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Crystallization of 2-amino-4-chloro-6-morpholinopyrimidine, C
8H
11ClN
4O, (I), yields two polymorphs, both with space group
P2
1/
c, having
Z' = 1 (from diethyl ether solution) and
Z' = 2 (from dichloromethane solution), denoted (I
a) and (I
b), respectively. In polymorph (I
a), the molecules are linked by an N-H
O and an N-H
N hydrogen bond into sheets built from alternating
R(8) and
R(40) rings. In polymorph (I
b), one molecule acts as a triple acceptor of hydrogen bonds and the other acts as a single acceptor; one N-H
O and three N-H
N hydrogen bonds link the molecules in a complex chain containing two types of
R(8) and one type of
R(18) ring. 2-Amino-4-chloro-6-piperidinopyrimidine, C
9H
13ClN
4, (II), which is isomorphous with polymorph (I
b), also has
Z' = 2 in
P2
1/
c, and the molecules are linked by three N-H
N hydrogen bonds into a centrosymmetric four-molecule aggregate containing three
R(8) rings.
Supporting information
CCDC references: 204035; 204036; 204037
Samples of (I) and (II) were synthesized from 2-amino-4,6-dichloropyrimidine (purchased from Aldrich). Morpholine [for (I)] or piperidine [for (II)] (3.1 mmol), and triethylamine (6.5 mmol) were added to a stirred solution of 2-amino-4,6-dichloropyrimidine (3.0 mmol) in 3-methylbutan-2-ol (20 ml). The mixtures were heated under reflux, with stirring, for 2 h. After cooling, the solvent was removed, excess distilled water was added, and the resulting solid was filtered off and washed with water. After drying, the solid products were recrystallized first from ethyl acetate and then from dichloromethane; m.p. 485 K [for (I)] and 431 K [for (II)]. NMR for (I), δ 1H (CHCl3): 3.55 (4H, t, J = 5.2 Hz, N—CH2), 3.74 (4H, t, J = 5.2 Hz, O—CH2), 4.90 (2H, br, NH2, exchanges with D2O), 5.94 [1H, s, C(5)—H]; δ 13C (CDCl3): 45.3, 66.6, 82.4, 160.2, 162.3, 163.3; NMR for (II), δ 1H (CHCl3): 1.58–1.68 (6H, m, 3 × CH2), 3.54 (4H, t, J = 45.0 Hz, N—CH2), 4.76 (2H, br, NH2, exchanges with D2O), 5.96 [1H, s, C(5)—H]; δ 13C (CDCl3): 24.6, 25.5, 45.3, 82.4, 160.2, 162.2, 163.3. Crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation of solutions in diethyl ether [for (Ia)] or dichloromethane [for (Ib) and (II)].
Polymorphs (Ia) and (Ib) and compound (II) all crystallize in space group P21/c, the space group being uniquely assigned from the systematic absences in each case. All H atoms were treated as riding atoms, with C—H distances of 0.95 (heteroaromatic) or 0.99 Å (CH2), and N—H distances of 0.88 Å.
For all compounds, data collection: KappaCCD Server Software (Nonius, 1997); cell refinement: DENZO–SMN (Otwinowski & Minor, 1997). Data reduction: DENZO–SMN for (Ia); DENZO–SMN (Otwinowski & Minor, 1997) for (Ib), (II). For all compounds, program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2002); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).
(Ia) 2-Amino-4-chloro-6-morpholinopyrimidine,
Z' = 1 polymorph
top
Crystal data top
C8H11ClN4O | F(000) = 448 |
Mr = 214.66 | Dx = 1.537 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 2102 reflections |
a = 9.4143 (4) Å | θ = 3.1–27.5° |
b = 13.0869 (4) Å | µ = 0.38 mm−1 |
c = 7.5774 (2) Å | T = 120 K |
β = 96.4260 (13)° | Block, colourless |
V = 927.70 (5) Å3 | 0.42 × 0.22 × 0.16 mm |
Z = 4 | |
Data collection top
Nonius KappaCCD diffractometer | 2102 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 1705 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.046 |
ϕ scans, and ω scans with κ offsets | θmax = 27.5°, θmin = 3.1° |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | h = −12→12 |
Tmin = 0.856, Tmax = 0.941 | k = −16→12 |
6031 measured reflections | l = −8→9 |
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)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.092 | H-atom parameters constrained |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0371P)2 + 0.4718P] where P = (Fo2 + 2Fc2)/3 |
2102 reflections | (Δ/σ)max < 0.001 |
127 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.38 e Å−3 |
Crystal data top
C8H11ClN4O | V = 927.70 (5) Å3 |
Mr = 214.66 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.4143 (4) Å | µ = 0.38 mm−1 |
b = 13.0869 (4) Å | T = 120 K |
c = 7.5774 (2) Å | 0.42 × 0.22 × 0.16 mm |
β = 96.4260 (13)° | |
Data collection top
Nonius KappaCCD diffractometer | 2102 independent reflections |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | 1705 reflections with I > 2σ(I) |
Tmin = 0.856, Tmax = 0.941 | Rint = 0.046 |
6031 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.092 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.35 e Å−3 |
2102 reflections | Δρmin = −0.38 e Å−3 |
127 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.71414 (14) | 0.68239 (10) | 0.31515 (17) | 0.0145 (3) | |
C2 | 0.61611 (17) | 0.61494 (13) | 0.3565 (2) | 0.0153 (3) | |
N2 | 0.64679 (15) | 0.51494 (11) | 0.33258 (19) | 0.0210 (3) | |
N3 | 0.48967 (14) | 0.63653 (10) | 0.41696 (17) | 0.0162 (3) | |
C4 | 0.46540 (16) | 0.73618 (13) | 0.4275 (2) | 0.0151 (3) | |
Cl4 | 0.29987 (4) | 0.76873 (3) | 0.49579 (5) | 0.02164 (14) | |
C5 | 0.55396 (16) | 0.81388 (12) | 0.3899 (2) | 0.0146 (3) | |
C6 | 0.68472 (17) | 0.78156 (12) | 0.3325 (2) | 0.0133 (3) | |
N61 | 0.78585 (14) | 0.84916 (10) | 0.28931 (18) | 0.0148 (3) | |
C62 | 0.78964 (18) | 0.95378 (13) | 0.3586 (2) | 0.0184 (4) | |
C63 | 0.88104 (18) | 1.02158 (13) | 0.2538 (2) | 0.0208 (4) | |
O64 | 1.01967 (12) | 0.97951 (9) | 0.24329 (15) | 0.0205 (3) | |
C65 | 1.00464 (18) | 0.88308 (13) | 0.1556 (2) | 0.0191 (4) | |
C66 | 0.92618 (17) | 0.80832 (13) | 0.2607 (2) | 0.0190 (4) | |
H1 | 0.7274 | 0.4976 | 0.2920 | 0.025* | |
H2 | 0.5861 | 0.4674 | 0.3577 | 0.025* | |
H51 | 0.5298 | 0.8839 | 0.4012 | 0.017* | |
H3 | 0.8293 | 0.9535 | 0.4852 | 0.022* | |
H4 | 0.6913 | 0.9815 | 0.3504 | 0.022* | |
H5 | 0.8323 | 1.0311 | 0.1323 | 0.025* | |
H6 | 0.8911 | 1.0896 | 0.3111 | 0.025* | |
H7 | 1.1004 | 0.8555 | 0.1401 | 0.023* | |
H8 | 0.9515 | 0.8922 | 0.0363 | 0.023* | |
H9 | 0.9142 | 0.7427 | 0.1957 | 0.023* | |
H10 | 0.9827 | 0.7952 | 0.3767 | 0.023* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0145 (6) | 0.0133 (7) | 0.0159 (7) | −0.0003 (5) | 0.0025 (5) | 0.0019 (5) |
C2 | 0.0160 (8) | 0.0151 (8) | 0.0146 (8) | −0.0018 (6) | 0.0001 (6) | 0.0012 (6) |
N2 | 0.0217 (8) | 0.0125 (7) | 0.0298 (8) | −0.0013 (6) | 0.0081 (6) | 0.0009 (6) |
N3 | 0.0142 (7) | 0.0163 (7) | 0.0182 (7) | −0.0019 (5) | 0.0017 (5) | 0.0035 (5) |
C4 | 0.0121 (7) | 0.0207 (9) | 0.0126 (8) | 0.0006 (6) | 0.0019 (6) | 0.0019 (6) |
Cl4 | 0.0133 (2) | 0.0262 (3) | 0.0268 (2) | 0.00021 (16) | 0.00769 (15) | 0.00222 (17) |
C5 | 0.0147 (8) | 0.0139 (8) | 0.0151 (8) | 0.0008 (6) | 0.0017 (6) | 0.0011 (6) |
C6 | 0.0139 (8) | 0.0147 (8) | 0.0110 (7) | −0.0002 (6) | 0.0002 (6) | 0.0024 (6) |
N61 | 0.0130 (7) | 0.0124 (7) | 0.0198 (7) | −0.0011 (5) | 0.0054 (5) | 0.0001 (5) |
C62 | 0.0192 (8) | 0.0146 (8) | 0.0225 (9) | −0.0022 (7) | 0.0075 (6) | −0.0032 (7) |
C63 | 0.0189 (8) | 0.0155 (9) | 0.0288 (9) | −0.0026 (7) | 0.0064 (7) | −0.0009 (7) |
O64 | 0.0169 (6) | 0.0189 (6) | 0.0263 (6) | −0.0054 (5) | 0.0053 (5) | −0.0027 (5) |
C65 | 0.0176 (8) | 0.0185 (9) | 0.0225 (9) | −0.0027 (7) | 0.0077 (6) | −0.0010 (7) |
C66 | 0.0144 (8) | 0.0163 (8) | 0.0272 (9) | 0.0014 (7) | 0.0071 (6) | 0.0021 (7) |
Geometric parameters (Å, º) top
N1—C6 | 1.337 (2) | N61—C62 | 1.465 (2) |
N1—C2 | 1.339 (2) | C62—C63 | 1.520 (2) |
C2—N3 | 1.352 (2) | C62—H3 | 0.99 |
C2—N2 | 1.357 (2) | C62—H4 | 0.99 |
N2—H1 | 0.88 | C63—O64 | 1.427 (2) |
N2—H2 | 0.88 | C63—H5 | 0.99 |
N3—C4 | 1.328 (2) | C63—H6 | 0.99 |
C4—C5 | 1.365 (2) | O64—C65 | 1.426 (2) |
C4—Cl4 | 1.7489 (16) | C65—C66 | 1.506 (2) |
C5—C6 | 1.415 (2) | C65—H7 | 0.99 |
C5—H51 | 0.95 | C65—H8 | 0.99 |
C6—N61 | 1.366 (2) | C66—H9 | 0.99 |
N61—C66 | 1.464 (2) | C66—H10 | 0.99 |
| | | |
C6—N1—C2 | 117.46 (14) | N61—C62—H4 | 109.5 |
N1—C2—N3 | 126.68 (15) | C63—C62—H4 | 109.5 |
N1—C2—N2 | 116.23 (15) | H3—C62—H4 | 108.1 |
N3—C2—N2 | 117.09 (15) | O64—C63—C62 | 112.25 (14) |
C2—N2—H1 | 120.0 | O64—C63—H5 | 109.2 |
C2—N2—H2 | 120.0 | C62—C63—H5 | 109.2 |
H1—N2—H2 | 120.0 | O64—C63—H6 | 109.2 |
C4—N3—C2 | 112.91 (14) | C62—C63—H6 | 109.2 |
N3—C4—C5 | 127.29 (15) | H5—C63—H6 | 107.9 |
N3—C4—Cl4 | 114.95 (12) | C65—O64—C63 | 108.90 (12) |
C5—C4—Cl4 | 117.75 (13) | O64—C65—C66 | 110.93 (13) |
C4—C5—C6 | 114.46 (15) | O64—C65—H7 | 109.5 |
C4—C5—H51 | 122.8 | C66—C65—H7 | 109.5 |
C6—C5—H51 | 122.8 | O64—C65—H8 | 109.5 |
N1—C6—N61 | 116.59 (14) | C66—C65—H8 | 109.5 |
N1—C6—C5 | 121.15 (14) | H7—C65—H8 | 108.0 |
N61—C6—C5 | 122.25 (15) | N61—C66—C65 | 110.21 (14) |
C6—N61—C66 | 117.64 (13) | N61—C66—H9 | 109.6 |
C6—N61—C62 | 120.60 (13) | C65—C66—H9 | 109.6 |
C66—N61—C62 | 114.08 (13) | N61—C66—H10 | 109.6 |
N61—C62—C63 | 110.55 (13) | C65—C66—H10 | 109.6 |
N61—C62—H3 | 109.5 | H9—C66—H10 | 108.1 |
C63—C62—H3 | 109.5 | | |
| | | |
C6—N1—C2—N3 | −1.0 (2) | N1—C6—N61—C66 | −11.2 (2) |
C6—N1—C2—N2 | 178.08 (14) | C5—C6—N61—C66 | 169.94 (14) |
N1—C2—N3—C4 | 2.3 (2) | N1—C6—N61—C62 | −158.81 (14) |
N2—C2—N3—C4 | −176.68 (14) | C5—C6—N61—C62 | 22.3 (2) |
C2—N3—C4—C5 | −2.1 (2) | C6—N61—C62—C63 | −164.05 (14) |
C2—N3—C4—Cl4 | 177.36 (11) | C66—N61—C62—C63 | 47.21 (19) |
N3—C4—C5—C6 | 0.5 (2) | N61—C62—C63—O64 | −52.48 (19) |
Cl4—C4—C5—C6 | −178.94 (11) | C62—C63—O64—C65 | 60.71 (17) |
C2—N1—C6—N61 | −179.85 (14) | C63—O64—C65—C66 | −63.06 (17) |
C2—N1—C6—C5 | −0.9 (2) | C6—N61—C66—C65 | 160.42 (14) |
C4—C5—C6—N1 | 1.1 (2) | C62—N61—C66—C65 | −49.86 (18) |
C4—C5—C6—N61 | −179.99 (14) | O64—C65—C66—N61 | 57.46 (18) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1···O64i | 0.88 | 2.44 | 3.288 (2) | 163 |
N2—H2···N3ii | 0.88 | 2.36 | 3.119 (2) | 145 |
Symmetry codes: (i) −x+2, y−1/2, −z+1/2; (ii) −x+1, −y+1, −z+1. |
(Ib) 2-Amino-4-chloro-6-morpholinopyrimidine,
Z' = 2 polymorph
top
Crystal data top
C8H11ClN4O | F(000) = 896 |
Mr = 214.66 | Dx = 1.497 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 4346 reflections |
a = 13.9215 (3) Å | θ = 3.0–27.5° |
b = 8.1803 (2) Å | µ = 0.37 mm−1 |
c = 19.6390 (4) Å | T = 150 K |
β = 121.6130 (12)° | Plate, colourless |
V = 1904.65 (8) Å3 | 0.30 × 0.25 × 0.02 mm |
Z = 8 | |
Data collection top
Nonius KappaCCD diffractometer | 4346 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 3612 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.046 |
ϕ scans, and ω scans with κ offsets | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | h = −18→16 |
Tmin = 0.961, Tmax = 0.995 | k = −10→10 |
17326 measured reflections | l = −25→25 |
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)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0488P)2 + 0.656P] where P = (Fo2 + 2Fc2)/3 |
4346 reflections | (Δ/σ)max = 0.001 |
253 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.40 e Å−3 |
Crystal data top
C8H11ClN4O | V = 1904.65 (8) Å3 |
Mr = 214.66 | Z = 8 |
Monoclinic, P21/c | Mo Kα radiation |
a = 13.9215 (3) Å | µ = 0.37 mm−1 |
b = 8.1803 (2) Å | T = 150 K |
c = 19.6390 (4) Å | 0.30 × 0.25 × 0.02 mm |
β = 121.6130 (12)° | |
Data collection top
Nonius KappaCCD diffractometer | 4346 independent reflections |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | 3612 reflections with I > 2σ(I) |
Tmin = 0.961, Tmax = 0.995 | Rint = 0.046 |
17326 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.097 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.32 e Å−3 |
4346 reflections | Δρmin = −0.40 e Å−3 |
253 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N11 | 0.79843 (10) | 0.20269 (15) | 0.47727 (7) | 0.0157 (3) | |
C12 | 0.87493 (13) | 0.31923 (18) | 0.49071 (9) | 0.0159 (3) | |
N12 | 0.83577 (11) | 0.46261 (16) | 0.45255 (8) | 0.0196 (3) | |
N13 | 0.98819 (10) | 0.30662 (16) | 0.53999 (7) | 0.0171 (3) | |
C14 | 1.02161 (12) | 0.16575 (18) | 0.57935 (9) | 0.0161 (3) | |
Cl14 | 1.16729 (3) | 0.14980 (5) | 0.64376 (2) | 0.02322 (12) | |
C15 | 0.95440 (12) | 0.03841 (18) | 0.57365 (9) | 0.0163 (3) | |
C16 | 0.83789 (12) | 0.06163 (18) | 0.51820 (8) | 0.0151 (3) | |
N161 | 0.76117 (10) | −0.05594 (16) | 0.50384 (7) | 0.0189 (3) | |
C162 | 0.78149 (14) | −0.19507 (19) | 0.55632 (10) | 0.0216 (3) | |
C163 | 0.68697 (13) | −0.2016 (2) | 0.57320 (9) | 0.0223 (3) | |
O164 | 0.57956 (9) | −0.21304 (13) | 0.50117 (7) | 0.0214 (2) | |
C165 | 0.55954 (13) | −0.07493 (19) | 0.45042 (9) | 0.0197 (3) | |
C166 | 0.65010 (12) | −0.0603 (2) | 0.43037 (9) | 0.0184 (3) | |
N21 | 0.41915 (10) | 0.52848 (15) | 0.36586 (7) | 0.0160 (3) | |
C22 | 0.52244 (12) | 0.47297 (18) | 0.38765 (8) | 0.0155 (3) | |
N22 | 0.57501 (11) | 0.37564 (16) | 0.45215 (8) | 0.0192 (3) | |
N23 | 0.57955 (10) | 0.50596 (15) | 0.35056 (7) | 0.0153 (3) | |
C24 | 0.52311 (12) | 0.60138 (18) | 0.28705 (8) | 0.0148 (3) | |
Cl24 | 0.59211 (3) | 0.64279 (5) | 0.23570 (2) | 0.01897 (11) | |
C25 | 0.41932 (13) | 0.66938 (18) | 0.25868 (9) | 0.0165 (3) | |
C26 | 0.36881 (12) | 0.62934 (18) | 0.30311 (9) | 0.0153 (3) | |
N261 | 0.26690 (11) | 0.69436 (16) | 0.28426 (8) | 0.0177 (3) | |
C262 | 0.19982 (13) | 0.78362 (19) | 0.20911 (9) | 0.0187 (3) | |
C263 | 0.10854 (14) | 0.8840 (2) | 0.20937 (10) | 0.0251 (4) | |
O264 | 0.04106 (10) | 0.78723 (16) | 0.22870 (7) | 0.0278 (3) | |
C265 | 0.11157 (14) | 0.7239 (2) | 0.30760 (10) | 0.0269 (4) | |
C266 | 0.20157 (13) | 0.6115 (2) | 0.31349 (9) | 0.0205 (3) | |
H11 | 0.7628 | 0.4775 | 0.4203 | 0.024* | |
H12 | 0.8832 | 0.5416 | 0.4598 | 0.024* | |
H151 | 0.9836 | −0.0584 | 0.6046 | 0.020* | |
H13 | 0.8550 | −0.1824 | 0.6069 | 0.026* | |
H14 | 0.7832 | −0.2976 | 0.5302 | 0.026* | |
H15 | 0.6981 | −0.2974 | 0.6074 | 0.027* | |
H16 | 0.6894 | −0.1021 | 0.6027 | 0.027* | |
H17 | 0.5580 | 0.0260 | 0.4777 | 0.024* | |
H18 | 0.4851 | −0.0868 | 0.4005 | 0.024* | |
H19 | 0.6457 | −0.1546 | 0.3972 | 0.022* | |
H110 | 0.6383 | 0.0409 | 0.3992 | 0.022* | |
H21 | 0.5419 | 0.3503 | 0.4785 | 0.023* | |
H22 | 0.6426 | 0.3372 | 0.4681 | 0.023* | |
H251 | 0.3839 | 0.7380 | 0.2129 | 0.020* | |
H23 | 0.1647 | 0.7051 | 0.1641 | 0.022* | |
H24 | 0.2497 | 0.8568 | 0.2011 | 0.022* | |
H25 | 0.1439 | 0.9736 | 0.2488 | 0.030* | |
H26 | 0.0598 | 0.9338 | 0.1560 | 0.030* | |
H27 | 0.0646 | 0.6634 | 0.3233 | 0.032* | |
H28 | 0.1479 | 0.8159 | 0.3454 | 0.032* | |
H29 | 0.2526 | 0.5779 | 0.3698 | 0.025* | |
H210 | 0.1660 | 0.5119 | 0.2813 | 0.025* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N11 | 0.0126 (6) | 0.0174 (6) | 0.0162 (6) | −0.0020 (5) | 0.0069 (5) | 0.0000 (5) |
C12 | 0.0148 (7) | 0.0184 (7) | 0.0149 (7) | −0.0014 (6) | 0.0080 (6) | −0.0011 (6) |
N12 | 0.0120 (6) | 0.0177 (6) | 0.0232 (7) | −0.0021 (5) | 0.0051 (5) | 0.0030 (5) |
N13 | 0.0125 (6) | 0.0180 (6) | 0.0187 (6) | −0.0022 (5) | 0.0068 (5) | 0.0001 (5) |
C14 | 0.0108 (7) | 0.0198 (7) | 0.0158 (7) | 0.0003 (5) | 0.0057 (6) | −0.0013 (6) |
Cl14 | 0.01039 (19) | 0.0251 (2) | 0.0273 (2) | −0.00093 (14) | 0.00509 (17) | 0.00521 (15) |
C15 | 0.0139 (7) | 0.0163 (7) | 0.0182 (7) | 0.0005 (6) | 0.0080 (6) | 0.0010 (6) |
C16 | 0.0149 (7) | 0.0172 (7) | 0.0145 (7) | −0.0024 (6) | 0.0086 (6) | −0.0030 (6) |
N161 | 0.0126 (6) | 0.0210 (7) | 0.0178 (6) | −0.0040 (5) | 0.0043 (5) | 0.0031 (5) |
C162 | 0.0172 (8) | 0.0184 (7) | 0.0256 (8) | −0.0018 (6) | 0.0087 (7) | 0.0040 (6) |
C163 | 0.0185 (8) | 0.0232 (8) | 0.0212 (8) | −0.0029 (6) | 0.0077 (7) | 0.0049 (6) |
O164 | 0.0161 (6) | 0.0202 (6) | 0.0254 (6) | −0.0028 (4) | 0.0092 (5) | 0.0048 (5) |
C165 | 0.0170 (7) | 0.0188 (8) | 0.0209 (7) | −0.0009 (6) | 0.0084 (6) | 0.0038 (6) |
C166 | 0.0139 (7) | 0.0216 (8) | 0.0157 (7) | −0.0045 (6) | 0.0049 (6) | −0.0003 (6) |
N21 | 0.0136 (6) | 0.0170 (6) | 0.0162 (6) | 0.0002 (5) | 0.0070 (5) | 0.0001 (5) |
C22 | 0.0143 (7) | 0.0143 (7) | 0.0140 (7) | −0.0028 (5) | 0.0047 (6) | −0.0021 (5) |
N22 | 0.0156 (6) | 0.0222 (7) | 0.0196 (7) | 0.0032 (5) | 0.0090 (6) | 0.0069 (5) |
N23 | 0.0131 (6) | 0.0151 (6) | 0.0152 (6) | −0.0011 (5) | 0.0057 (5) | −0.0001 (5) |
C24 | 0.0137 (7) | 0.0163 (7) | 0.0149 (7) | −0.0042 (6) | 0.0079 (6) | −0.0034 (6) |
Cl24 | 0.01498 (19) | 0.0246 (2) | 0.01833 (19) | −0.00025 (14) | 0.00942 (16) | 0.00275 (14) |
C25 | 0.0149 (7) | 0.0174 (7) | 0.0147 (7) | 0.0013 (6) | 0.0060 (6) | 0.0014 (6) |
C26 | 0.0118 (7) | 0.0148 (7) | 0.0153 (7) | −0.0021 (5) | 0.0044 (6) | −0.0036 (6) |
N261 | 0.0135 (6) | 0.0197 (6) | 0.0189 (6) | 0.0022 (5) | 0.0079 (5) | 0.0024 (5) |
C262 | 0.0155 (7) | 0.0191 (8) | 0.0192 (7) | 0.0032 (6) | 0.0076 (6) | 0.0022 (6) |
C263 | 0.0201 (8) | 0.0256 (8) | 0.0278 (9) | 0.0057 (7) | 0.0112 (7) | 0.0026 (7) |
O264 | 0.0161 (6) | 0.0385 (7) | 0.0269 (6) | 0.0065 (5) | 0.0099 (5) | 0.0041 (5) |
C265 | 0.0218 (9) | 0.0367 (10) | 0.0246 (8) | 0.0060 (7) | 0.0138 (7) | 0.0008 (7) |
C266 | 0.0162 (8) | 0.0263 (8) | 0.0194 (8) | 0.0006 (6) | 0.0095 (7) | 0.0015 (6) |
Geometric parameters (Å, º) top
N11—C16 | 1.348 (2) | N21—C26 | 1.3361 (19) |
N11—C12 | 1.3483 (19) | N21—C22 | 1.3460 (19) |
C12—N12 | 1.3440 (19) | C22—N22 | 1.3425 (19) |
C12—N13 | 1.354 (2) | C22—N23 | 1.3575 (19) |
N12—H11 | 0.88 | N22—H21 | 0.88 |
N12—H12 | 0.88 | N22—H22 | 0.88 |
N13—C14 | 1.328 (2) | N23—C24 | 1.3247 (19) |
C14—C15 | 1.365 (2) | C24—C25 | 1.365 (2) |
C14—Cl14 | 1.7438 (15) | C24—Cl24 | 1.7521 (14) |
C15—C16 | 1.415 (2) | C25—C26 | 1.417 (2) |
C15—H151 | 0.95 | C25—H251 | 0.95 |
C16—N161 | 1.3526 (19) | C26—N261 | 1.3719 (19) |
N161—C162 | 1.460 (2) | N261—C262 | 1.462 (2) |
N161—C166 | 1.4612 (19) | N261—C266 | 1.471 (2) |
C162—C163 | 1.517 (2) | C262—C263 | 1.515 (2) |
C162—H13 | 0.99 | C262—H23 | 0.99 |
C162—H14 | 0.99 | C262—H24 | 0.99 |
C163—O164 | 1.4242 (19) | C263—O264 | 1.424 (2) |
C163—H15 | 0.99 | C263—H25 | 0.99 |
C163—H16 | 0.99 | C263—H26 | 0.99 |
O164—C165 | 1.4339 (18) | O264—C265 | 1.428 (2) |
C165—C166 | 1.510 (2) | C265—C266 | 1.509 (2) |
C165—H17 | 0.99 | C265—H27 | 0.99 |
C165—H18 | 0.99 | C265—H28 | 0.99 |
C166—H19 | 0.99 | C266—H29 | 0.99 |
C166—H110 | 0.99 | C266—H210 | 0.99 |
| | | |
C16—N11—C12 | 117.09 (13) | C26—N21—C22 | 117.26 (13) |
N12—C12—N11 | 117.39 (13) | N22—C22—N21 | 117.59 (13) |
N12—C12—N13 | 116.43 (13) | N22—C22—N23 | 116.18 (13) |
N11—C12—N13 | 126.18 (14) | N21—C22—N23 | 126.22 (13) |
C12—N12—H11 | 120.0 | C22—N22—H21 | 120.0 |
C12—N12—H12 | 120.0 | C22—N22—H22 | 120.0 |
H11—N12—H12 | 120.0 | H21—N22—H22 | 120.0 |
C14—N13—C12 | 113.80 (13) | C24—N23—C22 | 113.40 (12) |
N13—C14—C15 | 126.74 (14) | N23—C24—C25 | 127.08 (13) |
N13—C14—Cl14 | 113.99 (11) | N23—C24—Cl24 | 114.98 (11) |
C15—C14—Cl14 | 119.27 (12) | C25—C24—Cl24 | 117.94 (11) |
C14—C15—C16 | 114.88 (13) | C24—C25—C26 | 114.54 (14) |
C14—C15—H151 | 122.6 | C24—C25—H251 | 122.7 |
C16—C15—H151 | 122.6 | C26—C25—H251 | 122.7 |
N11—C16—N161 | 117.00 (13) | N21—C26—N261 | 117.16 (13) |
N11—C16—C15 | 121.23 (13) | N21—C26—C25 | 121.41 (13) |
N161—C16—C15 | 121.77 (14) | N261—C26—C25 | 121.41 (14) |
C16—N161—C162 | 124.57 (12) | C26—N261—C262 | 119.26 (12) |
C16—N161—C166 | 122.30 (13) | C26—N261—C266 | 118.65 (13) |
C162—N161—C166 | 113.04 (12) | C262—N261—C266 | 115.19 (12) |
N161—C162—C163 | 108.21 (13) | N261—C262—C263 | 111.11 (13) |
N161—C162—H13 | 110.1 | N261—C262—H23 | 109.4 |
C163—C162—H13 | 110.1 | C263—C262—H23 | 109.4 |
N161—C162—H14 | 110.1 | N261—C262—H24 | 109.4 |
C163—C162—H14 | 110.1 | C263—C262—H24 | 109.4 |
H13—C162—H14 | 108.4 | H23—C262—H24 | 108.0 |
O164—C163—C162 | 111.39 (12) | O264—C263—C262 | 111.80 (14) |
O164—C163—H15 | 109.4 | O264—C263—H25 | 109.3 |
C162—C163—H15 | 109.4 | C262—C263—H25 | 109.3 |
O164—C163—H16 | 109.4 | O264—C263—H26 | 109.3 |
C162—C163—H16 | 109.4 | C262—C263—H26 | 109.3 |
H15—C163—H16 | 108.0 | H25—C263—H26 | 107.9 |
C163—O164—C165 | 111.04 (11) | C263—O264—C265 | 108.46 (13) |
O164—C165—C166 | 111.05 (12) | O264—C265—C266 | 112.04 (13) |
O164—C165—H17 | 109.4 | O264—C265—H27 | 109.2 |
C166—C165—H17 | 109.4 | C266—C265—H27 | 109.2 |
O164—C165—H18 | 109.4 | O264—C265—H28 | 109.2 |
C166—C165—H18 | 109.4 | C266—C265—H28 | 109.2 |
H17—C165—H18 | 108.0 | H27—C265—H28 | 107.9 |
N161—C166—C165 | 109.91 (12) | N261—C266—C265 | 110.33 (14) |
N161—C166—H19 | 109.7 | N261—C266—H29 | 109.6 |
C165—C166—H19 | 109.7 | C265—C266—H29 | 109.6 |
N161—C166—H110 | 109.7 | N261—C266—H210 | 109.6 |
C165—C166—H110 | 109.7 | C265—C266—H210 | 109.6 |
H19—C166—H110 | 108.2 | H29—C266—H210 | 108.1 |
| | | |
C16—N11—C12—N12 | −177.36 (13) | C26—N21—C22—N22 | 177.98 (13) |
C16—N11—C12—N13 | 1.8 (2) | C26—N21—C22—N23 | −2.0 (2) |
N12—C12—N13—C14 | 176.55 (13) | N22—C22—N23—C24 | 179.49 (13) |
N11—C12—N13—C14 | −2.6 (2) | N21—C22—N23—C24 | −0.6 (2) |
C12—N13—C14—C15 | 0.8 (2) | C22—N23—C24—C25 | 1.9 (2) |
C12—N13—C14—Cl14 | −179.31 (10) | C22—N23—C24—Cl24 | −178.38 (10) |
N13—C14—C15—C16 | 1.5 (2) | N23—C24—C25—C26 | −0.7 (2) |
Cl14—C14—C15—C16 | −178.35 (10) | Cl24—C24—C25—C26 | 179.62 (10) |
C12—N11—C16—N161 | −179.14 (12) | C22—N21—C26—N261 | −175.78 (13) |
C12—N11—C16—C15 | 0.9 (2) | C22—N21—C26—C25 | 3.3 (2) |
C14—C15—C16—N11 | −2.4 (2) | C24—C25—C26—N21 | −2.1 (2) |
C14—C15—C16—N161 | 177.63 (13) | C24—C25—C26—N261 | 176.93 (14) |
N11—C16—N161—C162 | −162.15 (14) | N21—C26—N261—C262 | −170.17 (13) |
C15—C16—N161—C162 | 17.8 (2) | C25—C26—N261—C262 | 10.8 (2) |
N11—C16—N161—C166 | 21.6 (2) | N21—C26—N261—C266 | −20.6 (2) |
C15—C16—N161—C166 | −158.45 (14) | C25—C26—N261—C266 | 160.32 (14) |
C16—N161—C162—C163 | 128.11 (15) | C26—N261—C262—C263 | −164.34 (13) |
C166—N161—C162—C163 | −55.31 (17) | C266—N261—C262—C263 | 45.09 (18) |
N161—C162—C163—O164 | 57.28 (17) | N261—C262—C263—O264 | −53.19 (18) |
C162—C163—O164—C165 | −59.90 (16) | C262—C263—O264—C265 | 62.16 (17) |
C163—O164—C165—C166 | 58.06 (16) | C263—O264—C265—C266 | −63.17 (18) |
C16—N161—C166—C165 | −128.64 (15) | C26—N261—C266—C265 | 163.75 (13) |
C162—N161—C166—C165 | 54.70 (17) | C262—N261—C266—C265 | −45.50 (18) |
O164—C165—C166—N161 | −54.54 (17) | O264—C265—C266—N261 | 54.32 (19) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N12—H11···N23 | 0.88 | 2.19 | 3.061 (2) | 174 |
N22—H22···N11 | 0.88 | 2.35 | 3.211 (2) | 165 |
N12—H12···N13i | 0.88 | 2.18 | 3.036 (2) | 165 |
N22—H21···O164ii | 0.88 | 2.23 | 3.051 (2) | 155 |
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, −y, −z+1. |
(II) 2-Amino-4-chloro-6-piperidinopyrimidine
top
Crystal data top
C9H13ClN4 | F(000) = 896 |
Mr = 212.68 | Dx = 1.414 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 4533 reflections |
a = 13.8139 (2) Å | θ = 3.0–27.5° |
b = 8.4804 (1) Å | µ = 0.35 mm−1 |
c = 19.8379 (3) Å | T = 120 K |
β = 120.6770 (9)° | Block, colourless |
V = 1998.74 (5) Å3 | 0.45 × 0.35 × 0.25 mm |
Z = 8 | |
Data collection top
Nonius KappaCCD diffractometer | 4533 independent reflections |
Radiation source: fine-focus sealed X-ray tube | 3726 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.042 |
ϕ scans, and ω scans with κ offsets | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | h = −17→16 |
Tmin = 0.826, Tmax = 0.911 | k = −10→11 |
15693 measured reflections | l = −25→25 |
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)] = 0.033 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.087 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0419P)2 + 0.5327P] where P = (Fo2 + 2Fc2)/3 |
4533 reflections | (Δ/σ)max = 0.001 |
250 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
Crystal data top
C9H13ClN4 | V = 1998.74 (5) Å3 |
Mr = 212.68 | Z = 8 |
Monoclinic, P21/c | Mo Kα radiation |
a = 13.8139 (2) Å | µ = 0.35 mm−1 |
b = 8.4804 (1) Å | T = 120 K |
c = 19.8379 (3) Å | 0.45 × 0.35 × 0.25 mm |
β = 120.6770 (9)° | |
Data collection top
Nonius KappaCCD diffractometer | 4533 independent reflections |
Absorption correction: multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | 3726 reflections with I > 2σ(I) |
Tmin = 0.826, Tmax = 0.911 | Rint = 0.042 |
15693 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.033 | 0 restraints |
wR(F2) = 0.087 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.25 e Å−3 |
4533 reflections | Δρmin = −0.28 e Å−3 |
250 parameters | |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N11 | 0.81471 (10) | 0.18328 (13) | 0.47002 (6) | 0.0157 (2) | |
C12 | 0.88591 (12) | 0.30463 (16) | 0.48551 (8) | 0.0152 (3) | |
N12 | 0.84403 (10) | 0.43638 (14) | 0.44331 (7) | 0.0191 (3) | |
N13 | 0.99700 (10) | 0.30808 (13) | 0.54099 (7) | 0.0167 (2) | |
C14 | 1.03363 (12) | 0.17721 (16) | 0.58336 (8) | 0.0163 (3) | |
Cl14 | 1.17375 (3) | 0.18345 (4) | 0.65928 (2) | 0.02326 (10) | |
C15 | 0.97273 (11) | 0.04391 (16) | 0.57347 (8) | 0.0169 (3) | |
C16 | 0.85855 (12) | 0.04946 (16) | 0.51163 (8) | 0.0153 (3) | |
N161 | 0.79034 (10) | −0.07770 (14) | 0.49192 (7) | 0.0181 (3) | |
C162 | 0.82073 (10) | −0.21876 (12) | 0.54089 (6) | 0.0234 (3) | |
C163 | 0.76888 (10) | −0.20812 (12) | 0.59229 (6) | 0.0256 (3) | |
C164 | 0.64137 (14) | −0.19517 (18) | 0.54122 (9) | 0.0254 (3) | |
C165 | 0.60693 (13) | −0.06015 (18) | 0.48212 (9) | 0.0233 (3) | |
C166 | 0.66895 (12) | −0.06769 (17) | 0.43709 (8) | 0.0200 (3) | |
N21 | 0.44603 (10) | 0.53187 (14) | 0.37572 (7) | 0.0176 (3) | |
C22 | 0.54302 (12) | 0.47010 (16) | 0.38853 (8) | 0.0177 (3) | |
N22 | 0.60167 (11) | 0.38106 (15) | 0.45416 (7) | 0.0237 (3) | |
N23 | 0.59066 (9) | 0.48844 (14) | 0.34421 (7) | 0.0175 (3) | |
C24 | 0.53063 (12) | 0.57948 (16) | 0.28197 (8) | 0.0166 (3) | |
Cl24 | 0.58707 (3) | 0.60594 (4) | 0.22147 (2) | 0.02286 (10) | |
C25 | 0.43078 (12) | 0.65039 (16) | 0.26070 (8) | 0.0174 (3) | |
C26 | 0.38803 (11) | 0.62230 (15) | 0.31114 (8) | 0.0153 (3) | |
N261 | 0.28892 (10) | 0.68526 (13) | 0.29758 (7) | 0.0164 (2) | |
C262 | 0.21643 (12) | 0.76963 (17) | 0.22408 (8) | 0.0180 (3) | |
C263 | 0.13674 (13) | 0.88200 (18) | 0.23172 (9) | 0.0237 (3) | |
C264 | 0.07035 (13) | 0.8005 (2) | 0.26391 (9) | 0.0270 (4) | |
C265 | 0.15162 (13) | 0.72011 (19) | 0.34120 (9) | 0.0239 (3) | |
C266 | 0.22795 (12) | 0.60598 (17) | 0.33079 (8) | 0.0182 (3) | |
H11 | 0.7723 | 0.4414 | 0.4070 | 0.023* | |
H12 | 0.8882 | 0.5180 | 0.4519 | 0.023* | |
H151 | 1.0044 | −0.0465 | 0.6057 | 0.020* | |
H13 | 0.9036 | −0.2268 | 0.5740 | 0.028* | |
H14 | 0.7926 | −0.3140 | 0.5074 | 0.028* | |
H15 | 0.7990 | −0.1146 | 0.6268 | 0.031* | |
H16 | 0.7889 | −0.3031 | 0.6258 | 0.031* | |
H17 | 0.6088 | −0.1771 | 0.5750 | 0.030* | |
H18 | 0.6106 | −0.2956 | 0.5127 | 0.030* | |
H19 | 0.5248 | −0.0654 | 0.4447 | 0.028* | |
H110 | 0.6234 | 0.0418 | 0.5102 | 0.028* | |
H111 | 0.6435 | −0.1611 | 0.4023 | 0.024* | |
H112 | 0.6517 | 0.0276 | 0.4041 | 0.024* | |
H21 | 0.5753 | 0.3665 | 0.4858 | 0.028* | |
H22 | 0.6660 | 0.3380 | 0.4650 | 0.028* | |
H251 | 0.3923 | 0.7143 | 0.2152 | 0.021* | |
H23 | 0.1720 | 0.6924 | 0.1820 | 0.022* | |
H24 | 0.2639 | 0.8300 | 0.2090 | 0.022* | |
H25 | 0.0836 | 0.9272 | 0.1796 | 0.028* | |
H26 | 0.1807 | 0.9699 | 0.2670 | 0.028* | |
H27 | 0.0245 | 0.8791 | 0.2723 | 0.032* | |
H28 | 0.0189 | 0.7213 | 0.2258 | 0.032* | |
H29 | 0.1980 | 0.8008 | 0.3807 | 0.029* | |
H210 | 0.1085 | 0.6621 | 0.3607 | 0.029* | |
H211 | 0.2828 | 0.5597 | 0.3822 | 0.022* | |
H212 | 0.1821 | 0.5191 | 0.2956 | 0.022* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N11 | 0.0130 (6) | 0.0191 (6) | 0.0141 (6) | −0.0005 (5) | 0.0063 (5) | −0.0001 (4) |
C12 | 0.0139 (7) | 0.0203 (7) | 0.0124 (6) | −0.0001 (5) | 0.0075 (6) | −0.0014 (5) |
N12 | 0.0129 (6) | 0.0197 (6) | 0.0183 (6) | −0.0016 (5) | 0.0032 (5) | 0.0022 (5) |
N13 | 0.0128 (6) | 0.0205 (6) | 0.0150 (6) | −0.0010 (5) | 0.0058 (5) | 0.0002 (5) |
C14 | 0.0115 (7) | 0.0232 (7) | 0.0136 (6) | 0.0008 (6) | 0.0060 (6) | −0.0015 (5) |
Cl14 | 0.01206 (18) | 0.0289 (2) | 0.02026 (19) | −0.00127 (14) | 0.00206 (15) | 0.00288 (14) |
C15 | 0.0138 (7) | 0.0187 (7) | 0.0166 (7) | 0.0023 (6) | 0.0065 (6) | 0.0025 (5) |
C16 | 0.0149 (7) | 0.0184 (7) | 0.0152 (7) | 0.0001 (5) | 0.0096 (6) | −0.0013 (5) |
N161 | 0.0131 (6) | 0.0200 (6) | 0.0179 (6) | −0.0019 (5) | 0.0055 (5) | 0.0005 (5) |
C162 | 0.0208 (8) | 0.0152 (7) | 0.0288 (8) | −0.0006 (6) | 0.0087 (7) | 0.0007 (6) |
C163 | 0.0314 (9) | 0.0193 (7) | 0.0224 (8) | −0.0032 (6) | 0.0110 (7) | 0.0048 (6) |
C164 | 0.0284 (9) | 0.0234 (8) | 0.0294 (8) | −0.0042 (6) | 0.0185 (7) | 0.0009 (6) |
C165 | 0.0182 (8) | 0.0228 (8) | 0.0275 (8) | −0.0009 (6) | 0.0105 (7) | 0.0007 (6) |
C166 | 0.0138 (7) | 0.0243 (7) | 0.0174 (7) | −0.0041 (6) | 0.0049 (6) | 0.0010 (6) |
N21 | 0.0136 (6) | 0.0186 (6) | 0.0167 (6) | 0.0003 (5) | 0.0049 (5) | 0.0025 (5) |
C22 | 0.0141 (7) | 0.0151 (7) | 0.0172 (7) | −0.0020 (5) | 0.0032 (6) | 0.0004 (5) |
N22 | 0.0173 (7) | 0.0288 (7) | 0.0221 (7) | 0.0064 (5) | 0.0079 (6) | 0.0100 (5) |
N23 | 0.0124 (6) | 0.0183 (6) | 0.0164 (6) | 0.0000 (5) | 0.0034 (5) | −0.0009 (5) |
C24 | 0.0139 (7) | 0.0187 (7) | 0.0146 (7) | −0.0029 (6) | 0.0054 (6) | −0.0032 (5) |
Cl24 | 0.01552 (19) | 0.0342 (2) | 0.01862 (18) | 0.00228 (15) | 0.00853 (15) | 0.00171 (14) |
C25 | 0.0152 (7) | 0.0187 (7) | 0.0142 (7) | 0.0009 (6) | 0.0045 (6) | 0.0021 (5) |
C26 | 0.0126 (7) | 0.0143 (7) | 0.0144 (7) | −0.0016 (5) | 0.0036 (6) | −0.0013 (5) |
N261 | 0.0130 (6) | 0.0185 (6) | 0.0164 (6) | 0.0022 (5) | 0.0064 (5) | 0.0037 (4) |
C262 | 0.0152 (7) | 0.0201 (7) | 0.0161 (7) | 0.0024 (6) | 0.0061 (6) | 0.0032 (5) |
C263 | 0.0229 (8) | 0.0242 (8) | 0.0230 (8) | 0.0086 (6) | 0.0110 (7) | 0.0056 (6) |
C264 | 0.0194 (8) | 0.0382 (9) | 0.0250 (8) | 0.0107 (7) | 0.0125 (7) | 0.0041 (7) |
C265 | 0.0239 (8) | 0.0316 (8) | 0.0194 (7) | 0.0034 (7) | 0.0134 (7) | 0.0005 (6) |
C266 | 0.0174 (7) | 0.0204 (7) | 0.0167 (7) | −0.0009 (6) | 0.0086 (6) | 0.0013 (5) |
Geometric parameters (Å, º) top
N11—C12 | 1.3463 (18) | N21—C22 | 1.3366 (18) |
N11—C16 | 1.3512 (17) | N21—C26 | 1.3505 (17) |
C12—N12 | 1.3377 (18) | C22—N23 | 1.3494 (18) |
C12—N13 | 1.3578 (18) | C22—N22 | 1.3583 (18) |
N12—H11 | 0.88 | N22—H21 | 0.88 |
N12—H12 | 0.88 | N22—H22 | 0.88 |
N13—C14 | 1.3267 (18) | N23—C24 | 1.3279 (18) |
C14—C15 | 1.3622 (19) | C24—C25 | 1.359 (2) |
C14—Cl14 | 1.7444 (14) | C24—Cl24 | 1.7474 (13) |
C15—C16 | 1.4215 (19) | C25—C26 | 1.4177 (19) |
C15—H151 | 0.95 | C25—H251 | 0.95 |
C16—N161 | 1.3519 (18) | C26—N261 | 1.3624 (17) |
N161—C162 | 1.4611 (15) | N261—C262 | 1.4666 (17) |
N161—C166 | 1.4632 (18) | N261—C266 | 1.4702 (17) |
C162—C163 | 1.5186 (19) | C262—C263 | 1.521 (2) |
C162—H13 | 0.99 | C262—H23 | 0.99 |
C162—H14 | 0.99 | C262—H24 | 0.99 |
C163—C164 | 1.5233 (19) | C263—C264 | 1.524 (2) |
C163—H15 | 0.99 | C263—H25 | 0.99 |
C163—H16 | 0.99 | C263—H26 | 0.99 |
C164—C165 | 1.531 (2) | C264—C265 | 1.523 (2) |
C164—H17 | 0.99 | C264—H27 | 0.99 |
C164—H18 | 0.99 | C264—H28 | 0.99 |
C165—C166 | 1.5221 (19) | C265—C266 | 1.521 (2) |
C165—H19 | 0.99 | C265—H29 | 0.99 |
C165—H110 | 0.99 | C265—H210 | 0.99 |
C166—H111 | 0.99 | C266—H211 | 0.99 |
C166—H112 | 0.99 | C266—H212 | 0.99 |
| | | |
C12—N11—C16 | 117.07 (12) | C22—N21—C26 | 117.06 (11) |
N12—C12—N11 | 117.60 (12) | N21—C22—N23 | 127.28 (12) |
N12—C12—N13 | 115.99 (12) | N21—C22—N22 | 116.74 (12) |
N11—C12—N13 | 126.40 (12) | N23—C22—N22 | 115.97 (12) |
C12—N12—H11 | 120.0 | C22—N22—H21 | 120.0 |
C12—N12—H12 | 120.0 | C22—N22—H22 | 120.0 |
H11—N12—H12 | 120.0 | H21—N22—H22 | 120.0 |
C14—N13—C12 | 113.80 (12) | C24—N23—C22 | 113.08 (11) |
N13—C14—C15 | 126.51 (13) | N23—C24—C25 | 126.81 (13) |
N13—C14—Cl14 | 114.72 (10) | N23—C24—Cl24 | 115.30 (10) |
C15—C14—Cl14 | 118.76 (11) | C25—C24—Cl24 | 117.87 (11) |
C14—C15—C16 | 115.38 (12) | C24—C25—C26 | 115.38 (13) |
C14—C15—H151 | 122.3 | C24—C25—H251 | 122.3 |
C16—C15—H151 | 122.3 | C26—C25—H251 | 122.3 |
N11—C16—N161 | 117.66 (12) | N21—C26—N261 | 117.38 (12) |
N11—C16—C15 | 120.60 (12) | N21—C26—C25 | 120.38 (12) |
N161—C16—C15 | 121.73 (12) | N261—C26—C25 | 122.23 (12) |
C16—N161—C162 | 122.64 (11) | C26—N261—C262 | 119.68 (11) |
C16—N161—C166 | 122.28 (12) | C26—N261—C266 | 118.69 (11) |
C162—N161—C166 | 111.92 (10) | C262—N261—C266 | 114.32 (11) |
N161—C162—C163 | 108.90 (6) | N261—C262—C263 | 111.62 (11) |
N161—C162—H13 | 109.9 | N261—C262—H23 | 109.3 |
C163—C162—H13 | 109.9 | C263—C262—H23 | 109.3 |
N161—C162—H14 | 109.9 | N261—C262—H24 | 109.3 |
C163—C162—H14 | 109.9 | C263—C262—H24 | 109.3 |
H13—C162—H14 | 108.3 | H23—C262—H24 | 108.0 |
C162—C163—C164 | 109.82 (7) | C262—C263—C264 | 112.24 (12) |
C162—C163—H15 | 109.7 | C262—C263—H25 | 109.2 |
C164—C163—H15 | 109.7 | C264—C263—H25 | 109.2 |
C162—C163—H16 | 109.7 | C262—C263—H26 | 109.2 |
C164—C163—H16 | 109.7 | C264—C263—H26 | 109.2 |
H15—C163—H16 | 108.2 | H25—C263—H26 | 107.9 |
C163—C164—C165 | 111.44 (11) | C265—C264—C263 | 109.43 (13) |
C163—C164—H17 | 109.3 | C265—C264—H27 | 109.8 |
C165—C164—H17 | 109.3 | C263—C264—H27 | 109.8 |
C163—C164—H18 | 109.3 | C265—C264—H28 | 109.8 |
C165—C164—H18 | 109.3 | C263—C264—H28 | 109.8 |
H17—C164—H18 | 108.0 | H27—C264—H28 | 108.2 |
C166—C165—C164 | 111.71 (12) | C266—C265—C264 | 110.75 (12) |
C166—C165—H19 | 109.3 | C266—C265—H29 | 109.5 |
C164—C165—H19 | 109.3 | C264—C265—H29 | 109.5 |
C166—C165—H110 | 109.3 | C266—C265—H210 | 109.5 |
C164—C165—H110 | 109.3 | C264—C265—H210 | 109.5 |
H19—C165—H110 | 107.9 | H29—C265—H210 | 108.1 |
N161—C166—C165 | 109.93 (11) | N261—C266—C265 | 111.42 (11) |
N161—C166—H111 | 109.7 | N261—C266—H211 | 109.3 |
C165—C166—H111 | 109.7 | C265—C266—H211 | 109.3 |
N161—C166—H112 | 109.7 | N261—C266—H212 | 109.3 |
C165—C166—H112 | 109.7 | C265—C266—H212 | 109.3 |
H111—C166—H112 | 108.2 | H211—C266—H212 | 108.0 |
| | | |
C16—N11—C12—N12 | 178.36 (11) | C26—N21—C22—N23 | 0.4 (2) |
C16—N11—C12—N13 | −2.62 (19) | C26—N21—C22—N22 | 179.12 (12) |
N12—C12—N13—C14 | 177.46 (11) | N21—C22—N23—C24 | 0.2 (2) |
N11—C12—N13—C14 | −1.57 (18) | N22—C22—N23—C24 | −178.53 (12) |
C12—N13—C14—C15 | 3.22 (19) | C22—N23—C24—C25 | −0.4 (2) |
C12—N13—C14—Cl14 | −175.95 (9) | C22—N23—C24—Cl24 | −179.26 (10) |
N13—C14—C15—C16 | −0.6 (2) | N23—C24—C25—C26 | 0.0 (2) |
Cl14—C14—C15—C16 | 178.51 (9) | Cl24—C24—C25—C26 | 178.83 (10) |
C12—N11—C16—N161 | −174.25 (11) | C22—N21—C26—N261 | 179.80 (12) |
C12—N11—C16—C15 | 5.34 (18) | C22—N21—C26—C25 | −0.83 (19) |
C14—C15—C16—N11 | −3.90 (18) | C24—C25—C26—N21 | 0.67 (19) |
C14—C15—C16—N161 | 175.68 (12) | C24—C25—C26—N261 | 180.00 (12) |
N11—C16—N161—C162 | −168.38 (11) | N21—C26—N261—C262 | −173.24 (12) |
C15—C16—N161—C162 | 12.03 (19) | C25—C26—N261—C262 | 7.4 (2) |
N11—C16—N161—C166 | −10.13 (18) | N21—C26—N261—C266 | −24.78 (18) |
C15—C16—N161—C166 | 170.29 (12) | C25—C26—N261—C266 | 155.87 (12) |
C16—N161—C162—C163 | 95.88 (11) | C26—N261—C262—C263 | −158.02 (13) |
C166—N161—C162—C163 | −64.39 (10) | C266—N261—C262—C263 | 52.21 (16) |
N161—C162—C163—C164 | 59.36 (9) | N261—C262—C263—C264 | −52.37 (17) |
C162—C163—C164—C165 | −53.16 (12) | C262—C263—C264—C265 | 54.62 (17) |
C163—C164—C165—C166 | 50.16 (16) | C263—C264—C265—C266 | −55.99 (17) |
C16—N161—C166—C165 | −99.61 (15) | C26—N261—C266—C265 | 155.60 (12) |
C162—N161—C166—C165 | 60.74 (14) | C262—N261—C266—C265 | −54.31 (15) |
C164—C165—C166—N161 | −52.69 (16) | C264—C265—C266—N261 | 55.86 (17) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N12—H11···N23 | 0.88 | 2.19 | 3.0479 (16) | 163 |
N22—H22···N11 | 0.88 | 2.40 | 3.2601 (17) | 167 |
N12—H12···N13i | 0.88 | 2.12 | 2.9862 (16) | 169 |
Symmetry code: (i) −x+2, −y+1, −z+1. |
Experimental details
| (Ia) | (Ib) | (II) |
Crystal data |
Chemical formula | C8H11ClN4O | C8H11ClN4O | C9H13ClN4 |
Mr | 214.66 | 214.66 | 212.68 |
Crystal system, space group | Monoclinic, P21/c | Monoclinic, P21/c | Monoclinic, P21/c |
Temperature (K) | 120 | 150 | 120 |
a, b, c (Å) | 9.4143 (4), 13.0869 (4), 7.5774 (2) | 13.9215 (3), 8.1803 (2), 19.6390 (4) | 13.8139 (2), 8.4804 (1), 19.8379 (3) |
β (°) | 96.4260 (13) | 121.6130 (12) | 120.6770 (9) |
V (Å3) | 927.70 (5) | 1904.65 (8) | 1998.74 (5) |
Z | 4 | 8 | 8 |
Radiation type | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.38 | 0.37 | 0.35 |
Crystal size (mm) | 0.42 × 0.22 × 0.16 | 0.30 × 0.25 × 0.02 | 0.45 × 0.35 × 0.25 |
|
Data collection |
Diffractometer | Nonius KappaCCD diffractometer | Nonius KappaCCD diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | Multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | Multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) | Multi-scan (DENZO–SMN; Otwinowski & Minor, 1997) |
Tmin, Tmax | 0.856, 0.941 | 0.961, 0.995 | 0.826, 0.911 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6031, 2102, 1705 | 17326, 4346, 3612 | 15693, 4533, 3726 |
Rint | 0.046 | 0.046 | 0.042 |
(sin θ/λ)max (Å−1) | 0.649 | 0.649 | 0.649 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.092, 1.05 | 0.037, 0.097, 1.04 | 0.033, 0.087, 1.04 |
No. of reflections | 2102 | 4346 | 4533 |
No. of parameters | 127 | 253 | 250 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.35, −0.38 | 0.32, −0.40 | 0.25, −0.28 |
Hydrogen-bond geometry (Å, º) for (Ia) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1···O64i | 0.88 | 2.44 | 3.288 (2) | 163 |
N2—H2···N3ii | 0.88 | 2.36 | 3.119 (2) | 145 |
Symmetry codes: (i) −x+2, y−1/2, −z+1/2; (ii) −x+1, −y+1, −z+1. |
Hydrogen-bond geometry (Å, º) for (Ib) top
D—H···A | D—H | H···A | D···A | D—H···A |
N12—H11···N23 | 0.88 | 2.19 | 3.061 (2) | 174 |
N22—H22···N11 | 0.88 | 2.35 | 3.211 (2) | 165 |
N12—H12···N13i | 0.88 | 2.18 | 3.036 (2) | 165 |
N22—H21···O164ii | 0.88 | 2.23 | 3.051 (2) | 155 |
Symmetry codes: (i) −x+2, −y+1, −z+1; (ii) −x+1, −y, −z+1. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N12—H11···N23 | 0.88 | 2.19 | 3.0479 (16) | 163 |
N22—H22···N11 | 0.88 | 2.40 | 3.2601 (17) | 167 |
N12—H12···N13i | 0.88 | 2.12 | 2.9862 (16) | 169 |
Symmetry code: (i) −x+2, −y+1, −z+1. |
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Aminochloropyrimidines are key intermediates for the synthesis of O6-benzyloxy-5-nitrosopyrimidines, which can themselves be converted into a wide range of alkoxy- and amino-substituted O6-benzyloxy-5-nitrosopyrimidines (Quesada, Marchal, Melguizo et al., 2002; Quesada, Marchal, Nogueras et al., 2002), important as potential, or proven, in vitro inhibitors of the human DNA-repair protein O6-alkylguanine-DNA-transferase (Chae et al., 1995; Quesada, Marchal, Melguizo et al., 2002). We report here the molecular and supramolecular structures of two examples of this class of pyrimidine, namely 2-amino-4-chloro-6-morpholinopyrimidine, (I), which crystallizes in two polymorphic forms, and 2-amino-4-chloro-6-piperidinopyrimidine, (II), which is isomorphous and almost isostructural with one of the polymorphs of (I).
The simpler polymorph (Ia) (Fig. 1) of compound (I) has Z' = 1 in P21/c, and the molecules are linked into sheets by two hydrogen bonds, one each of the N—H···O and N—H···N types (Table 1). Amino atom N2 in the molecule at (x, y, z) acts as hydrogen-bond donor, via H1, to the morpholine atom O64 in the molecule at (2 − x, −0.5 + y, 0.5 − z), while atom N2 at (2 − x, −0.5 + y, 0.5 − z) likewise acts as donor to O64 at (x, −1 + y, z), so producing a C(9) chain running parallel to the [010] direction and generated by the 21 screw axis along (1, y, 1/4) (Fig. 2). Adjacent [010] chains are linked into (102) sheets by means of N—H···N hydrogen bonding. Amine atom N2 in the molecule at (x, y, z), which lies in the [010] chain along (1, y, 1/4), acts as hydrogen-bond donor, via H2, to atom N3 in the molecule at (1 − x, 1 − y, 1 − z), which lies in the antiparallel chain along (0, −y, 3/4), so forming an R22(8) ring centred at (1/2, 1/2, 1/2). In a similar way, the molecule at (2 − x, −0.5 + y, 0.5 − z), a component of the (1, y, 1/4) chain, is linked via the R22(8) motif to the molecule at (1 + x, 0.5 − y, −0.5 + z), which lies in the chain along (2, −y, −0.25). In this manner, [010] chains are linked into a (102) sheet, built from alternating R22(8) and R66(40) rings (Fig. 2). If the individual molecules are regarded as the nodes of the net defining the (102) sheet, then this net is of the (6,3)-type (Batten & Robson, 1998), while if the R22(8) dimers are taken to be the nodes the net is of (4,4)-type. There are no direction-specific interactions between adjacent sheets.
In the Z' = 2 polymorph of compound (I), viz. (Ib), the two independent molecules (Fig. 3) exhibit different hydrogen-bonding behaviour and the hydrogen bonds (Table 2) generate a rather elaborate one-dimensional structure. In both molecules, the amino group acts as a double donor, but molecule 1 (containing atom N11; Fig. 3) acts as a triple acceptor of hydrogen bonds, via atoms N11, N13 and O164, whereas in molecule 2, there is just a single acceptor, N23. These facts alone preclude an additional symmetry. Within the selected asymmetric unit (Fig. 3), the molecules are linked by paired N—H···N hydrogen bonds, forming an R22(8) dimer in which the orientation of the morpholine substituents precludes even approximate additional symmetry. In analysing the structure of this polymorph, it is convenient to employ the substructure approach (Gregson et al., 2000), where the key substructural unit is the R22(8) dimer; the formation of this dimer leaves two N—H bonds, N12—H12 and N22—H21, available for the formation of further hydrogen bonds. Amino atom N12 in the type-1 molecule at (x, y, z) acts as hydrogen-bond donor, via H12, to atom N13 in the type-1 molecule at (2 − x, 1 − y, 1 − z), so generating a centrosymmetric R22(8) motif, centred at (1, 1/2, 1/2), while atom N22 in the type-2 molecule at (x, y, z) acts as donor, via H21, to atom O164 in the type-1 molecule at (1 − x, −y, 1 − z), so generating a centrosymmetric R44(18) motif centred at (1/2, 0, 1/2). Propagation by inversion of these hydrogen bonds thus leads to formation of a chain of rings running parallel to the [110] direction (Fig. 4), such that the type-2 morpholine groups containing atom O264 are pendent from the chain with no plausible hydrogen-bond donors within hydrogen-bonding distance.
Compound (II) has so far been isolated in only one crystalline form and this is isomorphous with the Z' = 2 polymorph of compound (I); the cell dimensions of these two P21/c, Z' = 2 phases are very similar and it is possible to refine either structure starting from the coordinates of the other, paying due regard to the difference in atom types between the morpholino substituent in (I) and the piperidine substituent in (II). Since, however, there can be no N—H···O hydrogen bonds in (II) (Table 3), the supramolecular aggregation in (II) must be different from that in either polymorph of (I), where such hydrogen bonds are present in both polymorphs, and hence the two Z' = 2 phases are not, strictly speaking, properly isostructural, although they are nearly so. The asymmetric unit selected for compound (II) resembles that for the Z' = 2 polymorph of (I) in forming an R22(8) dimer which itself exhibits no symmetry (Fig. 5). Pairs of these dimers are linked into a centrosymmetric four-molecule aggregate centred at (1, 1/2, 1/2); atom N12 at (x, y, z) acts as hydrogen-bond donor, via H12, to atom N13 at (2 − x, 1 − y, 1 − z), but the N22—H21 bond does not participate in the hydrogen bonding, so that this aggregate is strictly finite (Fig. 6).
It is notable that even in (II), where there is an exact match between the number of hard hydrogen-bond donors and the number of hard hydrogen-bond acceptors, not all of these donors and acceptors are involved in the supramolecular aggregation. Thus, atom N21 does not accept any hydrogen bond, nor is N22—H21 involved. In both (Ia) and (Ib), there is an excess of acceptors over donors, and in (Ia), atom N1 is unused as an acceptor, while in (Ib) both N21 and O264 are unused. The structures of (Ia), (Ib) and (II) do not contain any soft hydrogen bonds of the C—H···A (A = N or O) or D—H···π types (D = C or N), nor do they contain any π–π-stacking interactions; they thus have hydrogen-bonded supramolecular structures which are two-dimensional, one-dimensional and (finite) zero-dimensional, respectively.
In each of (Ib) and (II), there are rather short contacts between pairs of Cl atoms, across the inversion centre at (1, 1/2, 1/2) (Figs. 4 and 6); in (Ib), the Cl14···Cl24i distance is 3.375 (2) Å [symmetry code: (i) 2 − x, 1 − y, 1 − z], associated with a C—Cl···Cl angle of 145.14 (5)°, while in (II), the corresponding values are 3.425 (2) Å and 150.08 (5)°. For Cl bonded to neutral arene groups, Bondi (1964) recommended a van der Waals radius of 1.77 Å; the Cl···Cl contact distances in (Ib) and (II) are thus significantly shorter than twice the van der Waals radius. Database analysis of such halogen–halogen contacts has shown than when the X···X contact distance (X = halogen) is significantly less than the van der Waals sum, the associated C—X···X angles are clustered around 180 and 90° (Ramasabbu et al., 1986); the C—Cl···Cl angles observed are not particularly close to either cluster, and almost certainly their values are constrained by the formation of the centrosymmetric hydrogen-bonded R22(8) rings.
Within the molecules, the morpholine and piperidine substituents adopt the usual chair conformation, but with the N atoms in these rings almost planar; the sum of the angles at this N atom ranges from 352.3 (2)° in (Ia) to 359.9 (2)° in molecule 1 of (Ib). Consistent with this planarity, the associated C—N distances for the bond linking the two rings within each molecule range from 1.352 (2) to 1.372 (2) Å, with a mean of 1.361 (2) Å, typical of Ar—N(C)2 distances involving di-N-substituted anilines with a planar N atom (mean value 1.371 Å; Allen et al., 1987). By way of comparison, the C—NH2 distances here range from 1.338 (2) to 1.358 (2) Å, with a mean value of 1.348 (2) Å, again typical of Ar—NH2 distances in simple anilines with an unsubstituted planar N atom (mean value 1.355 Å; Allen et al., 1987). The other intramolecular distances and angles show no unusual features; in particular, there is no evidence for any bond fixation within the pyrimidine rings.
The very different cell dimensions for the two polymorphs (Ia) and (Ib) effectively rule out any possibility of a simple displacive phase transition between these two polymorphs. While we have not investigated the relative stability of these two polymorphs, we note that (Ia) has a significantly higher density than (Ib) and thus is probably the thermodynamically more stable form (Burger & Ramberger, 1979). Although polymorph (Ib) was the first to be isolated, both forms can readily be reproduced by crystallization from the appropriate solvent; hence there is no question here of any disappearing polymorph (Dunitz & Bernstein, 1995).