Abstract In the course of a liquid secondary ion mass spectrometric (SIMS) investigation on a bisquaternary ammonium antimicrobial agent, decamethoxinum, unusual pathways of fragmentation of the organic dication M 2+ of this bisquaternary salt, with preservation of the doubly charged state of the fragments, were observed. To reveal the structural and electronic parameters of decamethoxinum, which are responsible for the stabilization of its organic dication in the gas phase, a comprehensive SIMS study using metastable decay, collision‐induced dissociation and kinetic energy release techniques complemented by ab initio quantum chemical calculations was performed. Pathways of fragmentation of two main precursors originating from decamethoxinum—organic dication M 2+ and its cluster with a Cl − counterion [M · Cl] + —and a number of their primary fragments were established and systematized. Differences in the pathways of fragmentation of M 2+ and [M · Cl] + were revealed: the main directions of [M · Cl] + decay involve dequaternization similar to thermal degradation of this compound, while in M 2+ fragmentation via loss of one and two terminal radicals with preservation of the doubly charged state of the fragments dominates over charge separation processes. It was shown that pairing of the dication with a Cl − anion does not preserve the complex from fragmentation via separation of two positively charged centers or neutralization (dequaternization) of one such center. At the same time the low abundance of M 2+ in the SIMS spectra is to a larger extent controlled by a probability of M 2+ association with an anion than by the decay of the dication per se. Quantum chemical calculations of the structural and electronic parameters of the decamethoxinum dication have revealed at least three features which can provide stabilization of the doubly charged state. Firstly, in the most energetically favorable stretch conformation the distance between the quaternary nitrogens ( r N1‐N2 = 1.39 nm) is relatively large. Secondly, an intramolecular solvation of quaternary groups by carbonyl oxygens of the adjacent groups of the dication occurs, which contribute to structural stabilization. Thirdly, an important feature of the electronic structure of the dication is the presence of a partial negative charge on the nitrogen atoms and smearing of a positive charge mainly over the hydrogens of alkyl groups attached to the quaternary nitrogens, which reduces the net repulsion between the quaternary groups. The possible influence of charge smearing on the kinetic energy released on the dication fragmentation is discussed. Copyright © 2005 John Wiley & Sons, Ltd.