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

IF 4.7 2区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Molecular Structure Pub Date : 2025-09-27 DOI:10.1016/j.molstruc.2025.144176

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

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Abstract

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 ¹H, ¹³C, and ¹⁵N 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.

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N-（5-氨基嘧啶-2-酰基）-N-甲基-2-甲氧基甲基苯胺的固态（x射线晶体学）和溶液（核磁共振）结构及其质子化位点的测定

通过晶体学和核磁共振测定了该化合物在固态和溶液中的结构，特别是C2-N8键周围的构象。使用Crystal Explorer 25.09对该分子进行Hirshfeld表面（HS）分析，以评估晶体中潜在的分子间接触区域并确定所涉及的原子。由于嘧啶环快速分解，无法得到质子化形式的晶体，因此采用多核1H、13C和15N核磁共振波谱。结果表明，质子化作用以90/10的比例发生在环氮上。在Becke三参数Lee-Yang-Parr (B3LYP)/ 6-311 ++G（d,p）能级上进行了几何和能量的理论计算，并通过规范不变原子轨道（GIAO）方法将优化的结构用于计算化学位移。这些计算对于得出明确的结论至关重要。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Structure 化学-物理化学

CiteScore

7.10

自引率

15.80%

发文量

2384

审稿时长

45 days

期刊介绍： The Journal of Molecular Structure is dedicated to the publication of full-length articles and review papers, providing important new structural information on all types of chemical species including: • Stable and unstable molecules in all types of environments (vapour, molecular beam, liquid, solution, liquid crystal, solid state, matrix-isolated, surface-absorbed etc.) • Chemical intermediates • Molecules in excited states • Biological molecules • Polymers. The methods used may include any combination of spectroscopic and non-spectroscopic techniques, for example: • Infrared spectroscopy (mid, far, near) • Raman spectroscopy and non-linear Raman methods (CARS, etc.) • Electronic absorption spectroscopy • Optical rotatory dispersion and circular dichroism • Fluorescence and phosphorescence techniques • Electron spectroscopies (PES, XPS), EXAFS, etc. • Microwave spectroscopy • Electron diffraction • NMR and ESR spectroscopies • Mössbauer spectroscopy • X-ray crystallography • Charge Density Analyses • Computational Studies (supplementing experimental methods) We encourage publications combining theoretical and experimental approaches. The structural insights gained by the studies should be correlated with the properties, activity and/ or reactivity of the molecule under investigation and the relevance of this molecule and its implications should be discussed.