In 2-amino-4,6-dimethoxy-5-nitropyrimidine, C
6H
8N
4O
4, the molecules are linked by one N-H
N and one N-H
O hydrogen bond to form sheets built from alternating
R(8) and
R(32) rings. In isomeric 4-amino-2,6-dimethoxy-5-nitropyrimidine, C
6H
8N
4O
4, which crystallizes with
Z' = 2 in
P, the two independent molecules are linked into a dimer by two independent N-H
N hydrogen bonds. These dimers are linked into sheets by a combination of two-centre C-H
O and three-centre C-H
(O)
2 hydrogen bonds, and the sheets are further linked by two independent aromatic
-
-stacking interactions to form a three-dimensional structure.
Supporting information
CCDC references: 204041; 204042
Samples of (I) and (II) were prepared by oxidation of the corresponding nitroso compounds (Marchal et al., 2002) with 3-chloroperoxobenzoic acid (1.1 molar equivalents) in acetonitrile solution. After recrystallization from ethyl acetate, the products had m.p. of 462 [(I)] and 452 K [(II)]. Spectroscopic analysis for (III) Should this be (I)?: 1H NMR (δ, DMSO-d6, p.p.m.): 3.91 (s, 6H, O—CH3), 7.65 (bs, 2H, NH2, exchanges with D2O); 13C NMR (δ, DMSO-d6, p.p.m.): 54.6, 112.2, 160.7, 163.5. Spectroscopic analysis for (IV) Should this be (II)?: 1H NMR (δ, DMSO-d6, p.p.m.): 3.88 (s, 3H, O—CH3), 3.93 (s, 3H, O—CH3), 8.33 (bs, 2H, NH2, exchanges with D2O); 13C NMR (δ, DMSO-d6, p.p.m.): 54.8, 54.9, 111.6, 160.1, 163.3, 165.9. Crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation of solutions in ethyl acetate [(I)] or diethyl ether [(II)].
For compound (I), the space group P21/c was uniquely assigned from the systematic absences. Compound (II) is triclinic, and space group P1 was selected and confirmed by the subsequent analysis. H atoms were treated as riding atoms, with C—H distances of 0.98 and N—H distances of 0.88 Å.
For both compounds, data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997). Data reduction: DENZO-SMN for (I); DENZO-SMN (Otwinowski & Minor, 1997) for (II). For both compounds, program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2002); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
(I) 2-Amino-4,6-dimethoxy-5-nitropyrimidine
top
Crystal data top
C6H8N4O4 | F(000) = 416 |
Mr = 200.16 | Dx = 1.646 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1835 reflections |
a = 7.3443 (2) Å | θ = 3.0–27.5° |
b = 7.8437 (2) Å | µ = 0.14 mm−1 |
c = 14.9129 (4) Å | T = 120 K |
β = 109.9470 (13)° | Block, yellow |
V = 807.54 (4) Å3 | 0.50 × 0.40 × 0.15 mm |
Z = 4 | |
Data collection top
Nonius KappaCCD area-detector diffractometer | 1835 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 1569 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.062 |
ϕ scans, and ω scans with κ offsets | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −8→9 |
Tmin = 0.936, Tmax = 0.985 | k = −9→10 |
6065 measured reflections | l = −19→17 |
Refinement top
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)] = 0.040 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.110 | H-atom parameters constrained |
S = 1.00 | w = 1/[σ2(Fo2) + (0.0617P)2 + 0.2772P] where P = (Fo2 + 2Fc2)/3 |
1835 reflections | (Δ/σ)max < 0.001 |
129 parameters | Δρmax = 0.26 e Å−3 |
0 restraints | Δρmin = −0.32 e Å−3 |
Crystal data top
C6H8N4O4 | V = 807.54 (4) Å3 |
Mr = 200.16 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.3443 (2) Å | µ = 0.14 mm−1 |
b = 7.8437 (2) Å | T = 120 K |
c = 14.9129 (4) Å | 0.50 × 0.40 × 0.15 mm |
β = 109.9470 (13)° | |
Data collection top
Nonius KappaCCD area-detector diffractometer | 1835 independent reflections |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | 1569 reflections with I > 2σ(I) |
Tmin = 0.936, Tmax = 0.985 | Rint = 0.062 |
6065 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.040 | 0 restraints |
wR(F2) = 0.110 | H-atom parameters constrained |
S = 1.00 | Δρmax = 0.26 e Å−3 |
1835 reflections | Δρmin = −0.32 e Å−3 |
129 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.22558 (15) | 0.10695 (13) | 0.46351 (7) | 0.0133 (3) | |
C2 | 0.21598 (18) | 0.02873 (16) | 0.38128 (9) | 0.0131 (3) | |
N2 | 0.37375 (15) | −0.04917 (15) | 0.37713 (8) | 0.0164 (3) | |
N3 | 0.06003 (15) | 0.02311 (14) | 0.30037 (7) | 0.0136 (2) | |
C4 | −0.09743 (18) | 0.10148 (16) | 0.30191 (9) | 0.0127 (3) | |
O4 | −0.25573 (13) | 0.09551 (12) | 0.22500 (6) | 0.0150 (2) | |
C41 | −0.24346 (19) | −0.00391 (18) | 0.14537 (9) | 0.0176 (3) | |
C5 | −0.10622 (17) | 0.18542 (16) | 0.38375 (9) | 0.0130 (3) | |
N5 | −0.27988 (15) | 0.26800 (14) | 0.38510 (8) | 0.0140 (3) | |
O51 | −0.39187 (13) | 0.32829 (12) | 0.30986 (7) | 0.0193 (2) | |
O52 | −0.31205 (14) | 0.27579 (13) | 0.46063 (7) | 0.0206 (3) | |
C6 | 0.06565 (18) | 0.18391 (15) | 0.46433 (9) | 0.0127 (3) | |
O6 | 0.06585 (13) | 0.26712 (12) | 0.54186 (6) | 0.0164 (2) | |
C61 | 0.24604 (19) | 0.27703 (18) | 0.62109 (9) | 0.0172 (3) | |
H2A | 0.4808 | −0.0489 | 0.4271 | 0.020* | |
H2B | 0.3711 | −0.1010 | 0.3244 | 0.020* | |
H41A | −0.1467 | 0.0468 | 0.1216 | 0.026* | |
H41B | −0.3699 | −0.0047 | 0.0943 | 0.026* | |
H41C | −0.2054 | −0.1210 | 0.1664 | 0.026* | |
H61A | 0.2902 | 0.1617 | 0.6435 | 0.026* | |
H61B | 0.2263 | 0.3422 | 0.6731 | 0.026* | |
H61C | 0.3439 | 0.3338 | 0.6005 | 0.026* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0123 (5) | 0.0131 (5) | 0.0131 (5) | 0.0007 (4) | 0.0025 (4) | 0.0004 (4) |
C2 | 0.0129 (6) | 0.0120 (6) | 0.0134 (6) | −0.0009 (4) | 0.0030 (5) | 0.0019 (5) |
N2 | 0.0123 (5) | 0.0226 (6) | 0.0120 (5) | 0.0035 (4) | 0.0009 (4) | −0.0042 (4) |
N3 | 0.0124 (5) | 0.0145 (5) | 0.0125 (5) | 0.0007 (4) | 0.0026 (4) | −0.0003 (4) |
C4 | 0.0121 (6) | 0.0114 (6) | 0.0129 (6) | −0.0013 (4) | 0.0020 (5) | 0.0024 (5) |
O4 | 0.0121 (5) | 0.0175 (5) | 0.0124 (5) | 0.0012 (3) | 0.0004 (4) | −0.0025 (4) |
C41 | 0.0161 (6) | 0.0222 (7) | 0.0130 (6) | 0.0001 (5) | 0.0030 (5) | −0.0039 (5) |
C5 | 0.0118 (6) | 0.0118 (6) | 0.0146 (6) | 0.0014 (4) | 0.0035 (5) | 0.0010 (5) |
N5 | 0.0134 (5) | 0.0130 (5) | 0.0145 (5) | 0.0000 (4) | 0.0034 (4) | −0.0011 (4) |
O51 | 0.0177 (5) | 0.0224 (5) | 0.0153 (5) | 0.0074 (4) | 0.0024 (4) | 0.0047 (4) |
O52 | 0.0178 (5) | 0.0303 (6) | 0.0145 (5) | 0.0048 (4) | 0.0065 (4) | −0.0006 (4) |
C6 | 0.0142 (6) | 0.0102 (6) | 0.0129 (6) | −0.0009 (4) | 0.0037 (5) | 0.0005 (5) |
O6 | 0.0133 (5) | 0.0204 (5) | 0.0129 (5) | 0.0020 (3) | 0.0010 (4) | −0.0051 (4) |
C61 | 0.0138 (6) | 0.0215 (7) | 0.0136 (6) | −0.0015 (5) | 0.0014 (5) | −0.0056 (5) |
Geometric parameters (Å, º) top
N1—C2 | 1.3515 (17) | C6—O6 | 1.3273 (15) |
C2—N3 | 1.3515 (16) | N2—H2A | 0.88 |
N3—C4 | 1.3167 (16) | N2—H2B | 0.88 |
C4—C5 | 1.4076 (18) | O4—C41 | 1.4490 (15) |
C5—C6 | 1.4151 (17) | C41—H41A | 0.98 |
C6—N1 | 1.3244 (16) | C41—H41B | 0.98 |
C2—N2 | 1.3299 (16) | C41—H41C | 0.98 |
C5—N5 | 1.4367 (16) | O6—C61 | 1.4445 (15) |
N5—O51 | 1.2368 (14) | C61—H61A | 0.98 |
N5—O52 | 1.2287 (14) | C61—H61B | 0.98 |
C4—O4 | 1.3265 (15) | C61—H61C | 0.98 |
| | | |
C6—N1—C2 | 116.32 (11) | H41B—C41—H41C | 109.5 |
N2—C2—N1 | 118.31 (11) | C4—C5—C6 | 116.16 (11) |
N2—C2—N3 | 115.47 (11) | C4—C5—N5 | 121.78 (11) |
N1—C2—N3 | 126.22 (11) | C6—C5—N5 | 122.06 (11) |
C2—N2—H2A | 120.0 | O52—N5—O51 | 122.44 (11) |
C2—N2—H2B | 120.0 | O52—N5—C5 | 118.98 (11) |
H2A—N2—H2B | 120.0 | O51—N5—C5 | 118.58 (11) |
C4—N3—C2 | 116.82 (11) | N1—C6—O6 | 119.65 (11) |
N3—C4—O4 | 118.97 (11) | N1—C6—C5 | 122.21 (11) |
N3—C4—C5 | 122.26 (11) | O6—C6—C5 | 118.11 (11) |
O4—C4—C5 | 118.71 (11) | C6—O6—C61 | 117.87 (10) |
C4—O4—C41 | 116.52 (10) | O6—C61—H61A | 109.5 |
O4—C41—H41A | 109.5 | O6—C61—H61B | 109.5 |
O4—C41—H41B | 109.5 | H61A—C61—H61B | 109.5 |
H41A—C41—H41B | 109.5 | O6—C61—H61C | 109.5 |
O4—C41—H41C | 109.5 | H61A—C61—H61C | 109.5 |
H41A—C41—H41C | 109.5 | H61B—C61—H61C | 109.5 |
| | | |
C6—N1—C2—N2 | 179.55 (11) | C6—C5—N5—O52 | −30.26 (17) |
C6—N1—C2—N3 | 0.55 (18) | C4—C5—N5—O51 | −29.94 (17) |
N2—C2—N3—C4 | −178.97 (11) | C6—C5—N5—O51 | 149.95 (12) |
N1—C2—N3—C4 | 0.05 (19) | C2—N1—C6—O6 | −178.28 (11) |
C2—N3—C4—O4 | −178.20 (11) | C2—N1—C6—C5 | −0.25 (17) |
C2—N3—C4—C5 | −0.96 (18) | C4—C5—C6—N1 | −0.56 (18) |
C5—C4—O4—C41 | −175.20 (11) | N5—C5—C6—N1 | 179.55 (11) |
N3—C4—C5—C6 | 1.20 (18) | C4—C5—C6—O6 | 177.50 (11) |
O4—C4—C5—C6 | 178.45 (11) | N5—C5—C6—O6 | −2.40 (18) |
N3—C4—C5—N5 | −178.90 (11) | N1—C6—O6—C61 | 3.10 (17) |
O4—C4—C5—N5 | −1.66 (18) | N3—C4—O4—C41 | 2.14 (16) |
C4—C5—N5—O52 | 149.85 (12) | C5—C6—O6—C61 | −175.01 (11) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1i | 0.88 | 2.26 | 3.1210 (16) | 165 |
N2—H2B···O51ii | 0.88 | 2.13 | 2.9951 (15) | 166 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x, y−1/2, −z+1/2. |
(II) 4-amino-2,6-dimethoxy-5-nitropyrimidine
top
Crystal data top
C6H8N4O4 | Z = 4 |
Mr = 200.16 | F(000) = 416 |
Triclinic, P1 | Dx = 1.601 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.8427 (2) Å | Cell parameters from 3699 reflections |
b = 9.9742 (5) Å | θ = 3.2–27.5° |
c = 13.2752 (5) Å | µ = 0.14 mm−1 |
α = 79.007 (2)° | T = 120 K |
β = 75.577 (3)° | Block, colourless |
γ = 72.547 (2)° | 0.40 × 0.25 × 0.20 mm |
V = 830.46 (6) Å3 | |
Data collection top
Nonius KappaCCD area-detector diffractometer | 3699 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 2510 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.065 |
ϕ scans, and ω scans with κ offsets | θmax = 27.5°, θmin = 3.2° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −8→8 |
Tmin = 0.946, Tmax = 0.978 | k = −12→12 |
12543 measured reflections | l = −17→16 |
Refinement top
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)] = 0.050 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0779P)2] where P = (Fo2 + 2Fc2)/3 |
3699 reflections | (Δ/σ)max = 0.001 |
257 parameters | Δρmax = 0.50 e Å−3 |
0 restraints | Δρmin = −0.39 e Å−3 |
Crystal data top
C6H8N4O4 | γ = 72.547 (2)° |
Mr = 200.16 | V = 830.46 (6) Å3 |
Triclinic, P1 | Z = 4 |
a = 6.8427 (2) Å | Mo Kα radiation |
b = 9.9742 (5) Å | µ = 0.14 mm−1 |
c = 13.2752 (5) Å | T = 120 K |
α = 79.007 (2)° | 0.40 × 0.25 × 0.20 mm |
β = 75.577 (3)° | |
Data collection top
Nonius KappaCCD area-detector diffractometer | 3699 independent reflections |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | 2510 reflections with I > 2σ(I) |
Tmin = 0.946, Tmax = 0.978 | Rint = 0.065 |
12543 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.050 | 0 restraints |
wR(F2) = 0.135 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.50 e Å−3 |
3699 reflections | Δρmin = −0.39 e Å−3 |
257 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N11 | 0.24070 (19) | 0.04768 (13) | 1.08769 (9) | 0.0160 (3) | |
C12 | 0.2416 (2) | 0.13922 (16) | 1.00022 (12) | 0.0158 (3) | |
C121 | 0.2063 (3) | 0.31254 (17) | 1.10861 (12) | 0.0233 (4) | |
O12 | 0.23108 (18) | 0.27243 (11) | 1.00632 (8) | 0.0206 (3) | |
N13 | 0.25233 (19) | 0.11597 (13) | 0.90412 (10) | 0.0161 (3) | |
C14 | 0.2615 (2) | −0.01660 (16) | 0.89040 (11) | 0.0148 (3) | |
N14 | 0.2724 (2) | −0.03475 (14) | 0.79233 (9) | 0.0187 (3) | |
C15 | 0.2600 (2) | −0.12426 (15) | 0.97845 (11) | 0.0149 (3) | |
N15 | 0.2686 (2) | −0.26649 (14) | 0.96737 (10) | 0.0190 (3) | |
O152 | 0.2669 (3) | −0.35590 (13) | 1.04365 (10) | 0.0469 (4) | |
O151 | 0.27636 (18) | −0.29476 (12) | 0.87914 (8) | 0.0233 (3) | |
C16 | 0.2507 (2) | −0.08460 (16) | 1.07678 (11) | 0.0151 (3) | |
O16 | 0.25090 (17) | −0.17890 (11) | 1.16133 (8) | 0.0191 (3) | |
C161 | 0.2449 (3) | −0.13105 (17) | 1.25871 (11) | 0.0202 (4) | |
N21 | 0.2547 (2) | 0.31004 (13) | 0.46017 (10) | 0.0171 (3) | |
C22 | 0.2483 (2) | 0.21808 (16) | 0.54755 (12) | 0.0170 (3) | |
C221 | 0.2449 (3) | 0.05499 (17) | 0.43956 (12) | 0.0243 (4) | |
O22 | 0.24281 (18) | 0.08772 (11) | 0.54138 (8) | 0.0220 (3) | |
N23 | 0.2484 (2) | 0.23754 (13) | 0.64323 (10) | 0.0179 (3) | |
C24 | 0.2476 (2) | 0.36860 (16) | 0.65701 (12) | 0.0161 (3) | |
N24 | 0.2467 (2) | 0.38409 (14) | 0.75419 (10) | 0.0210 (3) | |
C25 | 0.2467 (2) | 0.47816 (15) | 0.56970 (11) | 0.0153 (3) | |
N25 | 0.23793 (19) | 0.61896 (13) | 0.58176 (10) | 0.0165 (3) | |
O252 | 0.2506 (2) | 0.70808 (12) | 0.50460 (9) | 0.0270 (3) | |
O251 | 0.21637 (19) | 0.64912 (11) | 0.67143 (8) | 0.0247 (3) | |
C26 | 0.2572 (2) | 0.43875 (16) | 0.47082 (12) | 0.0152 (3) | |
C261 | 0.2865 (3) | 0.48191 (17) | 0.28676 (11) | 0.0215 (4) | |
O26 | 0.26880 (17) | 0.53178 (11) | 0.38560 (8) | 0.0191 (3) | |
H12A | 0.0744 | 0.2984 | 1.1529 | 0.035* | |
H12B | 0.2045 | 0.4125 | 1.1015 | 0.035* | |
H12C | 0.3233 | 0.2539 | 1.1409 | 0.035* | |
H14A | 0.2732 | 0.0370 | 0.7422 | 0.022* | |
H14B | 0.2788 | −0.1185 | 0.7776 | 0.022* | |
H16A | 0.3687 | −0.0973 | 1.2518 | 0.030* | |
H16B | 0.2436 | −0.2098 | 1.3155 | 0.030* | |
H16C | 0.1183 | −0.0537 | 1.2747 | 0.030* | |
H22A | 0.1191 | 0.1150 | 0.4151 | 0.036* | |
H22B | 0.2475 | −0.0448 | 0.4448 | 0.036* | |
H22C | 0.3695 | 0.0726 | 0.3897 | 0.036* | |
H24A | 0.2467 | 0.3118 | 0.8040 | 0.025* | |
H24B | 0.2461 | 0.4666 | 0.7689 | 0.025* | |
H26A | 0.4152 | 0.4054 | 0.2734 | 0.032* | |
H26B | 0.2907 | 0.5602 | 0.2298 | 0.032* | |
H26C | 0.1655 | 0.4465 | 0.2906 | 0.032* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N11 | 0.0192 (7) | 0.0149 (7) | 0.0134 (7) | −0.0051 (5) | −0.0031 (5) | −0.0003 (5) |
C12 | 0.0154 (8) | 0.0149 (8) | 0.0165 (8) | −0.0050 (6) | −0.0028 (6) | 0.0001 (6) |
C121 | 0.0350 (10) | 0.0188 (9) | 0.0192 (9) | −0.0112 (7) | −0.0040 (7) | −0.0055 (7) |
O12 | 0.0326 (6) | 0.0144 (6) | 0.0167 (6) | −0.0088 (5) | −0.0059 (4) | −0.0008 (4) |
N13 | 0.0187 (7) | 0.0173 (7) | 0.0124 (7) | −0.0060 (5) | −0.0035 (5) | 0.0003 (5) |
C14 | 0.0119 (7) | 0.0164 (8) | 0.0156 (8) | −0.0037 (6) | −0.0023 (6) | −0.0017 (6) |
N14 | 0.0285 (8) | 0.0175 (7) | 0.0110 (7) | −0.0079 (6) | −0.0054 (5) | 0.0003 (5) |
C15 | 0.0175 (8) | 0.0130 (8) | 0.0145 (8) | −0.0043 (6) | −0.0038 (6) | −0.0011 (6) |
N15 | 0.0252 (7) | 0.0187 (7) | 0.0138 (7) | −0.0079 (6) | −0.0041 (5) | −0.0001 (5) |
O152 | 0.1079 (13) | 0.0205 (7) | 0.0194 (7) | −0.0285 (8) | −0.0207 (7) | 0.0091 (5) |
O151 | 0.0365 (7) | 0.0212 (6) | 0.0148 (6) | −0.0097 (5) | −0.0066 (5) | −0.0038 (5) |
C16 | 0.0143 (7) | 0.0146 (8) | 0.0152 (8) | −0.0043 (6) | −0.0034 (6) | 0.0024 (6) |
O16 | 0.0300 (6) | 0.0161 (6) | 0.0121 (6) | −0.0088 (5) | −0.0061 (4) | 0.0022 (4) |
C161 | 0.0316 (9) | 0.0201 (8) | 0.0108 (8) | −0.0088 (7) | −0.0059 (6) | −0.0015 (6) |
N21 | 0.0220 (7) | 0.0155 (7) | 0.0141 (7) | −0.0057 (5) | −0.0042 (5) | −0.0004 (5) |
C22 | 0.0208 (8) | 0.0129 (8) | 0.0160 (8) | −0.0044 (6) | −0.0032 (6) | 0.0004 (6) |
C221 | 0.0410 (10) | 0.0166 (8) | 0.0176 (9) | −0.0097 (7) | −0.0066 (7) | −0.0036 (6) |
O22 | 0.0381 (7) | 0.0132 (6) | 0.0167 (6) | −0.0096 (5) | −0.0072 (5) | 0.0004 (4) |
N23 | 0.0255 (7) | 0.0147 (7) | 0.0134 (7) | −0.0056 (6) | −0.0056 (5) | 0.0010 (5) |
C24 | 0.0161 (8) | 0.0170 (8) | 0.0141 (8) | −0.0044 (6) | −0.0026 (6) | −0.0001 (6) |
N24 | 0.0350 (8) | 0.0168 (7) | 0.0117 (7) | −0.0082 (6) | −0.0067 (5) | 0.0018 (5) |
C25 | 0.0194 (8) | 0.0128 (8) | 0.0134 (8) | −0.0043 (6) | −0.0038 (6) | −0.0003 (6) |
N25 | 0.0203 (7) | 0.0148 (7) | 0.0144 (7) | −0.0044 (5) | −0.0042 (5) | −0.0011 (5) |
O252 | 0.0484 (8) | 0.0155 (6) | 0.0167 (6) | −0.0115 (5) | −0.0060 (5) | 0.0030 (5) |
O251 | 0.0435 (7) | 0.0194 (6) | 0.0134 (6) | −0.0091 (5) | −0.0070 (5) | −0.0045 (5) |
C26 | 0.0155 (8) | 0.0152 (8) | 0.0142 (8) | −0.0042 (6) | −0.0045 (6) | 0.0020 (6) |
C261 | 0.0358 (10) | 0.0203 (8) | 0.0105 (8) | −0.0101 (7) | −0.0061 (6) | −0.0003 (6) |
O26 | 0.0307 (6) | 0.0154 (6) | 0.0126 (6) | −0.0081 (5) | −0.0064 (4) | 0.0007 (4) |
Geometric parameters (Å, º) top
N11—C12 | 1.3333 (19) | N21—C22 | 1.3348 (19) |
C12—N13 | 1.3201 (19) | C22—N23 | 1.3212 (19) |
N13—C14 | 1.3497 (19) | N23—C24 | 1.3522 (19) |
C14—C15 | 1.429 (2) | C24—C25 | 1.433 (2) |
C15—C16 | 1.416 (2) | C25—C26 | 1.420 (2) |
C16—N11 | 1.3341 (19) | C26—N21 | 1.323 (2) |
C14—N14 | 1.3292 (18) | C24—N24 | 1.3266 (19) |
C15—N15 | 1.4362 (19) | C25—N25 | 1.4254 (19) |
N15—O151 | 1.2411 (16) | N25—O251 | 1.2456 (16) |
N15—O152 | 1.2153 (17) | N25—O252 | 1.2255 (16) |
C12—O12 | 1.3259 (18) | C22—O22 | 1.3304 (18) |
C16—O16 | 1.3199 (17) | C26—O26 | 1.3215 (17) |
C121—O12 | 1.4438 (18) | C221—O22 | 1.4456 (18) |
C121—H12A | 0.98 | C221—H22A | 0.98 |
C121—H12B | 0.98 | C221—H22B | 0.98 |
C121—H12C | 0.98 | C221—H22C | 0.98 |
N14—H14A | 0.88 | N24—H24A | 0.88 |
N14—H14B | 0.88 | N24—H24B | 0.88 |
O16—C161 | 1.4483 (17) | C261—O26 | 1.4550 (17) |
C161—H16A | 0.98 | C261—H26A | 0.98 |
C161—H16B | 0.98 | C261—H26B | 0.98 |
C161—H16C | 0.98 | C261—H26C | 0.98 |
| | | |
C12—N11—C16 | 115.74 (13) | C26—N21—C22 | 115.96 (13) |
N13—C12—O12 | 113.04 (13) | N23—C22—O22 | 113.07 (13) |
N13—C12—N11 | 128.51 (14) | N23—C22—N21 | 128.57 (14) |
O12—C12—N11 | 118.45 (13) | O22—C22—N21 | 118.36 (13) |
O12—C121—H12A | 109.5 | O22—C221—H22A | 109.5 |
O12—C121—H12B | 109.5 | O22—C221—H22B | 109.5 |
H12A—C121—H12B | 109.5 | H22A—C221—H22B | 109.5 |
O12—C121—H12C | 109.5 | O22—C221—H22C | 109.5 |
H12A—C121—H12C | 109.5 | H22A—C221—H22C | 109.5 |
H12B—C121—H12C | 109.5 | H22B—C221—H22C | 109.5 |
C12—O12—C121 | 118.05 (12) | C22—O22—C221 | 117.41 (12) |
C12—N13—C14 | 117.27 (12) | C22—N23—C24 | 116.88 (12) |
N14—C14—N13 | 115.03 (12) | N24—C24—N23 | 115.08 (12) |
N14—C14—C15 | 125.40 (14) | N24—C24—C25 | 125.13 (14) |
N13—C14—C15 | 119.57 (13) | N23—C24—C25 | 119.79 (13) |
C14—N14—H14A | 120.0 | C24—N24—H24A | 120.0 |
C14—N14—H14B | 120.0 | C24—N24—H24B | 120.0 |
H14A—N14—H14B | 120.0 | H24A—N24—H24B | 120.0 |
C16—C15—C14 | 117.04 (13) | C26—C25—N25 | 121.93 (13) |
C16—C15—N15 | 121.60 (12) | C26—C25—C24 | 116.57 (13) |
C14—C15—N15 | 121.36 (13) | N25—C25—C24 | 121.49 (13) |
O151—N15—O152 | 121.45 (13) | O251—N25—O252 | 121.16 (12) |
O152—N15—C15 | 119.95 (13) | O252—N25—C25 | 119.91 (12) |
O151—N15—C15 | 118.60 (12) | O251—N25—C25 | 118.92 (12) |
O16—C16—N11 | 117.80 (13) | O26—C26—N21 | 117.74 (13) |
O16—C16—C15 | 120.35 (13) | O26—C26—C25 | 120.17 (13) |
N11—C16—C15 | 121.85 (13) | N21—C26—C25 | 122.09 (13) |
C16—O16—C161 | 117.17 (12) | O26—C261—H26A | 109.5 |
O16—C161—H16A | 109.5 | O26—C261—H26B | 109.5 |
O16—C161—H16B | 109.5 | H26A—C261—H26B | 109.5 |
H16A—C161—H16B | 109.5 | O26—C261—H26C | 109.5 |
O16—C161—H16C | 109.5 | H26A—C261—H26C | 109.5 |
H16A—C161—H16C | 109.5 | H26B—C261—H26C | 109.5 |
H16B—C161—H16C | 109.5 | C26—O26—C261 | 116.88 (12) |
| | | |
C16—N11—C12—N13 | −0.5 (2) | C26—N21—C22—N23 | −1.6 (2) |
C16—N11—C12—O12 | 179.75 (12) | C26—N21—C22—O22 | 179.13 (13) |
N13—C12—O12—C121 | 176.44 (12) | N23—C22—O22—C221 | −179.22 (13) |
O12—C12—N13—C14 | −179.38 (12) | O22—C22—N23—C24 | −178.10 (12) |
N11—C12—N13—C14 | 0.8 (2) | N21—C22—N23—C24 | 2.6 (2) |
C12—N13—C14—N14 | −179.93 (13) | C22—N23—C24—N24 | 179.68 (13) |
C12—N13—C14—C15 | −0.2 (2) | C22—N23—C24—C25 | 0.0 (2) |
N14—C14—C15—C16 | 179.08 (13) | N24—C24—C25—C26 | 177.32 (14) |
N13—C14—C15—C16 | −0.6 (2) | N23—C24—C25—C26 | −3.0 (2) |
N14—C14—C15—N15 | −0.6 (2) | N24—C24—C25—N25 | −2.0 (2) |
N13—C14—C15—N15 | 179.74 (12) | N23—C24—C25—N25 | 177.63 (12) |
C14—C15—N15—O152 | −179.91 (14) | C24—C25—N25—O252 | 175.43 (13) |
C16—C15—N15—O152 | 0.4 (2) | C26—C25—N25—O252 | −3.9 (2) |
C14—C15—N15—O151 | −0.4 (2) | C24—C25—N25—O251 | −4.9 (2) |
C16—C15—N15—O151 | 179.95 (13) | C26—C25—N25—O251 | 175.77 (13) |
N11—C12—O12—C121 | −3.7 (2) | N21—C22—O22—C221 | 0.2 (2) |
N11—C16—O16—C161 | −1.36 (19) | N21—C26—O26—C261 | −2.44 (19) |
C12—N11—C16—O16 | 179.81 (13) | C22—N21—C26—O26 | 178.35 (12) |
C12—N11—C16—C15 | −0.5 (2) | C22—N21—C26—C25 | −2.0 (2) |
C14—C15—C16—O16 | −179.33 (13) | N25—C25—C26—O26 | 3.1 (2) |
N15—C15—C16—O16 | 0.3 (2) | C24—C25—C26—O26 | −176.23 (13) |
C14—C15—C16—N11 | 1.0 (2) | N25—C25—C26—N21 | −176.53 (13) |
N15—C15—C16—N11 | −179.37 (13) | C24—C25—C26—N21 | 4.1 (2) |
C15—C16—O16—C161 | 178.93 (13) | C25—C26—O26—C261 | 177.89 (13) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N14—H14B···O151 | 0.88 | 2.00 | 2.624 (2) | 127 |
N24—H24B···O251 | 0.88 | 2.01 | 2.630 (2) | 126 |
N14—H14A···N23 | 0.88 | 2.16 | 3.027 (2) | 169 |
N24—H24A···N13 | 0.88 | 2.14 | 3.010 (2) | 170 |
C121—H12B···O152i | 0.98 | 2.42 | 3.378 (2) | 165 |
C221—H22B···O252ii | 0.98 | 2.44 | 3.394 (2) | 165 |
C161—H16B···O26iii | 0.98 | 2.54 | 3.438 (2) | 153 |
C161—H16B···O252iii | 0.98 | 2.50 | 3.356 (2) | 146 |
C261—H26B···O16iv | 0.98 | 2.54 | 3.441 (2) | 152 |
C261—H26B···O152iv | 0.98 | 2.48 | 3.338 (2) | 146 |
Symmetry codes: (i) x, y+1, z; (ii) x, y−1, z; (iii) x, y−1, z+1; (iv) x, y+1, z−1. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C6H8N4O4 | C6H8N4O4 |
Mr | 200.16 | 200.16 |
Crystal system, space group | Monoclinic, P21/c | Triclinic, P1 |
Temperature (K) | 120 | 120 |
a, b, c (Å) | 7.3443 (2), 7.8437 (2), 14.9129 (4) | 6.8427 (2), 9.9742 (5), 13.2752 (5) |
α, β, γ (°) | 90, 109.9470 (13), 90 | 79.007 (2), 75.577 (3), 72.547 (2) |
V (Å3) | 807.54 (4) | 830.46 (6) |
Z | 4 | 4 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.14 | 0.14 |
Crystal size (mm) | 0.50 × 0.40 × 0.15 | 0.40 × 0.25 × 0.20 |
|
Data collection |
Diffractometer | Nonius KappaCCD area-detector diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.936, 0.985 | 0.946, 0.978 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6065, 1835, 1569 | 12543, 3699, 2510 |
Rint | 0.062 | 0.065 |
(sin θ/λ)max (Å−1) | 0.649 | 0.650 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.040, 0.110, 1.00 | 0.050, 0.135, 1.02 |
No. of reflections | 1835 | 3699 |
No. of parameters | 129 | 257 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.26, −0.32 | 0.50, −0.39 |
Selected geometric parameters (Å, º) for (I) topN1—C2 | 1.3515 (17) | C2—N2 | 1.3299 (16) |
C2—N3 | 1.3515 (16) | C5—N5 | 1.4367 (16) |
N3—C4 | 1.3167 (16) | N5—O51 | 1.2368 (14) |
C4—C5 | 1.4076 (18) | N5—O52 | 1.2287 (14) |
C5—C6 | 1.4151 (17) | C4—O4 | 1.3265 (15) |
C6—N1 | 1.3244 (16) | C6—O6 | 1.3273 (15) |
| | | |
C4—C5—N5—O51 | −29.94 (17) | N1—C6—O6—C61 | 3.10 (17) |
C6—C5—N5—O51 | 149.95 (12) | N3—C4—O4—C41 | 2.14 (16) |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···N1i | 0.88 | 2.26 | 3.1210 (16) | 165 |
N2—H2B···O51ii | 0.88 | 2.13 | 2.9951 (15) | 166 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x, y−1/2, −z+1/2. |
Selected geometric parameters (Å, º) for (II) topN11—C12 | 1.3333 (19) | N21—C22 | 1.3348 (19) |
C12—N13 | 1.3201 (19) | C22—N23 | 1.3212 (19) |
N13—C14 | 1.3497 (19) | N23—C24 | 1.3522 (19) |
C14—C15 | 1.429 (2) | C24—C25 | 1.433 (2) |
C15—C16 | 1.416 (2) | C25—C26 | 1.420 (2) |
C16—N11 | 1.3341 (19) | C26—N21 | 1.323 (2) |
C14—N14 | 1.3292 (18) | C24—N24 | 1.3266 (19) |
C15—N15 | 1.4362 (19) | C25—N25 | 1.4254 (19) |
N15—O151 | 1.2411 (16) | N25—O251 | 1.2456 (16) |
N15—O152 | 1.2153 (17) | N25—O252 | 1.2255 (16) |
C12—O12 | 1.3259 (18) | C22—O22 | 1.3304 (18) |
C16—O16 | 1.3199 (17) | C26—O26 | 1.3215 (17) |
| | | |
C14—C15—N15—O151 | −0.4 (2) | C24—C25—N25—O251 | −4.9 (2) |
C16—C15—N15—O151 | 179.95 (13) | C26—C25—N25—O251 | 175.77 (13) |
N11—C12—O12—C121 | −3.7 (2) | N21—C22—O22—C221 | 0.2 (2) |
N11—C16—O16—C161 | −1.36 (19) | N21—C26—O26—C261 | −2.44 (19) |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N14—H14B···O151 | 0.88 | 2.00 | 2.624 (2) | 127 |
N24—H24B···O251 | 0.88 | 2.01 | 2.630 (2) | 126 |
N14—H14A···N23 | 0.88 | 2.16 | 3.027 (2) | 169 |
N24—H24A···N13 | 0.88 | 2.14 | 3.010 (2) | 170 |
C121—H12B···O152i | 0.98 | 2.42 | 3.378 (2) | 165 |
C221—H22B···O252ii | 0.98 | 2.44 | 3.394 (2) | 165 |
C161—H16B···O26iii | 0.98 | 2.54 | 3.438 (2) | 153 |
C161—H16B···O252iii | 0.98 | 2.50 | 3.356 (2) | 146 |
C261—H26B···O16iv | 0.98 | 2.54 | 3.441 (2) | 152 |
C261—H26B···O152iv | 0.98 | 2.48 | 3.338 (2) | 146 |
Symmetry codes: (i) x, y+1, z; (ii) x, y−1, z; (iii) x, y−1, z+1; (iv) x, y+1, z−1. |
Supramolecular aggregation in simple C-substituted nitroanilines is dominated by N—H···O hydrogen bonds. In 4-nitroanilines containing no other hydrogen-bonding substituents, there are two dominant patterns of supramolecular aggregation. Either each molecule is linked to four other molecules by means of such hydrogen bonds, giving rise to two-dimensional (Tonogaki et al., 1993; Glidewell, Low, McWilliam et al., 2002a) or three-dimensional (Ferguson et al., 2001) hydrogen-bonded structures, or else the molecules are linked into chains via paired N—H···O hydrogen bonds which form an R22(6) (Bernstein et al., 1995) motif (McWilliam et al., 2001; Glidewell, Low, McWilliam et al., 2002a). The dominant motif in simple 2-nitroanilines is a combination of intramolecular S(6) rings and simple C(6) or C22(12) chains, depending upon whether Z' = 1 or 2 (Dhaneshwar et al., 1978; Ellena et al., 1996; Cannon et al., 2001; Garden et al., 2002).
However, where other hydrogen-bond acceptors are present, whether a heteroatom within the aromatic ring or in a C-substituent, formation of N—H···N hydrogen bonds can effectively compete with N—H···O hydrogen-bond formation, leading to the production of very elegant sheets containing alternating large and small rings (Glidewell et al., 2001; Glidewell, Low, McWilliam et al., 2002b). Continuing our exploration of this theme, we have now investigated two isomeric examples, 2-amino-4,6-dimethoxy-5-nitropyrimidine, (I), and 4-amino-2,6-dimethoxy-5-nitropyrimidine, (II), containing two additional types of potential hydrogen-bond acceptor, namely a pair of N atoms within the ring and a pair of O atoms in C-substituents. \sch
Compounds (I) and (II) crystallize in space groups P21/c and P1 with Z' = 1 and 2, respectively. In (I) (Fig. 1), both methoxy groups have the methyl C atoms essentially in the plane of the pyrimidine ring, such that both methyl groups are directed away from the nitro substituent. This conformation matches that of the analogous 2-amino-4,6-dimethoxy-5-nitrosopyrimidine (Glidewell, Low, Marchal et al., 2002). Although there is no crystallographic symmetry relating the two halves of the molecule across the line N2···N5, the corresponding dimensions for the two halves (Table 1) are very similar. Both of the exocyclic C—N distances are very short for their types (Allen et al., 1987), while the N—O distances are long. The N1—C6 and N3—C4 distances are significantly shorter than the N1—C2 and C2—N3 distances, and these observations, taken together, point to the charge-separated form (Ia) as an important contributor to the overall molecular-electronic structure.
The two independent molecules in (II) (Fig. 2) have identical conformations, and in each the C—O bonds of the two methoxy groups are almost parallel. The intramolecular distances in the two molecules (Table 3) are very similar. As observed in (I), the exocyclic C—N bonds are short for their types, but in contrast to (I), in each molecule of (II) there is a significant difference between the two N—O bond lengths, with that involved in the characteristic intramolecular S(6) hydrogen-bonded motif being the longer in each molecule. These observations, together with the pattern of the C—N distances within the rings, point to (IIa) and (IIb) as important contributors to the overall molecular-electronic structure. The nitro groups in (II) are almost coplanar with the adjacent pyrimidine rings, presumably influenced by the intramolecular hydrogen bonds. In (I), the nitro group is twisted out of the ring plane by ca 30° (Tables 1 and 3).
The supramolecular structure of (I) is generated by just two hydrogen bonds, one each of the N—H···N and N—H···O types (Table 2). The amino atom N2 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H2A, to ring atom N1 in the molecule at (1 − x, −y, 1 − z), so generating a centrosymmetric R22(8) ring centred at (1/2,0,1/2) (Fig. 3). The same atom N2 also acts as a donor, but this time via atom H2B, to nitro atom O51 in the molecule at (-x, y − 1/2, 1/2 − z), and propagation of this hydrogen bond produces a C(8) chain running parallel to the [010] direction and generated by the 21 screw axis along (0,y,1/4). The combination of the R22(8) rings and the C(8) chains generates a (102) sheet, built from alternating centrosymmetric R22(8) and R66(32) rings and incorporating the C(8) chains along (0,y,1/4) and (1,-y,3/4) (Fig. 3).
Neither of the methoxy substituents participates directly in the hydrogen-bonding arrangement, but in each molecule, the two methoxy groups are directed into the interior of a different R66(32) ring, such that four methoxy groups are directed into each of these rings, effectively occupying the whole interior of these rings. Thus it may well be that these methoxy groups act as templates for the formation of the R66(32) rings, just as, in 3-trifluoromethyl-4-nitroaniline, there are pairs of CF3 groups lying within hydrogen-bonded R44(32) rings (Glidewell, Low, McWilliam et al., 2002a). There are neither C—H···π(arene) hydrogen bonds nor aromatic π···π stacking interactions in the structure of (I), which thus depends solely on hard hydrogen bonds as the only direction-specific interactions.
Within the asymmetric unit of (II) (Fig. 2), there are two independent N—H···O hydrogen bonds (Table 4), each generating an S(6) motif, and there are two independent N—H···N hydrogen bonds, which together generate a pseudo-centrosymmetric R22(8) ring. However, a search of possible additional symmetry revealed none. These dimeric units are then linked into sheets via a series of two C—H···O hydrogen bonds (Table 4). Methoxy atom C121 in the type 1 molecule (containing atoms N11 etc.) at (x, y, z) acts as a hydrogen-bond donor, via atom H12B, to nitro atom O151 in the type 1 molecule at (x, 1 + y, z), while atom C221 in the type 2 molecule (containing atoms N21 etc.) at (x, y, z) similarly acts as a donor, via atom H22B, to nitro atom O251 at (x, y − 1, z). In this manner, a chain of edge-fused R22(8) and R66(22) rings running parallel to [010] is generated by translation (Fig. 4).
Similarly, methoxy atom C161 in the type 1 molecule at (x, y, z) forms, via atom H16B, a planar three-centre C—H···(O)2 hydrogen bond, in which the two acceptors are methoxy atom O26 and nitro atom O252, both in the type 2 molecule at (x, y − 1, 1 + z). Methoxy atom C261 at (x, y, z) forms, via atom H26B, another such three-centre system, where the acceptors are methoxy atom O16 and nitro atom O152 at (x, 1 + y, z − 1). The combination of these two three-centre interactions generates a tricyclic R21(6)R22(6)R21(6) motif containing the unusual pseudo-anthracene synthon A (see Scheme), and propagation of this motif by translation generates a chain running parallel to the [011] direction (Fig. 5).
The combination of the [010] (Fig. 4) and [011] chains (Fig. 5) generates a sheet parallel to (100), and adjacent sheets are linked, to form a three-dimensional structure, by two independent aromatic π···π stacking interactions involving the type 1 molecules only. The pyrimidine ring of the type 1 molecule at (x, y, z) forms stacking interactions with the corresponding rings at both (-x, −y, 2 − z) and (1 − x, −y, 2 − z). The centroid separations are 3.462 (2) and 3.414 (2) Å, respectively, the interplanar spacings are 3.269 (2) and 3.241 (2) Å, respectively, and the centroid offsets are 1.140 (2) and 1.073 (2) Å, respectively. The combined effect of these two interactions is the generation of a π-stacked chain running parallel to the [100] direction (Fig. 6), linking the hydrogen-bonded (100) sheets.
The structural role of the methoxy substituents thus appears to be entirely different between (I) and (II). In (I), these substituents appear to act as templates for the formation of large hydrogen-bonded rings, while in (II), they link dimeric units into sheets.