J. Phys. Chem A 107 (2003) 6144-6159

Inner shell spectroscopy of the peptide bond: comparison of the C 1s, N 1s and O 1s spectra glycine, glycyl-glycine and glycyl-glycyl-glycine

M.L. Gordon (1), G. Cooper(1), T. Araki(1), C. Morin(1), C. C. Turci(2), K. Kaznatcheev(3), and A. P. Hitchcock (1)

1.Department of Chemistry, McMaster University, Hamilton, ON, L8S 4M1, Canada,
2. Instituto de Quimica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21910, Brazil,
3. Canadian Light Source, University of Saskatchewan, Saskatoon, SK S7N 5C6 Canada

Received: February 20, 2003; In Final Form: June 5, 2003

Abstract—Oscillator strengths for C 1s, N 1s, and O 1s excitation spectra of gaseous glycine and the dipeptide, glycylglycine, have been derived from inner-shell electron energy-loss spectroscopy recorded under scattering conditions where electric dipole transitions dominate (2.5 keV residual energy, ~2 deg). X-ray absorption spectra of solid glycine, glycyl-glycine, glycyl-glycyl-glycine, and a large protein, fibrinogen, were recorded in a scanning transmission X-ray microscope. The experimental spectra are assigned through interspecies comparisons and by comparison to ab initio computed spectra of various conformations of glycine and glycylglycine. Inner-shell excitation spectral features characteristic of the peptide bond are readily identified by comparison of the spectra of gas-phase glycine and glycyl-glycine. They include a clear broadening and a ~0.3 eV shift of the C 1s ->p*C=O peak and introduction of a new pre-edge feature in the N 1s spectrum. These effects are due to 1s f d*amide transitions introduced with formation of the peptide bond. Similar changes occur in the spectra of the solids. The computational results support the interpretation of the experimental inner-shell spectra and provide insight into electron density distributions in the core excited states. Possible conformational dependence of the inner-shell excitation spectra was explored by computing the spectra of neutral glycine in its four most common conformations, and of glycyl-glycine in planar and two twisted conformations. A strong dependence of the computed C 1s, N 1s, and O 1s spectra of glycylglycine on the conformation about the amide linkage was confirmed by additional ab initio calculations of the conformational dependence of the spectra of formamide

Keywords: peptide bond, glycine, Glycyl-glycine, tri-glycine, NEXAFS, delocalization, conformer dependence

10.1021/jp0344390     © 2003 American Chemical Society