I am looking for introduction to modeling of chemical reactions. I think there is the base approach, where concentrations of chemical species are given, plus ratios of each possible reaction / outcome. Is there a paper lightly explaining internal mechanics of such reactions, and their modeling via system of differential equations?
The topic you are asking about is called reaction dynamics, and is closely related to chemical kinetics (the former is more focussed on atomistic events, reactive and nonreactive collisions, while the later usually describes the mathematical treatment of the kinetic laws governing species concentrations). It was the topic of the 1986 Nobel Prize in Chemistry.
It is covered by most physical chemistry textbooks, and more in depth by specialized textbooks on that matter. It is sometimes taught together with basics of statistical mechanics or statistical thermodynamics. Check your favorite (or local) university for a list of reading material on this topic!