Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

Elizabeth Brunk; Ursula Rothlisberger

doi:10.1021/cr500628b

Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States

Chemical Reviews ◽

10.1021/cr500628b ◽

2015 ◽

Vol 115 (12) ◽

pp. 6217-6263 ◽

Cited By ~ 210

Author(s):

Elizabeth Brunk ◽

Ursula Rothlisberger

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Excited States ◽

Biological Systems ◽

Quantum Mechanical ◽

Electronically Excited States ◽

Electronically Excited ◽

Dynamics Simulations

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New Insights into the Jahn-Teller Effect through ab initio Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulations of CuII in Water

ChemPhysChem ◽

10.1002/cphc.200300659 ◽

2003 ◽

Vol 4 (9) ◽

pp. 931-943 ◽

Cited By ~ 56

Author(s):

Christian F. Schwenk ◽

Bernd M. Rode

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Teller Effect ◽

Quantum Mechanical ◽

Jahn Teller ◽

Jahn Teller Effect ◽

Dynamics Simulations

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Calculation of the Proton Transfer Rate Using Density Matrix Evolution and Molecular Dynamics Simulations: Inclusion of the Proton Excited States

The Journal of Physical Chemistry ◽

10.1021/j100034a005 ◽

1995 ◽

Vol 99 (34) ◽

pp. 12711-12717 ◽

Cited By ~ 33

Author(s):

Janez Mavri ◽

Herman J. C. Berendsen

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Density Matrix ◽

Molecular Dynamics Simulations ◽

Excited States ◽

Transfer Rate ◽

Dynamics Simulations ◽

Matrix Evolution

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Calculation of Local Water Densities in Biological Systems: A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation

The Journal of Physical Chemistry B ◽

10.1021/jp102587q ◽

2011 ◽

Vol 115 (2) ◽

pp. 319-328 ◽

Cited By ~ 65

Author(s):

Martin C. Stumpe ◽

Nikolay Blinov ◽

David Wishart ◽

Andriy Kovalenko ◽

Vijay S. Pande

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Biological Systems ◽

Molecular Theory ◽

Local Water ◽

Dynamics Simulations

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Characterization of a Catalytic Ligand Bridging Metal Ions in Phosphodiesterases 4 and 5 by Molecular Dynamics Simulations and Hybrid Quantum Mechanical/Molecular Mechanical Calculations

Biophysical Journal ◽

10.1529/biophysj.106.086835 ◽

2006 ◽

Vol 91 (5) ◽

pp. 1858-1867 ◽

Cited By ~ 32

Author(s):

Ying Xiong ◽

Hai-Ting Lu ◽

Yongjian Li ◽

Guang-Fu Yang ◽

Chang-Guo Zhan

Keyword(s):

Molecular Dynamics ◽

Metal Ions ◽

Molecular Dynamics Simulations ◽

Quantum Mechanical ◽

Dynamics Simulations

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Can’t we negotiate the importance of electron correlation? HF vs RIMP2 in ab initio quantum mechanical charge field molecular dynamics simulations of Cu+ in pure liquid ammonia

Journal of Molecular Liquids ◽

10.1016/j.molliq.2021.118286 ◽

2021 ◽

pp. 118286

Author(s):

Wahyu Dita Saputri ◽

Harno Dwi Pranowo ◽

Thomas S. Hofer

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Electron Correlation ◽

Liquid Ammonia ◽

Quantum Mechanical ◽

Pure Liquid ◽

Charge Field ◽

Dynamics Simulations ◽

Mechanical Charge

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Hybrid Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of HIV-1 Integrase/Inhibitor Complexes

Biophysical Journal ◽

10.1529/biophysj.107.108464 ◽

2007 ◽

Vol 93 (10) ◽

pp. 3613-3626 ◽

Cited By ~ 10

Author(s):

Nadtanet Nunthaboot ◽

Somsak Pianwanit ◽

Vudhichai Parasuk ◽

Jerry O. Ebalunode ◽

James M. Briggs ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Integrase Inhibitor ◽

Quantum Mechanical ◽

Dynamics Simulations ◽

Hiv 1

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Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Cytidine Deaminase: From Stabilization of Transition State Analogues to Catalytic Mechanisms

The Journal of Physical Chemistry B ◽

10.1021/jp037529d ◽

2004 ◽

Vol 108 (7) ◽

pp. 2477-2483 ◽

Cited By ~ 7

Author(s):

Qin Xu ◽

Hong Guo

Keyword(s):

Molecular Dynamics ◽

Transition State ◽

Molecular Dynamics Simulations ◽

Cytidine Deaminase ◽

Quantum Mechanical ◽

Transition State Analogues ◽

Catalytic Mechanisms ◽

Dynamics Simulations

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A Combined Car-Parrinello Quantum Mechanical-Molecular Mechanical Implementation for Ab Initio Molecular Dynamics Simulations of Extended Systems

ACS Symposium Series - Combined Quantum Mechanical and Molecular Mechanical Methods ◽

10.1021/bk-1998-0712.ch008 ◽

1998 ◽

pp. 128-147 ◽

Cited By ~ 8

Author(s):

Tom K. Woo ◽

Peter M. Margl ◽

Liqun Deng ◽

Tom Ziegler

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Quantum Mechanical ◽

Extended Systems ◽

Dynamics Simulations

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When Water Plays an Active Role in Electronic Structure. Insights from First-Principles Molecular Dynamics Simulations of Biological Systems

Springer Series on Bio- and Neurosystems - Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes ◽

10.1007/978-3-319-95843-9_22 ◽

2018 ◽

pp. 715-753

Author(s):

Giovanni La Penna ◽

Oliviero Andreussi

Keyword(s):

Molecular Dynamics ◽

Electronic Structure ◽

Molecular Dynamics Simulations ◽

First Principles ◽

Biological Systems ◽

Active Role ◽

Dynamics Simulations ◽

First Principles Molecular Dynamics

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Molecular mechanism for the encapsulation of the doxorubicin in the cucurbit[n]urils cavity and the effects of diameter, protonation on loading and releasing of the anticancer drug:Mixed quantum mechanical/ molecular dynamics simulations

Computer Methods and Programs in Biomedicine ◽

10.1016/j.cmpb.2020.105563 ◽

2020 ◽

Vol 196 ◽

pp. 105563

Author(s):

Zohre Hasanzade ◽

Heidar Raissi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Mechanism ◽

Quantum Mechanical ◽

Dynamics Simulations ◽

Quantum Mechanical Molecular Dynamics

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