scholarly journals The Coupling between Stability and Ion Pair Formation in Magnesium Electrolytes from First-Principles Quantum Mechanics and Classical Molecular Dynamics

2015 ◽  
Vol 137 (9) ◽  
pp. 3411-3420 ◽  
Author(s):  
Nav Nidhi Rajput ◽  
Xiaohui Qu ◽  
Niya Sa ◽  
Anthony K. Burrell ◽  
Kristin A. Persson
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
First Principles ◽  
Ion Pair ◽  
Pair Formation ◽  
Ion Pair Formation ◽  
Classical Molecular Dynamics

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.

Extraction of organic acids by ion-pair formation with tri-n-octylamine

1985 ◽  
Vol 178 ◽  
pp. 189-195 ◽  
Author(s):  
M. Puttemans ◽  
L. Dryon ◽  
D.L. Massart
Keyword(s):  
Organic Acids ◽  
Ion Pair ◽  
Pair Formation ◽  
Ion Pair Formation

scholarly journals Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

Charge-transfer stabilization of molecular bicimers: ion pair formation in diarylmethanes

1988 ◽  
Vol 92 (7) ◽  
pp. 1703-1705 ◽  
Author(s):  
R. J. Locke ◽  
Steve H. Modiano ◽  
E. C. Lim
Keyword(s):  
Charge Transfer ◽  
Ion Pair ◽  
Pair Formation ◽  
Ion Pair Formation
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