Simulations free energy profiles

In contrast, the term transition state refers to the properties of an ensemble of molecular entities at a finite (nonzero) temperature it may be associated with the maximum along a simulated free energy profile for an elementary step. We consider it useful to distinguish the two concepts in view of the significant difference between them the one is microscopic and related to a feature of an (unobservable)... 

Outer sphere electron transfer (e.g., [11-19,107,160-162]), ion transfer [10,109,163,164] and proton transfer [165] are among the reactions near electrodes and the hquid/liquid interface which have been studied by computer simulation. Much of this work has been reviewed recently [64,111,125,126] and will not be repeated here. All studies involve the calculation of a free energy profile as a function of a spatial or a collective solvent coordinate. 

Relative free energy changes along the reaction coordinate may be calculated via MD simulations. Subsequently, they may be combined with the QM total energies of the reacting QM subsystem to obtain the overall free energy profiles associated with the reaction steps in the following way... 

With the characterized mechanism, the next key question is the origin of its catalytic power. A prerequisite for this investigation is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio QM/MM approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9... 

It is interesting to note that the free energy profiles obtained with ABF are essentially identical to those derived by Park et al. [53] from a reversible, 200-ns steered molecular dynamics simulation and from a set of 100 shorter runs, pulling very... 

Schulten and coworkers coupled SMD [23] simulations with the Jarzynski identity [102] to derive the free energy profile for glycerol conduction in the facilitator GlpF, a channel that allows the selective passage of water and small, linear alcohols,... 

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