Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

Hiroya Nakata; Michael W. Schmidt; Dmitri G. Fedorov; Kazuo Kitaura; Shinichiro Nakamura; Mark S. Gordon

doi:10.1021/jp507726m

Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

The Journal of Physical Chemistry A ◽

10.1021/jp507726m ◽

2014 ◽

Vol 118 (41) ◽

pp. 9762-9771 ◽

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Author(s):

Hiroya Nakata ◽

Michael W. Schmidt ◽

Dmitri G. Fedorov ◽

Kazuo Kitaura ◽

Shinichiro Nakamura ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Orbital Method ◽

Radical Center ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Dynamics Simulations

Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials

Theoretical Chemistry Accounts ◽

10.1007/s00214-012-1136-8 ◽

2012 ◽

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Author(s):

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Dmitri G. Fedorov ◽

Kazuo Kitaura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Effective Potentials ◽

Fragment Molecular Orbital ◽

Dynamics Simulations

Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials

Highlights in Theoretical Chemistry - From Quantum Mechanics to Force Fields ◽

10.1007/978-3-642-34450-3_4 ◽

2012 ◽

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Author(s):

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Dmitri G. Fedorov ◽

Kazuo Kitaura

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Effective Potentials ◽

Fragment Molecular Orbital ◽

Dynamics Simulations

Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b01208 ◽

2016 ◽

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pp. 1423-1435 ◽

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Author(s):

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Hiroya Nakata ◽

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Maricris Mayes ◽

Yuri Alexeev ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Dynamics Simulations ◽

Three Body

Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations

Chemical Physics Letters ◽

10.1016/j.cplett.2008.11.044 ◽

2009 ◽

Vol 467 (4-6) ◽

pp. 417-423 ◽

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Hirofumi Watanabe ◽

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Tatsuya Nakano ◽

Yuji Mochizuki ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Force Fields ◽

Orbital Method ◽

Atomic Charges ◽

Molecular Orbital Method ◽

Classical Molecular Dynamics ◽

Dynamics Simulations

Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method

The Journal of Physical Chemistry Letters ◽

10.1021/acs.jpclett.5b02490 ◽

2015 ◽

Vol 6 (24) ◽

pp. 5034-5039 ◽

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Author(s):

Yoshio Nishimoto ◽

Hiroya Nakata ◽

Dmitri G. Fedorov ◽

Stephan Irle

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Density Functional ◽

Large Scale ◽

Tight Binding ◽

Quantum Mechanical ◽

Orbital Method ◽

Molecular Orbital Method ◽

Dynamics Simulations

Ab initioPath Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

Journal of the Physical Society of Japan ◽

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2009 ◽

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pp. 104723 ◽

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Author(s):

Takatoshi Fujita ◽

Hirofumi Watanabe ◽

Shigenori Tanaka

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital

Solvatochromic Shifts of Uracil and Cytosine Using a Combined Multireference Configuration Interaction/Molecular Dynamics Approach and the Fragment Molecular Orbital Method†

The Journal of Physical Chemistry A ◽

10.1021/jp901601u ◽

2009 ◽

Vol 113 (45) ◽

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Author(s):

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Spiridoula Matsika

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Configuration Interaction ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Solvatochromic Shifts

Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation

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2009 ◽

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Tatsuya Nakano

Keyword(s):

Molecular Dynamics ◽

Molecular Orbital ◽

Chemical Reactions ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital ◽

Explicit Solvation

Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics

Chemistry - A European Journal ◽

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Hiroshi Yamataka ◽

Yuto Komeiji ◽

Yuji Mochizuki ◽

Tatsuya Nakano

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Molecular Orbital ◽

Fragment Molecular Orbital ◽

Dynamics Simulations ◽

Zwitterionic Intermediate

Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’

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Yutaka Ueno ◽

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...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Ab Initio ◽

Molecular Orbital ◽

Dynamics Simulation ◽

Orbital Method ◽

Molecular Orbital Method ◽

Fragment Molecular Orbital