Then when ions are formed, energy is used up and when ions are neutralised energy is released, that i'd imagine would be as in depth as it'd be needed. The attraction of ions would be fun to play with.
Chemistry/organic chemistry is a little more complicated than that unfortunately. Many reactions do involve ions (for instance NADP+), but that's actually NADPH being broken down to release energy. That is, a neutral molecule being broken down (I think that's considered a reducing reaction if I remember my Chemistry, which is doubtful
) to ions to release
energy. Chemistry is rather a series of mutations of molecules from one form to another, with the difference in bond energy determining how much energy is required or released. As far as I know the amount of bond energy a molecule has is not immediately predictable just from the atoms in it (I think it's some complicated function of the various electron shells and you end up getting neck deep in quantum mechanics before long).
Now that said, a simplified chemistry model isn't impossible, but from a computational standpoint I'd want the role of particles that give off a charge to be minimal. As long as the particles in the sim are passive and only react to the fluid (or electromagnetic forces or whatever), they're O(n) to simulate. That is, double the number of particles and you double the computation time. If they also exert push or have mass or generally do anything to influence the simulation at all it starts to move towards O(n^2). There are ways around that using techniques like multipole methods, but they're really complicated
From a gameplay perspective, though, I think you can get a lot of the effects without doing much of the work. At its core a cell is a capacitor, and uses the voltage difference of the inside and outside of a cell to drive at least some of its reactions. We could do something like limit how fast things (fats, proteins, etc.) can by synthesized by how large the voltage difference is, which is a function of total charge and bot surface area. Building up charge could take time. Expending charge is less limited, but once its gone its gone, and has to be recharged.