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


J. H. Bowie, Department of Chemistry, The University of Adelaide, South Australia, 5005.




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)CO2H (or C-terminal CONH2) – 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).


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


The calculations suggest that RNH ions are formed by SNi cyclisation processes involving either (i) the C-terminal CO2 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. Copyright © 2012 John Wiley & Sons, Ltd.