Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions:  The Nucleophilic Attack in Subtilisin

1998 ◽  
Vol 102 (12) ◽  
pp. 2293-2301 ◽  
Author(s):  
J. Bentzien ◽  
R. P. Muller ◽  
J. Florián ◽  
A. Warshel
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Nucleophilic Attack ◽  
Enzymatic Reactions ◽  
Molecular Mechanics Calculations ◽  
Energy Surfaces

BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: from semi-empirical to ab initio

2019 ◽  
Vol 21 (39) ◽  
pp. 21942-21959 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Indirect Method ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Energy Simulations ◽  
Semi Empirical

The indirect method for the construction of quantum mechanics (QM)/molecular mechanics (MM) free energy landscapes provides a cheaper alternative for free energy simulations at the QM level.

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 Mechanism and kinetics for both thermal and electrochemical reduction of N2 catalysed by Ru(0001) based on quantum mechanics

2019 ◽  
Vol 21 (32) ◽  
pp. 17605-17612 ◽  
Author(s):  
Liang-Yu Chen ◽  
Tung-Chun Kuo ◽  
Zih-Siang Hong ◽  
Mu-Jeng Cheng ◽  
William A. Goddard
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Electrochemical Reduction ◽  
Mechanism And Kinetics ◽  
Energy Surfaces

QM calculations were used to predict the free energy surfaces for N2 thermal and electrochemical reduction (N2TR and N2ER) on Ru(0001), to find the detailed atomistic mechanism and kinetics, and provide the basis for improving the efficiency of N2ER.

Protonation structure of the photosynthetic water oxidizing complex in the S0 state as revealed by normal mode analysis using quantum mechanics/molecular mechanics calculations

2020 ◽  
Vol 22 (42) ◽  
pp. 24213-24225
Author(s):  
Masao Yamamoto ◽  
Shin Nakamura ◽  
Takumi Noguchi
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Molecular Vibrations ◽  
Molecular Mechanics Calculations ◽  
Water Oxidizing Complex

Protonation structure of the first intermediate of the water oxidizing complex was determined by QM/MM calculations of molecular vibrations.

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