Single and double protonated (E)-1,4-diamine-2-butenes were evaluated as a model system to probe isomerization during the ESI processes employing infrared multiple-photon dissociation (IRMPD) spectroscopy and density function theory (DFT) calculations, including implicit and explicit solvation models. Our results show that the preferential protonation takes place at the amines for singly protonated species and that the double bond is not protonated even under double protonation, as expected from known pK_a values. This behavior was shown to reflect the (E)–(Z) interconversion rate, as no interconversion was observed nor predicted by implicit solvation model based on density (SMD) calculations even by the olefin protonation pathway. Explicit solvent calculations show that the singly protonated (E) configuration observed in the gas phase is also the most stable configuration in solution due to molecular interactions with the solvent that are absent for the (Z) configuration. The explicit solvation calculation reverts the supposed gas-phase stability of the (Z) configuration in comparison to (E) from −9 kcal mol⁻¹ (in relative Gibbs free energy) in the gas phase to +89 kcal mol⁻¹ (in total potential energy) as depicted by explicit Monte Carlo (MC) simulations. Together with previous results for the saturated 1,4-diamines from Morton and coworkers that show the (Z) configuration related conformation to be the most stable geometry in the gas-phase due to intermolecular hydrogen bonding, our experiments clearly show that conformational reorganizations can take place during the ESI process. These results suggest that gas-phase experiments and vacuum calculations may not be valid as evidence for conformations in solution without prior testing to check for isomerization during the ESI process.