The Reveal atoms animation makes atoms (and bonds between them) appear progressively between two frames. This is done via the visibility of nodes and not via their transparency.
See also animations: Conceal atoms, Appear, Disappear, Flash, Pulse, Show, Shown, Hide, Hidden
First, choose atoms and bonds that you want to progressively disappear.
Then, double-click on the Reveal atoms animation effect in the Animation panel of the Animator.
This animation has 4 keyframes:
Move the keyframes of the animation as needed.
Note: You can always move the keyframes of the animation.
You can change how the parameters are interpolated between the frames by modifying the Easing curve.