Quantum Mechanical/Molecular Mechanical Molecular Dynamics and Free Energy Simulations of the ThiopurineS-Methyltransferase Reaction with 6-Mercaptopurine

2011 ◽  
Vol 115 (24) ◽  
pp. 8033-8037 ◽  
Author(s):  
Xiao-Liang Pan ◽  
Feng-Chao Cui ◽  
Jing-Yao Liu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Quantum Mechanical ◽  
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>

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.

Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the GlutathioneS-Transferase (M1-1) Reaction with Phenanthrene 9,10-Oxide

2002 ◽  
Vol 124 (33) ◽  
pp. 9926-9936 ◽  
Author(s):  
Lars Ridder ◽  
Ivonne M. C. M. Rietjens ◽  
Jacques Vervoort ◽  
Adrian J. Mulholland
Keyword(s):  
Free Energy ◽  
Quantum Mechanical ◽  
Energy Simulations

Spatial Redistribution of Niobium Additives Near Nickel Surfaces

1995 ◽  
Vol 408 ◽  
Author(s):  
Leonid S. Muratov ◽  
Bernard R. Cooper
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Harmonic Approximation ◽  
Lattice Relaxation ◽  
Pure Nickel ◽  
Quantum Mechanical ◽  
Concentration Limit ◽  
Vibrational Entropy ◽  
Quantum Mechanical Calculations ◽  
Spatial Redistribution

AbstractThe spatial redistribution of niobium atoms near the surface of pure nickel has been considered in the low niobium concentration limit. The calculation of free energy includes lattice relaxation around niobium atoms by using molecular dynamics (MD) incorporating atomistic potentials based on ab-initio quantum mechanical calculations and includes vibrational entropy phenomenologically within the local harmonic approximation.

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
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