Redetermination of cytosinium hydrogen maleate–cytosine (1/1) from the original data

The title structure has been redetermined from the data published by Benali-Cherif, Falek & Direm [Acta Cryst. (2009), E65, o3058–o3059]. The improvement of the present redetermination consists in the discovery of the disorder of one of the H atoms with occupancies equal to 0.55 (2) and 0.45 (2), respectively. These H atoms are involved in an N⋯N hydrogen bond and are shifted towards its centre.


Chemical context
Structures which contain hydroxyl, secondary and primary amine groups are often determined incorrectly because of an assumed geometry of these groups and the subsequent applied constraints or restraints. 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. In the course of recalculation of suspect structures which were retrieved from the Cambridge Crystallographic Database (Groom & Allen, 2014), a defect in the structure determination of 2-amino-4,6-dimethoxypyrimidine-4-aminobenzoic acid (1/1) by Benali-Cherif et al. (2009) has been found; the CSD refcode is DUJCAN. The aim of the present article is to demonstrate how the original structure determination can be improved.

Structural commentary
The structure of the title compound has been described by Benali-Cherif et al. (2009). In that article, the hydrogen atom H3b was attached to atom N3b and refined with a distance constraint of N3b-H3b = 0.86 Å with U iso (H3b) = 1.2U eq (N3b). This hydrogen is involved in the hydrogen bond N3b-H3bÁ Á ÁN3a (Fig. 1).
However, inspection of the difference electron density map of the recalculated structure has shown that hydrogen atom H3b is disordered over two positions (Fig. 2), between atoms N3a and N3b. Thus, atom H3b was split into two atoms, labelled as H1n3b and H1n3a, with respective occupancies 0.52 (2) and 0.48 (2). These hydrogen atoms remain involved in the N3aÁ Á ÁN3b hydrogen bond (Table 1), as shown in Fig. 3.
The observed disorder of the secondary amine hydrogen atoms is probably due to the chemical equality of two symmetry-independent cytosinium/cytosine molecules and their quite similar environments. Otherwise, the description of the hydrogen-bond pattern by Benali-Cherif et al. (2009) remains intact because locally one of the nitrogen atoms, N3a or N3b, acts as a donor while the other acts as an acceptor of the hydrogen bond.
The hydrogen atom H3, which was situated about the centre of the hydrogen bond O3-H3Á Á ÁO1 has also been checked (Fig. 4). It turns out that the build-up of the electron density is not split into two positions and the original position determined by Benali-Cherif et al. (2009) is correct.
In a broader sense, the present redetermination emphasizes how important it is to carefully examine the difference electron-density maps during structure determinations.  View of the constituent molecules and atoms of the present redetermined title structure. The displacement ellipsoids are drawn at the 50% probability level.

Figure 4
A section of the difference electron-density map for the present redetermined title structure, which shows the build up of the electron density between atoms O1 and O3. Positive and negative electron densities are indicated by continuous and dashed lines, respectively. The increment between the contours is 0.05 e Å À3 (JANA2006; Petříček et al., 2014).

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 atoms N1 and N3. Positive and negative electron densities are indicated by continuous and dashed lines, respectively. The increment between the contours is 0.05 e Å À3 (JANA2006; Petříček et al., 2014). View of the constituent molecules and atoms of the title structure in the original article [Benali-Cherif, Falek & Direm (2009). Acta Cryst. E65, o3058-o3059]. The displacement ellipsoids are drawn at the 50% probability level.

Supramolecular features
The graph set analysis (Etter et al., 1990) of the title compound has been described by Benali-Cherif et al. (2009).

Database survey
The CIF file of the article by Benali-Cherif et al. (2009) has been included in the Cambridge Crystallographic Database (Groom & Allen, 2014) under the refcode DUJCAN.

Synthesis and crystallization
The preparation of the title compound has been described by Benali-Cherif et al. (2009).

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 maps. The aryl hydrogen atoms were refined as constrained with C aryl -H aryl = 0.93 Å and U iso (H aryl ) = 1.2U eq (C aryl ). The displacement parameter of the hydroxyl hydrogen atom H3 was constrained by U iso (H3) = 1.5U eq (O3). The hydrogen atoms of the primary and secondary amine groups were constrained by U iso (H amine ) = 1.2U eq (N amine ). In addition, the distances of the disordered amine hydrogen atoms, H1n36 and H1n3b, were refined with the distance restraint N-H = 0.87 (1) Å , and their occupational parameters constrained to fulfill the condition that their sum = 1 [viz. 0.55 (2) (H1n3b) and 0.45 (2) (H1n3a)].