Nonmerohedrally twinned 6-amino-3-methyl­uracil-5-carbaldehyde: a hydrogen-bonded ribbon containing four types of ring

In the title compound [systematic name: 6-amino-5-formyl-3-methyl­pyrimidine-2,4(1H,3H)-dione], C₆H₇N₃O₃, the intra­molecular dimensions provide evidence for some polarization of the electronic structure. There is an intra­molecular N-H...O hydrogen bond; this and a combination of three inter­molecular N-H...O hydrogen bonds generate an almost planar ribbon containing S(6), R₂²(4), R₂¹(6) and R₄⁴(16) rings. These ribbons are linked into sheets by a dipolar carbonyl-carbonyl inter­action. The structure was refined as a nonmero­hedral twin, with twin fractions 0.7924 (1) and 0.2076 (10).

S1. Comment

The title compound, (I), has been prepared as an intermediate for the preparation of fused pyrimidine derivatives. Its synthesis utilized the Vilsmeier–Haack formylation procedure applied to 6-amino-3-methyl-2-(methylsulfanyl)pyrimidin-4(3H)-one in which the work-up using aqueous sodium hydroxide effected the hydrolysis of the methylsulfanyl group at C2, so providing the title compound in a single process. Compound (I) is closely related to the 1,3-dimethyl analogue (II), which, unlike (I), crystallizes as a monohydrate. The structure of (II) was first determined some years ago, using diffraction data collected at ambient temperature (Low et al., 1992); more recently, the structure of (II) was re-examined using data collected at 120 K (de la Torre et al., 2007), and the improved precision afforded by the low-temperature data enabled a detailed examination of the intramolecular dimensions, which were interpreted in terms of a polarized electronic structure. A combination of three N—H···O hydrogen bonds and two O—H···O hydrogen bonds links the molecular components of the monohydrate of (II) into two linked and interwoven three-dimensional frameworks.

Prompted by the interesting molecular and supramolecular structures found in (II), we have now taken the opportunity to make a detailed comparison with the monomethyl analogue (I) (Fig. 1). Compound (I) crystallizes in solvent-free form in a unit cell whose dimensions bear no resemblance to those of the unit cell of (II). However, a similar pattern of bond distances is found (Table 1). In particular, the C5—C51 and C6—N6 bonds are both short for their types (Allen et al., 1987), while C51—O5 is long for its type; in addition, the C4—O4 bond is significantly longer than C2—O2. These dimensions (Table 1) provide evidence for the importance of polarized forms (Ia) and (Ib) as contributors to the overall electronic structure. Despite the high degree of substitution of the rings in both (I) and (II), these rings are planar, although puckered pyrimidine rings are quite frequently observed in the presence of contiguous substituents (Melguizo et al., 2003; Quesada et al., 2003, 2004; Low et al., 2007; Trilleras et al., 2007; Cobo et al., 2008). In (I), the maximum deviation of any ring atom from the mean plane is that of atom N3, 0.013 (2) Å. In these respects, therefore, (I) and (II) show considerable similarity. They differ, however, in their patterns of hydrogen bonding, dominated firstly by the presence of a water molecule in (II), which acts as a single acceptor and as a double donor of hydrogen bonds, and secondly by the presence in (I) of an additional N—H bond at N1.

Within the molecule of (I), the N—H···O hydrogen bond (Table 2) generates an S(6) (Bernstein et al., 1995) motif; such an intramolecular motif is highly characteristic of both 6-amino-5-formyl pyrimidines and 6-amino-5-nitrosopyrimidines (Low et al., 1997, 1999, 2000; Quesada et al., 2002, 2004; Melguizo et al., 2003; Cobo et al., 2008), and it may well be a controlling factor in determining in (I) the near coplanarity of the formyl group with the uracil ring (Table 1): the formyl atom O5 deviates from the mean plane of the ring by only 0.008 (2) Å. This intramolecular interaction is, in fact, the shorter component of the three-centre N—H···(O)₂ system, the longer component of which links pairs of molecules into a centrosymmetric dimer, characterized by an R₂²(12) motif; this motif is itself partitioned into a central R₂²(4) ring flanked by two symmetry-related S(6) rings. Between the dimers related by translation along [100], atoms N1 and N6 both act as hydrogen-bond donors to the amidic carbonyl atom O4 in the adjacent dimer, so forming an R₂¹(6) ring. These interactions thus serve to link the centrosymmetric dimers into a ribbon along [100], in which R₂²(4) rings centred at (n + 1/2, 1/2, 1/2), where n represents an integer, alternate with R₄⁴(16) rings centred at (n, 1/2, 1/2) (Fig. 2). Although the centrosymmetric dimer motif containing an R₂²(4) ring flanked by two S(6) rings can also be identified within the three-dimensional structure of (II), the subsequent linking of these dimers is entirely different in (I) and (II), leading to hydrogen-bonded structures which are, respectively one-dimensional and three-dimensional. It is of interest to note that, in (I), the hydrogen-bond formation involves the acceptor atoms O4 and O5, which carry enhanced negative changes owing to the charge polarization, but it does not involve atom O2, which is not involved in the polarization. The hydrogen bonds may thus all be regarded as charge-assisted hydrogen bonds (Gilli et al., 1993).

With the exception of the H atoms in the methyl group, the ribbon is almost completely planar, providing a very compact structure. There are two hydrogen-bonded ribbons running through each unit cell in (I); although there are no hydrogen bonds between adjacent chains, the chains are weakly linked into sheets by a dipolar carbonyl–carbonyl interaction. The carbonyl atom O2 in the molecule at (x, y, z) makes a short contact with the carbonyl atom C2 in the molecule at (1 - x, 1/2 + y, 3/2 - z), with dimensions O2···C2ⁱⁱⁱ = 2.8978 (17) Å, C2···C2ⁱⁱⁱ = 3.1791 (13) Å and C2—O2···C2ⁱⁱⁱ = 142.14 (9)° [symmetry code: (iii) -x + 1, y + 1/2, -z + 3/2], so conforming rather closely to the perpendicular, type I carbonyl–carbonyl interaction (Allen et al., 1998). The two molecules concerned are components of the hydrogen-bonded chains along (x, 1/2, 1/2) and (x, 1, 1), respectively; hence propagation by the space-group symmetry of the carbonyl–carbonyl interaction links hydrogen-bonded ribbons into a sheet parallel to (011).

Related literature

For related literature, see: Allen et al. (1987, 1998); Bernstein et al. (1995); Cherdantseva et al. (1983); Cobo et al. (2008); Gilli et al. (1993); Low et al. (1992, 1997, 1999, 2000, 2007); Melguizo et al. (2003); Quesada et al. (2002, 2003, 2004); Sheldrick (2008).

S2. Experimental

To a suspension of 6-amino-3-methyl-2-(methylsulfanyl)pyrimidin-4(3H)-one (10 mmol) in dimethylformamide (30 ml) cooled in an ice–water bath, phosphoryl chloride (12 mmol) was added dropwise: the mixture was then stirred at room temperature for 1 h. The reaction mixture was poured onto crushed ice (400 ml), after which the whole was permitted to warm to ambient temperature; the mixture was then heated to boiling and sodium hydroxide pellets were added until the solution was basic. The resulting mixture was allowed to cool to ambient temperature, and the white solid thus formed was collected by filtration, washed with ethanol, dried and recrystallized from ethanol [yield 50%; decomposed without melting at 573 K; literature m.p. > 573 K (Cherdantseva et al., 1983]. Crystals suitable for single-crystal X-ray diffraction were grown from by slow evaporation of a solution in dimethylsulfoxide.

S3. Refinement

All H atoms were located from difference maps and then treated as riding atoms with C—H distances of 0.95 or 0.98 Å and N—H distances of 0.88 Å, and with U_iso(H) = kU_eq(carrier) (k = 1.2 or 1.5). Conventional refinement then converged to R of 0.165 for 1513 reflections (1284 labelled observed) with R_int = 0.057, but analysis with PLATON/TwinRotMat (Spek, 2009) of this solution indicated non-merohedral twinning about a twofold rotation axis (201) (which makes an angle of 0.26° with [100]). The TwinRotMat routine was used to prepare a modified hkl file for use with the HKLF5 option in SHELXL97 (Sheldrick, 2008). The resulting twin fractions were 0.2076 (10) and 0.7924 (10).

Computing details

Data collection: COLLECT (Hooft, 1999); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures

	Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. A stereoview of part of the crystal structure of (I), showing the formation of a hydrogen-bonded ribbon containing four types of ring and running parallel to [100].

6-amino-5-formyl-3-methylpyrimidine-2,4(1H,3H)-dione

Crystal data

C6H7N3O3	F(000) = 352
Mr = 169.14	Dx = 1.707 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1513 reflections
a = 6.6749 (4) Å	θ = 3.4–27.5°
b = 5.0712 (5) Å	µ = 0.14 mm^−1
c = 19.7422 (4) Å	T = 120 K
β = 99.996 (2)°	Block, colourless
V = 658.12 (8) Å^3	0.29 × 0.23 × 0.12 mm
Z = 4

Data collection

Bruker–Nonius KappaCCD diffractometer	9103 independent reflections
Radiation source: Bruker-Nonius FR591 rotating anode	7474 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.000
Detector resolution: 9.091 pixels mm^-1	θmax = 27.5°, θmin = 3.4°
ϕ & ω scans	h = −8→8
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	k = −6→6
Tmin = 0.972, Tmax = 0.983	l = −25→25
9103 measured reflections

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)] = 0.058	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.152	H-atom parameters constrained
S = 1.08	w = 1/[σ^2(Fo^2) + (0.0619P)^2 + 0.3795P] where P = (Fo^2 + 2Fc^2)/3
9103 reflections	(Δ/σ)max = 0.001
111 parameters	Δρmax = 0.30 e Å^−3
0 restraints	Δρmin = −0.32 e Å^−3

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

	x	y	z	Uiso*/Ueq
N1	0.57570 (16)	1.1821 (2)	0.63728 (5)	0.0193 (3)
H1	0.7075	1.2076	0.6407	0.023*
C2	0.47247 (19)	1.3483 (3)	0.67337 (7)	0.0185 (3)
N3	0.26579 (15)	1.3079 (2)	0.66410 (5)	0.0178 (2)
C4	0.16639 (19)	1.1091 (2)	0.62456 (7)	0.0182 (3)
C5	0.28259 (19)	0.9429 (3)	0.58818 (6)	0.0175 (3)
C6	0.49261 (18)	0.9817 (2)	0.59668 (6)	0.0177 (3)
O2	0.56033 (14)	1.51777 (18)	0.70932 (5)	0.0230 (2)
C31	0.1492 (2)	1.4724 (3)	0.70406 (7)	0.0225 (3)
H31A	0.1210	1.3727	0.7439	0.034*
H31B	0.0206	1.5240	0.6752	0.034*
H31C	0.2278	1.6306	0.7199	0.034*
O4	−0.01878 (13)	1.08385 (19)	0.62243 (5)	0.0231 (2)
C51	0.1867 (2)	0.7404 (3)	0.54487 (7)	0.0212 (3)
H51	0.0430	0.7265	0.5402	0.025*
O5	0.27217 (14)	0.58170 (18)	0.51294 (4)	0.0241 (2)
N6	0.61547 (16)	0.8349 (2)	0.56832 (6)	0.0214 (3)
H61	0.7469	0.8681	0.5759	0.026*
H62	0.5670	0.7026	0.5416	0.026*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0125 (5)	0.0261 (6)	0.0198 (6)	−0.0026 (4)	0.0047 (4)	−0.0025 (4)
C2	0.0170 (6)	0.0221 (7)	0.0170 (7)	0.0003 (5)	0.0045 (5)	0.0019 (5)
N3	0.0162 (5)	0.0226 (6)	0.0158 (5)	0.0000 (4)	0.0056 (4)	−0.0015 (4)
C4	0.0165 (7)	0.0216 (7)	0.0170 (6)	0.0001 (5)	0.0042 (5)	0.0027 (5)
C5	0.0141 (6)	0.0213 (7)	0.0172 (6)	−0.0002 (5)	0.0031 (5)	0.0006 (5)
C6	0.0172 (7)	0.0212 (6)	0.0155 (6)	0.0007 (5)	0.0050 (5)	0.0041 (5)
O2	0.0200 (5)	0.0254 (5)	0.0238 (5)	−0.0020 (4)	0.0041 (4)	−0.0045 (4)
C31	0.0194 (7)	0.0248 (7)	0.0245 (7)	0.0011 (5)	0.0072 (6)	−0.0056 (6)
O4	0.0136 (5)	0.0297 (5)	0.0271 (5)	−0.0006 (4)	0.0070 (4)	−0.0040 (4)
C51	0.0147 (7)	0.0276 (8)	0.0213 (7)	−0.0012 (6)	0.0034 (5)	0.0005 (6)
O5	0.0224 (5)	0.0261 (5)	0.0249 (5)	0.0001 (4)	0.0073 (4)	−0.0066 (4)
N6	0.0143 (6)	0.0273 (6)	0.0232 (6)	−0.0002 (4)	0.0052 (5)	−0.0036 (5)

Geometric parameters (Å, º)

N1—C2	1.3650 (16)	C51—O5	1.2229 (15)
C2—N3	1.3753 (16)	C6—N6	1.3037 (16)
N3—C4	1.3733 (17)	N1—H1	0.8800
C4—C5	1.4215 (18)	C31—H31A	0.9800
C5—C6	1.3966 (18)	C31—H31B	0.9800
C6—N1	1.3522 (16)	C31—H31C	0.9800
C2—O2	1.2006 (15)	C51—H51	0.9500
N3—C31	1.4619 (16)	N6—H61	0.8800
C4—O4	1.2360 (15)	N6—H62	0.8800
C5—C51	1.4163 (18)
C6—N1—C2	125.53 (11)	N6—C6—N1	117.38 (11)
C6—N1—H1	117.2	N6—C6—C5	124.13 (12)
C2—N1—H1	117.2	N1—C6—C5	118.49 (11)
O2—C2—N1	120.76 (12)	N3—C31—H31A	109.5
O2—C2—N3	124.14 (12)	N3—C31—H31B	109.5
N1—C2—N3	115.09 (11)	H31A—C31—H31B	109.5
C4—N3—C2	124.04 (11)	N3—C31—H31C	109.5
C4—N3—C31	118.40 (10)	H31A—C31—H31C	109.5
C2—N3—C31	117.31 (11)	H31B—C31—H31C	109.5
O4—C4—N3	118.48 (12)	O5—C51—C5	125.86 (13)
O4—C4—C5	123.48 (12)	O5—C51—H51	117.1
N3—C4—C5	118.04 (11)	C5—C51—H51	117.1
C6—C5—C51	120.93 (12)	C6—N6—H61	120.0
C6—C5—C4	118.69 (11)	C6—N6—H62	120.0
C51—C5—C4	120.38 (12)	H61—N6—H62	120.0
C6—N1—C2—O2	178.42 (12)	N3—C4—C5—C6	2.82 (17)
C6—N1—C2—N3	−2.61 (18)	O4—C4—C5—C51	2.07 (19)
O2—C2—N3—C4	−177.99 (12)	N3—C4—C5—C51	−177.92 (12)
N1—C2—N3—C4	3.08 (18)	C2—N1—C6—N6	−177.03 (12)
O2—C2—N3—C31	−3.87 (19)	C2—N1—C6—C5	2.39 (19)
N1—C2—N3—C31	177.19 (11)	C51—C5—C6—N6	−2.2 (2)
C2—N3—C4—O4	176.70 (12)	C4—C5—C6—N6	177.01 (12)
C31—N3—C4—O4	2.65 (18)	C51—C5—C6—N1	178.37 (11)
C2—N3—C4—C5	−3.31 (18)	C4—C5—C6—N1	−2.37 (18)
C31—N3—C4—C5	−177.36 (12)	C4—C5—C51—O5	−177.67 (13)
O4—C4—C5—C6	−177.19 (12)	C6—C5—C51—O5	1.6 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O4^i	0.88	2.02	2.8172 (14)	150
N6—H61···O4^i	0.88	2.00	2.7910 (14)	149
N6—H62···O5	0.88	2.05	2.6880 (14)	129
N6—H62···O5^ii	0.88	2.19	2.8314 (14)	130

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