X-ray charge density study of the 6-methyluracil derivative in the crystal: Revealing, consequences, and multipole refinement of minor static disorder

Abstract

The accurate X-ray diffraction experiment was performed on the crystal of 1,6-dimethyl-3-propargyl-2,4-pyrimidinedione at 100 K. The static electron density (ED) was obtained via multipole refinement against these data. The presence of low-intense but nonrandom positive residual density peaks revealed that the structure was complicated by the minor conformational static disorder. Further analysis of the number and positions of critical points (CPs) (3, +3) of Laplacian of ED ∇2ρ(r) and the ratio of eigenvalues of its Hessian matrix unambiguously proved that the multipole-modeled ED of the main disorder component was contaminated by the second one. A method of visualizing the Laplacian minima as CP-ellipsoids with semiaxes inversely proportional to the eigenvalues of Hessian matrix of ∇2ρ(r) was applied to evaluate the correctness of modeled ED. Extra Laplacian CPs (3, +3) were attributed to the incorrect multipole populations, while the elongated shape of the corresponding discoid CP-ellipsoids was mainly considered to be the effect of troublesome kappa-parameters. A number of different multipole models were constructed in order to minimize the undesirable effects of disorder on the multipole ED. The two-component multipole model showed that the heterocyclic moiety of the minor component with an occupancy of 2% underwent the 180° rotation about the N3–C7 bond axis. Furthermore, the partial transfer of multipole parameters from the model refined against theoretical structure factors was utilized on the most problematic atoms, which massively contributed to disorder treatment. This approach allowed us to restore the ED of the main component in the crystal environment, which quality was gauged by the quantum-topological analysis as well as by its conformity to the data obtained from ab initio periodic calculations. Attempts to speculate on reasons for the limited disordering observed were made: theoretical calculations suggest that moderate hydrogen bonds support the disordering in the structure, while multiple weak noncovalent contacts, e.g., pi interactions, may provide the restrictions on the 50:50 disorder.