Work

The structure of N-(5-aminopyrimidin-2-yl)-N-methyl-2-methoxymethylaniline in solid state (X-ray crystallography) and in solution (NMR) and determination of its protonation site

Year: 2025

Type: article

Abstract: • X-ray crystallography of N-(5-aminopyrimidin-2-yl)-N-methyl-2-methoxymethylaniline in solid state • Analysis of the Hirshfeld surface (HS) of this molecule has allowed to evaluate the areas of possible intermolecular contacts in the crystal, as well as to determine the atoms involved. • Multinuclear 1 H, 13 C and 15 N NMR spectroscopy has been used to study the behavior of the molecule and determine the protonation site. • DFT calculations of geometries and energies have been performed and optimized structures have been used to calculate chemical shifts using the GIAO method. The structure of the title compound was determined both in the solid state by crystallography and in solution by NMR, particularly concerning the conformation around the C2–N8 bond. Hirshfeld surface (HS) analysis of this molecule was performed, using Crystal Explorer 25.09, in order to evaluate the zones of potential intermolecular contacts in the crystal as well as to determine the atoms involved. As crystals of the protonated form could not be obtained due to the rapid decomposition of the pyrimidine ring, multinuclear 1 H, 13 C, and 15 N NMR spectroscopy was employed. This revealed that protonation occurs on the ring nitrogens in a 90/10 ratio. Theoretical calculations of geometries and energies have been carried out at the Becke Three-parameter Lee–Yang–Parr (B3LYP)/6-311++G(d,p) level, and the optimized structures used to calculate chemical shifts via the Gauge-Invariant Atomic Orbital (GIAO) method. These calculations were crucial to draw definitive conclusions.

Source: Journal of Molecular Structure

DOI: 10.1016/j.molstruc.2025.144176

Authors: Felipe Reviriego, Patricia Delgado-Martínez, M. Carmen Torralba, Rosa M. Claramunt, Ibon Alkorta, José Elguero