Calculating Chemically Accurate Redox Potentials for Engineered Flavoproteins from Classical Molecular Dynamics Free Energy Simulations†

2008 ◽  
Vol 112 (50) ◽  
pp. 13053-13057 ◽  
Author(s):  
Benedict M. Sattelle ◽  
Michael J. Sutcliffe
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Redox Potentials ◽  
Classical Molecular Dynamics ◽  
Energy Simulations

Displacement of carbonates in Ca2UO2(CO3)3 by amidoxime-based ligands from free-energy simulations

2018 ◽  
Vol 47 (5) ◽  
pp. 1604-1613 ◽  
Author(s):  
Bo Li ◽  
Chad Priest ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Nacl Solution ◽  
Classical Molecular Dynamics ◽  
Energy Profiles ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Free Energy Profiles

Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca2UO2(CO3)3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.

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>

Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations

2016 ◽  
Vol 120 (33) ◽  
pp. 8186-8192 ◽  
Author(s):  
Rainer Bomblies ◽  
Manuel P. Luitz ◽  
Martin Zacharias
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Simulations

Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation

2010 ◽  
Vol 110 (15) ◽  
pp. 2865-2879 ◽  
Author(s):  
Mahmoud Moradi ◽  
Jung-Goo Lee ◽  
Volodymyr Babin ◽  
Christopher Roland ◽  
Celeste Sagui
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Classical Molecular Dynamics

scholarly journals Effects of Base Substitutions in an RNA Hairpin from Molecular Dynamics and Free Energy Simulations

2003 ◽  
Vol 85 (6) ◽  
pp. 3445-3459 ◽  
Author(s):  
Joanna Sarzynska ◽  
Lennart Nilsson ◽  
Tadeusz Kulinski
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Base Substitutions ◽  
Energy Simulations ◽  
Rna Hairpin
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