The transformation of biomass-derived molecules into platform chemicals that can directly be employed by the chemical industry is one of the challenges in catalysis in this century. While some processes are cost-effective and industrially available, the molecular insight has been advancing at a slow pace when compared to other areas (like energy conversion). In the present review we describe the main challenges imposed on the theoretical simulations for the study of these complex molecules and how the most crucial issues are typically addressed. In particular, we focus on technical aspects like the need for London dispersion and solvation contributions. We also deal with the complexity of reaction networks, which requires new approaches and ways to compile the results in the form of databases. This allows the study of large reaction networks for the decomposition of C2 alcohols, or the plethora of functional groups of cyclic molecules such as lignin and sugars. Finally, we put forward a few applications that show the potential of atomistic simulations in the field