A theoretical framework for the formalization of chemical interaction and configuration based properties
Technically, one could argue that the entirety of chemistry is trying to formalize how properties of molecules change under a given perturbation. From a computational perspective, some work is being done in the context of machine learning towards developing a continuous mathematical representation of molecules, essentially mapping out chemical space. In this way, you could determine how properties change based on how close different configurations of a compound are in this chemical space. 

For details/an example, see 1. 
For more on this topic, search "chemical space" or, for some of the commonly used mathematical tools used, "principal component analysis" and "variational auto encoder". 

Overall, I think a chemical Theory of Everything would have to necessarily be much more qualitative than that of Physics, just due to the emergent complexity that comes from the vast number of combinatorial possibilities of different compounds. 


Aspuru-Guzik, A. et al. Automatic chemical design using a data-driven continuous representation of molecules. ACS Central Science. 2018, 4.