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

Gur, D.; Shimon, L.J.W.

doi:10.1107/S2056989015003163

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Volume 71| Part 3| March 2015| Pages 281-283

doi:10.1107/S2056989015003163

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

Dvir Gur ^a ^* and Linda J. W. Shimon ^b

^aDepartment of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and ^bChemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
^*Correspondence e-mail: dvir.gur@weizmann.ac.il

Edited by S. Parkin, University of Kentucky, USA (Received 2 December 2014; accepted 13 February 2015; online 18 February 2015)

In the title compound, disodium 2-amino-6-oxo-6,7-dihydro-1H-purine-1,7-diide heptahydrate, 2Na⁺·C₅H₃N₅O²⁻·7H₂O, the structure is composed of alternating (100) layers of guanine molecules and hydrated Na⁺ ions. Within the guanine layer, the molecules are arranged in centrosymmetric pairs, with a partial overlap between the guanine rings. In this compound, guanine exists as the amino–keto tautomer from which deprotonation from N₁ and N₇ has occurred (purine numbering). There are no direct interactions between the Na⁺ cations and the guanine anions. Guanine molecules are linked to neighboring water molecules by O—H⋯N and O—H⋯O hydrogen bonds into a network structure.

Keywords: crystal structure; guanine salt; nucleobase; hydrogen bonds.

CCDC reference: 1049453

1. Chemical context

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.

2. 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 1
A displacement ellipsoid plot of the asymmetric unit drawn at the 50% probability level. H atoms have been omitted for clarity.

3. Supramolecular features

The structure is composed of alternating (100) layers of guanine molecules and hydrated Na⁺ Ions (Fig. 2). Within the guanine layer, the molecules are arranged in centrosymmetric pairs, in which a partial overlap between the guanine rings is present. The distances between the overlapping atoms C₂–N₃ⁱ and C₄–N₁₀ⁱ are 3.415 (2) and 3.460 (2) Å, respectively [symmetry code: (i) = 1 − x, 1 − y, 1 − z]. The two molecules are offset presumably to separate the charged N⁻ ions of the two molecules and at the same time provide van der Waals contacts between the two rings. In most known guanine crystal structures, neighboring guanine molecules form hydrogen bonds that result in flat layers of guanine molecules, between which stacking interactions are present. Such layers are not present in the structure of the title compound. Instead, the guanine molecules form O—H⋯N and O—H⋯O hydrogen bonds with the neighboring water molecules (Table 1), satisfying all guanine donors and acceptors with the exception of the NH₂ 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).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2A⋯N9ⁱ	0.84 (3)	1.97 (3)	2.7875 (19)	168 (3)
O2—H2B⋯N3	0.89 (3)	2.08 (3)	2.9582 (19)	167 (2)
O3—H3A⋯O5ⁱⁱ	0.87 (3)	2.08 (3)	2.9200 (18)	163 (3)
O3—H3B⋯N3	0.87 (3)	1.95 (3)	2.8038 (18)	166 (3)
O4—H4A⋯N1ⁱⁱⁱ	0.85 (3)	1.96 (3)	2.8093 (19)	177 (3)
O4—H4B⋯N9	0.85 (3)	2.14 (3)	2.9866 (19)	176 (2)
O5—H5C⋯O1ⁱⁱⁱ	0.81 (3)	1.96 (3)	2.7581 (18)	168 (3)
O6—H6A⋯O2^iv	0.79 (3)	2.02 (3)	2.7938 (19)	167 (3)
O6—H6B⋯N7^v	0.90 (3)	2.01 (3)	2.909 (2)	173 (2)
O7—H7A⋯O1^v	0.88 (3)	1.95 (3)	2.7867 (17)	160 (3)
O7—H7B⋯O3	0.85 (3)	1.92 (3)	2.7608 (18)	168 (3)
O8—H8A⋯O1ⁱⁱⁱ	0.84 (3)	1.99 (3)	2.8303 (17)	171 (3)
O8—H8B⋯N7^vi	0.82 (3)	1.98 (3)	2.7938 (19)	171 (3)
O5—H5D⋯O1^vii	0.78 (3)	2.02 (3)	2.7835 (17)	164 (3)
Symmetry codes: (i) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (ii) $[-x, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iv) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (v) x-1, y, z; (vi) -x+1, -y, -z+1; (vii) $[x-1, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

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.

4. 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 µm), 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.

5. 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.

Table 2
Experimental details

Crystal data
Chemical formula	2Na⁺·C₅H₃N₅O²⁻·7H₂O
M_r	321.21
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	120
a, b, c (Å)	10.5520 (2), 11.6936 (3), 11.1938 (2)
β (°)	101.5758 (13)
V (Å³)	1353.12 (5)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.20
Crystal size (mm)	0.30 × 0.10 × 0.05

Data collection
Diffractometer	Nonius KappaCCD
Absorption correction	Multi-scan (DENZO-SMN; Otwinowski & Minor, 2006 )
T_min, T_max	0.977, 0.990
No. of measured, independent and observed [I > 2σ(I)] reflections	6648, 3931, 2981
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.704

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.147, 1.07
No. of reflections	3931
No. of parameters	248
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.57, −0.39
Computer programs: COLLECT (Nonius, 1998 ), DENZO-SMN (Otwinowski & Minor, 2006), SHELXS97 (Sheldrick, 2008 ), SHELXL2013 (Sheldrick, 2015 ), PLATON (Spek, 2009 ), CrystalMaker (CrystalMaker, 2010 ) and publCIF (Westrip, 2010 ).

Supporting information

CCDC reference: 1049453

Crystal structure: contains datablock I. DOI: 10.1107/S2056989015003163/pk2539sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015003163/pk2539Isup2.hkl

checkCIF report

Chemical context top

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., 2013, 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 top

Supramolecular features top

The structure is composed of alternating layers of guanine molecules and hydrated Na⁺ Ions (Fig. 2). Within the guanine layer, the molecules are arranged in centrosymmetric pairs, in which a partial overlap between the guanine rings is present. The distances between the overlapping atoms C₂–N₃ⁱ and C₄–N₁₀ⁱ are 3.415 (2) and 3.460 (2) Å respectively [symmetry code: (i) = 1 - x, 1 - y, 1 - z]. The two molecules are offset presumably to separate the charged N^- ions of the two molecules and at the same time provide van der Waals contacts between the two rings. In most known guanine crystal structures, neighboring guanine molecules form hydrogen bonds that result in flat layers of guanine molecules, between which stacking interactions are present. Such layers are not present in the structure of the title compound. Instead, the guanine molecules form N···H—O and O···H—O hydrogen bonds with the neighboring water molecules (Table 1), satisfying all guanine donors and acceptors with the exception of the NH₂ amine group, which surprisingly seems not 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 top

Disodium 2-amino-6-oxo-7,7-dihydro-1H-purine-1,7 diide-heptahydrate was prepared by dissolving 0.1 g guanine (powder Sigma–Aldrich ) in 5 ml NaOH 1 N. The solution was then filtered using a PVDF filter (0.22 µm), 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 top

Related literature top

For related literature, see: Blackburn et al. (2006); Broomhead (1951); Burrows & Muller (1998); Cooke et al. (2003); Guille & Clegg (2006); Gur et al. (2013, 2014); Iball & Wilson (1965); Kasai (1997); Land (1972); Melvin et al. (1995); Parker (2000); Steenken & Jovanovic (1997); Thewalt et al. (1971); Wei (1977).

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: DENZO-SMN (Otwinowski & Minor, 2006); data reduction: DENZO-SMN (Otwinowski & Minor, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009) and CrystalMaker (CrystalMaker, 2010); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2015) and publCIF (Westrip, 2010).

Figures top

	Fig. 1. A displacement ellipsoid plot of the asymmetric unit drawn at the 50% probability level. H atoms have been omitted for clarity.
	Fig. 2. The crystal structure viewed down the c axis, showing the alternating layers of guanine molecules and hydrated sodium ions.
	Fig. 3. A view down the a axis showing the herringbone crystal packing motif, including edge-to-face interactions between the guanine dimers.

Disodium 2-amino-6-oxo-6,7-dihydro-1H-purine-1,7-diide heptahydrate top

Crystal data top

2Na⁺·C₅H₃N₅O²⁻·7H₂O	F(000) = 672
M_r = 321.21	D_x = 1.577 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 10.5520 (2) Å	Cell parameters from 3810 reflections
b = 11.6936 (3) Å	θ = 2.6–30.0°
c = 11.1938 (2) Å	µ = 0.20 mm⁻¹
β = 101.5758 (13)°	T = 120 K
V = 1353.12 (5) Å³	Plate, colourless
Z = 4	0.30 × 0.10 × 0.05 mm

Data collection top

Nonius KappaCCD diffractometer	2981 reflections with I > 2σ(I)
Radiation source: sealed tube	R_int = 0.019
ϕ and ω scans	θ_max = 30.0°, θ_min = 3.7°
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 2006)	h = −14→14
T_min = 0.977, T_max = 0.990	k = −12→16
6648 measured reflections	l = −15→15
3931 independent reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F² > 2σ(F²)] = 0.049	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.147	w = 1/[σ²(F_o²) + (0.0862P)² + 0.5094P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max < 0.001
3931 reflections	Δρ_max = 0.57 e Å⁻³
248 parameters	Δρ_min = −0.39 e Å⁻³

Crystal data top

2Na⁺·C₅H₃N₅O²⁻·7H₂O	V = 1353.12 (5) Å³
M_r = 321.21	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 10.5520 (2) Å	µ = 0.20 mm⁻¹
b = 11.6936 (3) Å	T = 120 K
c = 11.1938 (2) Å	0.30 × 0.10 × 0.05 mm
β = 101.5758 (13)°

Data collection top

Nonius KappaCCD diffractometer	3931 independent reflections
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 2006)	2981 reflections with I > 2σ(I)
T_min = 0.977, T_max = 0.990	R_int = 0.019
6648 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.049	0 restraints
wR(F²) = 0.147	H atoms treated by a mixture of independent and constrained refinement
S = 1.07	Δρ_max = 0.57 e Å⁻³
3931 reflections	Δρ_min = −0.39 e Å⁻³
248 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.65524 (13)	0.48287 (13)	0.34832 (13)	0.0172 (3)
C2	0.52557 (16)	0.48307 (15)	0.33930 (15)	0.0175 (3)
N3	0.45252 (13)	0.40241 (13)	0.37665 (13)	0.0170 (3)
C4	0.52344 (15)	0.31289 (15)	0.43267 (14)	0.0158 (3)
C5	0.65775 (15)	0.30526 (15)	0.44968 (14)	0.0161 (3)
C6	0.72597 (15)	0.39376 (14)	0.40446 (14)	0.0156 (3)
N7	0.69798 (13)	0.20349 (13)	0.50957 (13)	0.0186 (3)
C8	0.58601 (16)	0.15733 (16)	0.52393 (16)	0.0193 (3)
H8	0.585 (2)	0.087 (2)	0.563 (2)	0.023*
N9	0.47610 (13)	0.21804 (13)	0.47962 (13)	0.0178 (3)
N10	0.46123 (16)	0.57498 (15)	0.27867 (15)	0.0235 (3)
H10A	0.378 (3)	0.585 (3)	0.290 (3)	0.057 (9)*
H10B	0.513 (3)	0.636 (3)	0.271 (3)	0.048 (8)*
O1	0.85043 (11)	0.39326 (11)	0.41331 (10)	0.0171 (3)
Na1	0.11549 (6)	0.25431 (6)	0.18356 (6)	0.01689 (17)
Na2	0.04858 (6)	0.04502 (6)	0.37257 (6)	0.01704 (17)
O2	0.30698 (12)	0.32592 (11)	0.13607 (12)	0.0194 (3)
H2A	0.355 (3)	0.303 (3)	0.090 (3)	0.043 (8)*
H2B	0.362 (3)	0.346 (2)	0.204 (2)	0.031 (6)*
O3	0.18432 (12)	0.38036 (11)	0.35525 (11)	0.0186 (3)
H3A	0.143 (3)	0.445 (3)	0.352 (3)	0.048 (8)*
H3B	0.267 (3)	0.391 (3)	0.374 (3)	0.042 (7)*
O4	0.24329 (12)	0.11485 (11)	0.32009 (11)	0.0177 (3)
H4A	0.276 (3)	0.075 (2)	0.271 (3)	0.035 (7)*
H4B	0.307 (3)	0.146 (2)	0.367 (2)	0.032 (7)*
O5	−0.00208 (13)	0.06838 (11)	0.14535 (11)	0.0174 (3)
H5C	0.050 (3)	0.024 (3)	0.128 (3)	0.042 (8)*
H5D	−0.051 (3)	0.089 (3)	0.087 (3)	0.040 (7)*
O6	−0.15505 (12)	0.02121 (12)	0.42404 (11)	0.0200 (3)
H6A	−0.207 (3)	−0.027 (3)	0.401 (3)	0.037 (7)*
H6B	−0.203 (3)	0.079 (2)	0.444 (2)	0.037 (7)*
O7	0.04292 (13)	0.22690 (11)	0.46296 (11)	0.0180 (3)
H7A	−0.030 (3)	0.265 (3)	0.447 (3)	0.041 (7)*
H7B	0.094 (3)	0.274 (2)	0.440 (3)	0.034 (7)*
O8	0.08223 (12)	−0.14985 (11)	0.31485 (11)	0.0175 (3)
H8A	0.108 (2)	−0.143 (2)	0.249 (3)	0.033 (7)*
H8B	0.145 (3)	−0.173 (2)	0.365 (3)	0.034 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0152 (6)	0.0196 (7)	0.0171 (6)	−0.0014 (5)	0.0042 (5)	0.0002 (5)
C2	0.0158 (7)	0.0205 (8)	0.0162 (7)	0.0002 (6)	0.0034 (6)	−0.0002 (6)
N3	0.0139 (6)	0.0197 (7)	0.0172 (6)	−0.0007 (5)	0.0030 (5)	0.0006 (5)
C4	0.0130 (7)	0.0214 (8)	0.0127 (7)	0.0011 (6)	0.0023 (5)	−0.0006 (6)
C5	0.0141 (7)	0.0201 (8)	0.0140 (7)	0.0015 (6)	0.0024 (5)	0.0016 (6)
C6	0.0131 (7)	0.0207 (8)	0.0128 (7)	−0.0008 (6)	0.0021 (5)	−0.0024 (6)
N7	0.0154 (6)	0.0205 (7)	0.0194 (7)	0.0015 (5)	0.0022 (5)	0.0026 (5)
C8	0.0163 (8)	0.0220 (9)	0.0196 (8)	0.0012 (6)	0.0033 (6)	0.0020 (6)
N9	0.0154 (6)	0.0209 (7)	0.0169 (6)	0.0000 (5)	0.0030 (5)	0.0016 (5)
N10	0.0180 (7)	0.0243 (8)	0.0282 (8)	0.0031 (6)	0.0045 (6)	0.0072 (6)
O1	0.0106 (5)	0.0232 (6)	0.0177 (5)	−0.0012 (4)	0.0034 (4)	−0.0005 (4)
Na1	0.0157 (3)	0.0191 (4)	0.0157 (3)	−0.0004 (2)	0.0028 (2)	0.0002 (2)
Na2	0.0166 (3)	0.0193 (3)	0.0158 (3)	0.0003 (2)	0.0045 (2)	−0.0001 (2)
O2	0.0159 (6)	0.0261 (7)	0.0167 (6)	−0.0009 (5)	0.0045 (5)	−0.0018 (5)
O3	0.0135 (6)	0.0207 (6)	0.0223 (6)	0.0008 (5)	0.0047 (4)	−0.0024 (5)
O4	0.0134 (5)	0.0220 (6)	0.0176 (6)	0.0002 (5)	0.0030 (4)	−0.0028 (5)
O5	0.0166 (6)	0.0202 (6)	0.0146 (5)	0.0028 (5)	0.0013 (4)	0.0013 (5)
O6	0.0159 (6)	0.0230 (7)	0.0213 (6)	−0.0008 (5)	0.0043 (5)	−0.0027 (5)
O7	0.0171 (6)	0.0198 (6)	0.0177 (6)	0.0017 (5)	0.0049 (4)	0.0003 (4)
O8	0.0147 (6)	0.0229 (6)	0.0147 (5)	0.0016 (5)	0.0022 (4)	0.0012 (4)

Geometric parameters (Å, º) top

N1—C2	1.352 (2)	Na2—O7	2.3612 (14)
N1—C6	1.360 (2)	Na2—O4	2.3912 (14)
C2—N3	1.337 (2)	Na2—O8	2.4142 (15)
C2—N10	1.375 (2)	Na2—O6ⁱⁱⁱ	2.4534 (14)
N3—C4	1.364 (2)	Na2—O5	2.5067 (14)
C4—N9	1.364 (2)	Na2—Na2ⁱⁱⁱ	3.3871 (13)
C4—C5	1.394 (2)	Na2—Na1^iv	3.8095 (9)
C5—N7	1.390 (2)	Na2—Na1^v	4.1397 (9)
C5—C6	1.411 (2)	O2—H2A	0.84 (3)
C6—O1	1.2970 (19)	O2—H2B	0.89 (3)
N7—C8	1.338 (2)	O3—H3A	0.87 (3)
C8—N9	1.365 (2)	O3—H3B	0.87 (3)
C8—H8	0.94 (2)	O4—H4A	0.85 (3)
N10—H10A	0.91 (3)	O4—H4B	0.85 (3)
N10—H10B	0.91 (3)	O5—H5C	0.81 (3)
Na1—O2	2.3447 (14)	O5—H5D	0.78 (3)
Na1—O8ⁱ	2.3715 (14)	O6—Na2ⁱⁱⁱ	2.4534 (14)
Na1—O3	2.4153 (14)	O6—H6A	0.79 (3)
Na1—O7ⁱⁱ	2.4440 (14)	O6—H6B	0.90 (3)
Na1—O4	2.4467 (14)	O7—Na1^v	2.4440 (14)
Na1—O5	2.4972 (14)	O7—H7A	0.88 (3)
Na1—Na2	3.4006 (9)	O7—H7B	0.85 (3)
Na1—Na2ⁱ	3.8095 (9)	O8—Na1^iv	2.3716 (14)
Na1—Na2ⁱⁱ	4.1397 (9)	O8—H8A	0.84 (3)
Na2—O6	2.3502 (14)	O8—H8B	0.82 (3)

C2—N1—C6	119.30 (14)	O4—Na2—O5	74.47 (4)
N3—C2—N1	127.87 (15)	O8—Na2—O5	81.04 (5)
N3—C2—N10	116.55 (15)	O6ⁱⁱⁱ—Na2—O5	160.17 (5)
N1—C2—N10	115.49 (15)	O6—Na2—Na2ⁱⁱⁱ	46.41 (3)
C2—N3—C4	112.80 (14)	O7—Na2—Na2ⁱⁱⁱ	83.17 (4)
N3—C4—N9	126.26 (14)	O4—Na2—Na2ⁱⁱⁱ	137.16 (5)
N3—C4—C5	124.10 (15)	O8—Na2—Na2ⁱⁱⁱ	91.01 (4)
N9—C4—C5	109.64 (14)	O6ⁱⁱⁱ—Na2—Na2ⁱⁱⁱ	43.93 (3)
N7—C5—C4	108.93 (14)	O5—Na2—Na2ⁱⁱⁱ	148.16 (5)
N7—C5—C6	132.26 (14)	O6—Na2—Na1	123.50 (4)
C4—C5—C6	118.80 (15)	O7—Na2—Na1	69.18 (4)
O1—C6—N1	119.48 (15)	O4—Na2—Na1	46.01 (3)
O1—C6—C5	123.43 (15)	O8—Na2—Na1	116.92 (4)
N1—C6—C5	117.09 (14)	O6ⁱⁱⁱ—Na2—Na1	133.71 (4)
C8—N7—C5	102.23 (14)	O5—Na2—Na1	47.07 (3)
N7—C8—N9	116.93 (16)	Na2ⁱⁱⁱ—Na2—Na1	152.07 (3)
N7—C8—H8	120.6 (14)	O6—Na2—Na1^iv	61.78 (4)
N9—C8—H8	122.5 (14)	O7—Na2—Na1^iv	145.56 (4)
C4—N9—C8	102.28 (13)	O4—Na2—Na1^iv	130.44 (4)
C2—N10—H10A	115 (2)	O8—Na2—Na1^iv	36.86 (3)
C2—N10—H10B	114.3 (19)	O6ⁱⁱⁱ—Na2—Na1^iv	88.83 (4)
H10A—N10—H10B	121 (3)	O5—Na2—Na1^iv	86.14 (4)
O2—Na1—O8ⁱ	129.23 (5)	Na2ⁱⁱⁱ—Na2—Na1^iv	69.95 (2)
O2—Na1—O3	80.05 (5)	Na1—Na2—Na1^iv	133.15 (2)
O8ⁱ—Na1—O3	80.22 (5)	O6—Na2—Na1^v	82.59 (4)
O2—Na1—O7ⁱⁱ	81.28 (5)	O7—Na2—Na1^v	31.10 (3)
O8ⁱ—Na1—O7ⁱⁱ	82.37 (5)	O4—Na2—Na1^v	90.17 (4)
O3—Na1—O7ⁱⁱ	137.08 (5)	O8—Na2—Na1^v	138.65 (4)
O2—Na1—O4	89.29 (5)	O6ⁱⁱⁱ—Na2—Na1^v	55.22 (4)
O8ⁱ—Na1—O4	133.29 (5)	O5—Na2—Na1^v	139.21 (4)
O3—Na1—O4	82.51 (5)	Na2ⁱⁱⁱ—Na2—Na1^v	59.82 (2)
O7ⁱⁱ—Na1—O4	135.46 (5)	Na1—Na2—Na1^v	95.369 (16)
O2—Na1—O5	133.89 (5)	Na1^iv—Na2—Na1^v	129.771 (19)
O8ⁱ—Na1—O5	90.29 (5)	Na1—O2—H2A	133 (2)
O3—Na1—O5	136.66 (5)	Na1—O2—H2B	110.3 (16)
O7ⁱⁱ—Na1—O5	82.01 (5)	H2A—O2—H2B	104 (2)
O4—Na1—O5	73.70 (5)	Na1—O3—H3A	115 (2)
O2—Na1—Na2	133.95 (4)	Na1—O3—H3B	114.2 (19)
O8ⁱ—Na1—Na2	92.44 (4)	H3A—O3—H3B	110 (3)
O3—Na1—Na2	90.63 (4)	Na2—O4—Na1	89.31 (5)
O7ⁱⁱ—Na1—Na2	129.14 (4)	Na2—O4—H4A	117.3 (18)
O4—Na1—Na2	44.68 (3)	Na1—O4—H4A	101.7 (18)
O5—Na1—Na2	47.31 (3)	Na2—O4—H4B	127.2 (17)
O2—Na1—Na2ⁱ	91.59 (4)	Na1—O4—H4B	112.0 (18)
O8ⁱ—Na1—Na2ⁱ	37.64 (3)	H4A—O4—H4B	105 (2)
O3—Na1—Na2ⁱ	68.95 (4)	Na1—O5—Na2	85.62 (4)
O7ⁱⁱ—Na1—Na2ⁱ	73.34 (4)	Na1—O5—H5C	105 (2)
O4—Na1—Na2ⁱ	150.82 (4)	Na2—O5—H5C	99 (2)
O5—Na1—Na2ⁱ	123.71 (4)	Na1—O5—H5D	96 (2)
Na2—Na1—Na2ⁱ	126.913 (19)	Na2—O5—H5D	148 (2)
O2—Na1—Na2ⁱⁱ	67.43 (4)	H5C—O5—H5D	111 (3)
O8ⁱ—Na1—Na2ⁱⁱ	74.73 (4)	Na2—O6—Na2ⁱⁱⁱ	89.65 (5)
O3—Na1—Na2ⁱⁱ	107.25 (4)	Na2—O6—H6A	128 (2)
O7ⁱⁱ—Na1—Na2ⁱⁱ	29.94 (3)	Na2ⁱⁱⁱ—O6—H6A	104 (2)
O4—Na1—Na2ⁱⁱ	151.97 (4)	Na2—O6—H6B	124.0 (17)
O5—Na1—Na2ⁱⁱ	110.76 (4)	Na2ⁱⁱⁱ—O6—H6B	100.6 (17)
Na2—Na1—Na2ⁱⁱ	155.43 (3)	H6A—O6—H6B	103 (3)
Na2ⁱ—Na1—Na2ⁱⁱ	50.230 (19)	Na2—O7—Na1^v	118.96 (6)
O6—Na2—O7	84.18 (5)	Na2—O7—H7A	117.7 (19)
O6—Na2—O4	166.81 (6)	Na1^v—O7—H7A	104.2 (19)
O7—Na2—O4	83.95 (5)	Na2—O7—H7B	112.8 (18)
O6—Na2—O8	98.31 (5)	Na1^v—O7—H7B	99.0 (18)
O7—Na2—O8	169.31 (5)	H7A—O7—H7B	101 (3)
O4—Na2—O8	94.41 (5)	Na1^iv—O8—Na2	105.50 (5)
O6—Na2—O6ⁱⁱⁱ	90.35 (5)	Na1^iv—O8—H8A	119.6 (18)
O7—Na2—O6ⁱⁱⁱ	86.16 (5)	Na2—O8—H8A	103.7 (19)
O4—Na2—O6ⁱⁱⁱ	94.57 (5)	Na1^iv—O8—H8B	115.2 (18)
O8—Na2—O6ⁱⁱⁱ	83.44 (5)	Na2—O8—H8B	105.6 (19)
O6—Na2—O5	104.03 (5)	H8A—O8—H8B	106 (3)
O7—Na2—O5	108.55 (5)

Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x, −y+1/2, z−1/2; (iii) −x, −y, −z+1; (iv) −x, y−1/2, −z+1/2; (v) x, −y+1/2, z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2A···N9ⁱⁱ	0.84 (3)	1.97 (3)	2.7875 (19)	168 (3)
O2—H2B···N3	0.89 (3)	2.08 (3)	2.9582 (19)	167 (2)
O3—H3A···O5ⁱ	0.87 (3)	2.08 (3)	2.9200 (18)	163 (3)
O3—H3B···N3	0.87 (3)	1.95 (3)	2.8038 (18)	166 (3)
O4—H4A···N1^vi	0.85 (3)	1.96 (3)	2.8093 (19)	177 (3)
O4—H4B···N9	0.85 (3)	2.14 (3)	2.9866 (19)	176 (2)
O5—H5C···O1^vi	0.81 (3)	1.96 (3)	2.7581 (18)	168 (3)
O6—H6A···O2^iv	0.79 (3)	2.02 (3)	2.7938 (19)	167 (3)
O6—H6B···N7^vii	0.90 (3)	2.01 (3)	2.909 (2)	173 (2)
O7—H7A···O1^vii	0.88 (3)	1.95 (3)	2.7867 (17)	160 (3)
O7—H7B···O3	0.85 (3)	1.92 (3)	2.7608 (18)	168 (3)
O8—H8A···O1^vi	0.84 (3)	1.99 (3)	2.8303 (17)	171 (3)
O8—H8B···N7^viii	0.82 (3)	1.98 (3)	2.7938 (19)	171 (3)
O5—H5D···O1^ix	0.78 (3)	2.02 (3)	2.7835 (17)	164 (3)

Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x, −y+1/2, z−1/2; (iv) −x, y−1/2, −z+1/2; (vi) −x+1, y−1/2, −z+1/2; (vii) x−1, y, z; (viii) −x+1, −y, −z+1; (ix) x−1, −y+1/2, z−1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2A···N9ⁱ	0.84 (3)	1.97 (3)	2.7875 (19)	168 (3)
O2—H2B···N3	0.89 (3)	2.08 (3)	2.9582 (19)	167 (2)
O3—H3A···O5ⁱⁱ	0.87 (3)	2.08 (3)	2.9200 (18)	163 (3)
O3—H3B···N3	0.87 (3)	1.95 (3)	2.8038 (18)	166 (3)
O4—H4A···N1ⁱⁱⁱ	0.85 (3)	1.96 (3)	2.8093 (19)	177 (3)
O4—H4B···N9	0.85 (3)	2.14 (3)	2.9866 (19)	176 (2)
O5—H5C···O1ⁱⁱⁱ	0.81 (3)	1.96 (3)	2.7581 (18)	168 (3)
O6—H6A···O2^iv	0.79 (3)	2.02 (3)	2.7938 (19)	167 (3)
O6—H6B···N7^v	0.90 (3)	2.01 (3)	2.909 (2)	173 (2)
O7—H7A···O1^v	0.88 (3)	1.95 (3)	2.7867 (17)	160 (3)
O7—H7B···O3	0.85 (3)	1.92 (3)	2.7608 (18)	168 (3)
O8—H8A···O1ⁱⁱⁱ	0.84 (3)	1.99 (3)	2.8303 (17)	171 (3)
O8—H8B···N7^vi	0.82 (3)	1.98 (3)	2.7938 (19)	171 (3)
O5—H5D···O1^vii	0.78 (3)	2.02 (3)	2.7835 (17)	164 (3)

Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x, y+1/2, −z+1/2; (iii) −x+1, y−1/2, −z+1/2; (iv) −x, y−1/2, −z+1/2; (v) x−1, y, z; (vi) −x+1, −y, −z+1; (vii) x−1, −y+1/2, z−1/2.

Experimental details

Crystal data
Chemical formula	2Na⁺·C₅H₃N₅O²⁻·7H₂O
M_r	321.21
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	120
a, b, c (Å)	10.5520 (2), 11.6936 (3), 11.1938 (2)
β (°)	101.5758 (13)
V (Å³)	1353.12 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.20
Crystal size (mm)	0.30 × 0.10 × 0.05

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	Multi-scan (DENZO-SMN; Otwinowski & Minor, 2006)
T_min, T_max	0.977, 0.990
No. of measured, independent and observed [I > 2σ(I)] reflections	6648, 3931, 2981
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.704

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.147, 1.07
No. of reflections	3931
No. of parameters	248
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.57, −0.39

Computer programs: COLLECT (Nonius, 1998), DENZO-SMN (Otwinowski & Minor, 2006), SHELXS97 (Sheldrick, 2008), PLATON (Spek, 2009) and CrystalMaker (CrystalMaker, 2010), SHELXL2013 (Sheldrick, 2015) and publCIF (Westrip, 2010).

Acknowledgements

We would like to thank Professor Lia Addadi, Professor Steve Weiner and Professor Leslie Schwartz for their helpful guidance and advice. This research was supported by a grant from the Israel Science foundation (grant No. 2012\224330*).

References

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Volume 71| Part 3| March 2015| Pages 281-283

doi:10.1107/S2056989015003163

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Synthesis and crystallization

5. Refinement

Supporting information

Acknowledgements

References

research communications

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

3. Supramolecular features