The relationship between time and atoms is complex and still not fully understood. On a basic level, time can be seen as a measurement of the change and movement of atoms. Atoms make up all matter in the universe and their interactions and movements are what create the concept of time.
It is believed that time cannot exist without atoms. As mentioned before, time is directly tied to the movement and interactions of atoms. Without atoms, there would be no change or movement to measure, and therefore no concept of time.
This question is a bit more complicated. Atoms are constantly in motion, so in a sense, they are always experiencing time. However, some theories suggest that time may be an emergent property of quantum mechanics and not a fundamental aspect of the universe. In this case, atoms would exist without time, but their movements would still create the illusion of time.
On a quantum level, time has a significant impact on atoms. The uncertainty principle states that the more precisely we measure the position of an atom, the less precise our measurement of its momentum becomes. This means that as we try to observe and measure the movement of atoms, time becomes a more uncertain factor.
It is currently believed that time and atoms cannot be separated. As mentioned before, time is a measurement of the movements of atoms, so without atoms, there would be no time. Similarly, time is a fundamental aspect of the universe, so it would not be possible to remove it from the equation and still have atoms exist.