Applications of ionization spectroscopy to study small bio-molecules

Abstract

Ionization potential provides a useful quantum mechanical diagnostic for the oxidative potential of a molecule. However, to accurately predict the ionization binding energy spectra for even small biomolecules using relatively simple models is still a challenge in theoretical spectroscopy. In the progress report, recent progresses targeting core and valence binding energy spectroscopy of small bio-molecules, such as amino acids and DNA/RNA bases and their fragments, are discussed using density functional theory based models.

Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry‐adapted cluster/configuration interaction methodology

“…In this case, a detailed understanding of their structures, dynamics and distinction between intrinsic properties and those due to environmental interactions can be obtained. 4 Valance (21.218 eV) photoelectron spectrum of HYP and its methyl-substituted derivatives were first recorded by Lin et al 5 using a helium (He) lamp (21.218 eV) as a radiation source. The authors also investigated the electronic structure and gas-phase tautomerism of HYP and its methyl-substituted derivatives by CNDO/S semi-empirical molecular orbital (MO) and HartreeFock (HF) ab initio calculations using floating spherical Gaussian type orbitals.…”

Intramolecular interactions of L‐phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules

“…18 Under appropriate approximations, orbitals of a molecule can be measured as MDs in momentum space. When combined with position space information, momentum space provides an additional dimension of chemical bonding information.…”

“…[18][19][20][21][22][23][24][25] Modern computational chemistry has made the accurate calculations of several one electron properties routine, shifting the focus of theoretical work from calculation to interpretation. 26 In this article, valence orbitals of L-phe are studied using DSA, with respect to its fragment species, ie., benzene and L-alanine, to reveal intramolecular interactions between phenyl and alaninyl.…”

Methylation of zebularine investigated using density functional theory calculations

“…Nevertheless, based on the ionization energy differences (e.g., SAOP energies), valence orbitals of the nucleoside pair are classified as primary methyl dominant group of MO8(57a), MO18(47a), and MO37(28a) (orbitals only for d5; Marked bold in Table 2); secondary methyl affected orbitals such as HOMO(as MO1 which refers to 60a in zeb and Accurate calculations of ionization energies for larger molecules have been always a challenge to theoreticians. 22 However, valence ionization spectra of molecules are usually more accessible than core ionization spectra, as smaller relaxation effects in valence space mean that even the Hartree-Fock orbital energies can be good approximations for ionization energies through the Koopman's theorem. For smaller molecules such as benzene, 35 the sophisticated ADC(3) model, 36 is able to produce accurate ionization energies for the valence orbitals.…”

“…A recent review given by Takahashi and their applications to biomolecules has been documented. 22,23 Combining the spectroscopic means to investigate methylation of zeb is able to provide a more comprehensive understanding of the important processes in nucleosides. In the present study, we reveal the methylation process from a combined spectroscopic method and from orbital based information in momentum space.…”