Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6)
The title compound, C5D6ClN2O+·Cl−, crystallizes in the orthorhombic space group, Pbcm, and consists of a 4-chloro-2-methyl-6-oxo-3,6-dihydropyrimidin-1-ium cation and a chloride anion where both moieties lie on a crystallographic mirror. The cation is disordered and was refined as two equivalent fo...
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| Format: | Article |
| Language: | English |
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International Union of Crystallography
2021-04-01
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| Series: | Acta Crystallographica Section E: Crystallographic Communications |
| Subjects: | |
| Online Access: | http://scripts.iucr.org/cgi-bin/paper?S205698902100270X |
| _version_ | 1818490672089399296 |
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| author | Ray J. Butcher Andrew P. Purdy Sean A. Fischer Daniel Gunlycke |
| author_facet | Ray J. Butcher Andrew P. Purdy Sean A. Fischer Daniel Gunlycke |
| author_sort | Ray J. Butcher |
| collection | DOAJ |
| description | The title compound, C5D6ClN2O+·Cl−, crystallizes in the orthorhombic space group, Pbcm, and consists of a 4-chloro-2-methyl-6-oxo-3,6-dihydropyrimidin-1-ium cation and a chloride anion where both moieties lie on a crystallographic mirror. The cation is disordered and was refined as two equivalent forms with occupancies of 0.750 (4)/0.250 (4), while the chloride anion is triply disordered with occupancies of 0.774 (12), 0.12 (2), and 0.11 (2). Unusually, the bond angles around the C=O unit range from 127.2 (6) to 115.2 (3)° and similar angles have been found in other structures containing a 6-oxo-3,6-dihydropyrimidin-1-ium cation, including the monclinic polymorph of the title compound, which crystallizes in the monoclinic space group P21/c [Kawai et al. (1973). Cryst. Struct. Comm. 2, 663–666]. The cations and anions pack into sheets in the ab plane linked by N—H...Cl hydrogen bonds as well as C—H...O and Cl...O interactions. In graph-set notation, these form R33(11) and R32(9) rings. Theoretical calculations seem to indicate that the reason for the unusual angles at the sp2 C is the electrostatic interaction between the oxygen atom and the adjacent N—H hydrogen. |
| first_indexed | 2024-12-10T17:20:06Z |
| format | Article |
| id | doaj.art-0cff7afba7734ec3baf6f2f324502588 |
| institution | Directory Open Access Journal |
| issn | 2056-9890 |
| language | English |
| last_indexed | 2024-12-10T17:20:06Z |
| publishDate | 2021-04-01 |
| publisher | International Union of Crystallography |
| record_format | Article |
| series | Acta Crystallographica Section E: Crystallographic Communications |
| spelling | doaj.art-0cff7afba7734ec3baf6f2f3245025882022-12-22T01:39:59ZengInternational Union of CrystallographyActa Crystallographica Section E: Crystallographic Communications2056-98902021-04-0177439039510.1107/S205698902100270Xru2073Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6)Ray J. Butcher0Andrew P. Purdy1Sean A. Fischer2Daniel Gunlycke3Department of Chemistry, Howard University, 525 College Street NW, Washington DC 20059, USAChemistry Division, Code 6100, Naval Research Laboratory, 4555 Overlook Av, SW, Washington DC 20375-5342, USAChemistry Division, Code 6189, Naval Research Laboratory, 4555 Overlook Av, SW, Washington DC 20375-5342, USAChemistry Division, Code 6189, Naval Research Laboratory, 4555 Overlook Av, SW, Washington DC 20375-5342, USAThe title compound, C5D6ClN2O+·Cl−, crystallizes in the orthorhombic space group, Pbcm, and consists of a 4-chloro-2-methyl-6-oxo-3,6-dihydropyrimidin-1-ium cation and a chloride anion where both moieties lie on a crystallographic mirror. The cation is disordered and was refined as two equivalent forms with occupancies of 0.750 (4)/0.250 (4), while the chloride anion is triply disordered with occupancies of 0.774 (12), 0.12 (2), and 0.11 (2). Unusually, the bond angles around the C=O unit range from 127.2 (6) to 115.2 (3)° and similar angles have been found in other structures containing a 6-oxo-3,6-dihydropyrimidin-1-ium cation, including the monclinic polymorph of the title compound, which crystallizes in the monoclinic space group P21/c [Kawai et al. (1973). Cryst. Struct. Comm. 2, 663–666]. The cations and anions pack into sheets in the ab plane linked by N—H...Cl hydrogen bonds as well as C—H...O and Cl...O interactions. In graph-set notation, these form R33(11) and R32(9) rings. Theoretical calculations seem to indicate that the reason for the unusual angles at the sp2 C is the electrostatic interaction between the oxygen atom and the adjacent N—H hydrogen.http://scripts.iucr.org/cgi-bin/paper?S205698902100270Xcrystal structurepyrimidinium cationdistorted sp2 c |
| spellingShingle | Ray J. Butcher Andrew P. Purdy Sean A. Fischer Daniel Gunlycke Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6) Acta Crystallographica Section E: Crystallographic Communications crystal structure pyrimidinium cation distorted sp2 c |
| title | Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6) |
| title_full | Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6) |
| title_fullStr | Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6) |
| title_full_unstemmed | Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6) |
| title_short | Structural and theoretical studies of 4-chloro-2-methyl-6-oxo-3,6-dideuteropyrimidin-1-ium chloride (d6) |
| title_sort | structural and theoretical studies of 4 chloro 2 methyl 6 oxo 3 6 dideuteropyrimidin 1 ium chloride d6 |
| topic | crystal structure pyrimidinium cation distorted sp2 c |
| url | http://scripts.iucr.org/cgi-bin/paper?S205698902100270X |
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