martínez ◽  
Rafael R. Pappalardo ◽  
Enrique Sánchez Marcos
Keyword(s):  
Molecular Dynamics ◽  
Water Structure ◽  
Structure Dynamics ◽  
Classical Molecular Dynamics ◽  
Hydrated Ion

Protic ammonium carboxylate ionic liquids: insight into structure, dynamics and thermophysical properties by alkyl group functionalization

2017 ◽  
Vol 19 (16) ◽  
pp. 10358-10370 ◽  
Author(s):  
Th. Dhileep N. Reddy ◽  
Bhabani S. Mallik
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Alkyl Group ◽  
Structure Dynamics ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Insight Into

This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations.

scholarly journals Cation and Water Structure, Dynamics, and Energetics in Smectite Clays: A Molecular Dynamics Study of Ca–Hectorite

2016 ◽  
Vol 120 (23) ◽  
pp. 12429-12439 ◽  
Author(s):  
Narasimhan Loganathan ◽  
A. Ozgur Yazaydin ◽  
Geoffrey M. Bowers ◽  
Andrey G. Kalinichev ◽  
R. James Kirkpatrick
Keyword(s):  
Molecular Dynamics ◽  
Water Structure ◽  
Structure Dynamics ◽  
Smectite Clays

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

scholarly journals Unveiling the Interplay Between Diffusing CO2 and Ethanol Molecules in Champagne Wines by Classical Molecular Dynamics and 13C NMR Spectroscopy

2014 ◽  
Vol 5 (24) ◽  
pp. 4232-4237 ◽  
Author(s):  
David A. Bonhommeau ◽  
Alexandre Perret ◽  
Jean-Marc Nuzillard ◽  
Clara Cilindre ◽  
Thibaud Cours ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
13C Nmr ◽  
13C Nmr Spectroscopy ◽  
Classical Molecular Dynamics
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