Buy article online - an online subscription or single-article purchase is required to access this article.
4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1
H)-one, C
12H
13N
3OS, crystallizes in two polymorphic forms, both having space group
P2
1/
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
-
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(1
H)-one, C
12H
12N
4O
2S, (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, C
12H
13N
3OS, (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
CCDC references: 219577; 219578; 219579; 219580
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.
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.
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).
(I) 4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1
H)-one, polymorph with
Z' = 1
top
Crystal data top
C12H13N3OS | F(000) = 520 |
Mr = 247.31 | Dx = 1.435 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 2600 reflections |
a = 9.7139 (2) Å | θ = 3.0–27.5° |
b = 9.5846 (2) Å | µ = 0.27 mm−1 |
c = 12.6431 (2) Å | T = 120 K |
β = 103.4465 (13)° | Block, colourless |
V = 1144.85 (4) Å3 | 0.30 × 0.26 × 0.20 mm |
Z = 4 | |
Data collection top
Nonius KappaCCD diffractometer | 2600 independent reflections |
Radiation source: rotating anode | 2249 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.032 |
ϕ scans, and ω scans with κ offsets | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan DENZO-SMN (Otwinowski & Minor, 1997) | h = −12→11 |
Tmin = 0.902, Tmax = 0.943 | k = −11→12 |
7564 measured reflections | l = −14→16 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.035 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.091 | H-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 parameters | Δρmax = 0.24 e Å−3 |
0 restraints | Δρmin = −0.31 e Å−3 |
Crystal data top
C12H13N3OS | V = 1144.85 (4) Å3 |
Mr = 247.31 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.7139 (2) Å | µ = 0.27 mm−1 |
b = 9.5846 (2) Å | T = 120 K |
c = 12.6431 (2) Å | 0.30 × 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 = 0.943 | Rint = 0.032 |
7564 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.035 | 0 restraints |
wR(F2) = 0.091 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.24 e Å−3 |
2600 reflections | Δρmin = −0.31 e Å−3 |
155 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
S2 | 0.78067 (4) | 0.10593 (4) | −0.09925 (3) | 0.01763 (12) | |
O6 | 0.50570 (11) | 0.29284 (11) | 0.15128 (8) | 0.0210 (2) | |
N1 | 0.63886 (12) | 0.19680 (12) | 0.04326 (9) | 0.0136 (2) | |
N3 | 0.70235 (12) | −0.04151 (12) | 0.05419 (9) | 0.0139 (2) | |
N4 | 0.63526 (13) | −0.18557 (13) | 0.17770 (10) | 0.0184 (3) | |
C2 | 0.70101 (14) | 0.08191 (14) | 0.01077 (11) | 0.0131 (3) | |
C4 | 0.63418 (13) | −0.05561 (15) | 0.13751 (11) | 0.0141 (3) | |
C5 | 0.56911 (14) | 0.05435 (15) | 0.17611 (11) | 0.0161 (3) | |
C6 | 0.56570 (14) | 0.18654 (15) | 0.12836 (11) | 0.0155 (3) | |
C11 | 0.78052 (14) | 0.41415 (14) | 0.05830 (11) | 0.0141 (3) | |
C12 | 0.89040 (15) | 0.34918 (15) | 0.13181 (11) | 0.0168 (3) | |
C13 | 1.01182 (15) | 0.42234 (16) | 0.18048 (12) | 0.0205 (3) | |
C14 | 1.02459 (16) | 0.56213 (16) | 0.15619 (12) | 0.0212 (3) | |
C15 | 0.91427 (16) | 0.62861 (16) | 0.08502 (12) | 0.0213 (3) | |
C16 | 0.79293 (15) | 0.55541 (15) | 0.03605 (11) | 0.0184 (3) | |
C17 | 0.65073 (15) | 0.33551 (14) | −0.00213 (11) | 0.0163 (3) | |
C21 | 0.82976 (18) | −0.07050 (16) | −0.12178 (13) | 0.0238 (3) | |
H12 | 0.8823 | 0.2535 | 0.1490 | 0.020* | |
H13 | 1.0863 | 0.3766 | 0.2305 | 0.025* | |
H14 | 1.1085 | 0.6119 | 0.1882 | 0.025* | |
H15 | 0.9217 | 0.7250 | 0.0696 | 0.026* | |
H16 | 0.7179 | 0.6018 | −0.0129 | 0.022* | |
H17A | 0.5652 | 0.3903 | 0.0004 | 0.020* | |
H17B | 0.6546 | 0.3258 | −0.0793 | 0.020* | |
H21A | 0.9102 | −0.0986 | −0.0634 | 0.036* | |
H21B | 0.8563 | −0.0765 | −0.1918 | 0.036* | |
H21C | 0.7495 | −0.1327 | −0.1224 | 0.036* | |
H4A | 0.6775 | −0.2534 | 0.1505 | 0.022* | |
H4B | 0.5937 | −0.2028 | 0.2312 | 0.022* | |
H5 | 0.5262 | 0.0405 | 0.2356 | 0.019* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S2 | 0.0213 (2) | 0.0165 (2) | 0.0183 (2) | −0.00184 (13) | 0.01094 (14) | 0.00022 (13) |
O6 | 0.0227 (5) | 0.0190 (5) | 0.0239 (5) | 0.0028 (4) | 0.0103 (4) | −0.0031 (4) |
N1 | 0.0133 (5) | 0.0134 (6) | 0.0149 (5) | −0.0004 (4) | 0.0047 (4) | −0.0003 (4) |
N3 | 0.0130 (5) | 0.0157 (6) | 0.0135 (5) | −0.0007 (4) | 0.0041 (4) | −0.0008 (4) |
N4 | 0.0211 (6) | 0.0170 (6) | 0.0191 (6) | 0.0005 (5) | 0.0085 (5) | 0.0027 (5) |
C2 | 0.0102 (6) | 0.0158 (7) | 0.0136 (6) | −0.0018 (5) | 0.0031 (5) | −0.0012 (5) |
C4 | 0.0108 (6) | 0.0177 (7) | 0.0127 (6) | −0.0029 (5) | 0.0006 (5) | 0.0007 (5) |
C5 | 0.0154 (7) | 0.0195 (7) | 0.0148 (6) | −0.0021 (5) | 0.0063 (5) | −0.0004 (6) |
C6 | 0.0122 (6) | 0.0193 (7) | 0.0153 (6) | −0.0016 (5) | 0.0039 (5) | −0.0042 (5) |
C11 | 0.0154 (7) | 0.0145 (7) | 0.0146 (6) | −0.0005 (5) | 0.0076 (5) | −0.0009 (5) |
C12 | 0.0187 (7) | 0.0142 (7) | 0.0181 (7) | 0.0006 (5) | 0.0052 (5) | −0.0001 (5) |
C13 | 0.0169 (7) | 0.0236 (8) | 0.0206 (7) | 0.0007 (6) | 0.0033 (6) | −0.0034 (6) |
C14 | 0.0201 (7) | 0.0237 (8) | 0.0224 (7) | −0.0073 (6) | 0.0101 (6) | −0.0075 (6) |
C15 | 0.0280 (8) | 0.0155 (7) | 0.0239 (8) | −0.0046 (6) | 0.0131 (6) | −0.0010 (6) |
C16 | 0.0217 (7) | 0.0159 (7) | 0.0186 (7) | 0.0019 (6) | 0.0072 (6) | 0.0016 (6) |
C17 | 0.0160 (7) | 0.0139 (7) | 0.0186 (7) | 0.0008 (5) | 0.0037 (5) | 0.0019 (5) |
C21 | 0.0311 (8) | 0.0211 (8) | 0.0247 (8) | 0.0004 (6) | 0.0177 (6) | −0.0034 (6) |
Geometric parameters (Å, º) top
C11—C12 | 1.389 (2) | N3—C4 | 1.375 (2) |
C11—C16 | 1.394 (2) | C4—C5 | 1.376 (2) |
C11—C17 | 1.514 (2) | C5—C6 | 1.401 (2) |
C12—C13 | 1.387 (2) | C6—N1 | 1.424 (2) |
C12—H12 | 0.95 | N1—C17 | 1.463 (2) |
C13—C14 | 1.387 (2) | C2—S2 | 1.757 (2) |
C13—H13 | 0.95 | C21—S2 | 1.798 (2) |
C14—C15 | 1.384 (2) | C4—N4 | 1.344 (2) |
C14—H14 | 0.95 | C6—O6 | 1.241 (2) |
C15—C16 | 1.388 (2) | C21—H21A | 0.98 |
C15—H15 | 0.95 | C21—H21B | 0.98 |
C16—H16 | 0.95 | C21—H21C | 0.98 |
C17—H17A | 0.99 | N4—H4A | 0.88 |
C17—H17B | 0.99 | N4—H4B | 0.88 |
N1—C2 | 1.364 (2) | C5—H5 | 0.95 |
C2—N3 | 1.303 (3) | | |
| | | |
C12—C11—C16 | 118.78 (13) | C2—N1—C17 | 122.31 (11) |
C12—C11—C17 | 122.31 (12) | C6—N1—C17 | 117.24 (11) |
C16—C11—C17 | 118.86 (12) | N3—C2—N1 | 124.59 (12) |
C13—C12—C11 | 120.80 (13) | N3—C2—S2 | 119.31 (10) |
C13—C12—H12 | 119.6 | N1—C2—S2 | 116.09 (10) |
C11—C12—H12 | 119.6 | S2—C21—H21A | 109.5 |
C14—C13—C12 | 120.06 (14) | S2—C21—H21B | 109.5 |
C14—C13—H13 | 120.0 | H21A—C21—H21B | 109.5 |
C12—C13—H13 | 120.0 | S2—C21—H21C | 109.5 |
C15—C14—C13 | 119.55 (14) | H21A—C21—H21C | 109.5 |
C15—C14—H14 | 120.2 | H21B—C21—H21C | 109.5 |
C13—C14—H14 | 120.2 | C2—S2—C21 | 100.61 (7) |
C14—C15—C16 | 120.42 (14) | C2—N3—C4 | 116.91 (12) |
C14—C15—H15 | 119.8 | N4—C4—N3 | 114.70 (12) |
C16—C15—H15 | 119.8 | N4—C4—C5 | 122.66 (12) |
C15—C16—C11 | 120.36 (14) | N3—C4—C5 | 122.64 (13) |
C15—C16—H16 | 119.8 | C4—N4—H4A | 120.0 |
C11—C16—H16 | 119.8 | C4—N4—H4B | 120.0 |
N1—C17—C11 | 112.75 (11) | H4A—N4—H4B | 120.0 |
N1—C17—H17A | 109.0 | C4—C5—C6 | 120.46 (12) |
C11—C17—H17A | 109.0 | C4—C5—H5 | 119.8 |
N1—C17—H17B | 109.0 | C6—C5—H5 | 119.8 |
C11—C17—H17B | 109.0 | O6—C6—C5 | 127.39 (13) |
H17A—C17—H17B | 107.8 | O6—C6—N1 | 117.63 (12) |
C2—N1—C6 | 120.35 (11) | C5—C6—N1 | 114.98 (12) |
| | | |
C16—C11—C12—C13 | −1.5 (2) | C17—N1—C2—S2 | −6.56 (17) |
C17—C11—C12—C13 | 175.80 (13) | N3—C2—S2—C21 | 4.53 (13) |
C11—C12—C13—C14 | 0.1 (2) | N1—C2—S2—C21 | −174.29 (11) |
C12—C13—C14—C15 | 1.4 (2) | N1—C2—N3—C4 | 0.9 (2) |
C13—C14—C15—C16 | −1.6 (2) | S2—C2—N3—C4 | −177.76 (9) |
C14—C15—C16—C11 | 0.2 (2) | C2—N3—C4—N4 | 178.32 (12) |
C12—C11—C16—C15 | 1.3 (2) | C2—N3—C4—C5 | −1.21 (19) |
C17—C11—C16—C15 | −176.10 (12) | N4—C4—C5—C6 | −177.24 (12) |
C12—C11—C17—N1 | 13.45 (18) | N3—C4—C5—C6 | 2.3 (2) |
C16—C11—C17—N1 | −169.27 (12) | C4—C5—C6—O6 | 176.46 (13) |
C11—C17—N1—C2 | −87.95 (15) | C4—C5—C6—N1 | −2.78 (19) |
C11—C17—N1—C6 | 88.57 (14) | C2—N1—C6—O6 | −176.80 (12) |
C6—N1—C2—N3 | −1.7 (2) | C17—N1—C6—O6 | 6.61 (18) |
C17—N1—C2—N3 | 174.70 (12) | C2—N1—C6—C5 | 2.52 (18) |
C6—N1—C2—S2 | 177.03 (9) | C17—N1—C6—C5 | −174.08 (12) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4B···O6i | 0.88 | 1.95 | 2.823 (2) | 170 |
Symmetry code: (i) −x+1, y−1/2, −z+1/2. |
(II) 4-Amino-1-benzyl-2-(methylsulfanyl)pyrimidin-6(1
H)-one, polymorph with
Z' = 2 'C12 H13 N3 O S'
top
Crystal data top
C24H25.95N6.05O2.05S2 | F(000) = 1042.8 |
Mr = 496.10 | Dx = 1.400 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5325 reflections |
a = 11.4629 (2) Å | θ = 3.1–27.5° |
b = 10.2603 (2) Å | µ = 0.26 mm−1 |
c = 20.9303 (4) Å | T = 120 K |
β = 107.0920 (14)° | Block, green |
V = 2352.95 (8) Å3 | 0.47 × 0.22 × 0.14 mm |
Z = 4 | |
Data collection top
Nonius KappaCCD diffractometer | 5325 independent reflections |
Radiation source: rotating anode | 4389 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.064 |
ϕ scans, and ω scans with κ offsets | θmax = 27.5°, θmin = 3.1° |
Absorption correction: multi-scan DENZO-SMN (Otwinowski & Minor, 1997) | h = −14→14 |
Tmin = 0.887, Tmax = 0.957 | k = −13→12 |
21205 measured reflections | l = −27→27 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.047 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.119 | H-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 parameters | Δρmax = 0.51 e Å−3 |
1 restraint | Δρmin = −0.41 e Å−3 |
Crystal data top
C24H25.95N6.05O2.05S2 | V = 2352.95 (8) Å3 |
Mr = 496.10 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.4629 (2) Å | µ = 0.26 mm−1 |
b = 10.2603 (2) Å | T = 120 K |
c = 20.9303 (4) Å | 0.47 × 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 = 0.957 | Rint = 0.064 |
21205 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.047 | 1 restraint |
wR(F2) = 0.119 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.51 e Å−3 |
5325 reflections | Δρmin = −0.41 e Å−3 |
318 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | Occ. (<1) |
S12 | 0.68767 (4) | 1.04108 (5) | 0.62530 (3) | 0.02764 (14) | |
O16 | 0.23861 (12) | 0.98605 (14) | 0.53972 (7) | 0.0281 (3) | |
N11 | 0.44857 (14) | 1.00240 (15) | 0.57375 (8) | 0.0201 (3) | |
N13 | 0.57460 (13) | 0.81516 (16) | 0.59210 (7) | 0.0200 (3) | |
N14 | 0.49396 (15) | 0.61296 (16) | 0.56142 (9) | 0.0266 (4) | |
C12 | 0.55905 (16) | 0.94083 (19) | 0.59392 (9) | 0.0197 (4) | |
C14 | 0.47183 (17) | 0.74009 (19) | 0.56759 (9) | 0.0206 (4) | |
C15 | 0.35499 (17) | 0.7926 (2) | 0.55082 (9) | 0.0229 (4) | |
C16 | 0.33808 (17) | 0.9275 (2) | 0.55350 (9) | 0.0219 (4) | |
C111 | 0.46488 (16) | 1.21470 (18) | 0.63496 (9) | 0.0204 (4) | |
C112 | 0.54567 (18) | 1.31854 (19) | 0.64946 (10) | 0.0244 (4) | |
C113 | 0.57217 (18) | 1.3822 (2) | 0.71062 (11) | 0.0267 (4) | |
C114 | 0.51775 (19) | 1.3408 (2) | 0.75809 (10) | 0.0278 (4) | |
C115 | 0.43498 (19) | 1.2385 (2) | 0.74369 (10) | 0.0279 (4) | |
C116 | 0.40859 (18) | 1.17588 (19) | 0.68242 (10) | 0.0244 (4) | |
C117 | 0.44110 (18) | 1.14517 (19) | 0.56873 (10) | 0.0231 (4) | |
C121 | 0.80787 (19) | 0.9232 (2) | 0.63789 (14) | 0.0394 (6) | |
S22 | −0.15062 (5) | 0.53540 (6) | 0.33956 (3) | 0.03293 (15) | |
O26 | 0.28185 (13) | 0.49245 (17) | 0.46960 (8) | 0.0389 (4) | |
N21 | 0.07893 (14) | 0.50607 (17) | 0.41394 (8) | 0.0243 (4) | |
N23 | −0.06500 (15) | 0.35550 (16) | 0.43280 (8) | 0.0252 (4) | |
N24 | −0.00230 (18) | 0.18370 (18) | 0.50577 (9) | 0.0343 (4) | |
C22 | −0.03717 (18) | 0.4569 (2) | 0.40205 (10) | 0.0238 (4) | |
C24 | 0.02910 (19) | 0.2928 (2) | 0.47850 (10) | 0.0270 (4) | |
C25 | 0.1475 (2) | 0.3388 (2) | 0.49531 (11) | 0.0321 (5) | |
C26 | 0.17820 (18) | 0.4461 (2) | 0.46216 (11) | 0.0293 (5) | |
C211 | 0.11361 (17) | 0.5758 (2) | 0.30691 (10) | 0.0248 (4) | |
C212 | 0.11064 (18) | 0.6716 (2) | 0.25963 (12) | 0.0322 (5) | |
C213 | 0.12672 (19) | 0.4468 (2) | 0.29044 (11) | 0.0284 (4) | |
C214 | 0.12100 (19) | 0.6397 (2) | 0.19740 (12) | 0.0369 (5) | |
C215 | 0.13327 (19) | 0.5107 (3) | 0.18102 (11) | 0.0363 (5) | |
C216 | 0.13613 (19) | 0.4140 (2) | 0.22757 (11) | 0.0321 (5) | |
C217 | 0.10436 (19) | 0.6154 (2) | 0.37514 (11) | 0.0296 (5) | |
C221 | −0.2845 (2) | 0.4511 (3) | 0.34457 (15) | 0.0455 (7) | |
N25 | 0.219 (4) | 0.322 (4) | 0.559 (2) | 0.054 (11)* | 0.05 |
O25 | 0.183 (2) | 0.216 (3) | 0.5860 (13) | 0.027 (6)* | 0.05 |
H11A | 0.3588 | 1.1695 | 0.5401 | 0.028* | |
H11B | 0.5009 | 1.1761 | 0.5463 | 0.028* | |
H112 | 0.5835 | 1.3466 | 0.6171 | 0.029* | |
H113 | 0.6273 | 1.4536 | 0.7199 | 0.032* | |
H114 | 0.5371 | 1.3825 | 0.8004 | 0.033* | |
H115 | 0.3964 | 1.2113 | 0.7759 | 0.033* | |
H116 | 0.3517 | 1.1060 | 0.6727 | 0.029* | |
H12A | 0.7932 | 0.8517 | 0.6656 | 0.059* | |
H12B | 0.8862 | 0.9647 | 0.6604 | 0.059* | |
H12C | 0.8099 | 0.8888 | 0.5946 | 0.059* | |
H14A | 0.5696 | 0.5841 | 0.5727 | 0.032* | |
H14B | 0.4329 | 0.5585 | 0.5461 | 0.032* | |
H15 | 0.2861 | 0.7366 | 0.5374 | 0.028* | |
H21A | 0.1820 | 0.6570 | 0.4007 | 0.035* | |
H21B | 0.0387 | 0.6811 | 0.3692 | 0.035* | |
H212 | 0.1014 | 0.7604 | 0.2702 | 0.039* | |
H213 | 0.1293 | 0.3802 | 0.3224 | 0.034* | |
H214 | 0.1197 | 0.7065 | 0.1658 | 0.044* | |
H215 | 0.1397 | 0.4888 | 0.1381 | 0.044* | |
H216 | 0.1445 | 0.3253 | 0.2166 | 0.039* | |
H22A | −0.2743 | 0.3574 | 0.3392 | 0.068* | |
H22B | −0.3555 | 0.4822 | 0.3091 | 0.068* | |
H22C | −0.2970 | 0.4677 | 0.3882 | 0.068* | |
H24A | −0.0788 | 0.1575 | 0.4939 | 0.041* | |
H24B | 0.0537 | 0.1389 | 0.5354 | 0.041* | |
H25 | 0.2089 | 0.2970 | 0.5298 | 0.039* | 0.95 |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N11 | 0.0215 (8) | 0.0220 (8) | 0.0183 (7) | 0.0024 (6) | 0.0081 (6) | −0.0005 (6) |
C117 | 0.0266 (9) | 0.0217 (10) | 0.0225 (9) | 0.0046 (8) | 0.0094 (8) | 0.0027 (7) |
C111 | 0.0207 (9) | 0.0198 (9) | 0.0208 (9) | 0.0048 (7) | 0.0063 (7) | 0.0010 (7) |
C112 | 0.0249 (9) | 0.0222 (10) | 0.0296 (10) | 0.0022 (8) | 0.0133 (8) | 0.0032 (8) |
C113 | 0.0224 (9) | 0.0213 (10) | 0.0364 (11) | 0.0008 (8) | 0.0088 (8) | −0.0025 (8) |
C114 | 0.0304 (10) | 0.0271 (11) | 0.0247 (10) | 0.0021 (8) | 0.0064 (8) | −0.0040 (8) |
C115 | 0.0370 (11) | 0.0269 (11) | 0.0229 (10) | −0.0013 (9) | 0.0136 (9) | 0.0008 (8) |
C116 | 0.0258 (9) | 0.0223 (10) | 0.0266 (10) | −0.0021 (8) | 0.0099 (8) | −0.0009 (8) |
C12 | 0.0189 (8) | 0.0252 (10) | 0.0149 (8) | 0.0000 (7) | 0.0052 (7) | −0.0014 (7) |
S12 | 0.0206 (2) | 0.0229 (3) | 0.0381 (3) | −0.00116 (19) | 0.0066 (2) | −0.0049 (2) |
C121 | 0.0184 (9) | 0.0338 (12) | 0.0614 (16) | 0.0034 (9) | 0.0047 (10) | −0.0111 (11) |
N13 | 0.0189 (7) | 0.0232 (8) | 0.0176 (7) | 0.0001 (6) | 0.0047 (6) | −0.0021 (6) |
C14 | 0.0241 (9) | 0.0238 (10) | 0.0160 (8) | −0.0013 (7) | 0.0092 (7) | −0.0008 (7) |
N14 | 0.0239 (8) | 0.0225 (9) | 0.0342 (9) | −0.0016 (7) | 0.0099 (7) | −0.0043 (7) |
C15 | 0.0214 (9) | 0.0266 (10) | 0.0215 (9) | −0.0038 (8) | 0.0074 (8) | −0.0020 (7) |
C16 | 0.0198 (9) | 0.0300 (10) | 0.0162 (8) | −0.0008 (8) | 0.0059 (7) | −0.0018 (7) |
O16 | 0.0201 (7) | 0.0341 (8) | 0.0297 (7) | 0.0043 (6) | 0.0065 (6) | −0.0014 (6) |
N21 | 0.0212 (8) | 0.0267 (9) | 0.0257 (8) | −0.0003 (7) | 0.0079 (7) | −0.0061 (7) |
C217 | 0.0282 (10) | 0.0249 (11) | 0.0393 (12) | −0.0052 (8) | 0.0156 (9) | −0.0079 (9) |
C211 | 0.0175 (8) | 0.0260 (10) | 0.0330 (10) | −0.0026 (7) | 0.0104 (8) | −0.0035 (8) |
C212 | 0.0221 (10) | 0.0295 (11) | 0.0441 (13) | −0.0006 (8) | 0.0085 (9) | 0.0024 (9) |
C213 | 0.0290 (10) | 0.0260 (11) | 0.0343 (11) | −0.0044 (8) | 0.0159 (9) | −0.0029 (8) |
C214 | 0.0231 (10) | 0.0478 (14) | 0.0383 (12) | −0.0001 (10) | 0.0068 (9) | 0.0144 (10) |
C215 | 0.0217 (10) | 0.0621 (16) | 0.0257 (11) | −0.0016 (10) | 0.0078 (9) | −0.0019 (10) |
C216 | 0.0278 (10) | 0.0357 (12) | 0.0358 (11) | −0.0053 (9) | 0.0139 (9) | −0.0114 (9) |
C22 | 0.0222 (9) | 0.0266 (10) | 0.0256 (9) | 0.0026 (8) | 0.0119 (8) | −0.0025 (8) |
S22 | 0.0232 (3) | 0.0368 (3) | 0.0385 (3) | 0.0011 (2) | 0.0085 (2) | 0.0158 (2) |
C221 | 0.0197 (10) | 0.0502 (15) | 0.0659 (17) | 0.0048 (10) | 0.0114 (11) | 0.0267 (13) |
N23 | 0.0257 (8) | 0.0261 (9) | 0.0256 (8) | 0.0040 (7) | 0.0105 (7) | −0.0003 (7) |
C24 | 0.0299 (10) | 0.0268 (11) | 0.0232 (9) | 0.0066 (8) | 0.0063 (8) | −0.0036 (8) |
N24 | 0.0357 (10) | 0.0291 (10) | 0.0334 (10) | 0.0051 (8) | 0.0030 (8) | 0.0063 (8) |
C25 | 0.0296 (11) | 0.0335 (12) | 0.0281 (10) | 0.0097 (9) | 0.0005 (9) | −0.0048 (9) |
C26 | 0.0224 (10) | 0.0337 (12) | 0.0314 (11) | 0.0021 (8) | 0.0071 (8) | −0.0141 (9) |
O26 | 0.0225 (8) | 0.0446 (10) | 0.0470 (10) | −0.0033 (7) | 0.0065 (7) | −0.0173 (8) |
Geometric parameters (Å, º) top
N11—C12 | 1.366 (2) | C22—N23 | 1.311 (3) |
C12—N13 | 1.304 (2) | N23—C24 | 1.373 (3) |
N13—C14 | 1.374 (2) | C24—C25 | 1.381 (3) |
C14—C15 | 1.390 (3) | C25—C26 | 1.400 (3) |
C15—C16 | 1.401 (3) | C26—N21 | 1.420 (3) |
C16—N11 | 1.435 (2) | N21—C217 | 1.464 (3) |
N11—C117 | 1.469 (2) | C22—S22 | 1.747 (2) |
C12—S12 | 1.759 (2) | S22—C221 | 1.791 (2) |
S12—C121 | 1.794 (2) | C24—N24 | 1.353 (3) |
C14—N14 | 1.342 (2) | C26—O26 | 1.246 (3) |
C16—O16 | 1.245 (2) | C217—C211 | 1.518 (3) |
C117—C111 | 1.511 (3) | C217—H21A | 0.99 |
C117—H11A | 0.99 | C217—H21B | 0.99 |
C117—H11B | 0.99 | C211—C213 | 1.387 (3) |
C111—C112 | 1.386 (3) | C211—C212 | 1.388 (3) |
C111—C116 | 1.392 (3) | C212—C214 | 1.382 (3) |
C112—C113 | 1.389 (3) | C212—H212 | 0.95 |
C112—H112 | 0.95 | C213—C216 | 1.393 (3) |
C113—C114 | 1.386 (3) | C213—H213 | 0.95 |
C113—H113 | 0.95 | C214—C215 | 1.384 (4) |
C114—C115 | 1.388 (3) | C214—H214 | 0.95 |
C114—H114 | 0.95 | C215—C216 | 1.385 (3) |
C115—C116 | 1.386 (3) | C215—H215 | 0.95 |
C115—H115 | 0.95 | C216—H216 | 0.95 |
C116—H116 | 0.95 | C221—H22A | 0.98 |
C121—H12A | 0.98 | C221—H22B | 0.98 |
C121—H12B | 0.98 | C221—H22C | 0.98 |
C121—H12C | 0.98 | N24—H24A | 0.88 |
N14—H14A | 0.88 | N24—H24B | 0.88 |
N14—H14B | 0.88 | C25—N25 | 1.36 (5) |
C15—H15 | 0.95 | C25—H25 | 0.95 |
N21—C22 | 1.376 (2) | N25—O25 | 1.34 (6) |
| | | |
C12—N11—C16 | 120.07 (16) | C26—N21—C217 | 118.54 (17) |
C12—N11—C117 | 120.82 (16) | N21—C217—C211 | 113.38 (16) |
C16—N11—C117 | 119.02 (15) | N21—C217—H21A | 108.9 |
N11—C117—C111 | 114.47 (15) | C211—C217—H21A | 108.9 |
N11—C117—H11A | 108.6 | N21—C217—H21B | 108.9 |
C111—C117—H11A | 108.6 | C211—C217—H21B | 108.9 |
N11—C117—H11B | 108.6 | H21A—C217—H21B | 107.7 |
C111—C117—H11B | 108.6 | C213—C211—C212 | 118.7 (2) |
H11A—C117—H11B | 107.6 | C213—C211—C217 | 122.15 (19) |
C112—C111—C116 | 118.93 (18) | C212—C211—C217 | 119.14 (19) |
C112—C111—C117 | 119.53 (17) | C214—C212—C211 | 120.9 (2) |
C116—C111—C117 | 121.54 (17) | C214—C212—H212 | 119.6 |
C111—C112—C113 | 120.96 (18) | C211—C212—H212 | 119.6 |
C111—C112—H112 | 119.5 | C211—C213—C216 | 120.7 (2) |
C113—C112—H112 | 119.5 | C211—C213—H213 | 119.7 |
C114—C113—C112 | 119.63 (19) | C216—C213—H213 | 119.7 |
C114—C113—H113 | 120.2 | C212—C214—C215 | 120.2 (2) |
C112—C113—H113 | 120.2 | C212—C214—H214 | 119.9 |
C113—C114—C115 | 119.94 (19) | C215—C214—H214 | 119.9 |
C113—C114—H114 | 120.0 | C214—C215—C216 | 119.6 (2) |
C115—C114—H114 | 120.0 | C214—C215—H215 | 120.2 |
C116—C115—C114 | 120.06 (19) | C216—C215—H215 | 120.2 |
C116—C115—H115 | 120.0 | C215—C216—C213 | 119.9 (2) |
C114—C115—H115 | 120.0 | C215—C216—H216 | 120.1 |
C115—C116—C111 | 120.46 (18) | C213—C216—H216 | 120.1 |
C115—C116—H116 | 119.8 | N23—C22—N21 | 124.36 (18) |
C111—C116—H116 | 119.8 | N23—C22—S22 | 119.91 (15) |
N13—C12—N11 | 124.79 (17) | N21—C22—S22 | 115.70 (15) |
N13—C12—S12 | 118.85 (14) | C22—S22—C221 | 101.28 (10) |
N11—C12—S12 | 116.36 (14) | S22—C221—H22A | 109.5 |
C12—S12—C121 | 100.60 (10) | S22—C221—H22B | 109.5 |
S12—C121—H12A | 109.5 | H22A—C221—H22B | 109.5 |
S12—C121—H12B | 109.5 | S22—C221—H22C | 109.5 |
H12A—C121—H12B | 109.5 | H22A—C221—H22C | 109.5 |
S12—C121—H12C | 109.5 | H22B—C221—H22C | 109.5 |
H12A—C121—H12C | 109.5 | C22—N23—C24 | 117.32 (17) |
H12B—C121—H12C | 109.5 | N24—C24—N23 | 115.45 (18) |
C12—N13—C14 | 117.11 (16) | N24—C24—C25 | 122.59 (19) |
N14—C14—N13 | 114.53 (16) | N23—C24—C25 | 122.0 (2) |
N14—C14—C15 | 123.21 (18) | C24—N24—H24A | 120.0 |
N13—C14—C15 | 122.26 (17) | C24—N24—H24B | 120.0 |
C14—N14—H14A | 120.0 | H24A—N24—H24B | 120.0 |
C14—N14—H14B | 120.0 | N25—C25—C24 | 118 (2) |
H14A—N14—H14B | 120.0 | N25—C25—C26 | 115 (2) |
C14—C15—C16 | 120.48 (18) | C24—C25—C26 | 120.90 (19) |
C14—C15—H15 | 119.8 | C24—C25—H25 | 119.6 |
C16—C15—H15 | 119.8 | C26—C25—H25 | 119.6 |
O16—C16—C15 | 126.54 (18) | O25—N25—C25 | 110 (4) |
O16—C16—N11 | 118.59 (18) | O26—C26—C25 | 127.4 (2) |
C15—C16—N11 | 114.87 (16) | O26—C26—N21 | 117.3 (2) |
C22—N21—C26 | 119.99 (18) | C25—C26—N21 | 115.29 (18) |
C22—N21—C217 | 121.38 (17) | | |
| | | |
C12—N11—C117—C111 | −76.8 (2) | N21—C217—C211—C212 | 166.01 (17) |
C16—N11—C117—C111 | 106.69 (19) | C213—C211—C212—C214 | −0.3 (3) |
N11—C117—C111—C112 | 131.59 (18) | C217—C211—C212—C214 | 178.83 (19) |
N11—C117—C111—C116 | −47.6 (2) | C212—C211—C213—C216 | −0.3 (3) |
C116—C111—C112—C113 | 1.0 (3) | C217—C211—C213—C216 | −179.37 (19) |
C117—C111—C112—C113 | −178.16 (18) | C211—C212—C214—C215 | 0.7 (3) |
C111—C112—C113—C114 | 0.4 (3) | C212—C214—C215—C216 | −0.5 (3) |
C112—C113—C114—C115 | −1.6 (3) | C214—C215—C216—C213 | 0.0 (3) |
C113—C114—C115—C116 | 1.3 (3) | C211—C213—C216—C215 | 0.5 (3) |
C114—C115—C116—C111 | 0.2 (3) | C26—N21—C22—N23 | 0.2 (3) |
C112—C111—C116—C115 | −1.3 (3) | C217—N21—C22—N23 | 176.66 (18) |
C117—C111—C116—C115 | 177.84 (18) | C26—N21—C22—S22 | −177.80 (14) |
C16—N11—C12—N13 | 5.1 (3) | C217—N21—C22—S22 | −1.3 (2) |
C117—N11—C12—N13 | −171.31 (17) | N23—C22—S22—C221 | 5.9 (2) |
C16—N11—C12—S12 | −174.06 (13) | N21—C22—S22—C221 | −176.01 (16) |
C117—N11—C12—S12 | 9.5 (2) | N21—C22—N23—C24 | −1.9 (3) |
N13—C12—S12—C121 | 5.49 (18) | S22—C22—N23—C24 | 176.03 (14) |
N11—C12—S12—C121 | −175.25 (15) | C22—N23—C24—N24 | −175.74 (18) |
N11—C12—N13—C14 | 0.5 (3) | C22—N23—C24—C25 | 4.4 (3) |
S12—C12—N13—C14 | 179.66 (13) | N24—C24—C25—N25 | −33.9 (18) |
C12—N13—C14—N14 | 174.47 (16) | N23—C24—C25—N25 | 145.9 (18) |
C12—N13—C14—C15 | −5.6 (3) | N24—C24—C25—C26 | 174.86 (19) |
N14—C14—C15—C16 | −175.05 (18) | N23—C24—C25—C26 | −5.3 (3) |
N13—C14—C15—C16 | 5.1 (3) | C24—C25—N25—O25 | 28 (2) |
C14—C15—C16—O16 | 179.93 (18) | C26—C25—N25—O25 | −179.5 (13) |
C14—C15—C16—N11 | 0.6 (3) | N25—C25—C26—O26 | 32.4 (16) |
C12—N11—C16—O16 | 175.19 (16) | C24—C25—C26—O26 | −175.5 (2) |
C117—N11—C16—O16 | −8.3 (2) | N25—C25—C26—N21 | −148.8 (16) |
C12—N11—C16—C15 | −5.4 (2) | C24—C25—C26—N21 | 3.3 (3) |
C117—N11—C16—C15 | 171.14 (16) | C22—N21—C26—O26 | 178.08 (17) |
C22—N21—C217—C211 | −79.4 (2) | C217—N21—C26—O26 | 1.5 (3) |
C26—N21—C217—C211 | 97.1 (2) | C22—N21—C26—C25 | −0.8 (3) |
N21—C217—C211—C213 | −14.9 (3) | C217—N21—C26—C25 | −177.44 (17) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N14—H14A···O26i | 0.88 | 2.28 | 3.029 (2) | 143 |
N14—H14B···O26 | 0.88 | 2.10 | 2.896 (2) | 151 |
N24—H24A···O16ii | 0.88 | 2.29 | 3.124 (2) | 157 |
N24—H24B···O16iii | 0.88 | 2.62 | 3.330 (2) | 138 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x, −y+1, −z+1; (iii) x, y−1, z. |
(III) 4-Amino-1-benzyl-2-(methylsulfanyl)-5-nitrosopyrimidin-6(1
H)-one
top
Crystal data top
C12H12N4O2S | Z = 4 |
Mr = 276.33 | F(000) = 576 |
Triclinic, P1 | Dx = 1.461 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 10.5035 (3) Å | Cell parameters from 4417 reflections |
b = 10.8741 (3) Å | θ = 3.0–25.0° |
c = 11.8261 (4) Å | µ = 0.26 mm−1 |
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 anode | 3498 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.094 |
ϕ scans, and ω scans with κ offsets | θmax = 25.0°, θmin = 3.0° |
Absorption correction: multi-scan DENZO-SMN (Otwinowski & Minor, 1997) | h = −12→12 |
Tmin = 0.920, Tmax = 0.991 | k = −12→12 |
24784 measured reflections | l = −14→14 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.107 | H-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 parameters | Δρmax = 0.21 e Å−3 |
0 restraints | Δρmin = −0.31 e Å−3 |
Crystal data top
C12H12N4O2S | γ = 93.7181 (14)° |
Mr = 276.33 | V = 1256.49 (7) Å3 |
Triclinic, P1 | Z = 4 |
a = 10.5035 (3) Å | Mo Kα radiation |
b = 10.8741 (3) Å | µ = 0.26 mm−1 |
c = 11.8261 (4) Å | T = 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 = 0.991 | Rint = 0.094 |
24784 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.107 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.21 e Å−3 |
4417 reflections | Δρmin = −0.31 e Å−3 |
345 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
S12 | −0.26530 (6) | 0.57441 (6) | 0.64908 (5) | 0.02699 (17) | |
O15 | 0.10003 (15) | 0.16677 (16) | 0.79411 (14) | 0.0305 (4) | |
O16 | −0.13462 (15) | 0.40714 (16) | 0.97953 (13) | 0.0269 (4) | |
N11 | −0.18937 (16) | 0.48009 (17) | 0.82222 (15) | 0.0186 (4) | |
N13 | −0.10917 (17) | 0.39198 (18) | 0.63424 (16) | 0.0205 (4) | |
N14 | 0.01962 (17) | 0.22653 (18) | 0.60112 (17) | 0.0250 (4) | |
N15 | 0.02623 (17) | 0.24354 (18) | 0.85497 (16) | 0.0229 (4) | |
C12 | −0.1775 (2) | 0.4719 (2) | 0.70564 (19) | 0.0192 (5) | |
C14 | −0.04164 (19) | 0.3107 (2) | 0.67778 (19) | 0.0190 (5) | |
C15 | −0.04068 (19) | 0.3155 (2) | 0.80047 (18) | 0.0177 (5) | |
C16 | −0.1214 (2) | 0.4010 (2) | 0.87679 (19) | 0.0192 (5) | |
C111 | −0.4107 (2) | 0.5422 (2) | 0.86319 (19) | 0.0208 (5) | |
C112 | −0.4873 (2) | 0.6355 (2) | 0.8450 (2) | 0.0282 (5) | |
C113 | −0.6206 (2) | 0.6073 (3) | 0.8171 (2) | 0.0334 (6) | |
C114 | −0.6779 (2) | 0.4857 (3) | 0.8066 (2) | 0.0340 (6) | |
C115 | −0.6030 (2) | 0.3921 (2) | 0.8245 (2) | 0.0322 (6) | |
C116 | −0.4700 (2) | 0.4203 (2) | 0.8533 (2) | 0.0265 (5) | |
C117 | −0.2670 (2) | 0.5761 (2) | 0.89777 (19) | 0.0205 (5) | |
C121 | −0.2054 (3) | 0.5476 (2) | 0.5065 (2) | 0.0318 (6) | |
S22 | 0.33254 (5) | −0.04886 (6) | 0.03064 (5) | 0.02635 (17) | |
O25 | −0.11416 (15) | 0.28444 (16) | 0.30060 (14) | 0.0310 (4) | |
O26 | 0.12194 (15) | 0.05295 (16) | 0.39780 (13) | 0.0282 (4) | |
N21 | 0.20812 (16) | 0.00550 (17) | 0.22155 (15) | 0.0186 (4) | |
N23 | 0.13959 (16) | 0.09661 (17) | 0.07124 (15) | 0.0192 (4) | |
N24 | −0.02023 (16) | 0.23108 (18) | 0.09427 (16) | 0.0211 (4) | |
N25 | −0.03844 (18) | 0.21262 (19) | 0.33404 (17) | 0.0254 (4) | |
C22 | 0.21383 (19) | 0.0260 (2) | 0.11387 (19) | 0.0193 (5) | |
C24 | 0.05003 (19) | 0.1582 (2) | 0.13947 (19) | 0.0181 (5) | |
C25 | 0.0373 (2) | 0.1467 (2) | 0.25404 (18) | 0.0191 (5) | |
C26 | 0.1205 (2) | 0.0682 (2) | 0.29980 (19) | 0.0209 (5) | |
C211 | 0.4293 (2) | 0.0051 (2) | 0.32323 (19) | 0.0194 (5) | |
C212 | 0.4515 (2) | 0.1402 (2) | 0.3548 (2) | 0.0310 (6) | |
C213 | 0.5726 (3) | 0.2054 (3) | 0.4088 (2) | 0.0391 (7) | |
C214 | 0.6716 (2) | 0.1374 (3) | 0.4312 (2) | 0.0385 (7) | |
C215 | 0.6504 (2) | 0.0033 (3) | 0.4009 (2) | 0.0354 (6) | |
C216 | 0.5297 (2) | −0.0631 (2) | 0.3471 (2) | 0.0266 (5) | |
C217 | 0.2991 (2) | −0.0706 (2) | 0.2654 (2) | 0.0215 (5) | |
C221 | 0.3068 (2) | 0.0015 (3) | −0.0993 (2) | 0.0303 (6) | |
H11A | −0.2433 | 0.6633 | 0.8921 | 0.025* | |
H11B | −0.2440 | 0.5835 | 0.9835 | 0.025* | |
H112 | −0.4482 | 0.7194 | 0.8517 | 0.034* | |
H113 | −0.6720 | 0.6719 | 0.8054 | 0.040* | |
H114 | −0.7688 | 0.4661 | 0.7871 | 0.041* | |
H115 | −0.6426 | 0.3082 | 0.8172 | 0.039* | |
H116 | −0.4192 | 0.3557 | 0.8662 | 0.032* | |
H12A | −0.2222 | 0.4542 | 0.4568 | 0.048* | |
H12B | −0.1124 | 0.5745 | 0.5216 | 0.048* | |
H12C | −0.2491 | 0.5996 | 0.4637 | 0.048* | |
H14A | 0.0157 | 0.2247 | 0.5258 | 0.030* | |
H14B | 0.0646 | 0.1719 | 0.6250 | 0.030* | |
H21A | 0.3112 | −0.1492 | 0.1964 | 0.026* | |
H21B | 0.2612 | −0.1014 | 0.3254 | 0.026* | |
H212 | 0.3834 | 0.1884 | 0.3394 | 0.037* | |
H213 | 0.5868 | 0.2981 | 0.4304 | 0.047* | |
H214 | 0.7546 | 0.1824 | 0.4676 | 0.046* | |
H215 | 0.7189 | −0.0441 | 0.4168 | 0.042* | |
H216 | 0.5160 | −0.1557 | 0.3267 | 0.032* | |
H22A | 0.2167 | −0.0237 | −0.1371 | 0.045* | |
H22B | 0.3633 | −0.0413 | −0.1578 | 0.045* | |
H22C | 0.3262 | 0.0971 | −0.0737 | 0.045* | |
H24A | −0.0081 | 0.2379 | 0.0241 | 0.025* | |
H24B | −0.0794 | 0.2730 | 0.1342 | 0.025* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N11 | 0.0191 (9) | 0.0197 (10) | 0.0180 (9) | 0.0034 (7) | 0.0039 (7) | 0.0072 (8) |
C117 | 0.0229 (11) | 0.0182 (12) | 0.0197 (11) | 0.0063 (9) | 0.0049 (9) | 0.0044 (9) |
C111 | 0.0218 (11) | 0.0222 (12) | 0.0171 (11) | 0.0055 (9) | 0.0076 (9) | 0.0031 (9) |
C112 | 0.0296 (13) | 0.0273 (13) | 0.0292 (13) | 0.0077 (10) | 0.0073 (10) | 0.0100 (11) |
C113 | 0.0270 (13) | 0.0418 (16) | 0.0307 (13) | 0.0151 (12) | 0.0032 (11) | 0.0100 (12) |
C114 | 0.0204 (12) | 0.0487 (17) | 0.0249 (13) | 0.0076 (12) | 0.0051 (10) | 0.0011 (12) |
C115 | 0.0302 (13) | 0.0289 (14) | 0.0295 (13) | −0.0048 (11) | 0.0112 (11) | −0.0010 (11) |
C116 | 0.0289 (13) | 0.0246 (13) | 0.0260 (12) | 0.0064 (10) | 0.0087 (10) | 0.0066 (10) |
C12 | 0.0200 (11) | 0.0185 (11) | 0.0174 (11) | −0.0026 (9) | 0.0000 (9) | 0.0058 (9) |
S12 | 0.0348 (3) | 0.0251 (3) | 0.0245 (3) | 0.0083 (3) | 0.0035 (3) | 0.0125 (3) |
C121 | 0.0440 (15) | 0.0316 (14) | 0.0232 (12) | 0.0033 (11) | 0.0039 (11) | 0.0146 (11) |
N13 | 0.0220 (10) | 0.0215 (10) | 0.0185 (9) | 0.0017 (8) | 0.0030 (8) | 0.0078 (8) |
C14 | 0.0158 (11) | 0.0201 (12) | 0.0193 (11) | −0.0041 (9) | 0.0037 (9) | 0.0051 (9) |
N14 | 0.0278 (10) | 0.0288 (11) | 0.0212 (10) | 0.0087 (9) | 0.0097 (8) | 0.0094 (9) |
C15 | 0.0170 (11) | 0.0197 (11) | 0.0161 (10) | 0.0006 (9) | 0.0019 (8) | 0.0063 (9) |
N15 | 0.0214 (10) | 0.0241 (10) | 0.0222 (10) | 0.0062 (8) | 0.0032 (8) | 0.0059 (8) |
O15 | 0.0299 (9) | 0.0361 (10) | 0.0281 (9) | 0.0163 (8) | 0.0080 (7) | 0.0111 (8) |
C16 | 0.0175 (11) | 0.0203 (12) | 0.0197 (12) | 0.0011 (9) | 0.0019 (9) | 0.0073 (9) |
O16 | 0.0317 (9) | 0.0357 (10) | 0.0190 (8) | 0.0124 (7) | 0.0103 (7) | 0.0134 (7) |
N21 | 0.0166 (9) | 0.0215 (10) | 0.0188 (9) | 0.0037 (7) | 0.0016 (7) | 0.0086 (8) |
C217 | 0.0201 (11) | 0.0195 (12) | 0.0258 (12) | 0.0045 (9) | 0.0008 (9) | 0.0093 (10) |
C211 | 0.0169 (11) | 0.0258 (13) | 0.0172 (11) | 0.0028 (9) | 0.0037 (9) | 0.0093 (9) |
C212 | 0.0273 (13) | 0.0281 (14) | 0.0366 (14) | 0.0003 (10) | −0.0019 (11) | 0.0125 (11) |
C213 | 0.0379 (15) | 0.0354 (16) | 0.0378 (15) | −0.0136 (12) | −0.0034 (12) | 0.0105 (13) |
C214 | 0.0224 (13) | 0.064 (2) | 0.0233 (13) | −0.0101 (13) | −0.0002 (10) | 0.0111 (13) |
C215 | 0.0212 (12) | 0.063 (2) | 0.0215 (12) | 0.0117 (12) | 0.0021 (10) | 0.0131 (12) |
C216 | 0.0277 (13) | 0.0322 (14) | 0.0204 (12) | 0.0126 (10) | 0.0055 (10) | 0.0074 (10) |
C22 | 0.0137 (10) | 0.0219 (12) | 0.0192 (11) | 0.0009 (9) | 0.0002 (9) | 0.0039 (9) |
S22 | 0.0202 (3) | 0.0366 (4) | 0.0226 (3) | 0.0113 (2) | 0.0060 (2) | 0.0082 (3) |
C221 | 0.0239 (12) | 0.0474 (16) | 0.0208 (12) | 0.0089 (11) | 0.0070 (10) | 0.0111 (11) |
N23 | 0.0175 (9) | 0.0225 (10) | 0.0167 (9) | 0.0028 (8) | 0.0033 (7) | 0.0050 (8) |
C24 | 0.0154 (10) | 0.0179 (11) | 0.0182 (11) | −0.0014 (9) | 0.0000 (8) | 0.0041 (9) |
N24 | 0.0193 (9) | 0.0283 (11) | 0.0199 (9) | 0.0080 (8) | 0.0067 (8) | 0.0115 (8) |
C25 | 0.0170 (11) | 0.0233 (12) | 0.0159 (11) | 0.0019 (9) | 0.0039 (9) | 0.0047 (9) |
N25 | 0.0223 (10) | 0.0307 (11) | 0.0251 (10) | 0.0082 (8) | 0.0048 (8) | 0.0106 (9) |
O25 | 0.0293 (9) | 0.0384 (10) | 0.0288 (9) | 0.0171 (8) | 0.0078 (7) | 0.0126 (8) |
C26 | 0.0175 (11) | 0.0247 (12) | 0.0196 (11) | 0.0014 (9) | 0.0034 (9) | 0.0065 (10) |
O26 | 0.0295 (9) | 0.0401 (10) | 0.0210 (8) | 0.0109 (7) | 0.0071 (7) | 0.0160 (8) |
Geometric parameters (Å, º) top
N11—C12 | 1.372 (3) | N21—C22 | 1.372 (3) |
C12—N13 | 1.306 (3) | C22—N23 | 1.305 (3) |
N13—C14 | 1.362 (3) | N23—C24 | 1.368 (3) |
C14—C15 | 1.433 (3) | C24—C25 | 1.422 (3) |
C15—C16 | 1.452 (3) | C25—C26 | 1.445 (3) |
C16—N11 | 1.419 (3) | C26—N21 | 1.420 (3) |
N11—C117 | 1.483 (3) | N21—C217 | 1.466 (3) |
C12—S12 | 1.743 (2) | C22—S22 | 1.747 (2) |
S12—C121 | 1.804 (2) | S22—C221 | 1.796 (2) |
C14—N14 | 1.312 (3) | C24—N24 | 1.316 (3) |
C15—N15 | 1.353 (3) | C25—N25 | 1.352 (3) |
N15—O15 | 1.273 (2) | N25—O25 | 1.272 (2) |
C16—O16 | 1.218 (3) | C26—O26 | 1.223 (3) |
C117—C111 | 1.507 (3) | C217—C211 | 1.511 (3) |
C117—H11A | 0.99 | C217—H21A | 0.99 |
C117—H11B | 0.99 | C217—H21B | 0.99 |
C111—C116 | 1.390 (3) | C211—C216 | 1.385 (3) |
C111—C112 | 1.392 (3) | C211—C212 | 1.385 (3) |
C112—C113 | 1.391 (3) | C212—C213 | 1.388 (3) |
C112—H112 | 0.95 | C212—H212 | 0.95 |
C113—C114 | 1.377 (4) | C213—C214 | 1.368 (4) |
C113—H113 | 0.95 | C213—H213 | 0.95 |
C114—C115 | 1.382 (4) | C214—C215 | 1.375 (4) |
C114—H114 | 0.95 | C214—H214 | 0.95 |
C115—C116 | 1.389 (3) | C215—C216 | 1.387 (3) |
C115—H115 | 0.95 | C215—H215 | 0.95 |
C116—H116 | 0.95 | C216—H216 | 0.95 |
C121—H12A | 0.98 | C221—H22A | 0.98 |
C121—H12B | 0.98 | C221—H22B | 0.98 |
C121—H12C | 0.98 | C221—H22C | 0.98 |
N14—H14A | 0.88 | N24—H24A | 0.88 |
N14—H14B | 0.88 | N24—H24B | 0.88 |
| | | |
C12—N11—C16 | 120.61 (17) | C22—N21—C26 | 120.43 (17) |
C12—N11—C117 | 121.63 (17) | C22—N21—C217 | 121.77 (17) |
C16—N11—C117 | 117.67 (17) | C26—N21—C217 | 117.55 (17) |
N11—C117—C111 | 114.61 (17) | N21—C217—C211 | 113.89 (17) |
N11—C117—H11A | 108.6 | N21—C217—H21A | 108.8 |
C111—C117—H11A | 108.6 | C211—C217—H21A | 108.8 |
N11—C117—H11B | 108.6 | N21—C217—H21B | 108.8 |
C111—C117—H11B | 108.6 | C211—C217—H21B | 108.8 |
H11A—C117—H11B | 107.6 | H21A—C217—H21B | 107.7 |
C116—C111—C112 | 118.7 (2) | C216—C211—C212 | 118.9 (2) |
C116—C111—C117 | 121.28 (19) | C216—C211—C217 | 118.6 (2) |
C112—C111—C117 | 120.0 (2) | C212—C211—C217 | 122.50 (19) |
C113—C112—C111 | 120.7 (2) | C211—C212—C213 | 120.3 (2) |
C113—C112—H112 | 119.6 | C211—C212—H212 | 119.9 |
C111—C112—H112 | 119.6 | C213—C212—H212 | 119.9 |
C114—C113—C112 | 119.9 (2) | C214—C213—C212 | 120.6 (3) |
C114—C113—H113 | 120.0 | C214—C213—H213 | 119.7 |
C112—C113—H113 | 120.0 | C212—C213—H213 | 119.7 |
C113—C114—C115 | 120.0 (2) | C213—C214—C215 | 119.6 (2) |
C113—C114—H114 | 120.0 | C213—C214—H214 | 120.2 |
C115—C114—H114 | 120.0 | C215—C214—H214 | 120.2 |
C114—C115—C116 | 120.3 (2) | C214—C215—C216 | 120.5 (2) |
C114—C115—H115 | 119.9 | C214—C215—H215 | 119.7 |
C116—C115—H115 | 119.9 | C216—C215—H215 | 119.7 |
C115—C116—C111 | 120.4 (2) | C211—C216—C215 | 120.2 (2) |
C115—C116—H116 | 119.8 | C211—C216—H216 | 119.9 |
C111—C116—H116 | 119.8 | C215—C216—H216 | 119.9 |
N13—C12—N11 | 125.35 (19) | N23—C22—N21 | 125.28 (19) |
N13—C12—S12 | 118.36 (16) | N23—C22—S22 | 118.95 (16) |
N11—C12—S12 | 116.27 (16) | N21—C22—S22 | 115.76 (15) |
C12—S12—C121 | 101.02 (11) | C22—S22—C221 | 101.30 (11) |
S12—C121—H12A | 109.5 | S22—C221—H22A | 109.5 |
S12—C121—H12B | 109.5 | S22—C221—H22B | 109.5 |
H12A—C121—H12B | 109.5 | H22A—C221—H22B | 109.5 |
S12—C121—H12C | 109.5 | S22—C221—H22C | 109.5 |
H12A—C121—H12C | 109.5 | H22A—C221—H22C | 109.5 |
H12B—C121—H12C | 109.5 | H22B—C221—H22C | 109.5 |
C12—N13—C14 | 118.48 (18) | C22—N23—C24 | 118.21 (18) |
N14—C14—N13 | 116.64 (19) | N24—C24—N23 | 116.00 (19) |
N14—C14—C15 | 122.06 (19) | N24—C24—C25 | 122.43 (19) |
N13—C14—C15 | 121.28 (19) | N23—C24—C25 | 121.53 (19) |
C14—N14—H14A | 120.0 | C24—N24—H24A | 120.0 |
C14—N14—H14B | 120.0 | C24—N24—H24B | 120.0 |
H14A—N14—H14B | 120.0 | H24A—N24—H24B | 120.0 |
N15—C15—C14 | 126.59 (19) | N25—C25—C24 | 126.61 (19) |
N15—C15—C16 | 114.08 (18) | N25—C25—C26 | 113.64 (18) |
C14—C15—C16 | 119.29 (18) | C24—C25—C26 | 119.44 (19) |
O15—N15—C15 | 117.81 (18) | O25—N25—C25 | 117.41 (18) |
O16—C16—N11 | 120.09 (19) | O26—C26—N21 | 118.89 (19) |
O16—C16—C15 | 125.09 (19) | O26—C26—C25 | 126.1 (2) |
N11—C16—C15 | 114.81 (18) | N21—C26—C25 | 115.04 (18) |
| | | |
C12—N11—C117—C111 | 73.9 (3) | C22—N21—C217—C211 | 79.1 (2) |
C16—N11—C117—C111 | −109.5 (2) | C26—N21—C217—C211 | −95.2 (2) |
N11—C117—C111—C116 | 53.0 (3) | N21—C217—C211—C216 | −168.10 (19) |
N11—C117—C111—C112 | −129.5 (2) | N21—C217—C211—C212 | 12.9 (3) |
C116—C111—C112—C113 | −0.2 (3) | C216—C211—C212—C213 | 0.4 (3) |
C117—C111—C112—C113 | −177.8 (2) | C217—C211—C212—C213 | 179.4 (2) |
C111—C112—C113—C114 | −0.4 (3) | C211—C212—C213—C214 | 0.2 (4) |
C112—C113—C114—C115 | 0.4 (4) | C212—C213—C214—C215 | −0.6 (4) |
C113—C114—C115—C116 | 0.1 (4) | C213—C214—C215—C216 | 0.4 (4) |
C114—C115—C116—C111 | −0.6 (3) | C212—C211—C216—C215 | −0.6 (3) |
C112—C111—C116—C115 | 0.7 (3) | C217—C211—C216—C215 | −179.6 (2) |
C117—C111—C116—C115 | 178.2 (2) | C214—C215—C216—C211 | 0.2 (3) |
C16—N11—C12—N13 | 2.0 (3) | C26—N21—C22—N23 | −3.1 (3) |
C117—N11—C12—N13 | 178.59 (19) | C217—N21—C22—N23 | −177.23 (19) |
C16—N11—C12—S12 | −179.77 (15) | C26—N21—C22—S22 | 176.19 (15) |
C117—N11—C12—S12 | −3.2 (3) | C217—N21—C22—S22 | 2.1 (3) |
N13—C12—S12—C121 | −8.9 (2) | N23—C22—S22—C221 | −0.7 (2) |
N11—C12—S12—C121 | 172.74 (17) | N21—C22—S22—C221 | 179.95 (17) |
N11—C12—N13—C14 | −1.1 (3) | N21—C22—N23—C24 | 1.4 (3) |
S12—C12—N13—C14 | −179.28 (15) | S22—C22—N23—C24 | −177.83 (15) |
C12—N13—C14—N14 | 176.06 (19) | C22—N23—C24—N24 | 178.24 (18) |
C12—N13—C14—C15 | −2.5 (3) | C22—N23—C24—C25 | 0.2 (3) |
N14—C14—C15—N15 | 4.2 (3) | N24—C24—C25—N25 | −4.8 (3) |
N13—C14—C15—N15 | −177.4 (2) | N23—C24—C25—N25 | 173.1 (2) |
N14—C14—C15—C16 | −173.43 (19) | N24—C24—C25—C26 | −178.03 (19) |
N13—C14—C15—C16 | 5.0 (3) | N23—C24—C25—C26 | −0.1 (3) |
C14—C15—N15—O15 | 2.8 (3) | C24—C25—N25—O25 | 6.2 (3) |
C16—C15—N15—O15 | −179.49 (18) | C26—C25—N25—O25 | 179.72 (18) |
C12—N11—C16—O16 | −178.5 (2) | C22—N21—C26—O26 | −176.5 (2) |
C117—N11—C16—O16 | 4.8 (3) | C217—N21—C26—O26 | −2.2 (3) |
C12—N11—C16—C15 | 0.6 (3) | C22—N21—C26—C25 | 2.9 (3) |
C117—N11—C16—C15 | −176.07 (18) | C217—N21—C26—C25 | 177.26 (17) |
N15—C15—C16—O16 | −2.7 (3) | N25—C25—C26—O26 | 3.9 (3) |
C14—C15—C16—O16 | 175.2 (2) | C24—C25—C26—O26 | 178.0 (2) |
N15—C15—C16—N11 | 178.20 (17) | N25—C25—C26—N21 | −175.47 (18) |
C14—C15—C16—N11 | −3.9 (3) | C24—C25—C26—N21 | −1.4 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N14—H14A···N25 | 0.88 | 2.23 | 3.100 (3) | 168 |
N14—H14A···O26 | 0.88 | 2.40 | 2.879 (2) | 114 |
N14—H14B···O15 | 0.88 | 2.01 | 2.642 (2) | 128 |
N24—H24A···N15i | 0.88 | 2.09 | 2.970 (3) | 177 |
N24—H24A···O16i | 0.88 | 2.50 | 2.938 (2) | 112 |
N24—H24B···O25 | 0.88 | 2.01 | 2.631 (2) | 127 |
Symmetry code: (i) x, y, z−1. |
(IV) 4-Amino-6-benzyloxy-2-(methylsulfanyl)pyrimidine
top
Crystal data top
C12H13N3OS | F(000) = 520 |
Mr = 247.31 | Dx = 1.367 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 1177 reflections |
a = 15.747 (2) Å | θ = 2.7–20.5° |
b = 5.1044 (7) Å | µ = 0.26 mm−1 |
c = 15.501 (3) Å | T = 120 K |
β = 105.286 (5)° | Needle, colourless |
V = 1201.9 (3) Å3 | 0.60 × 0.04 × 0.03 mm |
Z = 4 | |
Data collection top
Nonius KappaCCD diffractometer | 1177 independent reflections |
Radiation source: rotating anode | 1006 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.147 |
ϕ scans, and ω scans with κ offsets | θmax = 20.5°, θmin = 2.7° |
Absorption correction: multi-scan DENZO-SMN (Otwinowski & Minor, 1997) | h = −15→15 |
Tmin = 0.862, Tmax = 0.992 | k = −5→5 |
9738 measured reflections | l = −14→15 |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.077 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.155 | H-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 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.35 e Å−3 |
Crystal data top
C12H13N3OS | V = 1201.9 (3) Å3 |
Mr = 247.31 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 15.747 (2) Å | µ = 0.26 mm−1 |
b = 5.1044 (7) Å | T = 120 K |
c = 15.501 (3) Å | 0.60 × 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 = 0.992 | Rint = 0.147 |
9738 measured reflections | θmax = 20.5° |
Refinement top
R[F2 > 2σ(F2)] = 0.077 | 0 restraints |
wR(F2) = 0.155 | H-atom parameters constrained |
S = 1.22 | Δρmax = 0.32 e Å−3 |
1177 reflections | Δρmin = −0.35 e Å−3 |
155 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
S2 | 0.27418 (12) | 0.1502 (4) | 0.49135 (12) | 0.0270 (6) | |
O6 | 0.3641 (3) | −0.3141 (9) | 0.2472 (3) | 0.0235 (12) | |
N1 | 0.3258 (3) | −0.1023 (10) | 0.3632 (3) | 0.0169 (14) | |
N3 | 0.4194 (4) | 0.2350 (10) | 0.4443 (3) | 0.0195 (14) | |
N4 | 0.5508 (3) | 0.3420 (11) | 0.4124 (4) | 0.0252 (15) | |
C2 | 0.3481 (4) | 0.0834 (13) | 0.4247 (4) | 0.0175 (17) | |
C4 | 0.4774 (4) | 0.1946 (13) | 0.3940 (4) | 0.0192 (17) | |
C5 | 0.4600 (4) | 0.0042 (13) | 0.3257 (4) | 0.0212 (18) | |
C6 | 0.3834 (4) | −0.1335 (13) | 0.3146 (4) | 0.0196 (17) | |
C21 | 0.1850 (4) | −0.0671 (14) | 0.4410 (5) | 0.0274 (19) | |
C61 | 0.2014 (4) | −0.3409 (13) | 0.2024 (4) | 0.0180 (17) | |
C62 | 0.1258 (5) | −0.4274 (14) | 0.2224 (5) | 0.0283 (19) | |
C63 | 0.0444 (5) | −0.3127 (16) | 0.1852 (5) | 0.035 (2) | |
C64 | 0.0377 (5) | −0.1017 (15) | 0.1269 (5) | 0.034 (2) | |
C65 | 0.1130 (5) | −0.0166 (15) | 0.1062 (5) | 0.033 (2) | |
C66 | 0.1945 (5) | −0.1309 (14) | 0.1431 (4) | 0.0266 (18) | |
C67 | 0.2874 (4) | −0.4794 (13) | 0.2411 (5) | 0.0246 (18) | |
H21A | 0.1633 | −0.0270 | 0.3771 | 0.041* | |
H21B | 0.1372 | −0.0440 | 0.4700 | 0.041* | |
H21C | 0.2058 | −0.2487 | 0.4485 | 0.041* | |
H4A | 0.5600 | 0.4590 | 0.4556 | 0.030* | |
H4B | 0.5897 | 0.3214 | 0.3813 | 0.030* | |
H5 | 0.4991 | −0.0267 | 0.2895 | 0.025* | |
H67A | 0.2885 | −0.5437 | 0.3017 | 0.030* | |
H67B | 0.2910 | −0.6337 | 0.2035 | 0.030* | |
H62 | 0.1296 | −0.5697 | 0.2627 | 0.034* | |
H63 | −0.0067 | −0.3782 | 0.1996 | 0.042* | |
H64 | −0.0173 | −0.0186 | 0.1020 | 0.041* | |
H65 | 0.1091 | 0.1246 | 0.0654 | 0.039* | |
H66 | 0.2454 | −0.0666 | 0.1280 | 0.032* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
S2 | 0.0268 (11) | 0.0283 (12) | 0.0289 (11) | −0.0019 (9) | 0.0129 (8) | −0.0051 (9) |
O6 | 0.021 (3) | 0.024 (3) | 0.026 (3) | −0.003 (2) | 0.008 (2) | −0.005 (2) |
N1 | 0.022 (3) | 0.012 (3) | 0.017 (3) | 0.003 (3) | 0.005 (3) | 0.000 (3) |
N3 | 0.024 (4) | 0.016 (3) | 0.019 (3) | 0.003 (3) | 0.006 (3) | −0.002 (3) |
N4 | 0.023 (4) | 0.028 (4) | 0.024 (3) | −0.010 (3) | 0.005 (3) | −0.011 (3) |
C2 | 0.015 (4) | 0.016 (4) | 0.020 (4) | 0.003 (3) | 0.002 (3) | 0.001 (4) |
C4 | 0.017 (4) | 0.020 (4) | 0.018 (4) | 0.006 (4) | −0.001 (3) | 0.004 (4) |
C5 | 0.016 (4) | 0.031 (5) | 0.015 (4) | −0.003 (4) | 0.000 (3) | 0.000 (4) |
C6 | 0.022 (4) | 0.018 (4) | 0.015 (4) | 0.002 (4) | −0.001 (3) | −0.003 (3) |
C21 | 0.022 (4) | 0.026 (4) | 0.035 (5) | −0.004 (3) | 0.009 (3) | 0.003 (4) |
C61 | 0.022 (4) | 0.016 (4) | 0.015 (4) | −0.001 (3) | 0.003 (3) | −0.005 (3) |
C62 | 0.032 (5) | 0.029 (5) | 0.023 (5) | −0.009 (4) | 0.007 (4) | 0.001 (4) |
C63 | 0.018 (5) | 0.044 (5) | 0.040 (5) | −0.003 (4) | 0.002 (4) | −0.005 (5) |
C64 | 0.028 (5) | 0.039 (5) | 0.031 (5) | 0.008 (4) | −0.002 (4) | −0.003 (4) |
C65 | 0.037 (5) | 0.033 (5) | 0.026 (5) | 0.005 (4) | 0.003 (4) | 0.002 (4) |
C66 | 0.028 (5) | 0.027 (5) | 0.025 (4) | 0.000 (4) | 0.008 (3) | −0.007 (4) |
C67 | 0.029 (5) | 0.020 (4) | 0.025 (5) | −0.009 (4) | 0.007 (3) | −0.006 (3) |
Geometric parameters (Å, º) top
N1—C2 | 1.324 (8) | O6—C67 | 1.456 (7) |
N1—C6 | 1.333 (8) | C67—C61 | 1.505 (9) |
C2—N3 | 1.332 (8) | C67—H67A | 0.99 |
C2—S2 | 1.781 (7) | C67—H67B | 0.99 |
S2—C21 | 1.798 (7) | C61—C62 | 1.380 (9) |
C21—H21A | 0.98 | C61—C66 | 1.397 (9) |
C21—H21B | 0.98 | C62—C63 | 1.389 (10) |
C21—H21C | 0.98 | C62—H62 | 0.95 |
N3—C4 | 1.364 (8) | C63—C64 | 1.393 (10) |
C4—N4 | 1.345 (8) | C63—H63 | 0.95 |
C4—C5 | 1.410 (9) | C64—C65 | 1.379 (10) |
N4—H4A | 0.88 | C64—H64 | 0.95 |
N4—H4B | 0.88 | C65—C66 | 1.387 (9) |
C5—C6 | 1.366 (9) | C65—H65 | 0.95 |
C5—H5 | 0.95 | C66—H66 | 0.95 |
C6—O6 | 1.367 (8) | | |
| | | |
C2—N1—C6 | 113.7 (5) | O6—C67—C61 | 113.4 (5) |
N1—C2—N3 | 128.9 (6) | O6—C67—H67A | 108.9 |
N1—C2—S2 | 117.7 (5) | C61—C67—H67A | 108.9 |
N3—C2—S2 | 113.4 (5) | O6—C67—H67B | 108.9 |
C2—S2—C21 | 100.7 (3) | C61—C67—H67B | 108.9 |
S2—C21—H21A | 109.5 | H67A—C67—H67B | 107.7 |
S2—C21—H21B | 109.5 | C62—C61—C66 | 118.1 (6) |
H21A—C21—H21B | 109.5 | C62—C61—C67 | 119.9 (6) |
S2—C21—H21C | 109.5 | C66—C61—C67 | 121.9 (6) |
H21A—C21—H21C | 109.5 | C61—C62—C63 | 121.9 (7) |
H21B—C21—H21C | 109.5 | C61—C62—H62 | 119.0 |
C2—N3—C4 | 115.7 (5) | C63—C62—H62 | 119.0 |
N4—C4—N3 | 117.5 (6) | C62—C63—C64 | 119.9 (7) |
N4—C4—C5 | 122.1 (6) | C62—C63—H63 | 120.0 |
N3—C4—C5 | 120.4 (6) | C64—C63—H63 | 120.0 |
C4—N4—H4A | 120.0 | C65—C64—C63 | 118.2 (7) |
C4—N4—H4B | 120.0 | C65—C64—H64 | 120.9 |
H4A—N4—H4B | 120.0 | C63—C64—H64 | 120.9 |
C6—C5—C4 | 116.1 (6) | C64—C65—C66 | 122.0 (7) |
C6—C5—H5 | 121.9 | C64—C65—H65 | 119.0 |
C4—C5—H5 | 121.9 | C66—C65—H65 | 119.0 |
N1—C6—C5 | 125.2 (6) | C65—C66—C61 | 119.8 (7) |
N1—C6—O6 | 117.8 (6) | C65—C66—H66 | 120.1 |
C5—C6—O6 | 117.0 (6) | C61—C66—H66 | 120.1 |
C6—O6—C67 | 117.0 (5) | | |
| | | |
C6—N1—C2—N3 | −1.2 (9) | N1—C6—O6—C67 | −7.2 (8) |
C6—N1—C2—S2 | 178.0 (4) | C5—C6—O6—C67 | 173.9 (6) |
N1—C2—S2—C21 | −3.6 (6) | C6—O6—C67—C61 | 76.1 (7) |
N3—C2—S2—C21 | 175.7 (5) | O6—C67—C61—C62 | −155.4 (6) |
N1—C2—N3—C4 | 0.3 (9) | O6—C67—C61—C66 | 27.2 (8) |
S2—C2—N3—C4 | −178.9 (4) | C66—C61—C62—C63 | 0.2 (10) |
C2—N3—C4—N4 | −179.3 (6) | C67—C61—C62—C63 | −177.2 (6) |
C2—N3—C4—C5 | 0.5 (8) | C61—C62—C63—C64 | −0.9 (11) |
N4—C4—C5—C6 | 179.4 (6) | C62—C63—C64—C65 | 1.5 (10) |
N3—C4—C5—C6 | −0.5 (9) | C63—C64—C65—C66 | −1.4 (11) |
C2—N1—C6—C5 | 1.3 (9) | C64—C65—C66—C61 | 0.7 (10) |
C2—N1—C6—O6 | −177.5 (5) | C62—C61—C66—C65 | −0.1 (9) |
C4—C5—C6—N1 | −0.5 (10) | C67—C61—C66—C65 | 177.3 (6) |
C4—C5—C6—O6 | 178.2 (5) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4A···N3i | 0.88 | 2.16 | 3.044 (8) | 177 |
N4—H4B···O6ii | 0.88 | 2.40 | 3.209 (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 formula | C12H13N3OS | C24H25.95N6.05O2.05S2 | C12H12N4O2S | C12H13N3OS |
Mr | 247.31 | 496.10 | 276.33 | 247.31 |
Crystal system, space group | Monoclinic, P21/c | Monoclinic, P21/c | Triclinic, P1 | Monoclinic, P21/c |
Temperature (K) | 120 | 120 | 120 | 120 |
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), 90 | 90, 107.0920 (14), 90 | 109.6510 (13), 96.4203 (14), 93.7181 (14) | 90, 105.286 (5), 90 |
V (Å3) | 1144.85 (4) | 2352.95 (8) | 1256.49 (7) | 1201.9 (3) |
Z | 4 | 4 | 4 | 4 |
Radiation type | Mo Kα | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.27 | 0.26 | 0.26 | 0.26 |
Crystal size (mm) | 0.30 × 0.26 × 0.20 | 0.47 × 0.22 × 0.14 | 0.30 × 0.22 × 0.04 | 0.60 × 0.04 × 0.03 |
|
Data collection |
Diffractometer | Nonius KappaCCD diffractometer | Nonius KappaCCD diffractometer | Nonius KappaCCD diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-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, Tmax | 0.902, 0.943 | 0.887, 0.957 | 0.920, 0.991 | 0.862, 0.992 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7564, 2600, 2249 | 21205, 5325, 4389 | 24784, 4417, 3498 | 9738, 1177, 1006 |
Rint | 0.032 | 0.064 | 0.094 | 0.147 |
θmax (°) | 27.5 | 27.5 | 25.0 | 20.5 |
(sin θ/λ)max (Å−1) | 0.649 | 0.649 | 0.595 | 0.493 |
|
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 reflections | 2600 | 5325 | 4417 | 1177 |
No. of parameters | 155 | 318 | 345 | 155 |
No. of restraints | 0 | 1 | 0 | 0 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.24, −0.31 | 0.51, −0.41 | 0.21, −0.31 | 0.32, −0.35 |
Selected bond lengths (Å) for (I) topN1—C2 | 1.364 (2) | N1—C17 | 1.463 (2) |
C2—N3 | 1.303 (3) | C2—S2 | 1.757 (2) |
N3—C4 | 1.375 (2) | C21—S2 | 1.798 (2) |
C4—C5 | 1.376 (2) | C4—N4 | 1.344 (2) |
C5—C6 | 1.401 (2) | C6—O6 | 1.241 (2) |
C6—N1 | 1.424 (2) | | |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4B···O6i | 0.88 | 1.95 | 2.823 (2) | 170 |
Symmetry code: (i) −x+1, y−1/2, −z+1/2. |
Selected bond lengths (Å) for (II) topN11—C12 | 1.366 (2) | N21—C22 | 1.376 (2) |
C12—N13 | 1.304 (2) | C22—N23 | 1.311 (3) |
N13—C14 | 1.374 (2) | N23—C24 | 1.373 (3) |
C14—C15 | 1.390 (3) | C24—C25 | 1.381 (3) |
C15—C16 | 1.401 (3) | C25—C26 | 1.400 (3) |
C16—N11 | 1.435 (2) | C26—N21 | 1.420 (3) |
N11—C117 | 1.469 (2) | N21—C217 | 1.464 (3) |
C12—S12 | 1.759 (2) | C22—S22 | 1.747 (2) |
S12—C121 | 1.794 (2) | S22—C221 | 1.791 (2) |
C14—N14 | 1.342 (2) | C24—N24 | 1.353 (3) |
C16—O16 | 1.245 (2) | C26—O26 | 1.246 (3) |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N14—H14A···O26i | 0.88 | 2.28 | 3.029 (2) | 143 |
N14—H14B···O26 | 0.88 | 2.10 | 2.896 (2) | 151 |
N24—H24A···O16ii | 0.88 | 2.29 | 3.124 (2) | 157 |
N24—H24B···O16iii | 0.88 | 2.62 | 3.330 (2) | 138 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x, −y+1, −z+1; (iii) x, y−1, z. |
Selected bond lengths (Å) for (III) topN11—C12 | 1.372 (3) | N21—C22 | 1.372 (3) |
C12—N13 | 1.306 (3) | C22—N23 | 1.305 (3) |
N13—C14 | 1.362 (3) | N23—C24 | 1.368 (3) |
C14—C15 | 1.433 (3) | C24—C25 | 1.422 (3) |
C15—C16 | 1.452 (3) | C25—C26 | 1.445 (3) |
C16—N11 | 1.419 (3) | C26—N21 | 1.420 (3) |
N11—C117 | 1.483 (3) | N21—C217 | 1.466 (3) |
C12—S12 | 1.743 (2) | C22—S22 | 1.747 (2) |
S12—C121 | 1.804 (2) | S22—C221 | 1.796 (2) |
C14—N14 | 1.312 (3) | C24—N24 | 1.316 (3) |
C15—N15 | 1.353 (3) | C25—N25 | 1.352 (3) |
N15—O15 | 1.273 (2) | N25—O25 | 1.272 (2) |
C16—O16 | 1.218 (3) | C26—O26 | 1.223 (3) |
Hydrogen-bond geometry (Å, º) for (III) top
D—H···A | D—H | H···A | D···A | D—H···A |
N14—H14A···N25 | 0.88 | 2.23 | 3.100 (3) | 168 |
N14—H14A···O26 | 0.88 | 2.40 | 2.879 (2) | 114 |
N14—H14B···O15 | 0.88 | 2.01 | 2.642 (2) | 128 |
N24—H24A···N15i | 0.88 | 2.09 | 2.970 (3) | 177 |
N24—H24A···O16i | 0.88 | 2.50 | 2.938 (2) | 112 |
N24—H24B···O25 | 0.88 | 2.01 | 2.631 (2) | 127 |
Symmetry code: (i) x, y, z−1. |
Hydrogen-bond geometry (Å, º) for (IV) top
D—H···A | D—H | H···A | D···A | D—H···A |
N4—H4A···N3i | 0.88 | 2.16 | 3.044 (8) | 177 |
N4—H4B···O6ii | 0.88 | 2.40 | 3.209 (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.
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 C═O conjugated for C═C (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.