Predicting the properties of a new class of host–guest complexes: C60 fullerene and CB[9] cucurbituril

2014 ◽  
Vol 16 (41) ◽  
pp. 22823-22829 ◽  
Author(s):  
Eudes Fileti ◽  
Guilherme Colherinhas ◽  
Thaciana Malaspina
Keyword(s):  
Molecular Dynamics ◽  
Inclusion Complex ◽  
C60 Fullerene ◽  
Structure And Stability ◽  
New Class ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Methods ◽  
Semi Empirical

DFT, semi-empirical and classical molecular dynamics methods were used to describe the structure and stability of the inclusion complex formed by the fullerene C60 and the cucurbituril CB[9].

Evaluation of Mixed Quantum-Classical Molecular Dynamics on cis‐Azobenzene Photoisomerization

2021 ◽  
Author(s):  
Diandong Tang ◽  
Lin Shen ◽  
Wei-hai Fang
Keyword(s):  
Molecular Dynamics ◽  
Electronic State ◽  
Quantitative Prediction ◽  
Surface Hopping ◽  
Ultrafast Processes ◽  
Nonadiabatic Transitions ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Methods

The quantitative prediction on nonadiabatic transitions between different electronic state is important to understand ultrafast processes in photochemistry. A variety of mixed quantum-classical molecular dynamics methods such as surface hopping...

Molecular Dynamics Simulation of Femtosecond Pump-Probe Experiments on I2 in Ar Environments

2000 ◽  
Vol 214 (9) ◽  
Author(s):  
V.A. Ermoshin ◽  
V. Engel
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Time Resolved ◽  
Pump Probe ◽  
Classical Molecular Dynamics ◽  
Molecular Dynamics Methods

We present the application of classical molecular dynamics methods to the simulation of femtosecond time-resolved experiments. Choosing I

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 An Investigation into the Approximations Used in Wave Packet Molecular Dynamics for the Study of Warm Dense Matter

Plasma ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 294-308
Author(s):  
William A. Angermeier ◽  
Thomas G. White
Keyword(s):  
Molecular Dynamics ◽  
Wave Packet ◽  
Hydrogen Plasma ◽  
Valence Bond ◽  
Dense Matter ◽  
Basis Set ◽  
Warm Dense Matter ◽  
Scaling Parameters ◽  
Oppenheimer Approximation ◽  
Semi Empirical

Wave packet molecular dynamics (WPMD) has recently received a lot of attention as a computationally fast tool with which to study dynamical processes in warm dense matter beyond the Born–Oppenheimer approximation. These techniques, typically, employ many approximations to achieve computational efficiency while implementing semi-empirical scaling parameters to retain accuracy. We investigated three of the main approximations ubiquitous to WPMD: a restricted basis set, approximations to exchange, and the lack of correlation. We examined each of these approximations in regard to atomic and molecular hydrogen in addition to a dense hydrogen plasma. We found that the biggest improvement to WPMD comes from combining a two-Gaussian basis with a semi-empirical correction based on the valence-bond wave function. A single parameter scales this correction to match experimental pressures of dense hydrogen. Ultimately, we found that semi-empirical scaling parameters are necessary to correct for the main approximations in WPMD. However, reducing the scaling parameters for more ab-initio terms gives more accurate results and displays the underlying physics more readily.

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