Atoms are smaller that the waves that our ears detect. A sound is carried by a wave. If I were to blurt out, "I hate George W. Bush!", the sound isn't moving on its own, rather the sound would be carried on the wave.
Just imagine a pool of water. Drop a grape in the center of the pool. A rippling effect moves from the center of where the grape landed in the water. Now, the water itself isn't moving outwards from the grape drop, but rather, the wave is moving, causing the water, the medium, to move where the wave is. Or imagine yourself in a wave pool. When the wave comes, you bob up pretty much in the same position. You don't move horizontally, just vertically. This is how sound travels.
So imagine the sound is the grape and the ripples are what the sound piggybacks itself on. Now if you drop a grape in water, the water ripples. If you drop a grape in a vacuum, there will be no ripples because there is no medium for the ripples to travel on. This is why in outer space, sound doesn't travel well at all. There is no medium to be rippled.
Sound ripples the air, and the air consists of molecules. If we take out the air, there will no longer be any medium for the sound to ripple. Now look at the air zoomed out. There are billions of molecules just itching to be rippled. It feels REAL NICE you know. So a sound comes and then the air molecules ripple. Now zoom in and in and in. Now you see not a sea, but just individual molecules flying about waiting for that rippling thing. But there is nothing in between the molecules when you look so zoomed in, so the medium no longer exists at this zoomed in point. So if two atoms collided, there would be no sound because there is no medium which is so because the molecules or air is the medium.
Make sense? If not, spin in your chair five times real fast and respond to this post. ;)