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...

Proton transfer (PT) in organic crystals creates localized charges and strong hydrogen bonding (HB), making the self-consistent field (SCF) calculation of core-ionized and core-excited states challenging. Today most corresponding X-ray spectral measurements are interpreted based on empirical fitting and/or chemical intuitions. Here we present a systematic quantum mechanical/molecular mechanical (QM/MM) study of N 1s X-ray photoelectron (XPS) and absorption (XAS) spectra of three isonicotinamide (IN)-based organic crystals with full (1), half (2), and no (3) protonations. A complete picture of the structure–spectroscopy relation in different crystal environments was provided, and assignments to three unprotonated (pyridinic, p; amide, a 1 and a 2) sites and one protonated (pyridinic, h) N site were clearly made. We found that including distant residues as natural population analysis (NPA) point charges can effectively enhance the SCF convergence of the core states. The size of the QM part was tuned, and with some 140–170 atoms we achieved spectral convergence that can represent the infinite crystal. At the crystal structures, simulated relative binding energies deviate ≤0.3 eV to experiments. Simulated XAS spectra agree well with experiments, and with molecular orbital analysis we interpreted the π* structures as hybrid local excitation and charge transfer states (πLE–CT *) or pure LE states (πLE *). Analyses on both spectra helped understand the PT and HB nature in such organic crystals, and a debate in XPS interpretation of 3 was resolved and its XAS assignment corrected. Further, to model the dynamical effect of the proton in 2, XPS/XAS spectra were evaluated at snapshots with varying N–H distances. A continuous picture illustrates the sensitive influence of proton position to both spectra. Reduction of the N–H distance by only 0.2 Å from the crystal structure (1.1 Å) excellently reproduced both spectra. This perturbation phenomenologically models effects of vibration from the equilibrium crystal structure and environmental temperature and pressure factors.

Truncated cluster models represent an effective way for simulating X-ray spectra of 2D materials. Here we systematically assessed the influence of two key parameters, the cluster shape (honeycomb, rectangle, or parallelogram) and size, in X-ray photoelectron (XPS) and absorption (XAS) spectra simulations of three 2D materials at five K-edges (graphene, C 1s; C3N, C/N 1s; h-BN, B/N 1s) to pursue the accuracy limit of binding energy (BE) and spectral profile predictions. Several recent XPS experiments reported BEs with differences spanning 0.3, 1.5, 0.7, 0.3, and 0.3 eV, respectively. Our calculations favor the honeycomb model for stable accuracy and fast size convergence, and a honeycomb with ~10 nm side length (120 atoms) is enough to predict accurate 1s BEs for all 2D sheets. Compared to all these experiments, predicted BEs show absolute deviations as follows: 0.4-0.7, 0.0-1.0, 0.4-1.1, 0.6-0.9, and 0.1-0.4 eV. A mean absolute deviation of 0.3 eV was achieved if we compare only to the closest experiment. We found that the sensitivity of computed BEs to different model shapes depends on systems: graphene, sensitive; C3N, weak; h-BN, very weak. This can be attributed to their more or less delocalized π electrons in this series. For this reason, a larger cluster size is required for graphene than the other two to reproduce fine structures in XAS. The general profile of XAS shows weak dependence to model shape. Our calculations provide optimal parameters and accuracy estimations that are useful for X-ray spectral simulations of general graphene-like 2D materials.

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.

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