QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis

2010 ◽  
pp. 331-353
Author(s):  
Haiyan Liu
Keyword(s):  
Free Energy ◽  
Enzyme Catalysis ◽  
Energy Functions ◽  
Energy Simulations

scholarly journals Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

2018 ◽  
Vol 20 (31) ◽  
pp. 20650-20660 ◽  
Author(s):  
Heather J. Kulik
Keyword(s):  
Free Energy ◽  
Charge Transfer ◽  
Long Range ◽  
Enzyme Catalysis ◽  
Active Sites ◽  
Large Scale ◽  
Enzyme Active Sites ◽  
Energy Simulations

Large-scale QM/MM free energy simulations reveal long-range fluctuations in charges on residues in enzyme active sites during dynamics.

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

Inspection of free energy functions in gradient crystal plasticity

2013 ◽  
Vol 29 (6) ◽  
pp. 763-772 ◽  
Author(s):  
Samuel Forest ◽  
Nicolas Guéninchault
Keyword(s):  
Free Energy ◽  
Crystal Plasticity ◽  
Energy Functions

scholarly journals Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations

2018 ◽  
pp. 53-90 ◽  
Author(s):  
Daniel Roston ◽  
Xiya Lu ◽  
Dong Fang ◽  
Darren Demapan ◽  
Qiang Cui
Keyword(s):  
Free Energy ◽  
Phosphoryl Transfer ◽  
Energy Simulations
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