The molecular dimensions of both 2-amino-6-(
N-methylanilino)pyrimidin-4(3
H)-one, C
11H
12N
4O, (I), and 2-amino-6-(
N-methylanilino)-5-nitropyrimidin-4(3
H)-one, C
11H
11N
5O
3, (II), are consistent with considerable polarization of the molecular-electronic structures. The molecules of (I) are linked into a three-dimensional framework by a combination of one N-H
N hydrogen bond, two independent N-H
O hydrogen bonds and one C-H
(arene) hydrogen bond. The molecules of (II) are linked into ribbons containing three types of edge-fused ring by the combination of two independent three-centre N-H
(O)
2 hydrogen bonds.
Supporting information
CCDC references: 672539; 672540
For the synthesis of (I), a mixture of 2-amino-4-chloro-6-methoxypyrimidine
(1.82 mmol) and N-methylaniline (2.80 mmol) was heated to fusion
between 563–573 K for 4 min. The reaction mixture was cooled to ambient
temperature and the resulting solid mass was broken up; it was washed thrice
with ether, and then successively with a saturated aqueous solution of
potassium carbonate, with water and finally again with ether. the mixture was
then dried in an oven giving (I) as a pale-beige solid (yield 97%, m.p.
552–554 K). For the synthesis of (II), a mixture of
2-amino-6-chloro-5-nitro-4(3H)pyrimidinone (2.78 mmol),
N-methylaniline (3.13 mmol) and triethylamine (1 ml) in methanol (20 ml) was stirred magnetically at ambient temperature for 2 h. The resulting
yellow solid was collected by filtration, washed with methanol and then dried
in an oven to yield (II) (yield 83%, m.p. 585–588 K). Yellow crystals of (I)
and (II) suitable for single-crystal X-ray diffraction were obtained from
solutions in dimethylsulfoxide.
The space groups P21/c, for (I), and P212121, for
(II), were both uniquely assigned from the systematic absences. All H atoms
were located in difference maps and then treated as riding atoms, with C—H
distances of 0.95 Å (aromatic or heteroaromatic) or 0.98 Å (methyl), and
N—H 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, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997) and PRPKAPPA (Ferguson, 1999).
(I) 2-amino-6-(methylanilino)pyrimidin-4(3
H)-one
top
Crystal data top
C11H12N4O | F(000) = 456 |
Mr = 216.25 | Dx = 1.378 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 2396 reflections |
a = 10.6860 (12) Å | θ = 4.1–27.5° |
b = 7.1647 (14) Å | µ = 0.09 mm−1 |
c = 14.4911 (12) Å | T = 120 K |
β = 110.024 (9)° | Block, yellow |
V = 1042.4 (3) Å3 | 0.52 × 0.25 × 0.16 mm |
Z = 4 | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 2396 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 1568 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.057 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 4.1° |
ϕ & ω scans | h = −13→13 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −9→9 |
Tmin = 0.962, Tmax = 0.985 | l = −18→18 |
23278 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)] = 0.050 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.137 | H-atom parameters constrained |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0557P)2 + 0.7582P] where P = (Fo2 + 2Fc2)/3 |
2396 reflections | (Δ/σ)max < 0.001 |
146 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
Crystal data top
C11H12N4O | V = 1042.4 (3) Å3 |
Mr = 216.25 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 10.6860 (12) Å | µ = 0.09 mm−1 |
b = 7.1647 (14) Å | T = 120 K |
c = 14.4911 (12) Å | 0.52 × 0.25 × 0.16 mm |
β = 110.024 (9)° | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 2396 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 1568 reflections with I > 2σ(I) |
Tmin = 0.962, Tmax = 0.985 | Rint = 0.057 |
23278 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.050 | 0 restraints |
wR(F2) = 0.137 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.35 e Å−3 |
2396 reflections | Δρmin = −0.26 e Å−3 |
146 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.66081 (15) | 0.3959 (2) | 0.36165 (12) | 0.0190 (4) | |
C2 | 0.59095 (19) | 0.2415 (3) | 0.35541 (14) | 0.0194 (4) | |
N2 | 0.54735 (16) | 0.1509 (2) | 0.26918 (12) | 0.0234 (4) | |
N3 | 0.56134 (15) | 0.1688 (2) | 0.43183 (11) | 0.0192 (4) | |
C4 | 0.60352 (19) | 0.2548 (3) | 0.52379 (14) | 0.0190 (4) | |
O4 | 0.56750 (13) | 0.1799 (2) | 0.58994 (10) | 0.0226 (3) | |
C5 | 0.68257 (18) | 0.4133 (3) | 0.53313 (14) | 0.0196 (4) | |
C6 | 0.70970 (18) | 0.4795 (3) | 0.45137 (14) | 0.0193 (4) | |
N6 | 0.78848 (16) | 0.6308 (2) | 0.45421 (12) | 0.0219 (4) | |
C67 | 0.8052 (2) | 0.7070 (3) | 0.36560 (16) | 0.0322 (5) | |
C61 | 0.8560 (2) | 0.7336 (3) | 0.54195 (15) | 0.0212 (4) | |
C62 | 0.7878 (2) | 0.8511 (3) | 0.58287 (16) | 0.0255 (5) | |
C63 | 0.8565 (2) | 0.9632 (3) | 0.66180 (16) | 0.0284 (5) | |
C64 | 0.9941 (2) | 0.9555 (3) | 0.70086 (15) | 0.0263 (5) | |
C65 | 1.0629 (2) | 0.8378 (3) | 0.65976 (16) | 0.0270 (5) | |
C66 | 0.9943 (2) | 0.7277 (3) | 0.57988 (16) | 0.0256 (5) | |
H2A | 0.5655 | 0.1946 | 0.2184 | 0.028* | |
H2B | 0.5006 | 0.0477 | 0.2634 | 0.028* | |
H3 | 0.5145 | 0.0651 | 0.4233 | 0.023* | |
H5 | 0.7176 | 0.4755 | 0.5945 | 0.024* | |
H67A | 0.7709 | 0.6177 | 0.3116 | 0.048* | |
H67B | 0.8999 | 0.7300 | 0.3778 | 0.048* | |
H67C | 0.7558 | 0.8246 | 0.3480 | 0.048* | |
H62 | 0.6933 | 0.8553 | 0.5570 | 0.031* | |
H63 | 0.8091 | 1.0457 | 0.6892 | 0.034* | |
H64 | 1.0410 | 1.0309 | 0.7557 | 0.032* | |
H65 | 1.1573 | 0.8323 | 0.6863 | 0.032* | |
H66 | 1.0418 | 0.6481 | 0.5510 | 0.031* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0202 (8) | 0.0185 (8) | 0.0187 (9) | −0.0018 (7) | 0.0070 (7) | 0.0004 (7) |
C2 | 0.0201 (10) | 0.0193 (10) | 0.0188 (10) | 0.0031 (8) | 0.0068 (8) | 0.0026 (8) |
N2 | 0.0315 (9) | 0.0217 (9) | 0.0178 (9) | −0.0085 (8) | 0.0093 (7) | −0.0021 (7) |
N3 | 0.0211 (8) | 0.0186 (8) | 0.0181 (8) | −0.0057 (7) | 0.0071 (7) | −0.0010 (7) |
C4 | 0.0203 (10) | 0.0185 (10) | 0.0181 (10) | 0.0020 (8) | 0.0063 (8) | 0.0016 (8) |
O4 | 0.0278 (8) | 0.0226 (8) | 0.0201 (7) | −0.0043 (6) | 0.0117 (6) | 0.0011 (6) |
C5 | 0.0201 (10) | 0.0206 (10) | 0.0167 (10) | −0.0020 (8) | 0.0044 (8) | −0.0009 (8) |
C6 | 0.0167 (9) | 0.0176 (10) | 0.0224 (10) | 0.0015 (8) | 0.0052 (8) | 0.0011 (8) |
N6 | 0.0248 (9) | 0.0204 (9) | 0.0213 (9) | −0.0054 (7) | 0.0090 (7) | −0.0012 (7) |
C67 | 0.0394 (13) | 0.0318 (13) | 0.0259 (12) | −0.0131 (11) | 0.0116 (10) | 0.0022 (10) |
C61 | 0.0244 (10) | 0.0166 (10) | 0.0227 (10) | −0.0033 (8) | 0.0082 (8) | 0.0009 (8) |
C62 | 0.0209 (10) | 0.0263 (11) | 0.0283 (11) | 0.0001 (9) | 0.0072 (9) | 0.0000 (9) |
C63 | 0.0310 (12) | 0.0247 (11) | 0.0314 (12) | 0.0012 (9) | 0.0130 (10) | −0.0027 (10) |
C64 | 0.0285 (11) | 0.0235 (11) | 0.0251 (11) | −0.0035 (9) | 0.0069 (9) | −0.0031 (9) |
C65 | 0.0219 (10) | 0.0259 (11) | 0.0313 (12) | −0.0031 (9) | 0.0067 (9) | −0.0003 (10) |
C66 | 0.0248 (11) | 0.0221 (11) | 0.0314 (12) | 0.0000 (9) | 0.0115 (9) | −0.0028 (9) |
Geometric parameters (Å, º) top
N1—C2 | 1.321 (3) | C67—H67A | 0.98 |
N1—C6 | 1.363 (2) | C67—H67B | 0.98 |
C2—N2 | 1.342 (3) | C67—H67C | 0.98 |
C2—N3 | 1.355 (2) | C61—C62 | 1.374 (3) |
N2—H2A | 0.88 | C61—C66 | 1.390 (3) |
N2—H2B | 0.88 | C62—C63 | 1.385 (3) |
N3—C4 | 1.396 (2) | C62—H62 | 0.95 |
N3—H3 | 0.88 | C63—C64 | 1.384 (3) |
C4—O4 | 1.268 (2) | C63—H63 | 0.95 |
C4—C5 | 1.394 (3) | C64—C65 | 1.381 (3) |
C5—C6 | 1.396 (3) | C64—H64 | 0.95 |
C5—H5 | 0.95 | C65—C66 | 1.385 (3) |
C6—N6 | 1.365 (2) | C65—H65 | 0.95 |
N6—C61 | 1.432 (3) | C66—H66 | 0.95 |
N6—C67 | 1.461 (3) | | |
| | | |
C2—N1—C6 | 117.17 (17) | N6—C67—H67B | 109.5 |
N1—C2—N2 | 118.48 (17) | H67A—C67—H67B | 109.5 |
N1—C2—N3 | 123.41 (18) | N6—C67—H67C | 109.5 |
N2—C2—N3 | 118.11 (18) | H67A—C67—H67C | 109.5 |
C2—N2—H2A | 120.0 | H67B—C67—H67C | 109.5 |
C2—N2—H2B | 120.0 | C62—C61—C66 | 119.84 (19) |
H2A—N2—H2B | 120.0 | C62—C61—N6 | 121.15 (18) |
C2—N3—C4 | 121.40 (17) | C66—C61—N6 | 118.69 (18) |
C2—N3—H3 | 119.3 | C61—C62—C63 | 120.14 (19) |
C4—N3—H3 | 119.3 | C61—C62—H62 | 119.9 |
O4—C4—C5 | 127.03 (18) | C63—C62—H62 | 119.9 |
O4—C4—N3 | 116.90 (17) | C64—C63—C62 | 120.2 (2) |
C5—C4—N3 | 116.06 (17) | C64—C63—H63 | 119.9 |
C4—C5—C6 | 119.32 (18) | C62—C63—H63 | 119.9 |
C4—C5—H5 | 120.3 | C65—C64—C63 | 119.7 (2) |
C6—C5—H5 | 120.3 | C65—C64—H64 | 120.1 |
N1—C6—N6 | 114.14 (17) | C63—C64—H64 | 120.1 |
N1—C6—C5 | 122.50 (18) | C64—C65—C66 | 120.08 (19) |
N6—C6—C5 | 123.35 (18) | C64—C65—H65 | 120.0 |
C6—N6—C61 | 123.60 (17) | C66—C65—H65 | 120.0 |
C6—N6—C67 | 122.00 (17) | C65—C66—C61 | 119.98 (19) |
C61—N6—C67 | 114.33 (16) | C65—C66—H66 | 120.0 |
N6—C67—H67A | 109.5 | C61—C66—H66 | 120.0 |
| | | |
C6—N1—C2—N2 | −176.63 (17) | N1—C6—N6—C67 | 6.6 (3) |
C6—N1—C2—N3 | 3.1 (3) | C5—C6—N6—C67 | −174.3 (2) |
N1—C2—N3—C4 | 0.2 (3) | C6—N6—C61—C62 | −73.7 (3) |
N2—C2—N3—C4 | 179.84 (17) | C67—N6—C61—C62 | 103.3 (2) |
C2—N3—C4—O4 | 177.83 (17) | C6—N6—C61—C66 | 112.8 (2) |
C2—N3—C4—C5 | −3.0 (3) | C67—N6—C61—C66 | −70.1 (2) |
O4—C4—C5—C6 | −178.35 (19) | C66—C61—C62—C63 | −0.1 (3) |
N3—C4—C5—C6 | 2.6 (3) | N6—C61—C62—C63 | −173.43 (19) |
C2—N1—C6—N6 | 175.70 (17) | C61—C62—C63—C64 | −1.0 (3) |
C2—N1—C6—C5 | −3.4 (3) | C62—C63—C64—C65 | 1.1 (3) |
C4—C5—C6—N1 | 0.6 (3) | C63—C64—C65—C66 | −0.1 (3) |
C4—C5—C6—N6 | −178.46 (18) | C64—C65—C66—C61 | −1.0 (3) |
N1—C6—N6—C61 | −176.53 (17) | C62—C61—C66—C65 | 1.1 (3) |
C5—C6—N6—C61 | 2.6 (3) | N6—C61—C66—C65 | 174.58 (18) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O4i | 0.88 | 2.07 | 2.940 (2) | 168 |
N2—H2B···N1ii | 0.88 | 2.30 | 2.998 (2) | 136 |
N3—H3···O4iii | 0.88 | 1.94 | 2.818 (2) | 173 |
C64—H64···Cgiv | 0.95 | 2.82 | 3.695 (2) | 154 |
Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x+1, y−1/2, −z+1/2; (iii) −x+1, −y, −z+1; (iv) −x+2, y+1/2, −z+3/2. |
(II) 2-amino-6-(methylanilino)-5-nitropyrimidin-4(3
H)-one
top
Crystal data top
C11H11N5O3 | F(000) = 544 |
Mr = 261.25 | Dx = 1.493 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 1447 reflections |
a = 8.955 (3) Å | θ = 4.0–27.6° |
b = 11.2165 (15) Å | µ = 0.11 mm−1 |
c = 11.5670 (15) Å | T = 120 K |
V = 1161.8 (4) Å3 | Plate, yellow |
Z = 4 | 0.32 × 0.26 × 0.09 mm |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 1447 independent reflections |
Radiation source: Bruker-Nonius FR591 rotating anode | 879 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.102 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.6°, θmin = 4.0° |
ϕ & ω scans | h = −11→10 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −14→13 |
Tmin = 0.923, Tmax = 0.991 | l = −13→14 |
15997 measured reflections | |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.054 | H-atom parameters constrained |
wR(F2) = 0.138 | w = 1/[σ2(Fo2) + (0.079P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.05 | (Δ/σ)max < 0.001 |
1447 reflections | Δρmax = 0.28 e Å−3 |
173 parameters | Δρmin = −0.32 e Å−3 |
0 restraints | Absolute structure: Friedel pairs merged |
Primary atom site location: structure-invariant direct methods | |
Crystal data top
C11H11N5O3 | V = 1161.8 (4) Å3 |
Mr = 261.25 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 8.955 (3) Å | µ = 0.11 mm−1 |
b = 11.2165 (15) Å | T = 120 K |
c = 11.5670 (15) Å | 0.32 × 0.26 × 0.09 mm |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 1447 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 879 reflections with I > 2σ(I) |
Tmin = 0.923, Tmax = 0.991 | Rint = 0.102 |
15997 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.054 | 0 restraints |
wR(F2) = 0.138 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.28 e Å−3 |
1447 reflections | Δρmin = −0.32 e Å−3 |
173 parameters | Absolute structure: Friedel pairs merged |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.3771 (4) | 0.6396 (3) | 0.8030 (3) | 0.0256 (8) | |
C2 | 0.3091 (4) | 0.6763 (3) | 0.7084 (3) | 0.0225 (10) | |
N2 | 0.1616 (4) | 0.6755 (3) | 0.7050 (3) | 0.0311 (9) | |
N3 | 0.3820 (4) | 0.7154 (3) | 0.6128 (3) | 0.0248 (8) | |
C4 | 0.5375 (4) | 0.7283 (4) | 0.6109 (3) | 0.0227 (9) | |
O4 | 0.5987 (3) | 0.7719 (2) | 0.5250 (2) | 0.0299 (7) | |
C5 | 0.6088 (4) | 0.6946 (3) | 0.7157 (3) | 0.0221 (9) | |
N5 | 0.7627 (4) | 0.7276 (3) | 0.7223 (3) | 0.0269 (8) | |
O51 | 0.8462 (3) | 0.7031 (3) | 0.6411 (2) | 0.0348 (8) | |
O52 | 0.8067 (3) | 0.7805 (3) | 0.8104 (3) | 0.0358 (8) | |
C6 | 0.5281 (4) | 0.6463 (3) | 0.8086 (3) | 0.0219 (9) | |
N6 | 0.5892 (4) | 0.6038 (3) | 0.9073 (3) | 0.0252 (8) | |
C67 | 0.4899 (4) | 0.5663 (4) | 1.0026 (4) | 0.0339 (11) | |
C61 | 0.7436 (4) | 0.5716 (3) | 0.9177 (3) | 0.0248 (9) | |
C62 | 0.8086 (5) | 0.4956 (4) | 0.8391 (3) | 0.0280 (11) | |
C63 | 0.9581 (5) | 0.4656 (4) | 0.8498 (4) | 0.0335 (11) | |
C64 | 1.0402 (5) | 0.5102 (4) | 0.9414 (4) | 0.0353 (11) | |
C65 | 0.9747 (4) | 0.5831 (4) | 1.0209 (4) | 0.0341 (11) | |
C66 | 0.8255 (4) | 0.6142 (4) | 1.0112 (4) | 0.0289 (10) | |
H2A | 0.1103 | 0.6507 | 0.7652 | 0.037* | |
H2B | 0.1146 | 0.6997 | 0.6424 | 0.037* | |
H3 | 0.3303 | 0.7332 | 0.5505 | 0.030* | |
H67A | 0.4460 | 0.4886 | 0.9843 | 0.051* | |
H67B | 0.4102 | 0.6253 | 1.0125 | 0.051* | |
H67C | 0.5478 | 0.5603 | 1.0743 | 0.051* | |
H62 | 0.7511 | 0.4638 | 0.7774 | 0.034* | |
H63 | 1.0039 | 0.4146 | 0.7946 | 0.040* | |
H64 | 1.1428 | 0.4899 | 0.9490 | 0.042* | |
H65 | 1.0320 | 0.6129 | 1.0836 | 0.041* | |
H66 | 0.7799 | 0.6639 | 1.0675 | 0.035* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.023 (2) | 0.0324 (19) | 0.0218 (19) | 0.0003 (15) | 0.0027 (15) | 0.0009 (17) |
C2 | 0.019 (2) | 0.027 (2) | 0.021 (2) | 0.0012 (17) | 0.0026 (18) | 0.003 (2) |
N2 | 0.024 (2) | 0.046 (2) | 0.0233 (19) | −0.0042 (16) | 0.0017 (17) | 0.0079 (19) |
N3 | 0.0269 (19) | 0.0302 (19) | 0.0174 (18) | 0.0008 (16) | −0.0030 (15) | 0.0002 (15) |
C4 | 0.025 (2) | 0.022 (2) | 0.021 (2) | −0.0012 (19) | −0.001 (2) | −0.0020 (18) |
O4 | 0.0261 (16) | 0.0398 (17) | 0.0239 (15) | −0.0022 (13) | 0.0026 (13) | 0.0056 (14) |
C5 | 0.017 (2) | 0.026 (2) | 0.023 (2) | −0.0013 (17) | 0.0000 (17) | −0.0023 (19) |
N5 | 0.028 (2) | 0.0332 (19) | 0.0197 (18) | −0.0021 (17) | −0.0003 (18) | 0.0089 (17) |
O51 | 0.0226 (16) | 0.055 (2) | 0.0273 (16) | 0.0002 (14) | 0.0056 (15) | 0.0058 (15) |
O52 | 0.0423 (19) | 0.0390 (18) | 0.0261 (16) | −0.0127 (14) | −0.0073 (14) | −0.0001 (15) |
C6 | 0.025 (2) | 0.022 (2) | 0.018 (2) | 0.0005 (18) | 0.0012 (19) | −0.0032 (19) |
N6 | 0.025 (2) | 0.0307 (19) | 0.0195 (18) | 0.0002 (15) | 0.0017 (16) | 0.0029 (16) |
C67 | 0.035 (3) | 0.041 (3) | 0.026 (2) | 0.001 (2) | 0.006 (2) | 0.007 (2) |
C61 | 0.021 (2) | 0.030 (2) | 0.024 (2) | 0.0023 (19) | −0.002 (2) | 0.001 (2) |
C62 | 0.032 (3) | 0.027 (2) | 0.024 (2) | −0.005 (2) | −0.002 (2) | 0.001 (2) |
C63 | 0.036 (3) | 0.030 (2) | 0.034 (3) | 0.005 (2) | 0.009 (2) | 0.008 (2) |
C64 | 0.027 (2) | 0.038 (3) | 0.041 (3) | 0.002 (2) | −0.007 (2) | 0.012 (2) |
C65 | 0.026 (3) | 0.043 (3) | 0.033 (2) | −0.005 (2) | −0.009 (2) | 0.009 (2) |
C66 | 0.032 (2) | 0.032 (2) | 0.024 (2) | −0.0023 (18) | 0.003 (2) | 0.001 (2) |
Geometric parameters (Å, º) top
N1—C2 | 1.318 (5) | N6—C67 | 1.478 (5) |
N1—C6 | 1.356 (5) | C67—H67A | 0.98 |
C2—N2 | 1.322 (5) | C67—H67B | 0.98 |
C2—N3 | 1.357 (5) | C67—H67C | 0.98 |
N2—H2A | 0.88 | C61—C62 | 1.376 (5) |
N2—H2B | 0.88 | C61—C66 | 1.392 (5) |
N3—C4 | 1.400 (5) | C62—C63 | 1.386 (5) |
N3—H3 | 0.88 | C62—H62 | 0.95 |
C4—O4 | 1.235 (5) | C63—C64 | 1.384 (6) |
C4—C5 | 1.421 (5) | C63—H63 | 0.95 |
C5—C6 | 1.403 (5) | C64—C65 | 1.363 (6) |
C5—N5 | 1.430 (5) | C64—H64 | 0.95 |
N5—O51 | 1.231 (4) | C65—C66 | 1.385 (6) |
N5—O52 | 1.243 (4) | C65—H65 | 0.95 |
C6—N6 | 1.352 (5) | C66—H66 | 0.95 |
N6—C61 | 1.434 (5) | | |
| | | |
C2—N1—C6 | 118.9 (3) | N6—C67—H67A | 109.5 |
N1—C2—N2 | 119.0 (4) | N6—C67—H67B | 109.5 |
N1—C2—N3 | 123.7 (3) | H67A—C67—H67B | 109.5 |
N2—C2—N3 | 117.3 (4) | N6—C67—H67C | 109.5 |
C2—N2—H2A | 120.0 | H67A—C67—H67C | 109.5 |
C2—N2—H2B | 120.0 | H67B—C67—H67C | 109.5 |
H2A—N2—H2B | 120.0 | C62—C61—C66 | 120.2 (4) |
C2—N3—C4 | 121.7 (3) | C62—C61—N6 | 120.6 (4) |
C2—N3—H3 | 119.2 | C66—C61—N6 | 119.1 (4) |
C4—N3—H3 | 119.2 | C61—C62—C63 | 120.0 (4) |
O4—C4—N3 | 119.6 (3) | C61—C62—H62 | 120.0 |
O4—C4—C5 | 126.3 (3) | C63—C62—H62 | 120.0 |
N3—C4—C5 | 113.9 (3) | C64—C63—C62 | 119.6 (4) |
C6—C5—C4 | 121.7 (3) | C64—C63—H63 | 120.2 |
C6—C5—N5 | 123.7 (3) | C62—C63—H63 | 120.2 |
C4—C5—N5 | 114.2 (3) | C65—C64—C63 | 120.3 (4) |
O51—N5—O52 | 122.6 (3) | C65—C64—H64 | 119.9 |
O51—N5—C5 | 119.1 (3) | C63—C64—H64 | 119.9 |
O52—N5—C5 | 118.3 (3) | C64—C65—C66 | 120.8 (4) |
N6—C6—N1 | 115.1 (3) | C64—C65—H65 | 119.6 |
N6—C6—C5 | 125.0 (3) | C66—C65—H65 | 119.6 |
N1—C6—C5 | 119.9 (4) | C65—C66—C61 | 119.0 (4) |
C6—N6—C61 | 123.4 (3) | C65—C66—H66 | 120.5 |
C6—N6—C67 | 119.1 (3) | C61—C66—H66 | 120.5 |
C61—N6—C67 | 116.4 (3) | | |
| | | |
C6—N1—C2—N2 | −176.6 (4) | C4—C5—C6—N1 | −5.2 (6) |
C6—N1—C2—N3 | 3.4 (6) | N5—C5—C6—N1 | 166.8 (4) |
N1—C2—N3—C4 | −5.0 (6) | N1—C6—N6—C61 | 161.7 (4) |
N2—C2—N3—C4 | 175.1 (4) | C5—C6—N6—C61 | −18.1 (6) |
C2—N3—C4—O4 | −175.0 (4) | N1—C6—N6—C67 | −6.1 (5) |
C2—N3—C4—C5 | 1.2 (5) | C5—C6—N6—C67 | 174.1 (4) |
O4—C4—C5—C6 | 179.6 (4) | C6—N6—C61—C62 | −51.5 (5) |
N3—C4—C5—C6 | 3.6 (6) | C67—N6—C61—C62 | 116.6 (4) |
O4—C4—C5—N5 | 6.9 (6) | C6—N6—C61—C66 | 131.1 (4) |
N3—C4—C5—N5 | −169.1 (3) | C67—N6—C61—C66 | −60.7 (5) |
C6—C5—N5—O51 | 138.0 (4) | C66—C61—C62—C63 | −2.9 (6) |
C4—C5—N5—O51 | −49.4 (5) | N6—C61—C62—C63 | 179.7 (4) |
C6—C5—N5—O52 | −42.2 (5) | C61—C62—C63—C64 | 1.5 (6) |
C4—C5—N5—O52 | 130.4 (4) | C62—C63—C64—C65 | 0.2 (6) |
C2—N1—C6—N6 | −178.3 (3) | C63—C64—C65—C66 | −0.3 (6) |
C2—N1—C6—C5 | 1.6 (6) | C64—C65—C66—C61 | −1.1 (6) |
C4—C5—C6—N6 | 174.6 (3) | C62—C61—C66—C65 | 2.7 (6) |
N5—C5—C6—N6 | −13.3 (6) | N6—C61—C66—C65 | −179.9 (4) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2B···O4i | 0.88 | 1.97 | 2.783 (4) | 153 |
N2—H2B···O51ii | 0.88 | 2.40 | 2.936 (5) | 119 |
N3—H3···O4i | 0.88 | 2.25 | 3.000 (5) | 143 |
N3—H3···O51i | 0.88 | 2.33 | 3.093 (4) | 145 |
Symmetry codes: (i) x−1/2, −y+3/2, −z+1; (ii) x−1, y, z. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C11H12N4O | C11H11N5O3 |
Mr | 216.25 | 261.25 |
Crystal system, space group | Monoclinic, P21/c | Orthorhombic, P212121 |
Temperature (K) | 120 | 120 |
a, b, c (Å) | 10.6860 (12), 7.1647 (14), 14.4911 (12) | 8.955 (3), 11.2165 (15), 11.5670 (15) |
α, β, γ (°) | 90, 110.024 (9), 90 | 90, 90, 90 |
V (Å3) | 1042.4 (3) | 1161.8 (4) |
Z | 4 | 4 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.09 | 0.11 |
Crystal size (mm) | 0.52 × 0.25 × 0.16 | 0.32 × 0.26 × 0.09 |
|
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 | 0.962, 0.985 | 0.923, 0.991 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23278, 2396, 1568 | 15997, 1447, 879 |
Rint | 0.057 | 0.102 |
(sin θ/λ)max (Å−1) | 0.650 | 0.653 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.050, 0.137, 1.07 | 0.054, 0.138, 1.05 |
No. of reflections | 2396 | 1447 |
No. of parameters | 146 | 173 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.35, −0.26 | 0.28, −0.32 |
Absolute structure | ? | Friedel pairs merged |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2A···O4i | 0.88 | 2.07 | 2.940 (2) | 168 |
N2—H2B···N1ii | 0.88 | 2.30 | 2.998 (2) | 136 |
N3—H3···O4iii | 0.88 | 1.94 | 2.818 (2) | 173 |
C64—H64···Cgiv | 0.95 | 2.82 | 3.695 (2) | 154 |
Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x+1, y−1/2, −z+1/2; (iii) −x+1, −y, −z+1; (iv) −x+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 |
N2—H2B···O4i | 0.88 | 1.97 | 2.783 (4) | 153 |
N2—H2B···O51ii | 0.88 | 2.40 | 2.936 (5) | 119 |
N3—H3···O4i | 0.88 | 2.25 | 3.000 (5) | 143 |
N3—H3···O51i | 0.88 | 2.33 | 3.093 (4) | 145 |
Symmetry codes: (i) x−1/2, −y+3/2, −z+1; (ii) x−1, y, z. |
Selected geometric parameters (Å, °) topParameter | (I) | (II) |
N1-C2 | 1.321 (3) | 1.318 (5) |
C2-N3 | 1.355 (2) | 1.357 (5) |
N3-C4 | 1.396 (2) | 1.400 (5) |
C4-C5 | 1.394 (3) | 1.421 (5) |
C5-C6 | 1.396 (3) | 1.403 (5) |
C6-N1 | 1.363 (2) | 1.356 (5) |
C2-N2 | 1.342 (3) | 1.322 (5) |
C4-O4 | 1.268 (2) | 1.235 (5) |
C5-N5 | – | 1.430 (5) |
N5-O51 | – | 1.231 (4) |
N5-O52 | – | 1.243 (4) |
C6-N6 | 1.365 (2) | 1.352 (5) |
C4-C5-N5-O51 | – | -49.4 (5) |
N1-C6-N6-C61 | -176.53 (17) | 161.7 (4) |
N1-C6-N6-C67 | 6.6 (3) | -6.1 (5) |
C6-N6-C61-C62 | -73.7 (3) | -51.5 (5) |
As part of a wide-ranging investigation of biologically active heterocyclic compounds, we have initiated a study of pyrimido[4,5-b][1,4]benzodiazepine derivatives that are analogous to the well known benzodiazepine derivatives and which show related pharmacological properties, such as anti-anxiety or antidepressive activity (Dlugosz & Machon, 1990), as well as being candidates as effective anti-HIV-1 inhibitors (Di Braccio et al., 2001). We report here the molecular and supramolecular structures of two compounds, 2-amino-6-(N-methylanilino)pyrimidin-4(3H)-one, (I), and 2-amino-6-(N-methylanilino)-5-nitropyrimidin-4(3H)-one, (II), which were prepared, from the commercially available pyrimidines, (III) and (IV), respectively, for use as intermediates for the syntheses of pyrimido[4,5-b][1,4]benzodiazepines, (V).
In compounds (I) and (II) (Figs. 1 and 2), the coordination at N6 is planar and the methyl atom C67 and the ipso atom of the phenyl ring, atom C61, are very close to the plane of the pyrimidine ring, as indicated by the relevant torsion angles (Table 3). On the other hand, the planes of the phenyl group in each compound are well removed from the pyrimidine planes with dihedral angles between these two planes of 70.1 (2)° in (I) and 58.9 (2)° in (II). In (II), the dihedral angle between the CNO2 unit and the pyrimidine ring is 47.4 (2)°.
The molecules in each compound exhibit some unusual bond distances, which are indicative of polarized molecular–electronic structures. In compound (I), the C4—C5 and C5—C6 distances are identical within experimental uncertainty, although in the conventional representation these bonds are, respectively, single and double bonds. In addition, the C—O bond is long for its type (Allen et al., 1987), while the C6—N6 bond is short. These data together indicate that the polarized form (Ia) (Scheme 2) may be a significant contributor to the overall molecular–electronic structure of this compound, in addition to the unpolarized form (I).
Despite the large dihedral angle between the pyrimidine and nitro-group planes in (II), the C5—N5 bond is rather short for its type (mean value 1.486 Å; Allen et al., 1987); the C4—O4 bond is significantly shorter in (II) than in (I); and the N1—C2 and C2—N2 distances are effectively identical in (II). These observations indicate that the polarized forms (IIa) and (IIb) (Scheme 2) both contribute to the overall molecular–electronic structure of this compound, in addition to the unpolarized form (II).
The molecules of compound (I) are linked into sheets by three hydrogen bonds, one of N—H···N type and two of N—H···O type (Table 1). It is convenient to consider a centrosymmetric dimer unit, formed by paired N—H···O hydrogen bonds, as the basic building block forming the sheet. The ring atom N3 in the molecule at (x, y, z) acts as a donor, in an almost linear hydrogen bond, to atom O4 in the molecule at (1 - x, -y, 1 - z), so generating by inversion an R22(8) motif (Bernstein et al., 1995), centred at (1/2, 0, 1/2). This dimer is linked directly, by the other two hydrogen bonds, to the four dimers centred at (1/2, 1/2, 0), (1/2, -1/2, 0), (1/2, 1/2, 1) and (1/2, -1/2, 1), and propagation by the space group of these hydrogen bonds then generates a rather complex sheet parallel to (100) (Fig. 3). Each such sheet is weakly linked to the two adjacent sheets by a single C—H···π(arene) hydrogen bond (Table 2), so forming a continuous hydrogen-bonded framework structure in three dimensions.
The supramolecular aggregation of (II) is only one-dimensional; despite the presence of the two nitro-group O atoms as additional sites that are potential hydrogen-bond acceptors, one of the N—H bonds of the exocyclic amino group in (II) plays no part in the hydrogen bonding, and the supramolecular aggregation depends entirely on two independent three-centre N—H···(O)2 hydrogen-bond systems, both them effectively planar (Table 2).
Amino atom N2 in the molecule at (x, y, z) acts as a hydrogen-bond donor, via H2B, to atoms O4 and O51 in the molecules at (-1/2 + x, 3/2 - y, 1 - z) and (-1 + x, y, z), respectively. In the second three-centre system, the ring atom N3 acts as a hydrogen-bond donor to atoms O4 and O51, both in the molecule at (-1/2 + x, 3/2 - y, 1 - z). Hence two of the N—H bonds act as double donors of hydrogen bonds, while the third N—H bond does not participate in the hydrogen bonding; and two of the O atoms act as double acceptors of hydrogen bonds, while the third O atom does not participate in the hydrogen bonding. The combination of all these hydrogen bonds produces a ribbon of edge-fused rings running parallel to the [100] direction and generated by the 21 screw axis along (x, 3/4, 1/2) (Fig. 4). The ribbon contains an R12(6) ring where the sole acceptor is an O4 atom; an R21(6) ring where both hydrogen bonds involve an H3 atom; and an R22(6) ring containing both O4 and O51 atoms as the acceptors. A second ribbon, running antiparallel to the reference ribbon, is generated by the 21 screw axis along (x, 1/4, 1/2), but there are no direction-specific interactions between adjacent chains.