Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method

2008 ◽  
Vol 129 (6) ◽  
pp. 064108 ◽  
Author(s):  
Omololu Akin-Ojo ◽  
Yang Song ◽  
Feng Wang
Keyword(s):  
Quantum Mechanics ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Condensed Phase ◽  
Force Fields ◽  
Matching Method ◽  
Molecular Mechanics Calculations ◽  
Force Matching

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching

2007 ◽  
Vol 3 (2) ◽  
pp. 628-639 ◽  
Author(s):  
Patrick Maurer ◽  
Alessandro Laio ◽  
Håkan W. Hugosson ◽  
Maria Carola Colombo ◽  
Ursula Rothlisberger
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Force Fields ◽  
Force Matching

Protonation structure of the photosynthetic water oxidizing complex in the S0 state as revealed by normal mode analysis using quantum mechanics/molecular mechanics calculations

2020 ◽  
Vol 22 (42) ◽  
pp. 24213-24225
Author(s):  
Masao Yamamoto ◽  
Shin Nakamura ◽  
Takumi Noguchi
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Molecular Vibrations ◽  
Molecular Mechanics Calculations ◽  
Water Oxidizing Complex

Protonation structure of the first intermediate of the water oxidizing complex was determined by QM/MM calculations of molecular vibrations.

scholarly journals Unravelling novel synergies between organometallic and biological partners: a quantum mechanics/molecular mechanics study of an artificial metalloenzyme

2014 ◽  
Vol 11 (96) ◽  
pp. 20140090 ◽  
Author(s):  
Elisabeth Ortega-Carrasco ◽  
Agustí Lledós ◽  
Jean-Didier Maréchal
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Resting State ◽  
Structural Features ◽  
Activation Process ◽  
Biological Macromolecules ◽  
The Novel ◽  
Molecular Mechanics Calculations ◽  
Artificial Metalloenzymes ◽  
Artificial Metalloenzyme

In recent years, the design of artificial metalloenzymes obtained by the insertion of homogeneous catalysts into biological macromolecules has become a major field of research. These hybrids, and the corresponding X-ray structures of several of them, are offering opportunities to better understand the synergy between organometallic and biological subsystems. In this work, we investigate the resting state and activation process of a hybrid inspired by an oxidative haemoenzyme but presenting an unexpected reactivity and structural features. An extensive series of quantum mechanics/molecular mechanics calculations show that the resting state and the activation processes of the novel enzyme differ from naturally occurring haemoenzymes in terms of the electronic state of the metal, participation of the first coordination sphere of the metal and the dynamic process. This study presents novel insights into the sensitivity of the association between organometallic and biological partners and illustrates the molecular challenge that represents the design of efficient enzymes based on this strategy.

Sign in / Sign up

Export Citation Format

Share Document