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In each of 6-amino-3-methyl-2-(morpholin-4-yl)-5-nitrosopyrimidin-4(3
H)-one, C
9H
13N
5O
3, (I), morpholin-4-ium 4-amino-2-(morpholin-4-yl)-5-nitroso-6-oxo-1,6-dihydropyrimidin-1-ide, C
4H
10NO
+·C
8H
10N
5O
3−, (II), and 6-amino-2-(morpholin-4-yl)-5-nitrosopyrimidin-4(3
H)-one hemihydrate, C
8H
11N
5O
3·0.5H
2O, (III), the bond distances within the pyrimidine components are consistent with significant electronic polarization, which is most marked in (II) and least marked in (I). Despite the high level of substitution, the pyrimidine rings are all effectively planar, and in each of the pyrimidine components, there are intramolecular N—H
O hydrogen bonds. In each compound, the organic components are linked by multiple N—H
O hydrogen bonds to form sheets of widely differing construction, and in compound (III) adjacent sheets are linked by the water molecules, so forming a three-dimensional hydrogen-bonded framework. This study also contains the first direct geometric comparison between the electronic polarization in a neutral aminonitrosopyrimidine and that in its ring-deprotonated conjugate anion in a metal-free environment.
Supporting information
CCDC references: 686442; 686443; 686444
For the synthesis of compound (I), morpholine (100 mmol) was added dropwise and
with magnetic stirring to a suspension of
6-amino-3-methyl-2-methylsulfanyl-5-nitrosopyrimidin-4(3H)-one (26.8 mmol) in dry ethanol (80 ml). Stirring was continued for 18 h, when the colour
changed from blue to violet as methanethiol was liberated. The resulting solid
was collected by filtration and washed with cold ethanol. Crystals of (I)
suitable for single-crystal X-ray diffraction were grown by slow evaporation
of a solution in dimethylformamide–ethanol (10:1 v/v). Yield
57%; m.p. 508–509 K; MS (30 eV) m/z (%): 239 (M+, 89),
209 (2), 181 (6), 153 (4), 139 (10), 125 (20), 113 (13), 109 (13), 86 (29), 69 (92),
57 (76), 42 (100). A similar reaction, but using
6-amino-2-methylsulfanyl-5-nitrosopyrimidin-4(3H)-one in place of the
3-methyl analogue gave
6-amino-2-(morpholin-4-yl)-5-nitrosopyrimidin-4(3H)-one, (IV). Yield
99%, m.p. 507–508 K; MS (30 eV) m/z (%): 225 (M+, 72),
208 (94), 195 (2), 139 (2), 113 (49), 113 (49), 95 (24), 86 (21), 69 (100).
Recrystallization of this material from a dimethylformamide–ethanol (10:1
v/v) mixture containing a little morpholine gave crystals of
compound (II) suitable for single-crystal X-ray diffraction, whereas
crystallization from water yielded hemihydrate (III).
For each of (I) and (III), the space group P21/n was uniquely
assigned from the systematic absence. For compound (II), the systematic
absences permitted Cc and C2/c as possible space groups;
C2/c was selected and confirmed by the structure solution, but
the setting was then transformed to the alternative I2/a. All H atoms were
located in difference maps and then treated as riding atoms. H atoms bonded to
C or N atoms were allowed to ride in geometrically idealized positions, with
C—H = 0.98 (CH3) or 0.99 Å (CH2) and N—H = 0.92 Å for the cation
in (II) and 0.88 Å otherwise, and with Uiso(H) =
kUeq(C,N) where k = 1.5 for the methyl groups and 1.2
otherwise. H atoms bonded to O atoms were permitted to ride at the locations
deduced from the difference maps, with Uiso(H) = 1.5Ueq(O),
giving O—H distances of 0.89 and 1.19 Å in compound (III).
For all compounds, data collection: COLLECT (Hooft, 1999); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: OSCAIL (McArdle, 2003) and SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PRPKAPPA (Ferguson, 1999).
(I) 6-amino-3-methyl-2-(morpholin-4-yl)-5-nitrosopyrimidin-4(3
H)-one
top
Crystal data top
C9H13N5O3 | F(000) = 504 |
Mr = 239.24 | Dx = 1.494 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 2445 reflections |
a = 8.9122 (6) Å | θ = 3.2–27.5° |
b = 11.9051 (7) Å | µ = 0.12 mm−1 |
c = 10.4111 (4) Å | T = 120 K |
β = 105.649 (3)° | Block, violet |
V = 1063.68 (10) Å3 | 0.41 × 0.28 × 0.25 mm |
Z = 4 | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 2445 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 1516 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.068 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.2° |
ϕ and ω scans | h = −11→11 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −15→15 |
Tmin = 0.959, Tmax = 0.972 | l = −13→13 |
25676 measured reflections | |
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)] = 0.054 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.159 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0708P)2 + 0.8671P] where P = (Fo2 + 2Fc2)/3 |
2445 reflections | (Δ/σ)max < 0.001 |
155 parameters | Δρmax = 0.33 e Å−3 |
0 restraints | Δρmin = −0.31 e Å−3 |
Crystal data top
C9H13N5O3 | V = 1063.68 (10) Å3 |
Mr = 239.24 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 8.9122 (6) Å | µ = 0.12 mm−1 |
b = 11.9051 (7) Å | T = 120 K |
c = 10.4111 (4) Å | 0.41 × 0.28 × 0.25 mm |
β = 105.649 (3)° | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 2445 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 1516 reflections with I > 2σ(I) |
Tmin = 0.959, Tmax = 0.972 | Rint = 0.068 |
25676 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.054 | 0 restraints |
wR(F2) = 0.159 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.33 e Å−3 |
2445 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 | |
O4 | 0.5236 (2) | 0.28531 (14) | 0.73638 (16) | 0.0274 (4) | |
O5 | 0.7727 (2) | 0.56211 (15) | 0.86723 (17) | 0.0316 (5) | |
O24 | 0.6049 (2) | 0.21552 (14) | 0.07493 (16) | 0.0278 (4) | |
N1 | 0.7099 (2) | 0.45427 (16) | 0.47610 (18) | 0.0220 (5) | |
N3 | 0.5643 (2) | 0.30250 (16) | 0.53066 (19) | 0.0213 (5) | |
N5 | 0.6951 (2) | 0.47256 (18) | 0.82890 (19) | 0.0267 (5) | |
N6 | 0.8104 (2) | 0.59112 (16) | 0.6285 (2) | 0.0255 (5) | |
N21 | 0.6243 (2) | 0.31120 (16) | 0.32630 (18) | 0.0233 (5) | |
C2 | 0.6354 (3) | 0.3583 (2) | 0.4473 (2) | 0.0213 (5) | |
C3 | 0.4453 (3) | 0.2144 (2) | 0.4835 (2) | 0.0259 (6) | |
C4 | 0.5835 (3) | 0.3391 (2) | 0.6634 (2) | 0.0222 (5) | |
C5 | 0.6740 (3) | 0.4408 (2) | 0.7000 (2) | 0.0210 (5) | |
C6 | 0.7298 (3) | 0.49742 (19) | 0.6002 (2) | 0.0217 (5) | |
C22 | 0.6690 (3) | 0.1928 (2) | 0.3140 (2) | 0.0250 (6) | |
C23 | 0.5760 (3) | 0.1495 (2) | 0.1796 (2) | 0.0284 (6) | |
C25 | 0.5671 (3) | 0.3316 (2) | 0.0870 (2) | 0.0264 (6) | |
C26 | 0.6585 (3) | 0.3795 (2) | 0.2200 (2) | 0.0254 (6) | |
H3A | 0.4048 | 0.2192 | 0.3864 | 0.039* | |
H3B | 0.3599 | 0.2253 | 0.5250 | 0.039* | |
H3C | 0.4924 | 0.1404 | 0.5080 | 0.039* | |
H6A | 0.8488 | 0.6231 | 0.5680 | 0.031* | |
H6B | 0.8260 | 0.6218 | 0.7079 | 0.031* | |
H22A | 0.6466 | 0.1472 | 0.3862 | 0.030* | |
H22B | 0.7819 | 0.1877 | 0.3215 | 0.030* | |
H23A | 0.6049 | 0.0704 | 0.1689 | 0.034* | |
H23B | 0.4635 | 0.1518 | 0.1745 | 0.034* | |
H25A | 0.4541 | 0.3388 | 0.0784 | 0.032* | |
H25B | 0.5909 | 0.3751 | 0.0138 | 0.032* | |
H26A | 0.7714 | 0.3775 | 0.2270 | 0.030* | |
H26B | 0.6278 | 0.4586 | 0.2281 | 0.030* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O4 | 0.0303 (10) | 0.0281 (9) | 0.0263 (9) | −0.0014 (8) | 0.0120 (8) | 0.0044 (7) |
O5 | 0.0342 (10) | 0.0344 (11) | 0.0258 (10) | −0.0024 (8) | 0.0076 (8) | −0.0067 (8) |
O24 | 0.0336 (10) | 0.0282 (9) | 0.0228 (9) | 0.0014 (8) | 0.0098 (7) | −0.0017 (7) |
N1 | 0.0250 (11) | 0.0231 (11) | 0.0179 (10) | 0.0002 (9) | 0.0060 (8) | 0.0004 (8) |
N3 | 0.0201 (10) | 0.0237 (11) | 0.0212 (10) | −0.0010 (8) | 0.0075 (8) | 0.0005 (8) |
N5 | 0.0277 (11) | 0.0284 (12) | 0.0241 (11) | 0.0024 (9) | 0.0071 (9) | −0.0021 (9) |
N6 | 0.0351 (12) | 0.0228 (11) | 0.0196 (10) | −0.0038 (9) | 0.0089 (9) | −0.0009 (8) |
N21 | 0.0305 (11) | 0.0223 (11) | 0.0185 (10) | −0.0013 (9) | 0.0091 (8) | −0.0006 (8) |
C2 | 0.0198 (12) | 0.0237 (13) | 0.0199 (12) | 0.0014 (10) | 0.0049 (9) | 0.0023 (10) |
C3 | 0.0248 (13) | 0.0267 (13) | 0.0262 (13) | −0.0030 (11) | 0.0070 (10) | −0.0006 (10) |
C4 | 0.0222 (12) | 0.0246 (13) | 0.0198 (12) | 0.0045 (10) | 0.0060 (10) | 0.0027 (10) |
C5 | 0.0207 (12) | 0.0257 (13) | 0.0173 (12) | 0.0030 (10) | 0.0062 (9) | 0.0006 (9) |
C6 | 0.0223 (12) | 0.0218 (12) | 0.0211 (12) | 0.0046 (10) | 0.0059 (10) | 0.0025 (10) |
C22 | 0.0256 (13) | 0.0248 (13) | 0.0252 (13) | 0.0014 (10) | 0.0080 (10) | 0.0006 (10) |
C23 | 0.0346 (14) | 0.0244 (13) | 0.0277 (13) | −0.0036 (11) | 0.0108 (11) | −0.0046 (10) |
C25 | 0.0319 (14) | 0.0269 (13) | 0.0211 (13) | 0.0044 (11) | 0.0083 (10) | 0.0009 (10) |
C26 | 0.0327 (14) | 0.0240 (13) | 0.0208 (12) | −0.0017 (11) | 0.0095 (10) | 0.0005 (10) |
Geometric parameters (Å, º) top
O24—C23 | 1.422 (3) | C3—H3A | 0.98 |
O24—C25 | 1.436 (3) | C3—H3B | 0.98 |
O4—C4 | 1.221 (3) | C3—H3C | 0.98 |
O5—N5 | 1.275 (3) | C4—C5 | 1.447 (3) |
N1—C2 | 1.315 (3) | C5—C6 | 1.435 (3) |
N1—C6 | 1.357 (3) | C22—C23 | 1.512 (3) |
N3—C2 | 1.376 (3) | C22—H22A | 0.99 |
N3—C4 | 1.415 (3) | C22—H22B | 0.99 |
N3—C3 | 1.478 (3) | C23—H23A | 0.99 |
N5—C5 | 1.358 (3) | C23—H23B | 0.99 |
N6—C6 | 1.316 (3) | C25—C26 | 1.516 (3) |
N6—H6A | 0.88 | C25—H25A | 0.99 |
N6—H6B | 0.88 | C25—H25B | 0.99 |
N21—C2 | 1.358 (3) | C26—H26A | 0.99 |
N21—C26 | 1.470 (3) | C26—H26B | 0.99 |
N21—C22 | 1.480 (3) | | |
| | | |
C23—O24—C25 | 111.72 (18) | N6—C6—N1 | 117.2 (2) |
C2—N1—C6 | 118.31 (19) | N6—C6—C5 | 120.7 (2) |
C2—N3—C4 | 120.8 (2) | N1—C6—C5 | 122.0 (2) |
C2—N3—C3 | 123.00 (19) | N21—C22—C23 | 108.2 (2) |
C4—N3—C3 | 115.47 (18) | N21—C22—H22A | 110.1 |
O5—N5—C5 | 117.5 (2) | C23—C22—H22A | 110.1 |
C6—N6—H6A | 120.0 | N21—C22—H22B | 110.1 |
C6—N6—H6B | 120.0 | C23—C22—H22B | 110.1 |
H6A—N6—H6B | 120.0 | H22A—C22—H22B | 108.4 |
C2—N21—C26 | 119.48 (19) | O24—C23—C22 | 110.7 (2) |
C2—N21—C22 | 121.29 (19) | O24—C23—H23A | 109.5 |
C26—N21—C22 | 110.30 (18) | C22—C23—H23A | 109.5 |
N1—C2—N21 | 118.4 (2) | O24—C23—H23B | 109.5 |
N1—C2—N3 | 124.5 (2) | C22—C23—H23B | 109.5 |
N21—C2—N3 | 117.1 (2) | H23A—C23—H23B | 108.1 |
N3—C3—H3A | 109.5 | O24—C25—C26 | 111.2 (2) |
N3—C3—H3B | 109.5 | O24—C25—H25A | 109.4 |
H3A—C3—H3B | 109.5 | C26—C25—H25A | 109.4 |
N3—C3—H3C | 109.5 | O24—C25—H25B | 109.4 |
H3A—C3—H3C | 109.5 | C26—C25—H25B | 109.4 |
H3B—C3—H3C | 109.5 | H25A—C25—H25B | 108.0 |
O4—C4—N3 | 119.2 (2) | N21—C26—C25 | 108.1 (2) |
O4—C4—C5 | 125.5 (2) | N21—C26—H26A | 110.1 |
N3—C4—C5 | 115.26 (19) | C25—C26—H26A | 110.1 |
N5—C5—C6 | 127.0 (2) | N21—C26—H26B | 110.1 |
N5—C5—C4 | 114.3 (2) | C25—C26—H26B | 110.1 |
C6—C5—C4 | 118.7 (2) | H26A—C26—H26B | 108.4 |
| | | |
C6—N1—C2—N21 | −175.7 (2) | N3—C4—C5—N5 | −178.07 (19) |
C6—N1—C2—N3 | 5.7 (3) | O4—C4—C5—C6 | −176.8 (2) |
C26—N21—C2—N1 | −15.5 (3) | N3—C4—C5—C6 | 2.5 (3) |
C22—N21—C2—N1 | 128.6 (2) | C2—N1—C6—N6 | 177.2 (2) |
C26—N21—C2—N3 | 163.2 (2) | C2—N1—C6—C5 | 0.8 (3) |
C22—N21—C2—N3 | −52.7 (3) | N5—C5—C6—N6 | −0.4 (4) |
C4—N3—C2—N1 | −8.0 (3) | C4—C5—C6—N6 | 178.9 (2) |
C3—N3—C2—N1 | 161.9 (2) | N5—C5—C6—N1 | 175.9 (2) |
C4—N3—C2—N21 | 173.4 (2) | C4—C5—C6—N1 | −4.8 (3) |
C3—N3—C2—N21 | −16.8 (3) | C2—N21—C22—C23 | 152.8 (2) |
C2—N3—C4—O4 | −177.3 (2) | C26—N21—C22—C23 | −60.2 (2) |
C3—N3—C4—O4 | 12.1 (3) | C25—O24—C23—C22 | −58.3 (3) |
C2—N3—C4—C5 | 3.4 (3) | N21—C22—C23—O24 | 58.7 (3) |
C3—N3—C4—C5 | −167.2 (2) | C23—O24—C25—C26 | 57.8 (3) |
O5—N5—C5—C6 | 0.0 (3) | C2—N21—C26—C25 | −152.9 (2) |
O5—N5—C5—C4 | −179.4 (2) | C22—N21—C26—C25 | 59.4 (3) |
O4—C4—C5—N5 | 2.7 (3) | O24—C25—C26—N21 | −57.4 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···O24i | 0.88 | 1.98 | 2.848 (3) | 168 |
N6—H6B···O5 | 0.88 | 1.98 | 2.619 (3) | 129 |
N6—H6B···O4ii | 0.88 | 2.35 | 2.896 (3) | 121 |
Symmetry codes: (i) −x+3/2, y+1/2, −z+1/2; (ii) −x+3/2, y+1/2, −z+3/2. |
(II) morpholin-4-ium
4-amino-2-(morpholin-4-yl)-5-nitroso-6-oxo-1,6-dihydropyrimidin-1-ide
top
Crystal data top
C4H10NO+·C8H10N5O3− | F(000) = 1328 |
Mr = 312.34 | Dx = 1.430 Mg m−3 |
Monoclinic, I2/a | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -I 2ya | Cell parameters from 3354 reflections |
a = 9.4410 (11) Å | θ = 3.3–27.5° |
b = 16.347 (4) Å | µ = 0.11 mm−1 |
c = 18.799 (5) Å | T = 120 K |
β = 90.045 (15)° | Lath, violet |
V = 2901.3 (11) Å3 | 0.26 × 0.10 × 0.10 mm |
Z = 8 | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 3354 independent reflections |
Radiation source: Bruker–Nonius FR591 rotating anode | 2361 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.048 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.3° |
ϕ and ω scans | h = −12→12 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −21→21 |
Tmin = 0.977, Tmax = 0.989 | l = −24→24 |
33473 measured reflections | |
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)] = 0.049 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.109 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0306P)2 + 5.055P] where P = (Fo2 + 2Fc2)/3 |
3354 reflections | (Δ/σ)max < 0.001 |
199 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
Crystal data top
C4H10NO+·C8H10N5O3− | V = 2901.3 (11) Å3 |
Mr = 312.34 | Z = 8 |
Monoclinic, I2/a | Mo Kα radiation |
a = 9.4410 (11) Å | µ = 0.11 mm−1 |
b = 16.347 (4) Å | T = 120 K |
c = 18.799 (5) Å | 0.26 × 0.10 × 0.10 mm |
β = 90.045 (15)° | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 3354 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2361 reflections with I > 2σ(I) |
Tmin = 0.977, Tmax = 0.989 | Rint = 0.048 |
33473 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.049 | 0 restraints |
wR(F2) = 0.109 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.25 e Å−3 |
3354 reflections | Δρmin = −0.27 e Å−3 |
199 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O4 | 0.58426 (14) | 0.70724 (9) | 0.26537 (7) | 0.0239 (3) | |
O5 | 0.57948 (14) | 0.57129 (9) | 0.44197 (7) | 0.0227 (3) | |
O24 | −0.02092 (15) | 0.55270 (9) | 0.09133 (7) | 0.0290 (3) | |
N1 | 0.22162 (16) | 0.58424 (10) | 0.31405 (8) | 0.0188 (3) | |
N3 | 0.36442 (16) | 0.66628 (10) | 0.23262 (8) | 0.0189 (3) | |
N5 | 0.58145 (16) | 0.61396 (10) | 0.38319 (8) | 0.0207 (3) | |
N6 | 0.31265 (16) | 0.53870 (10) | 0.41996 (8) | 0.0206 (3) | |
N21 | 0.14231 (16) | 0.61936 (10) | 0.20370 (8) | 0.0209 (4) | |
C2 | 0.24766 (19) | 0.62398 (11) | 0.25230 (10) | 0.0173 (4) | |
C4 | 0.47342 (19) | 0.66716 (11) | 0.27884 (9) | 0.0176 (4) | |
C5 | 0.46347 (18) | 0.61945 (11) | 0.34506 (9) | 0.0165 (4) | |
C6 | 0.32895 (19) | 0.58026 (11) | 0.35985 (9) | 0.0168 (4) | |
C22 | 0.1527 (2) | 0.65210 (12) | 0.13147 (10) | 0.0236 (4) | |
C23 | 0.1166 (2) | 0.58570 (13) | 0.07847 (10) | 0.0254 (4) | |
C25 | −0.0256 (2) | 0.51830 (14) | 0.16095 (11) | 0.0298 (5) | |
C26 | 0.00630 (19) | 0.58025 (13) | 0.21814 (10) | 0.0222 (4) | |
O34 | 0.51265 (14) | 0.72728 (9) | 0.02394 (7) | 0.0247 (3) | |
N31 | 0.67247 (16) | 0.78042 (10) | 0.14380 (8) | 0.0219 (4) | |
C32 | 0.7156 (2) | 0.70778 (13) | 0.10134 (11) | 0.0244 (4) | |
C33 | 0.5859 (2) | 0.66997 (12) | 0.06768 (11) | 0.0246 (4) | |
C35 | 0.4659 (2) | 0.79510 (12) | 0.06570 (11) | 0.0233 (4) | |
C36 | 0.5901 (2) | 0.83871 (12) | 0.09899 (10) | 0.0224 (4) | |
H6A | 0.2317 | 0.5142 | 0.4291 | 0.025* | |
H6B | 0.3828 | 0.5356 | 0.4507 | 0.025* | |
H22A | 0.2500 | 0.6722 | 0.1227 | 0.028* | |
H22B | 0.0865 | 0.6986 | 0.1258 | 0.028* | |
H23A | 0.1201 | 0.6085 | 0.0297 | 0.031* | |
H23B | 0.1878 | 0.5414 | 0.0817 | 0.031* | |
H25A | 0.0440 | 0.4731 | 0.1640 | 0.036* | |
H25B | −0.1209 | 0.4950 | 0.1693 | 0.036* | |
H26A | −0.0695 | 0.6221 | 0.2194 | 0.027* | |
H26B | 0.0095 | 0.5528 | 0.2651 | 0.027* | |
H31A | 0.7518 | 0.8062 | 0.1614 | 0.026* | |
H31B | 0.6181 | 0.7639 | 0.1817 | 0.026* | |
H32A | 0.7629 | 0.6673 | 0.1325 | 0.029* | |
H32B | 0.7834 | 0.7244 | 0.0639 | 0.029* | |
H33A | 0.6146 | 0.6223 | 0.0386 | 0.029* | |
H33B | 0.5215 | 0.6502 | 0.1055 | 0.029* | |
H35A | 0.4014 | 0.7755 | 0.1035 | 0.028* | |
H35B | 0.4126 | 0.8337 | 0.0352 | 0.028* | |
H36A | 0.6518 | 0.8614 | 0.0613 | 0.027* | |
H36B | 0.5558 | 0.8846 | 0.1287 | 0.027* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O4 | 0.0203 (7) | 0.0311 (8) | 0.0203 (7) | −0.0089 (6) | −0.0016 (5) | 0.0041 (6) |
O5 | 0.0209 (7) | 0.0293 (8) | 0.0180 (7) | 0.0027 (6) | −0.0023 (5) | 0.0029 (6) |
O24 | 0.0320 (8) | 0.0330 (8) | 0.0220 (7) | −0.0090 (6) | −0.0062 (6) | −0.0010 (6) |
N1 | 0.0183 (8) | 0.0211 (8) | 0.0170 (8) | −0.0015 (6) | −0.0007 (6) | 0.0007 (6) |
N3 | 0.0181 (8) | 0.0204 (8) | 0.0181 (8) | −0.0018 (6) | −0.0019 (6) | 0.0007 (7) |
N5 | 0.0195 (8) | 0.0259 (9) | 0.0166 (8) | −0.0001 (7) | −0.0020 (6) | 0.0008 (7) |
N6 | 0.0181 (8) | 0.0267 (9) | 0.0170 (8) | −0.0044 (7) | −0.0011 (6) | 0.0024 (7) |
N21 | 0.0194 (8) | 0.0239 (9) | 0.0195 (8) | −0.0063 (7) | −0.0040 (6) | 0.0038 (7) |
C2 | 0.0180 (9) | 0.0164 (9) | 0.0176 (9) | 0.0006 (7) | −0.0017 (7) | −0.0005 (7) |
C4 | 0.0165 (9) | 0.0189 (9) | 0.0174 (9) | −0.0006 (7) | 0.0005 (7) | −0.0028 (7) |
C5 | 0.0165 (9) | 0.0173 (9) | 0.0157 (9) | 0.0007 (7) | 0.0006 (7) | −0.0031 (7) |
C6 | 0.0178 (9) | 0.0168 (9) | 0.0159 (9) | 0.0011 (7) | 0.0012 (7) | −0.0030 (7) |
C22 | 0.0217 (10) | 0.0269 (11) | 0.0222 (10) | −0.0063 (8) | −0.0067 (8) | 0.0102 (8) |
C23 | 0.0250 (10) | 0.0318 (11) | 0.0196 (10) | 0.0030 (9) | −0.0025 (8) | 0.0048 (9) |
C25 | 0.0328 (12) | 0.0299 (11) | 0.0267 (11) | −0.0107 (9) | −0.0034 (9) | 0.0016 (9) |
C26 | 0.0170 (9) | 0.0285 (11) | 0.0211 (9) | −0.0036 (8) | −0.0019 (7) | 0.0007 (8) |
O34 | 0.0279 (7) | 0.0241 (7) | 0.0221 (7) | 0.0003 (6) | −0.0091 (6) | −0.0021 (6) |
N31 | 0.0174 (8) | 0.0318 (9) | 0.0164 (8) | −0.0064 (7) | −0.0007 (6) | −0.0008 (7) |
C32 | 0.0223 (10) | 0.0305 (11) | 0.0206 (10) | 0.0047 (8) | −0.0026 (8) | 0.0002 (8) |
C33 | 0.0270 (10) | 0.0194 (10) | 0.0272 (11) | 0.0004 (8) | −0.0048 (8) | 0.0011 (8) |
C35 | 0.0225 (9) | 0.0212 (10) | 0.0262 (10) | 0.0015 (8) | −0.0022 (8) | 0.0046 (8) |
C36 | 0.0258 (10) | 0.0201 (10) | 0.0212 (9) | −0.0032 (8) | 0.0019 (8) | 0.0011 (8) |
Geometric parameters (Å, º) top
O4—C4 | 1.260 (2) | C25—C26 | 1.507 (3) |
O5—N5 | 1.307 (2) | C25—H25A | 0.99 |
O24—C25 | 1.425 (2) | C25—H25B | 0.99 |
O24—C23 | 1.426 (2) | C26—H26A | 0.99 |
N1—C6 | 1.331 (2) | C26—H26B | 0.99 |
N1—C2 | 1.353 (2) | O34—C33 | 1.425 (2) |
N3—C4 | 1.346 (2) | O34—C35 | 1.429 (2) |
N3—C2 | 1.353 (2) | N31—C32 | 1.488 (3) |
N5—C5 | 1.327 (2) | N31—C36 | 1.490 (2) |
N6—C6 | 1.328 (2) | N31—H31A | 0.92 |
N6—H6A | 0.88 | N31—H31B | 0.92 |
N6—H6B | 0.88 | C32—C33 | 1.511 (3) |
N21—C2 | 1.352 (2) | C32—H32A | 0.99 |
N21—C26 | 1.460 (2) | C32—H32B | 0.99 |
N21—C22 | 1.463 (2) | C33—H33A | 0.99 |
C4—C5 | 1.472 (3) | C33—H33B | 0.99 |
C5—C6 | 1.450 (2) | C35—C36 | 1.508 (3) |
C22—C23 | 1.512 (3) | C35—H35A | 0.99 |
C22—H22A | 0.99 | C35—H35B | 0.99 |
C22—H22B | 0.99 | C36—H36A | 0.99 |
C23—H23A | 0.99 | C36—H36B | 0.99 |
C23—H23B | 0.99 | | |
| | | |
C25—O24—C23 | 109.51 (15) | H25A—C25—H25B | 107.8 |
C6—N1—C2 | 116.09 (16) | N21—C26—C25 | 109.69 (16) |
C4—N3—C2 | 116.84 (16) | N21—C26—H26A | 109.7 |
O5—N5—C5 | 118.70 (15) | C25—C26—H26A | 109.7 |
C6—N6—H6A | 120.0 | N21—C26—H26B | 109.7 |
C6—N6—H6B | 120.0 | C25—C26—H26B | 109.7 |
H6A—N6—H6B | 120.0 | H26A—C26—H26B | 108.2 |
C2—N21—C26 | 123.06 (16) | C33—O34—C35 | 110.06 (14) |
C2—N21—C22 | 123.84 (16) | C32—N31—C36 | 110.48 (15) |
C26—N21—C22 | 113.10 (15) | C32—N31—H31A | 109.6 |
N21—C2—N1 | 114.76 (16) | C36—N31—H31A | 109.6 |
N21—C2—N3 | 116.29 (16) | C32—N31—H31B | 109.6 |
N1—C2—N3 | 128.94 (16) | C36—N31—H31B | 109.6 |
O4—C4—N3 | 120.68 (17) | H31A—N31—H31B | 108.1 |
O4—C4—C5 | 119.92 (16) | N31—C32—C33 | 109.21 (16) |
N3—C4—C5 | 119.39 (16) | N31—C32—H32A | 109.8 |
N5—C5—C6 | 126.99 (17) | C33—C32—H32A | 109.8 |
N5—C5—C4 | 116.01 (16) | N31—C32—H32B | 109.8 |
C6—C5—C4 | 116.92 (15) | C33—C32—H32B | 109.8 |
N6—C6—N1 | 119.14 (16) | H32A—C32—H32B | 108.3 |
N6—C6—C5 | 119.44 (16) | O34—C33—C32 | 111.43 (16) |
N1—C6—C5 | 121.41 (16) | O34—C33—H33A | 109.3 |
N21—C22—C23 | 109.49 (16) | C32—C33—H33A | 109.3 |
N21—C22—H22A | 109.8 | O34—C33—H33B | 109.3 |
C23—C22—H22A | 109.8 | C32—C33—H33B | 109.3 |
N21—C22—H22B | 109.8 | H33A—C33—H33B | 108.0 |
C23—C22—H22B | 109.8 | O34—C35—C36 | 110.76 (16) |
H22A—C22—H22B | 108.2 | O34—C35—H35A | 109.5 |
O24—C23—C22 | 111.38 (16) | C36—C35—H35A | 109.5 |
O24—C23—H23A | 109.4 | O34—C35—H35B | 109.5 |
C22—C23—H23A | 109.4 | C36—C35—H35B | 109.5 |
O24—C23—H23B | 109.4 | H35A—C35—H35B | 108.1 |
C22—C23—H23B | 109.4 | N31—C36—C35 | 109.73 (16) |
H23A—C23—H23B | 108.0 | N31—C36—H36A | 109.7 |
O24—C25—C26 | 112.56 (17) | C35—C36—H36A | 109.7 |
O24—C25—H25A | 109.1 | N31—C36—H36B | 109.7 |
C26—C25—H25A | 109.1 | C35—C36—H36B | 109.7 |
O24—C25—H25B | 109.1 | H36A—C36—H36B | 108.2 |
C26—C25—H25B | 109.1 | | |
| | | |
C26—N21—C2—N1 | 4.6 (3) | N5—C5—C6—N6 | 5.6 (3) |
C22—N21—C2—N1 | −174.86 (17) | C4—C5—C6—N6 | −177.80 (16) |
C26—N21—C2—N3 | −176.23 (17) | N5—C5—C6—N1 | −173.64 (18) |
C22—N21—C2—N3 | 4.3 (3) | C4—C5—C6—N1 | 3.0 (3) |
C6—N1—C2—N21 | 173.07 (17) | C2—N21—C22—C23 | 126.43 (19) |
C6—N1—C2—N3 | −6.0 (3) | C26—N21—C22—C23 | −53.1 (2) |
C4—N3—C2—N21 | −176.11 (17) | C25—O24—C23—C22 | −60.2 (2) |
C4—N3—C2—N1 | 2.9 (3) | N21—C22—C23—O24 | 56.9 (2) |
C2—N3—C4—O4 | −177.84 (17) | C23—O24—C25—C26 | 59.4 (2) |
C2—N3—C4—C5 | 3.3 (2) | C2—N21—C26—C25 | −127.7 (2) |
O5—N5—C5—C6 | −2.3 (3) | C22—N21—C26—C25 | 51.8 (2) |
O5—N5—C5—C4 | −178.96 (15) | O24—C25—C26—N21 | −54.8 (2) |
O4—C4—C5—N5 | −7.9 (3) | C36—N31—C32—C33 | −54.6 (2) |
N3—C4—C5—N5 | 170.98 (17) | C35—O34—C33—C32 | −61.1 (2) |
O4—C4—C5—C6 | 175.16 (17) | N31—C32—C33—O34 | 57.8 (2) |
N3—C4—C5—C6 | −6.0 (2) | C33—O34—C35—C36 | 60.9 (2) |
C2—N1—C6—N6 | −176.74 (17) | C32—N31—C36—C35 | 55.1 (2) |
C2—N1—C6—C5 | 2.5 (3) | O34—C35—C36—N31 | −58.0 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···O5i | 0.88 | 2.02 | 2.872 (2) | 163 |
N6—H6B···O5 | 0.88 | 1.95 | 2.608 (2) | 130 |
N31—H31A···O4ii | 0.92 | 2.08 | 2.868 (2) | 143 |
N31—H31A···N5ii | 0.92 | 2.21 | 2.939 (2) | 136 |
N31—H31B···O4 | 0.92 | 1.85 | 2.711 (2) | 154 |
Symmetry codes: (i) x−1/2, −y+1, z; (ii) −x+3/2, −y+3/2, −z+1/2. |
(III) 6-amino-2-(morpholin-4-yl)-5-nitrosopyrimidin-4(3
H)-one hemihydrate
top
Crystal data top
C8H11N5O3·0.5H2O | F(000) = 984 |
Mr = 234.23 | Dx = 1.546 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 4646 reflections |
a = 16.421 (2) Å | θ = 3.0–27.5° |
b = 7.3671 (12) Å | µ = 0.12 mm−1 |
c = 17.205 (4) Å | T = 120 K |
β = 104.794 (12)° | Block, purple |
V = 2012.4 (6) Å3 | 0.44 × 0.34 × 0.21 mm |
Z = 8 | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 4646 independent reflections |
Radiation source: Bruker–Nonius FR591 rotating anode | 2535 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.098 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.0° |
ϕ and ω scans | h = −21→21 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −9→9 |
Tmin = 0.953, Tmax = 0.975 | l = −22→22 |
47024 measured reflections | |
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)] = 0.058 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.162 | H-atom parameters constrained |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0672P)2 + 1.619P] where P = (Fo2 + 2Fc2)/3 |
4646 reflections | (Δ/σ)max < 0.001 |
298 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.41 e Å−3 |
Crystal data top
C8H11N5O3·0.5H2O | V = 2012.4 (6) Å3 |
Mr = 234.23 | Z = 8 |
Monoclinic, P21/n | Mo Kα radiation |
a = 16.421 (2) Å | µ = 0.12 mm−1 |
b = 7.3671 (12) Å | T = 120 K |
c = 17.205 (4) Å | 0.44 × 0.34 × 0.21 mm |
β = 104.794 (12)° | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 4646 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2535 reflections with I > 2σ(I) |
Tmin = 0.953, Tmax = 0.975 | Rint = 0.098 |
47024 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.162 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.32 e Å−3 |
4646 reflections | Δρmin = −0.41 e Å−3 |
298 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O4 | 0.43256 (12) | 0.1500 (3) | 0.26365 (11) | 0.0230 (5) | |
O5 | 0.29659 (11) | 0.0472 (3) | 0.42316 (12) | 0.0242 (5) | |
O24 | 0.82727 (11) | 0.4401 (3) | 0.51666 (12) | 0.0239 (5) | |
N1 | 0.53493 (14) | 0.2730 (3) | 0.49908 (14) | 0.0189 (5) | |
N3 | 0.54131 (14) | 0.2458 (3) | 0.36435 (13) | 0.0197 (5) | |
N5 | 0.33894 (14) | 0.0758 (3) | 0.37107 (14) | 0.0204 (5) | |
N6 | 0.42037 (14) | 0.1755 (3) | 0.53801 (14) | 0.0201 (5) | |
N21 | 0.65296 (14) | 0.3651 (3) | 0.46270 (14) | 0.0222 (6) | |
C2 | 0.57578 (16) | 0.2949 (4) | 0.44264 (16) | 0.0181 (6) | |
C4 | 0.46065 (17) | 0.1777 (4) | 0.33577 (17) | 0.0183 (6) | |
C5 | 0.41619 (16) | 0.1458 (4) | 0.39736 (16) | 0.0168 (6) | |
C6 | 0.45776 (16) | 0.1982 (4) | 0.47945 (16) | 0.0174 (6) | |
C22 | 0.70206 (17) | 0.4150 (4) | 0.40547 (17) | 0.0235 (7) | |
C23 | 0.79284 (17) | 0.3612 (4) | 0.43935 (18) | 0.0245 (7) | |
C25 | 0.78156 (17) | 0.3764 (4) | 0.57213 (18) | 0.0253 (7) | |
C26 | 0.68964 (17) | 0.4318 (4) | 0.54463 (17) | 0.0231 (7) | |
O14 | 0.26393 (12) | 0.1139 (3) | 0.58789 (11) | 0.0239 (5) | |
O15 | 0.11595 (12) | 0.2754 (3) | 0.73012 (12) | 0.0275 (5) | |
O124 | −0.01980 (12) | 0.1750 (3) | 0.19404 (12) | 0.0271 (5) | |
N11 | 0.01877 (14) | 0.2418 (3) | 0.48437 (14) | 0.0208 (6) | |
N13 | 0.15311 (14) | 0.1339 (3) | 0.47926 (13) | 0.0195 (5) | |
N15 | 0.16550 (15) | 0.2226 (3) | 0.68759 (14) | 0.0232 (6) | |
N16 | −0.00794 (14) | 0.3182 (3) | 0.60244 (14) | 0.0231 (6) | |
N121 | 0.04458 (14) | 0.1733 (3) | 0.36273 (13) | 0.0216 (6) | |
C12 | 0.07195 (16) | 0.1834 (4) | 0.44332 (16) | 0.0179 (6) | |
C14 | 0.18951 (17) | 0.1515 (4) | 0.56167 (16) | 0.0186 (6) | |
C15 | 0.13228 (16) | 0.2137 (4) | 0.60790 (16) | 0.0173 (6) | |
C16 | 0.04671 (17) | 0.2577 (4) | 0.56427 (17) | 0.0178 (6) | |
C122 | 0.09100 (17) | 0.0866 (4) | 0.31082 (17) | 0.0229 (7) | |
C123 | 0.06930 (18) | 0.1744 (4) | 0.22942 (17) | 0.0266 (7) | |
C125 | −0.06061 (18) | 0.2797 (4) | 0.24350 (17) | 0.0232 (7) | |
C126 | −0.04640 (17) | 0.1950 (5) | 0.32512 (17) | 0.0268 (7) | |
O1 | 0.26335 (14) | 0.4099 (3) | 0.27529 (13) | 0.0413 (6) | |
H3 | 0.5725 | 0.2584 | 0.3300 | 0.024* | |
H6A | 0.4460 | 0.2089 | 0.5873 | 0.024* | |
H6B | 0.3698 | 0.1270 | 0.5278 | 0.024* | |
H22A | 0.6982 | 0.5476 | 0.3957 | 0.028* | |
H22B | 0.6790 | 0.3525 | 0.3536 | 0.028* | |
H23A | 0.7967 | 0.2273 | 0.4439 | 0.029* | |
H23B | 0.8264 | 0.4007 | 0.4020 | 0.029* | |
H25A | 0.8068 | 0.4276 | 0.6261 | 0.030* | |
H25B | 0.7857 | 0.2425 | 0.5761 | 0.030* | |
H26A | 0.6583 | 0.3808 | 0.5816 | 0.028* | |
H26B | 0.6850 | 0.5657 | 0.5457 | 0.028* | |
H13 | 0.1840 | 0.0887 | 0.4489 | 0.023* | |
H16A | −0.0596 | 0.3455 | 0.5754 | 0.028* | |
H16B | 0.0072 | 0.3312 | 0.6550 | 0.028* | |
H22C | 0.0767 | −0.0441 | 0.3053 | 0.028* | |
H22D | 0.1523 | 0.0976 | 0.3354 | 0.028* | |
H23C | 0.0903 | 0.3009 | 0.2344 | 0.032* | |
H23D | 0.0978 | 0.1083 | 0.1937 | 0.032* | |
H25C | −0.1218 | 0.2861 | 0.2178 | 0.028* | |
H25D | −0.0380 | 0.4049 | 0.2489 | 0.028* | |
H26C | −0.0718 | 0.2724 | 0.3597 | 0.032* | |
H26D | −0.0742 | 0.0748 | 0.3202 | 0.032* | |
H1A | 0.2263 | 0.4282 | 0.2284 | 0.062* | |
H1B | 0.2993 | 0.2813 | 0.2580 | 0.062* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O4 | 0.0213 (11) | 0.0324 (12) | 0.0143 (11) | −0.0041 (9) | 0.0029 (8) | −0.0021 (9) |
O5 | 0.0160 (10) | 0.0365 (12) | 0.0224 (11) | −0.0029 (9) | 0.0092 (9) | −0.0029 (9) |
O24 | 0.0161 (10) | 0.0312 (12) | 0.0250 (12) | −0.0005 (9) | 0.0062 (9) | 0.0003 (9) |
N1 | 0.0155 (12) | 0.0231 (13) | 0.0186 (13) | −0.0010 (10) | 0.0054 (10) | −0.0012 (10) |
N3 | 0.0157 (12) | 0.0284 (14) | 0.0160 (13) | −0.0037 (10) | 0.0060 (10) | −0.0013 (10) |
N5 | 0.0159 (12) | 0.0255 (14) | 0.0214 (13) | 0.0004 (10) | 0.0075 (10) | −0.0023 (11) |
N6 | 0.0150 (12) | 0.0301 (14) | 0.0152 (12) | −0.0023 (10) | 0.0038 (10) | −0.0017 (11) |
N21 | 0.0162 (12) | 0.0337 (15) | 0.0164 (13) | −0.0048 (10) | 0.0038 (10) | −0.0034 (11) |
C2 | 0.0143 (14) | 0.0221 (15) | 0.0173 (15) | 0.0016 (11) | 0.0028 (11) | 0.0016 (12) |
C4 | 0.0161 (14) | 0.0191 (15) | 0.0194 (16) | 0.0021 (11) | 0.0039 (12) | 0.0007 (12) |
C5 | 0.0141 (13) | 0.0195 (15) | 0.0164 (14) | 0.0020 (11) | 0.0032 (11) | −0.0007 (12) |
C6 | 0.0138 (14) | 0.0207 (15) | 0.0184 (15) | 0.0023 (11) | 0.0052 (11) | −0.0007 (12) |
C22 | 0.0211 (15) | 0.0280 (17) | 0.0225 (16) | −0.0084 (13) | 0.0075 (12) | −0.0011 (13) |
C23 | 0.0221 (16) | 0.0288 (17) | 0.0251 (17) | −0.0014 (13) | 0.0103 (13) | −0.0024 (13) |
C25 | 0.0195 (15) | 0.0293 (17) | 0.0254 (17) | −0.0016 (13) | 0.0028 (13) | 0.0008 (13) |
C26 | 0.0189 (15) | 0.0348 (18) | 0.0153 (15) | −0.0034 (13) | 0.0038 (12) | −0.0053 (13) |
O14 | 0.0156 (10) | 0.0359 (13) | 0.0198 (11) | 0.0027 (9) | 0.0036 (8) | 0.0009 (9) |
O15 | 0.0266 (11) | 0.0404 (13) | 0.0174 (11) | 0.0049 (10) | 0.0092 (9) | −0.0011 (9) |
O124 | 0.0218 (11) | 0.0422 (13) | 0.0172 (11) | 0.0068 (9) | 0.0049 (9) | −0.0006 (9) |
N11 | 0.0169 (12) | 0.0299 (14) | 0.0162 (13) | 0.0029 (10) | 0.0051 (10) | 0.0004 (10) |
N13 | 0.0186 (12) | 0.0250 (13) | 0.0154 (12) | 0.0029 (10) | 0.0050 (10) | −0.0023 (10) |
N15 | 0.0216 (13) | 0.0309 (15) | 0.0175 (13) | 0.0009 (11) | 0.0057 (10) | −0.0024 (11) |
N16 | 0.0186 (12) | 0.0354 (15) | 0.0157 (13) | 0.0044 (11) | 0.0050 (10) | −0.0003 (11) |
N121 | 0.0161 (12) | 0.0342 (15) | 0.0147 (13) | 0.0018 (10) | 0.0043 (10) | −0.0018 (11) |
C12 | 0.0132 (13) | 0.0237 (15) | 0.0167 (15) | 0.0007 (11) | 0.0035 (11) | 0.0027 (12) |
C14 | 0.0183 (15) | 0.0210 (15) | 0.0165 (15) | −0.0029 (12) | 0.0047 (12) | 0.0017 (12) |
C15 | 0.0150 (14) | 0.0221 (15) | 0.0156 (14) | −0.0003 (11) | 0.0057 (11) | 0.0011 (12) |
C16 | 0.0184 (14) | 0.0191 (15) | 0.0172 (15) | −0.0013 (11) | 0.0069 (12) | 0.0028 (11) |
C122 | 0.0210 (15) | 0.0319 (17) | 0.0174 (15) | 0.0034 (13) | 0.0076 (12) | −0.0033 (13) |
C123 | 0.0215 (15) | 0.0391 (19) | 0.0207 (16) | 0.0049 (14) | 0.0083 (13) | 0.0014 (14) |
C125 | 0.0183 (14) | 0.0326 (18) | 0.0185 (16) | 0.0029 (13) | 0.0047 (12) | −0.0018 (13) |
C126 | 0.0137 (14) | 0.045 (2) | 0.0208 (16) | 0.0006 (13) | 0.0023 (12) | 0.0022 (14) |
O1 | 0.0385 (14) | 0.0480 (16) | 0.0317 (14) | 0.0030 (11) | −0.0015 (11) | 0.0038 (11) |
Geometric parameters (Å, º) top
O4—C4 | 1.225 (3) | O15—N15 | 1.286 (3) |
O5—N5 | 1.284 (3) | O124—C123 | 1.434 (3) |
O24—C23 | 1.429 (3) | O124—C125 | 1.435 (3) |
O24—C25 | 1.435 (3) | N11—C12 | 1.327 (3) |
N1—C2 | 1.323 (3) | N11—C16 | 1.339 (3) |
N1—C6 | 1.344 (3) | N13—C12 | 1.368 (3) |
N3—C2 | 1.370 (3) | N13—C14 | 1.397 (3) |
N3—C4 | 1.384 (3) | N13—H13 | 0.88 |
N3—H3 | 0.88 | N15—C15 | 1.341 (3) |
N5—C5 | 1.337 (3) | N16—C16 | 1.318 (3) |
N6—C6 | 1.317 (3) | N16—H16A | 0.88 |
N6—H6A | 0.88 | N16—H16B | 0.88 |
N6—H6B | 0.88 | N121—C12 | 1.346 (3) |
N21—C2 | 1.330 (3) | N121—C122 | 1.461 (3) |
N21—C26 | 1.469 (3) | N121—C126 | 1.477 (3) |
N21—C22 | 1.470 (3) | C14—C15 | 1.452 (4) |
C4—C5 | 1.451 (4) | C15—C16 | 1.451 (4) |
C5—C6 | 1.455 (4) | C122—C123 | 1.501 (4) |
C22—C23 | 1.508 (4) | C122—H22C | 0.99 |
C22—H22A | 0.99 | C122—H22D | 0.99 |
C22—H22B | 0.99 | C123—H23C | 0.99 |
C23—H23A | 0.99 | C123—H23D | 0.99 |
C23—H23B | 0.99 | C125—C126 | 1.499 (4) |
C25—C26 | 1.518 (4) | C125—H25C | 0.99 |
C25—H25A | 0.99 | C125—H25D | 0.99 |
C25—H25B | 0.99 | C126—H26C | 0.99 |
C26—H26A | 0.99 | C126—H26D | 0.99 |
C26—H26B | 0.99 | O1—H1A | 0.89 |
O14—C14 | 1.222 (3) | O1—H1B | 1.19 |
| | | |
C23—O24—C25 | 109.6 (2) | C12—N11—C16 | 118.4 (2) |
C2—N1—C6 | 119.2 (2) | C12—N13—C14 | 123.3 (2) |
C2—N3—C4 | 124.2 (2) | C12—N13—H13 | 118.3 |
C2—N3—H3 | 117.9 | C14—N13—H13 | 118.3 |
C4—N3—H3 | 117.9 | O15—N15—C15 | 116.4 (2) |
O5—N5—C5 | 117.6 (2) | C16—N16—H16A | 120.0 |
C6—N6—H6A | 120.0 | C16—N16—H16B | 120.0 |
C6—N6—H6B | 120.0 | H16A—N16—H16B | 120.0 |
H6A—N6—H6B | 120.0 | C12—N121—C122 | 124.4 (2) |
C2—N21—C26 | 120.6 (2) | C12—N121—C126 | 118.7 (2) |
C2—N21—C22 | 124.9 (2) | C122—N121—C126 | 114.0 (2) |
C26—N21—C22 | 113.5 (2) | N11—C12—N121 | 118.3 (2) |
N1—C2—N21 | 119.0 (3) | N11—C12—N13 | 122.9 (2) |
N1—C2—N3 | 122.0 (2) | N121—C12—N13 | 118.8 (2) |
N21—C2—N3 | 119.0 (2) | O14—C14—N13 | 118.8 (2) |
O4—C4—N3 | 119.9 (2) | O14—C14—C15 | 126.6 (3) |
O4—C4—C5 | 125.7 (2) | N13—C14—C15 | 114.6 (2) |
N3—C4—C5 | 114.4 (2) | N15—C15—C16 | 127.3 (2) |
N5—C5—C4 | 115.2 (2) | N15—C15—C14 | 115.1 (2) |
N5—C5—C6 | 126.9 (2) | C16—C15—C14 | 117.6 (2) |
C4—C5—C6 | 117.8 (2) | N16—C16—N11 | 116.3 (2) |
N6—C6—N1 | 117.0 (2) | N16—C16—C15 | 120.7 (2) |
N6—C6—C5 | 120.9 (2) | N11—C16—C15 | 123.0 (2) |
N1—C6—C5 | 122.1 (2) | N121—C122—C123 | 110.2 (2) |
N21—C22—C23 | 109.4 (2) | N121—C122—H22C | 109.6 |
N21—C22—H22A | 109.8 | C123—C122—H22C | 109.6 |
C23—C22—H22A | 109.8 | N121—C122—H22D | 109.6 |
N21—C22—H22B | 109.8 | C123—C122—H22D | 109.6 |
C23—C22—H22B | 109.8 | H22C—C122—H22D | 108.1 |
H22A—C22—H22B | 108.2 | O124—C123—C122 | 111.8 (2) |
O24—C23—C22 | 111.7 (2) | O124—C123—H23C | 109.3 |
O24—C23—H23A | 109.3 | C122—C123—H23C | 109.3 |
C22—C23—H23A | 109.3 | O124—C123—H23D | 109.3 |
O24—C23—H23B | 109.3 | C122—C123—H23D | 109.3 |
C22—C23—H23B | 109.3 | H23C—C123—H23D | 107.9 |
H23A—C23—H23B | 107.9 | O124—C125—C126 | 110.3 (2) |
O24—C25—C26 | 110.6 (2) | O124—C125—H25C | 109.6 |
O24—C25—H25A | 109.5 | C126—C125—H25C | 109.6 |
C26—C25—H25A | 109.5 | O124—C125—H25D | 109.6 |
O24—C25—H25B | 109.5 | C126—C125—H25D | 109.6 |
C26—C25—H25B | 109.5 | H25C—C125—H25D | 108.1 |
H25A—C25—H25B | 108.1 | N121—C126—C125 | 110.7 (2) |
N21—C26—C25 | 109.9 (2) | N121—C126—H26C | 109.5 |
N21—C26—H26A | 109.7 | C125—C126—H26C | 109.5 |
C25—C26—H26A | 109.7 | N121—C126—H26D | 109.5 |
N21—C26—H26B | 109.7 | C125—C126—H26D | 109.5 |
C25—C26—H26B | 109.7 | H26C—C126—H26D | 108.1 |
H26A—C26—H26B | 108.2 | H1A—O1—H1B | 99.4 |
C123—O124—C125 | 109.3 (2) | | |
| | | |
C6—N1—C2—N21 | −178.5 (3) | C16—N11—C12—N121 | −177.8 (3) |
C6—N1—C2—N3 | 0.9 (4) | C16—N11—C12—N13 | 2.0 (4) |
C26—N21—C2—N1 | −5.2 (4) | C122—N121—C12—N11 | −170.3 (3) |
C22—N21—C2—N1 | −173.2 (3) | C126—N121—C12—N11 | −10.9 (4) |
C26—N21—C2—N3 | 175.4 (2) | C122—N121—C12—N13 | 9.9 (4) |
C22—N21—C2—N3 | 7.5 (4) | C126—N121—C12—N13 | 169.3 (3) |
C4—N3—C2—N1 | 3.1 (4) | C14—N13—C12—N11 | −4.5 (4) |
C4—N3—C2—N21 | −177.6 (3) | C14—N13—C12—N121 | 175.3 (2) |
C2—N3—C4—O4 | 174.6 (3) | C12—N13—C14—O14 | −175.7 (3) |
C2—N3—C4—C5 | −5.3 (4) | C12—N13—C14—C15 | 4.6 (4) |
O5—N5—C5—C4 | −179.1 (2) | O15—N15—C15—C16 | 0.2 (4) |
O5—N5—C5—C6 | −1.6 (4) | O15—N15—C15—C14 | −179.3 (2) |
O4—C4—C5—N5 | 1.8 (4) | O14—C14—C15—N15 | −2.8 (4) |
N3—C4—C5—N5 | −178.4 (2) | N13—C14—C15—N15 | 176.9 (2) |
O4—C4—C5—C6 | −176.0 (3) | O14—C14—C15—C16 | 177.7 (3) |
N3—C4—C5—C6 | 3.8 (4) | N13—C14—C15—C16 | −2.7 (4) |
C2—N1—C6—N6 | 178.6 (2) | C12—N11—C16—N16 | 179.2 (3) |
C2—N1—C6—C5 | −2.1 (4) | C12—N11—C16—C15 | −0.2 (4) |
N5—C5—C6—N6 | 1.4 (4) | N15—C15—C16—N16 | 1.8 (4) |
C4—C5—C6—N6 | 179.0 (2) | C14—C15—C16—N16 | −178.7 (3) |
N5—C5—C6—N1 | −177.9 (3) | N15—C15—C16—N11 | −178.9 (3) |
C4—C5—C6—N1 | −0.3 (4) | C14—C15—C16—N11 | 0.6 (4) |
C2—N21—C22—C23 | −139.7 (3) | C12—N121—C122—C123 | −151.3 (3) |
C26—N21—C22—C23 | 51.6 (3) | C126—N121—C122—C123 | 48.5 (3) |
C25—O24—C23—C22 | 61.8 (3) | C125—O124—C123—C122 | 62.2 (3) |
N21—C22—C23—O24 | −56.0 (3) | N121—C122—C123—O124 | −54.6 (3) |
C23—O24—C25—C26 | −61.2 (3) | C123—O124—C125—C126 | −62.3 (3) |
C2—N21—C26—C25 | 138.8 (3) | C12—N121—C126—C125 | 149.0 (3) |
C22—N21—C26—C25 | −52.0 (3) | C122—N121—C126—C125 | −49.6 (3) |
O24—C25—C26—N21 | 56.0 (3) | O124—C125—C126—N121 | 55.7 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···N5i | 0.89 | 2.08 | 2.916 (3) | 157 |
O1—H1B···O4 | 1.19 | 2.37 | 3.423 (3) | 146 |
N3—H3···O15ii | 0.88 | 2.04 | 2.882 (3) | 161 |
N6—H6A···O124iii | 0.88 | 1.97 | 2.835 (3) | 166 |
N6—H6B···O5 | 0.88 | 1.98 | 2.623 (3) | 129 |
N6—H6B···O14 | 0.88 | 2.24 | 2.943 (3) | 137 |
N13—H13···O5 | 0.88 | 2.03 | 2.838 (3) | 152 |
N16—H16A···O24iv | 0.88 | 2.00 | 2.875 (3) | 173 |
N16—H16B···O15 | 0.88 | 1.96 | 2.605 (3) | 129 |
N16—H16B···O4v | 0.88 | 2.49 | 3.176 (3) | 136 |
C22—H22B···O15ii | 0.99 | 2.31 | 3.300 (4) | 175 |
C122—H22D···O5 | 0.99 | 2.49 | 3.447 (3) | 162 |
Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (ii) x+1/2, −y+1/2, z−1/2; (iii) x+1/2, −y+1/2, z+1/2; (iv) x−1, y, z; (v) x−1/2, −y+1/2, z+1/2. |
Experimental details
| (I) | (II) | (III) |
Crystal data |
Chemical formula | C9H13N5O3 | C4H10NO+·C8H10N5O3− | C8H11N5O3·0.5H2O |
Mr | 239.24 | 312.34 | 234.23 |
Crystal system, space group | Monoclinic, P21/n | Monoclinic, I2/a | Monoclinic, P21/n |
Temperature (K) | 120 | 120 | 120 |
a, b, c (Å) | 8.9122 (6), 11.9051 (7), 10.4111 (4) | 9.4410 (11), 16.347 (4), 18.799 (5) | 16.421 (2), 7.3671 (12), 17.205 (4) |
β (°) | 105.649 (3) | 90.045 (15) | 104.794 (12) |
V (Å3) | 1063.68 (10) | 2901.3 (11) | 2012.4 (6) |
Z | 4 | 8 | 8 |
Radiation type | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.12 | 0.11 | 0.12 |
Crystal size (mm) | 0.41 × 0.28 × 0.25 | 0.26 × 0.10 × 0.10 | 0.44 × 0.34 × 0.21 |
|
Data collection |
Diffractometer | Bruker–Nonius KappaCCD diffractometer | Bruker–Nonius KappaCCD diffractometer | Bruker–Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) | Multi-scan (SADABS; Sheldrick, 2003) | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.959, 0.972 | 0.977, 0.989 | 0.953, 0.975 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 25676, 2445, 1516 | 33473, 3354, 2361 | 47024, 4646, 2535 |
Rint | 0.068 | 0.048 | 0.098 |
(sin θ/λ)max (Å−1) | 0.650 | 0.649 | 0.650 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.054, 0.159, 1.06 | 0.049, 0.109, 1.09 | 0.058, 0.162, 1.05 |
No. of reflections | 2445 | 3354 | 4646 |
No. of parameters | 155 | 199 | 298 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.33, −0.31 | 0.25, −0.27 | 0.32, −0.41 |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···O24i | 0.88 | 1.98 | 2.848 (3) | 168 |
N6—H6B···O5 | 0.88 | 1.98 | 2.619 (3) | 129 |
N6—H6B···O4ii | 0.88 | 2.35 | 2.896 (3) | 121 |
Symmetry codes: (i) −x+3/2, y+1/2, −z+1/2; (ii) −x+3/2, y+1/2, −z+3/2. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···O5i | 0.88 | 2.02 | 2.872 (2) | 163 |
N6—H6B···O5 | 0.88 | 1.95 | 2.608 (2) | 130 |
N31—H31A···O4ii | 0.92 | 2.08 | 2.868 (2) | 143 |
N31—H31A···N5ii | 0.92 | 2.21 | 2.939 (2) | 136 |
N31—H31B···O4 | 0.92 | 1.85 | 2.711 (2) | 154 |
Symmetry codes: (i) x−1/2, −y+1, z; (ii) −x+3/2, −y+3/2, −z+1/2. |
Hydrogen-bond geometry (Å, º) for (III) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1A···N5i | 0.89 | 2.08 | 2.916 (3) | 157 |
O1—H1B···O4 | 1.19 | 2.37 | 3.423 (3) | 146 |
N3—H3···O15ii | 0.88 | 2.04 | 2.882 (3) | 161 |
N6—H6A···O124iii | 0.88 | 1.97 | 2.835 (3) | 166 |
N6—H6B···O5 | 0.88 | 1.98 | 2.623 (3) | 129 |
N6—H6B···O14 | 0.88 | 2.24 | 2.943 (3) | 137 |
N13—H13···O5 | 0.88 | 2.03 | 2.838 (3) | 152 |
N16—H16A···O24iv | 0.88 | 2.00 | 2.875 (3) | 173 |
N16—H16B···O15 | 0.88 | 1.96 | 2.605 (3) | 129 |
N16—H16B···O4v | 0.88 | 2.49 | 3.176 (3) | 136 |
Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (ii) x+1/2, −y+1/2, z−1/2; (iii) x+1/2, −y+1/2, z+1/2; (iv) x−1, y, z; (v) x−1/2, −y+1/2, z+1/2. |
Selected bond distances and angles (Å, °) for compounds (I)–(III) topParameter | | (I) | (II) | (III), mol 1 | (III), mol 2 |
| | x = nil | x = nil | x = nil | x = 1 |
Nx1—Cx2 | | 1.315 (3) | 1.353 (2) | 1.323 (3) | 1.327 (3) |
Cx2—Nx3 | | 1.376 (3) | 1.353 (2) | 1.370 (3) | 1.368 (3) |
Nx3—Cx4 | | 1.415 (3) | 1.346 (2) | 1.384 (3) | 1.397 (3) |
Cx4—Cx5 | | 1.447 (3) | 1.472 (3) | 1.451 (4) | 1.452 (4) |
Cx5—Cx6 | | 1.435 (3) | 1.450 (2) | 1.455 (4) | 1.451 (4) |
Cx6—Nx1 | | 1.357 (3) | 1.331 (2) | 1.344 (3) | 1.339 (3) |
Cx2—Nx21 | | 1.358 (3) | 1.352 (2) | 1.330 (3) | 1.346 (3) |
Cx4—Ox4 | | 1.221 (3) | 1.260 (2) | 1.225 (3) | 1.222 (3) |
Cx5—Nx5 | | 1.358 (3) | 1.327 (2) | 1.337 (3) | 1.341 (3) |
Nx5—Ox5 | | 1.275 (3) | 1.307 (2) | 1.284 (3) | 1.286 (3) |
Cx6—Nx6 | | 1.316 (3) | 1.328 (2) | 1.317 (3) | 1.318 (3) |
Δa | | 0.083 (3) | 0.020 (2) | 0.053 (3) | 0.055 (3) |
Cx6—Cx5—Nx5—Ox5 | | 0.0 (3) | -2.3 (3) | -1.6 (4) | 0.2 (4) |
Notes: (a) Δ is the bond-length difference [d(Cx5—Nx5) - d(Nx5—Ox5)]. |
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Substituted 6-amino-5-nitrosopyrimidines often form intramolecular N—H···O hydrogen bonds and hence they are isoelectronic and approximately isosteric with the correspondingly substituted purines. The presence of the 5-nitroso substituent strongly activates nucleophilic displacement of 2-methoxy or 2-methylsulfanyl substituents and this has proven to provide an effective and versatile synthetic route to a wide range of 2-substituted derivatives (Melguizo et al., 2002). The use of 2-methylsulfanyl derivatives as substrates is particular attractive as the low boiling temperature of the methanethiol by-product (ca 279 K at normal pressure) means that this component is readily removed as the reaction proceeds, so driving the substitution to completion.
Thus, reaction of 6-amino-3-methyl-2-methylsulfanyl-5-nitrosopyrimidin-4(3H)-one with morpholine gave 6-amino-3-methyl-2-(morpholin-4-yl)-5-nitrosopyrimidin-4(3H)-one, (I) (see reaction scheme below), while a similar reaction using 6-amino-2-methylsulfanyl-5-nitrosopyrimidin-4(3H)-one provided 6-amino-2-(morpholin-4-yl)-5-nitrosopyrimidin-4(3H)-one, (IV); recrystallization of (IV) from water gave the hemihydrate (III), while crystallization in the presence of morpholine gave the salt morpholin-4-ium 4-amino-2-(morpholin-4-yl)-5-nitroso-6-oxo-1,6-dihydropyrimidin-1-ide, (II). Accordingly, we have been able to compare the intramolecular metrics of both the neutral pyrimidinone (IV), as it occurs in the hemihydrate (III), and the corresponding conjugate anion, as it occurs in the salt (II).
While the morpholine rings in compounds (I)–(III) (Figs. 1–3) all adopt chair conformations, the pyrimidine rings are, in every case, effectively planar; the maximum deviation from the mean ring planes are 0.033 (2) Å for atom N3 in (I), 0.033 (2) Å for C4 and C5 in (II), and 0.028 (3) Å for N3 in (III). This may be contrasted with the boat conformation found for the pyrimidine ring in the related compound 2-amino-4,6-bis(morpholin-4-yl)-5-nitrosopyrimidine, (V) (Quesada et al., 2004), and the boat (Trilleras et al., 2008) and twist-boat (Quesada et al., 2002, 2003; Melguizo et al., 2003) conformations found in a number of other heavily substituted pyrimidines. In compounds (I)–(III), the three adjacent substituents at positions 4, 5 and 6 are of low steric bulk, and the planarity of the pyrimidine rings in these examples is consistent with our earlier suggestion that the ring puckering in substituted pyrmidines is a direct consequence of steric clashes between bulky substituents in these adjacent positions (Melguizo et al., 2003). The orientation of the nitrosyl substituents, which are all effectively coplanar with the adjacent pyrimidine rings, allowing the formation of intramolecular N—H···O hydrogen bonds (Table 1–3) are almost certainly controlled by the electronic structures discussed below.
The pyrimidine components of compounds (I)–(III) show a number of values (Table 4) which are atypical of their general types (Allen et al., 1987), but which are typical of those commonly observed in related aminonitrosopyrimidines (Low et al., 2000, 2001; Melguizo et al., 2003; Quesada et al., 2002, 2004). The discussion of these distances and their significance is based, to a large extent, on our earlier analysis (Low et al., 2000) of the molecular structures of some nitrosopyrimidinyl derivatives of amino acids, where the analysis of the experimental structures was supported by database and molecular-modelling studies. This analysis showed that the difference between the bond distances C—N and N—O, conveniently denoted as Δ, provides a powerful diagnostic tool for the identification of polarized molecular–electronic structures in such compounds. In simple C-nitroso compounds where there is no possibility of significant electronic delocalization, the difference between the C—N and N—O bond distances usually exceeds 0.20 Å (Talberg, 1977; Schlemper et al., 1986), while the N—O distances rarely exceed 1.25 Å (Davis et al., 1965; Bauer & Andreassen, 1972; Talberg, 1977; Schlemper et al., 1986). However, in each of compounds (I)–(III), the value of Δ is significantly less than 0.10 Å, while the N—O distances always exceed 1.27 Å (Table 4), and the observed values here can be taken as diagnostic of significant electronic delocalization (Low et al., 2000).
In the neutral compound (I), where the polarization is least marked, as judged by the magnitude of Δ, the C6—N6 bond is short for its type (Allen et al., 1987), while the C2—N21 bond distance is fairly typical of its type; in addition, the C4—C5 and C5—C6 distances have very similar lengths, although in the classical representation of (I), these are formally single and double bonds, respectively; on the other hand the N1—C2 bond, which is formally a double bond, is significantly shorter than any other C—N bond within the ring. These observations taken together point to the polarized form (Ia) (see second scheme) as an important contributor to the overall molecular–electronic structure, in addition to the classical unpolarized form (I).
The anionic component of the salt (II) shows the most marked polarization, as indicated by the very small value of Δ. In addition, the C6—N1 and C6—N6 bonds have effectively identical lengths, and the C—O bond is long for its type, while the N3—C4 bond is much shorter in (II) than in (I). The combination of these observations points to the importance of the polarized form (IIa) (see second scheme) as a contributor to the overall molecular–electronic structure. The additional observation that the C2—N1, C2—N3 and C2—N21 bonds have lengths which are identical within experimental uncertainty suggests that form (IIb), where the positive charge is delocalized over four N centres (N1, N3, N6 and N21) in an aminomethyleneguanidinium fragment, may also be significant.
In compound (III), the dimensions of the two independent pyrimidine components are very similar. The values of Δ are intermediate between those in compounds (I) and (II), but the general pattern in the intermolecular distances resembles that in (I). Thus, the Cx4—Cx5 and Cx5—Cx6 distances (x = nil or 1) are identical; the Cx6—Nx6 distances do not differ from the corresponding distance in (I); and the C—O distances are normal, although the Nx3—Cx4 distances are somewhat shorter than the N3—C4 distance in (I), whereas a modest lengthening might have been expected. A polarized structure of the same type as (Ia) is indicated, but with the degree of polarization somewhat enhanced over that in compound (I).
For each of compounds (I)–(III), the supramolecular aggregation is dominated by the formation of hydrogen-bonded sheets. In (I), the sheet is built from just three hydrogen bonds, all of N—H···O type (Table 1). Amino atom N6 in the molecule at (x, y, z) acts as hydrogen-bond donor, via H6A and H6B, respectively, to morpholine atom O24 in the molecule at (1.5 - x, 1/2 + y, 1/2 - z), and ketonic atom O4 in the molecule at (1.5 - x, 1/2 + y, 1.5 - z); the latter of these is, in fact, the longer component of a planar three-centre N—H···(O)2 system (Table 1). These intermolecular interactions, acting independently, generate C(9) and C(6) chains, respectively, both running parallel to the [010] direction, and in combination they generate a sheet lying parallel to (100) containing equal numbers of S(6) and R44(26) (Bernstein et al., 1995) rings (Fig. 4). Two sheets of this type, occupying the domains 0 < x < 1/2, and 0.5 < x < 1.0, respectively, and related to one another by inversion, pass through each unit cell, but there are no direction-specific interactions between adjacent sheets.
The formation of the sheet structure of compound (II) is somewhat more complex than that in compound (I); not only are there two independent molecular species present, but the number of hydrogen bonds (Table 2) is also greater. However, the sheet formation is quite easily analysed in terms of a centrosymmetric aggregate containing two ions of each type (Fig. 5). Within the asymmetric unit, ammonium atom N31 acts as hydrogen-bond donor, via H31B, to atom O4 in the anion. The same atom N31 at the cation at (x, y, z) also acts as hydrogen-bond donor, via H31A, to atoms O4 and N5 in the anion at (1.5 - x, 1.5 - y, 1/2 - z), in an effectively planar three-centre N—H···(N,O) system. The resulting centrosymmetric aggregate (Fig. 5), which is centred at (3/4, 3/4, 1/4), contains a central R42(8) ring along with two symmetry-related R12(5) rings and two S(6) rings. In the final hydrogen bond, atom N6 in the anion at (x, y, z) acts as donor to atom O4 in the anion at (-1/2 + x, 1 - y, z), and by this means the aggregate centred at (3/4, 3/4, 1/4) is directly linked to those at (1/4, 1/4, 1/4), (1/4, 1.25, 1/4), (1.25, 1/4, 1/4) and (1.25, 1.25, 1/4), so forming a sheet parallel to (001). This sheet thus contains four types of ring, S(6), R12(5), R42(8) and R88(30), the last two of which are both centrosymmetric (Fig. 6). Two sheets of this type, occupying the domains 0 < z < 1/2, and 0.5 < z < 1.0, respectively, and related to one another by inversion, pass through each unit cell, but there are no direction-specific interactions between adjacent sheets.
There are three independent molecular components, all neutral, in compound (III), and they are linked by a large number of hydrogen bonds, encompassing O—H···O, O—H···N and N—H···O types (Table 3), into a three-dimensional framework. The two organic components are linked into sheets built from six independent intermolecular N—H···O hydrogen bonds, and these sheets are linked by the water molecules to form the three-dimensional structure.
Within the asymmetric unit, atoms N6 and N13 act as hydrogen-bond donors to O14 and O5, respectively (Fig. 3). Similarly, atoms N16 and N3 act as donors, respectively, to O4 at (-1/2 + x, 1/2 - y, 1/2 + z) and O155 at (1/2 + x, 1/2 - y, -1/2 + z). This combination of four hydrogen bonds thus generates a chain of rings running parallel to the [101] direction and built from molecules related by the n-glide plane at y = 0.25 (Fig. 7). In addition, atom N6 at (x, y, z) acts as donor to morpholine atom O124 at (1/2 + x, 1/2 - y, 1/2 + z), so generating a second chain of rings, this time running parallel to the [101] direction, but again built from molecules related by the n-glide plane at y = 1/4, while atom N16 at (x, y, z) acts as donor to morpholine atom O24 at (-1 + x, y, z), so generating by translation a third chain of rings, this time running parallel to the [100] direction. The combination of the chains along [100], [101] and [101] then generates a sheet parallel to (010) and containing five independent types of ring, two each of S(6) and R22(6) types, together with one type of R44(24) ring (Fig. 7).
Two such sheets, occupying the domains 0 < y < 1/2, and 0.5 < y < 1.0, respectively, and related to one another by inversion, pass through each unit cell, and adjacent sheets are linked by the water molecules. A combination of O—H···O and O—H···N hydrogen bonds forms a C22(7) chain running parallel to the [010] direction (Fig. 8), which links the sheets into a continuous three-dimensional structure.
In summary, compounds (I)–(III) all show polarized molecular–electronic structures, albeit in differing degrees, and the organic fragments in each compound are linked by hydrogen bonds into sheets of markedly different types, despite the rather small differences in molecular constitution between the pyrimidine fragments involved.