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In the title compound, C
22H
23N
5O
4, the molecules are linked into chains by a three-centre N—H
(N,O) hydrogen bond, reinforced by a two-centre C—H
O hydrogen bond, and the chains are further linked into sheets by a combination of C—H
O and C—H
π(arene) hydrogen bonds.
Supporting information
CCDC reference: 192990
A solution of ethyl glycinate hydrochloride (0.51 mmol) in ethanol (5 ml) was
neutralized by KOH (0.51 mmol).
2-Benzylamino-4,6-bisbenzyloxy-5-nitosopyrimidine (0.47 mmol) were then added
and the mixture was kept at 333 K for 6 h. When the mixture had cooled to room
temperature, distilled water (50 ml) was added and ethanol was eliminated by
reduced pressure until a solid precipitate appeared. The solid was then
filtered off and washed with distilled water (yield 86%, m.p. 396 K). Analysis
found: C 62.70, H 5.50, N 16.62%; C22H23N5O4 requires C 62.40, H 5.62,
N 16.07%. Crystals suitable for single-crystal X-ray diffraction analysis were
grown from a solution in ethanol–water (1:1, v/v).
Compound (I) crystallized in the monoclinic system; the space group
P21/c was uniquely assigned from the systematic absences. H
atoms were treated as riding, with C—H distances in the range 0.95–0.99 Å
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).
Ethyl
N-[2-benzylamino-6-benzyloxy-5-nitrosopyrimidin-4-yl]glycinate
top
Crystal data top
C22H23N5O4 | F(000) = 888 |
Mr = 421.45 | Dx = 1.363 Mg m−3 |
Monoclinic, P21/c | Melting point: 396 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 15.2278 (8) Å | Cell parameters from 4644 reflections |
b = 15.8992 (5) Å | θ = 3.0–25.0° |
c = 8.5558 (3) Å | µ = 0.10 mm−1 |
β = 97.5860 (11)° | T = 120 K |
V = 2053.31 (14) Å3 | Needle, purple |
Z = 4 | 0.40 × 0.05 × 0.02 mm |
Data collection top
Nonius KappaCCD diffractometer | 1861 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed X-ray tube | Rint = 0.200 |
Graphite monochromator | θmax = 25.0°, θmin = 3.0° |
ϕ scans, and ω scans with κ offsets | h = −18→18 |
24714 measured reflections | k = −18→18 |
3619 independent reflections | l = −10→9 |
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)] = 0.069 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.176 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0658P)2 + 1.1859P] where P = (Fo2 + 2Fc2)/3 |
3619 reflections | (Δ/σ)max < 0.001 |
281 parameters | Δρmax = 0.28 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
Crystal data top
C22H23N5O4 | V = 2053.31 (14) Å3 |
Mr = 421.45 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 15.2278 (8) Å | µ = 0.10 mm−1 |
b = 15.8992 (5) Å | T = 120 K |
c = 8.5558 (3) Å | 0.40 × 0.05 × 0.02 mm |
β = 97.5860 (11)° | |
Data collection top
Nonius KappaCCD diffractometer | 1861 reflections with I > 2σ(I) |
24714 measured reflections | Rint = 0.200 |
3619 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.069 | 0 restraints |
wR(F2) = 0.176 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.28 e Å−3 |
3619 reflections | Δρmin = −0.28 e Å−3 |
281 parameters | |
Special details top
Geometry. Mean-plane data from the final SHELXL97 refinement run:- |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | −0.0187 (2) | 0.3075 (2) | 0.2239 (4) | 0.0245 (8) | |
C2 | 0.0506 (3) | 0.3350 (3) | 0.3311 (4) | 0.0239 (10) | |
N2 | 0.0590 (2) | 0.4176 (2) | 0.3421 (4) | 0.0253 (8) | |
C27 | 0.1239 (3) | 0.4596 (3) | 0.4548 (5) | 0.0263 (10) | |
C21 | 0.2143 (3) | 0.4660 (2) | 0.4009 (5) | 0.0248 (10) | |
C22 | 0.2867 (3) | 0.4234 (3) | 0.4784 (5) | 0.0269 (10) | |
C23 | 0.3690 (3) | 0.4312 (3) | 0.4307 (5) | 0.0330 (11) | |
C24 | 0.3813 (3) | 0.4810 (3) | 0.3038 (5) | 0.0325 (11) | |
C25 | 0.3102 (3) | 0.5240 (3) | 0.2236 (5) | 0.0324 (11) | |
C26 | 0.2276 (3) | 0.5166 (3) | 0.2734 (5) | 0.0309 (11) | |
N3 | 0.1087 (2) | 0.2870 (2) | 0.4246 (4) | 0.0239 (8) | |
C4 | 0.0945 (2) | 0.2044 (3) | 0.4154 (4) | 0.0214 (9) | |
N4 | 0.1494 (2) | 0.1539 (2) | 0.5065 (4) | 0.0254 (8) | |
C7 | 0.2333 (2) | 0.1838 (3) | 0.5859 (4) | 0.0263 (10) | |
C8 | 0.3013 (3) | 0.1837 (2) | 0.4729 (5) | 0.0251 (10) | |
O81 | 0.28688 (18) | 0.16395 (18) | 0.3365 (3) | 0.0336 (8) | |
O82 | 0.38064 (17) | 0.20902 (18) | 0.5446 (3) | 0.0307 (7) | |
C9 | 0.4508 (3) | 0.2097 (3) | 0.4442 (5) | 0.0356 (12) | |
C10 | 0.4846 (3) | 0.1237 (3) | 0.4187 (6) | 0.0457 (13) | |
C5 | 0.0225 (2) | 0.1675 (3) | 0.3114 (4) | 0.0223 (10) | |
N5 | 0.0049 (2) | 0.0859 (2) | 0.2857 (4) | 0.0284 (9) | |
O5 | 0.05466 (19) | 0.03165 (18) | 0.3646 (3) | 0.0345 (8) | |
C6 | −0.0312 (2) | 0.2273 (3) | 0.2183 (4) | 0.0225 (10) | |
O6 | −0.09866 (17) | 0.19484 (17) | 0.1202 (3) | 0.0285 (7) | |
C67 | −0.1553 (3) | 0.2533 (3) | 0.0206 (5) | 0.0295 (10) | |
C61 | −0.2196 (2) | 0.2975 (3) | 0.1104 (4) | 0.0248 (10) | |
C62 | −0.2114 (3) | 0.3827 (3) | 0.1432 (5) | 0.0298 (11) | |
C63 | −0.2713 (3) | 0.4233 (3) | 0.2247 (5) | 0.0369 (12) | |
C64 | −0.3403 (3) | 0.3792 (3) | 0.2756 (5) | 0.0411 (13) | |
C65 | −0.3501 (3) | 0.2950 (3) | 0.2425 (5) | 0.0387 (12) | |
C66 | −0.2908 (3) | 0.2541 (3) | 0.1583 (5) | 0.0310 (11) | |
H2 | 0.0231 | 0.4489 | 0.2772 | 0.030* | |
H27A | 0.1295 | 0.4285 | 0.5559 | 0.032* | |
H27B | 0.1024 | 0.5169 | 0.4743 | 0.032* | |
H22 | 0.2793 | 0.3883 | 0.5656 | 0.032* | |
H23 | 0.4180 | 0.4020 | 0.4859 | 0.040* | |
H24 | 0.4384 | 0.4858 | 0.2714 | 0.039* | |
H25 | 0.3180 | 0.5582 | 0.1354 | 0.039* | |
H26 | 0.1789 | 0.5468 | 0.2193 | 0.037* | |
H4 | 0.1342 | 0.1011 | 0.5186 | 0.030* | |
H7A | 0.2535 | 0.1471 | 0.6770 | 0.032* | |
H7B | 0.2263 | 0.2416 | 0.6258 | 0.032* | |
H9A | 0.5002 | 0.2453 | 0.4933 | 0.043* | |
H9B | 0.4278 | 0.2348 | 0.3410 | 0.043* | |
H10A | 0.5338 | 0.1271 | 0.3559 | 0.055* | |
H10B | 0.4369 | 0.0895 | 0.3627 | 0.055* | |
H10C | 0.5053 | 0.0977 | 0.5209 | 0.055* | |
H67A | −0.1885 | 0.2219 | −0.0682 | 0.035* | |
H67B | −0.1178 | 0.2955 | −0.0240 | 0.035* | |
H62 | −0.1639 | 0.4135 | 0.1092 | 0.036* | |
H63 | −0.2651 | 0.4819 | 0.2458 | 0.044* | |
H64 | −0.3809 | 0.4071 | 0.3334 | 0.049* | |
H65 | −0.3976 | 0.2646 | 0.2774 | 0.046* | |
H66 | −0.2990 | 0.1962 | 0.1332 | 0.037* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0219 (19) | 0.029 (2) | 0.0227 (19) | −0.0002 (17) | 0.0032 (14) | −0.0018 (15) |
C2 | 0.022 (2) | 0.030 (3) | 0.021 (2) | −0.001 (2) | 0.0071 (18) | 0.0003 (19) |
N2 | 0.023 (2) | 0.024 (2) | 0.028 (2) | 0.0002 (17) | 0.0008 (15) | −0.0005 (15) |
C27 | 0.028 (2) | 0.027 (3) | 0.025 (2) | −0.003 (2) | 0.0075 (18) | −0.0038 (18) |
C21 | 0.027 (2) | 0.021 (3) | 0.026 (2) | −0.0053 (19) | 0.0028 (18) | −0.0035 (18) |
C22 | 0.032 (3) | 0.027 (3) | 0.020 (2) | 0.000 (2) | −0.0008 (18) | −0.0007 (18) |
C23 | 0.023 (2) | 0.041 (3) | 0.034 (3) | 0.002 (2) | −0.0030 (18) | −0.003 (2) |
C24 | 0.026 (3) | 0.037 (3) | 0.036 (3) | −0.003 (2) | 0.008 (2) | 0.000 (2) |
C25 | 0.031 (3) | 0.032 (3) | 0.035 (3) | −0.008 (2) | 0.008 (2) | 0.003 (2) |
C26 | 0.027 (3) | 0.036 (3) | 0.029 (3) | 0.003 (2) | −0.0022 (18) | 0.001 (2) |
N3 | 0.025 (2) | 0.022 (2) | 0.0243 (19) | 0.0016 (16) | 0.0035 (15) | 0.0020 (15) |
C4 | 0.023 (2) | 0.022 (3) | 0.019 (2) | 0.000 (2) | 0.0056 (17) | 0.0010 (18) |
N4 | 0.023 (2) | 0.025 (2) | 0.027 (2) | −0.0027 (16) | 0.0017 (15) | 0.0026 (16) |
C7 | 0.025 (2) | 0.034 (3) | 0.020 (2) | 0.000 (2) | 0.0005 (17) | 0.0049 (18) |
C8 | 0.021 (2) | 0.023 (3) | 0.031 (3) | 0.0004 (19) | 0.0002 (18) | 0.0069 (19) |
O81 | 0.0330 (18) | 0.044 (2) | 0.0230 (18) | −0.0003 (15) | 0.0016 (12) | −0.0038 (14) |
O82 | 0.0253 (17) | 0.0385 (19) | 0.0286 (17) | 0.0002 (14) | 0.0050 (13) | −0.0020 (13) |
C9 | 0.023 (2) | 0.049 (3) | 0.036 (3) | 0.000 (2) | 0.009 (2) | −0.002 (2) |
C10 | 0.030 (3) | 0.049 (3) | 0.058 (3) | 0.008 (2) | 0.006 (2) | 0.000 (3) |
C5 | 0.024 (2) | 0.024 (3) | 0.019 (2) | 0.0011 (19) | 0.0044 (17) | −0.0007 (18) |
N5 | 0.029 (2) | 0.025 (2) | 0.032 (2) | 0.0043 (18) | 0.0085 (16) | 0.0009 (17) |
O5 | 0.0328 (17) | 0.0261 (19) | 0.0438 (19) | −0.0006 (15) | 0.0026 (14) | 0.0008 (14) |
C6 | 0.021 (2) | 0.029 (3) | 0.018 (2) | −0.006 (2) | 0.0043 (17) | −0.0049 (18) |
O6 | 0.0265 (16) | 0.0294 (18) | 0.0282 (17) | 0.0015 (14) | −0.0016 (12) | −0.0027 (13) |
C67 | 0.025 (2) | 0.042 (3) | 0.021 (2) | 0.000 (2) | −0.0022 (17) | −0.001 (2) |
C61 | 0.022 (2) | 0.033 (3) | 0.018 (2) | −0.004 (2) | −0.0008 (17) | 0.0025 (19) |
C62 | 0.030 (3) | 0.037 (3) | 0.022 (2) | 0.003 (2) | −0.0016 (18) | 0.003 (2) |
C63 | 0.042 (3) | 0.038 (3) | 0.028 (3) | 0.009 (2) | −0.006 (2) | −0.004 (2) |
C64 | 0.038 (3) | 0.059 (4) | 0.026 (3) | 0.021 (3) | 0.002 (2) | −0.003 (2) |
C65 | 0.031 (3) | 0.061 (4) | 0.024 (3) | 0.000 (3) | 0.002 (2) | 0.002 (2) |
C66 | 0.029 (3) | 0.038 (3) | 0.024 (2) | −0.003 (2) | −0.0022 (19) | 0.001 (2) |
Geometric parameters (Å, º) top
N1—C2 | 1.376 (5) | N4—H4 | 0.8800 |
C2—N3 | 1.348 (5) | C7—C8 | 1.507 (6) |
N3—C4 | 1.330 (5) | C7—H7A | 0.9900 |
C4—C5 | 1.443 (5) | C7—H7B | 0.9900 |
C5—C6 | 1.427 (6) | C8—O81 | 1.201 (5) |
C6—N1 | 1.288 (5) | C8—O82 | 1.343 (5) |
C2—N2 | 1.321 (5) | O82—C9 | 1.456 (5) |
C4—N4 | 1.334 (5) | C9—C10 | 1.488 (6) |
C5—N5 | 1.337 (5) | C9—H9A | 0.9900 |
N5—O5 | 1.280 (4) | C9—H9B | 0.9900 |
C6—O6 | 1.342 (5) | C10—H10A | 0.9800 |
N2—C27 | 1.450 (5) | C10—H10B | 0.9800 |
N2—H2 | 0.8800 | C10—H10C | 0.9800 |
C27—C21 | 1.512 (6) | O6—C67 | 1.462 (5) |
C27—H27A | 0.9900 | C67—C61 | 1.497 (6) |
C27—H27B | 0.9900 | C67—H67A | 0.9900 |
C21—C22 | 1.386 (6) | C67—H67B | 0.9900 |
C21—C26 | 1.392 (6) | C61—C62 | 1.386 (6) |
C22—C23 | 1.375 (6) | C61—C66 | 1.392 (6) |
C22—H22 | 0.9500 | C62—C63 | 1.380 (6) |
C23—C24 | 1.376 (6) | C62—H62 | 0.9500 |
C23—H23 | 0.9500 | C63—C64 | 1.381 (6) |
C24—C25 | 1.383 (6) | C63—H63 | 0.9500 |
C24—H24 | 0.9500 | C64—C65 | 1.373 (6) |
C25—C26 | 1.386 (6) | C64—H64 | 0.9500 |
C25—H25 | 0.9500 | C65—C66 | 1.388 (6) |
C26—H26 | 0.9500 | C65—H65 | 0.9500 |
N4—C7 | 1.447 (5) | C66—H66 | 0.9500 |
| | | |
C6—N1—C2 | 115.8 (3) | O82—C8—C7 | 111.1 (3) |
N2—C2—N3 | 118.1 (4) | C8—O82—C9 | 114.8 (3) |
N2—C2—N1 | 115.0 (4) | O82—C9—C10 | 112.0 (4) |
N3—C2—N1 | 126.9 (4) | O82—C9—H9A | 109.2 |
C2—N2—C27 | 123.8 (3) | C10—C9—H9A | 109.2 |
C2—N2—H2 | 118.1 | O82—C9—H9B | 109.2 |
C27—N2—H2 | 118.1 | C10—C9—H9B | 109.2 |
N2—C27—C21 | 113.4 (3) | H9A—C9—H9B | 107.9 |
N2—C27—H27A | 108.9 | C9—C10—H10A | 109.5 |
C21—C27—H27A | 108.9 | C9—C10—H10B | 109.5 |
N2—C27—H27B | 108.9 | H10A—C10—H10B | 109.5 |
C21—C27—H27B | 108.9 | C9—C10—H10C | 109.5 |
H27A—C27—H27B | 107.7 | H10A—C10—H10C | 109.5 |
C22—C21—C26 | 118.0 (4) | H10B—C10—H10C | 109.5 |
C22—C21—C27 | 121.3 (4) | N5—C5—C6 | 117.8 (4) |
C26—C21—C27 | 120.7 (4) | N5—C5—C4 | 128.0 (4) |
C23—C22—C21 | 120.8 (4) | C6—C5—C4 | 114.0 (4) |
C23—C22—H22 | 119.6 | O5—N5—C5 | 118.3 (3) |
C21—C22—H22 | 119.6 | N1—C6—O6 | 120.0 (4) |
C22—C23—C24 | 120.7 (4) | N1—C6—C5 | 124.6 (4) |
C22—C23—H23 | 119.7 | O6—C6—C5 | 115.3 (4) |
C24—C23—H23 | 119.7 | C6—O6—C67 | 117.7 (3) |
C23—C24—C25 | 119.8 (4) | O6—C67—C61 | 112.0 (3) |
C23—C24—H24 | 120.1 | O6—C67—H67A | 109.2 |
C25—C24—H24 | 120.1 | C61—C67—H67A | 109.2 |
C24—C25—C26 | 119.2 (4) | O6—C67—H67B | 109.2 |
C24—C25—H25 | 120.4 | C61—C67—H67B | 109.2 |
C26—C25—H25 | 120.4 | H67A—C67—H67B | 107.9 |
C25—C26—C21 | 121.4 (4) | C62—C61—C66 | 118.5 (4) |
C25—C26—H26 | 119.3 | C62—C61—C67 | 121.0 (4) |
C21—C26—H26 | 119.3 | C66—C61—C67 | 120.4 (4) |
C4—N3—C2 | 115.8 (3) | C63—C62—C61 | 120.8 (4) |
N3—C4—N4 | 118.4 (4) | C63—C62—H62 | 119.6 |
N3—C4—C5 | 122.8 (4) | C61—C62—H62 | 119.6 |
N4—C4—C5 | 118.8 (4) | C62—C63—C64 | 120.2 (5) |
C4—N4—C7 | 121.5 (3) | C62—C63—H63 | 119.9 |
C4—N4—H4 | 119.3 | C64—C63—H63 | 119.9 |
C7—N4—H4 | 119.3 | C65—C64—C63 | 119.8 (4) |
N4—C7—C8 | 109.7 (3) | C65—C64—H64 | 120.1 |
N4—C7—H7A | 109.7 | C63—C64—H64 | 120.1 |
C8—C7—H7A | 109.7 | C64—C65—C66 | 120.2 (4) |
N4—C7—H7B | 109.7 | C64—C65—H65 | 119.9 |
C8—C7—H7B | 109.7 | C66—C65—H65 | 119.9 |
H7A—C7—H7B | 108.2 | C65—C66—C61 | 120.4 (4) |
O81—C8—O82 | 124.1 (4) | C65—C66—H66 | 119.8 |
O81—C8—C7 | 124.9 (4) | C61—C66—H66 | 119.8 |
| | | |
C6—N1—C2—N2 | −176.0 (3) | N4—C7—C8—O82 | −178.2 (3) |
C6—N1—C2—N3 | 3.3 (6) | O81—C8—O82—C9 | −1.0 (6) |
N3—C2—N2—C27 | −3.5 (6) | C7—C8—O82—C9 | 179.2 (3) |
N1—C2—N2—C27 | 175.8 (3) | C8—O82—C9—C10 | −76.9 (4) |
C2—N2—C27—C21 | 83.1 (5) | N3—C4—C5—N5 | 175.8 (4) |
N2—C27—C21—C22 | −113.8 (4) | N4—C4—C5—N5 | −4.2 (6) |
N2—C27—C21—C26 | 67.6 (5) | N3—C4—C5—C6 | 0.7 (5) |
C26—C21—C22—C23 | 0.2 (6) | N4—C4—C5—C6 | −179.3 (3) |
C27—C21—C22—C23 | −178.5 (4) | C6—C5—N5—O5 | 177.5 (3) |
C21—C22—C23—C24 | −0.7 (6) | C4—C5—N5—O5 | 2.6 (6) |
C22—C23—C24—C25 | 0.3 (7) | C2—N1—C6—O6 | 178.3 (3) |
C23—C24—C25—C26 | 0.5 (6) | C2—N1—C6—C5 | −1.5 (5) |
C24—C25—C26—C21 | −0.9 (6) | N5—C5—C6—N1 | −175.9 (3) |
C22—C21—C26—C25 | 0.5 (6) | C4—C5—C6—N1 | −0.3 (6) |
C27—C21—C26—C25 | 179.3 (4) | N5—C5—C6—O6 | 4.3 (5) |
N2—C2—N3—C4 | 176.4 (3) | C4—C5—C6—O6 | 179.9 (3) |
N1—C2—N3—C4 | −2.8 (6) | N1—C6—O6—C67 | 0.9 (5) |
C2—N3—C4—N4 | −179.3 (3) | O6—C67—C61—C66 | −71.6 (5) |
C2—N3—C4—C5 | 0.7 (5) | C66—C61—C62—C63 | 1.5 (6) |
N3—C4—N4—C7 | −14.2 (5) | C67—C61—C62—C63 | 179.3 (4) |
C5—C4—N4—C7 | 165.8 (3) | C61—C62—C63—C64 | 0.4 (6) |
C4—N4—C7—C8 | −81.4 (5) | C62—C63—C64—C65 | −1.2 (6) |
N4—C7—C8—O81 | 1.9 (6) | C63—C64—C65—C66 | 0.1 (6) |
C5—C6—O6—C67 | −179.3 (3) | C64—C65—C66—C61 | 1.8 (6) |
C6—O6—C67—C61 | −77.5 (4) | C62—C61—C66—C65 | −2.5 (6) |
O6—C67—C61—C62 | 110.6 (4) | C67—C61—C66—C65 | 179.6 (4) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O5 | 0.88 | 2.00 | 2.621 (4) | 126 |
N2—H2···O5i | 0.88 | 2.06 | 2.933 (4) | 175 |
N2—H2···N5i | 0.88 | 2.27 | 3.004 (5) | 141 |
C62—H62···O5i | 0.95 | 2.50 | 3.369 (5) | 152 |
C7—H7B···O81ii | 0.99 | 2.43 | 3.265 (5) | 141 |
C22—H22···O81ii | 0.95 | 2.45 | 3.364 (4) | 161 |
C7—H7A···Cg2ii | 0.99 | 2.47 | 3.439 (4) | 165 |
C67—H67A···Cg3iii | 0.99 | 2.52 | 3.499 (4) | 172 |
Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x, −y+1/2, z+1/2; (iii) x, −y+1/2, z−1/2. |
Experimental details
Crystal data |
Chemical formula | C22H23N5O4 |
Mr | 421.45 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 120 |
a, b, c (Å) | 15.2278 (8), 15.8992 (5), 8.5558 (3) |
β (°) | 97.5860 (11) |
V (Å3) | 2053.31 (14) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.40 × 0.05 × 0.02 |
|
Data collection |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 24714, 3619, 1861 |
Rint | 0.200 |
(sin θ/λ)max (Å−1) | 0.595 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.069, 0.176, 1.04 |
No. of reflections | 3619 |
No. of parameters | 281 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.28, −0.28 |
Selected geometric parameters (Å, º) topN1—C2 | 1.376 (5) | C2—N2 | 1.321 (5) |
C2—N3 | 1.348 (5) | C4—N4 | 1.334 (5) |
N3—C4 | 1.330 (5) | C5—N5 | 1.337 (5) |
C4—C5 | 1.443 (5) | N5—O5 | 1.280 (4) |
C5—C6 | 1.427 (6) | C6—O6 | 1.342 (5) |
C6—N1 | 1.288 (5) | | |
| | | |
N1—C2—N2—C27 | 175.8 (3) | C5—C6—O6—C67 | −179.3 (3) |
C2—N2—C27—C21 | 83.1 (5) | C6—O6—C67—C61 | −77.5 (4) |
N2—C27—C21—C22 | −113.8 (4) | O6—C67—C61—C62 | 110.6 (4) |
C5—C4—N4—C7 | 165.8 (3) | N4—C7—C8—O82 | −178.2 (3) |
C4—N4—C7—C8 | −81.4 (5) | C7—C8—O82—C9 | 179.2 (3) |
N4—C7—C8—O81 | 1.9 (6) | C8—O82—C9—C10 | −76.9 (4) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4···O5 | 0.88 | 2.00 | 2.621 (4) | 126 |
N2—H2···O5i | 0.88 | 2.06 | 2.933 (4) | 175 |
N2—H2···N5i | 0.88 | 2.27 | 3.004 (5) | 141 |
C62—H62···O5i | 0.95 | 2.50 | 3.369 (5) | 152 |
C7—H7B···O81ii | 0.99 | 2.43 | 3.265 (5) | 141 |
C22—H22···O81ii | 0.95 | 2.45 | 3.364 (4) | 161 |
C7—H7A···Cg2ii | 0.99 | 2.47 | 3.439 (4) | 165 |
C67—H67A···Cg3iii | 0.99 | 2.52 | 3.499 (4) | 172 |
Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x, −y+1/2, z+1/2; (iii) x, −y+1/2, z−1/2. |
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We report here the molecular and supramolecular structure of the title compound, ethyl N-(2-benzylamino-6-benzyloxy-5-nitrosopyrimidin-4-yl)glycinate, (I) (Fig. 1), which we have studied in order to compare the interplay of the molecular and supramolecular structure in (I) with that in the analogue (II) (Quesada, Marchal et al., 2002; Quesada, Low et al., 2002), which differs from (I) in having an unsubstituted amino N2 atom, with no N2-benzyl group, as is present in (I). In (II), the molecules are linked into chains by a combination of a three-centred N—H···(N,O) hydrogen bond and an N—H···π(arene) interaction, involving different N—H bonds of the 2-amino group in the two types of interaction. In (I), with no NH2 group, a different pattern of supramolecular aggregation must occur.
In (I), the amino N4 forms the intramolecular N—H···O hydrogen bond typical of 4-amino-5-nitrosopyrimidines (Quesada, Marchal et al., 2002; Quesada, Low et al., 2002) and the amino N2 atom acts as hydrogen-bond donor to the nitroso atoms N5i and O5i in an almost planar three-centre interaction (see Table 2 for symmetry code), propagation of this interaction produces a chain running parallel to the [010] direction and generated by the 21-screw axis along (0, y, 1/4) (Fig. 2). This [010] chain is further reinforced by a C—H···O hydrogen bond, with the nitroso O5 atom again acting as the acceptor (Table 2 and Fig. 2), and the chain thus contains three different ring motifs of S(6), R21(3) and R12(11) types (Bernstein et al., 1995).
Two chains of this type, related to one another by centres of inversion and thus antiparallel, run through each unit cell, generated by the screw axes along (0, y, 1/4) and (0, -y, 3/4), and these chains are linked into (100) sheets by a combination of C—H···O and C—H···π(arene) hydrogen bonds (Table 2 and Fig. 3). Atoms C7 (via H7B) and C22, which are part of the chain along (0, y, 1/4), both act as hydrogen-bond donors to carbonyl O81ii which lies in the chain along (0, -y, 3/4) [symmetry code: (ii) x, -y + 1/2, z + 1/2]. Similarly, atoms C7 and C22 in the molecule at (-x, 0.5 + y, 0.5 - z), which also lies in the (0, y, 1/4) chain, act as donors to O81 in the molecule at (-x, 1 - y, -z), which itself lies in the chain along (0, -y, -0.25). In this manner, each [010] chain is linked by C—H···O hydrogen bonds to the two neighbouring chains in the [001] direction, so generating a (100) sheet.
The linking of the [010] chains is further reinforced by two distinct C—H···π(arene) interactions. Atoms C7 (via H7A) and C67 (via H67A) act as hydrogen-bond donors, respectively, to the centroid Cg2ii of the ring (C21–C26)ii and to the centroid Cg3iii of the ring (C61–C66)iii. These two molecules lie in the chains along (0, -y, 3/4) and (0, -y, -0.25), respectively, and hence these interactions (Fig. 3) reinforce the (100) sheet.
All of the C—H···O and C—H···π(arene) interactions have H···A and D···A distances which are reasonably short for their types and all except one have D—H···A angles above 150° (Table 2). However, the co-operative action of the many hydrogen bonds may be more significant than the properties of the individual interactions. It is striking that, in the enforced absence of an N—H···π(arene) hydrogen bond of the type found in (II), the structure of (I) nonetheless has adjusted to maximize the effects of the weaker hydrogen bonds, in particular, by engaging both of the aryl rings in the molecule.
Within the molecule of (I), the C—C, C—N and N—O distances (Table 1) exhibit the usual pattern found (Quesada, Marchal et al., 2002; Quesada, Low et al., 2002) in 2,4-diamino-5-nitrosopyrimidines, consistent with extensive charge delocalization, as in (Ia) (see Scheme). The conformation, as defined by the key torsion angles (Table 1), has atoms C27 and C67 effectively coplanar with the pyrimidine ring, but the phenyl rings are rotated out of this plane. The ester group has an unusual conformation (Fig. 1), as demonstrated by the (-)synclinal torsion angle C8—O82—C9—C10 (Table 1).