scholarly journals Application of classical molecular dynamics for evaluation of proton transfer mechanism on a protein

2005 ◽  
Vol 1710 (2-3) ◽  
pp. 67-77 ◽  
Author(s):  
Ran Friedman ◽  
Esther Nachliel ◽  
Menachem Gutman
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Transfer Mechanism ◽  
Classical Molecular Dynamics

First-principles molecular dynamics study of proton transfer mechanism in bovine cytochromecoxidase

2007 ◽  
Vol 19 (36) ◽  
pp. 365220 ◽  
Author(s):  
Katsumasa Kamiya ◽  
Mauro Boero ◽  
Masaru Tateno ◽  
Kenji Shiraishi ◽  
Atsushi Oshiyama
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
First Principles ◽  
Transfer Mechanism ◽  
First Principles Molecular Dynamics

On the proton transfer mechanism in ammonia-bridged 7-hydroxyquinoline: a TDDFT molecular dynamics study

2009 ◽  
Vol 11 (22) ◽  
pp. 4549 ◽  
Author(s):  
Matteo Guglielmi ◽  
Ivano Tavernelli ◽  
Ursula Rothlisberger
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Transfer Mechanism

scholarly journals The influence of external electric fields on proton transfer tautomerism in the guanine–cytosine base pair

2021 ◽  
Vol 23 (10) ◽  
pp. 6252-6265
Author(s):  
Alexander Gheorghiu ◽  
Peter V. Coveney ◽  
Alya A. Arabi
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Proton Transfer ◽  
Molecular Mechanics ◽  
Electric Fields ◽  
Base Pair ◽  
Realistic Model ◽  
External Electric Fields ◽  
Classical Molecular Dynamics

A detailed investigation is reported of mutagenic guanine–cytosine tautomerization in a realistic model of DNA bathed in intense electric fields using a combination of classical molecular dynamics and quantum mechanics/molecular mechanics methods.

Atomic Crystal and Molecular Dynamics Simulation Structures of Human Carbonic Anhydrase II:  Insights into the Proton Transfer Mechanism†,‡

Biochemistry ◽  
2007 ◽  
Vol 46 (11) ◽  
pp. 2930-2937 ◽  
Author(s):  
S. Zoë Fisher ◽  
C. Mark Maupin ◽  
Monika Budayova-Spano ◽  
Lakshmanan Govindasamy ◽  
Chingkuang Tu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Carbonic Anhydrase ◽  
Proton Transfer ◽  
Transfer Mechanism ◽  
Dynamics Simulation ◽  
Carbonic Anhydrase Ii ◽  
Human Carbonic Anhydrase ◽  
Atomic Crystal
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