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Molecules of the title compound, C6H9N3O2, are linked by an N-H...O hydrogen bond [H...O = 2.29 Å, N...O = 3.169 (2) Å and N-H...O = 173°] and an N-H...N hydrogen bond [H...N = 2.12 Å, N...N = 2.999 (2) Å and N-H...N = 175°] into sheets containing centrosymmetric R_2^2(8) and R_6^6(28) rings; the sheets are reinforced by a single aromatic [pi]-[pi]-stacking interaction.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S010827010300547X/sk1625sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S010827010300547X/sk1625Isup2.hkl
Contains datablock I

CCDC reference: 211747

Comment top

The supramolecular structure of 2-amino-4,6-dimethoxypyrimidine, (I) (Low et al., 2002), consists of chains of edge-fused R22(8) rings generated solely by N—H···N hydrogen bonds, and these chains are linked into a three-dimensional framework by means of aromatic ππ-stacking interactions. We now report the molecular and supramolecular structure of the isomeric compound 4-amino-2,6-dimethoxypyrimidine, (II), which proves to adopt a conformation different from that of (I) and a two-dimensional supramolecular structure involving both N—H···N and N—H···O hydrogen bonds, and aromatic ππ-stacking interactions.

Whereas compound (I), which could in principle adopt a conformation having C2v (mm2) molecular symmetry, adopts a conformation with one methoxy group anti to the amino and one syn to it, in compound (II), by contrast, both methoxy groups are anti to the amino substituent (Fig. 1 and Table 1). A similar pattern of molecular conformation has been observed in the isomeric tribenzyl compounds (III) and (IV) (Glidewell et al., 2003a); on the other hand, the 5-nitroso compounds (V) (Glidewell et al., 2002) and (VI) (Quesada, Low et al., 2002) both exhibit the third possible conformational arrangement of the alkoxy substituents. Of the two isomeric nitropyrimidines (VII) and (VIII) (Glidewell et al., 2003b), (VII) adopts an alkoxy conformation similar to those in (V) and (VI), while (VIII) adopts a conformation similar to those in (II) and (IV). The consistency of these conformational arrangements, independent of the nature, in particular the bulk, of the alkyl substituent suggests that the underlying causes determining the selection of the conformations may be intramolecular rather than intermolecular in origin.

There is no significant bond fixation within the pyrimidine ring of (II) (Table 1) and the exocyclic bond lengths are also normal for their types (Allen et al., 1987). In this respect, the molecular–electronic structure of (I) is markedly different from those in a large number of analogous pyrimidines carrying a 5-nitroso substituent, where highly polarized structures are the norm (Low et al., 2000; Low, Cannon et al., 2001; Low, Moreno et al., 2001; Quesada, Marchal et al., 2002).

The two-dimensional supramolecular structure of (II) is most readily analysed using the substructure approach (Gregson et al., 2000), which considers the effect of each of the intermolecular interactions in turn (Table 2). The amino atom N4 in the molecule at (x, y, z) acts as hydrogen-bond donor, via H4B, to O6 in the molecule at (1 − x, 0.5 + y, 1.5 − z), while N4 at (1 − x, 0.5 + y, 1.5 − z) in turn acts as donor to O6 at (x, 1 + y, z). In this manner, a C(6) chain is formed, running parallel to the [010] direction and generated by the 21 screw axis along (1/2, y, 3/4). Four such chains run through each unit cell. The same amino atom N4 also acts, this time via H4A, as hydrogen-bond donor to ring atom N3 in the molecule at (1 − x, 1 − y, 1 − z), so generating a centrosymmetric R22(8) ring. The molecule at (1 − x, 1 − y, 1 − z) forms part of the C(6) chain generated by the 21 screw axis along (1/2, −y, 1/4), and the effect of the N—H···N hydrogen bond is thus to link the C(6) chains into a sheet parallel to (100). This sheet contains R22(8) and R66(28) rings, both types centrosymmetric, arranged in a checkerboard fashion (Fig. 2). If the individual molecules are regarded as the nodes of the resulting net, then this is of the (6,3)-type, while if the R22(8) dimers are taken as the nodes, then the net is of the (4,4)-type (Batten & Robson, 1998).

The formation of the (100) sheet is reinforced by a single aromatic ππ-stacking interaction. The molecules at (x, y, z) and (1 − y, −y, 1 − z) are components of the same R66(28) ring, and the pyrimidine rings in these molecules are strictly parallel with an interplanar spacing of 3.371 (2) Å; the centroid–centroid separation is 3.624 (2) Å, corresponding to a centroid offset of 1.330 (2) Å.

There are two (100) sheets passing through each unit cell, in the domains 0.24 < x < 0.76 and 0.75 < x < 1.26, respectively; there are no direction-specific interactions between adjacent sheets, nor is there any interweaving of the sheets.

Finally, we note briefly here some common features in the supramolecular aggregation of compounds (I)–(VIII), i.e. paired N—H···N hydrogen bonds occur in each of (I), (III), (IV) and (VIII), giving chains in (I) and dimers in the remainder, while a combination of N—H···O and N—H···N hydrogen bonds occurs in both (II) and (VII), giving sheets in each case.

Experimental top

A sample of (II) was purchased from Aldrich. Crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation of a solution in tert-butanol.

Refinement top

Crystals of (II) are orthorhombic and the space group Pbca was uniquely assigned from the systematic absences. H atoms were treated as riding, with C—H distances of 0.95 (aromatic) and 0.98 Å (CH3), and N—H distances of 0.88 Å.

Computing details top

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 top
[Figure 1] Fig. 1. The molecule of (II), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. Stereoview of part of the crystal structure of (II), showing the formation of a (100) sheet of R22(8) and R66(28) rings, reinforced by a ππ-stacking interaction.
4-Amino-2,6-dimethoxypyrimidine top
Crystal data top
C6H9N3O2F(000) = 656
Mr = 155.16Dx = 1.379 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 1703 reflections
a = 13.5867 (6) Åθ = 2.9–27.4°
b = 7.8621 (2) ŵ = 0.11 mm1
c = 13.9932 (6) ÅT = 120 K
V = 1494.75 (10) Å3Needle, colourless
Z = 80.35 × 0.08 × 0.04 mm
Data collection top
Nonius KappaCCD
diffractometer
1703 independent reflections
Radiation source: rotating anode1056 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.081
ϕ scans, and ω scans with κ offsetsθmax = 27.4°, θmin = 2.9°
Absorption correction: multi-scan
(DENZO-SMN; Otwinowski & Minor, 1997)
h = 1717
Tmin = 0.968, Tmax = 0.995k = 810
13259 measured reflectionsl = 1814
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H-atom parameters constrained
wR(F2) = 0.125 w = 1/[σ2(Fo2) + (0.0626P)2 + 0.1218P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
1703 reflectionsΔρmax = 0.22 e Å3
103 parametersΔρmin = 0.22 e Å3
0 restraintsExtinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.010 (2)
Crystal data top
C6H9N3O2V = 1494.75 (10) Å3
Mr = 155.16Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 13.5867 (6) ŵ = 0.11 mm1
b = 7.8621 (2) ÅT = 120 K
c = 13.9932 (6) Å0.35 × 0.08 × 0.04 mm
Data collection top
Nonius KappaCCD
diffractometer
1703 independent reflections
Absorption correction: multi-scan
(DENZO-SMN; Otwinowski & Minor, 1997)
1056 reflections with I > 2σ(I)
Tmin = 0.968, Tmax = 0.995Rint = 0.081
13259 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0470 restraints
wR(F2) = 0.125H-atom parameters constrained
S = 1.05Δρmax = 0.22 e Å3
1703 reflectionsΔρmin = 0.22 e Å3
103 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.63250 (10)0.01875 (17)0.52126 (10)0.0268 (4)
C20.61115 (13)0.1620 (2)0.47552 (12)0.0274 (4)
O20.64422 (9)0.18170 (14)0.38552 (8)0.0357 (4)
C210.70292 (15)0.0465 (2)0.34752 (14)0.0428 (5)
N30.55987 (11)0.29530 (17)0.50602 (10)0.0297 (4)
C40.52533 (13)0.2825 (2)0.59663 (12)0.0290 (4)
N40.47082 (12)0.41308 (19)0.62885 (11)0.0376 (4)
C50.54495 (13)0.1403 (2)0.65327 (12)0.0298 (4)
C60.59770 (12)0.0125 (2)0.61067 (12)0.0270 (4)
O60.61665 (9)0.12925 (15)0.66255 (8)0.0339 (4)
C610.67240 (14)0.2620 (2)0.61635 (14)0.0374 (5)
H21A0.76170.03150.38720.064*
H21B0.72270.07450.28200.064*
H21C0.66450.05900.34730.064*
H4A0.45920.50100.59160.045*
H4B0.44670.41070.68720.045*
H50.52300.13260.71760.036*
H61A0.63720.30060.55920.056*
H61B0.68070.35770.66050.056*
H61C0.73720.21800.59800.056*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0258 (8)0.0309 (8)0.0237 (8)0.0022 (6)0.0017 (6)0.0014 (6)
C20.0268 (9)0.0320 (10)0.0234 (10)0.0063 (8)0.0021 (7)0.0015 (7)
O20.0454 (8)0.0362 (8)0.0254 (7)0.0014 (6)0.0115 (6)0.0006 (5)
C210.0467 (12)0.0457 (12)0.0359 (12)0.0013 (10)0.0182 (9)0.0072 (9)
N30.0321 (9)0.0307 (8)0.0262 (9)0.0016 (6)0.0032 (7)0.0011 (6)
C40.0288 (9)0.0328 (10)0.0252 (10)0.0014 (8)0.0026 (8)0.0035 (7)
N40.0506 (10)0.0338 (9)0.0285 (9)0.0089 (8)0.0104 (7)0.0010 (7)
C50.0309 (10)0.0368 (10)0.0216 (9)0.0016 (8)0.0024 (7)0.0003 (7)
C60.0235 (9)0.0319 (9)0.0257 (10)0.0024 (8)0.0029 (7)0.0021 (7)
O60.0395 (8)0.0344 (7)0.0279 (7)0.0091 (6)0.0024 (5)0.0050 (5)
C610.0414 (11)0.0341 (10)0.0367 (11)0.0107 (9)0.0019 (9)0.0016 (8)
Geometric parameters (Å, º) top
N1—C21.327 (2)O6—C611.443 (2)
C2—N31.329 (2)C21—H21A0.98
N3—C41.356 (2)C21—H21B0.98
C4—C51.396 (2)C21—H21C0.98
C5—C61.371 (2)N4—H4A0.88
C6—N11.338 (2)N4—H4B0.88
C2—O21.346 (2)C5—H50.95
O2—C211.431 (2)C61—H61A0.98
C4—N41.344 (2)C61—H61B0.98
C6—O61.355 (2)C61—H61C0.98
C2—N1—C6113.86 (14)C4—N4—H4B120.0
N1—C2—N3128.96 (16)H4A—N4—H4B120.0
N1—C2—O2118.41 (14)C6—C5—C4116.10 (15)
N3—C2—O2112.63 (14)C6—C5—H5122.0
C2—O2—C21116.63 (13)C4—C5—H5122.0
O2—C21—H21A109.5N1—C6—O6117.64 (14)
O2—C21—H21B109.5N1—C6—C5124.37 (15)
H21A—C21—H21B109.5O6—C6—C5117.99 (15)
O2—C21—H21C109.5C6—O6—C61117.06 (13)
H21A—C21—H21C109.5O6—C61—H61A109.5
H21B—C21—H21C109.5O6—C61—H61B109.5
C2—N3—C4115.05 (14)H61A—C61—H61B109.5
N4—C4—N3116.61 (15)O6—C61—H61C109.5
N4—C4—C5121.78 (16)H61A—C61—H61C109.5
N3—C4—C5121.61 (15)H61B—C61—H61C109.5
C4—N4—H4A120.0
C6—N1—C2—N31.0 (3)N4—C4—C5—C6177.18 (17)
C6—N1—C2—O2179.00 (14)N3—C4—C5—C62.4 (3)
N1—C2—O2—C211.9 (2)C2—N1—C6—O6179.71 (14)
N3—C2—O2—C21178.13 (15)C2—N1—C6—C50.2 (2)
N1—C2—N3—C40.4 (3)C4—C5—C6—N11.8 (3)
O2—C2—N3—C4179.60 (14)C4—C5—C6—O6178.71 (15)
C2—N3—C4—N4178.21 (16)N1—C6—O6—C610.4 (2)
C2—N3—C4—C51.4 (2)C5—C6—O6—C61179.92 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···N3i0.882.122.999 (2)175
N4—H4B···O6ii0.882.293.169 (2)173
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y+1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC6H9N3O2
Mr155.16
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)120
a, b, c (Å)13.5867 (6), 7.8621 (2), 13.9932 (6)
V3)1494.75 (10)
Z8
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.35 × 0.08 × 0.04
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(DENZO-SMN; Otwinowski & Minor, 1997)
Tmin, Tmax0.968, 0.995
No. of measured, independent and
observed [I > 2σ(I)] reflections
13259, 1703, 1056
Rint0.081
(sin θ/λ)max1)0.648
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.125, 1.05
No. of reflections1703
No. of parameters103
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.22, 0.22

Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO–SMN (Otwinowski & Minor, 1997), DENZO–SMN, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 and PRPKAPPA (Ferguson, 1999).

Selected geometric parameters (Å, º) top
N1—C21.327 (2)C2—O21.346 (2)
C2—N31.329 (2)O2—C211.431 (2)
N3—C41.356 (2)C4—N41.344 (2)
C4—C51.396 (2)C6—O61.355 (2)
C5—C61.371 (2)O6—C611.443 (2)
C6—N11.338 (2)
N1—C2—O2—C211.9 (2)N1—C6—O6—C610.4 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···N3i0.882.122.999 (2)175
N4—H4B···O6ii0.882.293.169 (2)173
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y+1/2, z+3/2.
 

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