Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations

1997 ◽  
Vol 101 (26) ◽  
pp. 5239-5248 ◽  
Author(s):  
Mafalda Nina ◽  
Dmitri Beglov ◽  
Benoît Roux
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Continuum Electrostatics ◽  
Energy Simulations ◽  
Atomic Radii

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>

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.

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

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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