Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

2000 ◽  
Vol 113 (12) ◽  
pp. 4863 ◽  
Author(s):  
Joost VandeVondele ◽  
Ursula Rothlisberger
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Free Energy Calculations ◽  
Ab Initio Molecular Dynamics ◽  
Energy Calculations

scholarly journals Full atomistic reaction mechanism with kinetics for CO reduction on Cu(100) from ab initio molecular dynamics free-energy calculations at 298 K

2017 ◽  
Vol 114 (8) ◽  
pp. 1795-1800 ◽  
Author(s):  
Tao Cheng ◽  
Hai Xiao ◽  
William A. Goddard
Keyword(s):  
Free Energy ◽  
Reaction Mechanism ◽  
Ab Initio ◽  
Rational Design ◽  
Major Product ◽  
Free Energy Calculations ◽  
Ab Initio Molecular Dynamics ◽  
Applied Potential ◽  
Hydrogen Electrode ◽  
Energy Calculations

A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of −0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than −0.6 V (RHE) ethylene, the major product, is produced via the Eley–Rideal (ER) mechanism using H2O +e–. The rate-determining step (RDS) is C–C coupling of two CO, with ΔG‡= 0.69 eV. For an applied potential less than −0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4along with CH4atUless than −0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4and C2H4. These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface.

scholarly journals Insight into the Binding of DFG-out Allosteric Inhibitors to B-Raf Kinase Using Molecular Dynamics and Free Energy Calculations

2015 ◽  
Vol 11 (2) ◽  
pp. 124-136 ◽  
Author(s):  
Luis Coronel ◽  
Jose Granadino-Roldán ◽  
Marta Pinto ◽  
Maria Tomas ◽  
Maria Pujol ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Allosteric Inhibitors ◽  
Energy Calculations ◽  
Raf Kinase ◽  
Insight Into

Small-to-Large Length Scale Transition of TMAO Interaction with Hydrophobic Solutes

2021 ◽  
Author(s):  
Angelina Folberth ◽  
Swaminath Bharadwaj ◽  
Nico van der Vegt
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Length Scale ◽  
Simulation Data ◽  
Energy Calculations ◽  
Large Length ◽  
Hydrophobic Solutes ◽  
Large Length Scale

We report the effect of trimethylamine N-oxide (TMAO) on the solvation of nonpolar solutes in water studied with molecular dynamics (MD) simulations and free-energy calculations. The simulation data indicate the...

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