Crystal structure of disodium 2-amino-6-oxo-6,7-dihydro-1H-purine-1,7-diide heptahydrate

In the title compound, the deprotonated guanine molecules are arranged in centrosymmetric pairs, and form hydrogen bonds with the neighboring water molecules.


Chemical context
Guanine is one of the five nucleic acids present in both DNA and RNA (Blackburn et al., 2006), and is also found in its crystalline form in the integument of many animals as a light reflector (Land, 1972;Parker, 2000;Gur et al., 2013Gur et al., , 2014. There are two known crystal structures of guanine; guanine monohydrate (Thewalt et al., 1971) and anhydrous guanine (Guille & Clegg, 2006). In addition there are also a few known guanine salts (Broomhead, 1951;Wei, 1977;Iball & Wilson, 1965). The crystal structure of the title compound was obtained as a part of a study into controlling the crystal phase of guanine using recrystallization.
Cation, anion and radical formation among nucleic acids are thought to be important steps in DNA damage (Cooke et al., 2003;Kasai, 1997). For that reason, protonation and deprotonation of nucleic acids and their role in processes like mutation has been widely studied both theoretically and experimentally. It is thought that the most prominent site for this kind of damage will be guanine because it has the lowest oxidation potential among the four DNA bases (Burrows & Muller, 1998;Steenken & Jovanovic, 1997). As a result, even initially different oxidized species may eventually migrate to guanine. Therefore, DNA damage is predicted to be produced at this site (Melvin et al., 1995). The crystal structure of the deprotonated guanine presented in this report may provide information about the deprotonated oxidized guanine state and its interactions with the neighboring water molecules.

Structural commentary
In the structure of the title compound, the asymmetric unit is composed of a guanine anion, two sodium counter-ions and seven water molecules (Fig. 1). In this compound, guanine exists as the amino-keto tautomer, the guanine molecules are doubly negatively charged, as a result of the deprotonation from N1 and N7 (purine numbering) that occurred due to the alkaline conditions of the solution from which recrystallization took place. There are no direct interactions between the Na + cations and the guanine anions.

Figure 2
The crystal structure viewed down the c axis, showing the alternating layers of guanine molecules and hydrated sodium ions.

Figure 3
A view down the a axis showing the herringbone crystal packing motif, including edge-to-face interactions between the guanine dimers.
present in the structure of the title compound. Instead, the guanine molecules form O-HÁ Á ÁN and O-HÁ Á ÁO hydrogen bonds with the neighboring water molecules (Table 1), satisfying all guanine donors and acceptors with the exception of the NH 2 amine group, which surprisingly does not seem to participate in any hydrogen bonding, and is not within hydrogen-bonding distance of any hydrogen acceptors. In addition, the guanine molecules form dimers that have an edge-to-face type orientation, resulting in the observed herringbone crystal packing motif with a dihedral angle of 123.917 (17) (Fig. 3).

Synthesis and crystallization
Disodium 2-amino-6-oxo-6,7-dihydro-1H-purine-1,7-diide heptahydrate was prepared by dissolving 0.1 g guanine (powder Sigma-Aldrich) in 5 ml NaOH 1 N (pH 14). The solution was then filtered using a PVDF filter (0.22 mm), and 0.1 ml of NaOH 1 N was added to the solution to ensure that all of the guanine was dissolved. The solution was then kept for 10 days under an IR lamp using 15 min. cycles (on/off) while open to the atmosphere. Large 3mm crystals were extracted from the suspension, broken to a suitable size and subjected to single crystal X-ray diffraction.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. All hydrogen atoms were refined freely with the exception of C8-bound H atom that was placed in a calculated position and refined in riding mode.  CrystalMaker (CrystalMaker, 2010); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2015) and publCIF (Westrip, 2010).