Download citation
Download citation
link to html
In order to correlate the reactivity and molecular structures of di­thio­carbamates, the crystal structures of 6-di­methyl­amino-5-nitro­pyrimidin-4-yl N,N-diethyl­di­thio­carbamate, C11H17N5O2S2, (Ia), and 6-methyl­amino-5-nitro­pyrimidin-4-yl N,N-diethyl­di­thio­carbamate, C10H15N5O2S2, (Ib), and of the product of thermolysis of (Ib), namely 4-diethyl­amino-6-methyl­amino-5-nitro­pyrimidinium chloride monohydrate, C9H16N5O2+·Cl·H2O, (II), have been determined from X-ray laboratory powder diffraction data. Conformational preferences in (Ia) and (Ib) 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

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100013457/br1303sup1.cif
Contains datablocks global, Ia, Ib, II

rtv

Rietveld powder data file (CIF format) https://doi.org/10.1107/S0108270100013457/br1303Iasup2.rtv
Contains datablock pattern_Ia

rtv

Rietveld powder data file (CIF format) https://doi.org/10.1107/S0108270100013457/br1303Ibsup3.rtv
Contains datablock pattern_Ib

rtv

Rietveld powder data file (CIF format) https://doi.org/10.1107/S0108270100013457/br1303IIsup4.rtv
Contains datablock pattern_II

CCDC references: 158254; 158255; 158256

Comment top

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].

Experimental top

Compounds (Ia), (Ib) and (II) were prepared in polycrystalline form according to the procedure of Makarov et al. (2000).

Refinement top

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.

Computing details top

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).

Figures top
[Figure 1] Fig. 1. The molecular structures of (a) (Ia) and (b) (Ib) with the atomic numbering. Displacement ellipsoids are drawn at the ??% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. A packing diagram for (II). Displacement ellipsoids are drawn at the ??% probability level and H atoms ahve been omitted for clarity.
[Figure 3] Fig. 3. The Rietveld plots, showing the observed and difference profiles, for (a) (Ia), (b) (Ib) and (c) (II). The reflection positions are shown above the difference profile.
(Ia) 6-Dimethylamino-5-nitropyrimidin-4-yl diethyldithiocarbamate top
Crystal data top
C11H17N5O2S2F(000) = 1328
Mr = 315.42Dx = 1.362 Mg m3
Orthorhombic, PbcaCu Kα radiation, λ = 1.54059 Å
Hall symbol: -P 2ac 2abµ = 3.23 mm1
a = 20.013 (6) ÅT = 295 K
b = 13.456 (3) ÅParticle morphology: no specific habit
c = 11.424 (3) Åintense yellow
V = 3076 (1) Å3flat_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 3502.223Data collection mode: transmission
Quartz monochromatorScan method: Stationary detector
Refinement top
Refinement on Inet155 parameters
Least-squares matrix: full with fixed elements per cycle122 restraints
Rp = 0.07318 constraints
Rwp = 0.098H-atom parameters constrained
Rexp = 0.030Weighting scheme based on measured s.u.'s
χ2 = 10.368(Δ/σ)max = 0.05
7598 data pointsBackground function: Chebyshev polynomial up to the 5th order
Excluded region(s): 4.03-7.99Preferred orientation correction: March-Dollase (Dollase, 1986)
Profile function: split-type pseudo-Voigt
Crystal data top
C11H17N5O2S2V = 3076 (1) Å3
Mr = 315.42Z = 8
Orthorhombic, PbcaCu Kα radiation, λ = 1.54059 Å
a = 20.013 (6) ŵ = 3.23 mm1
b = 13.456 (3) ÅT = 295 K
c = 11.424 (3) Åflat_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 cameraScan method: Stationary detector
Refinement top
Rp = 0.0737598 data points
Rwp = 0.098155 parameters
Rexp = 0.030122 restraints
χ2 = 10.368H-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
xyzUiso*/Ueq
N10.3906 (2)0.1648 (3)0.5588 (5)0.066 (2)*
C20.3696 (3)0.0882 (5)0.6208 (5)0.066 (2)*
N30.3695 (2)0.0092 (3)0.5902 (4)0.066 (2)*
C40.3954 (3)0.0298 (4)0.4842 (5)0.066 (2)*
C50.4222 (3)0.0491 (4)0.4153 (6)0.066 (2)*
C60.4194 (3)0.1519 (5)0.4533 (6)0.066 (2)*
N50.4461 (2)0.0229 (3)0.2952 (4)0.066 (2)*
O510.4908 (2)0.0335 (2)0.2807 (3)0.066 (2)*
O520.4137 (2)0.0564 (3)0.2149 (3)0.066 (2)*
N60.4451 (3)0.2341 (4)0.3978 (5)0.066 (2)*
C70.4324 (3)0.3310 (6)0.4471 (6)0.066 (2)*
C80.4906 (4)0.2215 (4)0.3020 (6)0.066 (2)*
S40.4022 (1)0.1558 (1)0.4306 (1)0.055 (1)*
C90.3193 (3)0.1760 (5)0.3820 (5)0.066 (2)*
S30.2698 (1)0.0855 (1)0.3605 (1)0.061 (1)*
N40.3065 (3)0.2758 (4)0.3657 (5)0.066 (2)*
C100.3568 (3)0.3514 (5)0.3923 (6)0.066 (2)*
C110.3484 (3)0.4032 (5)0.5106 (7)0.066 (2)*
C120.2415 (4)0.3034 (4)0.3165 (6)0.066 (2)*
C130.2414 (4)0.3152 (4)0.1833 (7)0.066 (2)*
H710.449 (2)0.391 (2)0.405 (3)0.051*
H720.384 (2)0.338 (3)0.460 (3)0.051*
H730.456 (2)0.332 (3)0.526 (3)0.051*
H810.511 (2)0.282 (2)0.265 (4)0.051*
H820.528 (2)0.181 (2)0.335 (3)0.051*
H830.466 (2)0.184 (3)0.242 (3)0.051*
H1310.197 (2)0.334 (3)0.150 (4)0.051*
H1320.255 (2)0.250 (2)0.147 (3)0.051*
H1330.275 (2)0.367 (2)0.161 (3)0.051*
H1110.384 (2)0.455 (2)0.528 (3)0.051*
H1120.353 (2)0.351 (3)0.573 (3)0.051*
H1130.305 (2)0.437 (3)0.515 (3)0.051*
H1210.209 (2)0.251 (2)0.338 (3)0.051*
H1220.228 (2)0.369 (2)0.352 (3)0.051*
H1010.402 (2)0.321 (2)0.388 (4)0.051*
H1020.353 (2)0.405 (2)0.330 (3)0.051*
H20.350 (2)0.105 (2)0.699 (3)0.051*
Geometric parameters (Å, º) top
N1—C21.319 (8)C8—H830.99 (4)
N1—C61.347 (9)S4—C91.771 (6)
C2—N31.356 (8)C9—S31.589 (7)
C2—H21.00 (3)C9—N41.380 (9)
N3—C41.346 (7)N4—C101.463 (9)
C4—C51.426 (8)N4—C121.46 (1)
C4—S41.808 (6)C10—C111.53 (1)
C5—C61.451 (9)C10—H1010.99 (3)
C5—N51.495 (8)C10—H1021.01 (3)
C6—N61.375 (9)C11—H1111.02 (3)
N5—O511.185 (5)C11—H1121.01 (4)
N5—O521.210 (6)C11—H1130.98 (3)
N6—C71.44 (1)C12—C131.53 (1)
N6—C81.434 (9)C12—H1211.00 (3)
C7—H711.00 (3)C12—H1221.00 (3)
C7—H720.99 (3)C13—H1311.00 (4)
C7—H731.02 (4)C13—H1321.01 (1)
C8—H810.99 (4)C13—H1331.00 (3)
C8—H821.00 (3)
C2—N1—C6121.1 (5)C4—S4—C9100.4 (3)
N1—C2—H2115 (2)S4—C9—N4111.5 (5)
N1—C2—N3128.1 (6)S4—C9—S3121.0 (4)
N3—C2—H2117 (2)S3—C9—N4127.5 (5)
C2—N3—C4115.5 (5)C9—N4—C12117.6 (5)
N3—C4—S4121.8 (4)C9—N4—C10121.4 (5)
N3—C4—C5119.2 (5)C10—N4—C12121.0 (6)
C5—C4—S4118.9 (4)N4—C10—H102107 (2)
C4—C5—N5116.8 (5)N4—C10—H101109 (2)
C4—C5—C6122.0 (5)N4—C10—C11115.1 (6)
C6—C5—N5120.8 (5)H101—C10—H102110 (3)
N1—C6—C5114.0 (6)C11—C10—H102107 (2)
C5—C6—N6127.9 (6)C11—C10—H101109 (2)
N1—C6—N6118.0 (6)C10—C11—H113111 (2)
C5—N5—O52115.9 (5)C10—C11—H112107 (2)
C5—N5—O51121.4 (4)C10—C11—H111114 (2)
O51—N5—O52122.5 (4)H112—C11—H113111 (3)
C6—N6—C8119.6 (6)H111—C11—H113107 (3)
C6—N6—C7118.8 (6)H111—C11—H112106 (3)
C7—N6—C8121.1 (5)N4—C12—H122108 (2)
N6—C7—H73106 (2)N4—C12—H121108 (2)
N6—C7—H72109 (2)N4—C12—C13114.2 (6)
N6—C7—H71119 (2)H121—C12—H122110 (3)
H72—C7—H73109 (3)C13—C12—H122108 (2)
H71—C7—H73106 (3)C13—C12—H121109 (2)
H71—C7—H72109 (3)C12—C13—H133109 (2)
N6—C8—H83106 (2)C12—C13—H132108 (2)
N6—C8—H82105 (2)C12—C13—H131114 (2)
N6—C8—H81119 (2)H132—C13—H133109 (2)
H82—C8—H83111 (3)H131—C13—H133108 (3)
H81—C8—H83109 (3)H131—C13—H132108 (3)
H81—C8—H82108 (3)
C5—C4—S4—C9103.9 (5)N1—C6—N6—C78.0 (9)
C4—C5—N5—O5162.6 (7)S3—C9—S4—C417.1 (5)
C5—C6—N6—C812 (1)
(Ib) 6-Methylamino-5-nitropyrimidin-4-yl diethyldithiocarbamate top
Crystal data top
C10H15N5O2S2F(000) = 632
Mr = 301.39Dx = 1.388 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54059 Å
a = 7.354 (3) ŵ = 3.42 mm1
b = 9.098 (4) ÅT = 295 K
c = 21.738 (8) ÅParticle morphology: parallelepipeds
β = 97.33 (2)°dark yellow
V = 1443 (1) Å3flat_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 3502.223Data collection mode: transmission
Quartz monochromatorScan method: Stationary detector
Refinement top
Refinement on Inet142 parameters
Least-squares matrix: full with fixed elements per cycle83 restraints
Rp = 0.07517 constraints
Rwp = 0.102H-atom parameters constrained
Rexp = 0.035Weighting scheme based on measured s.u.'s
χ2 = 8.644(Δ/σ)max = 0.05
7596 data pointsBackground function: Chebyshev polynomial up to the 5th order
Excluded region(s): 4.05-5.99Preferred orientation correction: March-Dollase (Dollase, 1986)
Profile function: split-type pseudo-Voigt
Crystal data top
C10H15N5O2S2V = 1443 (1) Å3
Mr = 301.39Z = 4
Monoclinic, P21/cCu Kα radiation, λ = 1.54059 Å
a = 7.354 (3) ŵ = 3.42 mm1
b = 9.098 (4) ÅT = 295 K
c = 21.738 (8) Åflat_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 cameraScan method: Stationary detector
Refinement top
Rp = 0.0757596 data points
Rwp = 0.102142 parameters
Rexp = 0.03583 restraints
χ2 = 8.644H-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
xyzUiso*/Ueq
N10.1935 (7)0.6766 (5)0.0773 (2)0.059 (2)*
C20.2112 (9)0.5761 (7)0.1252 (3)0.059 (2)*
N30.2627 (7)0.4352 (5)0.1250 (2)0.059 (2)*
C40.288 (10)0.3648 (6)0.0729 (3)0.059 (2)*
C50.2686 (9)0.4614 (8)0.0228 (3)0.059 (2)*
C60.215 (10)0.6127 (7)0.0211 (3)0.059 (2)*
N50.2912 (8)0.3860 (5)0.0359 (3)0.059 (2)*
O510.2945 (6)0.4570 (4)0.0836 (2)0.059 (2)*
O520.2871 (6)0.2537 (4)0.0385 (2)0.059 (2)*
N60.2034 (8)0.7037 (6)0.0285 (2)0.059 (2)*
C70.1612 (9)0.8546 (8)0.0236 (3)0.059 (2)*
S40.3563 (3)0.1882 (2)0.0803 (1)0.047 (1)*
C90.4572 (9)0.1976 (7)0.1603 (3)0.059 (2)*
N40.3404 (7)0.1586 (6)0.2007 (2)0.059 (2)*
S30.6672 (2)0.2286 (2)0.1818 (1)0.053 (1)*
C100.147 (11)0.1180 (7)0.1884 (3)0.059 (2)*
C110.082 (1)0.0406 (8)0.1707 (3)0.059 (2)*
C120.398 (1)0.1445 (8)0.2682 (4)0.059 (2)*
C130.406 (1)0.2976 (9)0.2988 (3)0.059 (2)*
H710.186 (6)0.915 (4)0.064 (2)0.051*
H720.252 (6)0.896 (4)0.016 (2)0.051*
H730.027 (6)0.865 (4)0.014 (2)0.051*
H20.192 (6)0.628 (4)0.169 (2)0.051*
H60.241 (5)0.667 (4)0.066 (2)0.051*
H1010.091 (5)0.184 (4)0.153 (2)0.051*
H1020.093 (7)0.142 (4)0.229 (2)0.051*
H1210.529 (6)0.104 (4)0.273 (2)0.051*
H1220.303 (6)0.083 (4)0.286 (2)0.051*
H1310.445 (6)0.282 (4)0.345 (1)0.051*
H1320.275 (5)0.341 (4)0.289 (2)0.051*
H1330.501 (6)0.358 (4)0.278 (2)0.051*
H1110.059 (6)0.037 (4)0.168 (2)0.051*
H1120.143 (6)0.105 (3)0.206 (2)0.051*
H1130.129 (6)0.062 (4)0.129 (2)0.051*
Geometric parameters (Å, º) top
N1—C21.379 (8)S4—C91.804 (7)
N1—C61.381 (8)C9—N41.352 (9)
C2—N31.337 (8)C9—S31.581 (7)
C2—H21.09 (4)N4—C101.459 (9)
N3—C41.335 (8)N4—C121.480 (9)
C4—C51.393 (9)C10—C111.55 (1)
C4—S41.685 (6)C10—H1011.03 (3)
C5—C61.43 (1)C10—H1021.04 (5)
C5—N51.477 (9)C11—H1111.03 (5)
C6—N61.353 (8)C11—H1121.03 (4)
N5—O511.225 (7)C11—H1131.03 (4)
N5—O521.205 (6)C12—C131.54 (1)
N6—C71.415 (9)C12—H1211.02 (4)
N6—H60.96 (4)C12—H1221.01 (4)
C7—H711.06 (4)C13—H1311.03 (3)
C7—H721.08 (4)C13—H1321.04 (4)
C7—H731.04 (4)C13—H1331.04 (4)
C2—N1—C6112.2 (5)N4—C9—S3122.2 (5)
N1—C2—H2111 (2)C9—N4—C12122.8 (5)
N1—C2—N3129.3 (6)C9—N4—C10129.2 (6)
N3—C2—H2119 (2)C10—N4—C12108.0 (5)
C2—N3—C4122.2 (5)N4—C10—H102105 (3)
N3—C4—S4116.7 (4)N4—C10—H101106 (2)
N3—C4—C5110.5 (6)N4—C10—C11123.0 (6)
C5—C4—S4132.5 (5)H101—C10—H102111 (3)
C4—C5—N5111.8 (6)C11—C10—H102105 (2)
C4—C5—C6128.9 (6)C11—C10—H101106 (2)
C6—C5—N5119.0 (6)C10—C11—H113105 (2)
N1—C6—C5116.4 (6)C10—C11—H112105 (2)
C5—C6—N6126.8 (6)C10—C11—H111105 (2)
N1—C6—N6116.4 (5)H112—C11—H113113 (3)
C5—N5—O52120.0 (5)H111—C11—H113113 (4)
C5—N5—O51120.2 (6)H111—C11—H112114 (3)
O51—N5—O52119.4 (5)N4—C12—H122108 (2)
C6—N6—H6118 (2)N4—C12—H121107 (3)
C6—N6—C7121.8 (5)N4—C12—C13109.9 (6)
C7—N6—H6119 (2)H121—C12—H122117 (4)
N6—C7—H73109 (2)C13—C12—H122109 (2)
N6—C7—H72106 (2)C13—C12—H121107 (2)
N6—C7—H71112 (2)C12—C13—H133106 (2)
H72—C7—H73109 (3)C12—C13—H132105 (2)
H71—C7—H73112 (3)C12—C13—H131107 (2)
H71—C7—H72108 (3)H132—C13—H133112 (3)
C4—S4—C997.4 (3)H131—C13—H133113 (3)
S4—C9—S3124.0 (4)H131—C13—H132114 (3)
S4—C9—N4113.4 (5)
C5—C4—S4—C9148.9 (7)C5—C6—N6—C7175.5 (6)
C4—C5—N5—O5214.3 (9)S3—C9—S4—C493.8 (5)
(II) 4-Diethylamino-6-methylamino-5-nitropyrimidinium chloride monohydrate top
Crystal data top
C9H16N5O2+·Cl·H2OF(000) = 592
Mr = 279.73Dx = 1.347 Mg m3
Orthorhombic, Pna21Cu Kα radiation, λ = 1.54059 Å
Hall symbol: P 2c -2nµ = 2.56 mm1
a = 10.271 (3) ÅT = 295 K
b = 6.8360 (2) ÅParticle morphology: needles
c = 19.642 (2) Åpale yellow
V = 1379.1 (6) Å3flat_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 3502.223Data collection mode: transmission
Quartz monochromatorScan method: Stationary detector
Refinement top
Refinement on Inet141 parameters
Least-squares matrix: full with fixed elements per cycle74 restraints
Rp = 0.08015 constraints
Rwp = 0.105H-atom parameters constrained
Rexp = 0.037Weighting scheme based on measured s.u.'s
χ2 = 8.180(Δ/σ)max = 0.05
7599 data pointsBackground function: Chebyshev polynomial up to the 5th order
Excluded region(s): 4.02-6.99Preferred orientation correction: March-Dollase (Dollase, 1986)
Profile function: split-type pseudo-Voigt
Crystal data top
C9H16N5O2+·Cl·H2OV = 1379.1 (6) Å3
Mr = 279.73Z = 4
Orthorhombic, Pna21Cu Kα radiation, λ = 1.54059 Å
a = 10.271 (3) ŵ = 2.56 mm1
b = 6.8360 (2) ÅT = 295 K
c = 19.642 (2) Åflat_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 cameraScan method: Stationary detector
Refinement top
Rp = 0.0807599 data points
Rwp = 0.105141 parameters
Rexp = 0.03774 restraints
χ2 = 8.180H-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
xyzUiso*/Ueq
N10.2620 (5)0.365 (1)0.0884 (3)0.062 (2)*
C20.2855 (9)0.228 (1)0.1358 (7)0.062 (2)*
N30.3470 (5)0.2626 (9)0.1960 (4)0.062 (2)*
C40.3853 (7)0.454 (1)0.2009 (5)0.062 (2)*
C50.3957 (6)0.5884 (9)0.1459 (4)0.062 (2)*
C60.3106 (5)0.551 (1)0.0901 (4)0.062 (2)*
N50.5005 (6)0.7323 (9)0.1396 (4)0.062 (2)*
O510.6050 (5)0.7066 (8)0.1663 (3)0.062 (2)*
O520.4849 (4)0.8722 (8)0.1007 (3)0.062 (2)*
N60.2953 (5)0.6685 (8)0.0346 (3)0.062 (2)*
C70.223 (1)0.603 (2)0.0262 (7)0.062 (2)*
N40.4347 (6)0.5083 (9)0.2646 (4)0.062 (2)*
C100.4593 (9)0.715 (2)0.2878 (5)0.062 (2)*
C110.3348 (9)0.807 (2)0.3133 (7)0.062 (2)*
C120.4493 (9)0.357 (2)0.3181 (6)0.062 (2)*
C130.570 (1)0.232 (2)0.3104 (8)0.062 (2)*
Cl0.0715 (2)0.1310 (3)0.00000.050 (1)*
Ow0.1319 (4)0.4556 (7)0.0376 (3)0.055 (2)*
H20.257 (4)0.090 (8)0.126 (3)0.051*
H10.198 (4)0.330 (7)0.051 (3)0.051*
H60.325 (4)0.808 (7)0.037 (3)0.051*
H710.222 (5)0.710 (7)0.061 (3)0.051*
H720.132 (4)0.570 (6)0.013 (3)0.051*
H730.266 (5)0.484 (7)0.045 (3)0.051*
H1210.371 (4)0.270 (7)0.317 (3)0.051*
H1220.452 (4)0.422 (8)0.364 (3)0.051*
H1010.525 (5)0.715 (7)0.325 (4)0.051*
H1020.494 (4)0.794 (8)0.249 (3)0.051*
H1110.353 (5)0.944 (8)0.329 (3)0.051*
H1120.301 (6)0.730 (8)0.353 (3)0.051*
H1130.269 (5)0.809 (6)0.276 (3)0.051*
H1310.572 (5)0.133 (7)0.348 (3)0.051*
H1320.649 (4)0.316 (8)0.313 (3)0.051*
H1330.567 (5)0.163 (7)0.266 (3)0.051*
Geometric parameters (Å, º) top
N1—C21.34 (1)C7—H721.00 (4)
N1—C61.372 (9)C7—H731.00 (5)
N1—H11.01 (5)N4—C101.50 (1)
C2—N31.36 (1)N4—C121.48 (1)
C2—H21.01 (5)C10—C111.51 (1)
N3—C41.366 (9)C10—H1011.00 (7)
C4—C51.42 (1)C10—H1021.00 (5)
C4—N41.40 (1)C11—H1111.00 (6)
C5—C61.43 (1)C11—H1121.00 (5)
C5—N51.463 (9)C11—H1131.00 (5)
C6—N61.362 (9)C12—C131.51 (2)
N5—O511.207 (8)C12—H1211.00 (5)
N5—O521.235 (9)C12—H1221.00 (6)
N6—C71.47 (1)C13—H1311.00 (5)
N6—H61.00 (5)C13—H1321.00 (5)
C7—H710.99 (5)C13—H1331.00 (5)
C6—N1—H1118 (3)C4—N4—C12118.9 (8)
C2—N1—H1117 (3)C4—N4—C10125.6 (7)
C2—N1—C6124.4 (7)C10—N4—C12115.0 (7)
N1—C2—H2118 (3)N4—C10—H102110 (3)
N1—C2—N3124 (1)N4—C10—H101110 (3)
N3—C2—H2118 (3)N4—C10—C11110.4 (8)
C2—N3—C4111.0 (7)H101—C10—H102108 (5)
N3—C4—N4115.0 (7)C11—C10—H102109 (3)
N3—C4—C5125.9 (6)C11—C10—H101109 (3)
C5—C4—N4118.5 (8)C10—C11—H113110 (3)
C4—C5—N5123.7 (6)C10—C11—H112110 (3)
C4—C5—C6115.0 (7)C10—C11—H111109 (3)
C6—C5—N5120.4 (6)H112—C11—H113110 (4)
N1—C6—C5114.0 (6)H111—C11—H113110 (4)
C5—C6—N6125.6 (6)H111—C11—H112109 (4)
N1—C6—N6119.1 (6)N4—C12—H122109 (3)
C5—N5—O52118.5 (6)N4—C12—H121109 (3)
C5—N5—O51121.3 (6)N4—C12—C13114.1 (9)
O51—N5—O52119.8 (6)H121—C12—H122108 (4)
C6—N6—H6119 (3)C13—C12—H122109 (3)
C6—N6—C7121.9 (7)C13—C12—H121108 (3)
C7—N6—H6118 (3)C12—C13—H133109 (3)
N6—C7—H73109 (3)C12—C13—H132109 (3)
N6—C7—H72109 (3)C12—C13—H131109 (3)
N6—C7—H71110 (3)H132—C13—H133110 (4)
H72—C7—H73109 (4)H131—C13—H133109 (4)
H71—C7—H73110 (4)H131—C13—H132110 (4)
H71—C7—H72110 (4)
N1—C6—N6—C73 (1)C4—C5—N5—O52162.3 (7)
N1—C6—C5—N5150.5 (6)C4—N4—C10—C1182 (1)
C4—C5—N5—O5125 (1)C4—N4—C12—C1380 (1)

Experimental details

(Ia)(Ib)(II)
Crystal data
Chemical formulaC11H17N5O2S2C10H15N5O2S2C9H16N5O2+·Cl·H2O
Mr315.42301.39279.73
Crystal system, space groupOrthorhombic, PbcaMonoclinic, P21/cOrthorhombic, Pna21
Temperature (K)295295295
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, 9090, 97.33 (2), 9090, 90, 90
V3)3076 (1)1443 (1)1379.1 (6)
Z844
Radiation typeCu Kα, λ = 1.54059 ÅCu Kα, λ = 1.54059 ÅCu Kα, λ = 1.54059 Å
µ (mm1)3.233.422.56
Specimen shape, size (mm)Flat_sheet, 7 × 7Flat_sheet, 7 × 7Flat_sheet, 7 × 7
Data collection
DiffractometerEnraf-Nonius Guinier Johannson camera FR 552
diffractometer
Enraf-Nonius Guinier Johannson camera FR 552
diffractometer
Enraf-Nonius Guinier Johannson camera FR 552
diffractometer
Specimen mountingPressed as a thin layer in the specimen holder of the cameraPressed as a thin layer in the specimen holder of the cameraPressed as a thin layer in the specimen holder of the camera
Data collection modeTransmissionTransmissionTransmission
Scan methodStationary detectorStationary detectorStationary detector
2θ values (°)2θfixed = ?2θfixed = ?2θfixed = ?
Refinement
R factors and goodness of fitRp = 0.073, Rwp = 0.098, Rexp = 0.030, χ2 = 10.368Rp = 0.075, Rwp = 0.102, Rexp = 0.035, χ2 = 8.644Rp = 0.080, Rwp = 0.105, Rexp = 0.037, χ2 = 8.180
No. of data points759875967599
No. of parameters155142141
No. of restraints1228374
H-atom treatmentH-atom parameters constrainedH-atom parameters constrainedH-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).

Experimental and DFT-calculated geometric parameters (Å, °) defining the conformations of (Ia) and (Ib) top
X-rayDFT
(Ia)
C5-C4-S4-C9103.9 (5)164
C4-C5-N5-O5162.6 (7)34
C5-C6-N6-C812 (1)19
N1-C6-N6-C78.0 (9)14
S3-C9-S4-C4-17.1 (5)-103
S4···O512.964 (7)2.687
(Ib)
C5-C4-S4-C9148.9 (7)169
C4-C5-N5-O5214.3 (9)2
C5-C6-N6-C7-175.5 (6)180
S3-C9-S4-C4-93.8 (5)-105
S4···O522.636 (7)2.591
 

Follow Acta Cryst. C
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds