Reaction coordinate
In
Molecular dynamics simulations often use collective variables to promote unusual but interesting states. The term collective variable may describe any function of the atom positions. Special collective variables that help to distinguish reactants from products are known as order parameters, terminology that originates in work on phase transitions.[2] Reaction coordinates are special order parameters that describe the entire pathway from reactants through transition states and on to products. Depending on the application, reaction coordinates may be defined by using chemically intuitive variables like bond lengths, or splitting probabilities (also called committors), or using the eigenfunction corresponding to the reactant-to-product transition as a progress coordinate.[3]
A reaction coordinate parameterizes reaction process at the level of the molecular entities involved. It differs from extent of reaction, which measures reaction progress in terms of the composition of the reaction system.
(Free) energy is often plotted against reaction coordinate(s) to demonstrate in schematic form the potential energy profile (an intersection of a potential energy surface) associated with the reaction.
In the formalism of
Notes and references