[6-Amino-3-methyl-5-nitro­so­pyrimidine-2,4(1H,3H)-dionato]­sodium dihydrate at 150 K: coordination-polymer ladders linked by hydrogen bonds

In the title compound, [Na(C₅H₅N₄O₃)]·2H₂O, each Na cation is linked to three C₅H₄N₄O₃⁻ anions and two water mol­ecules, forming approximately octahedral NaNO₅ units; the cations and the anions form molecular ladders, and each ladder is linked to four neighbouring ladders by O—H...O and O—H...N hydrogen bonds.

S1. Comment

In neutral nitrosopyrimidines of type (1) and in metal salts of the related glycinate anions (2) and (3), the close interplay of molecular, molecular-electronic, and supramolecular structures leads to an extensive polarization of the electronic structure of the organic fragment, consistently manifested in highly unusual interatomic distances (Low et al., 2000; Low, Arranz, Cobo, Fontecha, Godino, López & Glidewell et al., 2001; Low, Arranz, Cobo, Fontecha, Godino, López, Cannon et al., 2001; Low, Cannon et al., 2001; Low, Moreno et al., 2001). Continuing this study, we now report the molecular and supramolecular structure of the sodium salt (I) derived from the simpler derivative (4), from which the amino-acid unit is absent; compound (I) crystallizes as the dihydrate Na(C₅H₄N₄O₃)·2H₂O (Fig. 1). A very brief report on the room-temperature structure of (I) (Schwabenländer et al., 1998) contains neither description nor discussion of any of the key features of the overall structure: the pyrimidine geometry, the metal-ligand coordination geometry, the coordination-polymer formation, or the hydrogen bonding. The present study, undertaken at 150 (2) K, reveals a linear coordination polymer in the form of a molecular ladder, and the linking of the ladders into a continuous framework by extensive hydrogen bonding. \sch

The structure of the anion (Table 1), where the usual conformation having the nitroso group trans to the amidic O4 is reinforced by the formation of an intramolecular N—H···O hydrogen bond (Table 2), shows a number of the metrical features characteristic of 5-nitrosopyrimidine (Low et al., 2000; Low, Arranz, Cobo, Fontecha, Godino, López & Glidewell et al., 2001; Low, Arranz, Cobo, Fontecha, Godino, López, Cannon et al., 2001; Low, Cannon et al., 2001; Low, Moreno et al., 2001). In particular, the C4—C5 and C5—C6 distances are very similar; the difference between the C5—N5 and N5—O5 distances is less than 0.050 Å; and the C6—N6 bond is very short for a single C—N bond between three-connected atoms (Allen et al., 1987): while the very similar C2—O2 and C4—O4 distances are both typical of those in neutral amides (Allen et al., 1987), the N1—C6 bond is somewhat shorter than the N1—C2 bond. These observations taken together indicate polarization of the electronic structure, so that (4a) is a significantly better representation than (4 b).

The cations and anions together form a one-dimensional coordination polymer in the form of a molecular ladder, or chain of fused rings. The Na at (x, y, z) is bonded to both O2 at (x, y, z) and O4 at (x, y, -1 + z), and propagation of these interactions by translation generates a chain running parallel to the [001] direction (Fig. 2). At the same time, Na at (x, y, z) is also bonded to O2 at (1 - x, 2 - y, -z), and thus an antiparallel pair of chains is linked into a ladder. There are centrosymmetric rings centred at (1/2, 1.0, n) (n = zero or integer) alternating with twelve-membered rings centred at (1/2, 1.0, n + 1/2) (n = zero or integer) (Fig. 2). There is one of these chains of fused rings per unit cell and the chains lie along the lines (m + 1/2, n, z) (m, n = zero or integer).

There are also two water molecules bound to each Na and the resulting NaO₅ unit has approximate square pyramidal geometry (Table 1, Fig. 3). The mean value of the Na—O distances, 2.400 (2) Å, is biased by the outlier value, 2.6011 (16) Å, for the bond which links adjacent chains: this is probably due to steric repulsions between the organic ligands in the coupled chains. In addition, there is a (possibly adventitious) Na···N contact which completes an approximately octahedral geometry at Na (Fig. 3). The anion at (x, y, z) may thus be considered as monodentate to the Na centres at (x, y, z) and (1 - x, 2 - y, -z), via O2, and bidentate to the Na at (x, y, 1 + z) via O4 and N5, which make a bite angle at Na of 65.15 (5)°.

Both the metal coordination geometry and the metal-ligand coordination polymer in (I) may be contrasted with the corresponding Na salt of the anion (2) (Low, Moreno et al., 2001), where the two independent Na centres both have trigonal bipyramidal coordination and where centrosymmetric rings are linked into chains by isolated water molecules acting as single bridges between adjacent rings. In view of the polarized structure (4a), it is notable that the nitrosyl O5 is not coordinated to the metal in (I). By contrast, in the Na salt of (2), O5 is bonded to the metal, while in the K salts of (2) and (3), the nitrosyl group coordinates to the metal in η² and η¹ modes, respectively, (Low, Arranz, Cobo, Fontecha, Godino, López & Glidewell et al., 2001; Low, Moreno et al., 2001). On the other hand, in (I), O5 is the acceptor in the shortest, and presumably strongest, of the O—H···O hydrogen bonds.

Both of the water molecules in (I) act as double donors of hydrogen bonds (Table 2). Although the formation of the chain motif (Fig. 2) is not dependent upon hydrogen bonding, nonetheless the hydrogen bonds serve to link each [001] chain to four neighbouring chains, and thereby to link all the chains into a three-dimensional continuum. Water O7 at (x, y, z) is a component of the chain along (1/2, 1.0, z), and it acts as hydrogen-bond donor via H71 to N1 at (-x, 2 - y, -z) and via H72 to O5 at (-x, 2 - y, 1 - z), both of which are components of the chain along (-1/2, 1.0, z). Atom O8 at (x, y, z) is also a component of the chain along (1/2, 1.0, z) and it acts as hydrogen bond donor, via H81 to O4 at (1 - x, 1 - y, 1 - z), which is a component of the chain along (1/2, 0.0, z). Propagation by the space group of these hydrogen bonds links each [001] chain to its four immediate neighbours in the [100] and [010] directions, and hence all the [001] are linked into a single framework. The final, rather weak, hydrogen bond, from O8 at (x, y, z) to N1 at (1 - x, 2 - y, -z) falls within the reference chain along (1/2, 1.0, z). That N1 acts as a double acceptor of O—H···N hydrogen bonds (Table 2), with quasi-tetrahedral coordination (Fig. 4), is consistent with and supportive of the representation (4a).

The cell dimensions and refined coordinates indicate that the structure reported here at 150 K is the same phase as that studied earler at 293 K (Schwabenländer et al., 1998). The data set employed here is somewhat larger than that employed earlier, while in the earlier study all H parameters were refined. Consequently the data/parameter ratio here, 14.6, is c 50% higher than the 9.4 available previously.

Related literature

For related literature, see: Allen et al. (1987); Low et al. (2000); Low, Arranz, Cobo, Fontecha, Godino, López & Glidewell (2001); Low, Arranz, Cobo, Fontecha, Godino, López, Cannon, Quesada & Glidewell (2001); Low, Cannon, Quesada, Marchal, Melguizo, Nogueras, Sánchez & Glidewell (2001); Low, Moreno, Sánchez, Arranz Mascarós, Godino Salido, López Garzon, Cobo Domingo & Glidewell (2001); Schwabenländer et al. (1998).

S2. Experimental

An aqueous solution of Na₂[CO₃] (1.0 mmol in 10 cm³) was added to a suspension of (1c) (0.135 g, 0.5 mmol) in methanol (40 cm³): the mixture was heated under reflux for 1 h. The mixture was cooled to ambient temperature, and after several days, pink crystals of (I) formed.

S3. Refinement

Compound (I) crystallized in the triclinic system; space group P1 was assumed and confirmed by the analysis. H atoms were treated as riding atoms with C—H 0.98, N—H 0.88 and O—H 0.84 Å. The methyl group was modelled using six H sites, with occupancy 1/2, offset from one another by rotation of 60°.

Computing details

Data collection: Kappa-CCD Server Software (Nonius, 1997); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2001); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

Figures

	Fig. 1. The asymmetric unit of compound (I) showing the atom-labelling scheme (Author: please give probability level).
	Fig. 2. Part of the crystal structure of (I) showing formation of [001] chain containing the cations and anions only. For the sake of clarity H atoms are omitted. Atoms marked with a star (*), hash (#) or dollar sign ($) are at the symmetry positions (x, y, 1 + z), (1 - x, 2 - y, -z) and (1 - x, 2 - y, 1 - z), respectively.
	Fig. 3. Part of the crystal structure of (I) showing the coordination around the Na. Atoms marked with a star (*) or hash (#) are at the symmetry positions (x, y, -1 + z) and (1 - x, 2 - y, -z), respectively.
	Fig. 4. Part of the crystal structure of (I) showing the coordination at N1. Atoms marked with a hash (#) or ampersand (&) are at the symmetry position (1 - x, 2 - y, -z) and (-x, 2 - y, -z), respectively.

Diaqua[6-amino-3-methyl-5-nitrosopyrimidine-2,4(1H,3H)dionato]sodium

Crystal data

Na(C5H5N4O3)·2H2O	Z = 2
Mr = 228.15	F(000) = 236
Triclinic, P1	Dx = 1.680 Mg m^−3
a = 7.0529 (2) Å	Mo Kα radiation, λ = 0.71073 Å
b = 8.1852 (2) Å	Cell parameters from 1991 reflections
c = 8.7450 (6) Å	θ = 3.9–27.5°
α = 63.365 (2)°	µ = 0.19 mm^−1
β = 89.575 (2)°	T = 150 K
γ = 88.637 (3)°	Plate, pink
V = 451.14 (4) Å^3	0.20 × 0.10 × 0.02 mm

Data collection

Kappa-CCD diffractometer	1991 independent reflections
Radiation source: fine-focus sealed X-ray tube	1458 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.067
ϕ scans, and ω scans with κ offsets	θmax = 27.5°, θmin = 3.9°
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997)	h = −9→8
Tmin = 0.964, Tmax = 0.996	k = −10→10
4901 measured reflections	l = −11→11

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.049	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.136	H-atom parameters constrained
S = 0.98	w = 1/[σ^2(Fo^2) + (0.0779P)^2] where P = (Fo^2 + 2Fc^2)/3
1991 reflections	(Δ/σ)max < 0.001
136 parameters	Δρmax = 0.32 e Å^−3
0 restraints	Δρmin = −0.47 e Å^−3

Special details

Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm [Fox, G·C. & Holmes, K·C. (1966). Acta Cryst. 20, 886–891] which effectively corrects for absorption effects. High redundancy data were used in the scaling program hence the 'multi-scan' code word was used. No transmission coefficients are available from the program (only scale factors for each frame). The scale factors in the experimental table are calculated from the 'size' command in the SHELXL97 input file.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Na1	0.33332 (11)	0.85236 (10)	−0.03829 (9)	0.0208 (2)
N1	0.2136 (2)	1.1757 (2)	0.2375 (2)	0.0173 (4)
C2	0.2930 (3)	1.0124 (2)	0.2665 (2)	0.0161 (4)
O2	0.34758 (19)	0.98198 (18)	0.14710 (17)	0.0223 (3)
N3	0.3163 (2)	0.8730 (2)	0.4347 (2)	0.0168 (4)
C3	0.3853 (3)	0.6917 (3)	0.4593 (3)	0.0234 (5)
C4	0.2890 (3)	0.9018 (2)	0.5771 (2)	0.0164 (4)
O4	0.33343 (19)	0.78137 (17)	0.72124 (17)	0.0218 (3)
C5	0.2073 (3)	1.0790 (2)	0.5451 (2)	0.0159 (4)
N5	0.1774 (2)	1.1008 (2)	0.6860 (2)	0.0215 (4)
O5	0.0999 (2)	1.25185 (19)	0.66934 (18)	0.0268 (4)
C6	0.1694 (3)	1.2109 (2)	0.3691 (2)	0.0156 (4)
N6	0.0943 (2)	1.3722 (2)	0.3366 (2)	0.0223 (4)
O7	0.03812 (19)	0.72028 (17)	0.05121 (17)	0.0220 (3)
O8	0.5538 (2)	0.61206 (19)	0.0984 (2)	0.0378 (4)
H3A	0.4198	0.6974	0.3483	0.035*	0.50
H3B	0.2853	0.6025	0.5114	0.035*	0.50
H3C	0.4969	0.6546	0.5344	0.035*	0.50
H3D	0.3815	0.6056	0.5811	0.035*	0.50
H3E	0.5160	0.7005	0.4180	0.035*	0.50
H3F	0.3044	0.6484	0.3950	0.035*	0.50
H6A	0.0742	1.4542	0.2302	0.027*
H6B	0.0642	1.3979	0.4215	0.027*
H71	−0.0375	0.7447	−0.0303	0.033*
H72	−0.0203	0.7550	0.1160	0.033*
H81	0.5625	0.4975	0.1476	0.057*
H82	0.6407	0.6478	0.0254	0.057*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Na1	0.0288 (5)	0.0220 (4)	0.0114 (4)	0.0011 (3)	−0.0004 (3)	−0.0073 (3)
N1	0.0236 (9)	0.0184 (8)	0.0095 (8)	0.0021 (7)	−0.0006 (6)	−0.0059 (6)
C2	0.0188 (9)	0.0193 (9)	0.0098 (9)	−0.0009 (7)	−0.0003 (7)	−0.0061 (7)
O2	0.0316 (8)	0.0243 (7)	0.0142 (8)	0.0016 (6)	0.0026 (6)	−0.0116 (6)
N3	0.0222 (8)	0.0158 (8)	0.0124 (9)	0.0014 (6)	−0.0003 (6)	−0.0065 (6)
C3	0.0324 (11)	0.0169 (10)	0.0222 (11)	0.0024 (8)	0.0001 (9)	−0.0101 (8)
C4	0.0159 (9)	0.0195 (9)	0.0126 (9)	−0.0033 (7)	−0.0002 (7)	−0.0060 (7)
O4	0.0310 (8)	0.0196 (7)	0.0116 (7)	0.0024 (6)	−0.0035 (6)	−0.0040 (6)
C5	0.0178 (9)	0.0185 (9)	0.0120 (10)	−0.0009 (7)	0.0013 (7)	−0.0074 (8)
N5	0.0247 (9)	0.0226 (9)	0.0198 (9)	−0.0026 (7)	0.0026 (7)	−0.0117 (7)
O5	0.0367 (8)	0.0248 (8)	0.0198 (8)	0.0069 (6)	0.0009 (6)	−0.0112 (6)
C6	0.0168 (9)	0.0157 (9)	0.0138 (10)	0.0001 (7)	−0.0001 (7)	−0.0064 (8)
N6	0.0317 (9)	0.0201 (8)	0.0147 (9)	0.0050 (7)	0.0000 (7)	−0.0077 (7)
O7	0.0264 (7)	0.0269 (7)	0.0125 (7)	0.0040 (6)	−0.0006 (6)	−0.0089 (6)
O8	0.0395 (9)	0.0242 (8)	0.0340 (10)	0.0044 (7)	−0.0012 (7)	0.0006 (7)

Geometric parameters (Å, º)

Na1—O2	2.3052 (15)	C5—N5	1.336 (3)
Na1—O7	2.3325 (15)	N5—O5	1.287 (2)
Na1—O8	2.3431 (16)	C6—N6	1.318 (2)
N1—C2	1.352 (2)	C3—H3A	0.9800
C2—N3	1.408 (2)	C3—H3B	0.9800
N3—C4	1.378 (2)	C3—H3C	0.9800
C4—C5	1.454 (3)	C3—H3D	0.9800
C5—C6	1.452 (3)	C3—H3E	0.9800
C6—N1	1.339 (2)	C3—H3F	0.9800
Na1—O4^i	2.4198 (15)	N6—H6A	0.8800
Na1—N5^i	2.5872 (18)	N6—H6B	0.8800
Na1—O2^ii	2.6011 (16)	O7—H71	0.840
C2—O2	1.234 (2)	O7—H72	0.841
N3—C3	1.472 (2)	O8—H81	0.839
C4—O4	1.240 (2)	O8—H82	0.839
O2—Na1—O7	96.20 (6)	H3B—C3—H3C	109.5
O7—Na1—O4^i	91.45 (5)	N3—C3—H3D	109.5
O4^i—Na1—O2^ii	88.93 (5)	N3—C3—H3E	109.5
O2^ii—Na1—O2	82.90 (5)	H3D—C3—H3E	109.5
O8—Na1—O2	98.51 (6)	N3—C3—H3F	109.5
O8—Na1—O7	104.82 (6)	H3D—C3—H3F	109.5
O8—Na1—O4^i	88.71 (6)	H3E—C3—H3F	109.5
O8—Na1—O2^ii	78.50 (5)	O4—C4—N3	120.52 (18)
N5^i—Na1—O2	105.25 (6)	O4—C4—C5	123.74 (18)
N5^i—Na1—O7	89.58 (5)	N3—C4—C5	115.74 (16)
N5^i—Na1—O4^i	65.15 (5)	C4—O4—Na1^iii	119.72 (12)
N5^i—Na1—O2^ii	87.58 (5)	N5—C5—C6	127.50 (17)
O2—Na1—O4^i	167.76 (6)	N5—C5—C4	114.32 (16)
O7—Na1—O2^ii	176.67 (5)	C6—C5—C4	118.17 (17)
O8—Na1—N5^i	150.70 (7)	O5—N5—C5	118.24 (16)
Na1—O2—Na1^ii	97.10 (5)	O5—N5—Na1^iii	125.85 (12)
C6—N1—C2	120.06 (16)	C5—N5—Na1^iii	115.11 (12)
O2—C2—N1	121.06 (16)	N6—C6—N1	118.68 (17)
O2—C2—N3	118.45 (17)	N6—C6—C5	119.40 (17)
N1—C2—N3	120.48 (17)	N1—C6—C5	121.90 (16)
C2—O2—Na1	155.22 (12)	C6—N6—H6A	120.0
C2—O2—Na1^ii	107.64 (11)	C6—N6—H6B	120.0
C4—N3—C2	122.94 (16)	H6A—N6—H6B	120.0
C4—N3—C3	118.50 (16)	Na1—O7—H71	112.9
C2—N3—C3	118.42 (16)	Na1—O7—H72	114.2
N3—C3—H3A	109.5	H71—O7—H72	104.2
N3—C3—H3B	109.5	Na1—O8—H81	141.6
H3A—C3—H3B	109.5	Na1—O8—H82	99.2
N3—C3—H3C	109.5	H81—O8—H82	106.4
H3A—C3—H3C	109.5
C4—C5—N5—O5	−177.88 (17)	N1—C2—O2—Na1	−106.8 (3)
C6—C5—N5—O5	2.9 (3)	N1—C2—O2—Na1^ii	76.4 (2)
C5—C4—O4—Na1^iii	−10.0 (3)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N6—H6B···O5	0.88	1.96	2.621 (3)	130
O7—H71···N1^iv	0.84	2.05	2.884 (2)	176
O7—H72···O5^v	0.84	1.93	2.725 (2)	157
O8—H81···O4^vi	0.84	2.16	2.972 (2)	164
O8—H82···N1^ii	0.84	2.34	3.135 (2)	158

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