Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270102020991/sk1600sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270102020991/sk1600Isup2.hkl |
CCDC reference: 204043
A sample of 2-amino-4-butylamino-6-methoxy-5-nitrosopyrimidine (Marchal, 2001) Is a clause missing here? and then converted into (I) by oxidation using 3-chloroperoxobenzoic acid (1.1 molar equivalents) in acetonitrile solution. After recrystallization from ethyl acetate, (I) had a melting point of 378 K. Spectroscopic analysis: 1H NMR (δ, DMSO-d6, p.p.m.): 0.90 (t, 3H, C—CH3, J = 7.41 Hz), 1.32 (m, 2H, CH2), 1.55 (m, 2H, CH2), 3.45 (m, 2H, CH2), 3.88 (s, 3H, O—CH3), 7.37 (bs, 2H, NH2, exchanges with H2O), 8.84 (t, 1H, NH, J = 5.49 Hz); 13C NMR (δ, DMSO-d6, p.p.m.): 13.6, 19.5, 30.7, 54.2, 109.2, 157.9, 160.6, 165.3. Crystals of (I) suitable for single-crystal X-ray diffraction were grown by slow evaporation of a solution in water-ethanol-acetonitrile (1:1:1 v/v).
The systematic absences permitted Cc and C2/c as possible space groups; C2/c was selected, and confirmed by the successful structure analysis. It was apparent at an early stage that the structure contained a small proportion of molecules adopting an alternative orientation. The bond distances in the minor component were constrained using DFIX commands, and the non-H atoms were assigned a common isotropic displacement parameter. Refinement of the site occupancy factors for the two components, constrained to sum to unity, gave values of 0.912 (4) and 0.088 (4) for the major and minor components, respectively. However, in these circumstances, the common Uiso for the minor component was more than double the mean value of the Ueq values for the major component. Refinements were then carried out with a series of fixed values for the site occupancy factors, still constrained to sum to unity. The most satisfactory outcome, in terms of the values of Uiso and the mean Ueq for the two components, was achieved when the occupancies were 0.935 and 0.065, and accordingly the occupancies were thereafter fixed at these values. H atoms were treated as riding, with C—H distances of 0.98 (CH3) and 0.99 Å (CH2), 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, 2002); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
C9H15N5O3 | F(000) = 1024 |
Mr = 241.26 | Dx = 1.442 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 2482 reflections |
a = 20.5825 (13) Å | θ = 3.2–27.4° |
b = 8.8102 (4) Å | µ = 0.11 mm−1 |
c = 13.0289 (11) Å | T = 120 K |
β = 109.810 (3)° | Plate, colourless |
V = 2222.8 (3) Å3 | 0.22 × 0.08 × 0.02 mm |
Z = 8 |
Nonius KappaCCD area-detector diffractometer | 2482 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 1151 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.124 |
ϕ scans, and ω scans with κ offsets | θmax = 27.4°, θmin = 3.2° |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | h = −26→26 |
Tmin = 0.911, Tmax = 0.998 | k = −10→11 |
16040 measured 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)] = 0.063 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.163 | H-atom parameters constrained |
S = 0.94 | w = 1/[σ2(Fo2) + (0.0759P)2] where P = (Fo2 + 2Fc2)/3 |
2482 reflections | (Δ/σ)max < 0.001 |
211 parameters | Δρmax = 0.32 e Å−3 |
26 restraints | Δρmin = −0.31 e Å−3 |
C9H15N5O3 | V = 2222.8 (3) Å3 |
Mr = 241.26 | Z = 8 |
Monoclinic, C2/c | Mo Kα radiation |
a = 20.5825 (13) Å | µ = 0.11 mm−1 |
b = 8.8102 (4) Å | T = 120 K |
c = 13.0289 (11) Å | 0.22 × 0.08 × 0.02 mm |
β = 109.810 (3)° |
Nonius KappaCCD area-detector diffractometer | 2482 independent reflections |
Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) | 1151 reflections with I > 2σ(I) |
Tmin = 0.911, Tmax = 0.998 | Rint = 0.124 |
16040 measured reflections |
R[F2 > 2σ(F2)] = 0.063 | 26 restraints |
wR(F2) = 0.163 | H-atom parameters constrained |
S = 0.94 | Δρmax = 0.32 e Å−3 |
2482 reflections | Δρmin = −0.31 e Å−3 |
211 parameters |
Experimental. The program DENZO-SMN (Otwinowski & Minor, 1997) uses a scaling algorithm [Fox, G·C. & Holmes, K·C. (1966). Acta Cryst. 20, 886–891] which effectively corrects for absorption effects. High-redundancy data were used in the scaling program, hence the `multi-scan' code word was used. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
N1 | 0.31025 (15) | 0.4567 (3) | −0.0483 (2) | 0.0213 (8) | 0.935 |
C2 | 0.34067 (15) | 0.5240 (3) | 0.0504 (2) | 0.0201 (7) | 0.935 |
N2 | 0.33616 (13) | 0.6742 (3) | 0.0514 (2) | 0.0281 (7) | 0.935 |
N3 | 0.37390 (13) | 0.4557 (3) | 0.14522 (19) | 0.0203 (7) | 0.935 |
C4 | 0.37663 (14) | 0.3035 (3) | 0.1449 (2) | 0.0198 (7) | 0.935 |
N4 | 0.4105 (2) | 0.2373 (3) | 0.2402 (2) | 0.0209 (7) | 0.935 |
C41 | 0.44135 (16) | 0.3238 (3) | 0.3408 (2) | 0.0238 (7) | 0.935 |
C42 | 0.47305 (17) | 0.2170 (3) | 0.4360 (2) | 0.0222 (8) | 0.935 |
C43 | 0.50891 (16) | 0.3031 (3) | 0.5407 (2) | 0.0236 (7) | 0.935 |
C44 | 0.54224 (19) | 0.2029 (4) | 0.6395 (3) | 0.0321 (8) | 0.935 |
N5 | 0.34632 (13) | 0.0596 (3) | 0.0420 (2) | 0.0224 (6) | 0.935 |
O51 | 0.37716 (12) | −0.0112 (2) | 0.12942 (17) | 0.0316 (6) | 0.935 |
O52 | 0.31783 (12) | −0.0102 (2) | −0.04284 (16) | 0.0300 (6) | 0.935 |
C5 | 0.34477 (15) | 0.2192 (3) | 0.0452 (2) | 0.0183 (7) | 0.935 |
C6 | 0.31325 (14) | 0.3075 (3) | −0.0496 (2) | 0.0195 (7) | 0.935 |
C61 | 0.25712 (17) | 0.3330 (4) | −0.2406 (2) | 0.0323 (8) | 0.935 |
O6 | 0.28453 (14) | 0.2378 (3) | −0.14489 (17) | 0.0242 (7) | 0.935 |
N1A | 0.310 (2) | 0.0532 (19) | −0.0515 (14) | 0.026 (3)* | 0.065 |
C2A | 0.336 (2) | −0.0156 (17) | 0.0480 (15) | 0.026 (3)* | 0.065 |
N2A | 0.3339 (16) | −0.1667 (16) | 0.0456 (19) | 0.026 (3)* | 0.065 |
N3A | 0.372 (2) | 0.0514 (19) | 0.1435 (14) | 0.026 (3)* | 0.065 |
N4A | 0.405 (4) | 0.271 (3) | 0.238 (2) | 0.026 (3)* | 0.065 |
C4A | 0.376 (2) | 0.2028 (19) | 0.1414 (15) | 0.026 (3)* | 0.065 |
C41A | 0.438 (2) | 0.185 (3) | 0.3385 (15) | 0.026 (3)* | 0.065 |
C42A | 0.479 (3) | 0.279 (4) | 0.437 (2) | 0.026 (3)* | 0.065 |
C43A | 0.504 (2) | 0.181 (5) | 0.539 (3) | 0.026 (3)* | 0.065 |
C44A | 0.539 (3) | 0.286 (6) | 0.634 (3) | 0.026 (3)* | 0.065 |
C5A | 0.347 (3) | 0.2896 (16) | 0.0455 (18) | 0.026 (3)* | 0.065 |
O51A | 0.3776 (18) | 0.525 (4) | 0.134 (2) | 0.026 (3)* | 0.065 |
O52A | 0.318 (2) | 0.513 (5) | −0.038 (3) | 0.026 (3)* | 0.065 |
N5A | 0.347 (2) | 0.4477 (17) | 0.048 (2) | 0.026 (3)* | 0.065 |
C6A | 0.313 (2) | 0.1991 (19) | −0.0559 (14) | 0.026 (3)* | 0.065 |
O6A | 0.297 (3) | 0.266 (3) | −0.1520 (17) | 0.026 (3)* | 0.065 |
C61A | 0.259 (2) | 0.175 (4) | −0.2441 (15) | 0.026 (3)* | 0.065 |
H21 | 0.3546 | 0.7245 | 0.1128 | 0.034* | 0.935 |
H22 | 0.3147 | 0.7236 | −0.0094 | 0.034* | 0.935 |
H4 | 0.4144 | 0.1377 | 0.2426 | 0.025* | 0.935 |
H41A | 0.4055 | 0.3868 | 0.3551 | 0.029* | 0.935 |
H41B | 0.4774 | 0.3924 | 0.3327 | 0.029* | 0.935 |
H42A | 0.4364 | 0.1521 | 0.4460 | 0.027* | 0.935 |
H42B | 0.5069 | 0.1500 | 0.4194 | 0.027* | 0.935 |
H43A | 0.4748 | 0.3700 | 0.5563 | 0.028* | 0.935 |
H43B | 0.5449 | 0.3688 | 0.5294 | 0.028* | 0.935 |
H44A | 0.5072 | 0.1367 | 0.6512 | 0.048* | 0.935 |
H44B | 0.5628 | 0.2666 | 0.7040 | 0.048* | 0.935 |
H44C | 0.5783 | 0.1407 | 0.6269 | 0.048* | 0.935 |
H61A | 0.2210 | 0.3990 | −0.2319 | 0.048* | 0.935 |
H61B | 0.2375 | 0.2689 | −0.3052 | 0.048* | 0.935 |
H61C | 0.2943 | 0.3954 | −0.2494 | 0.048* | 0.935 |
H21A | 0.3555 | −0.2191 | 0.1049 | 0.032* | 0.065 |
H22A | 0.3109 | −0.2142 | −0.0153 | 0.032* | 0.065 |
H4A | 0.4047 | 0.3703 | 0.2418 | 0.032* | 0.065 |
H41C | 0.4689 | 0.1083 | 0.3241 | 0.032* | 0.065 |
H41D | 0.4015 | 0.1295 | 0.3572 | 0.032* | 0.065 |
H42C | 0.5198 | 0.3236 | 0.4234 | 0.032* | 0.065 |
H42D | 0.4504 | 0.3628 | 0.4477 | 0.032* | 0.065 |
H43C | 0.5362 | 0.1025 | 0.5316 | 0.032* | 0.065 |
H43D | 0.4637 | 0.1299 | 0.5502 | 0.032* | 0.065 |
H44D | 0.5748 | 0.3450 | 0.6173 | 0.040* | 0.065 |
H44E | 0.5602 | 0.2262 | 0.6999 | 0.040* | 0.065 |
H44F | 0.5049 | 0.3560 | 0.6450 | 0.040* | 0.065 |
H61D | 0.2886 | 0.0947 | −0.2556 | 0.040* | 0.065 |
H61E | 0.2422 | 0.2388 | −0.3094 | 0.040* | 0.065 |
H61F | 0.2193 | 0.1289 | −0.2300 | 0.040* | 0.065 |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0222 (16) | 0.022 (2) | 0.0177 (14) | −0.0008 (13) | 0.0048 (12) | −0.0012 (12) |
C2 | 0.0167 (17) | 0.0202 (18) | 0.0218 (17) | 0.0002 (13) | 0.0043 (13) | 0.0019 (14) |
N2 | 0.0355 (16) | 0.0179 (15) | 0.0241 (15) | 0.0005 (11) | 0.0010 (12) | 0.0006 (10) |
N3 | 0.0221 (15) | 0.0156 (15) | 0.0194 (15) | 0.0015 (11) | 0.0022 (11) | 0.0010 (11) |
C4 | 0.0157 (16) | 0.0252 (19) | 0.0165 (17) | −0.0033 (12) | 0.0027 (13) | −0.0031 (11) |
N4 | 0.0263 (17) | 0.0118 (14) | 0.0186 (13) | 0.0011 (16) | −0.0002 (10) | −0.0012 (11) |
C41 | 0.0307 (19) | 0.0176 (17) | 0.0173 (17) | −0.0027 (12) | 0.0006 (14) | −0.0031 (11) |
C42 | 0.0220 (18) | 0.0210 (19) | 0.0225 (17) | −0.0034 (14) | 0.0059 (13) | −0.0003 (12) |
C43 | 0.0231 (18) | 0.0264 (18) | 0.0194 (17) | −0.0013 (13) | 0.0046 (14) | −0.0038 (13) |
C44 | 0.041 (2) | 0.0314 (19) | 0.0190 (17) | −0.0012 (16) | 0.0042 (15) | 0.0024 (14) |
N5 | 0.0229 (14) | 0.0220 (14) | 0.0192 (14) | 0.0004 (11) | 0.0029 (11) | −0.0011 (12) |
O51 | 0.0436 (15) | 0.0182 (13) | 0.0238 (13) | 0.0042 (11) | −0.0004 (11) | 0.0012 (9) |
O52 | 0.0405 (15) | 0.0233 (13) | 0.0180 (12) | −0.0028 (11) | −0.0007 (10) | −0.0073 (9) |
C5 | 0.0205 (16) | 0.0132 (16) | 0.0218 (16) | −0.0003 (14) | 0.0082 (13) | −0.0019 (12) |
C6 | 0.0173 (17) | 0.0227 (19) | 0.0175 (18) | −0.0021 (12) | 0.0045 (14) | −0.0037 (11) |
C61 | 0.040 (2) | 0.0343 (19) | 0.0169 (18) | 0.0014 (14) | 0.0018 (15) | 0.0052 (13) |
O6 | 0.0263 (17) | 0.0297 (14) | 0.0146 (11) | −0.0032 (10) | 0.0044 (9) | −0.0008 (10) |
N1—C2 | 1.361 (4) | N1A—C6A | 1.290 (5) |
C2—N3 | 1.335 (4) | N1A—C2A | 1.365 (5) |
N3—C4 | 1.342 (4) | C2A—N2A | 1.333 (5) |
C4—C5 | 1.446 (4) | C2A—N3A | 1.349 (5) |
C5—C6 | 1.418 (4) | N2A—H21A | 0.88 |
C6—N1 | 1.316 (4) | N2A—H22A | 0.88 |
C2—N2 | 1.327 (4) | N3A—C4A | 1.337 (5) |
C4—N4 | 1.335 (4) | N4A—C4A | 1.343 (5) |
C5—N5 | 1.407 (4) | N4A—C41A | 1.458 (5) |
N5—O51 | 1.265 (3) | N4A—H4A | 0.88 |
N5—O52 | 1.227 (3) | C4A—C5A | 1.414 (10) |
C6—O6 | 1.330 (4) | C41A—C42A | 1.520 (5) |
N2—H21 | 0.88 | C41A—H41C | 0.99 |
N2—H22 | 0.88 | C41A—H41D | 0.99 |
N4—C41 | 1.463 (4) | C42A—C43A | 1.517 (5) |
N4—H4 | 0.88 | C42A—H42C | 0.99 |
C41—C42 | 1.517 (4) | C42A—H42D | 0.99 |
C41—H41A | 0.99 | C43A—C44A | 1.522 (5) |
C41—H41B | 0.99 | C43A—H43C | 0.99 |
C42—C43 | 1.516 (4) | C43A—H43D | 0.99 |
C42—H42A | 0.99 | C44A—H44D | 0.98 |
C42—H42B | 0.99 | C44A—H44E | 0.98 |
C43—C44 | 1.520 (4) | C44A—H44F | 0.98 |
C43—H43A | 0.99 | C5A—N5A | 1.393 (5) |
C43—H43B | 0.99 | C5A—C6A | 1.495 (10) |
C44—H44A | 0.98 | O51A—N5A | 1.274 (5) |
C44—H44B | 0.98 | O52A—N5A | 1.223 (5) |
C44—H44C | 0.98 | C6A—O6A | 1.322 (5) |
C61—O6 | 1.449 (4) | O6A—C61A | 1.440 (5) |
C61—H61A | 0.98 | C61A—H61D | 0.98 |
C61—H61B | 0.98 | C61A—H61E | 0.98 |
C61—H61C | 0.98 | C61A—H61F | 0.98 |
C6—N1—C2 | 116.1 (3) | H21A—N2A—H22A | 120.0 |
N2—C2—N3 | 117.2 (3) | C4A—N3A—C2A | 115.7 (5) |
N2—C2—N1 | 115.6 (3) | C4A—N4A—C41A | 122.4 (7) |
N3—C2—N1 | 127.2 (3) | C4A—N4A—H4A | 118.8 |
C2—N2—H21 | 120.0 | C41A—N4A—H4A | 118.8 |
C2—N2—H22 | 120.0 | N3A—C4A—N4A | 115.8 (6) |
H21—N2—H22 | 120.0 | N3A—C4A—C5A | 123.3 (5) |
C2—N3—C4 | 117.1 (3) | N4A—C4A—C5A | 120.8 (9) |
N4—C4—N3 | 116.3 (3) | N4A—C41A—C42A | 115 (2) |
N4—C4—C5 | 123.1 (3) | N4A—C41A—H41C | 108.4 |
N3—C4—C5 | 120.6 (3) | C42A—C41A—H41C | 108.4 |
C4—N4—C41 | 122.5 (3) | N4A—C41A—H41D | 108.4 |
C4—N4—H4 | 118.8 | C42A—C41A—H41D | 108.4 |
C41—N4—H4 | 118.8 | H41C—C41A—H41D | 107.5 |
N4—C41—C42 | 110.2 (3) | C43A—C42A—C41A | 111 (2) |
N4—C41—H41A | 109.6 | C43A—C42A—H42C | 109.5 |
C42—C41—H41A | 109.6 | C41A—C42A—H42C | 109.5 |
N4—C41—H41B | 109.6 | C43A—C42A—H42D | 109.5 |
C42—C41—H41B | 109.6 | C41A—C42A—H42D | 109.5 |
H41A—C41—H41B | 108.1 | H42C—C42A—H42D | 108.1 |
C43—C42—C41 | 111.6 (2) | C42A—C43A—C44A | 107 (3) |
C43—C42—H42A | 109.3 | C42A—C43A—H43C | 110.3 |
C41—C42—H42A | 109.3 | C44A—C43A—H43C | 110.3 |
C43—C42—H42B | 109.3 | C42A—C43A—H43D | 110.3 |
C41—C42—H42B | 109.3 | C44A—C43A—H43D | 110.3 |
H42A—C42—H42B | 108.0 | H43C—C43A—H43D | 108.6 |
C42—C43—C44 | 114.4 (3) | C43A—C44A—H44D | 109.5 |
C42—C43—H43A | 108.7 | C43A—C44A—H44E | 109.5 |
C44—C43—H43A | 108.7 | H44D—C44A—H44E | 109.5 |
C42—C43—H43B | 108.7 | C43A—C44A—H44F | 109.5 |
C44—C43—H43B | 108.7 | H44D—C44A—H44F | 109.5 |
H43A—C43—H43B | 107.6 | H44E—C44A—H44F | 109.5 |
O52—N5—O51 | 120.3 (3) | N5A—C5A—C4A | 121.4 (17) |
O52—N5—C5 | 121.3 (3) | N5A—C5A—C6A | 123.6 (17) |
O51—N5—C5 | 118.4 (3) | C4A—C5A—C6A | 115.0 (4) |
N5—C5—C6 | 122.0 (3) | O51A—N5A—O52A | 120 (3) |
N5—C5—C4 | 122.2 (3) | O52A—N5A—C5A | 117 (3) |
C6—C5—C4 | 115.8 (2) | O51A—N5A—C5A | 124 (3) |
N1—C6—O6 | 117.7 (3) | N1A—C6A—O6A | 119.3 (7) |
N1—C6—C5 | 123.1 (3) | N1A—C6A—C5A | 120.5 (5) |
O6—C6—C5 | 119.2 (3) | O6A—C6A—C5A | 119.4 (13) |
C6—O6—C61 | 117.2 (3) | C6A—O6A—C61A | 115.4 (10) |
C6A—N1A—C2A | 118.4 (5) | O6A—C61A—H61D | 109.5 |
N2A—C2A—N3A | 117.5 (8) | O6A—C61A—H61E | 109.5 |
N2A—C2A—N1A | 115.0 (7) | H61D—C61A—H61E | 109.5 |
N3A—C2A—N1A | 126.7 (6) | O6A—C61A—H61F | 109.5 |
C2A—N2A—H21A | 120.0 | H61D—C61A—H61F | 109.5 |
C2A—N2A—H22A | 120.0 | H61E—C61A—H61F | 109.5 |
C6—N1—C2—N2 | −178.7 (3) | C6A—N1A—C2A—N2A | −177 (4) |
C6—N1—C2—N3 | 1.0 (5) | C6A—N1A—C2A—N3A | −7 (7) |
N2—C2—N3—C4 | 178.0 (3) | N2A—C2A—N3A—C4A | 177 (4) |
N1—C2—N3—C4 | −1.7 (5) | N1A—C2A—N3A—C4A | 8 (7) |
C2—N3—C4—N4 | 179.5 (4) | C2A—N3A—C4A—N4A | 173 (6) |
C2—N3—C4—C5 | 0.1 (4) | C2A—N3A—C4A—C5A | −3 (7) |
N3—C4—N4—C41 | 1.8 (6) | C41A—N4A—C4A—N3A | 6 (10) |
C5—C4—N4—C41 | −178.8 (4) | C41A—N4A—C4A—C5A | −178 (6) |
C4—N4—C41—C42 | 177.3 (4) | C4A—N4A—C41A—C42A | 170 (7) |
N4—C41—C42—C43 | 176.9 (3) | N4A—C41A—C42A—C43A | 173 (5) |
C41—C42—C43—C44 | −179.7 (3) | C41A—C42A—C43A—C44A | −175 (4) |
C4—C5—N5—O51 | −0.5 (4) | N3A—C4A—C5A—N5A | 175 (5) |
C4—C5—N5—O52 | 178.5 (3) | N4A—C4A—C5A—N5A | −1 (8) |
C6—C5—N5—O51 | 178.0 (3) | N3A—C4A—C5A—C6A | −2 (7) |
C6—C5—N5—O52 | −3.0 (4) | N4A—C4A—C5A—C6A | −178 (6) |
N4—C4—C5—N5 | 1.0 (5) | C4A—C5A—N5A—O51A | 6 (8) |
N3—C4—C5—N5 | −179.7 (3) | C6A—C5A—N5A—O51A | −177 (5) |
N4—C4—C5—C6 | −177.6 (4) | C4A—C5A—N5A—O52A | −177 (5) |
N3—C4—C5—C6 | 1.8 (4) | C6A—C5A—N5A—O52A | 0 (7) |
C2—N1—C6—O6 | −179.5 (3) | C2A—N1A—C6A—O6A | 171 (5) |
C2—N1—C6—C5 | 1.2 (4) | C2A—N1A—C6A—C5A | 1 (6) |
N5—C5—C6—N1 | 178.9 (3) | N5A—C5A—C6A—N1A | −174 (5) |
C4—C5—C6—N1 | −2.5 (4) | C4A—C5A—C6A—N1A | 3 (7) |
N5—C5—C6—O6 | −0.4 (4) | N5A—C5A—C6A—O6A | 16 (7) |
C4—C5—C6—O6 | 178.2 (3) | C4A—C5A—C6A—O6A | −167 (4) |
N1—C6—O6—C61 | 4.7 (4) | N1A—C6A—O6A—C61A | 17 (7) |
C5—C6—O6—C61 | −175.9 (3) | C5A—C6A—O6A—C61A | −173 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O51 | 0.88 | 1.93 | 2.583 (3) | 130 |
N2—H21···O51i | 0.88 | 2.37 | 2.974 (3) | 126 |
N2—H22···O52i | 0.88 | 2.39 | 3.011 (3) | 128 |
N4A—H4A···O51A | 0.88 | 1.90 | 2.56 (4) | 133 |
N2A—H21A···O51Aii | 0.88 | 2.31 | 3.00 (4) | 132 |
N2A—H22A···O52Aii | 0.88 | 2.43 | 3.02 (4) | 123 |
Symmetry codes: (i) x, y+1, z; (ii) x, y−1, z. |
Experimental details
Crystal data | |
Chemical formula | C9H15N5O3 |
Mr | 241.26 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 120 |
a, b, c (Å) | 20.5825 (13), 8.8102 (4), 13.0289 (11) |
β (°) | 109.810 (3) |
V (Å3) | 2222.8 (3) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.22 × 0.08 × 0.02 |
Data collection | |
Diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (DENZO-SMN; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.911, 0.998 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 16040, 2482, 1151 |
Rint | 0.124 |
(sin θ/λ)max (Å−1) | 0.647 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.063, 0.163, 0.94 |
No. of reflections | 2482 |
No. of parameters | 211 |
No. of restraints | 26 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.32, −0.31 |
Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO-SMN (Otwinowski & Minor, 1997), DENZO-SMN, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2002), SHELXL97 and PRPKAPPA (Ferguson, 1999).
N1—C2 | 1.361 (4) | C2—N2 | 1.327 (4) |
C2—N3 | 1.335 (4) | C4—N4 | 1.335 (4) |
N3—C4 | 1.342 (4) | C5—N5 | 1.407 (4) |
C4—C5 | 1.446 (4) | N5—O51 | 1.265 (3) |
C5—C6 | 1.418 (4) | N5—O52 | 1.227 (3) |
C6—N1 | 1.316 (4) | C6—O6 | 1.330 (4) |
N4—C41—C42—C43 | 176.9 (3) | N4A—C41A—C42A—C43A | 173 (5) |
C41—C42—C43—C44 | −179.7 (3) | C41A—C42A—C43A—C44A | −175 (4) |
C4—C5—N5—O51 | −0.5 (4) | C4A—C5A—N5A—O51A | 6 (8) |
C4—C5—N5—O52 | 178.5 (3) | C4A—C5A—N5A—O52A | −177 (5) |
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O51 | 0.88 | 1.93 | 2.583 (3) | 130 |
N2—H21···O51i | 0.88 | 2.37 | 2.974 (3) | 126 |
N2—H22···O52i | 0.88 | 2.39 | 3.011 (3) | 128 |
N4A—H4A···O51A | 0.88 | 1.90 | 2.56 (4) | 133 |
N2A—H21A···O51Aii | 0.88 | 2.31 | 3.00 (4) | 132 |
N2A—H22A···O52Aii | 0.88 | 2.43 | 3.02 (4) | 123 |
Symmetry codes: (i) x, y+1, z; (ii) x, y−1, z. |
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An important mode of supramolecular aggregation in 4-nitroanilines is based on the formation of N—H···O hydrogen bonds, with each molecule acting as both a double donor and a double acceptor in these bonds. The resulting supramolecular structures can be two-dimensional (Tonogaki et al., 1993; Glidewell et al., 2002) or three-dimensional (Ferguson et al., 2001). An alternative aggregation mode can occur when there are bulky substituents present, which sometimes force an alternative one-dimensional aggregation mode, in which the molecules are linked by paired N—H···O hydrogen bonds to form an R22(6) (Bernstein et al., 1995) motif (McWilliam et al., 2001; Glidewell et al., 2002).
Continuing our study (Glidewell et al., 2003) of 2-amino-5-nitropyrimidines, which are closely analogous to 4-nitroanilines but which also offer the possibility that intermolecular N—H···N hydrogen bonds might be in competition with N—H···O hydrogen bonds, we report here the molecular and supramolecular structure of 2-amino-4-butylamino-6-methoxy-5-nitropyrimidine, (I). \sch
The molecules of (I), which lie in general positions, exhibit orientational disorder. The two components, whose site occupancy factors are 0.935 and 0.065, are related by an apparent rotation of 180° approximately around the N4···O6 line (Fig. 1). Within the molecules of the major component, the bond lengths (Table 1) show clear evidence of extensive bond fixation consequent upon the polarization of the molecular-electronic structure. Thus, the exocyclic bonds C2—N2 and C5—N5 are both very short for their types; the mean literature values for bonds of these types are 1.355 and 1.468 Å, respectively (Allen et al., 1987). The nitro group is essentially coplanar with the pyrimidine ring (Table 1), and the N—O distances are both longer than the mean literature value of 1.217 Å. It is noteworthy that the C2—N3 bond is shorter than C2—N1, and that N1—C6 is shorter than N3—C4, while N5—O52 is shorter than N5—O51. These observations taken together indicate that the polarized forms, (Ia), (Ib) and (Ic), are all significant contributors to the overall electronic structure.
The nature of the hydrogen bonding in (I) means that the supramolecular structures of the major and minor components are essentially the same, differing only in the direction of the chain formation (Table 2), and hence we discuss here only the major form. There is an intramolecular N—H···O hydrogen bond involving atoms N4 and O51, typical of those found in 2-nitroanilines (Dhaneshwar et al., 1978; Ellena et al., 1999; Cannon et al., 2001), but the principal interest in (I) lies in the intermolecular hydrogen bonding. The amino atom N2 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atoms H11 and H22, respectively, to atoms O51 and O52 in the molecule at (x, 1 + y, z), so generating a C(8) C(8)[R22(6)] chain of rings (Bernstein et al., 1995) running parallel to the [010] direction (Fig. 2). The R22(6) ring is effectively planar, with a sum of internal angles of 718°. It is notable that the supramolecular aggregation in (I) involves only N—H···O hydrogen bonds, whereas in the analogous 2-amino-4,6-dimethoxy-5-nitropyrimidine (Glidewell et al., 2003), both N—H···O and N—H···N hydrogen bonds contribute to the supramolecular structure.
Eight chains of rings pass through each unit cell of (I), but there are neither hydrogen bonds nor aromatic π–π stacking interactions between adjacent chains, so that the supramolecular structure defined by the direction-specific interactions is just one-dimensional. The total number of hydrogen bonds within the structure is maximized if the orientation of the molecules is fully correlated within a given chain. There is no necessary correlation between the molecular orientations in different chains, and chains containing the minor orientation are thus likely to be randomly distributed throughout the structure.
In the previously observed examples of such a chain of rings, the chains in the triclinic polymorph of 2-iodo-4-nitroaniline are linked into sheets by means of a two-centre iodo···nitro interaction (McWilliam et al., 2002), and in 2-trifluoromethyl-4-nitroaniline, a single C—H···O hydrogen bond links the molecules into a ladder generated by a 21 screw axis (Glidewell et al., 2002). It seems probable that direction-specific interactions between the chains in (I) are prevented by the presence of the N-butyl substituent which, in both components, adopts the usual all-trans chain-extended conformation (Table 1).