Chocolate is a complex structure containing consisting of cocoa powder, sugar, fat solids (primarily cocoa butter). The cocoa powder and cocoa butter both come from the cocoa bean following roasting, grinding, and liquification. The flavor and mouth feel of chocolate will depend on the ratios of these components, as well as their size and structure. For the cocoa butter alone, there are six different crystalline structures that it can assume depending on its processing, which will impact how shiny the finished product is, how it melts in your mouth, and if it will undergo blooming, the development of a gray coating on some inferior brands of chocolate.
Cambridge Polymer Group analyzed multiple types of chocolates, looking at their chemistry, morphology, rheology, and mechanical behavior. Alkaloid content, primarily caffeine and theobromine, was analyzed with chromatographic techniques, along with microstructural information by scanning electron microscopy.
The full application note can be found here.