To quickly create an animation of two or more molecules assembling, select them and double-click the Assemble button in the Animator (Ctrl / Cmd + 7).
This will automatically determine the initial and final position of each molecule, and add the assemble animation to the active presentation.
You can then change the begin and end keyframes in the animator, and change the amplitude and easing curve of the motion in the Inspector (Ctrl / Cmd + 2).