I am doing geometry optimizations (DFT) on a series of molecules with different structures and numbers of electrons. I am wondering if I can compare the single point energies of the optimized structures as a way to gauge stability or if, because they have different numbers of electrons, I can't make direct comparisons.
The short answer is, no.
If you want to compare "stability", you have to consider; "Stable with respect to what?" Stable with respect to reaction with something in the environment? Stable with respect to unimolecular dissociation? Stable with respect to ionization?
A direct comparison of the DFT total energies of two different molecules just compares how much energy is released when they are assembled from their separated electrons and atomic nuclei. That tells you very little about their relative reactivity.
For a longer answer, see my response to a related question here:
https://www.researchgate.net/post/what_is_the_more_perfect_parameter_for_the_stability_of_a_molecule_using_DFT_calculations
Unless these molecules are somehow related to each other (e.g., reactant-product) I do not think we can make any meaning out of the energies. Since stability is a relative parameter in absence of any connection between the corresponding molecules individual molecules are infinitely stable. If we want study photophysics the absolute energy is not going to make any differences. But if we are looking for some reaction mechanisms these values are needed. But again we have some product(s) to make a comparison.
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