ogg said:
Anyway, there are two important cases: one in which the E.S. is below the Products, and one in which it is above.
This is not true. The "E.S." as you call it -- though, transition state is the more appropriate term -- is
never lower in energy (more stable) than the products. As a matter of fact, this is completely counterintuitive! One would think that if there were to be progress along a reaction coordinate, and the system encountered some lower energy state on its way to the products, that this conformation would be the true product. In other words, at the geometry of the "products" in the scheme that you mentioned, there would exist a negative gradient along some coordinate q_i, i.e. \frac{\partial^2f}{\partial q_i^2}<0. This is never the case! In fact, according to the variational principle, there should always be a positive gradient along all coordinates at the best structure for the given model.
gabede said:
Is it this simple for any chemical reaction between complex molecules and simple atoms, or are there other key factors I should consider? Also, when determining what product a reaction will create, I am guessing that the most stable product will [...] require the movement of less electrons from the octet-satisfied oxygen ions.
Borek is correct. What you are saying is, unfortunately, indeed simplifed. We use supercomputers and high precision experiments to elaborate upon exactly this. The problem is that chemistry is nasty due to the fact that reactivity depends on individual molecules/atoms, which are many-body problems in themselves. When you consider the interaction between
just two of these many-body systems, the problem becomes even more challenging. In wave function theory (a 3N-dimensional interacting model), this problem is unwieldy. In density functional theory (a 3-dimensional non-interacting model), we encounter problems such as mixing of quantum states, and necessary treatments of quantum subsystems as being open, fluctuating in their number of electrons. These approximations leads to ugly results -- discontinuities in parts of the framework needed to describe essential parts of the picture, and interpretively challenging physical results such as non-integer numbers of electrons.
The point is, chemistry is often a subjective science (I was a chemistry major at one point, so I empathize with this), and it is most commonly the job of the theoretical or quantum chemist to worry about the technicalities of the aforementioned issues. If you are a motivated chemist who was as bothered with this as I was, I would learn a bit more about quantum chemistry (see Levine for a popular and accessible description, or Szabo and Ostlund for a more rigorous treatment).
Importantly, if you want to understand some of these concepts a bit better at the more fundamental level, you will need to understand the definition of some of these terms such as electronegativity, which has been interpreted as the negative of the chemical potential,
1 i.e. \chi=-\mu=-\Big(\frac{\partial E[\rho]}{\partial N}\Big)_{\nu_{ext}}
I would urge you to check out these two papers for more info:
1:
http://scitation.aip.org/content/aip/journal/jcp/68/8/10.1063/1.436185
2:
http://www.pnas.org/content/83/22/8440.full.pdf