5-(1-Hydroxy­ethyl­idene)-1,3-di­methyl­pyrimidine-2,4,6(1H,3H,5H)-trione and four amino derivatives

Silva, E.T. da; Ribiero, R.S.; Lima, E.L.S.; Wardell, J.L.; Skakle, J.M.S.; Low, J.N.; Glidewell, C.

doi:10.1107/S0108270104028859

Volume 61
Part 1
Pages o15-o20
January 2005

Received 5 November 2004
Accepted 8 November 2004
Online 11 December 2004

5-(1-Hydroxyethylidene)-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione and four amino derivatives

Emerson T. da Silva,^a Rodrigo S. Ribiero,^a Edson L. S. Lima,^a James L. Wardell,^b Janet M. S. Skakle,^c John N. Low ^c and Christopher Glidewell ^d ^*

^aInstituto de Química, Departamento de Química Orgânica, Universidade Federal do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil,^bInstituto de Química, Departamento de Química Inorgânica, Universidade Federal do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil,^cDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and ^dSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
Correspondence e-mail: cg@st-andrews.ac.uk

In the structures of 5-(1-hydroxyethylidene)-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione, C₈H₁₀N₂O₄, (I), 1,3-dimethyl-5-[1-(propylamino)ethylidene]pyrimidine-2,4,6(1H,3H,5H)-trione, C₁₁H₁₇N₃O₃, (II), and 5-[1-(2,2-dimethoxyethylamino)ethylidene]-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione, C₁₂H₁₉N₃O₅, (III), there are no direction-specific intermolecular interactions. The molecules in 5-[1-(benzylamino)ethylidene]-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione, C₁₅H₁₇N₃O₃, (IV), are linked into chains of edge-fused rings by a combination of one C-HO hydrogen bond and one C-H [pi] (arene) hydrogen bond, while the molecules in 5-(1-hydrazinoethylidene)-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione, C₈H₁₂N₄O₃, (V), are linked into a continuous framework structure by three distinct N-HO hydrogen bonds, each involving a different O-atom acceptor. Each of compounds (I)-(V) contains an intramolecular hydrogen bond, of the O-HO type in (I) and of the N-HO type in (II)-(V).

Comment

It has recently been reported (da Silva & Lima, 2003) that the title compound, (I), which is the enol tautomer of 1,3-dimethyl-5-acetylbarbituric acid, reacts readily with primary amines to form enamines. We report here the structures of (I), of three representative enamine derivatives, (II)-(IV), and of the hydrazine derivative (V) (Figs. 1 -5).

The bond distances in (I) (Table 1), in particular the C4-O4 and C51-O51 distances on the one hand and the C4-C5 and C5-C51 distances on the other, clearly demonstrate the enol constitution, consistent with the location of atom H51 as deduced from a difference map. In each of compounds (II)-(V), atom N51 has a planar configuration, and the C51-N51 distances are all typical of their type (Allen et al., 1987). Atom N52 in (V) has a distinctly pyramidal coordination environment, with a sum of bond angles, based on H-atom coordinates derived from difference maps, of 328.8°. The N51-N52 distance in (V) corresponds closely to the mean value of 1.420 Å for >N-N< distances where the coordination of one N atom is planar and that of the other is pyramidal.

There is an intramolecular hydrogen bond in each of (I)-(V), of O-HO type in (I) and of N-HO type in (II)-(V) (Table 2). There are no direction-specific intermolecular interactions in (I)-(III), but the molecules in (IV) and (V) are linked by intermolecular hydrogen bonds (Table 2) into supramolecular structures that are one- and three-dimensional, respectively.

The one-dimensional supramolecular structure of (IV) is generated by a combination of C-HO and C-H [pi] (arene) hydrogen bonds (Table 2). Aryl atom C514 in the molecule at (x, y, z) acts as a hydrogen-bond donor to carbonyl atom O4 in the molecule at (1 - x, 1 - y, 1 - z), so generating a centrosymmetric R₂²(22) ring (Bernstein et al., 1995) centred at ( $[1\over2]$ , $[1\over2]$ , $[1\over2]$ ) (Fig. 6). In addition, methylene atom C53 in the molecule at (x, y, z) acts as a hydrogen-bond donor to the C511-C516 aryl ring in the molecule at (1 - x, -y, 1 - z), so generating a second centrosymmetric ring, this time centred at ( $[1\over2]$ , 0, $[1\over2]$ ). The combination of these two centrosymmetric motifs thus generates a chain of edge-fused rings running parallel to the [010] direction, with the larger rings centred at ( $[1\over2]$ , $[1\over2]$ + n, $[1\over2]$ ) (n = zero or integer) and the smaller rings centred at ( $[1\over2]$ , n, $[1\over2]$ ) (n = zero or integer) (Fig. 6).

The three-dimensional supramolecular structure of (V) is of some complexity but can readily be analysed in terms of a series of one-dimensional substructures and their simple combinations. In the first substructure, atom N52 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H52D, to atom O4 in the molecule at (- $[1\over2]$ + x, $[1\over2]$ - y, -z), so producing a C(7) chain running parallel to the [100] direction and generated by the 2₁ screw axis along (x, $[1\over4]$ , 0) (Fig. 7). In the second substructure, atom N52 at (x, y, z) acts as a donor, via atom H52E, to atom O2 in the molecule at (2 - x, - $[1\over2]$ + y, $[1\over2]$ - z), so producing a C(9) chain running parallel to the [010] direction, now generated by the 2₁ screw axis along (1, y, $[1\over4]$ ) (Fig. 8).

Each of these chains, along [100] and [010], respectively, utilizes just one N-HO hydrogen bond, but the combination of these two interactions produces a third chain motif, running parallel to the [001] direction. Atom N52 in the molecule at (- $[1\over2]$ + x, $[1\over2]$ - y, -z) acts as a hydrogen-bond donor, via atom H52E, to atom O2 in the molecule at ( $[3\over2]$ - x, 1 - y, - $[1\over2]$ + z), while atom N52 at ( $[3\over2]$ - x, 1 - y, - $[1\over2]$ + z) acts as a donor, via atom H52D, to atom O4 at (2 - x, $[1\over2]$ + y, - $[1\over2]$ - z); finally, atom N52 at (2 - x, $[1\over2]$ + y, - $[1\over2]$ - z) acts as a donor, via atom H52E, to atom O2 in the molecule at (x, y, -1 + z). In this manner a C₂²(16) chain is generated along [001] (Fig. 9).

These three chain motifs (Figs. 7 -9) together produce a three-dimensional framework structure, which is generated solely by the action of 2₁ screw axes and which utilizes only half of the molecules within the unit cell. There is, accordingly, a second such framework present, which is interwoven with the first framework and related to it by inversion. These two three-dimensional substructures are, however, linked by the final N-HO hydrogen bond; this is, in fact, one component of an effectively planar three-centre N-H(O)₂ system (Table 2). Atom N51 in the molecule at (x, y, z) acts as a donor, not only intramolecularly to atom O4 but also to atom O6 in the molecule at (x, $[1\over2]$ - y, - $[1\over2]$ + z), so producing a C(6) chain running parallel to the [001] direction and generated by the c-glide plane at y = $[1\over4]$ (Fig. 10). This final motif suffices to link the two frameworks and hence to link all of the molecules into a single three-dimensional structure.