4-Chloro-6-meth­oxy­pyrimidin-2-amine–succinic acid (2/1)

Kaliyaperumal Thanigaimani; Nuridayanti Che Khalib; Suhana Arshad; Ibrahim Abdul Razak

doi:10.1107/S1600536812046156

. 2012 Nov 14;68(Pt 12):o3343. doi: 10.1107/S1600536812046156

4-Chloro-6-methoxypyrimidin-2-amine–succinic acid (2/1)

Kaliyaperumal Thanigaimani ^a, Nuridayanti Che Khalib ^a, Suhana Arshad ^a, Ibrahim Abdul Razak ^a,^*,^‡

PMCID: PMC3588944 PMID: 23476180

Abstract

The asymmetric unit of the title compound, 2C₅H₆ClN₃O·C₄H₆O₄, consists of one 4-chloro-6-methoxypyrimidin-2-amine molecule and one half-molecule of succinic acid which lies about an inversion centre. In the crystal, the acid and base molecules are linked through N—H⋯O and O—H⋯N hydrogen bonds, forming a tape along [1-10] in which R ₂ ²(8) and R ₄ ²(8) hydrogen-bond motifs are observed. The tapes are further interlinked through a pair of C—H⋯O hydrogen bonds into a sheet parallel to (11-2).

Related literature

For applications of pyrimidine derivatives, see: Condon et al. (1993 ▶); Maeno et al. (1990 ▶); Gilchrist (1997 ▶). For applications of succinic acid, see: Zeikus et al. (1999 ▶); Song & Lee (2006 ▶). 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 ▶). graphic file with name e-68-o3343-scheme1.jpg

Experimental

Crystal data

2C₅H₆ClN₃O·C₄H₆O₄
M _r = 437.24
Triclinic,
a = 5.0094 (2) Å
b = 8.5459 (4) Å
c = 10.8736 (5) Å
α = 82.337 (1)°
β = 88.952 (1)°
γ = 86.904 (1)°
V = 460.64 (4) Å³
Z = 1
Mo Kα radiation
μ = 0.40 mm⁻¹
T = 100 K
0.60 × 0.22 × 0.14 mm

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.796, T _max = 0.945
7766 measured reflections
1875 independent reflections
1808 reflections with I > 2σ(I)
R _int = 0.016

Refinement

R[F ² > 2σ(F ²)] = 0.024
wR(F ²) = 0.069
S = 1.09
1875 reflections
140 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.26 e Å⁻³

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

Supplementary Material

Click here for additional data file.^{(19.7KB, cif)}

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812046156/is5213sup1.cif

e-68-o3343-sup1.cif^{(19.7KB, cif)}

Click here for additional data file.^{(92.3KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812046156/is5213Isup2.hkl

e-68-o3343-Isup2.hkl^{(92.3KB, hkl)}

Click here for additional data file.^{(7KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536812046156/is5213Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H1N3⋯O3	0.847 (17)	2.223 (17)	3.0055 (13)	153.7 (14)
N3—H2N3⋯O3ⁱ	0.844 (16)	2.095 (16)	2.9369 (13)	175.4 (15)
O2—H1O2⋯N2ⁱ	0.806 (16)	1.923 (16)	2.7266 (13)	174.6 (18)
C3—H3A⋯O1ⁱⁱ	0.95	2.45	3.3911 (14)	172

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Symmetry codes: (i) Inline graphic ; (ii) .

Acknowledgments

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.

supplementary crystallographic information

Comment

Pyrimidine derivatives are very important molecules in biology and have many application in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, such as AZT, which is the most widely-used anti-AIDS drug (Gilchrist, 1997). The dicarboxylic acid, succinic acid, is a precursor for many chemicals of industrial importance (Zeikus et al., 1999; Song & Lee, 2006). In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound, (I), is presented here.

The asymmetric unit of the title compound consists of a 4-chloro-6-methoxypyrimidin-2-amine molecule and a half of the succinic acid molecule (Fig. 1). The acid molecule is lying about an inversion centre. The 4-chloro-6-methoxypyrimidin-2-amine molecule is approximately planar, with a maximum deviation of 0.037 (1) Å for atom O1. The bond lengths (Allen et al., 1987) and angle are normal.

In the crystal packing, the 4-chloro-6-methoxypyrimidin-2-amine molecules interact with the carboxylic group of the respective succinic acid molecules through N3—H2N3···O3ⁱ and O2—H1O2···N2ⁱ hydrogen bonds (symmetry code in Table 1), forming a hydrogen-bonded ring motif R₂²(8) (Bernstein et al., 1995). These motifs are centrosymmetrically paired via N3—H2N3···O3 hydrogen bonds, forming a complementary DADA array. These arrays are further interlinked with a neighboring array through a couple of C3—H3A···O1ⁱⁱ hydrogen bonds (symmetry code in Table 1) combine together to form a large ring motif, with graph-set notation R₆⁶(34). These ring motifs extend to give a sheet parallel to (112) plane as shown in Fig. 2.

Experimental

Hot methanol solutions (20 ml) of 4-chloro-6-methoxypyrimidin-2-amine (36 mg, Aldrich) and succinic acid (29 mg, Merck) were mixed and warmed over a heating magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature and crystals of the title compound (I) appeared after a few days.