Buy article online - an online subscription or single-article purchase is required to access this article.
In order to correlate the reactivity and molecular structures of dithiocarbamates, the crystal structures of 6-dimethylamino-5-nitropyrimidin-4-yl
N,
N-diethyldithiocarbamate, C
11H
17N
5O
2S
2, (I
a), and 6-methylamino-5-nitropyrimidin-4-yl
N,
N-diethyldithiocarbamate, C
10H
15N
5O
2S
2, (I
b), and of the product of thermolysis of (I
b), namely 4-diethylamino-6-methylamino-5-nitropyrimidinium chloride monohydrate, C
9H
16N
5O
2+·Cl
−·H
2O, (II), have been determined from X-ray laboratory powder diffraction data. Conformational preferences in (I
a) and (I
b) were studied on the density functional theory (DFT) level. Deviation of the reaction centre of the molecule from planarity and breakage of the secondary S
O contact cause switching between two alternative pathways of thermolysis.
Supporting information
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).
(Ia) 6-Dimethylamino-5-nitropyrimidin-4-yl diethyldithiocarbamate
top
Crystal data top
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 | |
Data collection top
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 top
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 | |
Crystal data top
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 |
Data collection top
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 |
Refinement top
Rp = 0.073 | 7598 data points |
Rwp = 0.098 | 155 parameters |
Rexp = 0.030 | 122 restraints |
χ2 = 10.368 | H-atom parameters constrained |
Special details top
Experimental. Specimen was rotated in its plane |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | 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* | |
Geometric parameters (Å, º) top
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) | | |
(Ib) 6-Methylamino-5-nitropyrimidin-4-yl diethyldithiocarbamate
top
Crystal data top
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 | |
Data collection top
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 top
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 | |
Crystal data top
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)° | |
Data collection top
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 |
Refinement top
Rp = 0.075 | 7596 data points |
Rwp = 0.102 | 142 parameters |
Rexp = 0.035 | 83 restraints |
χ2 = 8.644 | H-atom parameters constrained |
Special details top
Experimental. Specimen was rotated in its plane |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | 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* | |
Geometric parameters (Å, º) top
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) |
(II) 4-Diethylamino-6-methylamino-5-nitropyrimidinium chloride monohydrate
top
Crystal data top
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 | |
Data collection top
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 top
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 | |
Crystal data top
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 |
Data collection top
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 |
Refinement top
Rp = 0.080 | 7599 data points |
Rwp = 0.105 | 141 parameters |
Rexp = 0.037 | 74 restraints |
χ2 = 8.180 | H-atom parameters constrained |
Special details top
Experimental. Specimen was rotated in its plane |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | 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* | |
Geometric parameters (Å, º) top
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 |
Experimental and DFT-calculated geometric parameters (Å, °) defining the
conformations of (Ia) and (Ib) top | 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 |
Subscribe to Acta Crystallographica Section C: Structural Chemistry
The full text of this article is available to subscribers to the journal.
If you have already registered and are using a computer listed in your registration details, please email
support@iucr.org for assistance.
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].