When I started my PhD research, I was fairly enthusiastic about the future, but I soon got disillusioned. Before my supervisor went on summer holidays, he gave me a choice of two projects. Neither were any good, and when the Head of Department saw me, he suggested (probably to keep me quiet) that I find my own project. Accordingly, I elected to enter a major controversy, namely were the wave functions of a cyclopropane ring localized (i.e., each chemical bond could be described by wave interference between a given pair of atoms, but there was no further wave interference) or were they delocalized, (i.e. the wave function representing a pair of electrons spread over more than one pair of atoms) and in particular, did they delocalize into substituents? Now, without getting too technical, I knew my supervisor had done quite a bit of work on something called the Hammett equation, which measures the effect or substituents on reactive sites, and in which, certain substituents that had different values when such delocalization was involved. If I could make the right sort of compounds, this equation would actually solve a problem.
This was not to be a fortunate project. First, my reserve synthetic method took 13 steps to get to the desired product, and while no organic synthesis gives a yield much better than 95%, one of these struggled to get over 35%, and another was not as good as desirable, which meant that I had to start with a lot of material. I did explore some shorter routes. One involved a reaction that was published in a Letter by someone who would go on to win a Nobel prize. The very key requirement to get the reaction to work was omitted in the Letter. I got a second reaction to work, but I had to order special chemicals. They turned up after I had submitted my thesis. They travelled via Hong Kong, where they got put aside and forgotten. After discovering that my supervisor was not going to provide any useful advice on chemical synthesis, he went on sabbatical, and I was on my own. After a lot of travail, I did what I had set out to do, but an unexpected problem arose. The standard compounds worked well and I got the required straight line set with minimum deviation, but for the key compound at one extreme of the line, the substituent at one end reacted quickly with the other end in the amine form. No clear result.
My supervisor made a cameo appearance before heading back to North America, where he was looking for a better paying job, and he made a suggestion, which involved reacting carboxylic acids that I already had in toluene. These had already been reported in water and aqueous alcohol, but the slope of the line was too shallow to be conclusive. What the toluene did was to greatly amplify the effect. The results were clear: there was no delocalization.
The next problem was the controversy was settling down, and the general consensus that there was such delocalization. This was based on one main observational fact, namely adjacent positive charge was stabilized, and there were many papers stating that it must on theoretical grounds. The theory used was exactly the same type of programs that “proved” the existence of polywater. Now the interesting thing was that soon everybody admitted there was no polywater, but the theory was “obviously” right in this case. Of course I still had to explain the stabilization of positive charge, and I found a way, namely strain involved mechanical polarization.
So, where did this get me? Largely, nowhere. My supervisor did not want to stick his head above the parapet, so he never published the work on the acids that was my key finding. I published a sequence of papers based on the polarization hypothesis, but in my first one I made an error: I left out what I thought was too obvious to waste the time of the scientific community, and in any case, I badly needed the space to keep within page limits. Being brief is NOT always a virtue.
The big gain was that while both explanations explained why positive charge was stabilized, (and my theory got the energy of stabilization of the gas phase carbenium ion right, at least as measured by another PhD student in America) the two theories differed on adjacent negative charge. The theory involving quantum delocalization required it to be stabilized too, while mine required it to be destabilized. As it happens, negative charge adjacent to a cyclopropane ring is so unstable it is almost impossible to make it, but that may not be convincing. However, there is one UV transition where the excited state has more negative charge adjacent to the cyclopropane ring, and my calculations gave the exact spectral shift, to within 1 nm. The delocalization theory cannot even get the direction of the shift right. That was published.
So, what did I learn from this? First, my supervisor did not have the nerve to go against the flow. (Neither, seemingly, did the supervisor of the student who measured the energy of the carbenium ion, and all I could do was to rely on the published thesis.) My spectral shifts were dismissed by one reviewer as “not important” and they were subsequently ignored. Something that falsifies the standard theory is unimportant? I later met a chemist who rose to the top of the academic tree, and he had started with a paper that falsified the standard theory, but when it too was ignored, he moved on. I asked him about this, and he seemed a little embarrassed as he said it was far better to ignore that and get a reputation doing something more in accord with a standard paradigm.
Much later (I had a living to earn) I had the time to make a review. I found over 60 different types of experiment that falsified the standard theory that was now in textbooks. That could not get published. There are few review journals that deal with chemistry, and one rejected the proposal on the grounds the matter was settled. (No interest in finding out why that might be wrong.) For another, it exceeded their page limit. For another, not enough diagrams and too many equations. For others, they did not publish logic analyses. So there is what I have discovered about modern science: in practice it may not live up to its ideals.