The grid calculation should result in the identification of the transition
state of a reaction: the point with the highest energy when going from
reactants to products. A true transition state can be characterized
mathematically as a saddle point on the potential energy surface.
The second derivatives of the energy with respect to the coordinates should all be positive, with one exception: following the reaction coordinate the energy should decrease. This gives a negative second derivative, that is written as an imaginary frequency with a negative sign.
Starting from a structure close to the transition state (a 'refinement' grid calculation may be necessary to get the TS closer to the center of the grid), MOPAC can 'optimize' it, and subsequently walk the path down in two directions: towards the product and towards the reactants. All these instructions have been automated in the present version of the editor.
Just by selecting the point closest to the TS, and clicking the IRC-link at the bottom of a grid calculation,
a process is started that may take a good 10 minutes to complete.
The transition state is refined, the IRC paths calculated, and the results are combined in one animation. This describes the whole path from reactant to product, with energy diagram.
The whole point is that from this diagram the activation energy for this particular reaction can be read: E(TS)-E(Reactants).
By comparing the activation energies for several substitution patterns, the preferred product for a substituted diene/dienophile combination can be derived.
These last calculations are not performed in Nijmegen, but in Paderborn (Prof. Fels' group), where Oliver Stüker linked his modules to ours.