organic compounds
The molecular structure of the title compound, C9H12N6O5, shows extensive electronic delocalization involving the pyrimidine ring and the attached N atom of the glycylglycinate, the amino and the nitroso groups. A unique O—HN(nitroso) hydrogen bond of 2.748 (2) Å is found in the structure. The supramolecular structure is a three-dimensional network, derived from two sets of antiparallel chains, which link chains of alternating dimers which are formed by the action of two different crystallographic centres of symmetry.
Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536802013405/bt6170sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536802013405/bt6170Isup2.hkl |
CCDC reference: 193784
Key indicators
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C) = 0.002 Å
- R factor = 0.044
- wR factor = 0.122
- Data-to-parameter ratio = 12.8
checkCIF results
No syntax errors found ADDSYM reports no extra symmetry
Computing details top
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, 2002); software used to prepare material for publication: SHELXL97 and WORDPERFECT macro PRPKAPPA (Ferguson, 1999).
N-(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)glycylglycinate top
Crystal data top
C9H12N6O5 | Z = 2 |
Mr = 284.25 | F(000) = 296 |
Triclinic, P1 | Dx = 1.654 Mg m−3 |
a = 7.4727 (6) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 8.2356 (4) Å | Cell parameters from 2321 reflections |
c = 9.6678 (8) Å | θ = 2.8–26.4° |
α = 81.208 (5)° | µ = 0.14 mm−1 |
β = 88.722 (3)° | T = 150 K |
γ = 76.169 (4)° | Lath, pink |
V = 570.87 (7) Å3 | 0.30 × 0.10 × 0.05 mm |
Data collection top
Nonius KappaCCD diffractometer | 1775 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed X-ray tube | Rint = 0.055 |
Graphite monochromator | θmax = 26.4°, θmin = 2.8° |
φ scans, and ω scans with κ offsets | h = −9→9 |
9202 measured reflections | k = −10→10 |
2321 independent reflections | l = −12→12 |
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)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.122 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0708P)2 + 0.0612P] where P = (Fo2 + 2Fc2)/3 |
2321 reflections | (Δ/σ)max < 0.001 |
182 parameters | Δρmax = 0.21 e Å−3 |
0 restraints | Δρmin = −0.29 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
x | y | z | Uiso*/Ueq | ||
N1 | 0.05280 (18) | 0.18922 (17) | 0.89256 (15) | 0.0192 (3) | |
C2 | −0.0767 (2) | 0.14057 (19) | 0.82871 (17) | 0.0173 (4) | |
N21 | −0.03039 (19) | 0.06320 (17) | 0.71766 (15) | 0.0209 (3) | |
O21 | 0.19347 (18) | 0.13079 (15) | 0.42403 (13) | 0.0279 (3) | |
C21 | 0.1581 (2) | 0.0233 (2) | 0.66617 (19) | 0.0228 (4) | |
C22 | 0.1881 (2) | 0.1563 (2) | 0.54673 (18) | 0.0199 (4) | |
C23 | 0.2292 (2) | 0.4355 (2) | 0.46741 (18) | 0.0216 (4) | |
N22 | 0.20505 (19) | 0.30442 (17) | 0.57857 (15) | 0.0207 (3) | |
C24 | 0.4118 (2) | 0.3857 (2) | 0.39476 (18) | 0.0212 (4) | |
O22 | 0.40469 (17) | 0.46401 (16) | 0.26383 (13) | 0.0285 (3) | |
O23 | 0.54798 (17) | 0.29061 (15) | 0.45079 (13) | 0.0285 (3) | |
N3 | −0.25716 (18) | 0.16244 (16) | 0.87142 (14) | 0.0186 (3) | |
C3 | −0.3936 (2) | 0.1091 (2) | 0.79169 (19) | 0.0247 (4) | |
C4 | −0.3177 (2) | 0.2441 (2) | 0.98567 (18) | 0.0193 (4) | |
O4 | −0.47819 (17) | 0.26204 (16) | 1.02333 (14) | 0.0295 (3) | |
C5 | −0.1799 (2) | 0.3025 (2) | 1.05510 (17) | 0.0190 (4) | |
N5 | −0.24506 (19) | 0.38923 (17) | 1.15932 (15) | 0.0209 (3) | |
O5 | −0.13407 (17) | 0.44616 (16) | 1.22710 (13) | 0.0276 (3) | |
C6 | 0.0068 (2) | 0.26640 (19) | 1.00554 (18) | 0.0182 (4) | |
N6 | 0.13781 (19) | 0.30838 (18) | 1.07150 (15) | 0.0225 (3) | |
H21 | −0.1170 | 0.0347 | 0.6732 | 0.025* | |
H21A | 0.1838 | −0.0882 | 0.6337 | 0.027* | |
H21B | 0.2455 | 0.0157 | 0.7437 | 0.027* | |
H23A | 0.2236 | 0.5409 | 0.5065 | 0.026* | |
H23B | 0.1273 | 0.4584 | 0.3981 | 0.026* | |
H22A | 0.2015 | 0.3217 | 0.6663 | 0.025* | |
H22B | 0.5341 | 0.4205 | 0.2209 | 0.034* | |
H3A | −0.3988 | 0.1655 | 0.6944 | 0.037* | |
H3B | −0.5152 | 0.1403 | 0.8337 | 0.037* | |
H3C | −0.3574 | −0.0138 | 0.7940 | 0.037* | |
H6A | 0.2517 | 0.2857 | 1.0412 | 0.027* | |
H6B | 0.1113 | 0.3590 | 1.1458 | 0.027* |
Atomic displacement parameters (Å2) top
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0161 (7) | 0.0220 (7) | 0.0209 (8) | −0.0060 (5) | 0.0037 (6) | −0.0056 (6) |
C2 | 0.0189 (9) | 0.0156 (8) | 0.0168 (9) | −0.0052 (6) | 0.0016 (7) | 0.0008 (6) |
N21 | 0.0195 (8) | 0.0256 (7) | 0.0209 (8) | −0.0094 (6) | 0.0043 (6) | −0.0080 (6) |
O21 | 0.0375 (8) | 0.0314 (7) | 0.0213 (7) | −0.0165 (6) | 0.0068 (6) | −0.0117 (5) |
C21 | 0.0215 (9) | 0.0236 (9) | 0.0245 (10) | −0.0059 (7) | 0.0074 (7) | −0.0072 (7) |
C22 | 0.0145 (9) | 0.0252 (9) | 0.0213 (9) | −0.0050 (6) | 0.0034 (7) | −0.0074 (7) |
C23 | 0.0207 (9) | 0.0228 (9) | 0.0225 (10) | −0.0069 (7) | 0.0042 (7) | −0.0056 (7) |
N22 | 0.0229 (8) | 0.0248 (7) | 0.0171 (8) | −0.0082 (6) | 0.0048 (6) | −0.0080 (6) |
C24 | 0.0216 (10) | 0.0208 (8) | 0.0232 (10) | −0.0076 (7) | 0.0017 (7) | −0.0059 (7) |
O22 | 0.0263 (7) | 0.0352 (7) | 0.0196 (7) | −0.0015 (5) | 0.0070 (5) | −0.0003 (5) |
O23 | 0.0201 (7) | 0.0331 (7) | 0.0291 (8) | −0.0030 (5) | 0.0027 (6) | −0.0004 (6) |
N3 | 0.0168 (8) | 0.0220 (7) | 0.0186 (8) | −0.0069 (5) | 0.0013 (6) | −0.0048 (6) |
C3 | 0.0182 (9) | 0.0343 (10) | 0.0249 (10) | −0.0095 (7) | −0.0021 (7) | −0.0092 (8) |
C4 | 0.0165 (9) | 0.0213 (8) | 0.0198 (9) | −0.0048 (6) | 0.0024 (7) | −0.0023 (7) |
O4 | 0.0173 (7) | 0.0443 (8) | 0.0307 (8) | −0.0102 (5) | 0.0058 (5) | −0.0136 (6) |
C5 | 0.0184 (9) | 0.0214 (8) | 0.0175 (9) | −0.0052 (6) | 0.0023 (7) | −0.0031 (7) |
N5 | 0.0212 (8) | 0.0249 (7) | 0.0180 (8) | −0.0085 (6) | 0.0025 (6) | −0.0031 (6) |
O5 | 0.0268 (7) | 0.0359 (7) | 0.0251 (7) | −0.0116 (5) | 0.0015 (5) | −0.0135 (6) |
C6 | 0.0178 (9) | 0.0193 (8) | 0.0176 (9) | −0.0064 (6) | 0.0011 (7) | −0.0007 (6) |
N6 | 0.0156 (8) | 0.0322 (8) | 0.0226 (8) | −0.0076 (6) | 0.0030 (6) | −0.0101 (6) |
Geometric parameters (Å, º) top
N1—C2 | 1.329 (2) | C24—O23 | 1.207 (2) |
N1—C6 | 1.344 (2) | C24—O22 | 1.326 (2) |
C2—N21 | 1.329 (2) | O22—H22B | 1.0477 |
C2—N3 | 1.380 (2) | N3—C4 | 1.392 (2) |
N21—C21 | 1.462 (2) | N3—C3 | 1.476 (2) |
N21—H21 | 0.88 | C3—H3A | 0.98 |
O21—C22 | 1.234 (2) | C3—H3B | 0.98 |
C21—C22 | 1.517 (2) | C3—H3C | 0.98 |
C21—H21A | 0.99 | C4—O4 | 1.227 (2) |
C21—H21B | 0.99 | C4—C5 | 1.452 (2) |
C22—N22 | 1.338 (2) | C5—N5 | 1.340 (2) |
C23—N22 | 1.443 (2) | C5—C6 | 1.442 (2) |
C23—C24 | 1.517 (2) | N5—O5 | 1.2811 (18) |
C23—H23A | 0.99 | C6—N6 | 1.320 (2) |
C23—H23B | 0.99 | N6—H6A | 0.88 |
N22—H22A | 0.88 | N6—H6B | 0.88 |
C2—N1—C6 | 118.63 (14) | O23—C24—C23 | 124.05 (16) |
N21—C2—N1 | 118.47 (15) | O22—C24—C23 | 111.58 (14) |
N21—C2—N3 | 117.23 (14) | C24—O22—H22B | 106.7 |
N1—C2—N3 | 124.29 (15) | C2—N3—C4 | 120.91 (13) |
C2—N21—C21 | 122.88 (14) | C2—N3—C3 | 120.71 (13) |
C2—N21—H21 | 118.6 | C4—N3—C3 | 118.27 (13) |
C21—N21—H21 | 118.6 | N3—C3—H3A | 109.5 |
N21—C21—C22 | 111.63 (14) | N3—C3—H3B | 109.5 |
N21—C21—H21A | 109.3 | H3A—C3—H3B | 109.5 |
C22—C21—H21A | 109.3 | N3—C3—H3C | 109.5 |
N21—C21—H21B | 109.3 | H3A—C3—H3C | 109.5 |
C22—C21—H21B | 109.3 | H3B—C3—H3C | 109.5 |
H21A—C21—H21B | 108.0 | O4—C4—N3 | 120.40 (15) |
O21—C22—N22 | 120.79 (16) | O4—C4—C5 | 123.73 (15) |
O21—C22—C21 | 121.54 (15) | N3—C4—C5 | 115.87 (14) |
N22—C22—C21 | 117.66 (15) | N5—C5—C6 | 127.04 (15) |
N22—C23—C24 | 111.66 (14) | N5—C5—C4 | 114.32 (14) |
N22—C23—H23A | 109.3 | C6—C5—C4 | 118.63 (14) |
C24—C23—H23A | 109.3 | O5—N5—C5 | 119.06 (14) |
N22—C23—H23B | 109.3 | N6—C6—N1 | 118.20 (15) |
C24—C23—H23B | 109.3 | N6—C6—C5 | 120.24 (15) |
H23A—C23—H23B | 107.9 | N1—C6—C5 | 121.56 (14) |
C22—N22—C23 | 119.25 (14) | C6—N6—H6A | 120.0 |
C22—N22—H22A | 120.4 | C6—N6—H6B | 120.0 |
C23—N22—H22A | 120.4 | H6A—N6—H6B | 120.0 |
O23—C24—O22 | 124.34 (16) | ||
C6—N1—C2—N21 | −179.51 (14) | C2—N3—C4—O4 | −179.56 (15) |
C6—N1—C2—N3 | −0.7 (2) | C3—N3—C4—O4 | 4.2 (2) |
N1—C2—N21—C21 | 2.5 (2) | C2—N3—C4—C5 | −0.3 (2) |
N3—C2—N21—C21 | −176.41 (14) | C3—N3—C4—C5 | −176.52 (14) |
C2—N21—C21—C22 | −96.96 (18) | O4—C4—C5—N5 | −4.5 (2) |
N21—C21—C22—O21 | −103.45 (18) | N3—C4—C5—N5 | 176.26 (14) |
N21—C21—C22—N22 | 75.27 (19) | O4—C4—C5—C6 | 176.84 (15) |
O21—C22—N22—C23 | 0.2 (2) | N3—C4—C5—C6 | −2.4 (2) |
C21—C22—N22—C23 | −178.48 (14) | C6—C5—N5—O5 | −1.4 (3) |
C24—C23—N22—C22 | −66.09 (19) | C4—C5—N5—O5 | −179.98 (13) |
N22—C23—C24—O23 | −28.4 (2) | C2—N1—C6—N6 | 177.42 (14) |
N22—C23—C24—O22 | 153.69 (14) | C2—N1—C6—C5 | −2.3 (2) |
N21—C2—N3—C4 | −179.17 (14) | N5—C5—C6—N6 | 5.6 (3) |
N1—C2—N3—C4 | 2.0 (2) | C4—C5—C6—N6 | −175.85 (14) |
N21—C2—N3—C3 | −3.0 (2) | N5—C5—C6—N1 | −174.68 (16) |
N1—C2—N3—C3 | 178.13 (15) | C4—C5—C6—N1 | 3.8 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O22—H22B···N5i | 1.05 | 1.72 | 2.748 (2) | 168 |
N21—H21···O21ii | 0.88 | 1.96 | 2.755 (2) | 149 |
N22—H22A···N1 | 0.88 | 2.64 | 3.300 (2) | 133 |
N22—H22A···O5iii | 0.88 | 2.26 | 2.940 (2) | 135 |
N6—H6A···O4iv | 0.88 | 1.99 | 2.840 (2) | 163 |
N6—H6B···O5 | 0.88 | 1.99 | 2.638 (2) | 129 |
Symmetry codes: (i) x+1, y, z−1; (ii) −x, −y, −z+1; (iii) −x, −y+1, −z+2; (iv) x+1, y, z. |