6-Amino-3-methyl-5-nitro­so­pyrimi­dine-2,4(1H,3H)-dione forms a three-dimensional hydrogen-bonded framework structure

Molecules of the title compound, C₅H₆N₄O₃, are linked into a single three-dimensional framework by a two-centre N-H...O hydrogen bond [H...O = 1.92 Å, N...O = 2.785 (2) Å and N-H...O = 168°], a two-centre N-H...H hydrogen bond [H...N = 2.19 Å, N...N = 3.017 (2) Å and N-H...N = 157°] and the intermolecular component of an effectively planar three-centre N-H...(O)₂ hydrogen bond [H...O = 2.03 and 2.31 Å, N...O = 2.645 (2) and 2.957 (2) Å, N-H...O = 126 and 130°, and O...H...O = 101°].

S1. Comment

We have recently reported (Cuesta et al., 2001; Low et al., 2003; López Garzón et al., 2003) on the structures of the hydrated sodium, strontium and barium complexes of the 6-amino-3-methyl-5-nitrosopyrimidine-2,4(1H,3H)-dionate anion, derived from the neutral pyrimidine (I), and here we report the molecular and supramolecular structures of neutral (I) itself.

Within the molecule of (I) (Fig. 1), the C5–C6 bond distance (Table 1) is much longer than the mean value (1.330 Å; Allen et al., 1987) for a double bond between two three-connected C atoms, whereas the C4—C5 distance does not differ significantly from the mean value (1.455 Å) for a single bond between a pair of three connected C atoms in a conjugated system. At the same time the C6—N6 distance is significantly smaller than the mean value (1.355 Å) for a C_aryl—NH₂ distance involving a planar N atom, while the C5—N5 and N5—O5 distances differ by only ca 0.08 Å. The remaining distances show no unexpected values. Hence, it can be concluded that the polarized form, (Ia), is a significant contributor to the overall molecular–electronic structure, alongside the classically localized form, (I).

The molecules exhibit the usual intramolecular N—H···O hydrogen bonding, with nitroso atom O5 as the acceptor (Table 2) and, in addition, there are three intermolecular hydrogen bonds, of both N—H···O and N—H···N types, which link the molecules into layers. Amino atom N6 in the molecule at (x, y, z) acts as hydrogen-bond donor, via H6A, to nitroso atom N5 in the molecule at (x, 0.5 − y, 0.5 + z), while amino atom N6 at (x, 0.5 − y, 0.5 + z) in turn acts as donor to atom N5 at (x, y, 1 + z), so forming a zigzag C(5) chain (Bernstein et al., 1995) running parallel to the [001] direction and generated by the c-glide plane at y = 0.25. Atom N6 also utilizes atom H6B to form an effectively planar three-centre N—H···(O)₂ hydrogen bond, in which the two acceptors are nitroso atom O5 at (x, y, z), so forming an S(6) motif, and amide atom O4 in the molecule at (1 + x, 0.5 − y, 0.5 + z). This latter interaction gives rise to a zigzag C(6) chain running parallel to the [201] direction and generated by the same c-glide plane at y = 0.25. The combination of the [001] and [201] chains generates a sheet parallel to (010) in the form of a (4,4) net (Batten & Robson, 1998) containing equal numbers of S(6) and R⁵₄(16) rings (Fig. 2). Two sheets of this type pass through each unit cell, in the domains −0.03 < y < 0.53 and 0.47 < y < 1.03, and one further hydrogen bond serves to link the (010) sheets.

Atom N1 in the molecule at (x, y, z) acts as hydrogen-bond donor to atom O4 in the molecule at (1 − x, 1 − y, 1 − z), so forming an R²₂(8) ring centred at (1/2, 1/2, 1/2) (Fig. 3). The molecules at (x, y, z) and (1 − x, 1 − y, 1 − z) are components of sheets lying in the −0.03 < y < 0.53 and 0.47 < y < 1.03 domains, respectively, and propagation of this R²₂(8) motif by the space group links all the (010) sheets into a single three-dimensional framework. In this manner, all potential donors and all potential acceptors of hard hydrogen bonds are involved in the overall molecular aggregation.

The supramolecular aggregation of (I) can be contrasted with that of the dimethyl analogue, (II), which crystallizes as a monohydrate (Low et al., 1992). In this hydrate, the atoms all lie on mirror planes in space group Pnam (Pnma; No. 62), and the molecules are linked into sheets by a combination of O—H···O, O—H···N and N—H···O hydrogen bonds (Fig. 4).

S2. Experimental

An aqueous solution of potassium 6-amino-3-methyl-5-nitrosopyrimidine-2,4(1H,3H)-dionate was neutralized using excess potassium aluminium sulfate dodecahydrate. The gelatinous precipitate that formed initially was filtered off, and the resulting solution was set aside to crystallize, providing analytically pure crystals of (I), which were washed with cold water and then with ethanol. Analysis found: C 34.9, H 3.6, N 32.4%; C₅H₆N₄O₃ requires: C 35.2, H 3.5, N 32.9%.

S3. Refinement

Crystals of (I) are monoclinic and the space group P2₁/c was assigned uniquely from the systematic absences. All H atoms were treated as riding atoms, with C—H distances of 0.98 Å and N—H distances of 0.88 Å.

Computing details

Data collection: KappaCCD 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, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

Figures

	Fig. 1. The molecule of (I), showing the atom-labelling scheme. Displacement ellipsoids have been drawn at the 30% probability level.
	Fig. 2. A stereoview of part of the crystal structure of (I), showing the combination of [001] and [201] chains to form a (010) sheet. For the sake of clarity, H atoms bonded to C atoms have been omitted.
	Fig. 3. Part of the crystal structure of (I), showing the formation of the centrosymmetric R^22(8) motif that links the (010) sheets. For the sake of clarity, the unit-cell box and H atoms bonded to C atoms have been omitted.
	Fig. 4. Part of the crystal structure of (II), showing the formation of a (001) sheet. The original cell setting and atoms labels (Low et al., 1992) have been employed. For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*), hash (#), dollar sign ($) or ampersand (&) are at the symmetry positions (0.5 + x, −0.5 − y, 1/4), (0.5 + x, 0.5 − y, 1/4), (−0.5 + x, 0.5 − y, 1/4) and (−0.5 + x, −0.5 − y, 1/4), respectively.

6-Amino-3-methyl-5-nitrosopyrimidine-2,4(1H,3H)-dione

Crystal data

C5H6N4O3	F(000) = 352
Mr = 170.14	Dx = 1.769 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1399 reflections
a = 4.9634 (3) Å	θ = 3.5–27.4°
b = 11.1829 (9) Å	µ = 0.15 mm^−1
c = 11.7960 (8) Å	T = 120 K
β = 102.665 (4)°	Prism, pink
V = 638.81 (8) Å^3	0.15 × 0.10 × 0.06 mm
Z = 4

Data collection

Nonius KappaCCD diffractometer	1399 independent reflections
Radiation source: rotating anode	1106 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.040
ϕ scans, and ω scans with κ offsets	θmax = 27.4°, θmin = 3.5°
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997)	h = −5→6
Tmin = 0.972, Tmax = 0.991	k = −14→13
4417 measured reflections	l = −15→13

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)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.118	H-atom parameters constrained
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0702P)^2 + 0.0762P] where P = (Fo^2 + 2Fc^2)/3
1399 reflections	(Δ/σ)max < 0.001
110 parameters	Δρmax = 0.27 e Å^−3
0 restraints	Δρmin = −0.37 e Å^−3

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

	x	y	z	Uiso*/Ueq
N1	0.6958 (3)	0.40093 (12)	0.41374 (12)	0.0169 (3)
C2	0.4930 (3)	0.45663 (15)	0.33287 (14)	0.0156 (4)
O2	0.3284 (2)	0.52409 (11)	0.36355 (10)	0.0208 (3)
N3	0.4814 (3)	0.43161 (12)	0.21777 (11)	0.0148 (3)
C31	0.2701 (3)	0.49157 (15)	0.12970 (14)	0.0182 (4)
C4	0.6580 (3)	0.35010 (14)	0.17997 (14)	0.0151 (4)
O4	0.6195 (2)	0.32622 (11)	0.07656 (10)	0.0194 (3)
C5	0.8787 (3)	0.29996 (14)	0.26872 (14)	0.0154 (4)
N5	1.0602 (3)	0.23116 (12)	0.22777 (12)	0.0169 (3)
O5	1.2584 (2)	0.18399 (11)	0.30075 (11)	0.0218 (3)
C6	0.8911 (3)	0.32605 (14)	0.38832 (14)	0.0148 (4)
N6	1.0775 (3)	0.28214 (13)	0.47405 (12)	0.0189 (3)
H1	0.6999	0.4147	0.4876	0.020*
H31A	0.1662	0.5475	0.1678	0.027*
H31B	0.1439	0.4318	0.0864	0.027*
H31C	0.3592	0.5355	0.0760	0.027*
H6A	1.0750	0.3011	0.5462	0.023*
H6B	1.2055	0.2336	0.4596	0.023*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0193 (8)	0.0202 (7)	0.0113 (7)	0.0027 (6)	0.0032 (6)	−0.0008 (5)
C2	0.0172 (8)	0.0147 (8)	0.0152 (8)	−0.0024 (6)	0.0042 (7)	0.0005 (6)
O2	0.0229 (7)	0.0220 (7)	0.0176 (6)	0.0059 (5)	0.0045 (5)	−0.0002 (5)
N3	0.0168 (7)	0.0145 (7)	0.0125 (7)	0.0002 (5)	0.0019 (6)	0.0009 (5)
C31	0.0215 (9)	0.0176 (9)	0.0146 (8)	0.0031 (6)	0.0018 (7)	0.0018 (6)
C4	0.0158 (8)	0.0150 (8)	0.0150 (8)	−0.0041 (6)	0.0047 (7)	−0.0004 (6)
O4	0.0211 (7)	0.0237 (7)	0.0132 (6)	−0.0011 (5)	0.0032 (5)	−0.0024 (5)
C5	0.0174 (9)	0.0142 (8)	0.0148 (8)	−0.0024 (6)	0.0036 (7)	0.0008 (6)
N5	0.0173 (7)	0.0153 (7)	0.0181 (7)	−0.0008 (5)	0.0041 (6)	0.0022 (5)
O5	0.0196 (7)	0.0231 (7)	0.0218 (6)	0.0032 (5)	0.0029 (5)	0.0029 (5)
C6	0.0144 (8)	0.0138 (8)	0.0163 (8)	−0.0024 (6)	0.0034 (6)	0.0016 (6)
N6	0.0198 (8)	0.0222 (8)	0.0144 (7)	0.0024 (6)	0.0031 (6)	0.0015 (6)

Geometric parameters (Å, º)

N1—C2	1.375 (2)	C5—N5	1.352 (2)
C2—N3	1.375 (2)	N5—O5	1.271 (2)
N3—C4	1.403 (2)	C6—N6	1.308 (2)
C4—C5	1.452 (2)	N1—H1	0.88
C5—C6	1.429 (2)	C31—H31A	0.98
C6—N1	1.363 (2)	C31—H31B	0.98
C2—O2	1.224 (2)	C31—H31C	0.98
N3—C31	1.466 (2)	N6—H6A	0.88
C4—O4	1.222 (2)	N6—H6B	0.88
C6—N1—C2	124.99 (14)	H31B—C31—H31C	109.5
C6—N1—H1	117.5	O4—C4—N3	119.16 (15)
C2—N1—H1	117.5	O4—C4—C5	124.29 (15)
O2—C2—N1	120.59 (15)	N3—C4—C5	116.55 (14)
O2—C2—N3	122.10 (15)	N5—C5—C6	125.56 (15)
N1—C2—N3	117.30 (14)	N5—C5—C4	114.75 (14)
C2—N3—C4	123.51 (14)	C6—C5—C4	119.69 (15)
C2—N3—C31	118.37 (14)	O5—N5—C5	118.13 (13)
C4—N3—C31	118.12 (13)	N6—C6—N1	118.51 (15)
N3—C31—H31A	109.5	N6—C6—C5	123.84 (15)
N3—C31—H31B	109.5	N1—C6—C5	117.65 (15)
H31A—C31—H31B	109.5	C6—N6—H6A	120.0
N3—C31—H31C	109.5	C6—N6—H6B	120.0
H31A—C31—H31C	109.5	H6A—N6—H6B	120.0
C6—N1—C2—O2	−178.84 (15)	N3—C4—C5—N5	−173.81 (13)
C6—N1—C2—N3	2.2 (2)	O4—C4—C5—C6	−174.67 (15)
O2—C2—N3—C4	−176.66 (14)	N3—C4—C5—C6	5.7 (2)
N1—C2—N3—C4	2.2 (2)	C6—C5—N5—O5	0.7 (2)
O2—C2—N3—C31	2.2 (2)	C4—C5—N5—O5	−179.76 (13)
N1—C2—N3—C31	−178.89 (13)	C2—N1—C6—N6	177.85 (14)
C2—N3—C4—O4	174.33 (14)	C2—N1—C6—C5	−2.3 (2)
C31—N3—C4—O4	−4.5 (2)	N5—C5—C6—N6	−2.5 (3)
C2—N3—C4—C5	−6.0 (2)	C4—C5—C6—N6	177.97 (15)
C31—N3—C4—C5	175.08 (13)	N5—C5—C6—N1	177.64 (14)
O4—C4—C5—N5	5.8 (2)	C4—C5—C6—N1	−1.8 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2^i	0.88	1.92	2.785 (2)	168
N6—H6A···N5^ii	0.88	2.19	3.017 (2)	157
N6—H6B···O5	0.88	2.03	2.645 (2)	126
N6—H6B···O4^iii	0.88	2.31	2.957 (2)	130

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