How do we predict the properties of the materials we make through chemical reactions?
Well, you've described one of the goals of computational chemistry. It turns out that this problem is harder than intuition might predict. I recently read an article on the state of quantum computing that happens to summarize the issue for chemists nicely.


  We do not have enough computing power to do this well.


Computational quantum chemical models have become more and more sophisticated to take advantage of increasing computing power, but there still is not enough computing power. Part of the issue is that at the center of what we are trying to do is a multibody problem, which means that any attempts to optimize the electronic state for one electron in a molecule perturbs the state for other electrons. Then we go and adjust those other electrons, which perturbs our first electrons. This is a certified Really Hard ProblemTM. 

At the end of the day, we currently cannot determine exact solutions to multielectron wavefunctions. So approximations get made, and the approximations are getting better. In fact for smallish molecules, we are getting quite close to a variety of known experimental properties. However, for larger molecules, the algorithms still need trained and calibrated on real experimental data. As the molecules get bigger, or the materials being modeled become more complex, our ability to throw quantum chemical calculations at them diminishes. Modeling of proteins mostly uses molecular mechanics and statistical dynamics.