Deadline?

This isn't the first time I don't understand what I'm posting, and I'm sure it won't be the last (I am exceptionally ignorant). I understand the clock, we're one minute to midnight, and builder The Chosen One calls this "Deadline!", which I assume is connected to the time. I don't know enough about chemistry to understand what molecule that is. And is that a huge clock or a tiny katana? So many questions...