Ab initio and MS/MS studies on protonated peptides containing basic and acidic amino acid residues - I. Solvated proton vs. salt-bridged structures and the cleavage of the terminal amide bond of protonated RD-NH₂

The results of a detailed ab initio investigation on one of the simplest model peptides, RD-NH₂, containing both basic (R) and acidic (D) residues are presented here. The ab initio (B3LYP/6-31+G(d,p)) relative energies of several internally solvated (IS) and salt-bridged (SB) structures are in the range of 0-33kcal/mol. Upon ion activation in a tandem mass spectrometer, the conversion of IS into SB structures is energetically feasible but very probably kinetically controlled. Several theoretical pathways are suggested for the NH₃ loss from the amide terminus of protonated RD-NH₂. The loss of NH₃ is proposed to occur either via "four-center-one-step" (FCOS) processes or an "oxazolone ring" formation (OX). The FCOS pathways indicate that the formation of a SB structure is not a prerequisite for the loss of NH₃ from the amide terminus. The ab initio results clearly show the complexity of the potential energy surface of even such a small protonated peptide that is manifested in different protonated structures and pathways for a "simple" NH₃ loss. Low-energy CID MS² and MS³ spectra of the singly charged RD-NH₂ have also been recorded and discussed in conjunction with the theoretical results. A brief discussion on the limitations of our current model to the fragmentation behavior of larger peptides containing both basic and acidic amino acids is also presented.