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Universal mechanism for breaking amide bonds by ionizing radiation
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10.1063/1.3613638
/content/aip/journal/jcp/135/4/10.1063/1.3613638
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/4/10.1063/1.3613638
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Figures

Image of FIG. 1.
FIG. 1.

N 1s absorption spectra versus irradiation for a variety of amides. Arrows indicate increasing radiation exposure. (a) Alanine anhydride, (b) hexaglycine, (c) polyglycine, (d) cytochrome c, (e) bovine serum albumine (BSA), and (f) nylon 6. In all cases, the characteristic π* orbital of the amide bond at about 401.4 eV is quenched, and two new π* orbitals appear at about 398.9 eV and 400.0 eV. That suggests a universal bond breaking mechanism.

Image of FIG. 2.
FIG. 2.

O 1s absorption spectra versus irradiation for hexaglycine, BSA, and nylon 6. The π* and σ* peaks both decay with irradiation. This indicates removal of oxygen from the amide bond. The amide π* orbital at ≈532.2 eV includes the C=O double bond.

Image of FIG. 3.
FIG. 3.

C 1s absorption spectrum of hexaglycine versus irradiation. The π* peak of the amide bond at 288.1 eV decays with irradiation. Since this π* orbital includes the C=O bond, its decay confirms the removal of oxygen. The difference spectrum reveals the appearance of extra features below the amide π*. Two arrows at 284.9 eV and 286.5 eV indicate typical positions of imine and nitrile π* transitions.

Image of FIG. 4.
FIG. 4.

Model for the dissociation of the amide bond, which is compatible with the absorption spectra at the N, O, and C 1s edges. The amide bond is a conjugated π system which can be viewed as a superposition of the “covalent” configuration (a1) and the “(zwitter)-ionic” configuration (a2). Configuration (a1) is required to observe a π* orbital at the O 1s edge (Fig. 2) and Configuration (a2) to observe it at the N 1s edge (Fig. 1). (b) shows the intermediate state after removing the oxygen atom by irradiation. To repair the broken C=O bond, the H atom bonded to the N can migrate to one of the two adjacent carbon atoms (C or Cα), as indicated by two arrows. The two final reaction products are an imine in (c1) or a nitrile in (c2). They give rise to the two π* peaks appearing at the N 1s absorption edge in Fig. 1.

Image of FIG. 5.
FIG. 5.

N 1s absorption spectra of an imine and a nitrile, the two reaction products of the mechanism shown in Fig. 4. Their sum approximates the π* doublet seen in Fig. 1 after irradiation, with dashed vertical lines indicating the average peak positions in Fig. 1. The data for s-triazine are from Apen et al. (Ref. 49).

Image of FIG. 6.
FIG. 6.

N 1s absorption spectra of reference molecules for testing a variety of bond-breaking models. The two dashed vertical lines indicate the positions of the radiation-induced π* orbitals in Fig. 1. (a) 2,4,6-Tris(2-pyridyl)-s-triazine, an example for the π-bonded C=N network. (b) Polyacrylonitrile (PAN), a nitrile with two degenerate π* orbitals. (c) 8CB, a nitrile where the degeneracy is lifted by the attached phenyl ring. (d) Dimethyl cyclohexadiene diylidene biscyanamide, a molecule containing both nitrile and imine bonds. (e) Melamine, containing two types of N atoms. (f) Ethyl violet, a molecule with an overall positive charge. (g) Dimethyl adipimidate·2 HCl = DMA, a positively charged imine. (h) Cytosine, with three inequivalent N atoms, two of them π-bonded. (i) 4,6-Dihydroxypyrimidine, with two of its tautomers. (j) Nitrosobenzopyrone, where a single N atom produces two π* peaks.

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/content/aip/journal/jcp/135/4/10.1063/1.3613638
2011-07-25
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Universal mechanism for breaking amide bonds by ionizing radiation
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/4/10.1063/1.3613638
10.1063/1.3613638
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