Nature of matter is too complex to be fully predictable, so what is not predictable at current chemistry level is discovered accidentally, not being foreseen until encountered.
The first paragraph is incorrect, being rational and making accidental discoveries does not exclude each other. Ability to predict unknown phenomena is rather rare (like prediction of antimatter).
Ability to predict behavior of some molecule within the known is easier.
But all is very case dependent, there is hardly any general approach.
In several last decades, applying advances of quantum chemistry, there have been developed a screening method of evaluation of various compounds before them being synthetized yet, eliminating the ones not being promising. One of the leading scientists on this field was the late prof. Rudolf Zahradník Researchgate.net - scientific-contributions 1959-2013, a former head of the Czech Academy of Science.
In recent years, there are being developed AI powered screening computational methods, based on learn structural patterns of biological objects, organic molecules and their relations and interactions.