I don't know much about Chemistry, ok? 

You are seeking the best possible molecule to store energy and release that energy at will. 

You simulate a molecule that breaks down into products. I'm assuming here that there is a theoretical way to predict the outcome and occurence of chemical reactions, and to calculate the enthalpy of the molecule before and after it has broken down into products.

You calculate this, and register each reaction with corresponding enthalpies.

Then you try another molecule, and another, and keep iterating until you have the best fuel possible.

Another goal is inspired by the Omega molecule in Star Trek. To find the most energetically stable molecule that can exist, using the computer. Then, try to sinthesize it in the lab.