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The title compound [systematic name: 6-amino-5-formyl-1,3-dimethylpyrimidine-2,4(1H,3H)-dione monohydrate], C7H9N3O3·H2O, has been reexamined at 120 K. The improved precision of the intra­molecular dimensions provides evidence for a polarized mol­ecular–electronic structure, and the mol­ecular components are linked by one N—H...O and two O—H...O hydrogen bonds into two inter­woven three-dimensional frameworks, which are weakly linked by the longer component of a three-centre N—H...(O)2 hydrogen bond.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270107044563/ln3062sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270107044563/ln3062Isup2.hkl
Contains datablock I

CCDC reference: 669183

Comment top

Recent studies (Low et al., 2000; Quesada et al., 2002; Melguizo et al., 2003) of amino-substituted 5-nitrosopyrimidines have provided compelling evidence for the development of extensively-polarized molecular-electronic structures, in which forms such as (A) (Low et al., 2000) and (B) (Quesada et al., 2002; Melguizo et al., 2003) (see scheme) make important contributions to the overall molecular-electronic structures, normally represented by forms such as (C) and (D). These polarized structures in turn lead to the formation of supramolecular networks built from charge-assisted (Gilli et al., 1993) hydrogen bonds. With these recent findings in mind, we have now reinvestigated the structure of the title compound, (I) (Fig. 1). The structure of (I) was reported some years ago from diffraction data collected at ambient temperature (Low et al., 1992), but the precision of that determination does not permit a detailed analysis of the intramolecular dimensions; nor did the earlier report contain any discussion of the supramolecular aggregation. We have now redetermined the structure of (I) using diffraction data collected at 120 K and we present here an analysis of the intramolecular geometry and a description of the supramolecular aggregation. The unit-cell dimensions, space group and atomic coordinates show that no phase transition occurs between ambient temperature and 120 K.

The organic component of compound (I) is effectively planar, apart from the H atoms in the methyl groups, and the coplanarity of the formyl unit with the ring may be associated with the intramolecular N—H···O hydrogen bond (Table 2). The intramolecular bond distances (Table 1) show a number of unusual features. The C6—N6 bond is short for its type (Allen et al., 1987) and C51—O51 is long for its type, while C4—O4 is somewhat longer than C2—O2. At the same time, the lengths of the three bonds involving C5 span only a very small range, whereas in the classical representation the C5—C6 bond is a double bond, while the C5—C4 and C5—C51 bonds are single bonds. Finally, the C6—N1 bond is the shortest of the four independent C—N bonds within the ring. These observations, taken together, provide evidence for the importance of the polarized form (Ia) of the organic component as a contributor to the overall molecular-electronic structure, in addition to the classical form (Ib). It should perhaps be emphasized here that the similarity of the bond lengths involving C5, in particular, is not apparent from the results of the ambient-temperature study, nor is the lengthening of the C4—O4 bond. In form (Ia), the anionic fragment resembles a 1,3-diketonate unit in the syn–anti conformation, while the cationic fragment most closely resembles an amidinium cation.

Within the selected asymmetric unit, the independent components of (I) are linked by an N—H···O hydrogen bond (Fig. 1 and Table 2). These bimolecular aggregates are then linked by two independent O—H···O hydrogen bonds and an N—H···O hydrogen bond which is, in fact, the longer weaker component of a planar three-centre N—H···(O)2 hydrogen bond, in which both acceptors are formyl O atoms (Table 2). It is convenient to consider the actions of the two independent O—H···O hydrogen bonds, firstly acting in isolation, and secondly acting together. Water atom O1 at (x, y, z) acts as a hydrogen-bond donor, via atom H1A, to amidic atom O4 at (x, 1 − y, 1/2 + z), so completing a C22(8) (Bernstein et al., 1995) chain running parallel to the [001] direction and generated by the c-glide plane at y = 1/2. The same water atom also acts as a hydrogen-bond donor, this time via atom H1B, to atom O2 at (1/2 + x, 1/2 − y, 1/2 + z), so completing a second C22(8) chain, now running parallel to the [101] direction and generated by the n-glide plane at y = 1/4. These two chain motifs, generated by different glide planes, are sufficient to generate a three-dimensional framework, within which it is possible to identify a third simple chain motif, involving both O—H···O hydrogen bonds and this time running parallel to the [010] direction (Fig. 2). The combination of the hydrogen-bonded chains along [010], [001] and [101] necessarily generates a three-dimensional structure. The framework thus formed encompasses only half of the molecules within the unit cell, and this three-dimensional sub-structure conforms exactly to Cc symmetry. A second such sub-structure is related to the first by the twofold rotation axes, and the two sub-structural frameworks are continuously interwoven. They are linked by the inter-aggregate N—H···O hydrogen bond, which is the weaker component of the three-centre system in which the amino atom N6 at (x, y, z) acts as donor to the formyl atoms O51 at both (x, y, z) and (2 − x, y, 3/2 − z), so forming a cyclic motif generated by the twofold rotation axis along (1, y, 3/4) in which an R22(4) motif comprising two double donors and two double acceptors is embedded within an outer R22(12) ring (Fig. 3).

In view of the interesting three-dimensional supramolecular structure found for compound (I), we have also briefly analysed the supramolecular aggregation of the isoelectronic analogue (II), using the published atomic coordinates. This structure was reported (Low et al., 1992) in space group Pnam, a non-standard setting of Pnma, although the CIF retrieved (17 August 2007) from the IUCr archive records the structure as having space group Pna21, which had been considered by the authors and rejected by them. Scrutiny of the Pna21 structure using the ADDSYM option in PLATON (Spek, 2003) showed a 100% fit to space group Pnam, as deduced by the earlier authors. A combination of three hydrogen bonds, one each of N—H···O, O—H···O and O—H···N types, links the molecular components of (II) into complex sheets parallel to (001) and containing four types of ring, with chains of edge-fused R65(19) rings along [100] alternating with strings of edge-fused S(6), R21(5) and R23(6) rings (Fig. 4). Thus, a rather modest change in the constitution of the organic component between compounds (I) and (II) leads to a major change in the hydrogen-bonded supramolecular aggregation.

Experimental top

A mixture of phosphoryl chloride (10.7 mmol) and dimethylformamide (2 ml) was stirred at 273 K for 15 min, and then a suspension of 6-amino-1,3-dimethyluracil (6.4 mmol) in dimethylformamide (8 ml) was added. The mixture was heated at 323–333 K in a water-bath for another 15 min, and then poured on to crushed ice. The resultant solution was heated to boiling and neutralized with solid sodium hydroxide. The mixture was allowed to cool to ambient temperature, and the resulting solid product was collected by filtration, washed with a little ice-cold water, and then recrystallized from water (yield 98%, m.p. 465–467 K). Crystals of (I) suitable for single-crystal X-ray diffraction were obtained by slow evaporation of a solution in ethanol–water (97:3 v/v).

Refinement top

The systematic absences permitted Cc and C2/c as possible space groups. C2/c was selected, and confirmed by the refinement. All H atoms were located in difference maps and then treated as riding atoms, with distances C—H = 0.95 Å (formyl) or 0.98 Å (methyl), N—H = 0.86 Å and O—H = 0.82 Å, and with Uiso(H) = kUeq(carrier), with k = 1.5 for the methyl groups and the water molecule, and 1.2 for all other H atoms.

Computing details top

Data collection: COLLECT (Nonius, 1999); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997) and PRPKAPPA (Ferguson, 1999).

Figures top
[Figure 1] Fig. 1. The independent molecular components of compound (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the ??% probability level [Please complete] and H atoms are shown as small spheres of arbitrary radii. The dashed line indicates the N—H···O hydrogen bond linking the components within the selected asymmetric unit.
[Figure 2] Fig. 2. A stereoview of part of the crystal structure of compound (I), showing the formation of a hydrogen-bonded chain along the [010] direction containing three types of intermolecular hydrogen bond. For the sake of clarity, H atoms bonded to C atoms have been omitted
[Figure 3] Fig. 3. Part of the crystal structure of compound (I), showing the formation of the cyclic motif which links the two frameworks. For the sake of clarity, the unit-cell outline and H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) are at the symmetry position (2 − x, y, 3/2 − z).
[Figure 4] Fig. 4. A stereoview of part of the crystal structure of compound (II), showing the formation of a hydrogen-bonded sheet parallel to (001). The published atomic coordinates (Low et al., 1992) have been used. For the sake of clarity, H atoms bonded to C atoms have been omitted.
6-amino-5-formyl-1,3-dimethyl-2,4(1H,3H)-pyrimidinedione monohydrate top
Crystal data top
C7H9N3O3·H2OF(000) = 848
Mr = 201.19Dx = 1.526 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 2012 reflections
a = 15.5815 (4) Åθ = 4.5–27.5°
b = 7.4458 (4) ŵ = 0.13 mm1
c = 16.8575 (8) ÅT = 120 K
β = 116.408 (4)°Plate, colourless
V = 1751.67 (15) Å30.60 × 0.50 × 0.10 mm
Z = 8
Data collection top
Bruker Nonius KappaCCD area-detector
diffractometer
2012 independent reflections
Radiation source: Bruker-Nonius FR591 rotating anode1418 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.042
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 4.5°
ϕ and ω scansh = 2020
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
k = 99
Tmin = 0.946, Tmax = 0.988l = 2121
19726 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.142H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0686P)2 + 2.5767P]
where P = (Fo2 + 2Fc2)/3
2012 reflections(Δ/σ)max < 0.001
129 parametersΔρmax = 0.34 e Å3
0 restraintsΔρmin = 0.33 e Å3
Crystal data top
C7H9N3O3·H2OV = 1751.67 (15) Å3
Mr = 201.19Z = 8
Monoclinic, C2/cMo Kα radiation
a = 15.5815 (4) ŵ = 0.13 mm1
b = 7.4458 (4) ÅT = 120 K
c = 16.8575 (8) Å0.60 × 0.50 × 0.10 mm
β = 116.408 (4)°
Data collection top
Bruker Nonius KappaCCD area-detector
diffractometer
2012 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
1418 reflections with I > 2σ(I)
Tmin = 0.946, Tmax = 0.988Rint = 0.042
19726 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0480 restraints
wR(F2) = 0.142H-atom parameters constrained
S = 1.06Δρmax = 0.34 e Å3
2012 reflectionsΔρmin = 0.33 e Å3
129 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O20.53806 (9)0.29514 (19)0.50090 (8)0.0255 (3)
O40.73512 (9)0.58435 (19)0.41009 (8)0.0246 (3)
O510.96720 (9)0.5403 (2)0.65066 (9)0.0292 (4)
N10.69341 (10)0.3306 (2)0.60190 (10)0.0187 (4)
N30.63564 (10)0.4483 (2)0.45721 (10)0.0188 (4)
N60.84835 (11)0.3867 (2)0.70719 (10)0.0220 (4)
C20.61758 (13)0.3552 (3)0.51864 (12)0.0195 (4)
C40.72645 (13)0.5119 (2)0.47217 (12)0.0190 (4)
C50.80167 (12)0.4861 (2)0.55911 (12)0.0189 (4)
C60.78231 (12)0.4013 (2)0.62465 (11)0.0174 (4)
C110.67413 (14)0.2366 (3)0.66887 (13)0.0240 (4)
C310.55415 (13)0.4727 (3)0.36957 (12)0.0239 (4)
C510.89574 (13)0.5501 (3)0.57899 (13)0.0236 (4)
O10.85212 (9)0.22018 (19)0.85966 (9)0.0246 (3)
H6A0.83870.33650.74850.026*
H6B0.90320.43220.71800.026*
H11A0.61010.18260.64060.036*
H11B0.67730.32220.71420.036*
H11C0.72210.14220.69650.036*
H31A0.57510.54010.33130.036*
H31B0.50330.53930.37580.036*
H31C0.52980.35500.34310.036*
H510.90370.60570.53200.028*
H1A0.81860.27400.87800.037*
H1B0.90800.22010.89770.037*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O20.0180 (7)0.0338 (8)0.0227 (7)0.0061 (6)0.0073 (6)0.0011 (6)
O40.0218 (7)0.0299 (7)0.0218 (7)0.0008 (6)0.0094 (6)0.0054 (6)
O510.0171 (7)0.0408 (9)0.0247 (7)0.0046 (6)0.0047 (6)0.0041 (6)
N10.0154 (7)0.0217 (8)0.0188 (8)0.0023 (6)0.0075 (6)0.0013 (6)
N30.0151 (7)0.0229 (8)0.0166 (8)0.0002 (6)0.0053 (6)0.0001 (6)
N60.0167 (7)0.0293 (9)0.0199 (8)0.0032 (6)0.0080 (6)0.0007 (7)
C20.0183 (9)0.0199 (9)0.0206 (9)0.0005 (7)0.0090 (7)0.0016 (7)
C40.0186 (9)0.0170 (9)0.0231 (9)0.0008 (7)0.0108 (8)0.0016 (7)
C50.0157 (9)0.0204 (9)0.0207 (9)0.0001 (7)0.0083 (7)0.0011 (7)
C60.0158 (8)0.0171 (9)0.0188 (9)0.0011 (7)0.0073 (7)0.0023 (7)
C110.0201 (9)0.0320 (11)0.0213 (9)0.0018 (8)0.0104 (8)0.0050 (8)
C310.0175 (9)0.0321 (11)0.0198 (9)0.0018 (8)0.0061 (8)0.0011 (8)
C510.0204 (9)0.0255 (10)0.0247 (10)0.0001 (8)0.0098 (8)0.0033 (8)
O10.0183 (6)0.0333 (8)0.0215 (7)0.0032 (6)0.0083 (5)0.0004 (6)
Geometric parameters (Å, º) top
N1—C21.387 (2)N3—C311.470 (2)
C2—N31.375 (2)N6—H6A0.8604
N3—C41.405 (2)N6—H6B0.8604
C4—C51.425 (3)C11—H11A0.98
C5—C61.417 (2)C11—H11B0.98
C6—N11.368 (2)C11—H11C0.98
C2—O21.223 (2)C31—H31A0.98
C4—O41.237 (2)C31—H31B0.98
C5—C511.432 (3)C31—H31C0.98
C51—O511.228 (2)C51—H510.95
C6—N61.317 (2)O1—H1A0.8205
N1—C111.468 (2)O1—H1B0.8204
C6—N1—C2122.24 (15)N6—C6—C5121.58 (16)
C6—N1—C11119.74 (15)N1—C6—C5119.57 (16)
C2—N1—C11117.86 (15)N1—C11—H11A109.5
C2—N3—C4124.20 (15)N1—C11—H11B109.5
C2—N3—C31116.41 (14)H11A—C11—H11B109.5
C4—N3—C31119.31 (15)N1—C11—H11C109.5
C6—N6—H6A123.8H11A—C11—H11C109.5
C6—N6—H6B115.3H11B—C11—H11C109.5
H6A—N6—H6B120.9N3—C31—H31A109.5
O2—C2—N3121.64 (16)N3—C31—H31B109.5
O2—C2—N1120.91 (16)H31A—C31—H31B109.5
N3—C2—N1117.45 (15)N3—C31—H31C109.5
O4—C4—N3118.40 (16)H31A—C31—H31C109.5
O4—C4—C5125.42 (16)H31B—C31—H31C109.5
N3—C4—C5116.18 (16)O51—C51—C5126.60 (18)
C6—C5—C4119.94 (16)O51—C51—H51116.7
C6—C5—C51121.10 (16)C5—C51—H51116.7
C4—C5—C51118.94 (16)H1A—O1—H1B109.8
N6—C6—N1118.85 (16)
C4—N3—C2—O2176.42 (17)N3—C4—C5—C60.3 (3)
C31—N3—C2—O20.5 (3)O4—C4—C5—C511.0 (3)
C4—N3—C2—N13.2 (3)N3—C4—C5—C51179.21 (16)
C31—N3—C2—N1179.94 (16)C2—N1—C6—N6173.81 (17)
C6—N1—C2—O2177.73 (17)C11—N1—C6—N61.5 (3)
C11—N1—C2—O22.4 (3)C2—N1—C6—C57.0 (3)
C6—N1—C2—N32.7 (3)C11—N1—C6—C5177.69 (16)
C11—N1—C2—N3178.01 (16)C4—C5—C6—N6175.12 (17)
C2—N3—C4—O4175.61 (17)C51—C5—C6—N63.7 (3)
C31—N3—C4—O41.2 (3)C4—C5—C6—N15.8 (3)
C2—N3—C4—C54.2 (3)C51—C5—C6—N1175.41 (17)
C31—N3—C4—C5179.00 (16)C6—C5—C51—O510.1 (3)
O4—C4—C5—C6179.85 (17)C4—C5—C51—O51178.91 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···O10.861.992.831 (2)166
N6—H6B···O510.861.982.686 (2)138
N6—H6B···O51i0.862.383.030 (2)133
O1—H1A···O4ii0.821.932.7465 (18)174
O1—H1B···O2iii0.822.002.8177 (18)172
Symmetry codes: (i) x+2, y, z+3/2; (ii) x, y+1, z+1/2; (iii) x+1/2, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC7H9N3O3·H2O
Mr201.19
Crystal system, space groupMonoclinic, C2/c
Temperature (K)120
a, b, c (Å)15.5815 (4), 7.4458 (4), 16.8575 (8)
β (°) 116.408 (4)
V3)1751.67 (15)
Z8
Radiation typeMo Kα
µ (mm1)0.13
Crystal size (mm)0.60 × 0.50 × 0.10
Data collection
DiffractometerBruker Nonius KappaCCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.946, 0.988
No. of measured, independent and
observed [I > 2σ(I)] reflections
19726, 2012, 1418
Rint0.042
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.142, 1.06
No. of reflections2012
No. of parameters129
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.34, 0.33

Computer programs: COLLECT (Nonius, 1999), DIRAX/LSQ (Duisenberg et al., 2000), EVALCCD (Duisenberg et al., 2003), SIR2004 (Burla et al., 2005), OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 (Sheldrick, 1997) and PRPKAPPA (Ferguson, 1999).

Selected geometric parameters (Å, º) top
N1—C21.387 (2)C2—O21.223 (2)
C2—N31.375 (2)C4—O41.237 (2)
N3—C41.405 (2)C5—C511.432 (3)
C4—C51.425 (3)C51—O511.228 (2)
C5—C61.417 (2)C6—N61.317 (2)
C6—N11.368 (2)
C4—C5—C51—O51178.91 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···O10.861.992.831 (2)166
N6—H6B···O510.861.982.686 (2)138
N6—H6B···O51i0.862.383.030 (2)133
O1—H1A···O4ii0.821.932.7465 (18)174
O1—H1B···O2iii0.822.002.8177 (18)172
Symmetry codes: (i) x+2, y, z+3/2; (ii) x, y+1, z+1/2; (iii) x+1/2, y+1/2, z+1/2.
 

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