Towards sensitive identification of fluorinated graphdiyne configurations by computational X-ray spectroscopy

Fluorinated graphdiyne (F-GDY) materials exhibit exceptional performance in various applications, such as luminescent devices, electron transport, and energy conversion. Although F-GDY has been successfully synthesized, there is a lack of comprehensive identification of fluorinated configurations, either by theory or experiment. In this work, we investigated seven representative F-GDY configurations with low dopant concentrations and simulated their carbon and fluorine 1s X-ray photoelectron spectroscopy (XPS) and carbon 1s near-edge X-ray absorption fine-structure (NEXAFS) spectra. The goal was to establish the structure-spectroscopy relation for these materials. The simulated XPS spectra closely match the experimental data, providing sensitive identifications of certain fluorinated structures, although challenges still persist in distinguishing a few similar configurations. In contrast, the NEXAFS spectra, generated by three non-equivalent carbon atoms at the K-edges, offer more detailed information and are more sensitive for identifying all different F-GDY structures. Our theoretical study provides valuable insights for future experimental identification of F-GDY structures. These findings underscore the utility of computational X-ray spectroscopy in advancing the understanding and development of novel carbon-based materials.

Simulating temperature and tautomeric effects for vibrationally resolved XPS of biomolecules: Combining time-dependent and time-independent approaches to fingerprint carbonyl groups

Carbonyl groups (C=O) play crucial roles in the photophysics and photochemistry of biological systems. O1s x-ray photoelectron spectroscopy allows for targeted investigation of the C=O group, and the coupling between C=O vibration and O1s ionization is reflected in the fine structures. To elucidate its characteristic vibronic features, systematic Franck-Condon simulations were conducted for six common biomolecules, including three purines (xanthine, caffeine, and hypoxanthine) and three pyrimidines (thymine, 5F-uracil, and uracil). The complexity of simulation for these biomolecules lies in accounting for temperature effects and potential tautomeric variations. We combined the time-dependent and time-independent methods to efficiently account for the temperature effects and to provide explicit assignments, respectively. For hypoxanthine, the tautomeric effect was considered by incorporating the Boltzmann population ratios of two tautomers. The simulations demonstrated good agreement with experimental spectra, enabling differentiation of two types of carbonyl oxygens with subtle local structural differences, positioned between two nitrogens (O1) or between one carbon and one nitrogen (O2). The analysis provided insights into the coupling between C=O vibration and O1s ionization, consistently showing an elongation of the C=O bond length (by 0.08-0.09 Å) upon O1s ionization.

Simulating transient X-ray photoelectron spectra of Fe(CO)5 and its photodissociation products with multireference algebraic diagrammatic construction theory

Accurate simulations of transient X-ray photoelectron spectra (XPS) provide unique opportunities to bridge the gap between theory and experiment in understanding the photoactivated dynamics in molecules and materials. However, simulating X-ray photoelectron spectra along a photochemical reaction pathway is challenging as it requires accurate description of electronic structure incorporating core-hole screening, orbital relaxation, electron correlation, and spin-orbit coupling in excited states or at nonequilibrium ground-state geometries. In this work, we employ the recently developed multireference algebraic diagrammatic construction theory (MR-ADC) to investigate the core-ionized states and X-ray photoelectron spectra of Fe(CO)5 and its photodissociation products (Fe(CO)4, Fe(CO)3) following excitation with 266 nm light. The simulated transient Fe 3p and CO 3σ XPS spectra incorporating spin-orbit coupling and high-order electron correlation effects are shown to be in a good agreement with the experimental measurements by Leitner et al. [J. Chem. Phys., 2018, 149, 044307]. Our calculations suggest that core-hole screening, spin-orbit coupling, and ligand-field splitting effects are similarly important in reproducing the experimentally observed chemical shifts in transient Fe 3p XPS spectra of iron carbonyl complexes. Our results also demonstrate that the MR-ADC methods can be very useful in interpreting the transient XPS spectra of transition metal compounds.

First-principles simulation of X-ray spectra of graphdiyne and graphdiyne oxides at the carbon K-edge

The experimental C 1s near-edge X-ray absorption fine-structure (NEXAFS) spectra of graphdiyne (GDY) show an evident change at different exposure periods, which is explained by oxidation. Herein, to better understand the structure-spectra relationship and the influence of oxidization, we performed a first-principles simulation of the NEXAFS spectra and X-ray photoelectron spectra (XPS) of both pure GDY and its four typical graphdiyne oxides (GDO) at the carbon K-edge. Pure GDY contains one sp2-hybridized (C1) and two sp-hybridized (C2, C3) carbons, while oxidation introduces more nonequivalent carbons. The experimental NEXAFS spectrum exhibits the lowest peak at ca. 285.8 eV. It was found that the C 1s → π* excitation from the sp2-hybridized carbon atoms (C1) in pure GDY and the sp-hybridized atoms (C2, C3) in GDOs contributes to this peak. The two weak resonances at around 289.0 and 290.6 eV in the experiment are contributed by the carbon atoms bonded to the oxygen atoms. Meanwhile, we found that oxidization leads to an increase in the C 1s ionization potentials (IPs) by 0.3-2.7 eV, which is consistent with the XPS experiments. Our calculations provide a clear explanation of the structure-spectra relationships of GDY and GDOs, and the signatures are useful for estimating the degree of oxidation.

Vibrationally-Resolved X-ray Photoelectron Spectra of Six Polycyclic Aromatic Hydrocarbons from First-Principles Simulations

Vibrationally resolved C 1s X-ray photoelectron spectra (XPS) of a series of six polycyclic aromatic hydrocarbons (PAHs; phenanthrene, coronene, naphthalene, anthracene, tetracene, and pentacene) were computed by combining the full core hole density functional theory and the Franck-Condon simulations with the inclusion of the Duschinsky rotation effect. Simulated spectra of phenanthrene, coronene, and naphthalene agree well with experiments both in core binding energies (BEs) and profiles, which validate the accuracy of our predictions for the rest molecules with no high-resolution experiments. We found that three types of carbons i (inner C), p (peripheral C bonded to three C atoms), and h (peripheral C bonded to an H atom) show decreasing BEs. In linear PAHs (the latter four), h-type carbons further split into h1 or h2 (on inner or edge benzene ring) subtypes with chemical shifts of ca. 0.2-0.4 eV. All major Franck-Condon-active modes are characterized to be in-plane vibrations: low-frequency (<800 cm^-1) C-C ring deformation modes play an essential role in determining the peak asymmetries; and for each h-type carbon a high-frequency (ca. 3600 cm^-1) C*-H stretching mode is responsible for the high-energy tail. We found that core ionization leads to reduction of all C*-C and C*-H bond lengths and ring deformation with a definite direction. Based on theoretical spectra of four linear PAHs, we found asymptotic relations and anticipated possible spectral features for even larger linear PAHs. Our calculations provide accurate reference spectra for XPS characterizations of PAHs, which are useful in understanding the vibronic coupling effects in this family.

Soft X-ray Spectroscopy Simulations with Multiconfigurational Wave Function Theory: Spectrum Completeness, Sub-eV Accuracy, and Quantitative Reproduction of Line Shapes

Multireference methods are known for their ability to accurately treat states of very different nature in many molecular systems, facilitating high-quality simulations of a large variety of spectroscopic techniques. Here, we couple the multiconfigurational restricted active space self-consistent field RASSCF/RASPT2 method (of the CASSCF/CASPT2 methods family) to the displaced harmonic oscillator (DHO) model, to simulate soft X-ray spectroscopy. We applied such an RASSCF/RASPT2+DHO approach at the K-edges of various second-row elements for a set of small organic molecules that have been recently investigated at other levels of theory. X-ray absorption near-edge structure (XANES) and X-ray photoelectron spectroscopy (XPS) are simulated with a sub-eV accuracy and a correct description of the spectral line shapes. The method is extremely sensitive to the observed spectral shifts on a series of differently fluorinated ethylene systems, provides spectral fingerprints to distinguish between stable conformers of the glycine molecule, and accurately captures the vibrationally resolved carbon K-edge spectrum of formaldehyde. Differences with other theoretical methods are demonstrated, which show the advantages of employing a multireference/multiconfigurational approach. A protocol to systematically increase the number of core-excited states considered while maintaining a contained computational cost is presented. Insight is eventually provided for the effects caused by removing core-electrons from a given atom in terms of bond rearrangement and influence on the resulting spectral shapes within a unitary orbital-based framework for both XPS and XANES spectra.

A theoretical library of N1s core binding energies of polynitrogen molecules and ions in the gas phase

Polynitrogen molecules and ions are important building blocks of high energy density compounds(HEDCs). High energy bonds formed at the N sites can be effectively probed by the X-ray photoelectron spectroscopy...

Breaking inversion symmetry by protonation: experimental and theoretical NEXAFS study of the diazynium ion, N2H. Phys Chem Chem Phys 2021;23:17166-17176. [PMID: 34346432 DOI: 10.1039/d1cp02002a]

As an example of symmetry breaking in NEXAFS spectra of protonated species we present a high resolution NEXAFS spectrum of protonated dinitrogen, the diazynium ion N₂H⁺. By ab initio calculations we show that the spectrum consists of a superposition of two nitrogen 1s absorption spectra, each including a π* band, and a nitrogen 1s to H⁺ charge transfer band followed by a weak irregular progression of high energy excitations. Calculations also show that, as an effect of symmetry breaking by protonation, the π* transitions are separated by 0.23 eV, only slightly exceeding the difference in the corresponding dark (symmetry forbidden) and bright (symmetry allowed) core excitations of neutral N₂. By DFT and calculations and vibrational analysis, the complex π* excitation band of N₂H⁺ is understood as due to the superposition of the significantly different vibrational progressions of excitations from terminal and central nitrogen atoms, both leading to bent final state geometries. We also show computationally that the electronic structure of the charge transfer excitation smoothly depends on the nitrogen-proton distance and that there is a clear extension of the spectra going from infinity to close nitrogen-proton distance where fine structures show some, although not fully detailed, similarities. An interesting feature of partial localization of the nitrogen core orbitals, with a strong, non-monotonous, variation with nitrogen-proton distance could be highlighted. Specific effects could be unraveled when comparing molecular cation NEXAFS spectra, as represented by recently recorded spectra of N₂⁺ and CO⁺, and spectra of protonated molecules as represented here by the N₂H⁺ ion. Both types containing rich physical effects not represented in NEXAFS of neutral molecules because of the positive charge, whereas protonation also breaks the symmetry. The effect of the protonation on dinitrogen can be separated in charge, which extends the high-energy part of the spectrum, and symmetry-breaking, which is most clearly seen in the low-energy π* transition.

TD-DFT simulations of K-edge resonant inelastic X-ray scattering within the restricted subspace approximation

Truncation of orbital subspaces in TD-DFT yields an accurate description of RIXS spectra for soft X-ray K-edges.

Limitations of the equivalent core model for understanding core-level spectroscopies

The equivalent core model, or the Z + 1 approximation, has been used to interpret the binding energy, BE, shifts observed in X-ray photoelectron spectroscopy, XPS; in particular to relate these shifts to their origin in the electronic structure of the system. Indeed, a recent paper has claimed that the equivalent core model provides an intuitive chemical view of XPS BE shifts. In the present paper, we present a detailed comparison of the electronic structure provided from rigorous core-hole theory and from the equivalent core model to assess the validity and the utility of the use of the equivalent core model. This comparison shows that the equivalent core model provides a qualitative view of the different properties of initial and core-hole electronic structure. It is also shown that a very serious limitation of the equivalent core model is that it fails to distinguish between initial and final state contributions to the shifts of BEs which seriously reduces the utility of the information obtained with the equivalent core model. Indeed, there is a danger of making an incorrect assignment of the importance of relaxation because the equivalent core model appears to stress the role of final state effects. Given the importance of the distinction of initial and final state effects, we provide rigorous definitions of these two effects and we discuss an example where an incorrect interpretation was made based on the use of the equivalent core model.