Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270103010266/ln1168sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270103010266/ln1168Isup2.hkl | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270103010266/ln1168IIsup3.hkl |
CCDC references: 217139; 217140
For the preparation of 5,7-dimethoxyimidazo[1,2-c]pyrimidine, (I), a mixture of bromoacetaldehyde diethyl acetal (6.9 ml, 45.4 mmol) and water (25 ml) was treated with concentrated hydrochloric acid (2.5 ml) and heated until a homogeneous solution was obtained. The pH was adjusted to 5–6 by addition of solid sodium acetate and the resulting solution was added dropwise to a suspension of 4-amino-2,6-dimethoxypyrimidine (0.51 g, 3.2 mmol) in water (13 ml) containing sodium acetate (0.27 g, 3.2 mmol). The mixture was refluxed for 20 min and, after cooling, 1 N NaOH was added until a pH of 8 was achieved. The crude reaction mixture was extracted with dichloromethane. The extract was dried over anhydrous sodium sulfate and the solvent removed in vacuo. The residue was chromatographed on a silica-gel flash column to afford 0.214 g (1.19 mmol, 37%) of compound (I). 1H NMR (300 MHz, CDCl3/TMS): δ 3.92 (s, 3H, CH3O-7), 4.21 (s, 3H, CH3O-5), 6.37 (s, 1H, H-8), 7.42 (s, 2H, H-2 and H-3); 13C NMR (75 MHz, CDCl3/TMS): δ 55.26, 55.87, 82.19, 107,02, 134.03, 148.13, 150.05, 160.56. Recrystallization from ethyl acetate produced a crystalline sample suitable for single-crystal X-ray diffraction analysis (m.p. 387 K).
7-Methoxy-1-methylimidazo[1,2-a]pyrimidin-5(1H)-one, (II), was prepared using a procedure similar to that for compound (I). 5,7-Dimethoxyimidazo[1,2-a]pyrimidine (150 mg, 0.837 mmol) was obtained from 2-amino-4,6-dimethoxypyrimidine (1.64 g, 10.3 mmol) and bromoacetaldehyde diethyl acetal (6.25 ml, 41.2 mmol) (reaction time: 40 min). M.p. 399 K. 1H NMR (300 MHz, CDCl3/TMS): δ 4.03 (s, 3H, CH3O-7), 4.08 (s, 3H, CH3O-5), 5.67 (s, 1H, H-6), 7.34 (d, J = 1,7 Hz, 1H, H-3), 7.42 (d, J = 1,7 Hz, 1H, H-2). 13C NMR (75 MHz, CDCl3/TMS): δ 54.35, 56.72, 77.12, 105.87, 132.06, 149.06, 156.36, 165.12. This compound was placed in a Pyrex tube and heated in an oil bath at 403 K for 20 min. During this period, melting and resolidification of the starting material was observed. The solid residue was directly recrystallized from ethyl acetate to afford 113 mg (0.631 mmol, 75% yield) of compound (II) as crystals suitable for X-ray diffraction analysis (m. p. 449 K). 1H NMR (300 MHz, CDCl3/TMS): δ 3.67 (s, 3H, CH3N), 3.89 (s, 3H, CH3O), 5.39 (s, 1H, H-6), 6.86 (d, J = 3.1 Hz, 1H, H-2), 7.48 (d, J = 3.1 Hz, 1H, H-3). 13C NMR (75 MHz, CDCl3/TMS): δ 31.51, 54.28, 80.01, 106.89, 118.28, 145.72, 158.97, 170.37
Compound (I) crystallized in the triclinic system; space group P1 was assumed and confirmed by the analysis. Compound (II) crystallized in the monoclinic system; space group P21/c was assumed from the systematic absences. In both compounds, H atoms were treated as riding atoms, with C—H distances of 0.95 (aromatic) and 0.98 Å (CH3).
For both compounds, 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: ORTEPII (Johnson, 1976) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).
C8H9N3O2 | Z = 2 |
Mr = 179.18 | F(000) = 188 |
Triclinic, P1 | Dx = 1.484 Mg m−3 |
Hall symbol: -P 1 | Melting point: 387 K |
a = 3.8798 (3) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 8.9183 (6) Å | Cell parameters from 1756 reflections |
c = 12.6224 (11) Å | θ = 3.5–27.4° |
α = 69.426 (3)° | µ = 0.11 mm−1 |
β = 83.093 (4)° | T = 120 K |
γ = 79.189 (4)° | Block, colourless |
V = 400.94 (5) Å3 | 0.22 × 0.14 × 0.10 mm |
Nonius KappaCCD diffractometer | 1182 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed X-ray tube | Rint = 0.058 |
Graphite monochromator | θmax = 27.4°, θmin = 3.5° |
ϕ scans and ω scans with κ offsets | h = −5→4 |
6415 measured reflections | k = −11→11 |
1756 independent reflections | l = −16→16 |
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)] = 0.053 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.134 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0751P)2] where P = (Fo2 + 2Fc2)/3 |
1756 reflections | (Δ/σ)max < 0.001 |
120 parameters | Δρmax = 0.31 e Å−3 |
0 restraints | Δρmin = −0.32 e Å−3 |
C8H9N3O2 | γ = 79.189 (4)° |
Mr = 179.18 | V = 400.94 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 3.8798 (3) Å | Mo Kα radiation |
b = 8.9183 (6) Å | µ = 0.11 mm−1 |
c = 12.6224 (11) Å | T = 120 K |
α = 69.426 (3)° | 0.22 × 0.14 × 0.10 mm |
β = 83.093 (4)° |
Nonius KappaCCD diffractometer | 1182 reflections with I > 2σ(I) |
6415 measured reflections | Rint = 0.058 |
1756 independent reflections |
R[F2 > 2σ(F2)] = 0.053 | 0 restraints |
wR(F2) = 0.134 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.31 e Å−3 |
1756 reflections | Δρmin = −0.32 e Å−3 |
120 parameters |
Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm (Fox & Holmes, 1966) which effectively corrects for absorption effects. High redundancy data were used in the scaling program hence the 'multi-scan' code word was used. No transmission coefficients are available from the program (only scale factors for each frame). The scale factors in the experimental table are calculated from the 'size' command in the SHELXL97 input file. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.0425 (4) | 0.37339 (18) | 0.37285 (12) | 0.0269 (4) | |
C2 | −0.0218 (5) | 0.3154 (2) | 0.28995 (15) | 0.0268 (5) | |
C3 | 0.0311 (5) | 0.4191 (2) | 0.18361 (15) | 0.0258 (4) | |
N4 | 0.1346 (4) | 0.55052 (17) | 0.19891 (11) | 0.0224 (4) | |
C5 | 0.2346 (5) | 0.6905 (2) | 0.12447 (14) | 0.0216 (4) | |
O5 | 0.2332 (3) | 0.70044 (14) | 0.01661 (9) | 0.0263 (4) | |
C51 | 0.3399 (5) | 0.8458 (2) | −0.06818 (14) | 0.0272 (5) | |
N6 | 0.3217 (4) | 0.80121 (17) | 0.15539 (11) | 0.0235 (4) | |
C7 | 0.3118 (5) | 0.7735 (2) | 0.27021 (14) | 0.0233 (4) | |
O7 | 0.3967 (3) | 0.90308 (14) | 0.28836 (9) | 0.0282 (4) | |
C71 | 0.4070 (5) | 0.8903 (2) | 0.40490 (14) | 0.0288 (5) | |
C8 | 0.2278 (5) | 0.6363 (2) | 0.35239 (15) | 0.0245 (4) | |
C9 | 0.1371 (5) | 0.5168 (2) | 0.31598 (14) | 0.0221 (4) | |
H2 | −0.0954 | 0.2135 | 0.3060 | 0.032* | |
H3 | 0.0036 | 0.4051 | 0.1141 | 0.031* | |
H51A | 0.1643 | 0.9401 | −0.0676 | 0.041* | |
H51B | 0.3592 | 0.8346 | −0.1433 | 0.041* | |
H51C | 0.5681 | 0.8605 | −0.0508 | 0.041* | |
H71A | 0.1755 | 0.8743 | 0.4438 | 0.043* | |
H71B | 0.4695 | 0.9900 | 0.4081 | 0.043* | |
H71C | 0.5828 | 0.7978 | 0.4422 | 0.043* | |
H8 | 0.2301 | 0.6217 | 0.4306 | 0.029* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0326 (9) | 0.0241 (8) | 0.0249 (8) | −0.0088 (7) | −0.0017 (7) | −0.0075 (6) |
C2 | 0.0338 (11) | 0.0220 (9) | 0.0268 (10) | −0.0079 (8) | −0.0031 (8) | −0.0087 (8) |
C3 | 0.0329 (11) | 0.0224 (10) | 0.0255 (9) | −0.0061 (8) | −0.0044 (8) | −0.0104 (8) |
N4 | 0.0265 (9) | 0.0204 (8) | 0.0205 (8) | −0.0050 (7) | −0.0020 (6) | −0.0065 (6) |
C5 | 0.0241 (10) | 0.0227 (9) | 0.0187 (9) | −0.0026 (8) | −0.0023 (7) | −0.0077 (7) |
O5 | 0.0389 (8) | 0.0238 (7) | 0.0177 (6) | −0.0096 (6) | −0.0013 (5) | −0.0064 (5) |
C51 | 0.0354 (11) | 0.0250 (10) | 0.0193 (9) | −0.0090 (8) | 0.0016 (8) | −0.0040 (7) |
N6 | 0.0295 (9) | 0.0212 (8) | 0.0206 (8) | −0.0065 (7) | −0.0019 (6) | −0.0064 (6) |
C7 | 0.0263 (10) | 0.0234 (9) | 0.0223 (9) | −0.0037 (8) | −0.0041 (7) | −0.0095 (7) |
O7 | 0.0424 (9) | 0.0250 (7) | 0.0211 (7) | −0.0118 (6) | −0.0027 (6) | −0.0088 (5) |
C71 | 0.0381 (12) | 0.0304 (11) | 0.0230 (10) | −0.0099 (9) | −0.0044 (8) | −0.0121 (8) |
C8 | 0.0279 (10) | 0.0262 (10) | 0.0201 (9) | −0.0047 (8) | −0.0021 (8) | −0.0084 (7) |
C9 | 0.0231 (10) | 0.0236 (9) | 0.0188 (9) | −0.0018 (8) | −0.0032 (7) | −0.0064 (7) |
N1—C9 | 1.324 (2) | C51—H51B | 0.98 |
N1—C2 | 1.384 (2) | C51—H51C | 0.98 |
C2—C3 | 1.353 (3) | N6—C7 | 1.379 (2) |
C2—H2 | 0.95 | C7—O7 | 1.358 (2) |
C3—N4 | 1.388 (2) | C7—C8 | 1.362 (2) |
C3—H3 | 0.95 | O7—C71 | 1.4398 (19) |
N4—C5 | 1.364 (2) | C71—H71A | 0.98 |
N4—C9 | 1.402 (2) | C71—H71B | 0.98 |
C5—N6 | 1.292 (2) | C71—H71C | 0.98 |
C5—O5 | 1.3335 (19) | C8—C9 | 1.412 (2) |
O5—C51 | 1.455 (2) | C8—H8 | 0.95 |
C51—H51A | 0.98 | ||
C9—N1—C2 | 104.59 (15) | H51B—C51—H51C | 109.5 |
C3—C2—N1 | 112.94 (16) | C5—N6—C7 | 117.12 (14) |
C3—C2—H2 | 123.5 | O7—C7—C8 | 125.53 (15) |
N1—C2—H2 | 123.5 | O7—C7—N6 | 109.84 (14) |
C2—C3—N4 | 104.55 (15) | C8—C7—N6 | 124.63 (15) |
C2—C3—H3 | 127.7 | C7—O7—C71 | 116.35 (13) |
N4—C3—H3 | 127.7 | O7—C71—H71A | 109.5 |
C5—N4—C3 | 132.45 (14) | O7—C71—H71B | 109.5 |
C5—N4—C9 | 120.28 (14) | H71A—C71—H71B | 109.5 |
C3—N4—C9 | 107.23 (13) | O7—C71—H71C | 109.5 |
N6—C5—O5 | 123.74 (15) | H71A—C71—H71C | 109.5 |
N6—C5—N4 | 123.52 (15) | H71B—C71—H71C | 109.5 |
O5—C5—N4 | 112.75 (14) | C7—C8—C9 | 116.92 (16) |
C5—O5—C51 | 116.14 (13) | C7—C8—H8 | 121.5 |
O5—C51—H51A | 109.5 | C9—C8—H8 | 121.5 |
O5—C51—H51B | 109.5 | N1—C9—N4 | 110.69 (14) |
H51A—C51—H51B | 109.5 | N1—C9—C8 | 131.85 (16) |
O5—C51—H51C | 109.5 | N4—C9—C8 | 117.44 (15) |
H51A—C51—H51C | 109.5 | ||
C9—N1—C2—C3 | 0.1 (2) | C5—N6—C7—C8 | 2.2 (3) |
N1—C2—C3—N4 | 0.0 (2) | C8—C7—O7—C71 | 1.9 (3) |
C2—C3—N4—C5 | 177.70 (18) | N6—C7—O7—C71 | −178.37 (14) |
C2—C3—N4—C9 | 0.0 (2) | O7—C7—C8—C9 | 178.19 (16) |
C3—N4—C5—N6 | 179.63 (18) | N6—C7—C8—C9 | −1.5 (3) |
C9—N4—C5—N6 | −2.9 (3) | C2—N1—C9—N4 | −0.1 (2) |
C3—N4—C5—O5 | −0.5 (3) | C2—N1—C9—C8 | 178.37 (19) |
C9—N4—C5—O5 | 177.01 (14) | C5—N4—C9—N1 | −177.97 (15) |
N6—C5—O5—C51 | 0.4 (2) | C3—N4—C9—N1 | 0.1 (2) |
N4—C5—O5—C51 | −179.47 (15) | C5—N4—C9—C8 | 3.3 (2) |
O5—C5—N6—C7 | −179.72 (16) | C3—N4—C9—C8 | −178.62 (16) |
N4—C5—N6—C7 | 0.1 (3) | C7—C8—C9—N1 | −179.59 (19) |
C5—N6—C7—O7 | −177.62 (15) | C7—C8—C9—N4 | −1.2 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C8—H8···N1i | 0.95 | 2.59 | 3.476 (2) | 155 |
C3—H3···O5ii | 0.95 | 2.50 | 3.391 (2) | 157 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, −y+1, −z. |
C8H9N3O2 | F(000) = 376 |
Mr = 179.18 | Dx = 1.436 Mg m−3 |
Monoclinic, P21/c | Melting point: 449 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 8.5917 (6) Å | Cell parameters from 1855 reflections |
b = 6.7484 (5) Å | θ = 3.3–27.5° |
c = 14.3054 (14) Å | µ = 0.11 mm−1 |
β = 91.648 (3)° | T = 120 K |
V = 829.09 (12) Å3 | Plate, colourless |
Z = 4 | 0.30 × 0.28 × 0.02 mm |
Nonius KappaCCD diffractometer | 993 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed X-ray tube | Rint = 0.087 |
Graphite monochromator | θmax = 27.5°, θmin = 3.3° |
ϕ scans and ω scans with κ offsets | h = −11→10 |
6217 measured reflections | k = −8→8 |
1855 independent reflections | l = −13→18 |
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)] = 0.052 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.122 | H-atom parameters constrained |
S = 0.94 | w = 1/[σ2(Fo2) + (0.0513P)2] where P = (Fo2 + 2Fc2)/3 |
1855 reflections | (Δ/σ)max < 0.001 |
120 parameters | Δρmax = 0.21 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
C8H9N3O2 | V = 829.09 (12) Å3 |
Mr = 179.18 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.5917 (6) Å | µ = 0.11 mm−1 |
b = 6.7484 (5) Å | T = 120 K |
c = 14.3054 (14) Å | 0.30 × 0.28 × 0.02 mm |
β = 91.648 (3)° |
Nonius KappaCCD diffractometer | 993 reflections with I > 2σ(I) |
6217 measured reflections | Rint = 0.087 |
1855 independent reflections |
R[F2 > 2σ(F2)] = 0.052 | 0 restraints |
wR(F2) = 0.122 | H-atom parameters constrained |
S = 0.94 | Δρmax = 0.21 e Å−3 |
1855 reflections | Δρmin = −0.29 e Å−3 |
120 parameters |
Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm (Fox & Holmes, 1966) which effectively corrects for absorption effects. High redundancy data were used in the scaling program hence the 'multi-scan' code word was used. No transmission coefficients are available from the program (only scale factors for each frame). The scale factors in the experimental table are calculated from the 'size' command in the SHELXL97 input file. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.6851 (2) | 1.0258 (3) | 0.62431 (13) | 0.0233 (5) | |
C1 | 0.7393 (3) | 1.1826 (3) | 0.68716 (17) | 0.0317 (6) | |
C2 | 0.5884 (3) | 0.8698 (3) | 0.64538 (17) | 0.0249 (5) | |
C3 | 0.5694 (3) | 0.7536 (3) | 0.56916 (16) | 0.0269 (6) | |
N4 | 0.6585 (2) | 0.8409 (3) | 0.49968 (12) | 0.0223 (5) | |
C5 | 0.6857 (3) | 0.7744 (3) | 0.40684 (15) | 0.0242 (5) | |
O5 | 0.61694 (19) | 0.6226 (2) | 0.37863 (11) | 0.0310 (4) | |
C6 | 0.7908 (3) | 0.8954 (3) | 0.36131 (16) | 0.0243 (5) | |
C7 | 0.8540 (3) | 1.0617 (3) | 0.40352 (16) | 0.0236 (5) | |
O7 | 0.95467 (18) | 1.1700 (2) | 0.35333 (11) | 0.0266 (4) | |
C71 | 1.0034 (3) | 1.3575 (3) | 0.39178 (17) | 0.0316 (6) | |
N8 | 0.8256 (2) | 1.1255 (3) | 0.49053 (12) | 0.0223 (5) | |
C9 | 0.7291 (2) | 1.0068 (3) | 0.53494 (16) | 0.0210 (5) | |
H1A | 0.6859 | 1.3067 | 0.6707 | 0.048* | |
H1B | 0.8518 | 1.1999 | 0.6814 | 0.048* | |
H1C | 0.7164 | 1.1467 | 0.7517 | 0.048* | |
H2 | 0.5425 | 0.8478 | 0.7041 | 0.030* | |
H3 | 0.5083 | 0.6366 | 0.5637 | 0.032* | |
H6 | 0.8198 | 0.8624 | 0.2996 | 0.029* | |
H71A | 1.0548 | 1.3365 | 0.4530 | 0.047* | |
H71B | 0.9123 | 1.4430 | 0.3989 | 0.047* | |
H71C | 1.0763 | 1.4209 | 0.3497 | 0.047* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0243 (10) | 0.0259 (10) | 0.0195 (11) | −0.0008 (9) | −0.0002 (8) | −0.0026 (9) |
C1 | 0.0351 (14) | 0.0360 (14) | 0.0240 (14) | −0.0051 (12) | 0.0000 (11) | −0.0053 (11) |
C2 | 0.0231 (12) | 0.0298 (12) | 0.0220 (13) | −0.0004 (11) | 0.0032 (10) | 0.0034 (11) |
C3 | 0.0279 (12) | 0.0284 (13) | 0.0244 (14) | −0.0003 (11) | 0.0033 (10) | 0.0041 (11) |
N4 | 0.0261 (10) | 0.0243 (10) | 0.0166 (10) | 0.0018 (9) | 0.0017 (8) | 0.0009 (8) |
C5 | 0.0276 (12) | 0.0254 (12) | 0.0196 (13) | 0.0017 (11) | −0.0011 (10) | −0.0019 (10) |
O5 | 0.0412 (10) | 0.0283 (9) | 0.0234 (9) | −0.0047 (8) | 0.0021 (8) | −0.0033 (8) |
C6 | 0.0270 (12) | 0.0292 (13) | 0.0169 (12) | 0.0035 (11) | 0.0011 (10) | −0.0002 (10) |
C7 | 0.0224 (12) | 0.0284 (12) | 0.0198 (13) | 0.0047 (11) | 0.0002 (10) | 0.0060 (10) |
O7 | 0.0289 (9) | 0.0295 (9) | 0.0217 (9) | −0.0036 (7) | 0.0052 (7) | 0.0010 (7) |
C71 | 0.0351 (14) | 0.0317 (13) | 0.0283 (14) | −0.0069 (12) | 0.0041 (11) | −0.0009 (11) |
N8 | 0.0212 (10) | 0.0273 (10) | 0.0186 (11) | 0.0009 (9) | 0.0014 (8) | 0.0012 (8) |
C9 | 0.0199 (11) | 0.0233 (12) | 0.0195 (12) | 0.0045 (10) | −0.0023 (10) | 0.0010 (10) |
N1—C9 | 1.350 (3) | C5—O5 | 1.244 (3) |
N1—C2 | 1.380 (3) | C5—C6 | 1.393 (3) |
N1—C1 | 1.456 (3) | C6—C7 | 1.378 (3) |
C1—H1A | 0.98 | C6—H6 | 0.95 |
C1—H1B | 0.98 | C7—N8 | 1.346 (3) |
C1—H1C | 0.98 | C7—O7 | 1.354 (3) |
C2—C3 | 1.349 (3) | O7—C71 | 1.437 (3) |
C2—H2 | 0.95 | C71—H71A | 0.98 |
C3—N4 | 1.401 (3) | C71—H71B | 0.98 |
C3—H3 | 0.95 | C71—H71C | 0.98 |
N4—C9 | 1.363 (3) | N8—C9 | 1.328 (3) |
N4—C5 | 1.428 (3) | ||
C9—N1—C2 | 108.71 (18) | O5—C5—N4 | 118.16 (19) |
C9—N1—C1 | 124.14 (19) | C6—C5—N4 | 112.10 (19) |
C2—N1—C1 | 127.10 (19) | C7—C6—C5 | 121.7 (2) |
N1—C1—H1A | 109.5 | C7—C6—H6 | 119.2 |
N1—C1—H1B | 109.5 | C5—C6—H6 | 119.2 |
H1A—C1—H1B | 109.5 | N8—C7—O7 | 117.0 (2) |
N1—C1—H1C | 109.5 | N8—C7—C6 | 125.9 (2) |
H1A—C1—H1C | 109.5 | O7—C7—C6 | 117.1 (2) |
H1B—C1—H1C | 109.5 | C7—O7—C71 | 117.10 (18) |
C3—C2—N1 | 109.1 (2) | O7—C71—H71A | 109.5 |
C3—C2—H2 | 125.5 | O7—C71—H71B | 109.5 |
N1—C2—H2 | 125.5 | H71A—C71—H71B | 109.5 |
C2—C3—N4 | 105.82 (19) | O7—C71—H71C | 109.5 |
C2—C3—H3 | 127.1 | H71A—C71—H71C | 109.5 |
N4—C3—H3 | 127.1 | H71B—C71—H71C | 109.5 |
C9—N4—C3 | 109.22 (18) | C9—N8—C7 | 112.43 (18) |
C9—N4—C5 | 121.30 (18) | N8—C9—N1 | 126.2 (2) |
C3—N4—C5 | 129.39 (19) | N8—C9—N4 | 126.6 (2) |
O5—C5—C6 | 129.7 (2) | N1—C9—N4 | 107.17 (18) |
C9—N1—C2—C3 | −0.8 (3) | C6—C7—O7—C71 | 171.5 (2) |
C1—N1—C2—C3 | −178.2 (2) | O7—C7—N8—C9 | −178.21 (18) |
N1—C2—C3—N4 | 0.4 (2) | C6—C7—N8—C9 | 1.2 (3) |
C2—C3—N4—C9 | 0.1 (2) | C7—N8—C9—N1 | 176.4 (2) |
C2—C3—N4—C5 | 176.8 (2) | C7—N8—C9—N4 | −2.1 (3) |
C9—N4—C5—O5 | −179.57 (19) | C2—N1—C9—N8 | −177.9 (2) |
C3—N4—C5—O5 | 4.0 (3) | C1—N1—C9—N8 | −0.5 (3) |
C9—N4—C5—C6 | 0.9 (3) | C2—N1—C9—N4 | 0.8 (2) |
C3—N4—C5—C6 | −175.5 (2) | C1—N1—C9—N4 | 178.30 (19) |
O5—C5—C6—C7 | 178.8 (2) | C3—N4—C9—N8 | 178.2 (2) |
N4—C5—C6—C7 | −1.8 (3) | C5—N4—C9—N8 | 1.1 (3) |
C5—C6—C7—N8 | 0.8 (4) | C3—N4—C9—N1 | −0.5 (2) |
C5—C6—C7—O7 | −179.8 (2) | C5—N4—C9—N1 | −177.62 (18) |
N8—C7—O7—C71 | −9.1 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C3—H3···O5i | 0.95 | 2.22 | 3.104 (3) | 153 |
C2—H2···O5ii | 0.95 | 2.57 | 3.339 (3) | 139 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z+1/2. |
Experimental details
(I) | (II) | |
Crystal data | ||
Chemical formula | C8H9N3O2 | C8H9N3O2 |
Mr | 179.18 | 179.18 |
Crystal system, space group | Triclinic, P1 | Monoclinic, P21/c |
Temperature (K) | 120 | 120 |
a, b, c (Å) | 3.8798 (3), 8.9183 (6), 12.6224 (11) | 8.5917 (6), 6.7484 (5), 14.3054 (14) |
α, β, γ (°) | 69.426 (3), 83.093 (4), 79.189 (4) | 90, 91.648 (3), 90 |
V (Å3) | 400.94 (5) | 829.09 (12) |
Z | 2 | 4 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.11 | 0.11 |
Crystal size (mm) | 0.22 × 0.14 × 0.10 | 0.30 × 0.28 × 0.02 |
Data collection | ||
Diffractometer | Nonius KappaCCD diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | – | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6415, 1756, 1182 | 6217, 1855, 993 |
Rint | 0.058 | 0.087 |
(sin θ/λ)max (Å−1) | 0.647 | 0.649 |
Refinement | ||
R[F2 > 2σ(F2)], wR(F2), S | 0.053, 0.134, 1.03 | 0.052, 0.122, 0.94 |
No. of reflections | 1756 | 1855 |
No. of parameters | 120 | 120 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.31, −0.32 | 0.21, −0.29 |
Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO–SMN (Otwinowski & Minor, 1997), DENZO–SMN, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1976) and PLATON (Spek, 2003), SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).
N1—C9 | 1.324 (2) | C5—O5 | 1.3335 (19) |
N1—C2 | 1.384 (2) | O5—C51 | 1.455 (2) |
C2—C3 | 1.353 (3) | N6—C7 | 1.379 (2) |
C3—N4 | 1.388 (2) | C7—O7 | 1.358 (2) |
N4—C5 | 1.364 (2) | C7—C8 | 1.362 (2) |
N4—C9 | 1.402 (2) | O7—C71 | 1.4398 (19) |
C5—N6 | 1.292 (2) | C8—C9 | 1.412 (2) |
C9—N1—C2 | 104.59 (15) | C5—N6—C7 | 117.12 (14) |
C3—C2—N1 | 112.94 (16) | O7—C7—C8 | 125.53 (15) |
C2—C3—N4 | 104.55 (15) | O7—C7—N6 | 109.84 (14) |
C5—N4—C3 | 132.45 (14) | C8—C7—N6 | 124.63 (15) |
C5—N4—C9 | 120.28 (14) | C7—O7—C71 | 116.35 (13) |
C3—N4—C9 | 107.23 (13) | C7—C8—C9 | 116.92 (16) |
N6—C5—O5 | 123.74 (15) | N1—C9—N4 | 110.69 (14) |
N6—C5—N4 | 123.52 (15) | N1—C9—C8 | 131.85 (16) |
O5—C5—N4 | 112.75 (14) | N4—C9—C8 | 117.44 (15) |
C5—O5—C51 | 116.14 (13) | ||
N6—C5—O5—C51 | 0.4 (2) | C8—C7—O7—C71 | 1.9 (3) |
N4—C5—O5—C51 | −179.47 (15) | N6—C7—O7—C71 | −178.37 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
C8—H8···N1i | 0.95 | 2.59 | 3.476 (2) | 155 |
C3—H3···O5ii | 0.95 | 2.50 | 3.391 (2) | 157 |
Symmetry codes: (i) −x, −y+1, −z+1; (ii) −x, −y+1, −z. |
N1—C9 | 1.350 (3) | C5—O5 | 1.244 (3) |
N1—C2 | 1.380 (3) | C5—C6 | 1.393 (3) |
N1—C1 | 1.456 (3) | C6—C7 | 1.378 (3) |
C2—C3 | 1.349 (3) | C7—N8 | 1.346 (3) |
C3—N4 | 1.401 (3) | C7—O7 | 1.354 (3) |
N4—C9 | 1.363 (3) | O7—C71 | 1.437 (3) |
N4—C5 | 1.428 (3) | N8—C9 | 1.328 (3) |
C9—N1—C2 | 108.71 (18) | C6—C5—N4 | 112.10 (19) |
C9—N1—C1 | 124.14 (19) | C7—C6—C5 | 121.7 (2) |
C2—N1—C1 | 127.10 (19) | N8—C7—O7 | 117.0 (2) |
C3—C2—N1 | 109.1 (2) | N8—C7—C6 | 125.9 (2) |
C2—C3—N4 | 105.82 (19) | O7—C7—C6 | 117.1 (2) |
C9—N4—C3 | 109.22 (18) | C7—O7—C71 | 117.10 (18) |
C9—N4—C5 | 121.30 (18) | C9—N8—C7 | 112.43 (18) |
C3—N4—C5 | 129.39 (19) | N8—C9—N1 | 126.2 (2) |
O5—C5—C6 | 129.7 (2) | N8—C9—N4 | 126.6 (2) |
O5—C5—N4 | 118.16 (19) | N1—C9—N4 | 107.17 (18) |
N8—C7—O7—C71 | −9.1 (3) | C6—C7—O7—C71 | 171.5 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C3—H3···O5i | 0.95 | 2.22 | 3.104 (3) | 153 |
C2—H2···O5ii | 0.95 | 2.57 | 3.339 (3) | 139 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z+1/2. |
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Imidazopyrimidine derivatives are a group of fused heterocyclic systems of particular interest due to their resemblance to the ubiquitous biologically important purine, and thence their potential as antimetabolites showing useful biological activities. In fact, some imidazo[1,2-a]pyrimidines have shown antifungal (Rival et al., 1991) and anti-inflammatory/analgesic activities (Sacchi et al., 1997). In this paper, we report the molecular and supramolecular structure of two isomeric examples of such fused heterocyclic derivatives, namely 5,7-dimethoxyimidazo[1,2-c]pyrimidine, (I), and 7-methoxy-1-methylimidazo [1,2-a]pyrimidin-5(1H)-one, (II). The former was prepared by reaction of commercial 4-amino-2,6-dimethoxypyrimidine with bromoacetaldehyde (Quijano et al. 1994). The latter was obtained in good yield by fusion of the crystalline intermediate 5,7-dimethoxyimidazo[1,2-a]pyrimidine, which was prepared by reaction of commercial 2-amino-4,6-dimethoxypyrimidine with bromoacetaldehyde.
There are no unusual bond lengths or angles in (I) and (II), however, the bond distances along the fused heterocycle perimeter of (I) show a clear alternation in single- and double-bond character, so pointing to the low aromatic nature of this compound (Table 1). In both compounds, the six- and five-membered rings are planar, with the angle between the rings in being 1.40 (10) and 3.13 (12)° in (I) and (II), respectively. In (I), the torsion angles about the C5—O5 and C7—O7 bonds show that the methoxy groups are coplanar with the ring system. In (II), however, the torsion angles about the C7—O7 bond show that the methoxy group is tilted out of the plane of the ring system (Table 3).
In the absence of any donors for conventional hydrogen bonds, the supramolecular structures are controlled by the formation of weak C—H···N and C—H···O hydrogen bonds in (I) and by weak C—H···O hydrogen bonds in (II). In the case of (I), these are weaker than in (II), as evidenced by the C8···N1 and C3···O5 distances of 3.476 (2) and 3.391 (2) Å, respectively, for (I), and the C3···O5 and C2···O5 distances of 3.104 (3) and 3.339 (3) Å, respectively, in for (II). Details of the hydrogen bonding are given in Tables 2 and 4.
In (I), the molecules are linked to form one-dimensional ribbons of centrosymmetric dimers which run parallel to the c axis (Fig. 3). Atom C8 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H8, to ring atom N1 in the molecule at (-x, 1 − y, 1 − z), so generating a centrosymmetric R22(8) ring (Bernstein et al., 1995) centred at (0, 1/2, 1/2). Atom C3 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H3, to methoxy atom O5 in the molecule at (-x, 1 − y, −z), so generating a centrosymmetric R22(10) ring centred at (0, 1/2, 0). Alternatively, the molecules can be viewed as being linked head-to-tail by two centrosymmetrically related C22(10) chains. There are no other direction-specific contacts in the structure.
In (II), atom C2 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H2, to O5 in the molecule at (x, 1.5 − y, 0.5 + z), so generating a C(6) chain which runs parallel to the c axis (Fig. 4). This chain is produced by the action of the c-glide plane at y = 0.75. This chain is then linked to an antiparallel chain produced by the action of centres-of-symmetry to form a corrugated ribbon which lies approximately parallel to the (010) plane. In the crosslink, atom C3 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H3, to atom O5 in the molecule at (1 − x, 1 − y, 1 − z), so generating a centrosymmetric R22(10) ring centred at (1/2, 1/2, 1/2). An R44(22) ring centred at (1/2, 1/2, 1) is also formed involving six molecules, with four C2–H2···O5 and two C3–H3···O5 interactions. In this ring, two molecules donate and accept one interaction each, two accept two interactions to the same atom and two donate two interactions via two different H atoms each (Fig. 4). These ribbons are then linked via further C3–H3···O5 crosslinks, extending the structure parallel to the b axis, thereby forming corrugated sheets which lie in the (100) plane.
The molecules stack above each other such that atom N4 of the five-membered ring lies almost directly above the centroid of the five-membered ring at (1 − x, 1 − y, −z). The inter-centroid distance is 3.5221 (14) Å, the perpedicular distance between the centroid of one ring and the plane of the other is 3.301 Å, and the offset between centroids is 1.228 Å. A view of the stacking is shown in Fig. 5. Fig. 6 shows a stereoview of the three-dimensional structure formed by the interaction of the sheets and also the molecular stacking.