Reaction coordinate
In chemistry, a reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway. It is usually a geometric parameter that changes during the conversion of one or more molecular entities. In molecular dynamics simulations, a reaction coordinate is called collective variable.
These coordinates can sometimes represent a real coordinate system, although, for more complex reactions especially, this can be difficult.
Reaction coordinates are often plotted against free energy to demonstrate in some schematic form the potential energy profile associated to the reaction.
In the formalism of transition-state theory the reaction coordinate is that coordinate in set of curvilinear coordinates obtained from the conventional ones for the reactants which, for each reaction step, leads smoothly from the configuration of the reactants through that of the transition state to the configuration of the products. The reaction coordinate is typically chosen to follow the path along the gradient of potential energy from reactants to products.
For example, in the homolytic dissociation of molecular hydrogen, an apt coordinate system to choose would be the coordinate corresponding to the bond length.
