organic compounds
4-Chloro-6-methoxypyrimidin-2-amine
aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my
The title compound, C5H6ClN3O, is essentially planar with a maximum deviation of 0.0256 (11) Å for all non-H atoms. In the crystal, adjacent molecules are linked by a pair of N—H⋯N hydrogen bonds, forming an inversion dimer with an R22(8) ring motif. The dimers are further linked via N—H⋯O hydrogen bonds into an undulating sheet structure parallel to the bc plane.
Related literature
For the biological activity of pyrimidine and aminopyrimidine derivatives, see: Hunt et al. (1980); Baker & Santi (1965). For related structures, see: Schwalbe & Williams (1982); Hu et al. (2002); Chinnakali et al. (1999); Skovsgaard & Bond (2009). For hydrogen-bond motifs, see: Bernstein et al. (1995). For bond-length data, see: Allen et al. (1987). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
Supporting information
10.1107/S160053681204528X/is5214sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S160053681204528X/is5214Isup2.hkl
Supporting information file. DOI: 10.1107/S160053681204528X/is5214Isup3.cml
A hot ethanol solutions (20 ml) of 2-amino-4-chloro-6-methoxypyrimidine (36 mg, Aldrich) was warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature. Single crystals of the title compound (I) appeared from the mother liquor after a few days.
N-bound H atoms were located in a difference Fourier maps and refined freely [N—H = 0.828 (16) and 0.850 (16) Å]. The remaining H atoms were positioned geometrically (C–H = 0.95–0.98 Å) and were refined using a riding model, with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C). A rotating group model was used for the methyl group. Two outliers were omitted (1 8 14 and 0 1 2) in the final refinement.
Data collection: APEX2 (Bruker, 2009); cell
SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).C5H6ClN3O | F(000) = 328 |
Mr = 159.58 | Dx = 1.591 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 6060 reflections |
a = 3.7683 (2) Å | θ = 3.8–32.6° |
b = 16.4455 (2) Å | µ = 0.50 mm−1 |
c = 10.7867 (2) Å | T = 100 K |
β = 94.550 (1)° | Block, colourless |
V = 666.36 (4) Å3 | 0.49 × 0.28 × 0.21 mm |
Z = 4 |
Bruker SMART APEXII CCD area-detector diffractometer | 2436 independent reflections |
Radiation source: fine-focus sealed tube | 2266 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.016 |
ϕ and ω scans | θmax = 32.6°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −5→5 |
Tmin = 0.791, Tmax = 0.904 | k = −24→21 |
9524 measured reflections | l = −16→14 |
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)] = 0.027 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.070 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0306P)2 + 0.3355P] where P = (Fo2 + 2Fc2)/3 |
2436 reflections | (Δ/σ)max = 0.001 |
100 parameters | Δρmax = 0.67 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
C5H6ClN3O | V = 666.36 (4) Å3 |
Mr = 159.58 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 3.7683 (2) Å | µ = 0.50 mm−1 |
b = 16.4455 (2) Å | T = 100 K |
c = 10.7867 (2) Å | 0.49 × 0.28 × 0.21 mm |
β = 94.550 (1)° |
Bruker SMART APEXII CCD area-detector diffractometer | 2436 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 2266 reflections with I > 2σ(I) |
Tmin = 0.791, Tmax = 0.904 | Rint = 0.016 |
9524 measured reflections |
R[F2 > 2σ(F2)] = 0.027 | 0 restraints |
wR(F2) = 0.070 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.67 e Å−3 |
2436 reflections | Δρmin = −0.26 e Å−3 |
100 parameters |
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 1.11362 (6) | 0.546310 (13) | 0.64838 (2) | 0.01425 (6) | |
O1 | 0.57563 (19) | 0.80520 (4) | 0.79576 (6) | 0.01449 (13) | |
N1 | 0.9448 (2) | 0.57688 (5) | 0.87272 (7) | 0.01299 (14) | |
N2 | 0.6906 (2) | 0.70257 (5) | 0.93883 (7) | 0.01284 (14) | |
N3 | 0.8057 (3) | 0.59594 (5) | 1.07440 (8) | 0.01996 (17) | |
C1 | 0.8338 (2) | 0.68624 (5) | 0.72638 (8) | 0.01284 (15) | |
H1A | 0.8437 | 0.7075 | 0.6448 | 0.015* | |
C2 | 0.9490 (2) | 0.60954 (5) | 0.76040 (8) | 0.01137 (14) | |
C3 | 0.8137 (2) | 0.62570 (5) | 0.95924 (8) | 0.01305 (15) | |
C4 | 0.7000 (2) | 0.73004 (5) | 0.82415 (8) | 0.01155 (15) | |
C5 | 0.4336 (3) | 0.85141 (6) | 0.89378 (9) | 0.01568 (16) | |
H5A | 0.3073 | 0.8992 | 0.8583 | 0.024* | |
H5B | 0.6286 | 0.8691 | 0.9532 | 0.024* | |
H5C | 0.2680 | 0.8174 | 0.9366 | 0.024* | |
H2N3 | 0.722 (4) | 0.6245 (10) | 1.1281 (15) | 0.027 (4)* | |
H1N3 | 0.876 (4) | 0.5475 (10) | 1.0891 (15) | 0.023 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.01773 (10) | 0.01199 (10) | 0.01346 (10) | 0.00039 (7) | 0.00388 (7) | −0.00276 (7) |
O1 | 0.0206 (3) | 0.0093 (3) | 0.0136 (3) | 0.0025 (2) | 0.0019 (2) | 0.0013 (2) |
N1 | 0.0169 (3) | 0.0103 (3) | 0.0119 (3) | 0.0017 (2) | 0.0022 (2) | 0.0000 (2) |
N2 | 0.0170 (3) | 0.0092 (3) | 0.0124 (3) | 0.0018 (2) | 0.0017 (2) | 0.0004 (2) |
N3 | 0.0359 (5) | 0.0129 (4) | 0.0119 (3) | 0.0084 (3) | 0.0069 (3) | 0.0022 (3) |
C1 | 0.0171 (4) | 0.0105 (3) | 0.0110 (3) | 0.0002 (3) | 0.0014 (3) | 0.0003 (3) |
C2 | 0.0128 (3) | 0.0099 (3) | 0.0116 (3) | −0.0006 (3) | 0.0018 (3) | −0.0018 (3) |
C3 | 0.0171 (4) | 0.0103 (3) | 0.0118 (3) | 0.0014 (3) | 0.0020 (3) | 0.0005 (3) |
C4 | 0.0130 (3) | 0.0086 (3) | 0.0130 (3) | −0.0001 (3) | 0.0004 (3) | 0.0003 (3) |
C5 | 0.0176 (4) | 0.0115 (4) | 0.0182 (4) | 0.0029 (3) | 0.0026 (3) | −0.0013 (3) |
Cl1—C2 | 1.7449 (9) | N3—H2N3 | 0.828 (16) |
O1—C4 | 1.3485 (10) | N3—H1N3 | 0.850 (16) |
O1—C5 | 1.4393 (11) | C1—C2 | 1.3743 (12) |
N1—C2 | 1.3266 (11) | C1—C4 | 1.4035 (12) |
N1—C3 | 1.3539 (11) | C1—H1A | 0.9500 |
N2—C4 | 1.3201 (11) | C5—H5A | 0.9800 |
N2—C3 | 1.3584 (11) | C5—H5B | 0.9800 |
N3—C3 | 1.3378 (12) | C5—H5C | 0.9800 |
C4—O1—C5 | 117.38 (7) | N3—C3—N1 | 117.35 (8) |
C2—N1—C3 | 114.89 (8) | N3—C3—N2 | 117.28 (8) |
C4—N2—C3 | 115.86 (8) | N1—C3—N2 | 125.37 (8) |
C3—N3—H2N3 | 118.7 (11) | N2—C4—O1 | 119.46 (8) |
C3—N3—H1N3 | 119.1 (11) | N2—C4—C1 | 124.50 (8) |
H2N3—N3—H1N3 | 122.1 (15) | O1—C4—C1 | 116.04 (8) |
C2—C1—C4 | 113.28 (8) | O1—C5—H5A | 109.5 |
C2—C1—H1A | 123.4 | O1—C5—H5B | 109.5 |
C4—C1—H1A | 123.4 | H5A—C5—H5B | 109.5 |
N1—C2—C1 | 126.09 (8) | O1—C5—H5C | 109.5 |
N1—C2—Cl1 | 114.95 (6) | H5A—C5—H5C | 109.5 |
C1—C2—Cl1 | 118.96 (7) | H5B—C5—H5C | 109.5 |
C3—N1—C2—C1 | −0.18 (13) | C4—N2—C3—N1 | 0.61 (14) |
C3—N1—C2—Cl1 | −179.36 (6) | C3—N2—C4—O1 | 178.63 (8) |
C4—C1—C2—N1 | −0.63 (13) | C3—N2—C4—C1 | −1.55 (13) |
C4—C1—C2—Cl1 | 178.52 (6) | C5—O1—C4—N2 | −0.73 (12) |
C2—N1—C3—N3 | −179.55 (9) | C5—O1—C4—C1 | 179.44 (8) |
C2—N1—C3—N2 | 0.22 (13) | C2—C1—C4—N2 | 1.55 (13) |
C4—N2—C3—N3 | −179.62 (9) | C2—C1—C4—O1 | −178.62 (8) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H2N3···O1i | 0.828 (16) | 2.251 (17) | 3.0699 (11) | 170.1 (15) |
N3—H1N3···N1ii | 0.850 (16) | 2.183 (16) | 3.0335 (12) | 180 (2) |
Symmetry codes: (i) x, −y+3/2, z+1/2; (ii) −x+2, −y+1, −z+2. |
Experimental details
Crystal data | |
Chemical formula | C5H6ClN3O |
Mr | 159.58 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 3.7683 (2), 16.4455 (2), 10.7867 (2) |
β (°) | 94.550 (1) |
V (Å3) | 666.36 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.50 |
Crystal size (mm) | 0.49 × 0.28 × 0.21 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.791, 0.904 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9524, 2436, 2266 |
Rint | 0.016 |
(sin θ/λ)max (Å−1) | 0.759 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.027, 0.070, 1.06 |
No. of reflections | 2436 |
No. of parameters | 100 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.67, −0.26 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H2N3···O1i | 0.828 (16) | 2.251 (17) | 3.0699 (11) | 170.1 (15) |
N3—H1N3···N1ii | 0.850 (16) | 2.183 (16) | 3.0335 (12) | 180 (2) |
Symmetry codes: (i) x, −y+3/2, z+1/2; (ii) −x+2, −y+1, −z+2. |
Footnotes
‡Thomson Reuters ResearcherID: A-5599-2009.
Acknowledgements
The authors thank the Malaysian Government and Universiti Sains Malaysia (USM) for the research facilities and Fundamental Research Grant Scheme (FRGS) No. 203/PFIZIK/6711171 to conduct this work. KT thanks The Academy of Sciences for the Developing World and USM for a TWAS–USM fellowship.
References
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Pyrimidine and aminopyrimidine derivatives are biologically important compounds as they occur in nature as components of nucleic acids. Some aminopyrimidine derivatives are used as antifolate drugs (Hunt et al., 1980; Baker & Santi, 1965). The crystal structures of aminopyrimidine derivatives (Schwalbe & Williams, 1982), aminopyrimidine carboxylates (Hu et al., 2002) and co-crystal structures (Chinnakali et al., 1999; Skovsgaard & Bond, 2009) have been reported. In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound, (I), is presented here.
The title compound (Fig. 1) is essentially planar, with atom C5 deviating a maximum of 0.0256 (11) Å from a mean plane of non-H atoms. The bond lengths (Allen et al., 1987) and angles are normal. In the crystal structure (Fig. 2), molecules are linked by a pair of N3—H1N3···N1ii hydrogen bonds (symmetry code in Table 1) into an inversion dimer, forming an R22(8) (Bernstein et al., 1995) ring motif. These molecules are self-assembled via N3—H2N3···O1i hydrogen bonds (graph-set notation C(6); symmetry code in Table 1), which interconnect the dimers resulting in a wavy sheet parallel to the bc plane.