Bis(2,6-di­amino-4-chloro­pyrimidin-1-ium) fumarate

In the title salt, 2C₄H₆ClN₄⁺·C₄H₂O₄²⁻, the complete fumarate dianion is generated by crystallographic inversion symmetry. The cation is essentially planar, with a maximum deviation of 0.018 (1) Å. In the anion, the carboxyl­ate group is twisted slightly away from the attached plane, the dihedral angle between the carboxyl­ate and (E)-but-2-ene planes being 12.78 (13)°. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl­ate O atoms of the anion via a pair of N—H⋯O hydrogen bonds, forming an R₂²(8) ring motif. In addition, another type of R₂²(8) motif is formed by centrosymmetrically related pyrimidinium cations via N—H⋯N hydrogen bonds. These two combined motifs form a heterotetra­mer. The crystal structure is further stabilized by stong N—H⋯O, N—H⋯Cl and weak C—H⋯O hydrogen bonds, resulting a three-dimensional network.

Related literature

For applications of pyrimidine derivatives, see: Condon et al. (1993); Maeno et al. (1990); Gilchrist (1997). For details of fumaric acid, see: Batchelor et al. (2000). For hydrogen-bonded synthons, see: Thakur & Desiraju (2008). 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

• C₄H₆ClN₄⁺·0.5C₄H₂O₄²⁻

• M_r = 202.61

• Monoclinic, P 2₁ /c

• a = 5.4478 (7) Å

• b = 10.5187 (14) Å

• c = 14.8171 (18) Å

• β = 100.990 (4)°

• V = 833.50 (18) ų

• Z = 4

• Mo Kα radiation

• μ = 0.43 mm⁻¹

• T = 100 K

• 0.71 × 0.31 × 0.17 mm

Data collection

• Bruker SMART APEXII DUO CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2009) T_min = 0.749, T_max = 0.931

• 9206 measured reflections

• 2984 independent reflections

• 2708 reflections with I > 2σ(I)

• R_int = 0.033

Refinement

• R[F² > 2σ(F²)] = 0.042

• wR(F²) = 0.127

• S = 1.08

• 2984 reflections

• 138 parameters

• 1 restraint

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

• Δρ_max = 0.78 e Å⁻³

• Δρ_min = −0.78 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H1⋯O2^i	0.86 (1)	1.69 (1)	2.5281 (14)	165 (3)
N3—H2⋯O1^i	0.81 (2)	2.12 (2)	2.9233 (15)	168 (2)
N3—H3⋯N1^ii	0.85 (2)	2.15 (2)	3.0014 (16)	176 (2)
N4—H4⋯O1^iii	0.78 (2)	2.08 (2)	2.8307 (16)	161 (2)
N4—H5⋯Cl1^iv	0.77 (2)	2.78 (2)	3.3671 (13)	135.0 (19)
N4—H5⋯O2^i	0.77 (2)	2.56 (2)	3.1458 (15)	134.2 (19)
C3—H3A⋯O2^v	0.95	2.39	3.3085 (16)	162
Symmetry codes: (i) ; (ii) -x+1, -y+1, -z+2; (iii) x+1, y, z; (iv) ; (v) -x+1, -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). Fumaric acid is among the organic compounds widely found in nature, and is a key intermediate in the biosynthesis of organic acids. Fumaric acid is of interest since it is known to form supramolecular assemblies with N-aromatic complexes (Batchelor et al., 2000). In order to study some interesting hydrogen bonding interactions, the synthesis and structure of the title compound is presented here.

The asymmetric unit of title compound (Fig. 1), consists of a 2,6-diamino-4-chloropyrimidinium cation and a half of a fumarate dianion where the complete fumarate dianion is generated by crystallographic inversion symmetry (-x + 1, -y + 1, -z + 1). In the 2,6-diamino-4-chloropyridinium cation, protonatation of N1 atom has lead to a slight increase in the C1—N2—C2 angle (120.34 (10)°). The 2,6-diamino-4-chloropyridinium cation is essentially planar, with a maximum deviation of 0.018 (1) Å for atom C3. In the fumarate dianion, C5/C6/C5A/C6A plane makes a dihedral angle of 81.89 (6)° with 2,6-diamino-4-chloropyridinium cation. In the anion, the carboxylate group is twisted slightly away from the attached plane; the dihedral angle between the C5/C6/C5A/C6A and O1/O2/C5/C6 planes is 12.78 (13)°. The bond lengths (Allen et al., 1987) and angles are normal.

In the crystal structure (Fig. 2), the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxylate O atoms of the anion via a pair of N—H···O hydrogen bonds, forming R₂²(8) (Bernstein et al., 1995) ring motifs. In addition, another type of R₂²(8) motif is formed by centrosymmetrically related pyrimidinium cation through a pair of N3—H3···N1ⁱⁱⁱ hydrogen bonds (symmetry codes in Table 1). These two different motifs generate a linear heterotetrameric unit known to be one of the most stable synthons (Thakur & Desiraju, 2008). One of the O atoms of the carboxylate group acts as an acceptors of bifurcated N2—H1···O2ⁱⁱ and N4—H5···O2ⁱⁱ hydrogen bonds (symmetry codes in Table 1). The crystal structure is further stabilized by strong N4—H4···O1^iv, N4—H5···Cl1^V and weak C3—H3A···O2ⁱ hydrogen bonds (symmetry codes in Table 1), resulting in a three-dimensional network.

Related literature

For applications of pyrimidine derivatives, see: Condon et al. (1993); Maeno et al. (1990); Gilchrist (1997). For details of fumaric acid, see: Batchelor et al. (2000). For hydrogen-bonded synthons, see: Thakur & Desiraju (2008). 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 2,6-diamino-4-chloropyrimidine (36 mg, Aldrich) and fumaric 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 appeared after a few days.

S3. Refinement

N-bound H Atoms were located in a difference Fourier maps and refined isotropically. The N2–H1 bond length was constrained to 0.85 (1) Å. The remaining hydrogen atoms were positioned geometrically [C–H= 0.95 Å] and were refined using a riding model, with U_iso(H) = 1.2 U_eq(C).

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 50% probability displacement ellipsoids.
	Fig. 2. The crystal packing of the title compound viewed down the a axis. Hydrogen atoms not involved in the intermolecular interactions (dashed lines) have been omitted for clarity.

Bis(2,6-diamino-4-chloropyrimidin-1-ium) fumarate

Crystal data

C4H6ClN4^+·0.5C4H2O4^2^−	F(000) = 416
Mr = 202.61	Dx = 1.615 Mg m^−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 6512 reflections
a = 5.4478 (7) Å	θ = 3.4–32.6°
b = 10.5187 (14) Å	µ = 0.43 mm^−1
c = 14.8171 (18) Å	T = 100 K
β = 100.990 (4)°	Block, colourless
V = 833.50 (18) Å^3	0.71 × 0.31 × 0.17 mm
Z = 4

Data collection

Bruker SMART APEXII DUO CCD area-detector diffractometer	2984 independent reflections
Radiation source: fine-focus sealed tube	2708 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.033
ϕ and ω scans	θmax = 32.6°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −8→8
Tmin = 0.749, Tmax = 0.931	k = −15→11
9206 measured reflections	l = −22→20

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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.127	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ^2(Fo^2) + (0.0781P)^2 + 0.3432P] where P = (Fo^2 + 2Fc^2)/3
2984 reflections	(Δ/σ)max < 0.001
138 parameters	Δρmax = 0.78 e Å^−3
1 restraint	Δρmin = −0.78 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	0.40235 (6)	0.33920 (3)	0.76706 (2)	0.01926 (11)
N1	0.60987 (19)	0.49304 (10)	0.89510 (7)	0.0145 (2)
N2	0.94266 (19)	0.63383 (10)	0.88172 (7)	0.01248 (19)
N3	0.7774 (2)	0.62835 (11)	1.01344 (8)	0.0172 (2)
N4	1.1199 (2)	0.64457 (11)	0.75251 (8)	0.0155 (2)
C1	0.7751 (2)	0.58432 (11)	0.92934 (8)	0.0128 (2)
C2	0.9508 (2)	0.59135 (11)	0.79616 (8)	0.0121 (2)
C3	0.7835 (2)	0.49584 (11)	0.75646 (8)	0.0139 (2)
H3A	0.7827	0.4627	0.6968	0.017*
C4	0.6220 (2)	0.45442 (11)	0.81056 (8)	0.0138 (2)
O1	0.1038 (2)	0.65131 (9)	0.56049 (7)	0.0197 (2)
O2	0.2393 (2)	0.68272 (9)	0.42877 (7)	0.0196 (2)
C5	0.2377 (2)	0.62262 (11)	0.50395 (8)	0.0145 (2)
C6	0.4095 (2)	0.51141 (11)	0.52358 (8)	0.0148 (2)
H6A	0.3894	0.4547	0.5715	0.018*
H1	1.054 (4)	0.688 (2)	0.9060 (19)	0.054 (8)*
H2	0.874 (4)	0.685 (2)	1.0338 (16)	0.031 (6)*
H3	0.662 (4)	0.597 (2)	1.0383 (16)	0.035 (6)*
H4	1.118 (4)	0.629 (2)	0.7009 (16)	0.024 (5)*
H5	1.208 (4)	0.697 (2)	0.7770 (15)	0.025 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Cl1	0.01810 (17)	0.01552 (16)	0.02516 (18)	−0.00602 (9)	0.00670 (12)	−0.00792 (10)
N1	0.0156 (4)	0.0128 (4)	0.0160 (5)	−0.0033 (3)	0.0054 (3)	−0.0023 (3)
N2	0.0156 (4)	0.0097 (4)	0.0130 (4)	−0.0027 (3)	0.0050 (3)	−0.0008 (3)
N3	0.0212 (5)	0.0169 (5)	0.0153 (5)	−0.0072 (4)	0.0082 (4)	−0.0037 (4)
N4	0.0205 (5)	0.0133 (4)	0.0138 (4)	−0.0028 (4)	0.0063 (4)	−0.0010 (4)
C1	0.0144 (5)	0.0103 (5)	0.0145 (5)	−0.0017 (4)	0.0047 (4)	0.0002 (4)
C2	0.0139 (5)	0.0094 (4)	0.0135 (5)	0.0008 (3)	0.0041 (4)	0.0004 (3)
C3	0.0155 (5)	0.0114 (5)	0.0154 (5)	−0.0015 (4)	0.0047 (4)	−0.0020 (4)
C4	0.0141 (5)	0.0101 (4)	0.0178 (5)	−0.0014 (4)	0.0040 (4)	−0.0022 (4)
O1	0.0235 (5)	0.0206 (5)	0.0174 (4)	0.0087 (3)	0.0096 (4)	0.0032 (3)
O2	0.0270 (5)	0.0178 (4)	0.0159 (4)	0.0112 (4)	0.0089 (4)	0.0055 (3)
C5	0.0167 (5)	0.0132 (5)	0.0138 (5)	0.0039 (4)	0.0039 (4)	0.0004 (4)
C6	0.0179 (5)	0.0126 (5)	0.0143 (5)	0.0049 (4)	0.0039 (4)	0.0023 (4)

Geometric parameters (Å, º)

Cl1—C4	1.7385 (12)	N4—H4	0.78 (2)
N1—C4	1.3305 (15)	N4—H5	0.77 (2)
N1—C1	1.3474 (15)	C2—C3	1.4076 (16)
N2—C2	1.3529 (15)	C3—C4	1.3695 (16)
N2—C1	1.3592 (14)	C3—H3A	0.9500
N2—H1	0.862 (10)	O1—C5	1.2482 (14)
N3—C1	1.3273 (15)	O2—C5	1.2824 (14)
N3—H2	0.81 (2)	C5—C6	1.4919 (16)
N3—H3	0.85 (2)	C6—C6^i	1.334 (2)
N4—C2	1.3444 (15)	C6—H6A	0.9500
C4—N1—C1	114.99 (10)	N4—C2—C3	122.99 (11)
C2—N2—C1	120.34 (10)	N2—C2—C3	119.54 (10)
C2—N2—H1	118 (2)	C4—C3—C2	114.80 (10)
C1—N2—H1	122 (2)	C4—C3—H3A	122.6
C1—N3—H2	119.5 (17)	C2—C3—H3A	122.6
C1—N3—H3	113.3 (16)	N1—C4—C3	127.36 (11)
H2—N3—H3	127 (2)	N1—C4—Cl1	114.05 (9)
C2—N4—H4	120.1 (17)	C3—C4—Cl1	118.59 (9)
C2—N4—H5	119.4 (16)	O1—C5—O2	124.44 (11)
H4—N4—H5	120 (2)	O1—C5—C6	118.95 (11)
N3—C1—N1	119.22 (10)	O2—C5—C6	116.61 (10)
N3—C1—N2	117.81 (11)	C6^i—C6—C5	122.53 (14)
N1—C1—N2	122.97 (10)	C6^i—C6—H6A	118.7
N4—C2—N2	117.47 (11)	C5—C6—H6A	118.7
C4—N1—C1—N3	−179.71 (11)	N2—C2—C3—C4	0.33 (17)
C4—N1—C1—N2	−0.05 (17)	C1—N1—C4—C3	0.85 (19)
C2—N2—C1—N3	179.15 (11)	C1—N1—C4—Cl1	−178.65 (9)
C2—N2—C1—N1	−0.51 (18)	C2—C3—C4—N1	−0.99 (19)
C1—N2—C2—N4	179.70 (11)	C2—C3—C4—Cl1	178.50 (9)
C1—N2—C2—C3	0.34 (17)	O1—C5—C6—C6^i	−167.18 (16)
N4—C2—C3—C4	−178.98 (11)	O2—C5—C6—C6^i	12.7 (2)

Symmetry code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H1···O2^ii	0.86 (1)	1.69 (1)	2.5281 (14)	165 (3)
N3—H2···O1^ii	0.81 (2)	2.12 (2)	2.9233 (15)	168 (2)
N3—H3···N1^iii	0.85 (2)	2.15 (2)	3.0014 (16)	176 (2)
N4—H4···O1^iv	0.78 (2)	2.08 (2)	2.8307 (16)	161 (2)
N4—H5···Cl1^v	0.77 (2)	2.78 (2)	3.3671 (13)	135.0 (19)
N4—H5···O2^ii	0.77 (2)	2.56 (2)	3.1458 (15)	134.2 (19)
C3—H3A···O2^i	0.95	2.39	3.3085 (16)	162

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x+1, −y+3/2, z+1/2; (iii) −x+1, −y+1, −z+2; (iv) x+1, y, z; (v) −x+2, y+1/2, −z+3/2.

 

Footnotes

‡Thomson Reuters ResearcherID: A-5599-2009.