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Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.

The empirical Lewis picture of the chemical bond dominates the view chemists have of molecules, of their stability and reactivity. Within the mathematical framework of quantum mechanics, all this chemical information is hidden in the many-particle wave function Ψ. Thus, to reveal and understand it, there is great interest in enhancing the Lewis model and connecting it to computable quantities. As has previously been shown, the Lewis picture can often be recovered from the probability density |Ψ|2 with probabilities in agreement with valence bond weights: the structures appear as most likely positions in the all-electron configuration space. Here, we systematically expand this topological probability density analysis to molecules with multiple bonds and lone pairs, employing correlated Slater-Jastrow wave functions. In contrast to earlier studies, non-Lewis structures are obtained that disagree with the prevalent picture and have a potentially better predictive capability. While functional groups are still recovered with these ab initio structures, the boundary between bonds and lone pairs is mostly blurred or non-existent. In order to understand the newly found structures, the Lewis electron pairs are replaced with spin-coupled electron motifs as the fundamental electronic fragment. These electron motifs—which coincide with Lewis’ electron pairs for many single bonds—arise naturally from the generally applicable analysis presented. An attempt is made to rationalize the geometry of the newly-found structures by considering the Coulomb force and the Pauli repulsion.