Why Are B ions stable species in peptide spectra?

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Abstract
Protonated amino acids and derivatives RCH(NH2)C(+O)X · H+ (X = OH, NH2, OCH3) do not form stable acylium ions on loss of HX, but rather the acylium ion eliminates CO to form the immonium ion RCH = NH 2 + . By contrast, protonated dipeptide derivatives H2NCH(R)C(+O)NHCH(R′)C(+O)X · H+ [X = OH, OCH3, NH2, NHCH(R″)COOH] form stable B2 ions by elimination of HX. These B2 ions fragment on the metastable ion time scale by elimination of CO with substantial kinetic energy release (T 1/2 = 0.3–0.5 eV). Similarly, protonated N-acetyl amino acid derivatives CH3C(+O)NHCH(R′)C(+O)X · H+ [X = OH, OCH3, NH2, NHCH(R″)COOH] form stable B ions by loss of HX. These B ions also fragment unimolecularly by loss of CO with T 1/2 values of ∼ 0.5 eV. These large kinetic energy releases indicate that a stable configuration of the B ions fragments by way of activation to a reacting configuration that is higher in energy than the products, and some of the fragmentation exothermicity of the final step is partitioned into kinetic energy of the separating fragments. We conclude that the stable configuration is a protonated oxazolone, which is formed by interaction of the developing charge (as HX is lost) with the N-terminus carbonyl group and that the reacting configuration is the acyclic acylium ion. This conclusion is supported by the similar fragmentation behavior of protonated 2-phenyl-5-oxazolone and the B ion derived by loss of H-Gly-OH from protonated C6H5C(+O)-Gly-Gly-OH. In addition, ab initio calculations on the simplest B ion, nominally HC(+O)NHCH2CO+, show that the lowest energy structure is the protonated oxazolone. The acyclic acylium isomer is 1.49 eV higher in energy than the protonated oxazolone and 0.88 eV higher in energy than the fragmentation products, HC(+O)N+H = CH2 + CO, which is consistent with the kinetic energy releases measured.

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