The Role of Bonded Terms in Free Energy Simulations:  1. Theoretical Analysis

1999 ◽  
Vol 103 (1) ◽  
pp. 103-118 ◽  
Author(s):  
Stefan Boresch ◽  
Martin Karplus
Keyword(s):  
Free Energy ◽  
Theoretical Analysis ◽  
Energy Simulations

scholarly journals Role of the Active Site Guanine in theglmSRibozyme Self-Cleavage Mechanism: Quantum Mechanical/Molecular Mechanical Free Energy Simulations

2015 ◽  
Vol 137 (2) ◽  
pp. 784-798 ◽  
Author(s):  
Sixue Zhang ◽  
Abir Ganguly ◽  
Puja Goyal ◽  
Jamie L. Bingaman ◽  
Philip C. Bevilacqua ◽  
...  
Keyword(s):  
Free Energy ◽  
Active Site ◽  
Quantum Mechanical ◽  
Energy Simulations

The Role of Bonded Terms in Free Energy Simulations. 2. Calculation of Their Influence on Free Energy Differences of Solvation

1999 ◽  
Vol 103 (1) ◽  
pp. 119-136 ◽  
Author(s):  
Stefan Boresch ◽  
Martin Karplus
Keyword(s):  
Free Energy ◽  
Energy Simulations

The Role of Bonded Energy Terms in Free Energy Simulations - Insights from Analytical Results

2002 ◽  
Vol 28 (1-2) ◽  
pp. 13-37 ◽  
Author(s):  
Stefan Boresch
Keyword(s):  
Free Energy ◽  
Analytical Results ◽  
Energy Simulations

scholarly journals Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations

2018 ◽  
Vol 140 (28) ◽  
pp. 8965-8969 ◽  
Author(s):  
David R. Stevens ◽  
Sharon Hammes-Schiffer
Keyword(s):  
Free Energy ◽  
Dna Polymerase ◽  
Active Site ◽  
Metal Ion ◽  
The Third ◽  
Energy Simulations

QM/MM Free-Energy Simulations of Reaction in Serratia marcescens Chitinase B Reveal the Protonation State of Asp142 and the Critical Role of Tyr214

2014 ◽  
Vol 118 (18) ◽  
pp. 4771-4783 ◽  
Author(s):  
Jitrayut Jitonnom ◽  
Michael A. L. Limb ◽  
Adrian J. Mulholland
Keyword(s):  
Free Energy ◽  
Serratia Marcescens ◽  
Critical Role ◽  
Protonation State ◽  
Energy Simulations

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>

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