Arrhenius activation parameters for the loss of neutral nucleobases from deprotonated oligonucleotide anions in the gas phase

Abstract

Arrhenius activation parameters ( E a and A) for the loss of neutral nucleobase from a series of doubly deprotonated oligodexoynucleotide 10-mers of the type XT 9, T 9X, and T 5XT 4, where X = A, C, and G, have been determined using the blackbody infrared radiative dissociation technique. At temperatures of 120 to 190 °C, the anions dissociate exclusively by the loss of a neutral nucleobase (XH), followed by cleavage of the sugar 3′ CO bond leading to (a-XH) and w type ions or, in the case of the T 9X 2− ions, the loss of H 2O. The dissociation kinetics and energetics are sensitive to the nature and position of X. Over the temperature range investigated, the kinetics for the loss of AH and GH were similar, but ∼100 times faster than for the loss of CH. For the loss of AH and GH, the values of E a are sensitive to the position of the base. The order of the E a s for the loss of XH from the 5′ and 3′ termini is: C > G > A; while for T 5XT 4 the order is: C > A > G. The trends in the values of E a do not parallel the trend in deprotonation enthalpies or proton affinities of the nucleobases in the gas phase, indicating that the energetic differences do not simply reflect differences in their gas phase acidity or basicity. The pre-exponential factors ( A) vary from 10 10 to 10 15 s −1, depending on the nature and position of X. These results suggest that the reactivity of individual nucleobases is influenced by stabilizing intramolecular interactions.