A patent on a molecular structure is a very specific and easily interpreted patent. Most software patents are extremely vague and open to overly broad interpretations. The potential for abuse is far, far greater.
A friend working with polymers told me recently that their patents tend to be vague as well, in order to block as many variations and modifications to given formula as possible, while not revealing the exact chemical process used to obtain the polymer (e.g. saying that the temperature used is between XX and YY, instead of providing the exact value).
