An atom is a basic unit of matter in SpaceChem. They are provided in order to be manipulated and then sent to the desired output location. Most atoms can be bonded to form molecules, fused with other atoms using fusion lasers or split using fission laser.
Only the noble gases cannot be bonded with other atoms. Also, hydrogen, being element number 1, cannot be split. Moreover, no pairs of atoms whose atomic numbers together would be above 109 can be fused. If you try to split unsplittable atoms or fuse unfusable atoms, nothing happens and the waldo just continues as if it had not even just passed any instructions.
All about Atoms see Periodic Table.