Applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. Chemical bonding and binding features in the crystal and dimer of 1,3-bis­­(2-hy­dr­oxy­ethyl)-6-methyl­uracil

• Published in: IUCrJ 2023-09, Vol.10 (5), p.584-602
• Main Authors: Saifina, Alina F, Kartashov, Sergey V, Saifina, Liliya F, Fayzullin, Robert R
• Format: Article
• Language: English
• Subjects: Charge transfer; Chemical bonds; Chemical elements; Crystallography; Crystals; Density; Dimers; Electron transfer; Electronegativity; Electropositivity; Hydrogen atoms; Hydrogen bonds; Lewis acid; Lewis base; Multipoles; Nitrogen atoms; Quantum physics; Research Papers; Uracil
• ISSN: 2052-2525
• DOI: 10.1107/S2052252523007108

This article accompanies the award of the Struchkov Prize to Robert Fayzullin. It is part of a collection of articles from the IUCr 2023 Congress in Melbourne, Australia, and commemorates the 75th anniversary of the IUCr. We considered it timely to test the applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. The procedure was carried out on the crystal of 1,3-bis­(2-hy­droxy­ethyl)-6-methyl­uracil, and some derived properties of the scalar potential and vector force fields were compared with those obtained from the experimental multipole model and from the aspherical pseudo-atom model with parameters fitted to the calculated structure factors. The procedure was shown to accurately replicate the general vector-field behavior, the peculiarities of the quantum potentials and the characteristics of the force-field pseudoatoms, such as charge, shape and volume, as well as to reproduce the relative arrangement of atomic and pseudoatomic zero-flux surfaces along internuclear regions. It was found that, in addition to the quantum-topological atoms, the force-field pseudoatoms are spatially reproduced within a single structural fragment and similar environment. In addition, the classical and nonclassical hydrogen bonds in the uracil derivative crystal, as well as the H⋯O, N⋯O and N⋯C interactions in the free π-stacked dimer of the uracil derivative molecules, were studied using the potential and force fields within the concepts of interatomic charge transfer and electron lone pair donation–acceptance. Remarkably, the nitro­gen atoms in the N⋯O and N⋯C interactions behave rather like a Lewis base and an electron contributor. At the same time, the hydrogen atom in the H⋯O interaction, being a Lewis acid, also participates in the interatomic electron transfer by acting as a contributor. Thus, it has been argued that, when describing polar interatomic interactions within orbital-free considerations, it makes more physical sense to identify electronegative (electron occupier) and electropositive (electron contributor) atoms or subatomic fragments rather than nucleophilic and electrophilic sites.