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

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 NR(1)R(2), 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...N hydrogen bonds link pairs of molecules into centrosymmetric R2(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 R2(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 R2(2)(8) dimer motif, N-H...O and N-H...N hydrogen bonds cooperate to generate a three-dimensional framework structure.

2-Amino-4-chloro-5-formyl-6-[methyl(2-methylphenyl)amino]pyrimidine and 2-amino-4-chloro-5-formyl-6-[(2-methoxyphenyl)methylamino]pyrimidine are isostructural and form hydrogen-bonded sheets ofR22(8) andR66(32) rings

“…The corresponding bond distances and torsion angles for (I) and (II) are very similar (Table 1). The distances show many of the characteristics observed previously in other compounds of this type (Cobo et al, 2008). Thus, the ring distances N1-C2 and C6-N1 and the exocyclic distances C2-N2 are all very similar, while the ring distances N3-C4 are, by some margin, the shortest of all the N-C distances; the formyl C51-O51 bonds are long for their type [mean value (Allen et al, 1987) 1.192 Å ], while the C5-C51 bonds are short (mean value = 1.488 Å ).…”

“…Of the analogues studied previously (Cobo et al, 2008), those closest in constitution to (I) and (II) are (III), which differs from (I) and (II) only in carrying no substituent on the phenyl ring, and (IV), which is an isomer of (I). Compounds (III) and (IV) both adopt type B conformations, but while (III) contains a planar pyrimidine ring, in (IV) this ring adopts a boat conformation.…”

“…We have recently reported the molecular and supramolecular structures of a number of N 6 -substituted 2-amino-4-chloro-5formylpyrimidines (Cobo et al, 2008). Two features of the molecular structures that vary independently amongst the 12 examples studied are the orientation of the formyl group and the shape of the pyrimidine ring, while in all cases the bond distances provide strong evidence for the development of polarized electronic structures.…”

“…Two features of the molecular structures that vary independently amongst the 12 examples studied are the orientation of the formyl group and the shape of the pyrimidine ring, while in all cases the bond distances provide strong evidence for the development of polarized electronic structures. In the majority of the compounds studied earlier (Cobo et al, 2008), the formyl orientation has the formyl C-H bond approximately parallel to the C-Cl bond, while in the remainder, the formyl C O bond is approximately parallel to the C-Cl bond; these two conformations are denoted A and B, respectively. For both conformers, examples were observed in which the pyrimidine rings were planar within experimental uncertainty, while in others these rings were significantly puckered into boat, screwboat or twist-boat conformations.…”

Nonmerohedrally twinned 6-amino-3-methyluracil-5-carbaldehyde: a hydrogen-bonded ribbon containing four types of ring

“…These dimensions (Table 1) provide evidence for the importance of polarized forms (Ia) and (Ib) as contributors to the overall electronic structure. Despite the high degree of substitution of the rings in both (I) and (II), these rings are planar, although puckered pyrimidine rings are quite frequently observed in the presence of contiguous substituents (Melguizo et al, 2003;Quesada et al, 2003Quesada et al, , 2004Low et al, 2007;Trilleras et al, 2007;Cobo et al, 2008). In (I), the maximum deviation of any ring atom from the mean plane is seen for atom N3 [0.013 (2) Å ].…”