Probing the conformational energetics of alkyl thiols on gold surfaces by means of a morphing/steering non-equilibrium tool

2015 ◽  
Vol 17 (12) ◽  
pp. 8038-8052 ◽  
Author(s):  
Andrea Piserchia ◽  
Mirco Zerbetto ◽  
Diego Frezzato
Keyword(s):  
Free Energy ◽  
Gold Surface ◽  
Gold Surfaces ◽  
Jarzynski’S Equality ◽  
Torsion Free ◽  
Non Equilibrium

Jarzynski's equality is applied to compute the torsion free energy, bond-by-bond, for a probe alkyl thiol tethered to a gold surface.

scholarly journals Exploring the Sulfatase 1 Catch Bond Free Energy Landscape using Jarzynski’s Equality

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Volker Walhorn ◽  
Ann-Kristin Möller ◽  
Christian Bartz ◽  
Thomas Dierks ◽  
Dario Anselmetti
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Catch Bond ◽  
Jarzynski’S Equality

scholarly journals Size dependence of hydrophobic hydration at electrified gold/water interfaces

2021 ◽  
Vol 118 (15) ◽  
pp. e2023867118
Author(s):  
Alessandra Serva ◽  
Mathieu Salanne ◽  
Martina Havenith ◽  
Simone Pezzotti
Keyword(s):  
Free Energy ◽  
Energy Cost ◽  
Correction Term ◽  
Hydrophobic Hydration ◽  
Outer Sphere ◽  
Gold Surface ◽  
Electrochemical Reactions ◽  
Water Interface ◽  
Hydrophobic Solutes ◽  
Small Hydrophobic

Hydrophobic hydration at metal/water interfaces actively contributes to the energetics of electrochemical reactions, e.g. CO2 and N2 reduction, where small hydrophobic molecules are involved. In this work, constant applied potential molecular dynamics is employed to study hydrophobic hydration at a gold/water interface. We propose an adaptation of the Lum–Chandler–Weeks (LCW) theory to describe the free energy of hydrophobic hydration at the interface as a function of solute size and applied voltage. Based on this model we are able to predict the free energy cost of cavity formation at the interface directly from the free energy cost in the bulk plus an interface-dependent correction term. The interfacial water network contributes significantly to the free energy, yielding a preference for outer-sphere adsorption at the gold surface for ideal hydrophobes. We predict an accumulation of small hydrophobic solutes of sizes comparable to CO or N2, while the free energy cost to hydrate larger hydrophobes, above 2.5-Å radius, is shown to be greater at the interface than in the bulk. Interestingly, the transition from the volume dominated to the surface dominated regimes predicted by the LCW theory in the bulk is also found to take place for hydrophobes at the Au/water interface but occurs at smaller cavity radii. By applying the adapted LCW theory to a simple model addition reaction, we illustrate some implications of our findings for electrochemical reactions.

scholarly journals Duality and hidden equilibrium in transport models

2020 ◽  
Vol 9 (4) ◽  
Author(s):  
Rouven Frassek ◽  
Cristian Giardina ◽  
Jorge Kurchan
Keyword(s):  
Free Energy ◽  
Time Reversal ◽  
Large Family ◽  
Equilibrium States ◽  
Transport Models ◽  
Good Opportunity ◽  
The Past ◽  
Non Equilibrium

A large family of diffusive models of transport that have been considered in the past years admit a transformation into the same model in contact with an equilibrium bath. This mapping holds at the full dynamical level, and is independent of dimension or topology. It provides a good opportunity to discuss questions of time reversal in out of equilibrium contexts. In particular, thanks to the mapping one may define the free energy in the non-equilibrium states very naturally as the (usual) free energy of the mapped system.

Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations

2020 ◽  
Vol 100 ◽  
pp. 107648 ◽  
Author(s):  
Nguyen Thi Mai ◽  
Ngo Thi Lan ◽  
Thien Y Vu ◽  
Phuong Thi Mai Duong ◽  
Nguyen Thanh Tung ◽  
...  
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Binding Free Energy ◽  
Md Simulations ◽  
Checkpoint Kinase ◽  
Checkpoint Kinase 1 ◽  
Non Equilibrium

A method to estimate the Gibbs free energy of non-equilibrium alloys by thermal analysis

2011 ◽  
Vol 110 (3) ◽  
pp. 1153-1160 ◽  
Author(s):  
Linping Zhang ◽  
Xianlei Song ◽  
Yanyan Song ◽  
Zhanbo Sun ◽  
Qian Li ◽  
...  
Keyword(s):  
Thermal Analysis ◽  
Free Energy ◽  
Gibbs Free Energy ◽  
Equilibrium Alloys ◽  
Non Equilibrium
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