The crystal and molecular structures of 2-[1-(2-aminoethyl)-2-imidazolidinylidene]-2-nitroacetonitrile [C7H11N5O2; space group P21/n; Z = 4; a = 7.4889 (8), b = 17.273 (2), c = 7.4073 (8) Å, β = 111.937 (6)°], (I), and 2,6-diamino-5-hydroxy-3-nitro-4H-pyrazolo[1,5-a]pyrimidin-7-one monohydrate [C6H6N6O4·H2O; space group P21/n; Z = 4; a = 17.576 (3), b = 10.900 (2), c = 4.6738 (6) Å, β = 92.867 (8)°], (II), have been determined from X-ray, synchrotron and neutron powder diffraction data using various methods. The structures were originally solved from Guinier photographs with a grid search procedure and the program MRIA using a priori information from NMR and mass spectra on the possible geometry of the molecules. Because the conformation of molecule (I) changed during the bond-restrained Rietveld refinement, solvent water was found in (II) and, moreover, as both Guinier patterns were corrupted by texture, high-resolution texture-free synchrotron data were collected at the BM16 beamline, ESRF, to confirm the original results. Using the set of |F|2 values derived from the synchrotron patterns after full-pattern decomposition procedures, the structures of (I) and (II) were solved by direct methods via SHELXS96, SIRPOW.92 and POWSIM without any preliminary models of the molecules, and by Patterson search methods via DIRDIF96 and PATSEE with the use of rigid fragments from each of the molecules. The neutron patterns allowed (I) and (II) to be solved using the grid search procedure and correct initial models of the molecules including H atoms. The results obtained from powder patterns measured on different devices demonstrate the high level of reproducibility and reliability of various powder software and equipment, with a certain preference for synchrotron facilities.
Supporting information
| Portable Document Format (PDF) file Supplementary material |
| Crystallographic Information File (CIF) Contains datablocks cher, I2, II2 |
| Rietveld powder data file (CIF format) Contains datablock I2 |
| Structure factor file (SHELXL table format) Supplementary material |
| Rietveld powder data file (CIF format) Contains datablock cher_fitch_synchro_1 |
| Rietveld powder data file (CIF format) Contains datablock I2 |
| Rietveld powder data file (CIF format) Contains datablock II2 |
| Structure factor file (SHELXL table format) Supplementary material |
| Rietveld powder data file (CIF format) Contains datablock cher_fitch_synchro_2 |
| Rietveld powder data file (CIF format) Supplementary material |
CCDC references: 1207685; 1207686; 1207687; 1207688
For both compounds, cell refinement: LSPAID (Visser et al., 1986); data reduction: MRIA (Zlokazov et al., 1992); program(s) used to solve structure: DIRDIF92, MRIA, PATSEE, POWSIM, SIRPOW.92, SHELXS96; program(s) used to refine structure: MRIA; molecular graphics: PLUTON92 (Spek, 1992); software used to prepare material for publication: MRIA.
(I2) [1-(2-aminoethyl)-1,2-dihydroimidazolidene-2]nitroacetonitrile
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Crystal data top
C7H11N5O2 | F(000) = 416 |
Mr = 197.21 | Dx = 1.474 Mg m−3 |
Monoclinic, P21/n | Synchrotron radiation, λ = 0.85617(3) Å |
a = 7.4889 (8) Å | µ = 0.11 mm−1 |
b = 17.273 (2) Å | T = 295 K |
c = 7.4073 (8) Å | Particle morphology: lump-like |
β = 111.937 (6)° | light yellow |
V = 888.8 (2) Å3 | cylinder, 15 × 1 mm |
Z = 4 | |
Data collection top
ESRF powder diffractometer | Data collection mode: transmission |
Radiation source: BM16 bending magnet at ESRF, synchrotron radiation | Scan method: continuous |
Si 111 double crystal monochromator | 2θmin = 4°, 2θmax = 44°, 2θstep = 0.004° |
Specimen mounting: specimen was sealed in a 1 mm diameter borosilicate glass capillary | |
Refinement top
Refinement on Inet | 135 parameters |
Least-squares matrix: full with fixed elements per cycle | 112 restraints |
Rp = 0.050 | 10 constraints |
Rwp = 0.064 | H atoms treated by a mixture of independent and constrained refinement |
Rexp = 0.050 | Weighting scheme based on measured s.u.'s |
χ2 = 2.103 | (Δ/σ)max = 0.10 |
10001 data points | Background function: Chebyshev polynomial up to the 5th order |
Profile function: split-type pseudo-Voigt | Preferred orientation correction: March-Dollase (Dollase, 1986), direction of preferred orientation [010],
March-Dollase texture parameter r=1.066(4). |
Crystal data top
C7H11N5O2 | V = 888.8 (2) Å3 |
Mr = 197.21 | Z = 4 |
Monoclinic, P21/n | Synchrotron radiation, λ = 0.85617(3) Å |
a = 7.4889 (8) Å | µ = 0.11 mm−1 |
b = 17.273 (2) Å | T = 295 K |
c = 7.4073 (8) Å | cylinder, 15 × 1 mm |
β = 111.937 (6)° | |
Data collection top
ESRF powder diffractometer | Scan method: continuous |
Specimen mounting: specimen was sealed in a 1 mm diameter borosilicate glass capillary | 2θmin = 4°, 2θmax = 44°, 2θstep = 0.004° |
Data collection mode: transmission | |
Refinement top
Rp = 0.050 | 135 parameters |
Rwp = 0.064 | 112 restraints |
Rexp = 0.050 | H atoms treated by a mixture of independent and constrained refinement |
χ2 = 2.103 | (Δ/σ)max = 0.10 |
10001 data points | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.2150 (8) | 0.6302 (3) | 0.3818 (9) | 0.065 (6)* | |
O2 | 0.4715 (7) | 0.5869 (3) | 0.3457 (9) | 0.070 (6)* | |
N1 | 0.4562 (8) | 0.4475 (3) | 0.185 (1) | 0.032 (4)* | |
N2 | 0.2009 (7) | 0.3757 (3) | 0.1460 (8) | 0.048 (5)* | |
N3 | 0.1403 (8) | 0.3163 (3) | 0.5002 (7) | 0.057 (5)* | |
N4 | 0.3019 (9) | 0.5788 (4) | 0.334 (1) | 0.043 (5)* | |
N5 | −0.1526 (8) | 0.5103 (3) | 0.253 (1) | 0.063 (5)* | |
C2 | 0.2798 (9) | 0.4461 (5) | 0.205 (1) | 0.050 (6)* | |
C3 | 0.5080 (9) | 0.3741 (4) | 0.126 (1) | 0.069 (7)* | |
C4 | 0.3237 (9) | 0.3276 (5) | 0.0779 (9) | 0.081 (7)* | |
C5 | 0.1975 (9) | 0.5107 (5) | 0.257 (1) | 0.032 (5)* | |
C6 | 0.0017 (9) | 0.5084 (6) | 0.255 (1) | 0.026 (4)* | |
C7 | 0.0181 (9) | 0.3423 (4) | 0.1388 (8) | 0.072 (7)* | |
C8 | 0.0489 (9) | 0.2865 (4) | 0.3077 (9) | 0.054 (6)* | |
H1 | 0.525 (6) | 0.495 (3) | 0.188 (6) | 0.12 (3)* | |
H3 | 0.612 (7) | 0.352 (3) | 0.235 (7) | 0.12 (3)* | |
H31 | 0.548 (8) | 0.378 (3) | 0.017 (6) | 0.12 (3)* | |
H4 | 0.265 (8) | 0.320 (3) | −0.063 (6) | 0.12 (3)* | |
H41 | 0.345 (8) | 0.279 (3) | 0.145 (6) | 0.12 (3)* | |
H7 | −0.042 (8) | 0.315 (3) | 0.018 (7) | 0.12 (3)* | |
H71 | −0.068 (7) | 0.384 (3) | 0.140 (7) | 0.12 (3)* | |
H8 | −0.079 (7) | 0.272 (3) | 0.301 (6) | 0.12 (3)* | |
H81 | 0.115 (6) | 0.242 (3) | 0.290 (7) | 0.12 (3)* | |
H9 | 0.141 (6) | 0.369 (3) | 0.535 (6) | 0.12 (3)* | |
H91 | 0.230 (7) | 0.283 (3) | 0.601 (6) | 0.12 (3)* | |
Geometric parameters (Å, º) top
O1—N4 | 1.23 (1) | C2—C5 | 1.398 (9) |
O2—N4 | 1.247 (9) | C3—C4 | 1.520 (9) |
N1—C2 | 1.38 (1) | C3—H3 | 0.97 (4) |
N1—C3 | 1.441 (9) | C3—H31 | 0.96 (6) |
N1—H1 | 0.97 (5) | C4—H4 | 0.98 (4) |
N2—C2 | 1.351 (7) | C4—H41 | 0.96 (5) |
N2—C4 | 1.462 (9) | C5—C6 | 1.46 (1) |
N2—C7 | 1.468 (8) | C7—C8 | 1.527 (8) |
N3—C8 | 1.427 (8) | C7—H7 | 0.96 (5) |
N3—H9 | 0.95 (5) | C7—H71 | 0.97 (5) |
N3—H91 | 0.98 (4) | C8—H8 | 0.98 (6) |
N4—C5 | 1.409 (8) | C8—H81 | 0.94 (5) |
N5—C6 | 1.15 (1) | | |
| | | |
C2—N1—C3 | 113.2 (6) | N2—C4—H4 | 111 (3) |
C2—N1—H1 | 122 (3) | C3—C4—H4 | 109 (3) |
C3—N1—H1 | 124 (3) | N2—C4—H41 | 109 (3) |
C2—N2—C4 | 111.6 (5) | C3—C4—H41 | 113 (3) |
C2—N2—C7 | 130.9 (5) | H4—C4—H41 | 110 (4) |
C4—N2—C7 | 117.5 (5) | C2—C5—N4 | 122.8 (5) |
C8—N3—H9 | 125 (3) | C2—C5—C6 | 121.3 (6) |
C8—N3—H91 | 119 (2) | N4—C5—C6 | 115.6 (6) |
H9—N3—H91 | 115 (4) | N5—C6—C5 | 176.8 (8) |
O1—N4—O2 | 122.2 (7) | N2—C7—C8 | 111.4 (5) |
O1—N4—C5 | 116.4 (6) | N2—C7—H7 | 109 (3) |
O2—N4—C5 | 121.3 (7) | C8—C7—H7 | 109 (3) |
N2—C2—N1 | 107.5 (5) | N2—C7—H71 | 109 (3) |
N2—C2—C5 | 128.6 (5) | C8—C7—H71 | 111 (3) |
N1—C2—C5 | 123.6 (6) | H7—C7—H71 | 107 (4) |
N1—C3—C4 | 102.2 (5) | N3—C8—C7 | 117.4 (5) |
N1—C3—H3 | 108 (3) | N3—C8—H8 | 104 (3) |
C4—C3—H3 | 111 (3) | C7—C8—H8 | 106 (3) |
N1—C3—H31 | 113 (3) | N3—C8—H81 | 111 (3) |
C4—C3—H31 | 112 (4) | C7—C8—H81 | 109 (3) |
H3—C3—H31 | 109 (4) | H8—C8—H81 | 110 (4) |
N2—C4—C3 | 104.7 (5) | | |
(II2) 3,7-diamino-4-nitro-6-hydroxy-8-oxopyrazolo[1,5-
a]pyrimidine monohydrate
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Crystal data top
C6H6N6O4·H2O | F(000) = 504 |
Mr = 244.18 | Dx = 1.814 Mg m−3 |
Monoclinic, P21/n | Synchrotron radiation, λ = 0.95044(2) Å |
a = 17.576 (3) Å | µ = 1.39 mm−1 |
b = 10.900 (2) Å | T = 295 K |
c = 4.6738 (6) Å | Particle morphology: feather-like |
β = 92.867 (8)° | yellow-orange |
V = 894.3 (3) Å3 | cylinder, 15 × 1.5 mm |
Z = 4 | |
Data collection top
ESRF powder diffractometer | Data collection mode: transmission |
Radiation source: BM16 bending magnet at ESRF, synchrotron radiation | Scan method: continuous |
Si 111 double crystal monochromator | 2θmin = 5°, 2θmax = 55°, 2θstep = 0.005° |
Specimen mounting: specimen was sealed in a 1.5 mm diameter borosilicate glass capillary | |
Refinement top
Refinement on Inet | 126 parameters |
Least-squares matrix: full with fixed elements per cycle | 99 restraints |
Rp = 0.057 | 17 constraints |
Rwp = 0.068 | H atoms treated by a mixture of independent and constrained refinement |
Rexp = 0.043 | Weighting scheme based on measured s.u.'s |
χ2 = 3.062 | (Δ/σ)max = 0.10 |
10001 data points | Background function: Chebyshev polynomial up to the 5th order |
Profile function: split-type pseudo-Voigt | Preferred orientation correction: March-Dollase (Dollase, 1986), direction of preferred orientation [100],
March-Dollase texture parameter r=1.053(3). |
Crystal data top
C6H6N6O4·H2O | V = 894.3 (3) Å3 |
Mr = 244.18 | Z = 4 |
Monoclinic, P21/n | Synchrotron radiation, λ = 0.95044(2) Å |
a = 17.576 (3) Å | µ = 1.39 mm−1 |
b = 10.900 (2) Å | T = 295 K |
c = 4.6738 (6) Å | cylinder, 15 × 1.5 mm |
β = 92.867 (8)° | |
Data collection top
ESRF powder diffractometer | Scan method: continuous |
Specimen mounting: specimen was sealed in a 1.5 mm diameter borosilicate glass capillary | 2θmin = 5°, 2θmax = 55°, 2θstep = 0.005° |
Data collection mode: transmission | |
Refinement top
Rp = 0.057 | 126 parameters |
Rwp = 0.068 | 99 restraints |
Rexp = 0.043 | H atoms treated by a mixture of independent and constrained refinement |
χ2 = 3.062 | (Δ/σ)max = 0.10 |
10001 data points | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.3574 (2) | 0.2495 (3) | 0.3957 (8) | 0.013 (1)* | |
O2 | 0.4173 (2) | 0.5256 (3) | −0.3330 (8) | 0.019 (2)* | |
O3 | 0.6433 (2) | 0.2693 (3) | −0.3727 (8) | 0.022 (2)* | |
O4 | 0.6913 (2) | 0.1096 (3) | −0.1366 (8) | 0.025 (2)* | |
O5 | 0.2484 (3) | 0.6438 (3) | −0.237 (1) | 0.020 (2)* | |
N1 | 0.4909 (3) | 0.1227 (4) | 0.293 (1) | 0.010 (1)* | |
N2 | 0.4644 (3) | 0.2226 (4) | 0.1357 (8) | 0.010 (1)* | |
N3 | 0.6025 (3) | 0.0020 (4) | 0.2864 (9) | 0.010 (1)* | |
N4 | 0.6403 (3) | 0.1871 (4) | −0.1899 (9) | 0.020 (2)* | |
N5 | 0.4948 (3) | 0.3590 (4) | −0.236 (1) | 0.010 (1)* | |
N6 | 0.3226 (3) | 0.4734 (4) | 0.1177 (9) | 0.010 (1)* | |
C2 | 0.5585 (3) | 0.0934 (5) | 0.188 (1) | 0.010 (1)* | |
C3 | 0.5739 (3) | 0.1794 (5) | −0.040 (1) | 0.010 (1)* | |
C4 | 0.5141 (4) | 0.2633 (5) | −0.059 (1) | 0.010 (1)* | |
C6 | 0.4308 (4) | 0.4286 (4) | −0.178 (1) | 0.010 (1)* | |
C7 | 0.3843 (3) | 0.3970 (4) | 0.044 (1) | 0.010 (1)* | |
C8 | 0.3972 (3) | 0.2866 (4) | 0.202 (1) | 0.010 (1)* | |
H3 | 0.580 (3) | −0.070 (4) | 0.38 (1) | 0.16 (3)* | |
H31 | 0.645 (3) | −0.026 (4) | 0.16 (1) | 0.16 (3)* | |
H5 | 0.534 (3) | 0.388 (4) | −0.37 (1) | 0.16 (3)* | |
H6 | 0.307 (3) | 0.537 (4) | −0.02 (1) | 0.16 (3)* | |
H61 | 0.280 (3) | 0.425 (4) | 0.20 (1) | 0.16 (3)* | |
H7 | 0.401 (3) | 0.505 (4) | −0.53 (1) | 0.16 (3)* | |
H8 | 0.252 (3) | 0.710 (4) | −0.120 (9) | 0.16 (3)* | |
H9 | 0.254 (3) | 0.667 (4) | −0.42 (1) | 0.16 (3)* | |
Geometric parameters (Å, º) top
O1—C8 | 1.239 (6) | N3—H31 | 1.02 (5) |
O2—C6 | 1.297 (6) | N4—C3 | 1.393 (7) |
O2—H7 | 0.98 (5) | N5—C4 | 1.364 (7) |
O3—N4 | 1.241 (6) | N5—C6 | 1.395 (8) |
O4—N4 | 1.248 (6) | N5—H5 | 1.00 (5) |
O5—H8 | 0.91 (4) | N6—C7 | 1.423 (7) |
O5—H9 | 0.90 (5) | N6—H6 | 0.98 (5) |
N1—C2 | 1.346 (7) | N6—H61 | 1.01 (5) |
N1—N2 | 1.382 (6) | C2—C3 | 1.455 (7) |
N2—C4 | 1.367 (8) | C3—C4 | 1.393 (8) |
N2—C8 | 1.419 (7) | C6—C7 | 1.396 (8) |
N3—C2 | 1.329 (7) | C7—C8 | 1.424 (6) |
N3—H3 | 0.99 (5) | | |
| | | |
C6—O2—H7 | 112 (3) | N3—C2—N1 | 124.1 (5) |
H8—O5—H9 | 110 (4) | N3—C2—C3 | 127.6 (5) |
C2—N1—N2 | 105.9 (4) | N1—C2—C3 | 108.3 (4) |
C4—N2—N1 | 113.6 (4) | C4—C3—N4 | 125.2 (5) |
C4—N2—C8 | 123.5 (5) | C4—C3—C2 | 107.6 (5) |
N1—N2—C8 | 122.2 (4) | N4—C3—C2 | 126.7 (5) |
C2—N3—H3 | 121 (3) | N5—C4—N2 | 120.3 (5) |
C2—N3—H31 | 117 (3) | N5—C4—C3 | 134.8 (5) |
H3—N3—H31 | 110 (4) | N2—C4—C3 | 104.5 (5) |
O3—N4—O4 | 124.9 (4) | O2—C6—N5 | 117.5 (4) |
O3—N4—C3 | 117.1 (4) | O2—C6—C7 | 121.3 (4) |
O4—N4—C3 | 118.1 (5) | N5—C6—C7 | 121.2 (5) |
C4—N5—C6 | 118.5 (5) | C6—C7—N6 | 121.1 (5) |
C4—N5—H5 | 117 (3) | C6—C7—C8 | 120.7 (4) |
C6—N5—H5 | 122 (3) | N6—C7—C8 | 118.2 (4) |
C7—N6—H6 | 117 (3) | O1—C8—N2 | 120.4 (5) |
C7—N6—H61 | 112 (3) | O1—C8—C7 | 125.0 (4) |
H6—N6—H61 | 116 (4) | N2—C8—C7 | 114.5 (4) |
Experimental details
| (I2) | (II2) |
Crystal data |
Chemical formula | C7H11N5O2 | C6H6N6O4·H2O |
Mr | 197.21 | 244.18 |
Crystal system, space group | Monoclinic, P21/n | Monoclinic, P21/n |
Temperature (K) | 295 | 295 |
a, b, c (Å) | 7.4889 (8), 17.273 (2), 7.4073 (8) | 17.576 (3), 10.900 (2), 4.6738 (6) |
β (°) | 111.937 (6) | 92.867 (8) |
V (Å3) | 888.8 (2) | 894.3 (3) |
Z | 4 | 4 |
Radiation type | Synchrotron, λ = 0.85617(3) Å | Synchrotron, λ = 0.95044(2) Å |
µ (mm−1) | 0.11 | 1.39 |
Specimen shape, size (mm) | Cylinder, 15 × 1 | Cylinder, 15 × 1.5 |
|
Data collection |
Diffractometer | ESRF powder diffractometer | ESRF powder diffractometer |
Specimen mounting | Specimen was sealed in a 1 mm diameter borosilicate glass capillary | Specimen was sealed in a 1.5 mm diameter borosilicate glass capillary |
Data collection mode | Transmission | Transmission |
Scan method | Continuous | Continuous |
2θ values (°) | 2θmin = 4 2θmax = 44 2θstep = 0.004 | 2θmin = 5 2θmax = 55 2θstep = 0.005 |
|
Refinement |
R factors and goodness of fit | Rp = 0.050, Rwp = 0.064, Rexp = 0.050, χ2 = 2.103 | Rp = 0.057, Rwp = 0.068, Rexp = 0.043, χ2 = 3.062 |
No. of data points | 10001 | 10001 |
No. of parameters | 135 | 126 |
No. of restraints | 112 | 99 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement | H atoms treated by a mixture of independent and constrained refinement |
(Δ/σ)max | 0.10 | 0.10 |