This paper describes non-covalent complexes between zwitterionic 3-(1-alkyl-3N-imidazolio)-propane-1-sulfonates and different amines. Electrospray ionization (ESI) mass spectrometry and collision-induced dissociation were used to measure the stability of such complexes in solution and in the gas phase. Generally, zwitterionic sulfonates formed more abundant complexes with protonated 5-methylcytosine (5-MCH) than with aliphatic amines. The results show that the association constants and half-dissociation threshold energies of these complexes nonlinearly depend on the alkyl chain length of the zwitterion. It is shown that the complexes with the lowest stability exist in acetonitrile solution or in the gas phase. The factors responsible for this complicated behavior are discussed.The structure of the complexes was investigated by quantum chemical calculations using molecular mechanics and density functional theory. Hydrogen bonding is proposed as the main type of interaction responsible for the stability of ion-zwitterion complexes. In summary, the information obtained in this study could be used for the development of the new derivatization reagents for some compounds containing amidinium groups, like 5-MCH, to increase selectivity of ESI-based methods.

5-Methylcytosine (5-MC) is an important epigenetic modification of DNA. Abnormally high concentrations of this substance appear because of the hypermethylation of cytosine. Therefore, the measurement of the quantity of this compound in mammals is of great importance. Recently, we reported that several imidazolium-based zwitterionic sulfonates form complexes with 5-MC in solution, which can be studied by electrospray ionisation mass spectrometry (ESI-MS). It is shown in this paper that such an association can be utilised for the detection of 5-MC in a DNA sample using high-throughput a flow injection analysis ESI-MS method. A variety of the sulfonate zwitterions have been tested as m/z shift reagents to increase the selectivity of the analysis. It is shown that either of the zwitterions can be used without the loss of sensitivity. The performance of the method was tested in terms of linearity range, sensitivity, intra- and between-day precision and accuracy, matrix effect and carryover. The method described is characterised by simplicity, a good limit of quantitation (1 pg injected) and low run times (at least 50 injections per hour). In addition, high-performance liquid chromatography and tandem mass spectrometry are not required. The possibility exists to widen the scope of the method to other amidine-containing compounds present in more complicated matrices.