Employing atomistic molecular dynamics (MD) simulations, we scrutinize the relationship between sub-molecular motions in a glassy polymer and its glass-transition temperature (T-g). This molecular understanding allows us to modify the polymer to manipulate atomistic motions, thereby controlling the glass transition temperature. We demonstrate this using a high performance polymer, HFPE-30, which has applications in aerospace industry. Control over sub-molecular motion is achieved by chemical substitution and it leads to increase in the glass transition temperature without affecting its mechanical properties. The approach laid out here could pave a way to achieve highly cross-linked high temperature polymers with better thermo-chemical stability. (C) 2014 Elsevier B.V. All rights reserved.