organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 12| December 2012| Pages o3321-o3322

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

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

(Received 22 October 2012; accepted 2 November 2012; online 10 November 2012)

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[Condon, M. E., Brady, T. E., Feist, D., Malefyt, T., Marc, P., Quakenbush, L. S., Rodaway, S. J., Shaner, D. L. & Tecle, B. (1993). Brighton Crop Protection Conference on Weeds, pp. 41-46. Alton, Hampshire, England: BCPC Publications.]); Maeno et al. (1990[Maeno, S., Miura, I., Masuda, K. & Nagata, T. (1990). Brighton Crop Protection Conference on Pests and Diseases, pp. 415-422. Alton, Hampshire, England: BCPC Publications.]); Gilchrist (1997[Gilchrist, T. L. (1997). Heterocyclic Chemistry, 3rd ed., pp. 261-276. Singapore: Addison Wesley Longman.]). For details of fumaric acid, see: Batchelor et al. (2000[Batchelor, E., Klinowski, J. & Jones, W. (2000). J. Mater. Chem. 10, 839-848.]). For hydrogen-bonded synthons, see: Thakur & Desiraju (2008[Thakur, T. S. & Desiraju, G. R. (2008). Cryst. Growth Des. 8, 4031-4044.]). 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
  • C4H6ClN4+·0.5C4H2O42−

  • Mr = 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) Å3

  • 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[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.749, Tmax = 0.931

  • 9206 measured reflections

  • 2984 independent reflections

  • 2708 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.78 e Å−3

  • Δρmin = −0.78 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H1⋯O2i 0.86 (1) 1.69 (1) 2.5281 (14) 165 (3)
N3—H2⋯O1i 0.81 (2) 2.12 (2) 2.9233 (15) 168 (2)
N3—H3⋯N1ii 0.85 (2) 2.15 (2) 3.0014 (16) 176 (2)
N4—H4⋯O1iii 0.78 (2) 2.08 (2) 2.8307 (16) 161 (2)
N4—H5⋯Cl1iv 0.77 (2) 2.78 (2) 3.3671 (13) 135.0 (19)
N4—H5⋯O2i 0.77 (2) 2.56 (2) 3.1458 (15) 134.2 (19)
C3—H3A⋯O2v 0.95 2.39 3.3085 (16) 162
Symmetry codes: (i) [x+1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (ii) -x+1, -y+1, -z+2; (iii) x+1, y, z; (iv) [-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (v) -x+1, -y+1, -z+1.

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 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···O1iv, N4—H5···Cl1V and weak C3—H3A···O2i hydrogen bonds (symmetry codes in Table 1), resulting in a three-dimensional network.

Related literature top

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 top

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.

Refinement top

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 Uiso(H) = 1.2 Ueq(C).

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 50% probability displacement ellipsoids.
[Figure 2] 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 top
Crystal data top
C4H6ClN4+·0.5C4H2O42F(000) = 416
Mr = 202.61Dx = 1.615 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 6512 reflections
a = 5.4478 (7) Åθ = 3.4–32.6°
b = 10.5187 (14) ŵ = 0.43 mm1
c = 14.8171 (18) ÅT = 100 K
β = 100.990 (4)°Block, colourless
V = 833.50 (18) Å30.71 × 0.31 × 0.17 mm
Z = 4
Data collection top
Bruker SMART APEXII DUO CCD area-detector
diffractometer
2984 independent reflections
Radiation source: fine-focus sealed tube2708 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.033
ϕ and ω scansθmax = 32.6°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 88
Tmin = 0.749, Tmax = 0.931k = 1511
9206 measured reflectionsl = 2220
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.127H atoms treated by a mixture of independent and constrained refinement
S = 1.08 w = 1/[σ2(Fo2) + (0.0781P)2 + 0.3432P]
where P = (Fo2 + 2Fc2)/3
2984 reflections(Δ/σ)max < 0.001
138 parametersΔρmax = 0.78 e Å3
1 restraintΔρmin = 0.78 e Å3
Crystal data top
C4H6ClN4+·0.5C4H2O42V = 833.50 (18) Å3
Mr = 202.61Z = 4
Monoclinic, P21/cMo Kα radiation
a = 5.4478 (7) ŵ = 0.43 mm1
b = 10.5187 (14) ÅT = 100 K
c = 14.8171 (18) Å0.71 × 0.31 × 0.17 mm
β = 100.990 (4)°
Data collection top
Bruker SMART APEXII DUO CCD area-detector
diffractometer
2984 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
2708 reflections with I > 2σ(I)
Tmin = 0.749, Tmax = 0.931Rint = 0.033
9206 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0421 restraint
wR(F2) = 0.127H atoms treated by a mixture of independent and constrained refinement
S = 1.08Δρmax = 0.78 e Å3
2984 reflectionsΔρmin = 0.78 e Å3
138 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
Cl10.40235 (6)0.33920 (3)0.76706 (2)0.01926 (11)
N10.60987 (19)0.49304 (10)0.89510 (7)0.0145 (2)
N20.94266 (19)0.63383 (10)0.88172 (7)0.01248 (19)
N30.7774 (2)0.62835 (11)1.01344 (8)0.0172 (2)
N41.1199 (2)0.64457 (11)0.75251 (8)0.0155 (2)
C10.7751 (2)0.58432 (11)0.92934 (8)0.0128 (2)
C20.9508 (2)0.59135 (11)0.79616 (8)0.0121 (2)
C30.7835 (2)0.49584 (11)0.75646 (8)0.0139 (2)
H3A0.78270.46270.69680.017*
C40.6220 (2)0.45442 (11)0.81056 (8)0.0138 (2)
O10.1038 (2)0.65131 (9)0.56049 (7)0.0197 (2)
O20.2393 (2)0.68272 (9)0.42877 (7)0.0196 (2)
C50.2377 (2)0.62262 (11)0.50395 (8)0.0145 (2)
C60.4095 (2)0.51141 (11)0.52358 (8)0.0148 (2)
H6A0.38940.45470.57150.018*
H11.054 (4)0.688 (2)0.9060 (19)0.054 (8)*
H20.874 (4)0.685 (2)1.0338 (16)0.031 (6)*
H30.662 (4)0.597 (2)1.0383 (16)0.035 (6)*
H41.118 (4)0.629 (2)0.7009 (16)0.024 (5)*
H51.208 (4)0.697 (2)0.7770 (15)0.025 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.01810 (17)0.01552 (16)0.02516 (18)0.00602 (9)0.00670 (12)0.00792 (10)
N10.0156 (4)0.0128 (4)0.0160 (5)0.0033 (3)0.0054 (3)0.0023 (3)
N20.0156 (4)0.0097 (4)0.0130 (4)0.0027 (3)0.0050 (3)0.0008 (3)
N30.0212 (5)0.0169 (5)0.0153 (5)0.0072 (4)0.0082 (4)0.0037 (4)
N40.0205 (5)0.0133 (4)0.0138 (4)0.0028 (4)0.0063 (4)0.0010 (4)
C10.0144 (5)0.0103 (5)0.0145 (5)0.0017 (4)0.0047 (4)0.0002 (4)
C20.0139 (5)0.0094 (4)0.0135 (5)0.0008 (3)0.0041 (4)0.0004 (3)
C30.0155 (5)0.0114 (5)0.0154 (5)0.0015 (4)0.0047 (4)0.0020 (4)
C40.0141 (5)0.0101 (4)0.0178 (5)0.0014 (4)0.0040 (4)0.0022 (4)
O10.0235 (5)0.0206 (5)0.0174 (4)0.0087 (3)0.0096 (4)0.0032 (3)
O20.0270 (5)0.0178 (4)0.0159 (4)0.0112 (4)0.0089 (4)0.0055 (3)
C50.0167 (5)0.0132 (5)0.0138 (5)0.0039 (4)0.0039 (4)0.0004 (4)
C60.0179 (5)0.0126 (5)0.0143 (5)0.0049 (4)0.0039 (4)0.0023 (4)
Geometric parameters (Å, º) top
Cl1—C41.7385 (12)N4—H40.78 (2)
N1—C41.3305 (15)N4—H50.77 (2)
N1—C11.3474 (15)C2—C31.4076 (16)
N2—C21.3529 (15)C3—C41.3695 (16)
N2—C11.3592 (14)C3—H3A0.9500
N2—H10.862 (10)O1—C51.2482 (14)
N3—C11.3273 (15)O2—C51.2824 (14)
N3—H20.81 (2)C5—C61.4919 (16)
N3—H30.85 (2)C6—C6i1.334 (2)
N4—C21.3444 (15)C6—H6A0.9500
C4—N1—C1114.99 (10)N4—C2—C3122.99 (11)
C2—N2—C1120.34 (10)N2—C2—C3119.54 (10)
C2—N2—H1118 (2)C4—C3—C2114.80 (10)
C1—N2—H1122 (2)C4—C3—H3A122.6
C1—N3—H2119.5 (17)C2—C3—H3A122.6
C1—N3—H3113.3 (16)N1—C4—C3127.36 (11)
H2—N3—H3127 (2)N1—C4—Cl1114.05 (9)
C2—N4—H4120.1 (17)C3—C4—Cl1118.59 (9)
C2—N4—H5119.4 (16)O1—C5—O2124.44 (11)
H4—N4—H5120 (2)O1—C5—C6118.95 (11)
N3—C1—N1119.22 (10)O2—C5—C6116.61 (10)
N3—C1—N2117.81 (11)C6i—C6—C5122.53 (14)
N1—C1—N2122.97 (10)C6i—C6—H6A118.7
N4—C2—N2117.47 (11)C5—C6—H6A118.7
C4—N1—C1—N3179.71 (11)N2—C2—C3—C40.33 (17)
C4—N1—C1—N20.05 (17)C1—N1—C4—C30.85 (19)
C2—N2—C1—N3179.15 (11)C1—N1—C4—Cl1178.65 (9)
C2—N2—C1—N10.51 (18)C2—C3—C4—N10.99 (19)
C1—N2—C2—N4179.70 (11)C2—C3—C4—Cl1178.50 (9)
C1—N2—C2—C30.34 (17)O1—C5—C6—C6i167.18 (16)
N4—C2—C3—C4178.98 (11)O2—C5—C6—C6i12.7 (2)
Symmetry code: (i) x+1, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H1···O2ii0.86 (1)1.69 (1)2.5281 (14)165 (3)
N3—H2···O1ii0.81 (2)2.12 (2)2.9233 (15)168 (2)
N3—H3···N1iii0.85 (2)2.15 (2)3.0014 (16)176 (2)
N4—H4···O1iv0.78 (2)2.08 (2)2.8307 (16)161 (2)
N4—H5···Cl1v0.77 (2)2.78 (2)3.3671 (13)135.0 (19)
N4—H5···O2ii0.77 (2)2.56 (2)3.1458 (15)134.2 (19)
C3—H3A···O2i0.952.393.3085 (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.

Experimental details

Crystal data
Chemical formulaC4H6ClN4+·0.5C4H2O42
Mr202.61
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)5.4478 (7), 10.5187 (14), 14.8171 (18)
β (°) 100.990 (4)
V3)833.50 (18)
Z4
Radiation typeMo Kα
µ (mm1)0.43
Crystal size (mm)0.71 × 0.31 × 0.17
Data collection
DiffractometerBruker SMART APEXII DUO CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.749, 0.931
No. of measured, independent and
observed [I > 2σ(I)] reflections
9206, 2984, 2708
Rint0.033
(sin θ/λ)max1)0.757
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.127, 1.08
No. of reflections2984
No. of parameters138
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.78, 0.78

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
N2—H1···O2i0.862 (10)1.686 (12)2.5281 (14)165 (3)
N3—H2···O1i0.81 (2)2.12 (2)2.9233 (15)168 (2)
N3—H3···N1ii0.85 (2)2.15 (2)3.0014 (16)176 (2)
N4—H4···O1iii0.78 (2)2.08 (2)2.8307 (16)161 (2)
N4—H5···Cl1iv0.77 (2)2.78 (2)3.3671 (13)135.0 (19)
N4—H5···O2i0.77 (2)2.56 (2)3.1458 (15)134.2 (19)
C3—H3A···O2v0.95002.39003.3085 (16)162.00
Symmetry codes: (i) x+1, y+3/2, z+1/2; (ii) x+1, y+1, z+2; (iii) x+1, y, z; (iv) x+2, y+1/2, z+3/2; (v) x+1, y+1, z+1.
 

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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Volume 68| Part 12| December 2012| Pages o3321-o3322
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