The prototypical pillared layer MOFs, formed by a square lattice of paddle-wheel units and connected by dinitrogen pillars, can undergo a breathing phase transition by a "wine-rack" type motion of the square lattice. We studied this behavior, which is not yet fully understood, using an accurate first principles parameterized force field (MOF-FF) for larger nanocrystallites on the example of Zn2(bdc)2(dabco) [bdc: benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)], and found clear indications for an interface between a closed and an open pore phase traveling through the system during the phase transformation [J. Keupp and R. Schmid, Adv. Theory Simul., 2019, 2, 1900117]. In conventional simulations in small supercells this mechanism is prevented by periodic boundary conditions (PBCs), enforcing a synchronous transformation of the entire crystal. Here, we extend this investigation to pillared layer MOFs with flexible side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimentally known to have different properties with the side-chains acting as fixed guest molecules. First, in order to extend the parameterization for such flexible groups, a new parameterization strategy for MOF-FF had to be developed, using a multi-structure force based fit method. The resulting parameterization for a library of fu-MOFs is then validated with respect to a set of reference systems and shows very good accuracy. In the second step, a series of fu-MOFs with increasing side-chain length is studied with respect to the influence of the side-chains on the breathing behavior. For small supercells in PBCs a systematic trend of the closed pore volume with the chain length is observed. However, for a nanocrystallite model a distinct interface between a closed and an open pore phase is visible only for the short chain length, whereas for longer chains the interface broadens and a nearly concerted transformation is observed. Only by molecular dynamics simulations using accurate force fields can such complex phenomena can be studied on a molecular level.