A series of thermometer molecules (benzyl-substituted benzyl-pyridinium salts) were successfully used to determine the internal energy of ions generated by electrospray ionization. We used the chlorine salts of 4-chloro- (4C) 4-floro- (4F), 3-methoxy- (3MO), 4-methoxy- (4MO), 2-methyl- (2M), 3-methyl- (3M) and 4-methyl- (4M) benzyl-pyridinium to probe the energy deposited in analytes by different matrixes (CHCA, DHB and SA) during desorption process in MALDI.

The molecules in this series have a very simple fragmentation pathway. The energy deposited in the molecular ion at generation, induces its fragmentation according to the following reaction (shown here for 4MO molecule):

Their MALDI spectrum shows only 2 analyte peaks corresponding to the molecular ion (M+) and to the fragment ion (F+). Using the intensities of these peaks - I(M+) and I(F+) - we calculate the survival yields (SY):

Survival yields help us calculate the experimental fragmentation reaction rate coefficients (kexp). Theoretical rate coefficients (kRRKM) are evaluated using the Rice-Ramsperger-Kassel-Marcus theory. The internal energy of the ions is considered the energy E that leads to a theoretical rate coefficient kRRKM similar to the experimental rate coefficient kexp.

The sums and the densities of states were calculated using the Beyer-Swinehart direct count method. Critical energies were obtained from literature while frequencies of the equilibrium geometries and transition states were evaluated by AM1 semiempirical calculations.