Theoretical calculations and solid-state NMR have been used to determine the conformation, relative energies, and behavior of organic functional groups covalently bound within the pores of mesoporous silica nanoparticles (MSNs). The calculations were performed using the ReaxFF reactive force field for model surfaces consisting of a four-layer silica slab with one or two functional groups: N-(2-aminoethyl)3-aminopropyl- (AAP), N-[N-(2-aminoethyl)-2-aminoethyl]-3-aminopropyl- (AEP), or 3-cyanopropyl- (CP). The results indicate that the AAP and AEP groups exist primarily in the prone orientation, while CP can almost equally occupy both the prone and upright orientations in CP-MSN. This is in agreement with the solid-state C-13 NMR experiments, which suggest that the AAP and AEP functionalities remain rigid on the NMR. time scale (in this case sub-millisecond), whereas the CP substituent executes faster motions. These conformations are most likely governed by the hydrogen bonds between the amine moieties of the functional groups and the silanol groups on the silica surface. ReaxFF can be used to study a system that requires a large-scale model, such as the surface of an organo-functionalized heterogeneous catalyst, with higher accuracy than the conventional MM and at a lower computational cost than ab initio quantum mechanical calculations.