Backbone fragmentations of [M-H]- anions from peptides. Reinvestigation of the mechanism of the beta prime cleavage.

Rationale: An experimental study has shown that the structure of a β' ion proposed earlier is incorrect. Backbone cleavage β' anions have structures R(NH(-)) from systems [[RNHCH(X)CONHCH(Y)CO(2)H (or C-terminal CONH(2))-H](-) (where R is the rest of the peptide molecule and X and Y represent the α side chains of the individual amino acid residues).

Methods: Ab initio calculations were carried out at the CAM-B3LYP/6-311++g(d,p) level of theory.

Conclusions: The calculations suggest that RNH(-) ions are formed by S(N)i cyclisation processes involving either (i) the C-terminal CO(2)(-) or C-terminal [CONH](-) as appropriate, or (ii) an enolate ion [-NHC(-)(Y)-] cyclising at the backbone CH of the -CH(X)- group. Concomitant C-N bond cleavage then liberates an RNH(-) ion, processes which can occur along the peptide backbone.