Sampling the Proton Transfer Reaction Coordinate in Mixed Quantum-Classical Molecular Dynamics Simulations

Transfer Reaction ◽

Reaction Coordinate ◽

Molecular Dynamics Simulations of the Proton Transfer Reaction Between the Catalytic Residues in HTLV-I Protease

Biophysical Journal ◽

10.1016/j.bpj.2013.11.3745 ◽

2014 ◽

Vol 106 (2) ◽

pp. 676a

Author(s):

Shuhua Ma ◽

Natalie Petrillo ◽

Kimberly Vogt

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Transfer Reaction ◽

Catalytic Residues ◽

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations

Physical Review E ◽

10.1103/physreve.87.023301 ◽

2013 ◽

Vol 87 (2) ◽

Cited By ~ 10

Author(s):

Yoshiharu Mori ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Proton Transfer ◽

First Principles ◽

Transfer Reaction ◽

Umbrella Sampling ◽

Simulated Tempering ◽

Hybrid Quantum Classical Molecular Dynamics Simulation of the Proton-Transfer Reaction of HO-with HBr in Aqueous Clusters

The Journal of Physical Chemistry A ◽

10.1021/jp983678y ◽

1999 ◽

Vol 103 (26) ◽

pp. 5105-5112 ◽

Cited By ~ 12

Author(s):

M. Dolores Elola ◽

Dario A. Estrin ◽

Daniel Laria

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Transfer Reaction ◽

Dynamics Simulation ◽

Classical Molecular Dynamics

Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath

The Journal of Chemical Physics ◽

10.1063/1.2206175 ◽

2006 ◽

Vol 124 (24) ◽

pp. 244102 ◽

Cited By ~ 32

Author(s):

Soo Young Kim ◽

Sharon Hammes-Schiffer

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Transfer Reaction ◽

Classical Molecular Dynamics

Quantum-Classical Molecular Dynamics Simulations of Proton Transfer Processes in Molecular Complexes and in Enzymes

The Journal of Physical Chemistry ◽

10.1021/jp952642s ◽

1996 ◽

Vol 100 (7) ◽

pp. 2535-2545 ◽

Cited By ~ 67

Author(s):

P. Bała ◽

P. Grochowski ◽

B. Lesyng ◽

J. A. McCammon

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Molecular Complexes ◽

Transfer Processes ◽

Explicit proton transfer in classical molecular dynamics simulations

Journal of Computational Chemistry ◽

10.1002/jcc.23536 ◽

2014 ◽

Vol 35 (8) ◽

pp. 657-671 ◽

Cited By ~ 31

Author(s):

Maarten G. Wolf ◽

Gerrit Groenhof

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

Biochemistry ◽

10.1021/bi901353v ◽

2009 ◽

Vol 48 (44) ◽

pp. 10608-10619 ◽

Cited By ~ 28

Author(s):

Dhruva K. Chakravorty ◽

Alexander V. Soudackov ◽

Sharon Hammes-Schiffer

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bonding ◽

Proton Transfer ◽

Transfer Reactions ◽

Ketosteroid Isomerase ◽

Proton Transfer Reactions ◽

AB Initio Studies and Quantum-Classical Molecular Dynamics Simulations for Proton Transfer Processes in Model Systems and in Enzymes

Molecular Aspects of Biotechnology: Computational Models and Theories ◽

10.1007/978-94-011-2538-3_13 ◽

1992 ◽

pp. 299-326 ◽

Cited By ~ 8

Author(s):

P. Bala ◽

B. Lesyng ◽

T. N. Truong ◽

J. A. McCammon

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Ab Initio ◽

Model Systems ◽

Transfer Processes ◽

Enzymatic and Inhibition Mechanism of Human Aromatase (CYP19A1) Enzyme. A Computational Perspective from QM/MM and Classical Molecular Dynamics Simulations

Mini-Reviews in Medicinal Chemistry ◽

10.2174/1389557516666160623101129 ◽

2016 ◽

Vol 16 (14) ◽

pp. 1112-1124 ◽

Cited By ~ 13

Author(s):

Jacopo Sgrignani ◽

Andrea Cavalli ◽

Giorgio Colombo ◽

Alessandra Magistrato

Keyword(s):

Molecular Dynamics ◽

Inhibition Mechanism ◽

Computational Perspective ◽

Human Aromatase ◽

Characterization of amorphous Si generated through classical molecular dynamics simulations

2017 Spanish Conference on Electron Devices (CDE) ◽

10.1109/cde.2017.7905213 ◽

2017 ◽

Author(s):

Ivan Santos ◽

Pedro Lopez ◽

Maria Aboy ◽

Luis A. Marques ◽

Lourdes Pelaz

Keyword(s):

Molecular Dynamics ◽

Amorphous Si ◽