Predicting Core Level Photoelectron Spectra of Amino Acids Using Density Functional Theory

Abstract

Core level photoelectron spectroscopy is a widely used technique to study amino acids. Interpretation of the individual contributions from functional groups and their local chemical environments to overall spectra requires both high-resolution reference spectra and theoretical insights, for example from density functional theory calculations. This is a particular challenge for crystalline amino acids due to the lack of experimental data and the limitation of previous calculations to gas phase molecules. Here, a state of the art multiresolution approach is used for high precision gas phase calculations and to validate core hole pseudopotentials for plane-wave calculations. This powerful combination of complementary numerical techniques provides a framework for accurate ΔSCF calculations for molecules and solids in systematic basis sets. It is used to successfully predict C and O 1s core level spectra of glycine, alanine and serine and identify chemical state contributions to experimental spectra of crystalline amino acids. File list (3) download file view on ChemRxiv amino_paper.pdf (2.77 MiB) download file view on ChemRxiv amino_paper_SI.pdf (2.92 MiB) download file view on ChemRxiv amino_structures.zip (12.01 KiB)

The nuts and bolts of core-hole constrained ab initio simulation for K-shell x-ray photoemission and absorption spectra

“…It should also be noted that the use of the double hybrid functional xD-PBE0 brings no improvement relative to the regular hybrids. The better performance of hybrid functionals for K-shell XPS energies was also reported in the literature [112], while other studies found a better performance of regular GGAs [113]. However, many test sets used to judge the performance of binding energy calculations include only molecules with more moderate shifts [24,63,112,113].…”

“…Nevertheless, approximate core-hole simulation methods remain essential workhorses for highly complex spectroscopy simulations with applications ranging from in-operando electrocatalysis [124] to ultrafast dynamics [125] and pump-probe spectroscopy [126]. The efficiency of these methods enables the creation of high-volume data [112,127,128] which can be used for machine-learning-assisted spectral assignment [129][130][131]. The here presented ΔSCF and ΔIP-TP approaches as implemented in CASTEP are versatile and reliable for organic molecules in different environments and represent important tools in this context.…”

A combined density functional theory and x-ray photoelectron spectroscopy study of the aromatic amino acids

“…Following geometry optimisation and BE calculations, the two conformers of each amino acid with the most distinct BEs were retained for further investigation. For Ala, only the lowest energy conformer used in reference [3] was considered. The structures of each conformer are presented in the supplementary information (https://stacks.iop.org/EST/2/044005/mmedia).…”

“…Here, we expand and improve our previous approach to amino acids with aromatic side chains, including phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), and histidine (His). Figure 1 shows a schematic of their atomic structures, including alanine (Ala) which is used as a reference throughout and which we have reported previously [3]. As for XPS studies on amino acids in general, very few studies exist on the aromatic subgroup.…”

Local electronic structure of histidine in aqueous solution

“…This model at various levels of theory have been implemented in studying the core level shifts in aqueous glycine. 36,50,51 The calculated spectra, based on binding energies summarized in Table 2, are convoluted with a Gaussian with FWHM = 1.2 eV to resemble experimental spectra and are shown in Fig. 3.…”