scholarly journals The influence of external electric fields on proton transfer tautomerism in the guanine–cytosine base pair

2021 ◽  
Vol 23 (10) ◽  
pp. 6252-6265
Author(s):  
Alexander Gheorghiu ◽  
Peter V. Coveney ◽  
Alya A. Arabi
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Proton Transfer ◽  
Molecular Mechanics ◽  
Electric Fields ◽  
Base Pair ◽  
Realistic Model ◽  
External Electric Fields ◽  
Classical Molecular Dynamics

A detailed investigation is reported of mutagenic guanine–cytosine tautomerization in a realistic model of DNA bathed in intense electric fields using a combination of classical molecular dynamics and quantum mechanics/molecular mechanics methods.

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.

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 Molecular Dynamics Simulations of Liquid-Liquid Interfaces in an Electric Field: the Water-1,2-Dichloroethane Interface

2020 ◽  
Author(s):  
Paolo Raiteri ◽  
Peter Kraus ◽  
Julian Gale
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Molecular Dynamics Simulations ◽  
External Electric Field ◽  
Electric Fields ◽  
Liquid Interfaces ◽  
Ewald Summation ◽  
External Electric Fields ◽  
Simulation Cell ◽  
Dynamics Simulations

Molecular dynamics simulations of the liquid-liquid interface between water and 1,2-Dichloroethane in the presence of weak external electric fields.<div>The effect of the use of 3D periodic Ewald summation and the effect of the simulation setup are discussed.</div><div>A new simple geometric method for designing the simulation cell is proposed. This method was thoroughly tested shown that it mitigates any artefacts to the use of 3D Ewald summation with external electric field.</div>

The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics†

2012 ◽  
Vol 34 (9) ◽  
pp. 750-756 ◽  
Author(s):  
Marcin Nowosielski ◽  
Marcin Hoffmann ◽  
Aneta Kuron ◽  
Malgorzata Korycka-Machala ◽  
Jaroslaw Dziadek
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics

scholarly journals Possibility of realizing superionic ice VII in external electric fields of planetary bodies

2020 ◽  
Vol 6 (21) ◽  
pp. eaaz2915 ◽  
Author(s):  
Zdenek Futera ◽  
John S. Tse ◽  
Niall J. English
Keyword(s):  
Molecular Dynamics ◽  
Electric Field ◽  
Ab Initio ◽  
Electric Fields ◽  
State Of The Art ◽  
Ab Initio Molecular Dynamics ◽  
Theoretical Studies ◽  
Potential Candidate ◽  
External Electric Fields ◽  
Ice Phase

In a superionic (SI) ice phase, oxygen atoms remain crystallographically ordered while protons become fully diffusive as a result of intramolecular dissociation. Ice VII’s importance as a potential candidate for a SI ice phase has been conjectured from anomalous proton diffusivity data. Theoretical studies indicate possible SI prevalence in large-planet mantles (e.g., Uranus and Neptune) and exoplanets. Here, we realize sustainable SI behavior in ice VII by means of externally applied electric fields, using state-of-the-art nonequilibrium ab initio molecular dynamics to witness at first hand the protons’ fluid dance through a dipole-ordered ice VII lattice. We point out the possibility of SI ice VII on Venus, in its strong permanent electric field.

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