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, 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.

Localization of nuclear wave functions of lithium in [Li+@C60]PF6−: molecular insights into two-site disorder–order transition

“…, the nonperiodic nearest-neighbor truncation, the second-order perturbation treatment of the electron correlation, and the parametric potential fitting) and (ii) the decoupling of the motion of a Li + ion from the motions of its surrounding ions and molecules. The quantum mechanics/molecular mechanics (QM/MM) method, 69–74 particularly its polarizable variants, 75–77 and the ONIOM method 78 may help alleviate the nearest-neighbor truncation problem and clarify the contributions of the antiferroelectric ordering and interactions to the THz spectra. The contributions of the coupled dynamics ( e.g.…”

“…Possible reasons for the peak frequency discrepancies between theory and experiment may include (i) approximations in the adsorbent potential modeling (e.g., the nonperiodic nearest-neighbor truncation, the second-order perturbation treatment of the electron correlation, and the parametric potential fitting) and (ii) the decoupling of the motion of a Li + ion from the motions of its surrounding ions and molecules. The quantum mechanics/molecular mechanics (QM/MM) method, [69][70][71][72][73][74] particularly its polarizable variants, [75][76][77] and the ONIOM method 78 may help alleviate the nearest-neighbor truncation problem and clarify the contributions of the antiferroelectric ordering and interactions to the THz spectra. The contributions of the coupled dynamics (e.g., the collective Li + motions and the coupling of Li + motion with lattice motions) are also of great fundamental interest but beyond the scope of this study.…”

Fraction of Free-Base Nicotine in Simulated Vaping Aerosol Particles Determined by X-ray Spectroscopies

“…In Figure B for pH 2, two peaks of almost equal intensity show up at 399.0 and 401.0 eV, the second peak originating from a π 2 * orbital, with an absolute value of 399.1 eV. Ge et al suggest the second peak has a major contribution from a protonated nitrogen orbital, with an absolute value of 401.2 eV calculated by theory. In addition, the peak shape at the post edge region between 400 and 415 eV shown in Figure B is captured very well by the theoretical calculations of Ge et al for both NEXAFS spectra at low and high pH.…”

“…The observed N 1s shift of ∼2 eV upon nicotine protonation is qualitatively similar to our previously reported observations for amino acids analyzed under similar conditions. 29,30 Recently there have been a number of experimental 31,32 and theoretical 33 studies exploring protonation of organic crystals containing the pyridinic moiety particularly on isonicotinamide. The results are very similar to what is observed here.…”

“…While there are no X-ray studies of nicotine in the aqueous phase and/or in the presence of alcohols, there are both experimental and theoretical studies on organic crystals that can help decipher the spectra and provide a qualitative analysis of the peak positions and shape. In the recent theoretical work of Ge et al 33 who performed a quantum mechanical/molecular mechanical study on isonicotimide, calculated X-ray absorption spectra were shown to be sensitive to proton transfer and the nature of hydrogen bonding. The theoretical work was also compared to the experimental and theoretical results obtained by Edwards et al 34 Based on these two studies, we interpret the strong peak shown in Figure 2B for pH 10.4 at 399.0 eV emanating from the π 1 * orbital of the pyridinyl nitrogen.…”