The easiest way I can think of is Having a spawn state Boolean attached to the game/player state.
If PlayerState = CutScene
Set Var CanSpawn false
Then add a condition on the call function like
If CanSpawn = true
Call function.
If that makes sense. That would be the easiest way to do it.
Then if you want it to spawn one on a timer, You can attach a timer to each molecule,
When spawn, start timer, after X seconds set CanSpawn to true. Spawn the molcule then set CanSpawn to False....