Susanoo is a manifestation of one's chakra. Chakra is basically a mixture of spiritual and physical energy. It has a physical element to it (as evident when Madara stood on top of it), meaning it does consist of matter. Thus, Jinton should be able to remove Susanoo easily.
Amaterasu isn't made of atoms. Fire is composed of the oxygen it burns the fuel that it burns and the carbon it produces. Amaterasu does not require oxygen, requires no fuel and burns even carbon. Nothing exists inside Amaterasu therefore amaterasu is composed of nothing, but chakra and extreme heat.
Jinton bypasses susano'o's structure just like gaara's sand does disintegrate all molecular structures. Madara's clones were destroyed therefore the susano'o ceased to exist.
All of which are destroyed in Amaterasu. Therefore Amaterasu is composed of no physical element.
Where do you get that idea from? Jinton destroyed madara's susano, and even damaged his armor.
Gases, can't be destroyed? XD
Since Amaterasu burns everything even chakra. Jinton will lose the chakra that is made to keep the attack going. Either two things happen.
Jinton destroyed another Jinton (which is made of chakra), the two techniques clashed and destroyed each other, if Jinton doesn't work on chakra then it should've gone through the other Jinton (which is made of chakra) and do nothing to it.
