Simulating Ionization Spectra for Small Biomolecules in Inner and Valence Shells

摘要

Accurate prediction of ionization spectra of biomolecules has been a challenge for theoretical spectroscopy. There is no single model which is the best for all biomolecules due to their diversity, leading to a variety of methods. Comparing to inner-shell, valence-shell ionization spectra have been studied more extensively [1-7]. Good agreement with experiment has been achieved from relevantly well developed models, such as the outer valence Green's function (OVGF) model [8]. Energetics of a molecule are usually more sensitive to radial displacements rather than angular variations in the development of quantum chemistry in coordinate space. Energy differences among conformers of a biomolecule can be subtle, when the conformers are dominated by angular changes. However, such conformational changes can be significantly local, such as the shape of a particular orbital [2]. Dual space analysis (DSA) [9], is therefore applied to reveal details from both position space and momentum space of orbitals. Core-shell information was largely ignored in the past few decades, such as the applications of the frozen core model in computational chemistry. Quantitative treatment of NEXAFS spectra for even small biomolecules such as amino acids [10,11] and DNA bases [12-14] has yet been fully understood. Experimentally, congested spectra caused by energy source or resolution of the techniques have prevented from more detailed understanding [12,14]. Theoretically, calculations far from trivial are necessary to accurately reveal inner-shell properties and simple models are usually unable to reveal the subtle differences caused by various chemical environment and conformation of biomolecules. For example, tautomers of DNA bases [2,5,7] exhibit only minor differences in energy, but reveal significant configurational changes in the core shell [16,17]. This paper reports recent applications in simulating ionization spectroscopy including synchrotron sourced X-ray spectroscopy and electron momentum spectroscopy (EMS) to study both core and valence structures for biomolecules.