Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated

2015 ◽  
Vol 143 (12) ◽  
pp. 124304 ◽  
Author(s):  
Sergei D. Ivanov ◽  
Ian M. Grant ◽  
Dominik Marx
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Formic Acid ◽  
Ab Initio ◽  
Path Integral ◽  
Energy Landscapes ◽  
Double Proton Transfer ◽  
Free Energy Landscapes

Solvent Dependence of Double Proton Transfer in the Formic Acid–Formamidine Complex: Path Integral Molecular Dynamics Investigation

2017 ◽  
Vol 121 (39) ◽  
pp. 7324-7334 ◽  
Author(s):  
Nawee Kungwan ◽  
Chanisorn Ngaojampa ◽  
Yudai Ogata ◽  
Tsutomu Kawatsu ◽  
Yuki Oba ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Formic Acid ◽  
Path Integral ◽  
Double Proton Transfer ◽  
Solvent Dependence

BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: from semi-empirical to ab initio

2019 ◽  
Vol 21 (39) ◽  
pp. 21942-21959 ◽  
Author(s):  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Indirect Method ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Energy Simulations ◽  
Semi Empirical

The indirect method for the construction of quantum mechanics (QM)/molecular mechanics (MM) free energy landscapes provides a cheaper alternative for free energy simulations at the QM level.

scholarly journals The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases

2015 ◽  
Vol 6 (2) ◽  
pp. 1167-1177 ◽  
Author(s):  
Javier Iglesias-Fernández ◽  
Lluís Raich ◽  
Albert Ardèvol ◽  
Carme Rovira
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Dynamics Simulations ◽  
Conformational Free Energy

Ab initio conformational free energy landscapes, together with molecular dynamics simulations, enable to predict the catalytic itineraries of β-xylanase enzymes.

scholarly journals Distributions of experimental protein structures on coarse-grained free energy landscapes

2015 ◽  
Vol 143 (24) ◽  
pp. 243153 ◽  
Author(s):  
Kannan Sankar ◽  
Jie Liu ◽  
Yuan Wang ◽  
Robert L. Jernigan
Keyword(s):  
Free Energy ◽  
Protein Structures ◽  
Coarse Grained ◽  
Energy Landscapes ◽  
Free Energy Landscapes
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