The effect of protonation site on bond strengths in simple peptides: Application of Ab initio and modified neglect of differential overlap bond orders and modified neglect of differential overlap energy partitioning.

A comparative study of ab initio 6-31G() and semiempirical modified neglect of differential overlap (MNDO) bond orders and MNDO diatomic energy contributions for the description of bond strengths in neutral and protonated glycine, diglycine, triglycine, and dialanine is presented. Good correlations were found between 6-31G() and MNDO bond orders and between MNDO bond orders and diatomic energy contributions. Although bond orders and diatomic energy contributions are inherently different quantities, both predict the changes in bond strengths due to protonation to be qualitatively the same. The theoretically predicted differences in bond strengths for different protonated forms clearly indicate that in peptide fragmentation schemes one should consider even those protonated forms whose formation is not preferred energetically.