first off, AA is good (in concept), but don't do it on the outside of a piece (against a transparent background) because if somebody has a dark theme, it looks bad.

as for suggestions, try this (don't worry if it looks bad at first, i'll help you fix it, trust me)

don't use letters to distinguish the atoms, draw them. protons nutrons and electrons... hydrogen is easy, 1 proton, 1 electron. oxygen has 8 protons 8 neutrons, and 8 electrons. try to draw each up individually, then we can work on the bonds between them. you can use circles for P N & E, we'll color them different later, (trust me, it'll be fun)

I hope this helps, and feel free to ask for more help.

ok, good.

but keep in mind that protons and neutrons are in the center of an atom, electrons are on the outside.

try combining the protons and neutrons in pairs, then over lappting them to make a sphere, (its ok if some aren't visible)

you can also increase the size a little bit, we're going to compress them, then give it more depth.

as for the aliasing on the original, good fix, its correct now.