HF-STEX and RASSCF calculations on nitrogen K-shell X-ray absorption of purine base and its derivative

Abstract

The nitrogen K-shell X-ray absorption spectra of the purine bases present in nucleic acids, adenine and guanine, were analyzed by using ab initio Hartree-Fock static exchange and restrictedactive-space self-consistent-field calculations. A variety of derivative molecules were calculated to investigate the energetic shifts due to environmental effects on the nitrogen atoms. Shake-up excitations were also addressed.

N-K spectra of adenine amino tautomers

“…When the N @ -K sites locate in the hexagon ring of the tautomer, such as ade n9 and ade n7, the chemical environment in energy term seems more similar as the three imino N-K peaks are closely positioned. When the N @ -K sites locate in the pentagon ring of the tautomer, such as ade n1 and ade n3, the N-K sites in the hexagon ring, N (7) and N (9) , exhibit similar energy environment. In summary, the adenine tautomers are apparently different in their inner-shell N-K spectra.…”

“…Molecules of biological relevance often are thermally labile and hardly be brought into the gas phase by sample heating, and for most of DNA bases the spectra of different tautomers superimpose and make the spectra congested [5,6]. As a result, the study of DNA base tautomers has been largely based on computational methods [7,8,9,10,11,12,13]. Most of structural studies with respect to tautomerism of DNA bases, however, has concerned on the valence space [6,7,9,11,12,14,15], which hardly provides a thorough understanding of the role of possible proton transfer reactions without the recognition of inner-shell re-configuration process.…”

“…As a result, the study of DNA base tautomers has been largely based on computational methods [7,8,9,10,11,12,13]. Most of structural studies with respect to tautomerism of DNA bases, however, has concerned on the valence space [6,7,9,11,12,14,15], which hardly provides a thorough understanding of the role of possible proton transfer reactions without the recognition of inner-shell re-configuration process. For example, valence shell information has yet to interpret the reason why the preferential protonation sites [16,14,6] of ade n9 is in the order of N (1) , N (3) and N (7) (N (10) , N (9) ) andor why proton affinity of these sites is in such the order.…”

“…Most of structural studies with respect to tautomerism of DNA bases, however, has concerned on the valence space [6,7,9,11,12,14,15], which hardly provides a thorough understanding of the role of possible proton transfer reactions without the recognition of inner-shell re-configuration process. For example, valence shell information has yet to interpret the reason why the preferential protonation sites [16,14,6] of ade n9 is in the order of N (1) , N (3) and N (7) (N (10) , N (9) ) andor why proton affinity of these sites is in such the order. Unfortunately, many DNA base tautomeric studies have treated proton transfer as small perturbations, and frozen core (FC) treatment [6] are popular in these studies, which miss the most important information on tautomerism.…”

Electron Momentum Spectroscopy and Its Applications to Molecules of Biological Interest

“…Accurate prediction of electron spectra, particularly for core shell, is still largely for small molecules. A simple mean for the IPs was employed using the B3LYP and RHF orbital energies without any rigorous scientific basis in a spectral analysis of L-alanine (Mochzuki et al, 2001). In the most recent photoabsorption spectra of small amino acids in gas phase (Plekan et al, 2006), the observed results were semi-empirically assigned for the core ionization potentials (IPs) by subtracting the number of 2.6 eV from the DFT calculated core energies.…”