Acta Crystallographica Section B

Structural Science

Volume 64, Part 5 (October 2008)

research papers

Acta Cryst. (2008). B64, 596-609 [ doi:10.1107/S0108768108019915 ]

N⁶-Substituted 2-amino-4-chloro-5-formylpyrimidines: puckered versus planar pyrimidine rings, and hydrogen-bonded aggregation in zero, one, two and three dimensions

J. Cobo, J. Trilleras, J. Quiroga, A. Marchal, M. Nogueras, J. N. Low and C. Glidewell

Abstract: The structures of 12 new N⁶-substituted 2-amino-4-chloro-5-formylpyrimidines, where the N⁶ substituent is of the type NHR or NR¹R², 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-HN hydrogen bonds link pairs of molecules into centrosymmetric 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 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 dimer motif, N-HO and N-HN hydrogen bonds cooperate to generate a three-dimensional framework structure.

Keywords: hydrogen bonding; conformation; polarization; ring puckering.


	Structure factor file (CIF format) (140.6 kbytes) [ doi:10.1107/S0108768108019915/bm5057Isup2.fcf ] Contains datablock I

	Structure factor file (CIF format) (118.2 kbytes) [ doi:10.1107/S0108768108019915/bm5057IIsup3.fcf ] Contains datablock II

	Structure factor file (CIF format) (120.9 kbytes) [ doi:10.1107/S0108768108019915/bm5057IIIsup4.fcf ] Contains datablock III

	Structure factor file (CIF format) (147.7 kbytes) [ doi:10.1107/S0108768108019915/bm5057IVsup5.fcf ] Contains datablock IV

	Structure factor file (CIF format) (159.7 kbytes) [ doi:10.1107/S0108768108019915/bm5057Vsup6.fcf ] Contains datablock V

	Structure factor file (CIF format) (145.3 kbytes) [ doi:10.1107/S0108768108019915/bm5057VIsup7.fcf ] Contains datablock VI

	Structure factor file (CIF format) (136.7 kbytes) [ doi:10.1107/S0108768108019915/bm5057VIIsup8.fcf ] Contains datablock VII

	Structure factor file (CIF format) (134.3 kbytes) [ doi:10.1107/S0108768108019915/bm5057VIIIsup9.fcf ] Contains datablock VIII

	Structure factor file (CIF format) (182.2 kbytes) [ doi:10.1107/S0108768108019915/bm5057IXsup10.fcf ] Contains datablock IX

	Structure factor file (CIF format) (157.6 kbytes) [ doi:10.1107/S0108768108019915/bm5057Xsup11.fcf ] Contains datablock X

	Structure factor file (CIF format) (147.0 kbytes) [ doi:10.1107/S0108768108019915/bm5057XIsup12.fcf ] Contains datablock XI

	Structure factor file (CIF format) (123.3 kbytes) [ doi:10.1107/S0108768108019915/bm5057XIIsup13.fcf ] Contains datablock XII

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