5,5-Di-chloro-6-hy-droxy-dihydro-pyrimidine-2,4(1H,3H)-dione: mol-ecular and crystal structure, Hirshfeld surface analysis and the new route for synthesis with Mg(ReO4)2 as a new catalyst.

Anton P Novikov,Alexey V Safonov,Sergey N Ryagin,Konstantin E German,Mikhail S Grigoriev

doi:10.1107/s2056989020011809

Abstract

The mol-ecular and crystal structures of the title compound, C4H4Cl2N2O3, were investigated by single-crystal X-ray diffraction and a Hirshfeld surface analysis. The title compound was synthesized by a new type of reaction using Mg(ReO4)2 as a new catalyst and a possible mechanism for this reaction is proposed. The six-membered ring adopts a half-chair conformation. In the crystal, hydrogen bonds connect the mol-ecules into double layers, which are connected to each other by halogen bonds. The Hirshfeld surface analysis revealed that the most important contributions for the crystal packing are from O⋯H/H⋯O (35.8%), Cl⋯Cl (19.6%), Cl⋯H/H⋯Cl (17.0%), H⋯H (8.3%), C⋯O/O⋯C (4.3%), Cl⋯O/O⋯Cl (4.2%) and O⋯O (4.1%) contacts.

Highlights

The molecular and crystal structures of the title compound, C4H4Cl2N2O3, were investigated by single-crystal X-ray diffraction and a Hirshfeld surface analysis
The title compound was synthesized by a new type of reaction using Mg(ReO4)2 as a new catalyst and a possible mechanism for this reaction is proposed
The Hirshfeld surface analysis revealed that the most important contributions for the crystal packing are from OÁ Á ÁH/HÁ Á ÁO (35.8%), ClÁ Á ÁCl (19.6%), ClÁ Á ÁH/HÁ Á ÁCl (17.0%), HÁ Á ÁH (8.3%), CÁ Á ÁO/OÁ Á ÁC (4.3%), ClÁ Á ÁO/ OÁ Á ÁCl (4.2%) and OÁ Á ÁO (4.1%) contacts

Summary

Chemical context

Nitrogen heterocycles and pyrimidines are examples of the most important biologically active compounds and find a wide use in modern medicine (Pałasz et al, 2015; Takeshita et al, 2006; Henderson et al, 2003). Uracil is widespread in nature as a pyrimidine derivative, and is found as a part of nucleic acids. Halogen derivatives of uracil serve as convenient intermediates for the preparation of compounds with various functional groups (Wamhoff et al, 1992). Pyrimidine derivatives are used as intermediates for the production of various complex organic molecules for the treatment of cancer and AIDS (Fawcett et al, 1996). 5,5-Dichloro-6-hydroxydihydropyrimidine-2,4(1H,3H)-dione (1) was earlier synthesized by two reaction schemes starting with uracil: (1) by addition of Cl2 in H2O (Johnson et al, 1943) or (2) by addition of Na2S2O8 and NaCl in acetic acid (Itahara et al, 1986). We have found a new reaction for the synthesis of 1 by the reaction of uracil with hydrochloric acid and water in the presence of Mg(ReO4) as a catalyst.

Structural commentary

Supramolecular features

Hirshfeld surface analysis

Database survey

Findings

Synthesis and crystallization