Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270108017356/hj3078sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270108017356/hj3078Isup2.hkl |
CCDC reference: 697586
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.
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 Uiso(H) = kUeq(C), where k = 1.5 for the methyl groups and k = 1.2 for the ring H atoms.
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).
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) Å3 | 0.37 × 0.24 × 0.22 mm |
Z = 4 |
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 on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.101 | H-atom parameters constrained |
S = 1.12 | w = 1/[σ2(Fo2) + (0.0353P)2 + 0.7987P] where P = (Fo2 + 2Fc2)/3 |
2893 reflections | (Δ/σ)max < 0.001 |
192 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.30 e Å−3 |
C14H11N3O4 | V = 1258.5 (3) Å3 |
Mr = 285.26 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 7.2904 (8) Å | µ = 0.11 mm−1 |
b = 13.896 (2) Å | T = 120 K |
c = 12.5021 (11) Å | 0.37 × 0.24 × 0.22 mm |
β = 96.476 (7)° |
Bruker–Nonius KappaCCD diffractometer | 2893 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2250 reflections with I > 2σ(I) |
Tmin = 0.953, Tmax = 0.975 | Rint = 0.042 |
29699 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.101 | H-atom parameters constrained |
S = 1.12 | Δρmax = 0.27 e Å−3 |
2893 reflections | Δρmin = −0.30 e Å−3 |
192 parameters |
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* |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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) |
D—H···A | D—H | H···A | D···A | D—H···A |
C6—H6···O16i | 0.95 | 2.47 | 3.3920 (19) | 163 |
Symmetry code: (i) x, y, z+1. |
Experimental details
Crystal data | |
Chemical formula | C14H11N3O4 |
Mr | 285.26 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 120 |
a, b, c (Å) | 7.2904 (8), 13.896 (2), 12.5021 (11) |
β (°) | 96.476 (7) |
V (Å3) | 1258.5 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.37 × 0.24 × 0.22 |
Data collection | |
Diffractometer | Bruker–Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.953, 0.975 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 29699, 2893, 2250 |
Rint | 0.042 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.101, 1.12 |
No. of reflections | 2893 |
No. of parameters | 192 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.27, −0.30 |
Computer programs: COLLECT (Hooft, 1999), DIRAX/LSQ (Duisenberg et al., 2000), EVALCCD (Duisenberg et al., 2003), SIR2004 (Burla et al., 2005), OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2003), SHELXL97 (Sheldrick, 2008) and PRPKAPPA (Ferguson, 1999).
N13—C14—O14 | 118.71 (14) | N11—C16—O16 | 119.05 (14) |
C15—C14—O14 | 117.79 (14) | C15—C16—O16 | 117.28 (13) |
C1—N2—C12—N11 | −136.10 (15) | C17—O14—C14—N13 | 1.3 (2) |
C1—N2—C12—N13 | 44.7 (2) | C18—O16—C16—N11 | −6.6 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C6—H6···O16i | 0.95 | 2.47 | 3.3920 (19) | 163 |
Symmetry code: (i) x, y, z+1. |
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.