A large series of similar non-covalent complexes were probed using ion mobility spectrometry, molecular mechanics/molecular dynamics (MM/MD), electrospray-tandem mass spectrometry (ESI-MS/MS) and RRKM theory in order to determine the effects of charge state and charge location upon the conformation, the 0 K activation energy (E0) and the entropy of activation (ΔS‡) of the dissociation of these complexes. The non-covalent complexes consisted of poly(methylmethacrylate) oligomers and singly and doubly charged diaminoalkanes of varying length. This allowed for control of the charge separation within the complexes, as well as the size of the complex. A destabilizing effect was observed in complexes containing protons in close proximity, and/or short oligomers. Interestingly, a multiple charge stabilizing effect was observed when charge sites were sufficiently separated and/or when the polymer moiety of the complex was large. ΔS‡ values of doubly charged complexes showed a greater increase with increasing polymer size in comparison to singly charged complexes. This entropic observation is explained by structure, where IMS and MM/MD determined that the charge location was the determining factor of the overall conformation of these complexes and multiple charging resulted in more rigid arrangements. Dissociation of a tightly bound complex is more entropically favorable than a loosely bound complex. Also presented is a MM/MD refinement regime derived from IMS measurements.