A QM/MM Study on the X-ray Spectra of Organic Proton Transfer Crystals of Isonicotinamides

Abstract

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, a1 and a2) 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.