Buy article online - an online subscription or single-article purchase is required to access this article.
Download citation
Download citation
link to html
4-Amino-1-benzyl-2-(methyl­sulfanyl)­pyrimidin-6(1H)-one, C12H13N3OS, crystallizes in two polymorphic forms, both having space group P21/c, with Z' = 1 for form (I) and Z' = 2 for form (II). In (I), the mol­ecules are linked by a single N-­H...O hydrogen bond into simple C(6) chains, which are themselves linked into sheets by aromatic [pi]-[pi] interactions, while in (II), chains of edge-fused R42(8) and R44(24) rings are generated by four distinct N-H...O hydrogen bonds. In 4-amino-1-benzyl-2-(methyl­sulfanyl)-5-nitroso­pyrimidin-6(1H)-one, C12H12N4O2S, (III), where Z' = 2, two independent three-centre N-H...(N,O) hydrogen bonds generate a C(5)C(6)[R12(5)] chain of rings. In 4-amino-6-benzyl­oxy-2-(methyl­sulfanyl)­pyrimidine, C12H13N3OS, (IV), which is isomeric with (I) and (II), a combination of N-H...N and N-H...O hydrogen bonds generates a sheet of alternating R22(8) and R66(28) rings.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270103013465/gg1172sup1.cif
Contains datablocks global, I, II, III, IV

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270103013465/gg1172Isup2.hkl
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270103013465/gg1172IIsup3.hkl
Contains datablock II

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270103013465/gg1172IIIsup4.hkl
Contains datablock III

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270103013465/gg1172IVsup5.hkl
Contains datablock IV

CCDC references: 219577; 219578; 219579; 219580

Comment top

Benzylation of 4-amino-2-(methylsulfanyl)pyrimidin-6(1H)-one using benzyl chloride yields a mixture of two isomeric benzyl derivatives, 4-amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one, (I), and 4-amino-6-benzyloxy-2-(methylsulfanyl)pyrimidine, (IV), which result from N-benzylation and O-benzylation, respectively, (see Scheme). Nitrosation of (I) and (IV) yields the corresponding 5-nitroso derivatives, (III) and (V), respectively. We have previously reported the molecular and supramolecular structure of (V) (Low, Quesada, Marchal, Nogueras et al., 2002b), and here we report on two polymorphs, (I) and (II), of 4-amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one and on compounds (III) and (IV). The nitrosation of (I), which has Z' = 1 in space group P21/c, yielded deep-blue (III) and a second, pale-green product, (II), which proved to be a polymorph of (I), having Z' = 2 in P21/c, which had co-crystallized with a very small quantity (less than 3%) of (III).

In the molecule of (I) (Fig. 1), the C2—N3 and N3—C4 distances (Table 1) are typical of those for double and single bonds of these types (Allen et al., 1987). On the other hand, the C4—C5 distance is very long for a double bond of this type (mean value = 1.326 Å and upper quartile value = 1.334 Å) and the C5—C6 distance is correspondingly short (mean value = 1.464 Å and lower quartile value = 1.453 Å; Allen et al., 1987); at the same time, C4—N4 is somewhat shorter than typical Ar—NH2 bonds (mean value = 1.355 Å and lower quartile value = 1.340 Å), while the C6—O6 distance is longer than is typical for CO conjugated for CC (mean value = 1.222 Å and upper quartile value = 1.229 Å). The two independent C—S distances differ as expected. Finally, the N1—C6 distance is much longer than usual in amides (mean value = 1.346 Å and upper quartile value = 1.356 Å). All of these observations point to the importance of the delocalized form, (A), as a significant contributor to the overall molecular-electronic structure, while effectively ruling out any significant contribution from form (B) (see Scheme).

In the polymorph (II), where Z' = 2, molecule 1 (Fig. 2a) contains no trace of a 5-nitroso substituent, but there is ca 5% occupancy by a 5-nitroso substituent in molecule 2 (Fig. 2 b). Accordingly, the pattern of the bond distances in both molecules (Table 3) is very similar to that in (I), which is again consistent with form (A) being a significant contributor to the overall molecular-electronic structure. In (III), which again crystallizes with Z' = 2 (Fig. 3), the bond lengths in the two independent molecules are similar (Table 5) but differ from those in (I) and (II) in several important respects. Firstly, the Cn4—Cn5 and Cn5—Cn6 bonds (n = 1 or 2) are both significantly longer than the corresponding bonds in (I) and (II), while the Cn4—Nn4 and Cn6—On6 bonds are both shorter, pointing to form (C) being an important contributor to the molecular-electronic structure of (III). This result is consistent with the deductions, on geometrical grounds of the importance of the analogous form, (D), in the isomeric compound (V) (Low, Quesada, Marchal, Nogueras et al., 2002b).

The development of form (A) in both (I) and (II), and of form (C) in (III), in which both the potential hydrogen-bond donor N4 and the potential acceptors [O6 in (I) and (II), and O5 in (III)] carry significant partial charges, suggests that the intermolecular hydrogen bonding may be dominated by these two components in the formation of so-called resonance-assisted hydrogen bonds (Gilli et al., 1989; Bertolasi et al., 1991; Gilli et al., 1994, 2000).

The crystal quality of (IV) (Fig. 4) was consistently very poor, giving very poor diffraction characteristics, with poor resolution and precision. Accordingly, we do not comment here on the intramolecular geometry, except to note the difference in the conformation of the MeS substituents from those in (I) and (II).

Consistent with the analysis above, emphasizing the importance of form (A) in (I), the molecules of (I) are indeed linked into simple C(6) chains (Fig. 5) by a single N—H···O hydrogen bond (Table 2). Amino atom N4 acts as hydrogen-bond donor, via H4B, to atom O6 in the molecule at (1 − x, −0.5 + y, 0.5 − z), and propagation of this hydrogen bond produces a chain running parallel to the [010] direction, generated by the 21 screw axis along (1/2, y, 1/4). A second, anti-parallel chain is generated by the screw axis along (1/2, −y, 3/4). However, the N4—H4A bond participates neither in any conventional hydrogen bond nor in an N—H···π(arene) hydrogen bond. Although an adjacent phenyl ring is available, the H4A···Cg1i distance is ca 3.42 Å [Cg1 is the centroid of the C11—C16 ring; symmetry code: (i) x, −1 + y, z]; nor does the ring N3 atom act as a hydrogen-bond acceptor, although such behaviour is commonly observed in compounds of this type (Low, Quesada, Marchal, Melguizo et al., 2002a; Low, Quesada, Marchal, Nogueras et al., 2002b).

The chains generated by the N—H···O hydrogen bonds are, however, linked by means of aromatic π···π stacking interactions. The phenyl rings in the molecules at (x, y, z) and (2 − x, 1 − y, −z) are parallel, with an interplanar spacing of 3.488 (2) Å and a centroid separation of 3.675 (2) Å, corresponding to a centroid offset of 1.157 (2) Å. These two molecules lie in the chains along (1/2, y, 1/4) and (1.5, −y, −0.25), respectively. Similarly, the molecule at (1 − x, −0.5 + y, 0.5 − z), which also lies in the (1/2, y, 1/4) chain, forms a π···π stacking interaction with that at (−1 + x, 0.5 − y, 0.5 + z), which lies in the chain along (−0.5, −y, 3/4). In this manner, the hydrogen-bonded chains are linked to form a (102) sheet (Fig. 6).

The two independent molecules in (II) are also linked by three N—H···O hydrogen bonds (Table 4). Amino atom N14 of molecule 1 acts as a hydrogen-bond donor, via atom H14B, to atom O26 of molecule 2 in the asymmetric unit. Atom N14 also acts as a donor, via atom H14A, to atom O26 in the molecule at (1 − x, 1 − y, 1 − z), and these two interactions generate a centrosymmetric R24(8) ring centred at (1/2, 1/2, 1/2) (Fig. 7). At the same time, amino atom N24 in molecule 2 at (x, y, z) acts as a donor to atom O16 in the type 1 molecule at (-x, 1 − y, 1 − z), so generating an R44(24) ring centred at (0, 1/2, 1/2). The combined effect of these hydrogen bonds is the formation of a chain of edge-fused rings running parallel to the [100] direction, with R24(8) rings centred at (n + 1/2, 1/2, 1/2) (n = zero or integer) alternating with R44(24) rings centred at (n, 1/2, 1/2) (n = zero or integer) (Fig. 7). The formation of this chain is reinforced by the overlap of centrosymmetrically related pairs of highly polarized pyrimidinone rings (Fig. 8). The interplanar spacing between these rings in the type ? molecules at (x, y, z) and (-x, 1 − y, 1 − z) is 3.444 (2) Å, and the centroid separation is 3.514 (2) Å, corresponding to a centroid offset of only 0.698 (2) Å.

Each of the two independent molecules of (III) contains an intramolecular N—H···O hydrogen bond, defining an S(6) motif, as is usual in molecules of this type with adjacent amino and nitroso substituents. The molecules of (III) are linked into chains by means of two independent three-centre N—H···(N,O) hydrogen bonds, each of which is asymmetric but essentially planar (Table 6). In the asymmetric unit, amino atom N14 in the type 1 molecule acts as hydrogen-bond donor, via atom H14A, to both atom N25 and atom O26 in the type 2 molecule. Similarly, atom N24 in the type 2 molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H24A, to atoms N15 and O16 in the type 1 molecule at (x, y, −1 + z). In this manner, a C(5) C(6)[R21(5)] chain of rings is generated by translation along [001] (Fig. 9). Two chains of this type run through each unit cell, but there are no direction-specific interactions between adjacent chains. The supramolecular structure of (III) may be contrasted with that of the isomeric compound (V); in this compound, which also crystallizes with Z' = 2, two independent R22(8) dimers are formed by paired N—H···N hydrogen bonds, and these dimers are linked into chains by mean of aromatic π···π stacking interactions (Low, Quesada, Marchal, Nogueras et al., 2002b).

In compound (IV), the molecules are linked into centrosymmetric dimer units by pairs of strong N—H···N hydrogen bonds (Table 7), and these units are linked into sheets by means of a weaker N—H···O hydrogen bond. Amino atom N4 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via atom H4A, to ring atom N3 in the molecule at (1 − x, 1 − y, 1 − z), so generating a dimer centred at (1/2, 1/2, 1/2) and containing an R22(8) ring. Amino atom N4 at (x, y, z) also acts as a hydrogen-bond donor, this time via atom H4B, to atom O6 in the molecule at (1 − z, 0.5 + y, 0.5 − z), which lies in the dimer centred at (1/2, 1, 0), while atom O6 at (x, y, z) accepts a hydrogen bond from atom N4 at (1 − z, −0.5 + y, 0.5 − z), which lies in the dimer centred at (1/2, 0, 0). At the same time, atom N4 at (1 − x, 1 − y, 1 − z) acts as donor to O6 at (x, 0.5 − y, 0.5 + z), which lies in the dimer centred at (1/2, 0, 1), while atom O6 at (1 − x, 1 − y, 1 − z) acts as an acceptor from atom N4 at (x, 1.5 − y, 0.5 + z), part of the dimer centred at (1/2, 1, 1). In this manner, the molecules are linked into a (100) sheet built from R22(8) and R66(28) rings alternating in checkerboard fashion (Fig. 10). If the individual molecules are regarded as the nodes of the resulting net, then this is of the (6,3) type, while if the R22(8) dimers are taken as the nodes, the net is of the (4,4) type (Batten & Robson, 1998). Thus, although the supramolecular structure of (IV) is entirely different from those of (I) and (II), it is, in fact, closely similar to that of 4-amino-2,6,-dimethoxypyrimidine, (VI) (Glidewell et al., 2003), as indeed the overall conformation of (IV) is similar to that of both (V) and (VI).

Thus, in summary, no two isomeric or polymorphic compounds in this series adopt the same pattern of supramolecular aggregation. The two polymorphs (I) and (II), respectively, form π-stacked chains and chains of edge-fused rings, while the isomeric compound (IV) forms sheets. Compound (III) forms a simple chain of rings, while its isomer (V) forms chains of π-stacked dimers.

Experimental top

A suspension of 6-amino-2-(methylsulfanyl)pyrimidin-4(3H)-one (10.00 g, 63.62 mmol) and finely ground K2CO3 (11.89 g, 86 mmol) in dimethylsulfoxide (90 cm3) was stirred at room temperature for 1 h. Benzyl chloride (10 ml, 86 mmol) was then added and the mixture was stirred at room temperature for 9 h. Cold water (270 cm3) was added to the mixture with continuous stirring to precipitate the water-insoluble reaction products. The resulting mixture was stirred for a further 2 h, and a white solid was then collected by filtration, washed with water and dried in vacuo. The dried solid was suspended in diethyl ether (300 cm3) and stirred for 24 h. The solid in suspension was collected by filtration, washed with diethyl ether and recrystallized from ethanol to afford the pure N-benzyl isomer, (I) (2.23 g, 9.02 mmol, 14%). The ethereal fitrate was evaporated under reduced pressure and the residue was chromatographed on silica gel with mixed dichloromethane-acetone to afford the corresponding O-benzyl isomer (IV) (5.42 g, 22.4 mmol, 35%) and further crystals of (I) (0.378 g, 1.53 mmol, 2.4%). Crystals of (I) and (IV) suitable for single-crystal X-ray diffraction were obtained by slow evaporation of solutions in ethyl acetate for (I) (m.p. 478 K) or in t-butanol for (IV) [m.p. 397 K; literature value for (IV) 396–397 K (Ward & Baker, 1977)]. The nitrosation methodology described by Low, Quesada, Marchal, Nogueras et al., (2002b), using (I) as starting material, provided a mixture of green (II) and blue (III). Crystals of (II) and (III) suitable for single-crystal X-ray diffraction were obtained by slow evaporation of a solution in acetone–water (1:1 v/v), followed by manual separation.

Refinement top

For (I), (II) and (IV), the space group P21/c was determined uniquely from the systematic absences. Crystals of (III) are triclinic, and space group P1 was selected and confirmed by the successful structure analysis. For (IV), it proved extremely difficult to obtain single crystals; the quality of those obtained was always extremely poor, of very fine hair-like habit and giving no detectable diffraction beyond theta of 20°, so that the overall resolution is poor. Nonetheless the overall conformation and supramolecular structure of (IV) were clearly determined as being different from those of the isomeric (I) and (II). For each compound, all H atoms were treated as riding atoms, with C—H distances of 0.95 (aromatic), 0.98 (CH3) or 0.99 Å (CH2), and N—H distances of 0.88 Å.

Computing details top

For all compounds, data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997) and PRPKAPPA (Ferguson, 1999).

Figures top
[Figure 1] Fig. 1. The molecule of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 2] Fig. 2. The two independent molecules of (II), showing the atom-labelling scheme for (a) molecule 1 and (b) molecule 2. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 3] Fig. 3. The two independent molecules of (III), showing the atom-labelling scheme for (a) molecule 1 and (b) molecule 2. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 4] Fig. 4. The molecule of (IV), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.
[Figure 5] Fig. 5. Part of the crystal structure of (I), showing the formation of a C(6) chain along [010]. Atoms marked with an asterisk (*), a hash(#) or an ampersand (&) are at the symmetry positions (1 − x, −0.5 + y, 0.5 − z), (1 − x, −0.5 + y, 0.5 − z) and (x, 1 + y, z), respectively.
[Figure 6] Fig. 6. Stereoview of part of the crystal structure of (I), showing the linking of the [010] chains into a (102) sheet by means of aromatic π···π stacking interactions. For clarity, H atoms bonded to C atoms have been omitted.
[Figure 7] Fig. 7. Stereoview of part of the crystal structure of (II), showing the formation of a chain of edge-fused rings along [100]. For clarity, H atoms bonded to C atoms have been omitted.
[Figure 8] Fig. 8. Part of the crystal structure of (II), showing the overlap of pairs of type 2 molecules. Atoms marked with an asterisk (*) are at the symmetry position (-x, 1 − y, 1 − z). For clarity, the unit-cell box and H atoms bonded to C atoms have been omitted.
[Figure 9] Fig. 9. Stereoview of part of the crystal structure of (III), showing the formation of a chain of rings along [001]. For clarity, H atoms bonded to C atoms have been omitted.
[Figure 10] Fig. 10. Stereoview of part of the crystal structure of (IV), showing the formation of a (100) sheet of R22(8) and R66(28) rings. For clarity, H atoms bonded to C atoms have been omitted.
(I) 4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one, polymorph with Z' = 1 top
Crystal data top
C12H13N3OSF(000) = 520
Mr = 247.31Dx = 1.435 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2600 reflections
a = 9.7139 (2) Åθ = 3.0–27.5°
b = 9.5846 (2) ŵ = 0.27 mm1
c = 12.6431 (2) ÅT = 120 K
β = 103.4465 (13)°Block, colourless
V = 1144.85 (4) Å30.30 × 0.26 × 0.20 mm
Z = 4
Data collection top
Nonius KappaCCD
diffractometer
2600 independent reflections
Radiation source: rotating anode2249 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
ϕ scans, and ω scans with κ offsetsθmax = 27.5°, θmin = 3.0°
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
h = 1211
Tmin = 0.902, Tmax = 0.943k = 1112
7564 measured reflectionsl = 1416
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.091H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0415P)2 + 0.4958P]
where P = (Fo2 + 2Fc2)/3
2600 reflections(Δ/σ)max = 0.001
155 parametersΔρmax = 0.24 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
C12H13N3OSV = 1144.85 (4) Å3
Mr = 247.31Z = 4
Monoclinic, P21/cMo Kα radiation
a = 9.7139 (2) ŵ = 0.27 mm1
b = 9.5846 (2) ÅT = 120 K
c = 12.6431 (2) Å0.30 × 0.26 × 0.20 mm
β = 103.4465 (13)°
Data collection top
Nonius KappaCCD
diffractometer
2600 independent reflections
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
2249 reflections with I > 2σ(I)
Tmin = 0.902, Tmax = 0.943Rint = 0.032
7564 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.091H-atom parameters constrained
S = 1.06Δρmax = 0.24 e Å3
2600 reflectionsΔρmin = 0.31 e Å3
155 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S20.78067 (4)0.10593 (4)0.09925 (3)0.01763 (12)
O60.50570 (11)0.29284 (11)0.15128 (8)0.0210 (2)
N10.63886 (12)0.19680 (12)0.04326 (9)0.0136 (2)
N30.70235 (12)0.04151 (12)0.05419 (9)0.0139 (2)
N40.63526 (13)0.18557 (13)0.17770 (10)0.0184 (3)
C20.70101 (14)0.08191 (14)0.01077 (11)0.0131 (3)
C40.63418 (13)0.05561 (15)0.13751 (11)0.0141 (3)
C50.56911 (14)0.05435 (15)0.17611 (11)0.0161 (3)
C60.56570 (14)0.18654 (15)0.12836 (11)0.0155 (3)
C110.78052 (14)0.41415 (14)0.05830 (11)0.0141 (3)
C120.89040 (15)0.34918 (15)0.13181 (11)0.0168 (3)
C131.01182 (15)0.42234 (16)0.18048 (12)0.0205 (3)
C141.02459 (16)0.56213 (16)0.15619 (12)0.0212 (3)
C150.91427 (16)0.62861 (16)0.08502 (12)0.0213 (3)
C160.79293 (15)0.55541 (15)0.03605 (11)0.0184 (3)
C170.65073 (15)0.33551 (14)0.00213 (11)0.0163 (3)
C210.82976 (18)0.07050 (16)0.12178 (13)0.0238 (3)
H120.88230.25350.14900.020*
H131.08630.37660.23050.025*
H141.10850.61190.18820.025*
H150.92170.72500.06960.026*
H160.71790.60180.01290.022*
H17A0.56520.39030.00040.020*
H17B0.65460.32580.07930.020*
H21A0.91020.09860.06340.036*
H21B0.85630.07650.19180.036*
H21C0.74950.13270.12240.036*
H4A0.67750.25340.15050.022*
H4B0.59370.20280.23120.022*
H50.52620.04050.23560.019*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S20.0213 (2)0.0165 (2)0.0183 (2)0.00184 (13)0.01094 (14)0.00022 (13)
O60.0227 (5)0.0190 (5)0.0239 (5)0.0028 (4)0.0103 (4)0.0031 (4)
N10.0133 (5)0.0134 (6)0.0149 (5)0.0004 (4)0.0047 (4)0.0003 (4)
N30.0130 (5)0.0157 (6)0.0135 (5)0.0007 (4)0.0041 (4)0.0008 (4)
N40.0211 (6)0.0170 (6)0.0191 (6)0.0005 (5)0.0085 (5)0.0027 (5)
C20.0102 (6)0.0158 (7)0.0136 (6)0.0018 (5)0.0031 (5)0.0012 (5)
C40.0108 (6)0.0177 (7)0.0127 (6)0.0029 (5)0.0006 (5)0.0007 (5)
C50.0154 (7)0.0195 (7)0.0148 (6)0.0021 (5)0.0063 (5)0.0004 (6)
C60.0122 (6)0.0193 (7)0.0153 (6)0.0016 (5)0.0039 (5)0.0042 (5)
C110.0154 (7)0.0145 (7)0.0146 (6)0.0005 (5)0.0076 (5)0.0009 (5)
C120.0187 (7)0.0142 (7)0.0181 (7)0.0006 (5)0.0052 (5)0.0001 (5)
C130.0169 (7)0.0236 (8)0.0206 (7)0.0007 (6)0.0033 (6)0.0034 (6)
C140.0201 (7)0.0237 (8)0.0224 (7)0.0073 (6)0.0101 (6)0.0075 (6)
C150.0280 (8)0.0155 (7)0.0239 (8)0.0046 (6)0.0131 (6)0.0010 (6)
C160.0217 (7)0.0159 (7)0.0186 (7)0.0019 (6)0.0072 (6)0.0016 (6)
C170.0160 (7)0.0139 (7)0.0186 (7)0.0008 (5)0.0037 (5)0.0019 (5)
C210.0311 (8)0.0211 (8)0.0247 (8)0.0004 (6)0.0177 (6)0.0034 (6)
Geometric parameters (Å, º) top
C11—C121.389 (2)N3—C41.375 (2)
C11—C161.394 (2)C4—C51.376 (2)
C11—C171.514 (2)C5—C61.401 (2)
C12—C131.387 (2)C6—N11.424 (2)
C12—H120.95N1—C171.463 (2)
C13—C141.387 (2)C2—S21.757 (2)
C13—H130.95C21—S21.798 (2)
C14—C151.384 (2)C4—N41.344 (2)
C14—H140.95C6—O61.241 (2)
C15—C161.388 (2)C21—H21A0.98
C15—H150.95C21—H21B0.98
C16—H160.95C21—H21C0.98
C17—H17A0.99N4—H4A0.88
C17—H17B0.99N4—H4B0.88
N1—C21.364 (2)C5—H50.95
C2—N31.303 (3)
C12—C11—C16118.78 (13)C2—N1—C17122.31 (11)
C12—C11—C17122.31 (12)C6—N1—C17117.24 (11)
C16—C11—C17118.86 (12)N3—C2—N1124.59 (12)
C13—C12—C11120.80 (13)N3—C2—S2119.31 (10)
C13—C12—H12119.6N1—C2—S2116.09 (10)
C11—C12—H12119.6S2—C21—H21A109.5
C14—C13—C12120.06 (14)S2—C21—H21B109.5
C14—C13—H13120.0H21A—C21—H21B109.5
C12—C13—H13120.0S2—C21—H21C109.5
C15—C14—C13119.55 (14)H21A—C21—H21C109.5
C15—C14—H14120.2H21B—C21—H21C109.5
C13—C14—H14120.2C2—S2—C21100.61 (7)
C14—C15—C16120.42 (14)C2—N3—C4116.91 (12)
C14—C15—H15119.8N4—C4—N3114.70 (12)
C16—C15—H15119.8N4—C4—C5122.66 (12)
C15—C16—C11120.36 (14)N3—C4—C5122.64 (13)
C15—C16—H16119.8C4—N4—H4A120.0
C11—C16—H16119.8C4—N4—H4B120.0
N1—C17—C11112.75 (11)H4A—N4—H4B120.0
N1—C17—H17A109.0C4—C5—C6120.46 (12)
C11—C17—H17A109.0C4—C5—H5119.8
N1—C17—H17B109.0C6—C5—H5119.8
C11—C17—H17B109.0O6—C6—C5127.39 (13)
H17A—C17—H17B107.8O6—C6—N1117.63 (12)
C2—N1—C6120.35 (11)C5—C6—N1114.98 (12)
C16—C11—C12—C131.5 (2)C17—N1—C2—S26.56 (17)
C17—C11—C12—C13175.80 (13)N3—C2—S2—C214.53 (13)
C11—C12—C13—C140.1 (2)N1—C2—S2—C21174.29 (11)
C12—C13—C14—C151.4 (2)N1—C2—N3—C40.9 (2)
C13—C14—C15—C161.6 (2)S2—C2—N3—C4177.76 (9)
C14—C15—C16—C110.2 (2)C2—N3—C4—N4178.32 (12)
C12—C11—C16—C151.3 (2)C2—N3—C4—C51.21 (19)
C17—C11—C16—C15176.10 (12)N4—C4—C5—C6177.24 (12)
C12—C11—C17—N113.45 (18)N3—C4—C5—C62.3 (2)
C16—C11—C17—N1169.27 (12)C4—C5—C6—O6176.46 (13)
C11—C17—N1—C287.95 (15)C4—C5—C6—N12.78 (19)
C11—C17—N1—C688.57 (14)C2—N1—C6—O6176.80 (12)
C6—N1—C2—N31.7 (2)C17—N1—C6—O66.61 (18)
C17—N1—C2—N3174.70 (12)C2—N1—C6—C52.52 (18)
C6—N1—C2—S2177.03 (9)C17—N1—C6—C5174.08 (12)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4B···O6i0.881.952.823 (2)170
Symmetry code: (i) x+1, y1/2, z+1/2.
(II) 4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1H)-one, polymorph with Z' = 2 'C12 H13 N3 O S' top
Crystal data top
C24H25.95N6.05O2.05S2F(000) = 1042.8
Mr = 496.10Dx = 1.400 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5325 reflections
a = 11.4629 (2) Åθ = 3.1–27.5°
b = 10.2603 (2) ŵ = 0.26 mm1
c = 20.9303 (4) ÅT = 120 K
β = 107.0920 (14)°Block, green
V = 2352.95 (8) Å30.47 × 0.22 × 0.14 mm
Z = 4
Data collection top
Nonius KappaCCD
diffractometer
5325 independent reflections
Radiation source: rotating anode4389 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.064
ϕ scans, and ω scans with κ offsetsθmax = 27.5°, θmin = 3.1°
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
h = 1414
Tmin = 0.887, Tmax = 0.957k = 1312
21205 measured reflectionsl = 2727
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0447P)2 + 1.7296P]
where P = (Fo2 + 2Fc2)/3
5325 reflections(Δ/σ)max = 0.001
318 parametersΔρmax = 0.51 e Å3
1 restraintΔρmin = 0.41 e Å3
Crystal data top
C24H25.95N6.05O2.05S2V = 2352.95 (8) Å3
Mr = 496.10Z = 4
Monoclinic, P21/cMo Kα radiation
a = 11.4629 (2) ŵ = 0.26 mm1
b = 10.2603 (2) ÅT = 120 K
c = 20.9303 (4) Å0.47 × 0.22 × 0.14 mm
β = 107.0920 (14)°
Data collection top
Nonius KappaCCD
diffractometer
5325 independent reflections
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
4389 reflections with I > 2σ(I)
Tmin = 0.887, Tmax = 0.957Rint = 0.064
21205 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0471 restraint
wR(F2) = 0.119H-atom parameters constrained
S = 1.06Δρmax = 0.51 e Å3
5325 reflectionsΔρmin = 0.41 e Å3
318 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
S120.68767 (4)1.04108 (5)0.62530 (3)0.02764 (14)
O160.23861 (12)0.98605 (14)0.53972 (7)0.0281 (3)
N110.44857 (14)1.00240 (15)0.57375 (8)0.0201 (3)
N130.57460 (13)0.81516 (16)0.59210 (7)0.0200 (3)
N140.49396 (15)0.61296 (16)0.56142 (9)0.0266 (4)
C120.55905 (16)0.94083 (19)0.59392 (9)0.0197 (4)
C140.47183 (17)0.74009 (19)0.56759 (9)0.0206 (4)
C150.35499 (17)0.7926 (2)0.55082 (9)0.0229 (4)
C160.33808 (17)0.9275 (2)0.55350 (9)0.0219 (4)
C1110.46488 (16)1.21470 (18)0.63496 (9)0.0204 (4)
C1120.54567 (18)1.31854 (19)0.64946 (10)0.0244 (4)
C1130.57217 (18)1.3822 (2)0.71062 (11)0.0267 (4)
C1140.51775 (19)1.3408 (2)0.75809 (10)0.0278 (4)
C1150.43498 (19)1.2385 (2)0.74369 (10)0.0279 (4)
C1160.40859 (18)1.17588 (19)0.68242 (10)0.0244 (4)
C1170.44110 (18)1.14517 (19)0.56873 (10)0.0231 (4)
C1210.80787 (19)0.9232 (2)0.63789 (14)0.0394 (6)
S220.15062 (5)0.53540 (6)0.33956 (3)0.03293 (15)
O260.28185 (13)0.49245 (17)0.46960 (8)0.0389 (4)
N210.07893 (14)0.50607 (17)0.41394 (8)0.0243 (4)
N230.06500 (15)0.35550 (16)0.43280 (8)0.0252 (4)
N240.00230 (18)0.18370 (18)0.50577 (9)0.0343 (4)
C220.03717 (18)0.4569 (2)0.40205 (10)0.0238 (4)
C240.02910 (19)0.2928 (2)0.47850 (10)0.0270 (4)
C250.1475 (2)0.3388 (2)0.49531 (11)0.0321 (5)
C260.17820 (18)0.4461 (2)0.46216 (11)0.0293 (5)
C2110.11361 (17)0.5758 (2)0.30691 (10)0.0248 (4)
C2120.11064 (18)0.6716 (2)0.25963 (12)0.0322 (5)
C2130.12672 (19)0.4468 (2)0.29044 (11)0.0284 (4)
C2140.12100 (19)0.6397 (2)0.19740 (12)0.0369 (5)
C2150.13327 (19)0.5107 (3)0.18102 (11)0.0363 (5)
C2160.13613 (19)0.4140 (2)0.22757 (11)0.0321 (5)
C2170.10436 (19)0.6154 (2)0.37514 (11)0.0296 (5)
C2210.2845 (2)0.4511 (3)0.34457 (15)0.0455 (7)
N250.219 (4)0.322 (4)0.559 (2)0.054 (11)*0.05
O250.183 (2)0.216 (3)0.5860 (13)0.027 (6)*0.05
H11A0.35881.16950.54010.028*
H11B0.50091.17610.54630.028*
H1120.58351.34660.61710.029*
H1130.62731.45360.71990.032*
H1140.53711.38250.80040.033*
H1150.39641.21130.77590.033*
H1160.35171.10600.67270.029*
H12A0.79320.85170.66560.059*
H12B0.88620.96470.66040.059*
H12C0.80990.88880.59460.059*
H14A0.56960.58410.57270.032*
H14B0.43290.55850.54610.032*
H150.28610.73660.53740.028*
H21A0.18200.65700.40070.035*
H21B0.03870.68110.36920.035*
H2120.10140.76040.27020.039*
H2130.12930.38020.32240.034*
H2140.11970.70650.16580.044*
H2150.13970.48880.13810.044*
H2160.14450.32530.21660.039*
H22A0.27430.35740.33920.068*
H22B0.35550.48220.30910.068*
H22C0.29700.46770.38820.068*
H24A0.07880.15750.49390.041*
H24B0.05370.13890.53540.041*
H250.20890.29700.52980.039*0.95
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N110.0215 (8)0.0220 (8)0.0183 (7)0.0024 (6)0.0081 (6)0.0005 (6)
C1170.0266 (9)0.0217 (10)0.0225 (9)0.0046 (8)0.0094 (8)0.0027 (7)
C1110.0207 (9)0.0198 (9)0.0208 (9)0.0048 (7)0.0063 (7)0.0010 (7)
C1120.0249 (9)0.0222 (10)0.0296 (10)0.0022 (8)0.0133 (8)0.0032 (8)
C1130.0224 (9)0.0213 (10)0.0364 (11)0.0008 (8)0.0088 (8)0.0025 (8)
C1140.0304 (10)0.0271 (11)0.0247 (10)0.0021 (8)0.0064 (8)0.0040 (8)
C1150.0370 (11)0.0269 (11)0.0229 (10)0.0013 (9)0.0136 (9)0.0008 (8)
C1160.0258 (9)0.0223 (10)0.0266 (10)0.0021 (8)0.0099 (8)0.0009 (8)
C120.0189 (8)0.0252 (10)0.0149 (8)0.0000 (7)0.0052 (7)0.0014 (7)
S120.0206 (2)0.0229 (3)0.0381 (3)0.00116 (19)0.0066 (2)0.0049 (2)
C1210.0184 (9)0.0338 (12)0.0614 (16)0.0034 (9)0.0047 (10)0.0111 (11)
N130.0189 (7)0.0232 (8)0.0176 (7)0.0001 (6)0.0047 (6)0.0021 (6)
C140.0241 (9)0.0238 (10)0.0160 (8)0.0013 (7)0.0092 (7)0.0008 (7)
N140.0239 (8)0.0225 (9)0.0342 (9)0.0016 (7)0.0099 (7)0.0043 (7)
C150.0214 (9)0.0266 (10)0.0215 (9)0.0038 (8)0.0074 (8)0.0020 (7)
C160.0198 (9)0.0300 (10)0.0162 (8)0.0008 (8)0.0059 (7)0.0018 (7)
O160.0201 (7)0.0341 (8)0.0297 (7)0.0043 (6)0.0065 (6)0.0014 (6)
N210.0212 (8)0.0267 (9)0.0257 (8)0.0003 (7)0.0079 (7)0.0061 (7)
C2170.0282 (10)0.0249 (11)0.0393 (12)0.0052 (8)0.0156 (9)0.0079 (9)
C2110.0175 (8)0.0260 (10)0.0330 (10)0.0026 (7)0.0104 (8)0.0035 (8)
C2120.0221 (10)0.0295 (11)0.0441 (13)0.0006 (8)0.0085 (9)0.0024 (9)
C2130.0290 (10)0.0260 (11)0.0343 (11)0.0044 (8)0.0159 (9)0.0029 (8)
C2140.0231 (10)0.0478 (14)0.0383 (12)0.0001 (10)0.0068 (9)0.0144 (10)
C2150.0217 (10)0.0621 (16)0.0257 (11)0.0016 (10)0.0078 (9)0.0019 (10)
C2160.0278 (10)0.0357 (12)0.0358 (11)0.0053 (9)0.0139 (9)0.0114 (9)
C220.0222 (9)0.0266 (10)0.0256 (9)0.0026 (8)0.0119 (8)0.0025 (8)
S220.0232 (3)0.0368 (3)0.0385 (3)0.0011 (2)0.0085 (2)0.0158 (2)
C2210.0197 (10)0.0502 (15)0.0659 (17)0.0048 (10)0.0114 (11)0.0267 (13)
N230.0257 (8)0.0261 (9)0.0256 (8)0.0040 (7)0.0105 (7)0.0003 (7)
C240.0299 (10)0.0268 (11)0.0232 (9)0.0066 (8)0.0063 (8)0.0036 (8)
N240.0357 (10)0.0291 (10)0.0334 (10)0.0051 (8)0.0030 (8)0.0063 (8)
C250.0296 (11)0.0335 (12)0.0281 (10)0.0097 (9)0.0005 (9)0.0048 (9)
C260.0224 (10)0.0337 (12)0.0314 (11)0.0021 (8)0.0071 (8)0.0141 (9)
O260.0225 (8)0.0446 (10)0.0470 (10)0.0033 (7)0.0065 (7)0.0173 (8)
Geometric parameters (Å, º) top
N11—C121.366 (2)C22—N231.311 (3)
C12—N131.304 (2)N23—C241.373 (3)
N13—C141.374 (2)C24—C251.381 (3)
C14—C151.390 (3)C25—C261.400 (3)
C15—C161.401 (3)C26—N211.420 (3)
C16—N111.435 (2)N21—C2171.464 (3)
N11—C1171.469 (2)C22—S221.747 (2)
C12—S121.759 (2)S22—C2211.791 (2)
S12—C1211.794 (2)C24—N241.353 (3)
C14—N141.342 (2)C26—O261.246 (3)
C16—O161.245 (2)C217—C2111.518 (3)
C117—C1111.511 (3)C217—H21A0.99
C117—H11A0.99C217—H21B0.99
C117—H11B0.99C211—C2131.387 (3)
C111—C1121.386 (3)C211—C2121.388 (3)
C111—C1161.392 (3)C212—C2141.382 (3)
C112—C1131.389 (3)C212—H2120.95
C112—H1120.95C213—C2161.393 (3)
C113—C1141.386 (3)C213—H2130.95
C113—H1130.95C214—C2151.384 (4)
C114—C1151.388 (3)C214—H2140.95
C114—H1140.95C215—C2161.385 (3)
C115—C1161.386 (3)C215—H2150.95
C115—H1150.95C216—H2160.95
C116—H1160.95C221—H22A0.98
C121—H12A0.98C221—H22B0.98
C121—H12B0.98C221—H22C0.98
C121—H12C0.98N24—H24A0.88
N14—H14A0.88N24—H24B0.88
N14—H14B0.88C25—N251.36 (5)
C15—H150.95C25—H250.95
N21—C221.376 (2)N25—O251.34 (6)
C12—N11—C16120.07 (16)C26—N21—C217118.54 (17)
C12—N11—C117120.82 (16)N21—C217—C211113.38 (16)
C16—N11—C117119.02 (15)N21—C217—H21A108.9
N11—C117—C111114.47 (15)C211—C217—H21A108.9
N11—C117—H11A108.6N21—C217—H21B108.9
C111—C117—H11A108.6C211—C217—H21B108.9
N11—C117—H11B108.6H21A—C217—H21B107.7
C111—C117—H11B108.6C213—C211—C212118.7 (2)
H11A—C117—H11B107.6C213—C211—C217122.15 (19)
C112—C111—C116118.93 (18)C212—C211—C217119.14 (19)
C112—C111—C117119.53 (17)C214—C212—C211120.9 (2)
C116—C111—C117121.54 (17)C214—C212—H212119.6
C111—C112—C113120.96 (18)C211—C212—H212119.6
C111—C112—H112119.5C211—C213—C216120.7 (2)
C113—C112—H112119.5C211—C213—H213119.7
C114—C113—C112119.63 (19)C216—C213—H213119.7
C114—C113—H113120.2C212—C214—C215120.2 (2)
C112—C113—H113120.2C212—C214—H214119.9
C113—C114—C115119.94 (19)C215—C214—H214119.9
C113—C114—H114120.0C214—C215—C216119.6 (2)
C115—C114—H114120.0C214—C215—H215120.2
C116—C115—C114120.06 (19)C216—C215—H215120.2
C116—C115—H115120.0C215—C216—C213119.9 (2)
C114—C115—H115120.0C215—C216—H216120.1
C115—C116—C111120.46 (18)C213—C216—H216120.1
C115—C116—H116119.8N23—C22—N21124.36 (18)
C111—C116—H116119.8N23—C22—S22119.91 (15)
N13—C12—N11124.79 (17)N21—C22—S22115.70 (15)
N13—C12—S12118.85 (14)C22—S22—C221101.28 (10)
N11—C12—S12116.36 (14)S22—C221—H22A109.5
C12—S12—C121100.60 (10)S22—C221—H22B109.5
S12—C121—H12A109.5H22A—C221—H22B109.5
S12—C121—H12B109.5S22—C221—H22C109.5
H12A—C121—H12B109.5H22A—C221—H22C109.5
S12—C121—H12C109.5H22B—C221—H22C109.5
H12A—C121—H12C109.5C22—N23—C24117.32 (17)
H12B—C121—H12C109.5N24—C24—N23115.45 (18)
C12—N13—C14117.11 (16)N24—C24—C25122.59 (19)
N14—C14—N13114.53 (16)N23—C24—C25122.0 (2)
N14—C14—C15123.21 (18)C24—N24—H24A120.0
N13—C14—C15122.26 (17)C24—N24—H24B120.0
C14—N14—H14A120.0H24A—N24—H24B120.0
C14—N14—H14B120.0N25—C25—C24118 (2)
H14A—N14—H14B120.0N25—C25—C26115 (2)
C14—C15—C16120.48 (18)C24—C25—C26120.90 (19)
C14—C15—H15119.8C24—C25—H25119.6
C16—C15—H15119.8C26—C25—H25119.6
O16—C16—C15126.54 (18)O25—N25—C25110 (4)
O16—C16—N11118.59 (18)O26—C26—C25127.4 (2)
C15—C16—N11114.87 (16)O26—C26—N21117.3 (2)
C22—N21—C26119.99 (18)C25—C26—N21115.29 (18)
C22—N21—C217121.38 (17)
C12—N11—C117—C11176.8 (2)N21—C217—C211—C212166.01 (17)
C16—N11—C117—C111106.69 (19)C213—C211—C212—C2140.3 (3)
N11—C117—C111—C112131.59 (18)C217—C211—C212—C214178.83 (19)
N11—C117—C111—C11647.6 (2)C212—C211—C213—C2160.3 (3)
C116—C111—C112—C1131.0 (3)C217—C211—C213—C216179.37 (19)
C117—C111—C112—C113178.16 (18)C211—C212—C214—C2150.7 (3)
C111—C112—C113—C1140.4 (3)C212—C214—C215—C2160.5 (3)
C112—C113—C114—C1151.6 (3)C214—C215—C216—C2130.0 (3)
C113—C114—C115—C1161.3 (3)C211—C213—C216—C2150.5 (3)
C114—C115—C116—C1110.2 (3)C26—N21—C22—N230.2 (3)
C112—C111—C116—C1151.3 (3)C217—N21—C22—N23176.66 (18)
C117—C111—C116—C115177.84 (18)C26—N21—C22—S22177.80 (14)
C16—N11—C12—N135.1 (3)C217—N21—C22—S221.3 (2)
C117—N11—C12—N13171.31 (17)N23—C22—S22—C2215.9 (2)
C16—N11—C12—S12174.06 (13)N21—C22—S22—C221176.01 (16)
C117—N11—C12—S129.5 (2)N21—C22—N23—C241.9 (3)
N13—C12—S12—C1215.49 (18)S22—C22—N23—C24176.03 (14)
N11—C12—S12—C121175.25 (15)C22—N23—C24—N24175.74 (18)
N11—C12—N13—C140.5 (3)C22—N23—C24—C254.4 (3)
S12—C12—N13—C14179.66 (13)N24—C24—C25—N2533.9 (18)
C12—N13—C14—N14174.47 (16)N23—C24—C25—N25145.9 (18)
C12—N13—C14—C155.6 (3)N24—C24—C25—C26174.86 (19)
N14—C14—C15—C16175.05 (18)N23—C24—C25—C265.3 (3)
N13—C14—C15—C165.1 (3)C24—C25—N25—O2528 (2)
C14—C15—C16—O16179.93 (18)C26—C25—N25—O25179.5 (13)
C14—C15—C16—N110.6 (3)N25—C25—C26—O2632.4 (16)
C12—N11—C16—O16175.19 (16)C24—C25—C26—O26175.5 (2)
C117—N11—C16—O168.3 (2)N25—C25—C26—N21148.8 (16)
C12—N11—C16—C155.4 (2)C24—C25—C26—N213.3 (3)
C117—N11—C16—C15171.14 (16)C22—N21—C26—O26178.08 (17)
C22—N21—C217—C21179.4 (2)C217—N21—C26—O261.5 (3)
C26—N21—C217—C21197.1 (2)C22—N21—C26—C250.8 (3)
N21—C217—C211—C21314.9 (3)C217—N21—C26—C25177.44 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N14—H14A···O26i0.882.283.029 (2)143
N14—H14B···O260.882.102.896 (2)151
N24—H24A···O16ii0.882.293.124 (2)157
N24—H24B···O16iii0.882.623.330 (2)138
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z+1; (iii) x, y1, z.
(III) 4-Amino-1-benzyl-2-(methylsulfanyl)-5-nitrosopyrimidin-6(1H)-one top
Crystal data top
C12H12N4O2SZ = 4
Mr = 276.33F(000) = 576
Triclinic, P1Dx = 1.461 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 10.5035 (3) ÅCell parameters from 4417 reflections
b = 10.8741 (3) Åθ = 3.0–25.0°
c = 11.8261 (4) ŵ = 0.26 mm1
α = 109.6510 (13)°T = 120 K
β = 96.4203 (14)°Plate, blue
γ = 93.7181 (14)°0.30 × 0.22 × 0.04 mm
V = 1256.49 (7) Å3
Data collection top
Nonius KappaCCD
diffractometer
4417 independent reflections
Radiation source: rotating anode3498 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.094
ϕ scans, and ω scans with κ offsetsθmax = 25.0°, θmin = 3.0°
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
h = 1212
Tmin = 0.920, Tmax = 0.991k = 1212
24784 measured reflectionsl = 1414
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.107H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0461P)2 + 0.5677P]
where P = (Fo2 + 2Fc2)/3
4417 reflections(Δ/σ)max = 0.001
345 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
C12H12N4O2Sγ = 93.7181 (14)°
Mr = 276.33V = 1256.49 (7) Å3
Triclinic, P1Z = 4
a = 10.5035 (3) ÅMo Kα radiation
b = 10.8741 (3) ŵ = 0.26 mm1
c = 11.8261 (4) ÅT = 120 K
α = 109.6510 (13)°0.30 × 0.22 × 0.04 mm
β = 96.4203 (14)°
Data collection top
Nonius KappaCCD
diffractometer
4417 independent reflections
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
3498 reflections with I > 2σ(I)
Tmin = 0.920, Tmax = 0.991Rint = 0.094
24784 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0440 restraints
wR(F2) = 0.107H-atom parameters constrained
S = 1.05Δρmax = 0.21 e Å3
4417 reflectionsΔρmin = 0.31 e Å3
345 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S120.26530 (6)0.57441 (6)0.64908 (5)0.02699 (17)
O150.10003 (15)0.16677 (16)0.79411 (14)0.0305 (4)
O160.13462 (15)0.40714 (16)0.97953 (13)0.0269 (4)
N110.18937 (16)0.48009 (17)0.82222 (15)0.0186 (4)
N130.10917 (17)0.39198 (18)0.63424 (16)0.0205 (4)
N140.01962 (17)0.22653 (18)0.60112 (17)0.0250 (4)
N150.02623 (17)0.24354 (18)0.85497 (16)0.0229 (4)
C120.1775 (2)0.4719 (2)0.70564 (19)0.0192 (5)
C140.04164 (19)0.3107 (2)0.67778 (19)0.0190 (5)
C150.04068 (19)0.3155 (2)0.80047 (18)0.0177 (5)
C160.1214 (2)0.4010 (2)0.87679 (19)0.0192 (5)
C1110.4107 (2)0.5422 (2)0.86319 (19)0.0208 (5)
C1120.4873 (2)0.6355 (2)0.8450 (2)0.0282 (5)
C1130.6206 (2)0.6073 (3)0.8171 (2)0.0334 (6)
C1140.6779 (2)0.4857 (3)0.8066 (2)0.0340 (6)
C1150.6030 (2)0.3921 (2)0.8245 (2)0.0322 (6)
C1160.4700 (2)0.4203 (2)0.8533 (2)0.0265 (5)
C1170.2670 (2)0.5761 (2)0.89777 (19)0.0205 (5)
C1210.2054 (3)0.5476 (2)0.5065 (2)0.0318 (6)
S220.33254 (5)0.04886 (6)0.03064 (5)0.02635 (17)
O250.11416 (15)0.28444 (16)0.30060 (14)0.0310 (4)
O260.12194 (15)0.05295 (16)0.39780 (13)0.0282 (4)
N210.20812 (16)0.00550 (17)0.22155 (15)0.0186 (4)
N230.13959 (16)0.09661 (17)0.07124 (15)0.0192 (4)
N240.02023 (16)0.23108 (18)0.09427 (16)0.0211 (4)
N250.03844 (18)0.21262 (19)0.33404 (17)0.0254 (4)
C220.21383 (19)0.0260 (2)0.11387 (19)0.0193 (5)
C240.05003 (19)0.1582 (2)0.13947 (19)0.0181 (5)
C250.0373 (2)0.1467 (2)0.25404 (18)0.0191 (5)
C260.1205 (2)0.0682 (2)0.29980 (19)0.0209 (5)
C2110.4293 (2)0.0051 (2)0.32323 (19)0.0194 (5)
C2120.4515 (2)0.1402 (2)0.3548 (2)0.0310 (6)
C2130.5726 (3)0.2054 (3)0.4088 (2)0.0391 (7)
C2140.6716 (2)0.1374 (3)0.4312 (2)0.0385 (7)
C2150.6504 (2)0.0033 (3)0.4009 (2)0.0354 (6)
C2160.5297 (2)0.0631 (2)0.3471 (2)0.0266 (5)
C2170.2991 (2)0.0706 (2)0.2654 (2)0.0215 (5)
C2210.3068 (2)0.0015 (3)0.0993 (2)0.0303 (6)
H11A0.24330.66330.89210.025*
H11B0.24400.58350.98350.025*
H1120.44820.71940.85170.034*
H1130.67200.67190.80540.040*
H1140.76880.46610.78710.041*
H1150.64260.30820.81720.039*
H1160.41920.35570.86620.032*
H12A0.22220.45420.45680.048*
H12B0.11240.57450.52160.048*
H12C0.24910.59960.46370.048*
H14A0.01570.22470.52580.030*
H14B0.06460.17190.62500.030*
H21A0.31120.14920.19640.026*
H21B0.26120.10140.32540.026*
H2120.38340.18840.33940.037*
H2130.58680.29810.43040.047*
H2140.75460.18240.46760.046*
H2150.71890.04410.41680.042*
H2160.51600.15570.32670.032*
H22A0.21670.02370.13710.045*
H22B0.36330.04130.15780.045*
H22C0.32620.09710.07370.045*
H24A0.00810.23790.02410.025*
H24B0.07940.27300.13420.025*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N110.0191 (9)0.0197 (10)0.0180 (9)0.0034 (7)0.0039 (7)0.0072 (8)
C1170.0229 (11)0.0182 (12)0.0197 (11)0.0063 (9)0.0049 (9)0.0044 (9)
C1110.0218 (11)0.0222 (12)0.0171 (11)0.0055 (9)0.0076 (9)0.0031 (9)
C1120.0296 (13)0.0273 (13)0.0292 (13)0.0077 (10)0.0073 (10)0.0100 (11)
C1130.0270 (13)0.0418 (16)0.0307 (13)0.0151 (12)0.0032 (11)0.0100 (12)
C1140.0204 (12)0.0487 (17)0.0249 (13)0.0076 (12)0.0051 (10)0.0011 (12)
C1150.0302 (13)0.0289 (14)0.0295 (13)0.0048 (11)0.0112 (11)0.0010 (11)
C1160.0289 (13)0.0246 (13)0.0260 (12)0.0064 (10)0.0087 (10)0.0066 (10)
C120.0200 (11)0.0185 (11)0.0174 (11)0.0026 (9)0.0000 (9)0.0058 (9)
S120.0348 (3)0.0251 (3)0.0245 (3)0.0083 (3)0.0035 (3)0.0125 (3)
C1210.0440 (15)0.0316 (14)0.0232 (12)0.0033 (11)0.0039 (11)0.0146 (11)
N130.0220 (10)0.0215 (10)0.0185 (9)0.0017 (8)0.0030 (8)0.0078 (8)
C140.0158 (11)0.0201 (12)0.0193 (11)0.0041 (9)0.0037 (9)0.0051 (9)
N140.0278 (10)0.0288 (11)0.0212 (10)0.0087 (9)0.0097 (8)0.0094 (9)
C150.0170 (11)0.0197 (11)0.0161 (10)0.0006 (9)0.0019 (8)0.0063 (9)
N150.0214 (10)0.0241 (10)0.0222 (10)0.0062 (8)0.0032 (8)0.0059 (8)
O150.0299 (9)0.0361 (10)0.0281 (9)0.0163 (8)0.0080 (7)0.0111 (8)
C160.0175 (11)0.0203 (12)0.0197 (12)0.0011 (9)0.0019 (9)0.0073 (9)
O160.0317 (9)0.0357 (10)0.0190 (8)0.0124 (7)0.0103 (7)0.0134 (7)
N210.0166 (9)0.0215 (10)0.0188 (9)0.0037 (7)0.0016 (7)0.0086 (8)
C2170.0201 (11)0.0195 (12)0.0258 (12)0.0045 (9)0.0008 (9)0.0093 (10)
C2110.0169 (11)0.0258 (13)0.0172 (11)0.0028 (9)0.0037 (9)0.0093 (9)
C2120.0273 (13)0.0281 (14)0.0366 (14)0.0003 (10)0.0019 (11)0.0125 (11)
C2130.0379 (15)0.0354 (16)0.0378 (15)0.0136 (12)0.0034 (12)0.0105 (13)
C2140.0224 (13)0.064 (2)0.0233 (13)0.0101 (13)0.0002 (10)0.0111 (13)
C2150.0212 (12)0.063 (2)0.0215 (12)0.0117 (12)0.0021 (10)0.0131 (12)
C2160.0277 (13)0.0322 (14)0.0204 (12)0.0126 (10)0.0055 (10)0.0074 (10)
C220.0137 (10)0.0219 (12)0.0192 (11)0.0009 (9)0.0002 (9)0.0039 (9)
S220.0202 (3)0.0366 (4)0.0226 (3)0.0113 (2)0.0060 (2)0.0082 (3)
C2210.0239 (12)0.0474 (16)0.0208 (12)0.0089 (11)0.0070 (10)0.0111 (11)
N230.0175 (9)0.0225 (10)0.0167 (9)0.0028 (8)0.0033 (7)0.0050 (8)
C240.0154 (10)0.0179 (11)0.0182 (11)0.0014 (9)0.0000 (8)0.0041 (9)
N240.0193 (9)0.0283 (11)0.0199 (9)0.0080 (8)0.0067 (8)0.0115 (8)
C250.0170 (11)0.0233 (12)0.0159 (11)0.0019 (9)0.0039 (9)0.0047 (9)
N250.0223 (10)0.0307 (11)0.0251 (10)0.0082 (8)0.0048 (8)0.0106 (9)
O250.0293 (9)0.0384 (10)0.0288 (9)0.0171 (8)0.0078 (7)0.0126 (8)
C260.0175 (11)0.0247 (12)0.0196 (11)0.0014 (9)0.0034 (9)0.0065 (10)
O260.0295 (9)0.0401 (10)0.0210 (8)0.0109 (7)0.0071 (7)0.0160 (8)
Geometric parameters (Å, º) top
N11—C121.372 (3)N21—C221.372 (3)
C12—N131.306 (3)C22—N231.305 (3)
N13—C141.362 (3)N23—C241.368 (3)
C14—C151.433 (3)C24—C251.422 (3)
C15—C161.452 (3)C25—C261.445 (3)
C16—N111.419 (3)C26—N211.420 (3)
N11—C1171.483 (3)N21—C2171.466 (3)
C12—S121.743 (2)C22—S221.747 (2)
S12—C1211.804 (2)S22—C2211.796 (2)
C14—N141.312 (3)C24—N241.316 (3)
C15—N151.353 (3)C25—N251.352 (3)
N15—O151.273 (2)N25—O251.272 (2)
C16—O161.218 (3)C26—O261.223 (3)
C117—C1111.507 (3)C217—C2111.511 (3)
C117—H11A0.99C217—H21A0.99
C117—H11B0.99C217—H21B0.99
C111—C1161.390 (3)C211—C2161.385 (3)
C111—C1121.392 (3)C211—C2121.385 (3)
C112—C1131.391 (3)C212—C2131.388 (3)
C112—H1120.95C212—H2120.95
C113—C1141.377 (4)C213—C2141.368 (4)
C113—H1130.95C213—H2130.95
C114—C1151.382 (4)C214—C2151.375 (4)
C114—H1140.95C214—H2140.95
C115—C1161.389 (3)C215—C2161.387 (3)
C115—H1150.95C215—H2150.95
C116—H1160.95C216—H2160.95
C121—H12A0.98C221—H22A0.98
C121—H12B0.98C221—H22B0.98
C121—H12C0.98C221—H22C0.98
N14—H14A0.88N24—H24A0.88
N14—H14B0.88N24—H24B0.88
C12—N11—C16120.61 (17)C22—N21—C26120.43 (17)
C12—N11—C117121.63 (17)C22—N21—C217121.77 (17)
C16—N11—C117117.67 (17)C26—N21—C217117.55 (17)
N11—C117—C111114.61 (17)N21—C217—C211113.89 (17)
N11—C117—H11A108.6N21—C217—H21A108.8
C111—C117—H11A108.6C211—C217—H21A108.8
N11—C117—H11B108.6N21—C217—H21B108.8
C111—C117—H11B108.6C211—C217—H21B108.8
H11A—C117—H11B107.6H21A—C217—H21B107.7
C116—C111—C112118.7 (2)C216—C211—C212118.9 (2)
C116—C111—C117121.28 (19)C216—C211—C217118.6 (2)
C112—C111—C117120.0 (2)C212—C211—C217122.50 (19)
C113—C112—C111120.7 (2)C211—C212—C213120.3 (2)
C113—C112—H112119.6C211—C212—H212119.9
C111—C112—H112119.6C213—C212—H212119.9
C114—C113—C112119.9 (2)C214—C213—C212120.6 (3)
C114—C113—H113120.0C214—C213—H213119.7
C112—C113—H113120.0C212—C213—H213119.7
C113—C114—C115120.0 (2)C213—C214—C215119.6 (2)
C113—C114—H114120.0C213—C214—H214120.2
C115—C114—H114120.0C215—C214—H214120.2
C114—C115—C116120.3 (2)C214—C215—C216120.5 (2)
C114—C115—H115119.9C214—C215—H215119.7
C116—C115—H115119.9C216—C215—H215119.7
C115—C116—C111120.4 (2)C211—C216—C215120.2 (2)
C115—C116—H116119.8C211—C216—H216119.9
C111—C116—H116119.8C215—C216—H216119.9
N13—C12—N11125.35 (19)N23—C22—N21125.28 (19)
N13—C12—S12118.36 (16)N23—C22—S22118.95 (16)
N11—C12—S12116.27 (16)N21—C22—S22115.76 (15)
C12—S12—C121101.02 (11)C22—S22—C221101.30 (11)
S12—C121—H12A109.5S22—C221—H22A109.5
S12—C121—H12B109.5S22—C221—H22B109.5
H12A—C121—H12B109.5H22A—C221—H22B109.5
S12—C121—H12C109.5S22—C221—H22C109.5
H12A—C121—H12C109.5H22A—C221—H22C109.5
H12B—C121—H12C109.5H22B—C221—H22C109.5
C12—N13—C14118.48 (18)C22—N23—C24118.21 (18)
N14—C14—N13116.64 (19)N24—C24—N23116.00 (19)
N14—C14—C15122.06 (19)N24—C24—C25122.43 (19)
N13—C14—C15121.28 (19)N23—C24—C25121.53 (19)
C14—N14—H14A120.0C24—N24—H24A120.0
C14—N14—H14B120.0C24—N24—H24B120.0
H14A—N14—H14B120.0H24A—N24—H24B120.0
N15—C15—C14126.59 (19)N25—C25—C24126.61 (19)
N15—C15—C16114.08 (18)N25—C25—C26113.64 (18)
C14—C15—C16119.29 (18)C24—C25—C26119.44 (19)
O15—N15—C15117.81 (18)O25—N25—C25117.41 (18)
O16—C16—N11120.09 (19)O26—C26—N21118.89 (19)
O16—C16—C15125.09 (19)O26—C26—C25126.1 (2)
N11—C16—C15114.81 (18)N21—C26—C25115.04 (18)
C12—N11—C117—C11173.9 (3)C22—N21—C217—C21179.1 (2)
C16—N11—C117—C111109.5 (2)C26—N21—C217—C21195.2 (2)
N11—C117—C111—C11653.0 (3)N21—C217—C211—C216168.10 (19)
N11—C117—C111—C112129.5 (2)N21—C217—C211—C21212.9 (3)
C116—C111—C112—C1130.2 (3)C216—C211—C212—C2130.4 (3)
C117—C111—C112—C113177.8 (2)C217—C211—C212—C213179.4 (2)
C111—C112—C113—C1140.4 (3)C211—C212—C213—C2140.2 (4)
C112—C113—C114—C1150.4 (4)C212—C213—C214—C2150.6 (4)
C113—C114—C115—C1160.1 (4)C213—C214—C215—C2160.4 (4)
C114—C115—C116—C1110.6 (3)C212—C211—C216—C2150.6 (3)
C112—C111—C116—C1150.7 (3)C217—C211—C216—C215179.6 (2)
C117—C111—C116—C115178.2 (2)C214—C215—C216—C2110.2 (3)
C16—N11—C12—N132.0 (3)C26—N21—C22—N233.1 (3)
C117—N11—C12—N13178.59 (19)C217—N21—C22—N23177.23 (19)
C16—N11—C12—S12179.77 (15)C26—N21—C22—S22176.19 (15)
C117—N11—C12—S123.2 (3)C217—N21—C22—S222.1 (3)
N13—C12—S12—C1218.9 (2)N23—C22—S22—C2210.7 (2)
N11—C12—S12—C121172.74 (17)N21—C22—S22—C221179.95 (17)
N11—C12—N13—C141.1 (3)N21—C22—N23—C241.4 (3)
S12—C12—N13—C14179.28 (15)S22—C22—N23—C24177.83 (15)
C12—N13—C14—N14176.06 (19)C22—N23—C24—N24178.24 (18)
C12—N13—C14—C152.5 (3)C22—N23—C24—C250.2 (3)
N14—C14—C15—N154.2 (3)N24—C24—C25—N254.8 (3)
N13—C14—C15—N15177.4 (2)N23—C24—C25—N25173.1 (2)
N14—C14—C15—C16173.43 (19)N24—C24—C25—C26178.03 (19)
N13—C14—C15—C165.0 (3)N23—C24—C25—C260.1 (3)
C14—C15—N15—O152.8 (3)C24—C25—N25—O256.2 (3)
C16—C15—N15—O15179.49 (18)C26—C25—N25—O25179.72 (18)
C12—N11—C16—O16178.5 (2)C22—N21—C26—O26176.5 (2)
C117—N11—C16—O164.8 (3)C217—N21—C26—O262.2 (3)
C12—N11—C16—C150.6 (3)C22—N21—C26—C252.9 (3)
C117—N11—C16—C15176.07 (18)C217—N21—C26—C25177.26 (17)
N15—C15—C16—O162.7 (3)N25—C25—C26—O263.9 (3)
C14—C15—C16—O16175.2 (2)C24—C25—C26—O26178.0 (2)
N15—C15—C16—N11178.20 (17)N25—C25—C26—N21175.47 (18)
C14—C15—C16—N113.9 (3)C24—C25—C26—N211.4 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N14—H14A···N250.882.233.100 (3)168
N14—H14A···O260.882.402.879 (2)114
N14—H14B···O150.882.012.642 (2)128
N24—H24A···N15i0.882.092.970 (3)177
N24—H24A···O16i0.882.502.938 (2)112
N24—H24B···O250.882.012.631 (2)127
Symmetry code: (i) x, y, z1.
(IV) 4-Amino-6-benzyloxy-2-(methylsulfanyl)pyrimidine top
Crystal data top
C12H13N3OSF(000) = 520
Mr = 247.31Dx = 1.367 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1177 reflections
a = 15.747 (2) Åθ = 2.7–20.5°
b = 5.1044 (7) ŵ = 0.26 mm1
c = 15.501 (3) ÅT = 120 K
β = 105.286 (5)°Needle, colourless
V = 1201.9 (3) Å30.60 × 0.04 × 0.03 mm
Z = 4
Data collection top
Nonius KappaCCD
diffractometer
1177 independent reflections
Radiation source: rotating anode1006 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.147
ϕ scans, and ω scans with κ offsetsθmax = 20.5°, θmin = 2.7°
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
h = 1515
Tmin = 0.862, Tmax = 0.992k = 55
9738 measured reflectionsl = 1415
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.077Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.155H-atom parameters constrained
S = 1.22 w = 1/[σ2(Fo2)P)2 + 5.5293P]
where P = (Fo2 + 2Fc2)/3
1177 reflections(Δ/σ)max < 0.001
155 parametersΔρmax = 0.32 e Å3
0 restraintsΔρmin = 0.35 e Å3
Crystal data top
C12H13N3OSV = 1201.9 (3) Å3
Mr = 247.31Z = 4
Monoclinic, P21/cMo Kα radiation
a = 15.747 (2) ŵ = 0.26 mm1
b = 5.1044 (7) ÅT = 120 K
c = 15.501 (3) Å0.60 × 0.04 × 0.03 mm
β = 105.286 (5)°
Data collection top
Nonius KappaCCD
diffractometer
1177 independent reflections
Absorption correction: multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
1006 reflections with I > 2σ(I)
Tmin = 0.862, Tmax = 0.992Rint = 0.147
9738 measured reflectionsθmax = 20.5°
Refinement top
R[F2 > 2σ(F2)] = 0.0770 restraints
wR(F2) = 0.155H-atom parameters constrained
S = 1.22Δρmax = 0.32 e Å3
1177 reflectionsΔρmin = 0.35 e Å3
155 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
S20.27418 (12)0.1502 (4)0.49135 (12)0.0270 (6)
O60.3641 (3)0.3141 (9)0.2472 (3)0.0235 (12)
N10.3258 (3)0.1023 (10)0.3632 (3)0.0169 (14)
N30.4194 (4)0.2350 (10)0.4443 (3)0.0195 (14)
N40.5508 (3)0.3420 (11)0.4124 (4)0.0252 (15)
C20.3481 (4)0.0834 (13)0.4247 (4)0.0175 (17)
C40.4774 (4)0.1946 (13)0.3940 (4)0.0192 (17)
C50.4600 (4)0.0042 (13)0.3257 (4)0.0212 (18)
C60.3834 (4)0.1335 (13)0.3146 (4)0.0196 (17)
C210.1850 (4)0.0671 (14)0.4410 (5)0.0274 (19)
C610.2014 (4)0.3409 (13)0.2024 (4)0.0180 (17)
C620.1258 (5)0.4274 (14)0.2224 (5)0.0283 (19)
C630.0444 (5)0.3127 (16)0.1852 (5)0.035 (2)
C640.0377 (5)0.1017 (15)0.1269 (5)0.034 (2)
C650.1130 (5)0.0166 (15)0.1062 (5)0.033 (2)
C660.1945 (5)0.1309 (14)0.1431 (4)0.0266 (18)
C670.2874 (4)0.4794 (13)0.2411 (5)0.0246 (18)
H21A0.16330.02700.37710.041*
H21B0.13720.04400.47000.041*
H21C0.20580.24870.44850.041*
H4A0.56000.45900.45560.030*
H4B0.58970.32140.38130.030*
H50.49910.02670.28950.025*
H67A0.28850.54370.30170.030*
H67B0.29100.63370.20350.030*
H620.12960.56970.26270.034*
H630.00670.37820.19960.042*
H640.01730.01860.10200.041*
H650.10910.12460.06540.039*
H660.24540.06660.12800.032*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S20.0268 (11)0.0283 (12)0.0289 (11)0.0019 (9)0.0129 (8)0.0051 (9)
O60.021 (3)0.024 (3)0.026 (3)0.003 (2)0.008 (2)0.005 (2)
N10.022 (3)0.012 (3)0.017 (3)0.003 (3)0.005 (3)0.000 (3)
N30.024 (4)0.016 (3)0.019 (3)0.003 (3)0.006 (3)0.002 (3)
N40.023 (4)0.028 (4)0.024 (3)0.010 (3)0.005 (3)0.011 (3)
C20.015 (4)0.016 (4)0.020 (4)0.003 (3)0.002 (3)0.001 (4)
C40.017 (4)0.020 (4)0.018 (4)0.006 (4)0.001 (3)0.004 (4)
C50.016 (4)0.031 (5)0.015 (4)0.003 (4)0.000 (3)0.000 (4)
C60.022 (4)0.018 (4)0.015 (4)0.002 (4)0.001 (3)0.003 (3)
C210.022 (4)0.026 (4)0.035 (5)0.004 (3)0.009 (3)0.003 (4)
C610.022 (4)0.016 (4)0.015 (4)0.001 (3)0.003 (3)0.005 (3)
C620.032 (5)0.029 (5)0.023 (5)0.009 (4)0.007 (4)0.001 (4)
C630.018 (5)0.044 (5)0.040 (5)0.003 (4)0.002 (4)0.005 (5)
C640.028 (5)0.039 (5)0.031 (5)0.008 (4)0.002 (4)0.003 (4)
C650.037 (5)0.033 (5)0.026 (5)0.005 (4)0.003 (4)0.002 (4)
C660.028 (5)0.027 (5)0.025 (4)0.000 (4)0.008 (3)0.007 (4)
C670.029 (5)0.020 (4)0.025 (5)0.009 (4)0.007 (3)0.006 (3)
Geometric parameters (Å, º) top
N1—C21.324 (8)O6—C671.456 (7)
N1—C61.333 (8)C67—C611.505 (9)
C2—N31.332 (8)C67—H67A0.99
C2—S21.781 (7)C67—H67B0.99
S2—C211.798 (7)C61—C621.380 (9)
C21—H21A0.98C61—C661.397 (9)
C21—H21B0.98C62—C631.389 (10)
C21—H21C0.98C62—H620.95
N3—C41.364 (8)C63—C641.393 (10)
C4—N41.345 (8)C63—H630.95
C4—C51.410 (9)C64—C651.379 (10)
N4—H4A0.88C64—H640.95
N4—H4B0.88C65—C661.387 (9)
C5—C61.366 (9)C65—H650.95
C5—H50.95C66—H660.95
C6—O61.367 (8)
C2—N1—C6113.7 (5)O6—C67—C61113.4 (5)
N1—C2—N3128.9 (6)O6—C67—H67A108.9
N1—C2—S2117.7 (5)C61—C67—H67A108.9
N3—C2—S2113.4 (5)O6—C67—H67B108.9
C2—S2—C21100.7 (3)C61—C67—H67B108.9
S2—C21—H21A109.5H67A—C67—H67B107.7
S2—C21—H21B109.5C62—C61—C66118.1 (6)
H21A—C21—H21B109.5C62—C61—C67119.9 (6)
S2—C21—H21C109.5C66—C61—C67121.9 (6)
H21A—C21—H21C109.5C61—C62—C63121.9 (7)
H21B—C21—H21C109.5C61—C62—H62119.0
C2—N3—C4115.7 (5)C63—C62—H62119.0
N4—C4—N3117.5 (6)C62—C63—C64119.9 (7)
N4—C4—C5122.1 (6)C62—C63—H63120.0
N3—C4—C5120.4 (6)C64—C63—H63120.0
C4—N4—H4A120.0C65—C64—C63118.2 (7)
C4—N4—H4B120.0C65—C64—H64120.9
H4A—N4—H4B120.0C63—C64—H64120.9
C6—C5—C4116.1 (6)C64—C65—C66122.0 (7)
C6—C5—H5121.9C64—C65—H65119.0
C4—C5—H5121.9C66—C65—H65119.0
N1—C6—C5125.2 (6)C65—C66—C61119.8 (7)
N1—C6—O6117.8 (6)C65—C66—H66120.1
C5—C6—O6117.0 (6)C61—C66—H66120.1
C6—O6—C67117.0 (5)
C6—N1—C2—N31.2 (9)N1—C6—O6—C677.2 (8)
C6—N1—C2—S2178.0 (4)C5—C6—O6—C67173.9 (6)
N1—C2—S2—C213.6 (6)C6—O6—C67—C6176.1 (7)
N3—C2—S2—C21175.7 (5)O6—C67—C61—C62155.4 (6)
N1—C2—N3—C40.3 (9)O6—C67—C61—C6627.2 (8)
S2—C2—N3—C4178.9 (4)C66—C61—C62—C630.2 (10)
C2—N3—C4—N4179.3 (6)C67—C61—C62—C63177.2 (6)
C2—N3—C4—C50.5 (8)C61—C62—C63—C640.9 (11)
N4—C4—C5—C6179.4 (6)C62—C63—C64—C651.5 (10)
N3—C4—C5—C60.5 (9)C63—C64—C65—C661.4 (11)
C2—N1—C6—C51.3 (9)C64—C65—C66—C610.7 (10)
C2—N1—C6—O6177.5 (5)C62—C61—C66—C650.1 (9)
C4—C5—C6—N10.5 (10)C67—C61—C66—C65177.3 (6)
C4—C5—C6—O6178.2 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···N3i0.882.163.044 (8)177
N4—H4B···O6ii0.882.403.209 (7)154
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y+1/2, z+1/2.

Experimental details

(I)(II)(III)(IV)
Crystal data
Chemical formulaC12H13N3OSC24H25.95N6.05O2.05S2C12H12N4O2SC12H13N3OS
Mr247.31496.10276.33247.31
Crystal system, space groupMonoclinic, P21/cMonoclinic, P21/cTriclinic, P1Monoclinic, P21/c
Temperature (K)120120120120
a, b, c (Å)9.7139 (2), 9.5846 (2), 12.6431 (2)11.4629 (2), 10.2603 (2), 20.9303 (4)10.5035 (3), 10.8741 (3), 11.8261 (4)15.747 (2), 5.1044 (7), 15.501 (3)
α, β, γ (°)90, 103.4465 (13), 9090, 107.0920 (14), 90109.6510 (13), 96.4203 (14), 93.7181 (14)90, 105.286 (5), 90
V3)1144.85 (4)2352.95 (8)1256.49 (7)1201.9 (3)
Z4444
Radiation typeMo KαMo KαMo KαMo Kα
µ (mm1)0.270.260.260.26
Crystal size (mm)0.30 × 0.26 × 0.200.47 × 0.22 × 0.140.30 × 0.22 × 0.040.60 × 0.04 × 0.03
Data collection
DiffractometerNonius KappaCCD
diffractometer
Nonius KappaCCD
diffractometer
Nonius KappaCCD
diffractometer
Nonius KappaCCD
diffractometer
Absorption correctionMulti-scan
DENZO-SMN (Otwinowski & Minor, 1997)
Multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
Multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
Multi-scan
DENZO-SMN (Otwinowski & Minor, 1997)
Tmin, Tmax0.902, 0.9430.887, 0.9570.920, 0.9910.862, 0.992
No. of measured, independent and
observed [I > 2σ(I)] reflections
7564, 2600, 2249 21205, 5325, 4389 24784, 4417, 3498 9738, 1177, 1006
Rint0.0320.0640.0940.147
θmax (°)27.527.525.020.5
(sin θ/λ)max1)0.6490.6490.5950.493
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.091, 1.06 0.047, 0.119, 1.06 0.044, 0.107, 1.05 0.077, 0.155, 1.22
No. of reflections2600532544171177
No. of parameters155318345155
No. of restraints0100
H-atom treatmentH-atom parameters constrainedH-atom parameters constrainedH-atom parameters constrainedH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.24, 0.310.51, 0.410.21, 0.310.32, 0.35

Computer programs: KappaCCD Server Software (Nonius, 1997), DENZO-SMN (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 (Sheldrick, 1997) and PRPKAPPA (Ferguson, 1999).

Selected bond lengths (Å) for (I) top
N1—C21.364 (2)N1—C171.463 (2)
C2—N31.303 (3)C2—S21.757 (2)
N3—C41.375 (2)C21—S21.798 (2)
C4—C51.376 (2)C4—N41.344 (2)
C5—C61.401 (2)C6—O61.241 (2)
C6—N11.424 (2)
Hydrogen-bond geometry (Å, º) for (I) top
D—H···AD—HH···AD···AD—H···A
N4—H4B···O6i0.881.952.823 (2)170
Symmetry code: (i) x+1, y1/2, z+1/2.
Selected bond lengths (Å) for (II) top
N11—C121.366 (2)N21—C221.376 (2)
C12—N131.304 (2)C22—N231.311 (3)
N13—C141.374 (2)N23—C241.373 (3)
C14—C151.390 (3)C24—C251.381 (3)
C15—C161.401 (3)C25—C261.400 (3)
C16—N111.435 (2)C26—N211.420 (3)
N11—C1171.469 (2)N21—C2171.464 (3)
C12—S121.759 (2)C22—S221.747 (2)
S12—C1211.794 (2)S22—C2211.791 (2)
C14—N141.342 (2)C24—N241.353 (3)
C16—O161.245 (2)C26—O261.246 (3)
Hydrogen-bond geometry (Å, º) for (II) top
D—H···AD—HH···AD···AD—H···A
N14—H14A···O26i0.882.283.029 (2)143
N14—H14B···O260.882.102.896 (2)151
N24—H24A···O16ii0.882.293.124 (2)157
N24—H24B···O16iii0.882.623.330 (2)138
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z+1; (iii) x, y1, z.
Selected bond lengths (Å) for (III) top
N11—C121.372 (3)N21—C221.372 (3)
C12—N131.306 (3)C22—N231.305 (3)
N13—C141.362 (3)N23—C241.368 (3)
C14—C151.433 (3)C24—C251.422 (3)
C15—C161.452 (3)C25—C261.445 (3)
C16—N111.419 (3)C26—N211.420 (3)
N11—C1171.483 (3)N21—C2171.466 (3)
C12—S121.743 (2)C22—S221.747 (2)
S12—C1211.804 (2)S22—C2211.796 (2)
C14—N141.312 (3)C24—N241.316 (3)
C15—N151.353 (3)C25—N251.352 (3)
N15—O151.273 (2)N25—O251.272 (2)
C16—O161.218 (3)C26—O261.223 (3)
Hydrogen-bond geometry (Å, º) for (III) top
D—H···AD—HH···AD···AD—H···A
N14—H14A···N250.882.233.100 (3)168
N14—H14A···O260.882.402.879 (2)114
N14—H14B···O150.882.012.642 (2)128
N24—H24A···N15i0.882.092.970 (3)177
N24—H24A···O16i0.882.502.938 (2)112
N24—H24B···O250.882.012.631 (2)127
Symmetry code: (i) x, y, z1.
Hydrogen-bond geometry (Å, º) for (IV) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···N3i0.882.163.044 (8)177
N4—H4B···O6ii0.882.403.209 (7)154
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1, y+1/2, z+1/2.
 

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.

Buy online

You may purchase this article in PDF and/or HTML formats. For purchasers in the European Community who do not have a VAT number, VAT will be added at the local rate. Payments to the IUCr are handled by WorldPay, who will accept payment by credit card in several currencies. To purchase the article, please complete the form below (fields marked * are required), and then click on `Continue'.
E-mail address* 
Repeat e-mail address* 
(for error checking) 

Format*   PDF (US $40)
   HTML (US $40)
   PDF+HTML (US $50)
In order for VAT to be shown for your country javascript needs to be enabled.

VAT number 
(non-UK EC countries only) 
Country* 
 

Terms and conditions of use
Contact us

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