4,6-Dimeth­oxy-2-phthalimidopyrimidine: sheets built from π-stacked hydrogen-bonded chains

The mol­ecules of the title compound, C₁₄H₁₁N₃O₄, have approximate but noncrystallographic twofold rotational symmetry. The mol­ecules are linked into chains by a C—H...O hydrogen bond, and these chains are linked into sheets by a π–π stacking inter­action. The significance of this study lies in its comparison of the modes of supra­molecular agg­re­gation in the title compound and those in some close ana­logues.

S1. Comment

An attractive possibility as a protecting group for aminopyrimidines is the phthalimide unit, readily introduced by reaction of the aminopyrimidine with phthalic anhydride using microwave irradiation under solvent-free conditions. We report the molecular and supramolecular structures of the title compound, (I) (Fig. 1), synthesized in this fashion from 2-amino-4,6-dimethoxypyrimidine, and we compare its mode of supramolecular aggregation with that observed in several closely analogous compounds.

The torsion angles defining the conformations of the two independent methoxy groups (Table 1) indicate that the molecule overall has approximate, although noncrystallographic, twofold rotational symmetry. The dihedral angle between the mean planes of the pyrimidine ring and the phthalimide fragment is 46.4 (2)°, while the two independent methoxy C atoms are displaced by only 0.186 (2) and 0.068 (2) Å from the plane of the pyrimidine ring. Despite this near coplanarity of the methoxy C atoms with the pyrimidine ring, the two exocyclic bond angles at each of C14 and C16 are fairly similar (Table 1), in contrast to the difference of ca 10° typically found in methoxyarene derivatives. The bond distances in (I) present no unusual values.

The molecules of (I) are linked by a single C—H···O hydrogen bond (Table 2) into C(10) (Bernstein et al., 1995) chains running parallel to the [001] direction and consisting of molecules related by translation. Chains of this type are weakly linked into sheets by a single π–π stacking interaction. The pyrimidine and arene rings in the molecules at (x, y, z) and (x + 1/2, -y + 3/2, z - 1/2), respectively, make a dihedral angle of 11.6 (2)°; the ring-centroid separation is 3.618 (2) Å and the interplanar spacing is ca 3.31°, corresponding to a ring-centroid offset of ca 1.46 Å. The effect of this interaction is to link the hydrogen-bonded [001] chains into a sheet parallel to (100) (Fig. 2). Two sheets of this type pass through each unit cell, containing molecules related by the n-glide planes at y = 1/4 and y = 3/4, respectively, but there are no direction-specific interactions between adjacent sheets.

There appear to be no analogues of (I) containing the same ring system, regardless of substituents, recorded in the Cambridge Structural Database (CSD; Allen, 2002). However, the structures of the disubstituted 2-pyridyl analogue (II) (CSD refcode JUBLOH; Rodier et al., 1992) and the unsubstituted 2-pyridyl compound (III) (CSD code VEXNES; Liang & Li, 2007) have been reported, although in neither of these reports is there any consideration of the intermolecular interactions and aggregation. It is thus of interest to analyse these two structures briefly here in order to compare them with the structure of (I).

In (II), the pattern of substitution matches that in (I), but on a pyridine ring rather than a pyrimidine ring. A combination of a C—H···O hydrogen bond and a π–π stacking interaction between strictly parallel arene rings generates a chain of π-stacked hydrogen-bonded dimers running parallel to the [111] direction of the triclinic cell. Hydrogen-bonded R²₂(16) rings centred at (n, n + 1/2, n) (where n represents zero or an integer) alternate with π–π stacking interactions across (n - 1/2, n, n - 1/2) (where n represents zero or an integer) (Fig. 3). By contrast, in the analogous compound (III), which differs from (II) only in its lack of the two methyl groups, a combination of a C—H···O hydrogen bond and a π–π stacking interaction gives rise to a sheet parallel to (100) (Fig. 4). This sheet is formed by the π stacking of hydrogen-bonded C(8) chains running parallel to the [010] direction; this type of aggregation is thus somewhat similar to that found in (I). The molecules of the dinitrophenyl analogue (IV), where the substituted ring now contains no N atoms, lie across twofold rotation axes in space group P2/n (Glidewell et al., 2004), and the supramolecular aggregation consists of hydrogen-bonded chains of rings linked into sheets by dipolar O···N and O···C interactions.

Hence, (I), (II) and (IV), which have similar constitutions and very similar molecular shapes, all exhibit distinctly different patterns of supramolecular aggregation, namely π-stacked hydrogen-bonded chains in (I), π-stacked hydrogen-bonded dimers in (II) and hydrogen-bonded chains linked by dipolar interactions in (IV). The most similar structure types are those in (I) and (III), where the molecules concerned are, in fact, the least similar within this series.

Related literature

For related literature, see: Allen (2002); Bernstein et al. (1995); Glidewell et al. (2004); Liang & Li (2007); Rodier et al. (1992).

S2. Experimental

Finely ground 2-amino-4,6-dimethoxypyrimidine (1.29 mmol) and phthalic anhydride (1.29 mmol) were mixed thoroughly, and the mixture was then subjected to microwave irradiation (8 min, maximum temperature 423 K, maximun power 150 W) in an monomode microwave CEM reactor. The resulting solid was shaken with sodium hydrogencarbonate (5 ml of a saturated aqueous solution), and the crude product (I) was then collected by filtation and washed with diethyl ether. Crystals suitable for single-crystal X-ray diffraction were obtained by slow evaporation of a solution in dimethylsulfoxide (yield 65%, m.p. 465–466 K). HRMS found 285.0741; C₁₄H₁₁N₃O₄ requires 285.0750.

S3. Refinement

The space group P2₁/n was uniquely assigned from the systematic absences. All H atoms were located in difference maps and subsequently treated as riding atoms with C—H distances of 0.95 Å (arene and pyrimidine) or 0.98 Å (methyl), and with U_iso(H) = kU_eq(C), where k = 1.5 for the methyl groups and k = 1.2 for the ring H atoms.

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: SIR2004 (Burla et al., 2005); program(s) used to refine structure: OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PRPKAPPA (Ferguson, 1999).

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 sheet parallel to (100) built by the π stacking of the hydrogen-bonded chains running parallel to [001]. For the sake of clarity, H atoms not involved in the motif shown have been omitted.
	Fig. 3. A stereoview of part of the crystal structure of (II), showing the formation of a chain of π-stacked hydrogen-bonded dimers. The original atom coordinates (Rodier et al., 1992) have been used. For the sake of clarity, H atoms not involved in the motif shown have been omitted.
	Fig. 4. A stereoview of part of the crystal structure of (III), showing the formation of a sheet of π-stacked hydrogen bonded chains. The original atom coordinates (Liang & Li, 2007) have been used. For the sake of clarity, the H atoms not involved in the motif shown have been omitted.

4,6-Dimethoxy-2-phthalimidopyrimidine

Crystal data

C14H11N3O4	F(000) = 592
Mr = 285.26	Dx = 1.506 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 2893 reflections
a = 7.2904 (8) Å	θ = 3.1–27.5°
b = 13.896 (2) Å	µ = 0.11 mm^−1
c = 12.5021 (11) Å	T = 120 K
β = 96.476 (7)°	Block, colourless
V = 1258.5 (3) Å^3	0.37 × 0.24 × 0.22 mm
Z = 4

Data collection

Bruker–Nonius KappaCCD diffractometer	2893 independent reflections
Radiation source: Bruker-Nonius FR591 rotating anode	2250 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.042
Detector resolution: 9.091 pixels mm^-1	θmax = 27.5°, θmin = 3.1°
ϕ and ω scans	h = −9→9
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	k = −18→18
Tmin = 0.953, Tmax = 0.975	l = −16→16
29699 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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.101	H-atom parameters constrained
S = 1.12	w = 1/[σ^2(Fo^2) + (0.0353P)^2 + 0.7987P] where P = (Fo^2 + 2Fc^2)/3
2893 reflections	(Δ/σ)max < 0.001
192 parameters	Δρmax = 0.27 e Å^−3
0 restraints	Δρmin = −0.30 e Å^−3

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

	x	y	z	Uiso*/Ueq
O1	0.14405 (16)	0.89393 (8)	0.41992 (9)	0.0227 (3)
O3	0.46134 (16)	0.61983 (8)	0.34527 (9)	0.0211 (3)
O14	0.43751 (16)	1.00914 (8)	0.12561 (9)	0.0193 (3)
O16	0.23515 (16)	0.71259 (8)	−0.01622 (9)	0.0208 (3)
N2	0.29822 (18)	0.76357 (9)	0.35257 (10)	0.0160 (3)
N11	0.26284 (17)	0.73571 (9)	0.16784 (10)	0.0154 (3)
N13	0.37076 (17)	0.88754 (9)	0.24055 (10)	0.0153 (3)
C1	0.2220 (2)	0.81813 (11)	0.43301 (12)	0.0162 (3)
C3	0.3781 (2)	0.67645 (11)	0.39433 (12)	0.0163 (3)
C3A	0.3428 (2)	0.67437 (12)	0.50915 (12)	0.0167 (3)
C4	0.3911 (2)	0.60566 (12)	0.58742 (13)	0.0200 (3)
C5	0.3527 (2)	0.62678 (13)	0.69155 (13)	0.0224 (4)
C6	0.2668 (2)	0.71236 (13)	0.71517 (13)	0.0226 (4)
C7	0.2147 (2)	0.78010 (12)	0.63550 (13)	0.0201 (3)
C7A	0.2562 (2)	0.75925 (12)	0.53254 (12)	0.0166 (3)
C12	0.3105 (2)	0.79774 (11)	0.24644 (12)	0.0154 (3)
C14	0.3789 (2)	0.91902 (11)	0.14009 (12)	0.0153 (3)
C15	0.3324 (2)	0.86317 (11)	0.04968 (12)	0.0167 (3)
C16	0.2778 (2)	0.77010 (11)	0.06947 (12)	0.0154 (3)
C17	0.4915 (2)	1.06470 (12)	0.22090 (13)	0.0235 (4)
C18	0.1944 (3)	0.61291 (12)	0.00401 (14)	0.0258 (4)
H4	0.4479	0.5468	0.5709	0.024*
H5	0.3859	0.5818	0.7476	0.027*
H6	0.2433	0.7248	0.7871	0.027*
H7	0.1535	0.8380	0.6510	0.024*
H15	0.3376	0.8870	−0.0211	0.020*
H17A	0.3879	1.0686	0.2643	0.035*
H17B	0.5266	1.1296	0.2004	0.035*
H17C	0.5968	1.0337	0.2630	0.035*
H18A	0.3022	0.5826	0.0444	0.039*
H18B	0.1644	0.5793	−0.0646	0.039*
H18C	0.0889	0.6092	0.0460	0.039*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0281 (6)	0.0206 (6)	0.0200 (6)	0.0037 (5)	0.0060 (5)	0.0001 (5)
O3	0.0264 (6)	0.0204 (6)	0.0167 (6)	0.0043 (5)	0.0036 (5)	0.0005 (5)
O14	0.0257 (6)	0.0165 (6)	0.0162 (6)	−0.0024 (5)	0.0045 (5)	0.0003 (4)
O16	0.0326 (7)	0.0181 (6)	0.0118 (5)	−0.0023 (5)	0.0027 (5)	−0.0011 (4)
N2	0.0204 (7)	0.0169 (7)	0.0109 (6)	0.0010 (5)	0.0024 (5)	0.0012 (5)
N11	0.0165 (6)	0.0171 (6)	0.0126 (6)	0.0006 (5)	0.0022 (5)	0.0008 (5)
N13	0.0156 (6)	0.0162 (7)	0.0142 (6)	0.0006 (5)	0.0021 (5)	0.0005 (5)
C1	0.0163 (7)	0.0190 (8)	0.0134 (7)	−0.0032 (6)	0.0020 (6)	−0.0017 (6)
C3	0.0181 (8)	0.0177 (8)	0.0125 (7)	−0.0025 (6)	−0.0001 (6)	0.0011 (6)
C3A	0.0165 (7)	0.0206 (8)	0.0129 (7)	−0.0038 (6)	0.0011 (6)	0.0008 (6)
C4	0.0194 (8)	0.0224 (8)	0.0177 (8)	−0.0048 (6)	−0.0004 (6)	0.0037 (6)
C5	0.0205 (8)	0.0302 (9)	0.0155 (8)	−0.0100 (7)	−0.0020 (6)	0.0075 (7)
C6	0.0227 (8)	0.0353 (10)	0.0099 (7)	−0.0129 (7)	0.0020 (6)	0.0000 (7)
C7	0.0196 (8)	0.0257 (9)	0.0155 (8)	−0.0075 (7)	0.0037 (6)	−0.0043 (6)
C7A	0.0152 (7)	0.0206 (8)	0.0139 (7)	−0.0051 (6)	0.0001 (6)	0.0003 (6)
C12	0.0153 (7)	0.0192 (8)	0.0119 (7)	0.0034 (6)	0.0028 (6)	0.0010 (6)
C14	0.0146 (7)	0.0152 (8)	0.0164 (8)	0.0018 (6)	0.0031 (6)	0.0025 (6)
C15	0.0184 (8)	0.0193 (8)	0.0126 (7)	0.0018 (6)	0.0028 (6)	0.0021 (6)
C16	0.0155 (7)	0.0180 (8)	0.0125 (7)	0.0020 (6)	0.0013 (6)	−0.0013 (6)
C17	0.0310 (9)	0.0177 (8)	0.0215 (9)	−0.0022 (7)	0.0020 (7)	−0.0028 (7)
C18	0.0412 (11)	0.0178 (9)	0.0185 (8)	−0.0038 (7)	0.0031 (7)	−0.0029 (7)

Geometric parameters (Å, º)

O1—C1	1.199 (2)	C4—C5	1.393 (2)
O3—C3	1.2032 (19)	C4—H4	0.95
O14—C14	1.3421 (19)	C5—C6	1.391 (3)
O14—C17	1.4367 (19)	C5—H5	0.95
O16—C16	1.3446 (19)	C6—C7	1.392 (2)
O16—C18	1.445 (2)	C6—H6	0.95
N2—C3	1.417 (2)	C7—C7A	1.386 (2)
N2—C12	1.4216 (19)	C7—H7	0.95
N2—C1	1.4216 (19)	C14—C15	1.381 (2)
N11—C12	1.324 (2)	C15—C16	1.384 (2)
N11—C16	1.3354 (19)	C15—H15	0.95
N13—C12	1.328 (2)	C17—H17A	0.98
N13—C14	1.3375 (19)	C17—H17B	0.98
C1—C7A	1.487 (2)	C17—H17C	0.98
C3—C3A	1.487 (2)	C18—H18A	0.98
C3A—C4	1.384 (2)	C18—H18B	0.98
C3A—C7A	1.384 (2)	C18—H18C	0.98
C14—O14—C17	116.82 (12)	C3A—C7A—C7	121.80 (15)
C16—O16—C18	117.64 (12)	C3A—C7A—C1	109.24 (13)
C3—N2—C12	124.23 (12)	C7—C7A—C1	128.96 (15)
C3—N2—C1	111.84 (12)	N11—C12—N13	129.17 (14)
C12—N2—C1	123.57 (13)	N11—C12—N2	115.88 (14)
C12—N11—C16	114.12 (13)	N13—C12—N2	114.94 (13)
C12—N13—C14	114.17 (13)	N13—C14—O14	118.71 (14)
O1—C1—N2	126.08 (14)	N13—C14—C15	123.50 (14)
O1—C1—C7A	129.04 (14)	C15—C14—O14	117.79 (14)
N2—C1—C7A	104.86 (13)	C14—C15—C16	115.32 (14)
O3—C3—N2	125.50 (14)	C14—C15—H15	122.3
O3—C3—C3A	129.16 (15)	C16—C15—H15	122.3
N2—C3—C3A	105.28 (13)	N11—C16—O16	119.05 (14)
C4—C3A—C7A	121.61 (15)	N11—C16—C15	123.66 (14)
C4—C3A—C3	129.64 (15)	C15—C16—O16	117.28 (13)
C7A—C3A—C3	108.66 (14)	O14—C17—H17A	109.5
C3A—C4—C5	116.96 (16)	O14—C17—H17B	109.5
C3A—C4—H4	121.5	H17A—C17—H17B	109.5
C5—C4—H4	121.5	O14—C17—H17C	109.5
C6—C5—C4	121.41 (15)	H17A—C17—H17C	109.5
C6—C5—H5	119.3	H17B—C17—H17C	109.5
C4—C5—H5	119.3	O16—C18—H18A	109.5
C5—C6—C7	121.29 (15)	O16—C18—H18B	109.5
C5—C6—H6	119.4	H18A—C18—H18B	109.5
C7—C6—H6	119.4	O16—C18—H18C	109.5
C7A—C7—C6	116.91 (16)	H18A—C18—H18C	109.5
C7A—C7—H7	121.5	H18B—C18—H18C	109.5
C6—C7—H7	121.5
C3—N2—C1—O1	−178.98 (15)	N2—C1—C7A—C3A	−1.59 (17)
C12—N2—C1—O1	7.5 (2)	O1—C1—C7A—C7	−3.7 (3)
C3—N2—C1—C7A	−0.56 (17)	N2—C1—C7A—C7	177.93 (15)
C12—N2—C1—C7A	−174.03 (13)	C16—N11—C12—N13	−0.3 (2)
C12—N2—C3—O3	−2.0 (2)	C16—N11—C12—N2	−179.43 (13)
C1—N2—C3—O3	−175.38 (15)	C14—N13—C12—N11	1.9 (2)
C12—N2—C3—C3A	175.73 (13)	C14—N13—C12—N2	−179.04 (13)
C1—N2—C3—C3A	2.31 (17)	C3—N2—C12—N11	51.2 (2)
O3—C3—C3A—C4	−2.4 (3)	C1—N2—C12—N11	−136.10 (15)
N2—C3—C3A—C4	−179.93 (16)	C3—N2—C12—N13	−127.98 (15)
O3—C3—C3A—C7A	174.29 (16)	C1—N2—C12—N13	44.7 (2)
N2—C3—C3A—C7A	−3.28 (17)	C12—N13—C14—O14	179.78 (13)
C7A—C3A—C4—C5	−1.5 (2)	C12—N13—C14—C15	−1.2 (2)
C3—C3A—C4—C5	174.78 (15)	C17—O14—C14—N13	1.3 (2)
C3A—C4—C5—C6	1.1 (2)	C17—O14—C14—C15	−177.78 (14)
C4—C5—C6—C7	0.4 (2)	N13—C14—C15—C16	−0.8 (2)
C5—C6—C7—C7A	−1.5 (2)	O14—C14—C15—C16	178.28 (13)
C4—C3A—C7A—C7	0.4 (2)	C12—N11—C16—O16	179.12 (13)
C3—C3A—C7A—C7	−176.53 (14)	C12—N11—C16—C15	−2.0 (2)
C4—C3A—C7A—C1	180.00 (14)	C18—O16—C16—N11	−6.6 (2)
C3—C3A—C7A—C1	3.03 (17)	C18—O16—C16—C15	174.45 (14)
C6—C7—C7A—C3A	1.0 (2)	C14—C15—C16—N11	2.5 (2)
C6—C7—C7A—C1	−178.42 (15)	C14—C15—C16—O16	−178.60 (13)
O1—C1—C7A—C3A	176.77 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C6—H6···O16^i	0.95	2.47	3.3920 (19)	163

Symmetry code: (i) x, y, z+1.