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In chemistry, a reaction coordinate [1] is an abstract one-dimensional coordinate chosen to represent progress along a reaction pathway. Where possible it is usually a geometric parameter that changes during the conversion of one or more molecular entities, such as bond length or bond angle. For example, in the homolytic dissociation of ...
Figure 6:Reaction Coordinate Diagrams showing reactions with 0, 1 and 2 intermediates: The double-headed arrow shows the first, second and third step in each reaction coordinate diagram. In all three of these reactions the first step is the slow step because the activation energy from the reactants to the transition state is the highest.
In physics and engineering, a free body diagram (FBD; also called a force diagram) [1] is a graphical illustration used to visualize the applied forces, moments, and resulting reactions on a free body in a given condition. It depicts a body or connected bodies with all the applied forces and moments, and reactions, which act on the body(ies).
The activation strain model was originally proposed and has been extensively developed by Bickelhaupt and coworkers. [4] This model breaks the potential energy curve as a function of reaction coordinate, ζ, of a reaction into 2 components as shown in equation 1: the energy due to straining the original reactant molecules (∆E strain) and the energy due to interaction between reactant ...
In the theory of many-particle systems, Jacobi coordinates often are used to simplify the mathematical formulation. These coordinates are particularly common in treating polyatomic molecules and chemical reactions, [3] and in celestial mechanics. [4] An algorithm for generating the Jacobi coordinates for N bodies may be based upon binary trees. [5]
The difference between states A and B may be in the atom types involved, in which case the ΔF obtained is for "mutating" one molecule onto another, or it may be a difference of geometry, in which case one obtains a free-energy map along one or more reaction coordinates. This free-energy map is also known as a potential of mean force (PMF).
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