You are only comparing a molecule with 2 other ones, which in fact might be anywhere.
Collision detection is a topic quite hard to solve, but if you want to have your idea
working quickly you might go for a n^2 algorithm with 2 nested for loops.
the code is quite expected :
// collision
for(var t = 0; t < molecules.length-1; t++)
for(var tt = t+1; tt < molecules.length; tt++) {
var p1 = molecules[t];
var p2 = molecules[tt];
if (sq(p1.x-p2.x) +sq(p1.y-p2.y) < sq(p1.radius+p2.radius) )
{
p1.collided = 8; // will diplay for next 8 frames
p2.collided = 8; // .
}
}
the fiddle is here : http://jsbin.com/arokuz/10