Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100013457/br1303sup1.cif | |
Rietveld powder data file (CIF format) https://doi.org/10.1107/S0108270100013457/br1303Iasup2.rtv | |
Rietveld powder data file (CIF format) https://doi.org/10.1107/S0108270100013457/br1303Ibsup3.rtv | |
Rietveld powder data file (CIF format) https://doi.org/10.1107/S0108270100013457/br1303IIsup4.rtv |
CCDC references: 158254; 158255; 158256
Compounds (Ia), (Ib) and (II) were prepared in polycrystalline form according to the procedure of Makarov et al. (2000).
The powder of each compound was pressed as a thin layer in the specimen holder of the camera. During the exposures the specimen was spun in its plane to improve particle statistics. The unit-cell dimensions were determined from the Guinier photographs using the indexing program ITO (Visser, 1969) and refined with the program LSPAID (Visser, 1986) to M20 = 25 and F30 = 69 (0.010, 41) for (Ia), M20 = 49 and F30 = 121 (0.006, 40) for (Ib), and M20 = 47 and F30 = 99 (0.009, 35) for (II), using the first 50 peak positions. The space groups Pbca, P21/c and Pna21 were chosen on the basis of systematic extinction rules for (Ia), (Ib) and (II), respectively. Intensities for the structure determination and refinement were measured from the Guinier photographs in 0.01° steps using a Johannson LS18 line scanner. The structures of (Ia) and (Ib) were solved by the grid search procedure (Chernyshev & Schenk, 1998). Preliminary information about the possible structures of (Ia) and (Ib) was obtained from IR and NMR spectroscopy and mass spectrometry. The approximate models of the molecules were built up with the program MOPAC6.0 (Stewart, 1990). In (II), the position of the Cl- anion was found first from the Patterson map. Subsequently, the cation was located in the unit cell using the grid search procedure. Finally, the position of the O atom from the solvent water, without H atoms, was also found by the grid search procedure. The conformations of all of the molecules (Ia), (Ib) and of the cation of (II) changed significantly during the subsequent bond-restrained Rietveld refinements, leading to the correct crystal structures. The strength of the restraints was a function of interatomic separation and for intramolecular bond lengths corresponds to an r.m.s. deviation of 0.03 Å. The diffraction profiles and the differences between the measured and calculated profiles are shown in Fig. 3. H atoms were placed in geometrically calculated positions and allowed to refine using bond restraints, with a common isotropic displacement parameter Uiso fixed to 0.05 Å2. The March-Dollase texture formalism (Dollase, 1986), with (010), (100) and (001) as the directions of preferred orientation, was applied for (Ia), (Ib) and (II), respectively. The texture parameter r refined to 0.86 (1), 1.08 (1) and 1.14 (1) for (Ia), (Ib) and (II), respectively. The DFT calculations were performed using the program provided by Dr D. N. Laikov (Laikov, 1997) employing the BLYP (Becke-Lee-Yang-Parr) exchange-correlation functional (Becke, 1988; Lee et al., 1988). For the representation of the Kohn-Sham one-electron wavefunctions the sets of contracted Gaussian-type functions were used; the contracted patterns were {311/1} for H, {611111/411/11} for C, N and O, and {6111111111/5111111/11} for S. For the expansion of the electron density the uncontracted basis sets, (5 s1p) for H, (10 s3p3d1f) for C, N and O, and (14 s7p7d1f1g) for S, were employed.
For all compounds, data collection: Johannson LS18 linescanner data collection program; cell refinement: LSPAID (Visser et al., 1986); data reduction: PROFIT (Philips, 1996); program(s) used to solve structure: MRIA (Zlokazov & Chernyshev, 1992); program(s) used to refine structure: MRIA; molecular graphics: PLUTON (Spek, 1992); software used to prepare material for publication: MRIA, SHELXL93 (Sheldrick, 1993) and PARST (Nardelli, 1983).
C11H17N5O2S2 | F(000) = 1328 |
Mr = 315.42 | Dx = 1.362 Mg m−3 |
Orthorhombic, Pbca | Cu Kα radiation, λ = 1.54059 Å |
Hall symbol: -P 2ac 2ab | µ = 3.23 mm−1 |
a = 20.013 (6) Å | T = 295 K |
b = 13.456 (3) Å | Particle morphology: no specific habit |
c = 11.424 (3) Å | intense yellow |
V = 3076 (1) Å3 | flat_sheet, 7 × 7 mm |
Z = 8 |
Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Specimen mounting: Pressed as a thin layer in the specimen holder of the camera |
Radiation source: fine focus X-ray tube, Nonius 3502.223 | Data collection mode: transmission |
Quartz monochromator | Scan method: Stationary detector |
Refinement on Inet | 155 parameters |
Least-squares matrix: full with fixed elements per cycle | 122 restraints |
Rp = 0.073 | 18 constraints |
Rwp = 0.098 | H-atom parameters constrained |
Rexp = 0.030 | Weighting scheme based on measured s.u.'s |
χ2 = 10.368 | (Δ/σ)max = 0.05 |
7598 data points | Background function: Chebyshev polynomial up to the 5th order |
Excluded region(s): 4.03-7.99 | Preferred orientation correction: March-Dollase (Dollase, 1986) |
Profile function: split-type pseudo-Voigt |
C11H17N5O2S2 | V = 3076 (1) Å3 |
Mr = 315.42 | Z = 8 |
Orthorhombic, Pbca | Cu Kα radiation, λ = 1.54059 Å |
a = 20.013 (6) Å | µ = 3.23 mm−1 |
b = 13.456 (3) Å | T = 295 K |
c = 11.424 (3) Å | flat_sheet, 7 × 7 mm |
Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Data collection mode: transmission |
Specimen mounting: Pressed as a thin layer in the specimen holder of the camera | Scan method: Stationary detector |
Rp = 0.073 | 7598 data points |
Rwp = 0.098 | 155 parameters |
Rexp = 0.030 | 122 restraints |
χ2 = 10.368 | H-atom parameters constrained |
x | y | z | Uiso*/Ueq | ||
N1 | 0.3906 (2) | −0.1648 (3) | 0.5588 (5) | 0.066 (2)* | |
C2 | 0.3696 (3) | −0.0882 (5) | 0.6208 (5) | 0.066 (2)* | |
N3 | 0.3695 (2) | 0.0092 (3) | 0.5902 (4) | 0.066 (2)* | |
C4 | 0.3954 (3) | 0.0298 (4) | 0.4842 (5) | 0.066 (2)* | |
C5 | 0.4222 (3) | −0.0491 (4) | 0.4153 (6) | 0.066 (2)* | |
C6 | 0.4194 (3) | −0.1519 (5) | 0.4533 (6) | 0.066 (2)* | |
N5 | 0.4461 (2) | −0.0229 (3) | 0.2952 (4) | 0.066 (2)* | |
O51 | 0.4908 (2) | 0.0335 (2) | 0.2807 (3) | 0.066 (2)* | |
O52 | 0.4137 (2) | −0.0564 (3) | 0.2149 (3) | 0.066 (2)* | |
N6 | 0.4451 (3) | −0.2341 (4) | 0.3978 (5) | 0.066 (2)* | |
C7 | 0.4324 (3) | −0.3310 (6) | 0.4471 (6) | 0.066 (2)* | |
C8 | 0.4906 (4) | −0.2215 (4) | 0.3020 (6) | 0.066 (2)* | |
S4 | 0.4022 (1) | 0.1558 (1) | 0.4306 (1) | 0.055 (1)* | |
C9 | 0.3193 (3) | 0.1760 (5) | 0.3820 (5) | 0.066 (2)* | |
S3 | 0.2698 (1) | 0.0855 (1) | 0.3605 (1) | 0.061 (1)* | |
N4 | 0.3065 (3) | 0.2758 (4) | 0.3657 (5) | 0.066 (2)* | |
C10 | 0.3568 (3) | 0.3514 (5) | 0.3923 (6) | 0.066 (2)* | |
C11 | 0.3484 (3) | 0.4032 (5) | 0.5106 (7) | 0.066 (2)* | |
C12 | 0.2415 (4) | 0.3034 (4) | 0.3165 (6) | 0.066 (2)* | |
C13 | 0.2414 (4) | 0.3152 (4) | 0.1833 (7) | 0.066 (2)* | |
H71 | 0.449 (2) | −0.391 (2) | 0.405 (3) | 0.051* | |
H72 | 0.384 (2) | −0.338 (3) | 0.460 (3) | 0.051* | |
H73 | 0.456 (2) | −0.332 (3) | 0.526 (3) | 0.051* | |
H81 | 0.511 (2) | −0.282 (2) | 0.265 (4) | 0.051* | |
H82 | 0.528 (2) | −0.181 (2) | 0.335 (3) | 0.051* | |
H83 | 0.466 (2) | −0.184 (3) | 0.242 (3) | 0.051* | |
H131 | 0.197 (2) | 0.334 (3) | 0.150 (4) | 0.051* | |
H132 | 0.255 (2) | 0.250 (2) | 0.147 (3) | 0.051* | |
H133 | 0.275 (2) | 0.367 (2) | 0.161 (3) | 0.051* | |
H111 | 0.384 (2) | 0.455 (2) | 0.528 (3) | 0.051* | |
H112 | 0.353 (2) | 0.351 (3) | 0.573 (3) | 0.051* | |
H113 | 0.305 (2) | 0.437 (3) | 0.515 (3) | 0.051* | |
H121 | 0.209 (2) | 0.251 (2) | 0.338 (3) | 0.051* | |
H122 | 0.228 (2) | 0.369 (2) | 0.352 (3) | 0.051* | |
H101 | 0.402 (2) | 0.321 (2) | 0.388 (4) | 0.051* | |
H102 | 0.353 (2) | 0.405 (2) | 0.330 (3) | 0.051* | |
H2 | 0.350 (2) | −0.105 (2) | 0.699 (3) | 0.051* |
N1—C2 | 1.319 (8) | C8—H83 | 0.99 (4) |
N1—C6 | 1.347 (9) | S4—C9 | 1.771 (6) |
C2—N3 | 1.356 (8) | C9—S3 | 1.589 (7) |
C2—H2 | 1.00 (3) | C9—N4 | 1.380 (9) |
N3—C4 | 1.346 (7) | N4—C10 | 1.463 (9) |
C4—C5 | 1.426 (8) | N4—C12 | 1.46 (1) |
C4—S4 | 1.808 (6) | C10—C11 | 1.53 (1) |
C5—C6 | 1.451 (9) | C10—H101 | 0.99 (3) |
C5—N5 | 1.495 (8) | C10—H102 | 1.01 (3) |
C6—N6 | 1.375 (9) | C11—H111 | 1.02 (3) |
N5—O51 | 1.185 (5) | C11—H112 | 1.01 (4) |
N5—O52 | 1.210 (6) | C11—H113 | 0.98 (3) |
N6—C7 | 1.44 (1) | C12—C13 | 1.53 (1) |
N6—C8 | 1.434 (9) | C12—H121 | 1.00 (3) |
C7—H71 | 1.00 (3) | C12—H122 | 1.00 (3) |
C7—H72 | 0.99 (3) | C13—H131 | 1.00 (4) |
C7—H73 | 1.02 (4) | C13—H132 | 1.01 (1) |
C8—H81 | 0.99 (4) | C13—H133 | 1.00 (3) |
C8—H82 | 1.00 (3) | ||
C2—N1—C6 | 121.1 (5) | C4—S4—C9 | 100.4 (3) |
N1—C2—H2 | 115 (2) | S4—C9—N4 | 111.5 (5) |
N1—C2—N3 | 128.1 (6) | S4—C9—S3 | 121.0 (4) |
N3—C2—H2 | 117 (2) | S3—C9—N4 | 127.5 (5) |
C2—N3—C4 | 115.5 (5) | C9—N4—C12 | 117.6 (5) |
N3—C4—S4 | 121.8 (4) | C9—N4—C10 | 121.4 (5) |
N3—C4—C5 | 119.2 (5) | C10—N4—C12 | 121.0 (6) |
C5—C4—S4 | 118.9 (4) | N4—C10—H102 | 107 (2) |
C4—C5—N5 | 116.8 (5) | N4—C10—H101 | 109 (2) |
C4—C5—C6 | 122.0 (5) | N4—C10—C11 | 115.1 (6) |
C6—C5—N5 | 120.8 (5) | H101—C10—H102 | 110 (3) |
N1—C6—C5 | 114.0 (6) | C11—C10—H102 | 107 (2) |
C5—C6—N6 | 127.9 (6) | C11—C10—H101 | 109 (2) |
N1—C6—N6 | 118.0 (6) | C10—C11—H113 | 111 (2) |
C5—N5—O52 | 115.9 (5) | C10—C11—H112 | 107 (2) |
C5—N5—O51 | 121.4 (4) | C10—C11—H111 | 114 (2) |
O51—N5—O52 | 122.5 (4) | H112—C11—H113 | 111 (3) |
C6—N6—C8 | 119.6 (6) | H111—C11—H113 | 107 (3) |
C6—N6—C7 | 118.8 (6) | H111—C11—H112 | 106 (3) |
C7—N6—C8 | 121.1 (5) | N4—C12—H122 | 108 (2) |
N6—C7—H73 | 106 (2) | N4—C12—H121 | 108 (2) |
N6—C7—H72 | 109 (2) | N4—C12—C13 | 114.2 (6) |
N6—C7—H71 | 119 (2) | H121—C12—H122 | 110 (3) |
H72—C7—H73 | 109 (3) | C13—C12—H122 | 108 (2) |
H71—C7—H73 | 106 (3) | C13—C12—H121 | 109 (2) |
H71—C7—H72 | 109 (3) | C12—C13—H133 | 109 (2) |
N6—C8—H83 | 106 (2) | C12—C13—H132 | 108 (2) |
N6—C8—H82 | 105 (2) | C12—C13—H131 | 114 (2) |
N6—C8—H81 | 119 (2) | H132—C13—H133 | 109 (2) |
H82—C8—H83 | 111 (3) | H131—C13—H133 | 108 (3) |
H81—C8—H83 | 109 (3) | H131—C13—H132 | 108 (3) |
H81—C8—H82 | 108 (3) | ||
C5—C4—S4—C9 | 103.9 (5) | N1—C6—N6—C7 | 8.0 (9) |
C4—C5—N5—O51 | 62.6 (7) | S3—C9—S4—C4 | −17.1 (5) |
C5—C6—N6—C8 | 12 (1) |
C10H15N5O2S2 | F(000) = 632 |
Mr = 301.39 | Dx = 1.388 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54059 Å |
a = 7.354 (3) Å | µ = 3.42 mm−1 |
b = 9.098 (4) Å | T = 295 K |
c = 21.738 (8) Å | Particle morphology: parallelepipeds |
β = 97.33 (2)° | dark yellow |
V = 1443 (1) Å3 | flat_sheet, 7 × 7 mm |
Z = 4 |
Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Specimen mounting: Pressed as a thin layer in the specimen holder of the camera |
Radiation source: fine focus X-ray tube, Nonius 3502.223 | Data collection mode: transmission |
Quartz monochromator | Scan method: Stationary detector |
Refinement on Inet | 142 parameters |
Least-squares matrix: full with fixed elements per cycle | 83 restraints |
Rp = 0.075 | 17 constraints |
Rwp = 0.102 | H-atom parameters constrained |
Rexp = 0.035 | Weighting scheme based on measured s.u.'s |
χ2 = 8.644 | (Δ/σ)max = 0.05 |
7596 data points | Background function: Chebyshev polynomial up to the 5th order |
Excluded region(s): 4.05-5.99 | Preferred orientation correction: March-Dollase (Dollase, 1986) |
Profile function: split-type pseudo-Voigt |
C10H15N5O2S2 | V = 1443 (1) Å3 |
Mr = 301.39 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54059 Å |
a = 7.354 (3) Å | µ = 3.42 mm−1 |
b = 9.098 (4) Å | T = 295 K |
c = 21.738 (8) Å | flat_sheet, 7 × 7 mm |
β = 97.33 (2)° |
Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Data collection mode: transmission |
Specimen mounting: Pressed as a thin layer in the specimen holder of the camera | Scan method: Stationary detector |
Rp = 0.075 | 7596 data points |
Rwp = 0.102 | 142 parameters |
Rexp = 0.035 | 83 restraints |
χ2 = 8.644 | H-atom parameters constrained |
x | y | z | Uiso*/Ueq | ||
N1 | 0.1935 (7) | 0.6766 (5) | 0.0773 (2) | 0.059 (2)* | |
C2 | 0.2112 (9) | 0.5761 (7) | 0.1252 (3) | 0.059 (2)* | |
N3 | 0.2627 (7) | 0.4352 (5) | 0.1250 (2) | 0.059 (2)* | |
C4 | 0.288 (10) | 0.3648 (6) | 0.0729 (3) | 0.059 (2)* | |
C5 | 0.2686 (9) | 0.4614 (8) | 0.0228 (3) | 0.059 (2)* | |
C6 | 0.215 (10) | 0.6127 (7) | 0.0211 (3) | 0.059 (2)* | |
N5 | 0.2912 (8) | 0.3860 (5) | −0.0359 (3) | 0.059 (2)* | |
O51 | 0.2945 (6) | 0.4570 (4) | −0.0836 (2) | 0.059 (2)* | |
O52 | 0.2871 (6) | 0.2537 (4) | −0.0385 (2) | 0.059 (2)* | |
N6 | 0.2034 (8) | 0.7037 (6) | −0.0285 (2) | 0.059 (2)* | |
C7 | 0.1612 (9) | 0.8546 (8) | −0.0236 (3) | 0.059 (2)* | |
S4 | 0.3563 (3) | 0.1882 (2) | 0.0803 (1) | 0.047 (1)* | |
C9 | 0.4572 (9) | 0.1976 (7) | 0.1603 (3) | 0.059 (2)* | |
N4 | 0.3404 (7) | 0.1586 (6) | 0.2007 (2) | 0.059 (2)* | |
S3 | 0.6672 (2) | 0.2286 (2) | 0.1818 (1) | 0.053 (1)* | |
C10 | 0.147 (11) | 0.1180 (7) | 0.1884 (3) | 0.059 (2)* | |
C11 | 0.082 (1) | −0.0406 (8) | 0.1707 (3) | 0.059 (2)* | |
C12 | 0.398 (1) | 0.1445 (8) | 0.2682 (4) | 0.059 (2)* | |
C13 | 0.406 (1) | 0.2976 (9) | 0.2988 (3) | 0.059 (2)* | |
H71 | 0.186 (6) | 0.915 (4) | −0.064 (2) | 0.051* | |
H72 | 0.252 (6) | 0.896 (4) | 0.016 (2) | 0.051* | |
H73 | 0.027 (6) | 0.865 (4) | −0.014 (2) | 0.051* | |
H2 | 0.192 (6) | 0.628 (4) | 0.169 (2) | 0.051* | |
H6 | 0.241 (5) | 0.667 (4) | −0.066 (2) | 0.051* | |
H101 | 0.091 (5) | 0.184 (4) | 0.153 (2) | 0.051* | |
H102 | 0.093 (7) | 0.142 (4) | 0.229 (2) | 0.051* | |
H121 | 0.529 (6) | 0.104 (4) | 0.273 (2) | 0.051* | |
H122 | 0.303 (6) | 0.083 (4) | 0.286 (2) | 0.051* | |
H131 | 0.445 (6) | 0.282 (4) | 0.345 (1) | 0.051* | |
H132 | 0.275 (5) | 0.341 (4) | 0.289 (2) | 0.051* | |
H133 | 0.501 (6) | 0.358 (4) | 0.278 (2) | 0.051* | |
H111 | −0.059 (6) | −0.037 (4) | 0.168 (2) | 0.051* | |
H112 | 0.143 (6) | −0.105 (3) | 0.206 (2) | 0.051* | |
H113 | 0.129 (6) | −0.062 (4) | 0.129 (2) | 0.051* |
N1—C2 | 1.379 (8) | S4—C9 | 1.804 (7) |
N1—C6 | 1.381 (8) | C9—N4 | 1.352 (9) |
C2—N3 | 1.337 (8) | C9—S3 | 1.581 (7) |
C2—H2 | 1.09 (4) | N4—C10 | 1.459 (9) |
N3—C4 | 1.335 (8) | N4—C12 | 1.480 (9) |
C4—C5 | 1.393 (9) | C10—C11 | 1.55 (1) |
C4—S4 | 1.685 (6) | C10—H101 | 1.03 (3) |
C5—C6 | 1.43 (1) | C10—H102 | 1.04 (5) |
C5—N5 | 1.477 (9) | C11—H111 | 1.03 (5) |
C6—N6 | 1.353 (8) | C11—H112 | 1.03 (4) |
N5—O51 | 1.225 (7) | C11—H113 | 1.03 (4) |
N5—O52 | 1.205 (6) | C12—C13 | 1.54 (1) |
N6—C7 | 1.415 (9) | C12—H121 | 1.02 (4) |
N6—H6 | 0.96 (4) | C12—H122 | 1.01 (4) |
C7—H71 | 1.06 (4) | C13—H131 | 1.03 (3) |
C7—H72 | 1.08 (4) | C13—H132 | 1.04 (4) |
C7—H73 | 1.04 (4) | C13—H133 | 1.04 (4) |
C2—N1—C6 | 112.2 (5) | N4—C9—S3 | 122.2 (5) |
N1—C2—H2 | 111 (2) | C9—N4—C12 | 122.8 (5) |
N1—C2—N3 | 129.3 (6) | C9—N4—C10 | 129.2 (6) |
N3—C2—H2 | 119 (2) | C10—N4—C12 | 108.0 (5) |
C2—N3—C4 | 122.2 (5) | N4—C10—H102 | 105 (3) |
N3—C4—S4 | 116.7 (4) | N4—C10—H101 | 106 (2) |
N3—C4—C5 | 110.5 (6) | N4—C10—C11 | 123.0 (6) |
C5—C4—S4 | 132.5 (5) | H101—C10—H102 | 111 (3) |
C4—C5—N5 | 111.8 (6) | C11—C10—H102 | 105 (2) |
C4—C5—C6 | 128.9 (6) | C11—C10—H101 | 106 (2) |
C6—C5—N5 | 119.0 (6) | C10—C11—H113 | 105 (2) |
N1—C6—C5 | 116.4 (6) | C10—C11—H112 | 105 (2) |
C5—C6—N6 | 126.8 (6) | C10—C11—H111 | 105 (2) |
N1—C6—N6 | 116.4 (5) | H112—C11—H113 | 113 (3) |
C5—N5—O52 | 120.0 (5) | H111—C11—H113 | 113 (4) |
C5—N5—O51 | 120.2 (6) | H111—C11—H112 | 114 (3) |
O51—N5—O52 | 119.4 (5) | N4—C12—H122 | 108 (2) |
C6—N6—H6 | 118 (2) | N4—C12—H121 | 107 (3) |
C6—N6—C7 | 121.8 (5) | N4—C12—C13 | 109.9 (6) |
C7—N6—H6 | 119 (2) | H121—C12—H122 | 117 (4) |
N6—C7—H73 | 109 (2) | C13—C12—H122 | 109 (2) |
N6—C7—H72 | 106 (2) | C13—C12—H121 | 107 (2) |
N6—C7—H71 | 112 (2) | C12—C13—H133 | 106 (2) |
H72—C7—H73 | 109 (3) | C12—C13—H132 | 105 (2) |
H71—C7—H73 | 112 (3) | C12—C13—H131 | 107 (2) |
H71—C7—H72 | 108 (3) | H132—C13—H133 | 112 (3) |
C4—S4—C9 | 97.4 (3) | H131—C13—H133 | 113 (3) |
S4—C9—S3 | 124.0 (4) | H131—C13—H132 | 114 (3) |
S4—C9—N4 | 113.4 (5) | ||
C5—C4—S4—C9 | 148.9 (7) | C5—C6—N6—C7 | −175.5 (6) |
C4—C5—N5—O52 | 14.3 (9) | S3—C9—S4—C4 | −93.8 (5) |
C9H16N5O2+·Cl−·H2O | F(000) = 592 |
Mr = 279.73 | Dx = 1.347 Mg m−3 |
Orthorhombic, Pna21 | Cu Kα radiation, λ = 1.54059 Å |
Hall symbol: P 2c -2n | µ = 2.56 mm−1 |
a = 10.271 (3) Å | T = 295 K |
b = 6.8360 (2) Å | Particle morphology: needles |
c = 19.642 (2) Å | pale yellow |
V = 1379.1 (6) Å3 | flat_sheet, 7 × 7 mm |
Z = 4 |
Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Specimen mounting: Pressed as a thin layer in the specimen holder of the camera |
Radiation source: fine focus X-ray tube, Nonius 3502.223 | Data collection mode: transmission |
Quartz monochromator | Scan method: Stationary detector |
Refinement on Inet | 141 parameters |
Least-squares matrix: full with fixed elements per cycle | 74 restraints |
Rp = 0.080 | 15 constraints |
Rwp = 0.105 | H-atom parameters constrained |
Rexp = 0.037 | Weighting scheme based on measured s.u.'s |
χ2 = 8.180 | (Δ/σ)max = 0.05 |
7599 data points | Background function: Chebyshev polynomial up to the 5th order |
Excluded region(s): 4.02-6.99 | Preferred orientation correction: March-Dollase (Dollase, 1986) |
Profile function: split-type pseudo-Voigt |
C9H16N5O2+·Cl−·H2O | V = 1379.1 (6) Å3 |
Mr = 279.73 | Z = 4 |
Orthorhombic, Pna21 | Cu Kα radiation, λ = 1.54059 Å |
a = 10.271 (3) Å | µ = 2.56 mm−1 |
b = 6.8360 (2) Å | T = 295 K |
c = 19.642 (2) Å | flat_sheet, 7 × 7 mm |
Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Data collection mode: transmission |
Specimen mounting: Pressed as a thin layer in the specimen holder of the camera | Scan method: Stationary detector |
Rp = 0.080 | 7599 data points |
Rwp = 0.105 | 141 parameters |
Rexp = 0.037 | 74 restraints |
χ2 = 8.180 | H-atom parameters constrained |
x | y | z | Uiso*/Ueq | ||
N1 | 0.2620 (5) | 0.365 (1) | 0.0884 (3) | 0.062 (2)* | |
C2 | 0.2855 (9) | 0.228 (1) | 0.1358 (7) | 0.062 (2)* | |
N3 | 0.3470 (5) | 0.2626 (9) | 0.1960 (4) | 0.062 (2)* | |
C4 | 0.3853 (7) | 0.454 (1) | 0.2009 (5) | 0.062 (2)* | |
C5 | 0.3957 (6) | 0.5884 (9) | 0.1459 (4) | 0.062 (2)* | |
C6 | 0.3106 (5) | 0.551 (1) | 0.0901 (4) | 0.062 (2)* | |
N5 | 0.5005 (6) | 0.7323 (9) | 0.1396 (4) | 0.062 (2)* | |
O51 | 0.6050 (5) | 0.7066 (8) | 0.1663 (3) | 0.062 (2)* | |
O52 | 0.4849 (4) | 0.8722 (8) | 0.1007 (3) | 0.062 (2)* | |
N6 | 0.2953 (5) | 0.6685 (8) | 0.0346 (3) | 0.062 (2)* | |
C7 | 0.223 (1) | 0.603 (2) | −0.0262 (7) | 0.062 (2)* | |
N4 | 0.4347 (6) | 0.5083 (9) | 0.2646 (4) | 0.062 (2)* | |
C10 | 0.4593 (9) | 0.715 (2) | 0.2878 (5) | 0.062 (2)* | |
C11 | 0.3348 (9) | 0.807 (2) | 0.3133 (7) | 0.062 (2)* | |
C12 | 0.4493 (9) | 0.357 (2) | 0.3181 (6) | 0.062 (2)* | |
C13 | 0.570 (1) | 0.232 (2) | 0.3104 (8) | 0.062 (2)* | |
Cl | 0.0715 (2) | 0.1310 (3) | 0.0000 | 0.050 (1)* | |
Ow | −0.1319 (4) | 0.4556 (7) | −0.0376 (3) | 0.055 (2)* | |
H2 | 0.257 (4) | 0.090 (8) | 0.126 (3) | 0.051* | |
H1 | 0.198 (4) | 0.330 (7) | 0.051 (3) | 0.051* | |
H6 | 0.325 (4) | 0.808 (7) | 0.037 (3) | 0.051* | |
H71 | 0.222 (5) | 0.710 (7) | −0.061 (3) | 0.051* | |
H72 | 0.132 (4) | 0.570 (6) | −0.013 (3) | 0.051* | |
H73 | 0.266 (5) | 0.484 (7) | −0.045 (3) | 0.051* | |
H121 | 0.371 (4) | 0.270 (7) | 0.317 (3) | 0.051* | |
H122 | 0.452 (4) | 0.422 (8) | 0.364 (3) | 0.051* | |
H101 | 0.525 (5) | 0.715 (7) | 0.325 (4) | 0.051* | |
H102 | 0.494 (4) | 0.794 (8) | 0.249 (3) | 0.051* | |
H111 | 0.353 (5) | 0.944 (8) | 0.329 (3) | 0.051* | |
H112 | 0.301 (6) | 0.730 (8) | 0.353 (3) | 0.051* | |
H113 | 0.269 (5) | 0.809 (6) | 0.276 (3) | 0.051* | |
H131 | 0.572 (5) | 0.133 (7) | 0.348 (3) | 0.051* | |
H132 | 0.649 (4) | 0.316 (8) | 0.313 (3) | 0.051* | |
H133 | 0.567 (5) | 0.163 (7) | 0.266 (3) | 0.051* |
N1—C2 | 1.34 (1) | C7—H72 | 1.00 (4) |
N1—C6 | 1.372 (9) | C7—H73 | 1.00 (5) |
N1—H1 | 1.01 (5) | N4—C10 | 1.50 (1) |
C2—N3 | 1.36 (1) | N4—C12 | 1.48 (1) |
C2—H2 | 1.01 (5) | C10—C11 | 1.51 (1) |
N3—C4 | 1.366 (9) | C10—H101 | 1.00 (7) |
C4—C5 | 1.42 (1) | C10—H102 | 1.00 (5) |
C4—N4 | 1.40 (1) | C11—H111 | 1.00 (6) |
C5—C6 | 1.43 (1) | C11—H112 | 1.00 (5) |
C5—N5 | 1.463 (9) | C11—H113 | 1.00 (5) |
C6—N6 | 1.362 (9) | C12—C13 | 1.51 (2) |
N5—O51 | 1.207 (8) | C12—H121 | 1.00 (5) |
N5—O52 | 1.235 (9) | C12—H122 | 1.00 (6) |
N6—C7 | 1.47 (1) | C13—H131 | 1.00 (5) |
N6—H6 | 1.00 (5) | C13—H132 | 1.00 (5) |
C7—H71 | 0.99 (5) | C13—H133 | 1.00 (5) |
C6—N1—H1 | 118 (3) | C4—N4—C12 | 118.9 (8) |
C2—N1—H1 | 117 (3) | C4—N4—C10 | 125.6 (7) |
C2—N1—C6 | 124.4 (7) | C10—N4—C12 | 115.0 (7) |
N1—C2—H2 | 118 (3) | N4—C10—H102 | 110 (3) |
N1—C2—N3 | 124 (1) | N4—C10—H101 | 110 (3) |
N3—C2—H2 | 118 (3) | N4—C10—C11 | 110.4 (8) |
C2—N3—C4 | 111.0 (7) | H101—C10—H102 | 108 (5) |
N3—C4—N4 | 115.0 (7) | C11—C10—H102 | 109 (3) |
N3—C4—C5 | 125.9 (6) | C11—C10—H101 | 109 (3) |
C5—C4—N4 | 118.5 (8) | C10—C11—H113 | 110 (3) |
C4—C5—N5 | 123.7 (6) | C10—C11—H112 | 110 (3) |
C4—C5—C6 | 115.0 (7) | C10—C11—H111 | 109 (3) |
C6—C5—N5 | 120.4 (6) | H112—C11—H113 | 110 (4) |
N1—C6—C5 | 114.0 (6) | H111—C11—H113 | 110 (4) |
C5—C6—N6 | 125.6 (6) | H111—C11—H112 | 109 (4) |
N1—C6—N6 | 119.1 (6) | N4—C12—H122 | 109 (3) |
C5—N5—O52 | 118.5 (6) | N4—C12—H121 | 109 (3) |
C5—N5—O51 | 121.3 (6) | N4—C12—C13 | 114.1 (9) |
O51—N5—O52 | 119.8 (6) | H121—C12—H122 | 108 (4) |
C6—N6—H6 | 119 (3) | C13—C12—H122 | 109 (3) |
C6—N6—C7 | 121.9 (7) | C13—C12—H121 | 108 (3) |
C7—N6—H6 | 118 (3) | C12—C13—H133 | 109 (3) |
N6—C7—H73 | 109 (3) | C12—C13—H132 | 109 (3) |
N6—C7—H72 | 109 (3) | C12—C13—H131 | 109 (3) |
N6—C7—H71 | 110 (3) | H132—C13—H133 | 110 (4) |
H72—C7—H73 | 109 (4) | H131—C13—H133 | 109 (4) |
H71—C7—H73 | 110 (4) | H131—C13—H132 | 110 (4) |
H71—C7—H72 | 110 (4) | ||
N1—C6—N6—C7 | 3 (1) | C4—C5—N5—O52 | −162.3 (7) |
N1—C6—C5—N5 | 150.5 (6) | C4—N4—C10—C11 | 82 (1) |
C4—C5—N5—O51 | 25 (1) | C4—N4—C12—C13 | 80 (1) |
Experimental details
(Ia) | (Ib) | (II) | |
Crystal data | |||
Chemical formula | C11H17N5O2S2 | C10H15N5O2S2 | C9H16N5O2+·Cl−·H2O |
Mr | 315.42 | 301.39 | 279.73 |
Crystal system, space group | Orthorhombic, Pbca | Monoclinic, P21/c | Orthorhombic, Pna21 |
Temperature (K) | 295 | 295 | 295 |
a, b, c (Å) | 20.013 (6), 13.456 (3), 11.424 (3) | 7.354 (3), 9.098 (4), 21.738 (8) | 10.271 (3), 6.8360 (2), 19.642 (2) |
α, β, γ (°) | 90, 90, 90 | 90, 97.33 (2), 90 | 90, 90, 90 |
V (Å3) | 3076 (1) | 1443 (1) | 1379.1 (6) |
Z | 8 | 4 | 4 |
Radiation type | Cu Kα, λ = 1.54059 Å | Cu Kα, λ = 1.54059 Å | Cu Kα, λ = 1.54059 Å |
µ (mm−1) | 3.23 | 3.42 | 2.56 |
Specimen shape, size (mm) | Flat_sheet, 7 × 7 | Flat_sheet, 7 × 7 | Flat_sheet, 7 × 7 |
Data collection | |||
Diffractometer | Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Enraf-Nonius Guinier Johannson camera FR 552 diffractometer | Enraf-Nonius Guinier Johannson camera FR 552 diffractometer |
Specimen mounting | Pressed as a thin layer in the specimen holder of the camera | Pressed as a thin layer in the specimen holder of the camera | Pressed as a thin layer in the specimen holder of the camera |
Data collection mode | Transmission | Transmission | Transmission |
Scan method | Stationary detector | Stationary detector | Stationary detector |
2θ values (°) | 2θfixed = ? | 2θfixed = ? | 2θfixed = ? |
Refinement | |||
R factors and goodness of fit | Rp = 0.073, Rwp = 0.098, Rexp = 0.030, χ2 = 10.368 | Rp = 0.075, Rwp = 0.102, Rexp = 0.035, χ2 = 8.644 | Rp = 0.080, Rwp = 0.105, Rexp = 0.037, χ2 = 8.180 |
No. of data points | 7598 | 7596 | 7599 |
No. of parameters | 155 | 142 | 141 |
No. of restraints | 122 | 83 | 74 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained | H-atom parameters constrained |
Computer programs: Johannson LS18 linescanner data collection program, LSPAID (Visser et al., 1986), PROFIT (Philips, 1996), MRIA (Zlokazov & Chernyshev, 1992), PLUTON (Spek, 1992), MRIA, SHELXL93 (Sheldrick, 1993) and PARST (Nardelli, 1983).
X-ray | DFT | |
(Ia) | ||
C5-C4-S4-C9 | 103.9 (5) | 164 |
C4-C5-N5-O51 | 62.6 (7) | 34 |
C5-C6-N6-C8 | 12 (1) | 19 |
N1-C6-N6-C7 | 8.0 (9) | 14 |
S3-C9-S4-C4 | -17.1 (5) | -103 |
S4···O51 | 2.964 (7) | 2.687 |
(Ib) | ||
C5-C4-S4-C9 | 148.9 (7) | 169 |
C4-C5-N5-O52 | 14.3 (9) | 2 |
C5-C6-N6-C7 | -175.5 (6) | 180 |
S3-C9-S4-C4 | -93.8 (5) | -105 |
S4···O52 | 2.636 (7) | 2.591 |
Dithiocarbamoyl derivatives of diverse heterocycles demonstrate a broad range of physiological activity: antifilarial (Gallay & Schweizer, 1980), antiviral (Bernstein et al., 1993) and antifungal agents (Itoh & Okonogi, 1995), and oncolytic (Lerchen et al., 1996) and lipoprotein disorder drugs (Tokuhisa et al., 1998) are known among this group of compounds. Therefore, the question of the possible metabolic pathways of such compounds is currently a very hot topic in medicinal chemistry and the systematic study of their reactivity can clarify this problem. Three such compounds, (Ia), (Ib) and (II), are discussed here. \sch
It has been demonstrated that the thermolysis of dithiocarbamoyl derivatives of pyridines and pyrimidines containing a nitro group ortho to the dithiocarbamoyl moiety can result in the formation of disulfide compounds with the elimination of the nitro group, (III) (Rasheed & Warkentin, 1977; Makarov et al., 1994). Recently, an alternative thermolysis pathway involving the elimination of carbon disulfide has been found, (IV) (Makarov et al., 2000). The different reactivity of (Ia) and (Ib) can be interpreted, in principle, in terms of the differences in their molecular structures, which are illustrated in Table 1 and Fig. 1: the twist of the nitro group out of the plane of the pyrimidine ring in (Ia) should lower its affinity for nucleophilic substitution compared with (Ib). Besides this, the twist of the nitro group in (Ia) breaks the secondary S···O contact, which is present in (Ib). Short intramolecular S···O contacts arise from the σ-interaction between the non-bonding orbital of the O atom and the p and d orbitals of the S atom, and this interaction affects the spectral and chemical properties of the corresponding compounds (Cohen-Addad et al., 1984).
The results of the density functional theory (DFT; Dewar et al., 1985?) geometrical optimization of (Ib) decribed below compare rather well with the crystallographic data. Therefore, only minor changes in the molecular geometry of (Ib) are expected upon transfer from the crystal to solution. The secondary S···O contact also maintains the orientation of the dithiocarbamate group with respect to the C4—S4 bond: according to the DFT data, the decrease of the C5—C4—S4—C9 torsion angle from 169 to 110° (close to the observed 103°) requires 26 kJ mol-1. The orienting effect of the S···O contacts is also confirmed by analysis of the data retrieved from the Cambridge Crystallographic Database (CSD; Allen & Kennard, 1993) on compounds with the SR group situated ortho to the nitro group; in all 98 structures where the twist angle of the nitro group is less than 30°, the R moiety lies close to the ring plane and the NO2 and SR groups behave like engaged gears. However, if the nitro group is twisted out of the ring plane, the R—S—C—C torsion angles fall in the range 50–175° (14 structures).
In contrast with (Ib), the geometrical optimization of (Ia) leads to a structure that is significantly different from that observed, not only in terms of geometry, but also in terms of energy (the optimization started from the X-ray molecular geometry). Recently, two energy minima have been found for 2-nitrobenzenethiolates on the AM1 level (Dewar et al., 1985), the main one corresponding to the in-plane orientation of the nitro group and the second, local, one corresponding to the broken S···O contact (Low et al., 2000). In compounds (Ia) and (Ib) the DFT study did not reveal the second energy minimum. This distinction is probably due to the known deficiences in the sulfur parametrization inherent in the AM1 Hamiltonian. In particular, AM1 overestimates the positive charge on the S atoms, as compared with the ab initio results (Storer et al., 1995). The heat of formation obtained in the geometrical optimization, with the C5—C4—S4—C9 torsion angle constrained at its experimental value, is 16 kJ mol-1 higher than that for the fully optimized geometry. Thus, there are good reasons to believe that (Ia) flattens upon transfer from a crystal to solution and this is the probable reason why the thermolysis of (Ia) proceeds faster in the solid state than in xylene solution at the same temperature (Makarov et al., 1994). On the other hand, this means that even moderate deviation of the reaction centre of the molecule from planarity is enough to switch between two thermolysis pathways. Short intermolecular contacts are absent from the structures of (Ia) and (Ib).
The thermolysis product of (Ib) was isolated as the monohydrochloride salt, (II). The protonation site was unambiguously determined from the analysis of cation-anion contacts; N1···Cl 3.07 (1) Å and N1—H1···Cl 152 (4)°. However, the DFT and AM1 calculations predict that the protonation sites at N1 and N3 are equivalent to within 4 kJ/mol; thus, this compound should exist in solution as a tautomeric mixture. The hydrogen-bonding motif in (II) is shown in Fig. 2. The OW···Cl distances are 3.14 (1) and 3.19 (1) Å, and the Cl···OW···Cl angle is 117 (1)°. Besides this, the water molecule forms a weak hydrogen bond to the methylamino group; OW···H6i 2.22 (5) Å [symmetry code: (i) x - 1/2, 1/2 - y, z].