N (6)-substituted 2-amino-4-chloro-5-formylpyrimidines: puckered versus planar pyrimidine rings, and hydrogen-bonded aggregation in zero, one, two and three dimensions

Justo Cobo, Jorge Trilleras, Jairo Quiroga, Antonio Marchal, Manuel Nogueras, John N. Low, Christopher Glidewell

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

Abstract

The structures of 12 new N-6-substituted 2-amino-4-chloro-5-formylpyrimidines, where the N-6 substituent is of the type NHR or (NRR2)-R-1, have been determined. The intramolecular dimensions provide strong evidence for the development of polarized, charge-separated molecular-electronic structures, with the positive charge delocalized over the two exocyclic amino N atoms and with negative charge on the formyl O atom. This polarization appears to be independent of the significant puckering, in seven of the compounds, of the pyrimidine rings from planarity towards boat, twist-boat or screw-boat conformations. In 11 of the compounds studied here, N - H center dot center dot center dot N hydrogen bonds link pairs of molecules into centrosymmetric R-2(2)(8) dimer units, and their overall crystal structures are determined by the patterns of hydrogen bonds by which these units are further linked. Examples are reported in which no further hydrogen bonding occurs; in which the R-2(2)(8) dimers are linked into chains of rings, or into sheets; and in which sheets are formed by the pi-stacking of hydrogen-bonded chains of rings. In the sole structure lacking the R-2(2)(8) dimer motif, N - H center dot center dot center dot O and N - H center dot center dot center dot N hydrogen bonds cooperate to generate a three-dimensional framework structure.

Original languageEnglish
Pages (from-to)596-609
Number of pages14
JournalActa Crystallographica. Section B, Structural Science
Volume64
Publication statusPublished - Oct 2008

Keywords

  • SUPRAMOLECULAR STRUCTURES
  • INTRAMOLECULAR MOTIONS
  • CP/MAS NMR
  • X-RAY
  • INTERPLAY
  • O-6-BENZYLGUANINE
  • DIFFRACTION
  • DERIVATIVES
  • MONOHYDRATE
  • BROMIDES

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