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

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 R₂²(8) and R₄²(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).

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) ų

• 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[F² > 2σ(F²)] = 0.024

• wR(F²) = 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

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⋯O3^i	0.844 (16)	2.095 (16)	2.9369 (13)	175.4 (15)
O2—H1O2⋯N2^i	0.806 (16)	1.923 (16)	2.7266 (13)	174.6 (18)
C3—H3A⋯O1^ii	0.95	2.45	3.3911 (14)	172
Symmetry codes: (i) -x, -y+1, -z; (ii) -x+2, -y+1, -z+1.

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).

Supporting information

S1. 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.

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).

S2. 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.

S3. Refinement

O- and N-bound H atoms were located in a difference Fourier map and refined freely [refined distances: N—H = 0.846 (17) and 0.842 (18) Å, O—H = 0.804 (19) Å]. The remaining hydrogen atoms were positioned geometrically (C—H= 0.95–0.99 Å) and were refined using a riding model, with U_iso(H) = 1.2U_eq(C) or 1.5U_eq(methyl C). A rotating group model was used for the methyl group. Three outliers were omitted (-4 5 3, -1 2 1 and 1 0 1) in the final refinement.

Computing details

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

	Fig. 1. The molecular structure of the title compound with atom labels with 50% probability displacement ellipsoids.
	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–succinic acid (2/1)

Crystal data

2C5H6ClN3O·C4H6O4	Z = 1
Mr = 437.24	F(000) = 226
Triclinic, P1	Dx = 1.576 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.0094 (2) Å	Cell parameters from 8335 reflections
b = 8.5459 (4) Å	θ = 3.3–32.6°
c = 10.8736 (5) Å	µ = 0.40 mm^−1
α = 82.337 (1)°	T = 100 K
β = 88.952 (1)°	Block, colourless
γ = 86.904 (1)°	0.60 × 0.22 × 0.14 mm
V = 460.64 (4) Å^3

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer	1875 independent reflections
Radiation source: fine-focus sealed tube	1808 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
ϕ and ω scans	θmax = 26.5°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −6→6
Tmin = 0.796, Tmax = 0.945	k = −10→10
7766 measured reflections	l = −13→13

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.024	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.069	H atoms treated by a mixture of independent and constrained refinement
S = 1.09	w = 1/[σ^2(Fo^2) + (0.0384P)^2 + 0.1625P] where P = (Fo^2 + 2Fc^2)/3
1875 reflections	(Δ/σ)max < 0.001
140 parameters	Δρmax = 0.33 e Å^−3
0 restraints	Δρmin = −0.26 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
Cl1	0.42007 (6)	0.86198 (3)	0.41239 (3)	0.02047 (11)
O1	0.94601 (17)	0.35939 (10)	0.35994 (8)	0.01945 (19)
N1	0.59391 (18)	0.43360 (11)	0.22863 (9)	0.0147 (2)
C3	0.7047 (2)	0.59435 (13)	0.38427 (10)	0.0166 (2)
H3A	0.8146	0.6130	0.4505	0.020*
N3	0.2475 (2)	0.52018 (12)	0.09782 (10)	0.0179 (2)
C1	0.3960 (2)	0.54346 (13)	0.19395 (10)	0.0140 (2)
N2	0.33618 (18)	0.67556 (11)	0.24763 (9)	0.0140 (2)
C2	0.4949 (2)	0.69401 (13)	0.34172 (10)	0.0144 (2)
C4	0.7434 (2)	0.46134 (13)	0.32110 (10)	0.0151 (2)
C5	0.9799 (3)	0.21688 (14)	0.30162 (12)	0.0227 (3)
H5A	1.1372	0.1540	0.3359	0.034*
H5B	1.0046	0.2451	0.2119	0.034*
H5C	0.8208	0.1550	0.3175	0.034*
O2	0.04847 (16)	0.09366 (10)	−0.17679 (8)	0.01766 (19)
O3	0.18536 (16)	0.23812 (9)	−0.03536 (8)	0.01799 (19)
C7	0.4170 (2)	−0.01172 (13)	−0.05581 (10)	0.0146 (2)
H7A	0.5370	−0.0179	−0.1285	0.018*
H7B	0.3287	−0.1133	−0.0381	0.018*
C6	0.2070 (2)	0.12009 (13)	−0.08705 (10)	0.0135 (2)
H1N3	0.286 (3)	0.439 (2)	0.0627 (15)	0.022 (4)*
H2N3	0.123 (3)	0.588 (2)	0.0758 (15)	0.026 (4)*
H1O2	−0.059 (3)	0.166 (2)	−0.1960 (16)	0.029 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.02672 (17)	0.01570 (16)	0.02024 (16)	0.00612 (11)	−0.00563 (11)	−0.00917 (11)
O1	0.0221 (4)	0.0146 (4)	0.0220 (4)	0.0072 (3)	−0.0089 (3)	−0.0058 (3)
N1	0.0155 (4)	0.0127 (4)	0.0160 (5)	0.0016 (4)	−0.0023 (4)	−0.0032 (4)
C3	0.0196 (5)	0.0153 (5)	0.0153 (5)	0.0010 (4)	−0.0051 (4)	−0.0037 (4)
N3	0.0180 (5)	0.0156 (5)	0.0215 (5)	0.0057 (4)	−0.0071 (4)	−0.0094 (4)
C1	0.0131 (5)	0.0128 (5)	0.0162 (5)	−0.0004 (4)	0.0004 (4)	−0.0028 (4)
N2	0.0144 (4)	0.0127 (4)	0.0152 (4)	0.0018 (3)	−0.0014 (4)	−0.0037 (3)
C2	0.0179 (5)	0.0115 (5)	0.0143 (5)	0.0000 (4)	0.0008 (4)	−0.0035 (4)
C4	0.0154 (5)	0.0129 (5)	0.0163 (5)	0.0017 (4)	−0.0014 (4)	−0.0007 (4)
C5	0.0275 (6)	0.0142 (5)	0.0264 (6)	0.0086 (5)	−0.0071 (5)	−0.0064 (5)
O2	0.0176 (4)	0.0145 (4)	0.0214 (4)	0.0050 (3)	−0.0078 (3)	−0.0057 (3)
O3	0.0181 (4)	0.0146 (4)	0.0220 (4)	0.0040 (3)	−0.0055 (3)	−0.0064 (3)
C7	0.0139 (5)	0.0124 (5)	0.0178 (5)	0.0020 (4)	−0.0021 (4)	−0.0036 (4)
C6	0.0121 (5)	0.0131 (5)	0.0152 (5)	−0.0011 (4)	0.0007 (4)	−0.0013 (4)

Geometric parameters (Å, º)

Cl1—C2	1.7370 (11)	N2—C2	1.3379 (15)
O1—C4	1.3379 (14)	C5—H5A	0.9800
O1—C5	1.4471 (14)	C5—H5B	0.9800
N1—C4	1.3184 (15)	C5—H5C	0.9800
N1—C1	1.3511 (14)	O2—C6	1.3191 (13)
C3—C2	1.3637 (16)	O2—H1O2	0.804 (19)
C3—C4	1.4075 (16)	O3—C6	1.2175 (14)
C3—H3A	0.9500	C7—C6	1.5080 (15)
N3—C1	1.3363 (15)	C7—C7^i	1.525 (2)
N3—H1N3	0.846 (17)	C7—H7A	0.9900
N3—H2N3	0.842 (18)	C7—H7B	0.9900
C1—N2	1.3556 (14)
C4—O1—C5	117.22 (9)	O1—C4—C3	116.16 (10)
C4—N1—C1	116.08 (9)	O1—C5—H5A	109.5
C2—C3—C4	113.88 (10)	O1—C5—H5B	109.5
C2—C3—H3A	123.1	H5A—C5—H5B	109.5
C4—C3—H3A	123.1	O1—C5—H5C	109.5
C1—N3—H1N3	117.9 (11)	H5A—C5—H5C	109.5
C1—N3—H2N3	117.7 (11)	H5B—C5—H5C	109.5
H1N3—N3—H2N3	124.4 (16)	C6—O2—H1O2	112.9 (12)
N3—C1—N1	117.06 (10)	C6—C7—C7^i	112.44 (11)
N3—C1—N2	117.23 (10)	C6—C7—H7A	109.1
N1—C1—N2	125.71 (10)	C7^i—C7—H7A	109.1
C2—N2—C1	114.50 (9)	C6—C7—H7B	109.1
N2—C2—C3	125.78 (10)	C7^i—C7—H7B	109.1
N2—C2—Cl1	115.19 (8)	H7A—C7—H7B	107.8
C3—C2—Cl1	119.02 (9)	O3—C6—O2	123.52 (10)
N1—C4—O1	119.81 (10)	O3—C6—C7	123.89 (10)
N1—C4—C3	124.03 (10)	O2—C6—C7	112.59 (9)
C4—N1—C1—N3	177.94 (10)	C1—N1—C4—O1	−179.08 (9)
C4—N1—C1—N2	−1.63 (16)	C1—N1—C4—C3	0.99 (16)
N3—C1—N2—C2	−178.75 (10)	C5—O1—C4—N1	−3.63 (15)
N1—C1—N2—C2	0.81 (16)	C5—O1—C4—C3	176.31 (10)
C1—N2—C2—C3	0.73 (16)	C2—C3—C4—N1	0.32 (17)
C1—N2—C2—Cl1	−179.61 (7)	C2—C3—C4—O1	−179.62 (9)
C4—C3—C2—N2	−1.25 (17)	C7^i—C7—C6—O3	5.35 (17)
C4—C3—C2—Cl1	179.10 (8)	C7^i—C7—C6—O2	−174.64 (11)

Symmetry code: (i) −x+1, −y, −z.

Hydrogen-bond geometry (Å, º)

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···O3^ii	0.844 (16)	2.095 (16)	2.9369 (13)	175.4 (15)
O2—H1O2···N2^ii	0.806 (16)	1.923 (16)	2.7266 (13)	174.6 (18)
C3—H3A···O1^iii	0.95	2.45	3.3911 (14)	172

Symmetry codes: (ii) −x, −y+1, −z; (iii) −x+2, −y+1, −z+1.

 

Footnotes

‡Thomson Reuters ResearcherID: A-5599-2009.