Recently, I have been reading the Nobel Lecture given by Kenichi Fukui when he won the Nobel Prize in 1981, for his contributions to the development of Frontier Molecular Orbital Theory. One of the most well-known ideas in this theory is that principally, the reactivity of molecules can be understood by looking at their HOMOs and LUMOs. On p. 15 of the lecture notes, it is written:
If HOMO or LUMO happens to be inadequate owing to its extension, the symmetry, or the nodal property, the next orbital should be sought for. One of the simplest examples of such an instance is the protonation of pyridine. In this case, the nitrogen lone-pair orbital is not HOMO, but the addition of proton to the nitrogen lone-pair so as not to disturb the π conjugation will evidently be more advantageous than the addition to higher occupied π orbitals which may intercept the π conjugation. Thus, the reason why proton dare not add to the positions of large amplitude of π HOMO in this case will easily be understood. It is not completely satisfactory to dispose of a disagreement between the HOMO-LUMO argument and the experimental fact formally as an exception to the theory. A so-called exception does possess its own reason. To investigate what the reason is will possibly yield a novel finding.
In the above paragraph, Fukui is essentially telling us that consideration of the HOMO of the pyridine molecule would not allow us to determine the site of protonation. As Fukui writes, the HOMO of this molecule is one of $\pi$ MOs of the aromatic system while in this protonation reaction, the lone pair orbital on the nitrogen atom reacts. He also ends off by saying that further investigation of this example may "possibly yield a novel finding".
Firstly, I would like to ask if any further investigation has been done into this and whether any novel finding has been derived to date? Secondly, I would like to put forth my own rationalisation of this phenomenon. Personally, I do not think that this example poses as an exception to the theory because this acid-base phenomenon is controlled by thermodynamics. That is to say, whether the protonation occurs, it should result in the resultant conjugate acid being of the greatest stability (i.e. Gibbs free energies need to be considered). Thus, kinetic factors, like orbital interactions between frontier orbitals, become much less relevant. Would you agree with my rationalisation?