Hi. I'm trying to make a chemical reaction simulator.

I have a first year undergraduate level understanding of chemistry, biology, physics, mathematics, and computer science and can make a (2D) Pong clone. I am familiar with things like classes, objects, modules, and event-driven programming as well as basic calculus and linear algebra. I also know a bit of Java and C++ but would like to use pygame for this project since I am most familiar with Python.

I plan to model each atom as a sphere with a:

1.) diameter
2.) electronegativity
3.) mass
4.) velocity
5.) valence number

Bonds would come in single, double, and triple forms.

The idea is that I should be able to add hydrogen and oxygen, have them collide, and get water molecules forming. Eventually I would like to make things like phospholipids that spontaneously arrange to form cell membranes, DNA base pairing, proteins, and maybe even the nanomachines that Eric Drexler envisioned.

What other parameters would I need in addition to the five above in order to accurately model an atom?

Thanks in advance.