Can I perform and publish studies on patented chemical compounds?
Patent law varies around the world, but in general doesn't prohibit study and discussion. Lots of things that are covered by patent are regularly discussed in popular and scientific literature. You don't need Apple's permission to analyze an iPhone, for example. 

One of the reasons behind patent law, in fact is to make the essence of the thing known to the world. The patent application has to reveal everything essential on which the patent claim lies. 

Patent is intended to prohibit you from reproducing the thing for most purposes, but you aren't doing that.