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2-Amino-4-chloro-5-formyl-6-[methyl(2-methylphenyl)amino]pyrimidine, C
13H
13ClN
4O, (I), and 2-amino-4-chloro-5-formyl-6-[(2-methoxyphenyl)methylamino]pyrimidine, C
13H
13ClN
4O
2, (II), are isostructural and essentially isomorphous. Although the pyrimidine rings in each compound are planar, the ring-substituent atoms show significant displacements from this plane, and the bond distances provide evidence for polarization of the electronic structures. In each compound, a combination of N-H
N and N-H
O hydrogen bonds links the molecules into sheets built from centrosymmetric
R22(8) and
R66(32) rings. The significance of this study lies in its observation of the isostructural nature of (I) and (II), and in the comparison of their crystal and molecular structures with those of analogous compounds.
Supporting information
CCDC references: 718121; 718122
A solution containing 1 mmol of each of 2-amino-4,6-dichloro-5-formylpyrimidine,
the appropriate secondary amine [methyl(2-methylphenyl)amine for (I) and
methyl(2-methoxyphenyl)amine for (II)] and triethylamine as a base, in ethanol
(5 ml), was heated under reflux for 3 h. The mixtures were cooled to ambient
temperature and the resulting solid products were collected by filtration,
washed with cold ethanol and dried in air before being recrystallized from
ethanol to give yellow crystals of (I) and (II) suitable for single-crystal
X-ray diffraction. Compound (I) (yield 80%, m.p. 456–458 K): MS (70 eV)
m/z (%) 278/276 (M+2/M+, 13/42), 261/260 (55/17),
259 (100), 212 (13), 198 (23), 129/128 (31/8), 92/91 (6/20); HR–MS calculated
for C13H13ClN4O: 276.0778, found 276.0780. Compound (II) (yield 81%,
m.p. 454–456 K): MS (70 eV) m/z (%) 294/292
(M+2/M+, 7/21), 263/261 (35/100), 234/233 (4/11), 131/129
(8/21); HR–MS calculated for C13H13ClN4O2 292.0727, found 292.0727.
All H atoms were located in difference maps and then treated as riding atoms
with C—H distances of 0.95 Å (aromatic) or 0.98 Å (methyl) and N—H
distances of 0.88 Å, and with Uiso(H) = kUeq(carrier),
where k = 1.5 for the methyl groups and k = 1.2 for all other H
atoms.
For both 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 and PRPKAPPA (Ferguson, 1999).
(I) 2-Amino-4-chloro-5-formyl-6-[methyl(2-methylphenyl)amino]pyrimidine
top
Crystal data top
C13H13ClN4O | F(000) = 576 |
Mr = 276.72 | Dx = 1.431 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 2946 reflections |
a = 11.1502 (8) Å | θ = 3.0–27.5° |
b = 8.7271 (8) Å | µ = 0.30 mm−1 |
c = 13.7129 (13) Å | T = 120 K |
β = 105.676 (7)° | Block, yellow |
V = 1284.75 (19) Å3 | 0.47 × 0.37 × 0.26 mm |
Z = 4 | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 2946 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 1999 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.059 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.0° |
ϕ & ω scans | h = −14→14 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −11→11 |
Tmin = 0.874, Tmax = 0.927 | l = −17→17 |
23784 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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.155 | H-atom parameters constrained |
S = 1.14 | w = 1/[σ2(Fo2) + (0.0691P)2 + 1.3411P] where P = (Fo2 + 2Fc2)/3 |
2946 reflections | (Δ/σ)max = 0.001 |
174 parameters | Δρmax = 0.38 e Å−3 |
0 restraints | Δρmin = −0.46 e Å−3 |
Crystal data top
C13H13ClN4O | V = 1284.75 (19) Å3 |
Mr = 276.72 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 11.1502 (8) Å | µ = 0.30 mm−1 |
b = 8.7271 (8) Å | T = 120 K |
c = 13.7129 (13) Å | 0.47 × 0.37 × 0.26 mm |
β = 105.676 (7)° | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 2946 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 1999 reflections with I > 2σ(I) |
Tmin = 0.874, Tmax = 0.927 | Rint = 0.059 |
23784 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.155 | H-atom parameters constrained |
S = 1.14 | Δρmax = 0.38 e Å−3 |
2946 reflections | Δρmin = −0.46 e Å−3 |
174 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
Cl4 | 0.27600 (6) | 0.19726 (7) | 0.66110 (5) | 0.0266 (2) | |
O51 | 0.33885 (18) | 0.5202 (2) | 0.66011 (14) | 0.0312 (5) | |
N1 | 0.0135 (2) | 0.3502 (2) | 0.37571 (16) | 0.0229 (5) | |
N2 | −0.0730 (2) | 0.1130 (3) | 0.37337 (17) | 0.0296 (6) | |
H21 | −0.1203 | 0.1273 | 0.3114 | 0.036* | |
H22 | −0.0780 | 0.0250 | 0.4034 | 0.036* | |
N3 | 0.09352 (19) | 0.1658 (2) | 0.50572 (16) | 0.0219 (5) | |
N61 | 0.10068 (19) | 0.5865 (2) | 0.37734 (16) | 0.0220 (5) | |
C2 | 0.0124 (2) | 0.2136 (3) | 0.4185 (2) | 0.0233 (6) | |
C4 | 0.1747 (2) | 0.2680 (3) | 0.55218 (19) | 0.0208 (5) | |
C5 | 0.1818 (2) | 0.4178 (3) | 0.52155 (19) | 0.0201 (5) | |
C6 | 0.0981 (2) | 0.4508 (3) | 0.42417 (19) | 0.0205 (5) | |
C51 | 0.2510 (2) | 0.5387 (3) | 0.58651 (19) | 0.0228 (6) | |
H51 | 0.2248 | 0.6412 | 0.5696 | 0.027* | |
C61 | 0.2129 (2) | 0.6742 (3) | 0.39104 (19) | 0.0236 (6) | |
C62 | 0.3198 (3) | 0.6077 (3) | 0.3760 (2) | 0.0260 (6) | |
C63 | 0.4239 (3) | 0.7010 (3) | 0.3885 (2) | 0.0303 (6) | |
H63 | 0.4989 | 0.6588 | 0.3798 | 0.036* | |
C64 | 0.4202 (3) | 0.8535 (4) | 0.4133 (2) | 0.0336 (7) | |
H64 | 0.4926 | 0.9151 | 0.4216 | 0.040* | |
C65 | 0.3128 (3) | 0.9177 (3) | 0.4261 (2) | 0.0314 (7) | |
H65 | 0.3106 | 1.0231 | 0.4427 | 0.038* | |
C66 | 0.2091 (3) | 0.8281 (3) | 0.4148 (2) | 0.0279 (6) | |
H66 | 0.1344 | 0.8716 | 0.4233 | 0.033* | |
C67 | 0.0030 (2) | 0.6215 (3) | 0.2848 (2) | 0.0273 (6) | |
H671 | 0.0264 | 0.5799 | 0.2262 | 0.041* | |
H672 | −0.0072 | 0.7328 | 0.2776 | 0.041* | |
H673 | −0.0756 | 0.5752 | 0.2888 | 0.041* | |
C68 | 0.3276 (3) | 0.4439 (3) | 0.3470 (2) | 0.0317 (7) | |
H681 | 0.2470 | 0.4112 | 0.3029 | 0.048* | |
H682 | 0.3489 | 0.3802 | 0.4081 | 0.048* | |
H683 | 0.3919 | 0.4327 | 0.3109 | 0.048* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Cl4 | 0.0291 (4) | 0.0224 (3) | 0.0232 (3) | −0.0017 (3) | −0.0019 (2) | 0.0032 (3) |
O51 | 0.0336 (11) | 0.0268 (11) | 0.0271 (10) | −0.0027 (8) | −0.0025 (8) | −0.0017 (8) |
N1 | 0.0236 (11) | 0.0198 (11) | 0.0239 (11) | −0.0013 (9) | 0.0037 (9) | 0.0000 (9) |
N2 | 0.0361 (13) | 0.0223 (12) | 0.0231 (12) | −0.0083 (10) | −0.0044 (10) | 0.0034 (9) |
N3 | 0.0239 (11) | 0.0190 (11) | 0.0200 (11) | −0.0019 (9) | 0.0013 (9) | 0.0007 (8) |
N61 | 0.0214 (10) | 0.0207 (11) | 0.0226 (11) | −0.0014 (9) | 0.0037 (9) | 0.0044 (9) |
C2 | 0.0234 (13) | 0.0218 (14) | 0.0241 (13) | −0.0014 (11) | 0.0053 (10) | −0.0002 (11) |
C4 | 0.0195 (12) | 0.0243 (14) | 0.0181 (12) | 0.0004 (10) | 0.0040 (10) | −0.0003 (10) |
C5 | 0.0185 (12) | 0.0191 (12) | 0.0222 (13) | −0.0005 (10) | 0.0046 (10) | −0.0010 (10) |
C6 | 0.0200 (12) | 0.0204 (13) | 0.0211 (12) | 0.0003 (10) | 0.0055 (10) | 0.0001 (10) |
C51 | 0.0257 (13) | 0.0215 (13) | 0.0213 (13) | −0.0012 (11) | 0.0062 (11) | −0.0003 (10) |
C61 | 0.0256 (13) | 0.0229 (14) | 0.0217 (13) | −0.0024 (11) | 0.0056 (10) | 0.0037 (10) |
C62 | 0.0299 (14) | 0.0262 (14) | 0.0231 (13) | −0.0002 (11) | 0.0092 (11) | 0.0015 (11) |
C63 | 0.0238 (13) | 0.0380 (17) | 0.0296 (15) | −0.0026 (12) | 0.0080 (11) | 0.0017 (13) |
C64 | 0.0299 (14) | 0.0364 (16) | 0.0347 (16) | −0.0120 (13) | 0.0088 (12) | −0.0031 (13) |
C65 | 0.0406 (16) | 0.0196 (14) | 0.0354 (16) | −0.0050 (12) | 0.0127 (13) | −0.0010 (12) |
C66 | 0.0306 (14) | 0.0255 (15) | 0.0281 (14) | −0.0007 (11) | 0.0088 (11) | 0.0024 (11) |
C67 | 0.0286 (14) | 0.0249 (14) | 0.0263 (14) | 0.0024 (11) | 0.0039 (11) | 0.0079 (11) |
C68 | 0.0324 (15) | 0.0287 (15) | 0.0352 (16) | 0.0003 (12) | 0.0113 (13) | −0.0043 (12) |
Geometric parameters (Å, º) top
Cl4—C4 | 1.725 (3) | C61—C62 | 1.391 (4) |
O51—C51 | 1.212 (3) | C62—C63 | 1.391 (4) |
N1—C6 | 1.328 (3) | C62—C68 | 1.492 (4) |
N1—C2 | 1.331 (3) | C63—C64 | 1.377 (4) |
N2—C2 | 1.320 (3) | C63—H63 | 0.9500 |
N2—H21 | 0.8800 | C64—C65 | 1.376 (4) |
N2—H22 | 0.8800 | C64—H64 | 0.9500 |
N3—C4 | 1.307 (3) | C65—C66 | 1.370 (4) |
N3—C2 | 1.355 (3) | C65—H65 | 0.9500 |
N61—C6 | 1.351 (3) | C66—H66 | 0.9500 |
N61—C61 | 1.435 (3) | C67—H671 | 0.9800 |
N61—C67 | 1.464 (3) | C67—H672 | 0.9800 |
C4—C5 | 1.382 (4) | C67—H673 | 0.9800 |
C5—C6 | 1.437 (3) | C68—H681 | 0.9800 |
C5—C51 | 1.460 (4) | C68—H682 | 0.9800 |
C51—H51 | 0.9500 | C68—H683 | 0.9800 |
C61—C66 | 1.385 (4) | | |
| | | |
C6—N1—C2 | 117.5 (2) | C63—C62—C68 | 119.2 (3) |
C2—N2—H21 | 121.8 | C61—C62—C68 | 123.6 (3) |
C2—N2—H22 | 119.3 | C64—C63—C62 | 121.2 (3) |
H21—N2—H22 | 118.6 | C64—C63—H63 | 119.4 |
C4—N3—C2 | 115.4 (2) | C62—C63—H63 | 119.4 |
C6—N61—C61 | 122.4 (2) | C65—C64—C63 | 120.6 (3) |
C6—N61—C67 | 119.2 (2) | C65—C64—H64 | 119.7 |
C61—N61—C67 | 114.9 (2) | C63—C64—H64 | 119.7 |
N2—C2—N1 | 118.7 (2) | C66—C65—C64 | 119.4 (3) |
N2—C2—N3 | 115.7 (2) | C66—C65—H65 | 120.3 |
N1—C2—N3 | 125.6 (2) | C64—C65—H65 | 120.3 |
N3—C4—C5 | 125.9 (2) | C65—C66—C61 | 120.1 (3) |
N3—C4—Cl4 | 112.53 (19) | C65—C66—H66 | 120.0 |
C5—C4—Cl4 | 121.58 (19) | C61—C66—H66 | 120.0 |
C4—C5—C6 | 113.3 (2) | N61—C67—H671 | 109.5 |
C4—C5—C51 | 124.2 (2) | N61—C67—H672 | 109.5 |
C6—C5—C51 | 121.7 (2) | H671—C67—H672 | 109.5 |
N1—C6—N61 | 116.4 (2) | N61—C67—H673 | 109.5 |
N1—C6—C5 | 121.9 (2) | H671—C67—H673 | 109.5 |
N61—C6—C5 | 121.7 (2) | H672—C67—H673 | 109.5 |
O51—C51—C5 | 125.9 (2) | C62—C68—H681 | 109.5 |
O51—C51—H51 | 117.0 | C62—C68—H682 | 109.5 |
C5—C51—H51 | 117.0 | H681—C68—H682 | 109.5 |
C66—C61—C62 | 121.5 (2) | C62—C68—H683 | 109.5 |
C66—C61—N61 | 117.9 (2) | H681—C68—H683 | 109.5 |
C62—C61—N61 | 120.6 (2) | H682—C68—H683 | 109.5 |
C63—C62—C61 | 117.2 (3) | | |
| | | |
C6—N1—C2—N2 | 178.1 (2) | C51—C5—C6—N61 | 16.0 (4) |
C6—N1—C2—N3 | −2.7 (4) | C4—C5—C51—O51 | 24.5 (4) |
C4—N3—C2—N2 | −177.4 (2) | C6—C5—C51—O51 | −165.8 (3) |
C4—N3—C2—N1 | 3.4 (4) | C6—N61—C61—C66 | −130.2 (3) |
C2—N3—C4—C5 | 1.8 (4) | C67—N61—C61—C66 | 71.3 (3) |
C2—N3—C4—Cl4 | −178.96 (18) | C6—N61—C61—C62 | 52.9 (3) |
N3—C4—C5—C6 | −6.7 (4) | C67—N61—C61—C62 | −105.7 (3) |
Cl4—C4—C5—C6 | 174.11 (18) | C66—C61—C62—C63 | 1.7 (4) |
N3—C4—C5—C51 | 163.7 (2) | N61—C61—C62—C63 | 178.6 (2) |
Cl4—C4—C5—C51 | −15.4 (4) | C66—C61—C62—C68 | −178.0 (3) |
C2—N1—C6—N61 | 177.4 (2) | N61—C61—C62—C68 | −1.1 (4) |
C2—N1—C6—C5 | −3.1 (4) | C61—C62—C63—C64 | −1.0 (4) |
C61—N61—C6—N1 | −150.2 (2) | C68—C62—C63—C64 | 178.7 (3) |
C67—N61—C6—N1 | 7.4 (3) | C62—C63—C64—C65 | −0.1 (5) |
C61—N61—C6—C5 | 30.3 (4) | C63—C64—C65—C66 | 0.5 (4) |
C67—N61—C6—C5 | −172.0 (2) | C64—C65—C66—C61 | 0.2 (4) |
C4—C5—C6—N1 | 7.3 (4) | C62—C61—C66—C65 | −1.4 (4) |
C51—C5—C6—N1 | −163.5 (2) | N61—C61—C66—C65 | −178.3 (2) |
C4—C5—C6—N61 | −173.3 (2) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H21···O51i | 0.88 | 2.38 | 3.052 (3) | 134 |
N2—H21···Cl4i | 0.88 | 2.58 | 3.377 (2) | 152 |
N2—H22···N3ii | 0.88 | 2.11 | 2.988 (3) | 171 |
Symmetry codes: (i) x−1/2, −y+1/2, z−1/2; (ii) −x, −y, −z+1. |
(II) 2-amino-4-chloro-5-formyl-6-[(2-methoxyphenyl)methylamino]pyrimidine,
top
Crystal data top
C13H13ClN4O2 | F(000) = 608 |
Mr = 292.72 | Dx = 1.465 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 3028 reflections |
a = 11.301 (4) Å | θ = 5.1–27.5° |
b = 8.642 (3) Å | µ = 0.30 mm−1 |
c = 14.568 (5) Å | T = 120 K |
β = 111.13 (3)° | Block, yellow |
V = 1327.1 (8) Å3 | 0.27 × 0.15 × 0.10 mm |
Z = 4 | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 3028 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 2010 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.103 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 5.1° |
ϕ & ω scans | h = −14→14 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −11→11 |
Tmin = 0.939, Tmax = 0.971 | l = −17→18 |
18363 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)] = 0.061 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.143 | H-atom parameters constrained |
S = 1.11 | w = 1/[σ2(Fo2) + (0.0331P)2 + 2.2466P] where P = (Fo2 + 2Fc2)/3 |
3028 reflections | (Δ/σ)max = 0.001 |
183 parameters | Δρmax = 0.52 e Å−3 |
0 restraints | Δρmin = −0.43 e Å−3 |
Crystal data top
C13H13ClN4O2 | V = 1327.1 (8) Å3 |
Mr = 292.72 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 11.301 (4) Å | µ = 0.30 mm−1 |
b = 8.642 (3) Å | T = 120 K |
c = 14.568 (5) Å | 0.27 × 0.15 × 0.10 mm |
β = 111.13 (3)° | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 3028 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2010 reflections with I > 2σ(I) |
Tmin = 0.939, Tmax = 0.971 | Rint = 0.103 |
18363 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.061 | 0 restraints |
wR(F2) = 0.143 | H-atom parameters constrained |
S = 1.11 | Δρmax = 0.52 e Å−3 |
3028 reflections | Δρmin = −0.43 e Å−3 |
183 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
Cl4 | 0.29508 (7) | 0.19761 (9) | 0.66058 (5) | 0.0241 (2) | |
O51 | 0.3466 (2) | 0.5266 (3) | 0.66721 (16) | 0.0321 (6) | |
O62 | 0.2775 (2) | 0.4567 (3) | 0.35443 (16) | 0.0278 (5) | |
N1 | 0.0035 (2) | 0.3539 (3) | 0.38243 (18) | 0.0209 (6) | |
N2 | −0.0827 (3) | 0.1147 (3) | 0.37770 (19) | 0.0278 (6) | |
H21 | −0.1363 | 0.1346 | 0.3180 | 0.033* | |
H22 | −0.0845 | 0.0245 | 0.4053 | 0.033* | |
N3 | 0.0973 (2) | 0.1654 (3) | 0.50714 (17) | 0.0201 (6) | |
N61 | 0.0854 (2) | 0.5970 (3) | 0.38828 (17) | 0.0200 (6) | |
C2 | 0.0078 (3) | 0.2147 (4) | 0.4235 (2) | 0.0220 (7) | |
C4 | 0.1823 (3) | 0.2694 (4) | 0.5542 (2) | 0.0190 (6) | |
C5 | 0.1841 (3) | 0.4226 (3) | 0.5264 (2) | 0.0195 (6) | |
C6 | 0.0915 (3) | 0.4556 (3) | 0.4320 (2) | 0.0192 (6) | |
C51 | 0.2564 (3) | 0.5449 (4) | 0.5920 (2) | 0.0207 (6) | |
H51 | 0.2300 | 0.6484 | 0.5738 | 0.025* | |
C61 | 0.1985 (3) | 0.6808 (4) | 0.3990 (2) | 0.0216 (6) | |
C62 | 0.2965 (3) | 0.6083 (4) | 0.3790 (2) | 0.0233 (7) | |
C63 | 0.4026 (3) | 0.6926 (4) | 0.3836 (2) | 0.0291 (7) | |
H63 | 0.4708 | 0.6435 | 0.3715 | 0.035* | |
C64 | 0.4090 (3) | 0.8477 (4) | 0.4057 (2) | 0.0329 (8) | |
H64 | 0.4814 | 0.9056 | 0.4080 | 0.039* | |
C65 | 0.3121 (3) | 0.9202 (4) | 0.4247 (2) | 0.0332 (8) | |
H65 | 0.3179 | 1.0274 | 0.4402 | 0.040* | |
C66 | 0.2063 (3) | 0.8368 (4) | 0.4212 (2) | 0.0262 (7) | |
H66 | 0.1390 | 0.8867 | 0.4341 | 0.031* | |
C67 | −0.0184 (3) | 0.6270 (4) | 0.2956 (2) | 0.0240 (7) | |
H671 | 0.0002 | 0.5782 | 0.2416 | 0.036* | |
H672 | −0.0280 | 0.7389 | 0.2844 | 0.036* | |
H673 | −0.0973 | 0.5840 | 0.2985 | 0.036* | |
C68 | 0.3775 (3) | 0.3746 (4) | 0.3389 (3) | 0.0337 (8) | |
H681 | 0.3985 | 0.4248 | 0.2864 | 0.051* | |
H682 | 0.3507 | 0.2678 | 0.3198 | 0.051* | |
H683 | 0.4523 | 0.3744 | 0.3998 | 0.051* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Cl4 | 0.0249 (4) | 0.0228 (4) | 0.0192 (4) | 0.0006 (3) | 0.0013 (3) | 0.0023 (3) |
O51 | 0.0321 (13) | 0.0264 (13) | 0.0283 (12) | −0.0041 (10) | −0.0004 (10) | −0.0012 (10) |
O62 | 0.0305 (12) | 0.0250 (12) | 0.0334 (13) | −0.0005 (10) | 0.0181 (10) | −0.0061 (10) |
N1 | 0.0257 (14) | 0.0181 (13) | 0.0170 (12) | −0.0019 (11) | 0.0054 (11) | 0.0007 (10) |
N2 | 0.0332 (15) | 0.0217 (14) | 0.0194 (13) | −0.0063 (12) | −0.0015 (11) | 0.0052 (11) |
N3 | 0.0239 (13) | 0.0184 (13) | 0.0170 (12) | −0.0024 (11) | 0.0060 (10) | −0.0001 (10) |
N61 | 0.0208 (13) | 0.0194 (13) | 0.0193 (13) | −0.0009 (11) | 0.0066 (10) | 0.0025 (10) |
C2 | 0.0265 (16) | 0.0210 (16) | 0.0182 (14) | −0.0018 (13) | 0.0075 (12) | 0.0008 (12) |
C4 | 0.0195 (14) | 0.0218 (16) | 0.0147 (13) | 0.0019 (12) | 0.0049 (11) | 0.0007 (11) |
C5 | 0.0212 (15) | 0.0202 (16) | 0.0174 (14) | −0.0021 (12) | 0.0074 (12) | −0.0008 (12) |
C6 | 0.0209 (15) | 0.0196 (15) | 0.0199 (15) | 0.0011 (12) | 0.0108 (12) | 0.0010 (12) |
C51 | 0.0227 (15) | 0.0212 (16) | 0.0208 (15) | −0.0029 (13) | 0.0109 (13) | 0.0010 (12) |
C61 | 0.0240 (15) | 0.0230 (16) | 0.0195 (15) | −0.0030 (13) | 0.0099 (12) | 0.0012 (12) |
C62 | 0.0264 (16) | 0.0247 (17) | 0.0185 (14) | −0.0022 (14) | 0.0078 (13) | 0.0004 (13) |
C63 | 0.0239 (16) | 0.0367 (19) | 0.0277 (17) | −0.0025 (15) | 0.0107 (13) | 0.0000 (15) |
C64 | 0.0322 (19) | 0.035 (2) | 0.0314 (18) | −0.0133 (16) | 0.0118 (15) | −0.0004 (15) |
C65 | 0.040 (2) | 0.0245 (18) | 0.0307 (18) | −0.0068 (16) | 0.0078 (16) | 0.0010 (14) |
C66 | 0.0310 (17) | 0.0235 (18) | 0.0261 (16) | −0.0024 (14) | 0.0126 (14) | 0.0011 (13) |
C67 | 0.0263 (16) | 0.0225 (16) | 0.0228 (16) | −0.0011 (13) | 0.0081 (13) | 0.0045 (13) |
C68 | 0.0337 (19) | 0.035 (2) | 0.0366 (19) | 0.0052 (16) | 0.0173 (16) | −0.0061 (16) |
Geometric parameters (Å, º) top
Cl4—C4 | 1.728 (3) | C51—H51 | 0.9500 |
O51—C51 | 1.208 (4) | C61—C66 | 1.382 (5) |
O62—C62 | 1.355 (4) | C61—C62 | 1.392 (4) |
O62—C68 | 1.420 (4) | C62—C63 | 1.383 (4) |
N1—C6 | 1.328 (4) | C63—C64 | 1.375 (5) |
N1—C2 | 1.336 (4) | C63—H63 | 0.9500 |
N2—C2 | 1.322 (4) | C64—C65 | 1.373 (5) |
N2—H21 | 0.8800 | C64—H64 | 0.9500 |
N2—H22 | 0.8800 | C65—C66 | 1.381 (5) |
N3—C4 | 1.314 (4) | C65—H65 | 0.9500 |
N3—C2 | 1.342 (4) | C66—H66 | 0.9500 |
N61—C6 | 1.369 (4) | C67—H671 | 0.9800 |
N61—C61 | 1.428 (4) | C67—H672 | 0.9800 |
N61—C67 | 1.458 (4) | C67—H673 | 0.9800 |
C4—C5 | 1.387 (4) | C68—H681 | 0.9800 |
C5—C6 | 1.425 (4) | C68—H682 | 0.9800 |
C5—C51 | 1.461 (4) | C68—H683 | 0.9800 |
| | | |
C62—O62—C68 | 117.8 (3) | O62—C62—C63 | 125.1 (3) |
C6—N1—C2 | 116.9 (3) | O62—C62—C61 | 115.3 (3) |
C2—N2—H21 | 120.2 | C63—C62—C61 | 119.6 (3) |
C2—N2—H22 | 119.3 | C64—C63—C62 | 119.8 (3) |
H21—N2—H22 | 120.3 | C64—C63—H63 | 120.1 |
C4—N3—C2 | 115.3 (3) | C62—C63—H63 | 120.1 |
C6—N61—C61 | 120.6 (3) | C65—C64—C63 | 120.9 (3) |
C6—N61—C67 | 118.6 (3) | C65—C64—H64 | 119.5 |
C61—N61—C67 | 113.6 (2) | C63—C64—H64 | 119.5 |
N2—C2—N1 | 117.8 (3) | C64—C65—C66 | 119.8 (3) |
N2—C2—N3 | 116.3 (3) | C64—C65—H65 | 120.1 |
N1—C2—N3 | 125.9 (3) | C66—C65—H65 | 120.1 |
N3—C4—C5 | 125.8 (3) | C65—C66—C61 | 119.9 (3) |
N3—C4—Cl4 | 112.8 (2) | C65—C66—H66 | 120.0 |
C5—C4—Cl4 | 121.4 (2) | C61—C66—H66 | 120.0 |
C4—C5—C6 | 112.9 (3) | N61—C67—H671 | 109.5 |
C4—C5—C51 | 124.2 (3) | N61—C67—H672 | 109.5 |
C6—C5—C51 | 122.0 (3) | H671—C67—H672 | 109.5 |
N1—C6—N61 | 115.8 (3) | N61—C67—H673 | 109.5 |
N1—C6—C5 | 122.6 (3) | H671—C67—H673 | 109.5 |
N61—C6—C5 | 121.6 (3) | H672—C67—H673 | 109.5 |
O51—C51—C5 | 126.1 (3) | O62—C68—H681 | 109.5 |
O51—C51—H51 | 116.9 | O62—C68—H682 | 109.5 |
C5—C51—H51 | 116.9 | H681—C68—H682 | 109.5 |
C66—C61—C62 | 120.0 (3) | O62—C68—H683 | 109.5 |
C66—C61—N61 | 120.0 (3) | H681—C68—H683 | 109.5 |
C62—C61—N61 | 119.8 (3) | H682—C68—H683 | 109.5 |
| | | |
C6—N1—C2—N2 | 176.6 (3) | C4—C5—C51—O51 | 20.8 (5) |
C6—N1—C2—N3 | −4.3 (5) | C6—C5—C51—O51 | −170.3 (3) |
C4—N3—C2—N2 | −176.4 (3) | C6—N61—C61—C66 | −134.2 (3) |
C4—N3—C2—N1 | 4.6 (4) | C67—N61—C61—C66 | 75.8 (3) |
C2—N3—C4—C5 | 2.0 (4) | C6—N61—C61—C62 | 51.2 (4) |
C2—N3—C4—Cl4 | −179.5 (2) | C67—N61—C61—C62 | −98.8 (3) |
N3—C4—C5—C6 | −7.6 (4) | C68—O62—C62—C63 | 4.7 (4) |
Cl4—C4—C5—C6 | 174.1 (2) | C68—O62—C62—C61 | −176.3 (3) |
N3—C4—C5—C51 | 162.2 (3) | C66—C61—C62—O62 | −177.6 (3) |
Cl4—C4—C5—C51 | −16.1 (4) | N61—C61—C62—O62 | −3.0 (4) |
C2—N1—C6—N61 | 179.8 (3) | C66—C61—C62—C63 | 1.4 (4) |
C2—N1—C6—C5 | −2.3 (4) | N61—C61—C62—C63 | 176.0 (3) |
C61—N61—C6—N1 | −145.5 (3) | O62—C62—C63—C64 | 177.5 (3) |
C67—N61—C6—N1 | 3.1 (4) | C61—C62—C63—C64 | −1.4 (5) |
C61—N61—C6—C5 | 36.6 (4) | C62—C63—C64—C65 | 0.9 (5) |
C67—N61—C6—C5 | −174.8 (3) | C63—C64—C65—C66 | −0.3 (5) |
C4—C5—C6—N1 | 7.6 (4) | C64—C65—C66—C61 | 0.2 (5) |
C51—C5—C6—N1 | −162.4 (3) | C62—C61—C66—C65 | −0.8 (5) |
C4—C5—C6—N61 | −174.6 (3) | N61—C61—C66—C65 | −175.4 (3) |
C51—C5—C6—N61 | 15.4 (4) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H21···O51i | 0.88 | 2.55 | 3.125 (4) | 124 |
N2—H21···Cl4i | 0.88 | 2.58 | 3.375 (3) | 150 |
N2—H22···N3ii | 0.88 | 2.12 | 2.983 (4) | 168 |
Symmetry codes: (i) x−1/2, −y+1/2, z−1/2; (ii) −x, −y, −z+1. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C13H13ClN4O | C13H13ClN4O2 |
Mr | 276.72 | 292.72 |
Crystal system, space group | Monoclinic, P21/n | Monoclinic, P21/n |
Temperature (K) | 120 | 120 |
a, b, c (Å) | 11.1502 (8), 8.7271 (8), 13.7129 (13) | 11.301 (4), 8.642 (3), 14.568 (5) |
β (°) | 105.676 (7) | 111.13 (3) |
V (Å3) | 1284.75 (19) | 1327.1 (8) |
Z | 4 | 4 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.30 | 0.30 |
Crystal size (mm) | 0.47 × 0.37 × 0.26 | 0.27 × 0.15 × 0.10 |
|
Data collection |
Diffractometer | Bruker–Nonius KappaCCD diffractometer | Bruker–Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.874, 0.927 | 0.939, 0.971 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23784, 2946, 1999 | 18363, 3028, 2010 |
Rint | 0.059 | 0.103 |
(sin θ/λ)max (Å−1) | 0.649 | 0.650 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.051, 0.155, 1.14 | 0.061, 0.143, 1.11 |
No. of reflections | 2946 | 3028 |
No. of parameters | 174 | 183 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.38, −0.46 | 0.52, −0.43 |
Selected geometric parameters (Å, °) for (I) and (II) top(a) Selected distances and angles | | |
Parameter | (I) | (II) |
N1—C2 | 1.331 (3) | 1.336 (4) |
C2—N3 | 1.355 (3) | 1.342 (4) |
N3—C4 | 1.307 (3) | 1.314 (4) |
C4—C5 | 1.382 (4) | 1.387 (4) |
C5—C6 | 1.437 (3) | 1.425 (4) |
C6—N1 | 1.328 (3) | 1.328 (4) |
C2—N2 | 1.320 (3) | 1.322 (4) |
C5—C51 | 1.460 (4) | 1.461 (4) |
C51—O51 | 1.212 (3) | 1.208 (4) |
C6—N61 | 1.351 (3) | 1.369 (4) |
| | |
C61—C62—O62 | | 115.3 (3) |
C63—C62—O62 | | 125.1 (3) |
| | |
C4—C5—C51—O51 | 24.5 (4) | 20.8 (5) |
N1—C6—N61—C61 | -150.2 (2) | -145.5 (3) |
C6—N61—C61—C62 | 52.9 (3) | 51.2 (4) |
C61—C62—O62—C68 | | -176.3 (3) |
N1—C6—N61—C67 | 7.4 (3) | 3.1 (4) |
| | |
(b) Substituent-atom deviations from the pyrimidine plane | | |
Atom | (I) | (II) |
N2 | -0.093 (2) | -0.125 (3) |
Cl4 | 0.106 (2) | 0.106 (2) |
C51 | -0.368 (2) | -0.402 (3) |
O51 | 0.218 (2) | 0.331 (2) |
N61 | 0.118 (2) | 0.085 (2) |
Hydrogen bonds and short intermolecular contacts (Å, °)
for compounds (I) and (II) topCompound | D-H···A | D-H | H···A | D···A | D-H···A |
(I) | N2—H21···O51i | 0.88 | 2.38 | 3.052 (3) | 134 |
| N2—H21···Cl1i | 0.88 | 2.58 | 3.377 (2) | 152 |
| N2—H22···N3ii | 0.88 | 2.11 | 2.988 (3) | 171 |
(II) | N2—H21···O51i | 0.88 | 2.55 | 3.125 (4) | 124 |
| N2—H21···Cl1i | 0.88 | 2.58 | 3.375 (3) | 150 |
| N2—H22···N3ii | 0.88 | 2.12 | 2.983 (4) | 168 |
Symmetry codes: (i) x-1/2, -y+1/2, z-1/2;
(ii) -x, -y, -z+1. |
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We have recently reported the molecular and supramolecular structures of a number of N6-substituted 2-amino-4-chloro-5-formyl pyrimidines (Cobo et al., 2008). Two features of the molecular structures that vary independently amongst the 12 examples studied are the orientation of the formyl group and the shape of the pyrimidine ring, while in all cases the bond distances provide strong evidence for the development of polarized electronic structures. In the majority of the compounds studied earlier (Cobo et al., 2008), the formyl orientation has the formyl C—H bond approximately parallel to the C—Cl bond, while in the remainder, the formyl C═O bond is approximately parallel to the C—Cl bond; these two conformations are denoted (A) and (B), respectively. For both conformers, examples were observed in which the pyrimidine rings were planar within experimental uncertainty, while in others these rings were significantly puckered into boat, screw-boat or twist-boat conformations. The puckering of the pyridine rings in these examples did not appear to inhibit to any degree the development of the polarized electronic structures, exactly as found in other heavily-substituted pyrimidines previously reported (Low et al., 2007; Melguizo et al., 2003; Quesada et al., 2003, 2004; Trilleras et al., 2007), In all, of the 12 compounds previously studied, nine had formyl conformations of type (A) and three of type (B); independently, five of them contained planar pyrimidine rings and seven contained puckered rings.
As a continuation of this study, we have now investigated two further examples, (I) and (II), which both turn out to have type (B) conformations and to contain planar pyrimidine rings. Compounds (I) and (II) were prepared by selective monosubstitution (Taylor & Gillespie, 1992; Quiroga et al., 2008) of the 6-chloro substituent in 2-amino-4,6-dichloro-5-formylpyrimidine (Seela & Sterker, 1986), and their constitutions differ only in the identity of the substituent in the aryl ring, i.e. 2-methyl in (I) and 2-methoxy in (II) (Figs. 1 and 2). Compounds (I) and (II) crystallize in the same space group with fairly similar unit-cell dimensions; the coordinates of corresponding atoms are also similar, while the patterns of the hydrogen bonds are identical (Table 2). Accordingly, the compounds are isostructural and effectively isomorphous.
The corresponding bond distances and torsion angles for compounds (I) and (II) are very similar (Table 1). The distances show many of the characteristics observed previously in other compounds of this type (Cobo et al., 2008). Thus, the ring distances N1—C2 and C6—N1 and the exocyclic distances C2—N2 are all very similar, while the ring distances N3—C4 are, by some margin, the shortest of all the N—C distances; the formyl C51—O51 bonds are long for their type [mean value (Allen et al., 1987) 1.192 Å], while the C5—C51 bonds are short (mean value 1.488 Å). Taken together these distances provide evidence for an important contribution to the overall electronic structure in (I) and (II) from the polarized forms (Ia) and (IIa). This is so despite the fact that the formyl O atom is not coplanar with the pyrimidine ring, as indicated by the non-zero values of the C4—C5—C51—O51 torsion angle (Table 1).
Although the pyrimidine ring in each of (I) and (II) is essentially planar, with the maximum deviation of a ring atom from the mean plane occurring in each compound for atom C5, displaced from the plane by 0.042 (3) Å in (I) and 0.048 (3) Å in (II), the substituent atoms attached to the pyrimidine ring all show significant deviations from the ring plane. In particular, the three adjacent substituent atoms Cl4, C51 and N61 are displaced to alternate sides of the ring plane, with the central substituent atom C51 showing much the largest displacement in each compound (Table 1). The methoxy atom C68 in (II) is almost coplanar with the adjacent phenyl ring, having a deviation from the ring plane of only 0.013 (4) Å; accordingly, the two exocyclic C—C—O angles associated with the methoxy substituent differ by ca 10°, as normally observed in such cases.
Compounds (I) and (II) exhibit identical patterns of hydrogen bonding (Table 2), with similar dimensions for the hydrogen bonds in the two compounds. The N—H···N hydrogen bond generates a centrosymmetric R22(8) (Bernstein et al., 1995) motif, centred at (0, 0, 1/2). The action of the N—H···O hydrogen bond is to link this dimeric unit at (0, 0, 1/2) to the four adjacent dimers centred at (-1/2, -1/2, 0), (-1/2, 1/2, 0), (1/2, -1/2, 1) and (1/2, 1/2, 1), thereby generating a sheet parallel to (101) and built from alternating R22(8) and R66(32) rings (Fig. 3), in which both ring types are centrosymmetric. There are no direction-specific interactions between adjacent sheets; in particular, both C—H···π(arene) hydrogen bonds and aromatic π–π stacking interactions are absent, nor does the methoxy O atom in (II) play any part in the hydrogen bonding.
Within the hydrogen-bonded sheets formed in each of (I) and (II) there is a fairly short N—H···Cl contact (Table 2). However, it has been amply shown (Aakeröy et al., 1999; Brammer et al., 2001; Thallapally & Nangia, 2001) that Cl atoms covalently bonded to C atoms are very poor hydrogen-bond acceptors, and that such contacts are probably no more than ordinary van der Waals contacts. It is thus safer to regard the N—H···Cl contacts in (I) and (II) as adventitious contacts consequent upon the geometry of the N—H···O hydrogen bonds and not of themselves structurally significant. In any event such an interaction would not have any bearing on the overall forms of the hydrogen-bonded structures.
Of the analogues studied previously (Cobo et al., 2008), those closest in constitution to (I) and (II) are (III) (see scheme), which differs from (I) and (II) only in carrying no substituent on the phenyl ring, and (IV), which is an isomer of (I). Compounds (III) and (IV) both adopt type (B) conformations, but while (III) contains a planar pyrimidine ring, in (IV) this ring adopts a boat conformation. Although dimers characterized by R22(8) motifs and built from paired N—H···N hydrogen bonds can be identified in the structures of each of (III) and (IV), just as in (I) and (II), the further linking of these dimeric units in (III) and (IV) does not resemble that in (I) and (II). In (III), a combination of N—H···N and C—H···π(arene) hydrogen bonds leads to the formation of a chain of edge-fused rings, but the formyl O atom plays no role in the hydrogen bonding. In (IV), by contrast, a combination of N—H···N and N—H···O hydrogen bonds generates a chain of alternating centrosymmetric R22(8) and R44(16) rings.
The only other example in this series of a sheet of alternating R22(8) and R66(32) rings built from N—H···N and N—H···O hydrogen bonds, as in (I) and (II), was found in the structure of (V). This differs from (I) and (II), both in adopting a type (A) conformation and in the constitution of the NR2 group bonded to C6. This substituent contains an N—H bond that forms an intramolecular N—H···O hydrogen bond to the formyl O atom but otherwise plays no role in the supramolecular aggregation.