A redetermination from the original data of the crystal structure of 2-amino-4,6-dimethoxypyrimidin-1-ium 4-aminobenzoate

The title structure, 2-amino-4,6-dimethoxypyrimidine-(μ2-hydrogen)-4-aminobenzoate, has been redetermined from the data published by Thanigaimani, Muthiah & Lynch [Acta Cryst. (2006), E62, o2976–o2978]. The improvement of the present redetermination consists in a released geometry of the primary amine groups, which were originally been assumed as planar, as well as in a redetermination of the position of the hydroxy H atom. This H atom, whose parameters were originally constrained, turns out to be situated about the centre of the O⋯N hydrogen bond in two disordered positions, each with 0.5 occupancy.


Chemical context
Structures which contain hydroxyl, secondary and primary amine groups are often determined incorrectly because of an assumed geometry of these groups from which the applied constraints or restraints were inferred. In such cases, the correct geometry is missed as it is not verified by inspection of the difference electron-density maps. Thus, a considerable number of structures could have been determined more correctly -cf. Figs. 1 and 2 in Fá bry et al. (2014). The inclusion of such structures causes bias in crystallographic databases such as the Cambridge Structural Database (CSD; Groom & Allen, 2014).
In the course of recalculation of suspect structures which were retrieved from the CSD, defects in the structure determination of 2-amino-4,6-dimethoxypyrimidine-4-aminobenzoic acid (1/1) by Thanigaimani et al. (2006) have been found; the pertinent CSD refcode is IFACUO.
The defects in the original structure concern positional parameters both of the hydroxyl and the primary amine hydrogen atoms, which follow from unsubstantiated constraints of these hydrogen atoms. This means that the amine groups were assumed to be planar while the disorder regarding atom H4 was neglected because atom H4 was forced to be situated at atom O4.
The aim of the present article is to demonstrate how the original structure determination can be improved.
The improved refinement by JANA2006 (Petříček et al., 2014) yielded a non-planar geometry of the primary amine groups and a considerably different position for the hydrogen atom H4. This atom turns out to be disordered over two positions at about the centre of the hydrogen bond O4Á Á ÁN1 (Fig. 1). Thus, the title structure can be envisaged as an example of a structure with a symmetric hydrogen bond where the bridging hydrogen atom is disordered over two positions (see: for example Olovsson et al., 2002). One of these positions is closer to atom N1 while the other is closer to atom O4, and correspondingly they were labelled as H4n1 and H4o4. Each of the occupancies of H4n1 and H4o4 turned out to be equal to 0.5 within the interval given by the refined standard uncertainties; cf. the section of the electron density map in Fig. 2. The pKa of the conjugate acid to 2-amino-4,6-dimethoxypyrimidine is equal to 3.36 (Baldwin & van den Broek, 1975), while pKa 1 and pKa 2 of 4-aminobenzoic acid are equal to 2.50 and 4.87, respectively (CRC Handbook of Chemistry and Physics, 2009). pKa 1 refers to the deprotonation of the hydrogen carboxylate into the carboxylate group, while pKa 2 refers to the deprotonation of the ammonium group into the primary amine group in the solution (cf. pKa for benzoic acid and aniline are equal to 4.20 and 4.87, respectively; CRC Handbook of Chemistry and Physics, 2009). Thus, 2-amino-4,6-dimethoxypyrimidine is a weaker acid while 4-aminobenzoic acid is a weaker base. These values favour the formation of the salt rather than of the co-crystal. Since differences in the dissociation constants are relatively mild, the hydrogen atom is situated about the centre of the hydrogen bond N1Á Á ÁO4 and the structure in the solid state can be envisaged as a mixture of a co-crystal 2-amino-4,6dimethoxypyrimidine-4-aminobenzoic acid (1:1) with a salt 2amino-4,6-dimethoxypyrimidin-1-ium 4-aminobenzoate in a 1:1 proportion. Alternatively -as has been stated above -it can be assumed to be a structure with a disordered bridging hydrogen involved in a symmetric hydrogen bond (Olovsson et al., 2002).
In the recalculated structure determination, the deviation from planarity of the primary amine groups (including the C atoms to which they are attached) is larger for the one that is research communications Table 1 Hydrogen-bond geometry (Å , ).

Figure 1
View of the constituent molecules of the title structure after the improved refinement. The displacement ellipsoids are depicted at the 50% probability level. The occupancies of atoms H4N1 and H4O4 are each equal to 0.5.

Figure 2
A section of the difference electron-density map for the present redetermined title structure, which shows the build-up of the electron density between the atom O4 (red) and N1 (blue In a broader sense, the present redetermination emphasizes the importance of careful examination of the difference electron-density maps during structure determinations.

Supramolecular features
The details of the hydrogen bonding and the N-HÁ Á Áelectron ring interaction involving N4-H4b are given in Table 1. The graph-set motifs (Etter et al., 1990) were described by Thanigaimani et al. (2006) for the title structure. The graph-set motif R 3 2 (7) (Fig. 3) is shown in Fig. 2 of the article by Thanigaimani et al. (2006) and described there as R 2 2 (6).
In the present article, the graph-set motif R 3 2 (7) includes the atoms O4-

Database survey
The structure determination by Thanigaimani et al. (2006) has been included in the Cambridge Structural Database (Groom & Allen, 2014) under the refcode IFACUO.

Synthesis and crystallization
The preparation of the title compound has been described by Thanigaimani et al. (2006).

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. All the hydrogen atoms were discernible in the difference electron-density map. The aryl hydrogen atoms were constrained by the constraints C aryl -H aryl = 0.93 Å and U iso (H aryl ) = 1.2U eq (C aryl ) while the methyl hydrogens were constrained by the constraints C methyl -H methyl = 0.96 Å and U iso (H methyl ) = 1.5U eq (C methyl ). The hydrogen atoms of the primary amine group N2 were constrained by U iso (H N2 ) = 1.2U eq (N2). The displacement parameters of the hydroxyl hydrogen H4O4 and of the secondary amine H4N1 were constrained by U iso (H4O4) = 1.5U eq (O4) and U iso (H4N1) = 1.5U eq (N1) while their positional parameters were refined freely. The model with the refinement of the occupational factors of H4N1 and H4O4 under the condition that the sum of these occupational factors should equal to 1 resulted in the values 0.499 (25) and 0.501 (25), respectively. Therefore the occupational parameters were set to 0.5 in the final model and not further refined. The section of the title structure which shows the graph-set motifs R(7) 3 2 O4-H4O4Á Á ÁN1-C6-O2Á Á ÁH4a i Á Á ÁN4 i and O4Á Á ÁH4N1-N1-C6-O2Á Á ÁH4a i Á Á ÁN4 i [symmetry code: (i) Àx + 1, y À 1 2 , Àz + 1 2 ; colour code for atoms: grey -C and H, blue -N; red -O; colour code for bonds: black: covalent bonds, dashed orange: HÁ Á Áhydrogen-bond acceptor; blue O2-N4: inclusion into the graph-set motif R(7) 3 2 ]. A redetermination from the original data of the crystal structure of 2amino-4,6-dimethoxypyrimidin-1-ium 4-aminobenzoate Jan Fábry