Experimental and theoretical investigations of the loss of amino acid side chains in electron capture dissociation of model peptides.

Loss of side chains from different amino acid residues in a model peptide framework of RGGGXGGGR under electron capture dissociation conditions were systematically investigated, where X represents one of the twenty common amino acid residues. The alpha-carbon radical cations initially formed by N-Calpha cleavage of peptide ions were shown to undergo secondary dissociation through losses of even-electron and/or odd-electron side-chain moieties. Among the twenty common amino acid residues studied, thirteen of them were found to lose their characteristic side chains in terms of odd-electron neutral fragments, and nine of them were found to lose even-electron neutral side chains. Several generalized dissociation pathways were proposed and were evaluated theoretically with truncated leucine-containing models using ab initio calculations at B3-PMP2/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level. Elimination of odd-electron side chain was associated with the initial abstraction of the hydrogen from the alpha-carbon bearing the side chain by the N-terminal alpha-carbon radical. Subsequent formation of alpha-beta carbon-carbon double bond leads to the elimination of the odd-electron side chain. The energy barrier for this reaction pathway was 89 kJmol-1. This reaction pathway was 111 kJmol-1 more favorable than the previously proposed pathway involving the formation of cyclic lactam. Elimination of even-electron side chain was associated with the initial abstraction of the gamma-hydrogen from the side chain by the N-terminal alpha-carbon radical. Subsequent formation of beta-gamma carbon-carbon double bond leads to the elimination of the even-electron side chain and the migration of the radical center to the alpha-carbon. The energy barrier for this fragmentation reaction was found to be 50 kJmol-1.