"- They are small (about 0,000 000 001 m that is 1 nanometer) - Spherical - Of constant shape Indivisible" In this list, you have a parallel construction problem, meaning these words are not all in the same tense or form. In formal technical writing, a list like this should be consistent in its voice. For example, if I made a list of things I like about my cat, I wouldn't say: Her fur, petting her, she is cute. I would say: Feeling her fur, petting her, looking at her. So for your list, I recommend something like: Small (approximately 1 nanometer); spherical; of uniform shape; indivisible.
NB: I don't know what "NB" means.
"all molecules have different masses but, when they belong to the same chemical species, their masses are identical." This is contradictory; it says every molecule has a different mass, but it goes on to say that some actually don't. I recommend something like: "Molecules that belong to the same chemical species have identical masses, but the individual mass of each molecule varies between chemical species."
"For instance, two molecules of water have the same mass but a molecule of water doesn’t have the same mass than a molecule of ozone." This is grammatically sound, but clumsy. I recommend something like: "For example, a molecule of water has the same mass as another molecule of water and a different mass from that of a molecule of ozone."