To (mis)quote Oscar Wilde again, ““To lose one methyl group may be regarded as a misfortune; to lose both looks like carelessness.” Here, I refer to the (past) tendency of molecular modellers to simplify molecular structures. Thus in 1977, quantum molecular modelling, even at the semi-empirical level, was beset by lost groups. One of my early efforts (DOI: 10.1021/ja00465a005) was selected for study because it had nothing left to lose; the mass spectrometric fragmentation of the radical cations of methane and ethane. Methyl, phenyl and other “large” groups were routinely replaced by hydrogen in order to enable the study. Cations indeed were always of interest to modellers; the relative lack of electrons almost always meant unusual or interesting structures and reactions (including this controversial species, DOI: 10.1021/ja00444a012). Inured to such functional loss, we modellers forgot that (unless in a mass spectrometer), cations have to have a counter anion. Here I explore one example of the model being complete(d).
In the earlier post on this topic I had explored the possibility of a new isomer of cyclobutadiene, induced by the presence nearby of a strong acid, in the form of guanidinium cation. You might note there was no mention of any counterion! Well, here I add it in to complete the model, using perchlorate. I was following in a sense my own advice on Steve Bachrach’s blog, where the NMR spectrum of the adamantly cation was discussed. I had argued there that the anion (I chose SnCl5–) might actually have an effect on the NMR. For the cyclobutadiene complex above without a counter-ion, this non-planar form of the cyclobutadiene was calculated earlier to be ~8.5 kcal/mol in free energy higher than the rectangular conventional geometry. Add the perchlorate as above, and this energy difference drops to 4.1 kcal/mol (modelled in water as a solvent). So the counter-ion CAN make a difference!
What are the implications to a modeller of adding counter ions? Well, when you start doing such calculations, you find that the practical matter of optimising the geometry is not quite as straightforward as it is found to be for what I would call covalently bonded systems. These latter have pretty predictable geometries, and these geometries are pretty rigid. Ion-pairs on the other hand are less predictable. Note for example in the above diagram that the perchlorate counterion sits to one side of the molecule, and is not symmetrical. The potential energy surface can be very flat indeed, which means that locating the optimal geometry can be quite a struggle. And unlike a covalent structure, where once the location of the covalent bonds is decided, there is little further ambiguity, ion-pairs may have many different possible relative orientations. Thus the above one may not be unique!
But the last word to this post should be: do not forget counter ions if you a looking at ionic species, and always strive to be complete!