Non-adiabatic Thouless pumping of electrons is studied in the framework of topological Floquet engineering, particularly with a focus on how atomistic changes to chemical moieties control the emergence of the Floquet topological phase. We employ real-time time-dependent density functional theory to investigate the extent to which the topological invariant, the winding number, is impacted by molecular-level changes to trans-polyacetylene. In particular, several substitutions to trans-polyacetylene are studied to examine different effects on the electronic structure, including the mesomeric effect, inductive effect, and electron conjugation effect. Maximally localized Wannier functions are employed to relate the winding number to the valence bond description by expressing the topological pumping as the transport dynamics of the localized Wannier functions. By further exploiting the gauge invariance of the quantum dynamics in terms of the minimal particle-hole excitations, the topological pumping of electrons can be also represented as a cyclic transition among the bonding and antibonding orbitals. Having connected the topological invariant to the chemical concepts, we demonstrate molecular-level control of the emergence of the Floquet topological phase, presenting an exciting opportunity for the intuitive engineering of molecular systems with such an exotic topological phase.