Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S010827010300547X/sk1625sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S010827010300547X/sk1625Isup2.hkl |
CCDC reference: 211747
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.
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.
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).
C6H9N3O2 | F(000) = 656 |
Mr = 155.16 | Dx = 1.379 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 1703 reflections |
a = 13.5867 (6) Å | θ = 2.9–27.4° |
b = 7.8621 (2) Å | µ = 0.11 mm−1 |
c = 13.9932 (6) Å | T = 120 K |
V = 1494.75 (10) Å3 | Needle, colourless |
Z = 8 | 0.35 × 0.08 × 0.04 mm |
Nonius KappaCCD diffractometer | 1703 independent reflections |
Radiation source: rotating anode | 1056 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.081 |
ϕ scans, and ω scans with κ offsets | θmax = 27.4°, θmin = 2.9° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −17→17 |
Tmin = 0.968, Tmax = 0.995 | k = −8→10 |
13259 measured reflections | l = −18→14 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.047 | H-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 reflections | Δρmax = 0.22 e Å−3 |
103 parameters | Δρmin = −0.22 e Å−3 |
0 restraints | Extinction correction: SHELXL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.010 (2) |
C6H9N3O2 | V = 1494.75 (10) Å3 |
Mr = 155.16 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 13.5867 (6) Å | µ = 0.11 mm−1 |
b = 7.8621 (2) Å | T = 120 K |
c = 13.9932 (6) Å | 0.35 × 0.08 × 0.04 mm |
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 = 0.995 | Rint = 0.081 |
13259 measured reflections |
R[F2 > 2σ(F2)] = 0.047 | 0 restraints |
wR(F2) = 0.125 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.22 e Å−3 |
1703 reflections | Δρmin = −0.22 e Å−3 |
103 parameters |
x | y | z | Uiso*/Ueq | ||
N1 | 0.63250 (10) | 0.01875 (17) | 0.52126 (10) | 0.0268 (4) | |
C2 | 0.61115 (13) | 0.1620 (2) | 0.47552 (12) | 0.0274 (4) | |
O2 | 0.64422 (9) | 0.18170 (14) | 0.38552 (8) | 0.0357 (4) | |
C21 | 0.70292 (15) | 0.0465 (2) | 0.34752 (14) | 0.0428 (5) | |
N3 | 0.55987 (11) | 0.29530 (17) | 0.50602 (10) | 0.0297 (4) | |
C4 | 0.52533 (13) | 0.2825 (2) | 0.59663 (12) | 0.0290 (4) | |
N4 | 0.47082 (12) | 0.41308 (19) | 0.62885 (11) | 0.0376 (4) | |
C5 | 0.54495 (13) | 0.1403 (2) | 0.65327 (12) | 0.0298 (4) | |
C6 | 0.59770 (12) | 0.0125 (2) | 0.61067 (12) | 0.0270 (4) | |
O6 | 0.61665 (9) | −0.12925 (15) | 0.66255 (8) | 0.0339 (4) | |
C61 | 0.67240 (14) | −0.2620 (2) | 0.61635 (14) | 0.0374 (5) | |
H21A | 0.7617 | 0.0315 | 0.3872 | 0.064* | |
H21B | 0.7227 | 0.0745 | 0.2820 | 0.064* | |
H21C | 0.6645 | −0.0590 | 0.3473 | 0.064* | |
H4A | 0.4592 | 0.5010 | 0.5916 | 0.045* | |
H4B | 0.4467 | 0.4107 | 0.6872 | 0.045* | |
H5 | 0.5230 | 0.1326 | 0.7176 | 0.036* | |
H61A | 0.6372 | −0.3006 | 0.5592 | 0.056* | |
H61B | 0.6807 | −0.3577 | 0.6605 | 0.056* | |
H61C | 0.7372 | −0.2180 | 0.5980 | 0.056* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0258 (8) | 0.0309 (8) | 0.0237 (8) | −0.0022 (6) | 0.0017 (6) | −0.0014 (6) |
C2 | 0.0268 (9) | 0.0320 (10) | 0.0234 (10) | −0.0063 (8) | 0.0021 (7) | −0.0015 (7) |
O2 | 0.0454 (8) | 0.0362 (8) | 0.0254 (7) | −0.0014 (6) | 0.0115 (6) | −0.0006 (5) |
C21 | 0.0467 (12) | 0.0457 (12) | 0.0359 (12) | −0.0013 (10) | 0.0182 (9) | −0.0072 (9) |
N3 | 0.0321 (9) | 0.0307 (8) | 0.0262 (9) | −0.0016 (6) | 0.0032 (7) | −0.0011 (6) |
C4 | 0.0288 (9) | 0.0328 (10) | 0.0252 (10) | −0.0014 (8) | 0.0026 (8) | −0.0035 (7) |
N4 | 0.0506 (10) | 0.0338 (9) | 0.0285 (9) | 0.0089 (8) | 0.0104 (7) | 0.0010 (7) |
C5 | 0.0309 (10) | 0.0368 (10) | 0.0216 (9) | 0.0016 (8) | 0.0024 (7) | −0.0003 (7) |
C6 | 0.0235 (9) | 0.0319 (9) | 0.0257 (10) | −0.0024 (8) | −0.0029 (7) | 0.0021 (7) |
O6 | 0.0395 (8) | 0.0344 (7) | 0.0279 (7) | 0.0091 (6) | 0.0024 (5) | 0.0050 (5) |
C61 | 0.0414 (11) | 0.0341 (10) | 0.0367 (11) | 0.0107 (9) | 0.0019 (9) | 0.0016 (8) |
N1—C2 | 1.327 (2) | O6—C61 | 1.443 (2) |
C2—N3 | 1.329 (2) | C21—H21A | 0.98 |
N3—C4 | 1.356 (2) | C21—H21B | 0.98 |
C4—C5 | 1.396 (2) | C21—H21C | 0.98 |
C5—C6 | 1.371 (2) | N4—H4A | 0.88 |
C6—N1 | 1.338 (2) | N4—H4B | 0.88 |
C2—O2 | 1.346 (2) | C5—H5 | 0.95 |
O2—C21 | 1.431 (2) | C61—H61A | 0.98 |
C4—N4 | 1.344 (2) | C61—H61B | 0.98 |
C6—O6 | 1.355 (2) | C61—H61C | 0.98 |
C2—N1—C6 | 113.86 (14) | C4—N4—H4B | 120.0 |
N1—C2—N3 | 128.96 (16) | H4A—N4—H4B | 120.0 |
N1—C2—O2 | 118.41 (14) | C6—C5—C4 | 116.10 (15) |
N3—C2—O2 | 112.63 (14) | C6—C5—H5 | 122.0 |
C2—O2—C21 | 116.63 (13) | C4—C5—H5 | 122.0 |
O2—C21—H21A | 109.5 | N1—C6—O6 | 117.64 (14) |
O2—C21—H21B | 109.5 | N1—C6—C5 | 124.37 (15) |
H21A—C21—H21B | 109.5 | O6—C6—C5 | 117.99 (15) |
O2—C21—H21C | 109.5 | C6—O6—C61 | 117.06 (13) |
H21A—C21—H21C | 109.5 | O6—C61—H61A | 109.5 |
H21B—C21—H21C | 109.5 | O6—C61—H61B | 109.5 |
C2—N3—C4 | 115.05 (14) | H61A—C61—H61B | 109.5 |
N4—C4—N3 | 116.61 (15) | O6—C61—H61C | 109.5 |
N4—C4—C5 | 121.78 (16) | H61A—C61—H61C | 109.5 |
N3—C4—C5 | 121.61 (15) | H61B—C61—H61C | 109.5 |
C4—N4—H4A | 120.0 | ||
C6—N1—C2—N3 | −1.0 (3) | N4—C4—C5—C6 | 177.18 (17) |
C6—N1—C2—O2 | 179.00 (14) | N3—C4—C5—C6 | −2.4 (3) |
N1—C2—O2—C21 | −1.9 (2) | C2—N1—C6—O6 | −179.71 (14) |
N3—C2—O2—C21 | 178.13 (15) | C2—N1—C6—C5 | −0.2 (2) |
N1—C2—N3—C4 | 0.4 (3) | C4—C5—C6—N1 | 1.8 (3) |
O2—C2—N3—C4 | −179.60 (14) | C4—C5—C6—O6 | −178.71 (15) |
C2—N3—C4—N4 | −178.21 (16) | N1—C6—O6—C61 | −0.4 (2) |
C2—N3—C4—C5 | 1.4 (2) | C5—C6—O6—C61 | −179.92 (15) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4A···N3i | 0.88 | 2.12 | 2.999 (2) | 175 |
N4—H4B···O6ii | 0.88 | 2.29 | 3.169 (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 formula | C6H9N3O2 |
Mr | 155.16 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 120 |
a, b, c (Å) | 13.5867 (6), 7.8621 (2), 13.9932 (6) |
V (Å3) | 1494.75 (10) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.35 × 0.08 × 0.04 |
Data collection | |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.968, 0.995 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 13259, 1703, 1056 |
Rint | 0.081 |
(sin θ/λ)max (Å−1) | 0.648 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.125, 1.05 |
No. of reflections | 1703 |
No. of parameters | 103 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 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).
N1—C2 | 1.327 (2) | C2—O2 | 1.346 (2) |
C2—N3 | 1.329 (2) | O2—C21 | 1.431 (2) |
N3—C4 | 1.356 (2) | C4—N4 | 1.344 (2) |
C4—C5 | 1.396 (2) | C6—O6 | 1.355 (2) |
C5—C6 | 1.371 (2) | O6—C61 | 1.443 (2) |
C6—N1 | 1.338 (2) | ||
N1—C2—O2—C21 | −1.9 (2) | N1—C6—O6—C61 | −0.4 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4A···N3i | 0.88 | 2.12 | 2.999 (2) | 175 |
N4—H4B···O6ii | 0.88 | 2.29 | 3.169 (2) | 173 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+1, y+1/2, −z+3/2. |
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 π–π-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 π–π-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 π–π-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.