The attachment of amino fragment to purine: inner-shell structures and spectra

Abstract

The impact of the amino fragment (-NH(2)) attachment on the inner-shell structures and spectra of unsubstituted purine and the purine ring of adenine are studied. Density functional theory calculations, using the LB94/TZ2P//B3LYP/TZVP model, reveal significant site-dependent electronic structural changes in the inner shell of the species. A condensed Fukui function indicates that all of the N and C sites, except for N((1)) and C((5)), demonstrate significant electrophilic reactivity (f(-) > 0.5 in |e|) in the unsubstituted purine. Once the amino fragment binds to the C((6)) position of purine to form adenine, the electrophilic reactivity of these N and C sites is greatly reduced. As expected, the C((6)) position experiences substantial changes in energy and charge transfer, owing to the formation of the C-NH(2) bond in adenine. The present study reveals that the N1s spectra of adenine inherit the N1s spectra of the unsubstituted purine, whereas the C1s spectra experience significant changes although purine and adenine have geometrically similar carbon frames. The findings also indicate that the attachment of the NH(2) fragment to purine exhibits deeply rooted influences to the inner-shell structures of DNA/RNA bases. The present study suggests that some fragment-based methods may not be applicable to spectral analyses in the inner shell.

Photoelectron spectra and structures of three cyclic dipeptides: PhePhe, TyrPro, and HisGly

“…The aim of this study is to determine the intrinsic structure-property relationship of a number of cyclic dipeptides, using the experimental [11][12][13][14] and theoretical methods [15][16][17] previously applied to modelling both valence and inner-shell electronic states of biomolecules.…”

N-K spectra of adenine amino tautomers

“…Our simulated x-ray photoemission spectroscopy (XPS) of the canonical adenine (ade n9) using the LB94/T2ZP model has been proved accurate when compare to recent XPS experiments [23,26]. As a result, this experimentally validated model is applied to study its amino tautomers theoretically in the present study.…”

“…The planar geometries of the four planar amino tautomers of adenine are optimized respectively using the hybrid density functional theory (DFT) B3LYP/TZVP model. The TZVP basis set is a reasonably large triple zeta with valence polarized (TZVP) basis set [20], which has been proved reliable in our previous investigations of valence electronic properties of adenine amino tautomers [8], amino acids [21] and core shell of bicyclic-hydrocarbons [22] and DNA bases such as purine and adenine [23]. Based on the B3LYP/TZVP geometries of the tautomers, core ionization orbital energies of each tautomer are produced from single point calculations emplying the LB94/TZ2P model.…”

From building blocks of proteins to drugs: a quantum chemical study on structure–property relationships of phenylalanine, tyrosine and dopa

“…What is the role that the OH groups play in L-dopa, which significantly improve its drug potency? Structure-related changes in L-dopa unravel the innate physico-chemical properties of the molecule, which can be useful for understanding biological phenomena 40,41 . Therefore, comparatively studying the structural and electronic properties of those aromatic molecules, i.e., L-phe and L-tyr against Ldopa, reveal information, which helps to understand the structure-property relationships of L-dopa.…”