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4-Chloro-6-meth­­oxy­pyrimidin-2-amine

aSchool of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: arazaki@usm.my

(Received 30 October 2012; accepted 2 November 2012; online 10 November 2012)

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[Hunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). J. Biochem. 187, 533-536.]); Baker & Santi (1965[Baker, B. R. & Santi, D. V. (1965). J. Pharm. Sci. 54, 1252-1257.]). For related structures, see: Schwalbe & Williams (1982[Schwalbe, C. H. & Williams, G. J. B. (1982). Acta Cryst. B38, 1840-1843.]); Hu et al. (2002[Hu, M.-L., Ye, M.-D., Zain, S. M. & Ng, S. W. (2002). Acta Cryst. E58, o1005-o1007.]); Chinnakali et al. (1999[Chinnakali, K., Fun, H.-K., Goswami, S., Mahapatra, A. K. & Nigam, G. D. (1999). Acta Cryst. C55, 399-401.]); Skovsgaard & Bond (2009[Skovsgaard, S. & Bond, A. D. (2009). CrystEngComm, 11, 444-453.]). For hydrogen-bond motifs, see: Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]). For bond-length data, see: Allen et al. (1987[Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-19.]). For stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data
  • C5H6ClN3O

  • Mr = 159.58

  • Monoclinic, P 21 /c

  • a = 3.7683 (2) Å

  • b = 16.4455 (2) Å

  • c = 10.7867 (2) Å

  • β = 94.550 (1)°

  • V = 666.36 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.50 mm−1

  • T = 100 K

  • 0.49 × 0.28 × 0.21 mm

Data collection
  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.791, Tmax = 0.904

  • 9524 measured reflections

  • 2436 independent reflections

  • 2266 reflections with I > 2σ(I)

  • Rint = 0.016

Refinement
  • R[F2 > 2σ(F2)] = 0.027

  • wR(F2) = 0.070

  • S = 1.06

  • 2436 reflections

  • 100 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.67 e Å−3

  • Δρmin = −0.26 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{3\over 2}}, z+{\script{1\over 2}}]; (ii) -x+2, -y+1, -z+2.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

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.

Related literature top

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 top

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.

Refinement top

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.

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with atom labels with 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The crystal packing of the title compound. The H atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity.
4-Chloro-6-methoxypyrimidin-2-amine top
Crystal data top
C5H6ClN3OF(000) = 328
Mr = 159.58Dx = 1.591 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 6060 reflections
a = 3.7683 (2) Åθ = 3.8–32.6°
b = 16.4455 (2) ŵ = 0.50 mm1
c = 10.7867 (2) ÅT = 100 K
β = 94.550 (1)°Block, colourless
V = 666.36 (4) Å30.49 × 0.28 × 0.21 mm
Z = 4
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
2436 independent reflections
Radiation source: fine-focus sealed tube2266 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
ϕ and ω scansθmax = 32.6°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 55
Tmin = 0.791, Tmax = 0.904k = 2421
9524 measured reflectionsl = 1614
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.027Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.070H 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 parametersΔρmax = 0.67 e Å3
0 restraintsΔρmin = 0.26 e Å3
Crystal data top
C5H6ClN3OV = 666.36 (4) Å3
Mr = 159.58Z = 4
Monoclinic, P21/cMo Kα radiation
a = 3.7683 (2) ŵ = 0.50 mm1
b = 16.4455 (2) ÅT = 100 K
c = 10.7867 (2) Å0.49 × 0.28 × 0.21 mm
β = 94.550 (1)°
Data collection top
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 = 0.904Rint = 0.016
9524 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0270 restraints
wR(F2) = 0.070H atoms treated by a mixture of independent and constrained refinement
S = 1.06Δρmax = 0.67 e Å3
2436 reflectionsΔρmin = 0.26 e Å3
100 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl11.11362 (6)0.546310 (13)0.64838 (2)0.01425 (6)
O10.57563 (19)0.80520 (4)0.79576 (6)0.01449 (13)
N10.9448 (2)0.57688 (5)0.87272 (7)0.01299 (14)
N20.6906 (2)0.70257 (5)0.93883 (7)0.01284 (14)
N30.8057 (3)0.59594 (5)1.07440 (8)0.01996 (17)
C10.8338 (2)0.68624 (5)0.72638 (8)0.01284 (15)
H1A0.84370.70750.64480.015*
C20.9490 (2)0.60954 (5)0.76040 (8)0.01137 (14)
C30.8137 (2)0.62570 (5)0.95924 (8)0.01305 (15)
C40.7000 (2)0.73004 (5)0.82415 (8)0.01155 (15)
C50.4336 (3)0.85141 (6)0.89378 (9)0.01568 (16)
H5A0.30730.89920.85830.024*
H5B0.62860.86910.95320.024*
H5C0.26800.81740.93660.024*
H2N30.722 (4)0.6245 (10)1.1281 (15)0.027 (4)*
H1N30.876 (4)0.5475 (10)1.0891 (15)0.023 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.01773 (10)0.01199 (10)0.01346 (10)0.00039 (7)0.00388 (7)0.00276 (7)
O10.0206 (3)0.0093 (3)0.0136 (3)0.0025 (2)0.0019 (2)0.0013 (2)
N10.0169 (3)0.0103 (3)0.0119 (3)0.0017 (2)0.0022 (2)0.0000 (2)
N20.0170 (3)0.0092 (3)0.0124 (3)0.0018 (2)0.0017 (2)0.0004 (2)
N30.0359 (5)0.0129 (4)0.0119 (3)0.0084 (3)0.0069 (3)0.0022 (3)
C10.0171 (4)0.0105 (3)0.0110 (3)0.0002 (3)0.0014 (3)0.0003 (3)
C20.0128 (3)0.0099 (3)0.0116 (3)0.0006 (3)0.0018 (3)0.0018 (3)
C30.0171 (4)0.0103 (3)0.0118 (3)0.0014 (3)0.0020 (3)0.0005 (3)
C40.0130 (3)0.0086 (3)0.0130 (3)0.0001 (3)0.0004 (3)0.0003 (3)
C50.0176 (4)0.0115 (4)0.0182 (4)0.0029 (3)0.0026 (3)0.0013 (3)
Geometric parameters (Å, º) top
Cl1—C21.7449 (9)N3—H2N30.828 (16)
O1—C41.3485 (10)N3—H1N30.850 (16)
O1—C51.4393 (11)C1—C21.3743 (12)
N1—C21.3266 (11)C1—C41.4035 (12)
N1—C31.3539 (11)C1—H1A0.9500
N2—C41.3201 (11)C5—H5A0.9800
N2—C31.3584 (11)C5—H5B0.9800
N3—C31.3378 (12)C5—H5C0.9800
C4—O1—C5117.38 (7)N3—C3—N1117.35 (8)
C2—N1—C3114.89 (8)N3—C3—N2117.28 (8)
C4—N2—C3115.86 (8)N1—C3—N2125.37 (8)
C3—N3—H2N3118.7 (11)N2—C4—O1119.46 (8)
C3—N3—H1N3119.1 (11)N2—C4—C1124.50 (8)
H2N3—N3—H1N3122.1 (15)O1—C4—C1116.04 (8)
C2—C1—C4113.28 (8)O1—C5—H5A109.5
C2—C1—H1A123.4O1—C5—H5B109.5
C4—C1—H1A123.4H5A—C5—H5B109.5
N1—C2—C1126.09 (8)O1—C5—H5C109.5
N1—C2—Cl1114.95 (6)H5A—C5—H5C109.5
C1—C2—Cl1118.96 (7)H5B—C5—H5C109.5
C3—N1—C2—C10.18 (13)C4—N2—C3—N10.61 (14)
C3—N1—C2—Cl1179.36 (6)C3—N2—C4—O1178.63 (8)
C4—C1—C2—N10.63 (13)C3—N2—C4—C11.55 (13)
C4—C1—C2—Cl1178.52 (6)C5—O1—C4—N20.73 (12)
C2—N1—C3—N3179.55 (9)C5—O1—C4—C1179.44 (8)
C2—N1—C3—N20.22 (13)C2—C1—C4—N21.55 (13)
C4—N2—C3—N3179.62 (9)C2—C1—C4—O1178.62 (8)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H2N3···O1i0.828 (16)2.251 (17)3.0699 (11)170.1 (15)
N3—H1N3···N1ii0.850 (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 formulaC5H6ClN3O
Mr159.58
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)3.7683 (2), 16.4455 (2), 10.7867 (2)
β (°) 94.550 (1)
V3)666.36 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.50
Crystal size (mm)0.49 × 0.28 × 0.21
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.791, 0.904
No. of measured, independent and
observed [I > 2σ(I)] reflections
9524, 2436, 2266
Rint0.016
(sin θ/λ)max1)0.759
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.070, 1.06
No. of reflections2436
No. of parameters100
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.67, 0.26

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H2N3···O1i0.828 (16)2.251 (17)3.0699 (11)170.1 (15)
N3—H1N3···N1ii0.850 (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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