The scientific competences point to the development of capabilities, abilities and aptitudes which help to solve problems according to the context where the facts take place. Referring to PISA, 2015 there are six levels of performances to develop scientific competences. The main purpose here is for the students to identify, explain, and put into practice consciously the scientific knowledge, and as well the knowledge about Science in a great range of possibilities, somehow complex or easy circumstances. Besides being able to use this knowledge, they can also use arguments, and apply some recommendations on how to make logical decisions. At the same time, they could show abilities to solve some daily problems analyzing, comparing and making relations among different difficult situations related to composition, isomery, and structures of chemical compounds. In this paper a proposal is made for teaching Chemistry through classes designed to learn the spatial structures, nomenclature and isomery of organic compounds. Some workshop plans have been included to represent the chemical compounds (formulae) and their spatial structures. Most important is the opportunity the students have to manipulate spatial structures in 3D.