Can I perform and publish studies on patented chemical compounds? If a set of chemical compounds is patented by somebody else, am I allowed to perform studies (e.g. Pharmacophore, structure-activity relationship or QSAR analysis) on these patented compounds and publish the studies ? Provided that I'll cite the patent (as citing articles) but without having any type of permission.

Thanks
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.