organic compounds
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
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 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
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell 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
10.1107/S1600536812045308/rz5019sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812045308/rz5019Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812045308/rz5019Isup3.cml
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.
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).
Data collection: APEX2 (Bruker, 2009); cell
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).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. |
C4H6ClN4+·0.5C4H2O42− | 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) Å3 | 0.71 × 0.31 × 0.17 mm |
Z = 4 |
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 on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.127 | H 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 parameters | Δρmax = 0.78 e Å−3 |
1 restraint | Δρmin = −0.78 e Å−3 |
C4H6ClN4+·0.5C4H2O42− | V = 833.50 (18) Å3 |
Mr = 202.61 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 5.4478 (7) Å | µ = 0.43 mm−1 |
b = 10.5187 (14) Å | T = 100 K |
c = 14.8171 (18) Å | 0.71 × 0.31 × 0.17 mm |
β = 100.990 (4)° |
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 = 0.931 | Rint = 0.033 |
9206 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 1 restraint |
wR(F2) = 0.127 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.08 | Δρmax = 0.78 e Å−3 |
2984 reflections | Δρmin = −0.78 e Å−3 |
138 parameters |
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. |
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)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
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) |
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—C6i | 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) | C6i—C6—C5 | 122.53 (14) |
N1—C1—N2 | 122.97 (10) | C6i—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—C6i | −167.18 (16) |
N4—C2—C3—C4 | −178.98 (11) | O2—C5—C6—C6i | 12.7 (2) |
Symmetry code: (i) −x+1, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1···O2ii | 0.86 (1) | 1.69 (1) | 2.5281 (14) | 165 (3) |
N3—H2···O1ii | 0.81 (2) | 2.12 (2) | 2.9233 (15) | 168 (2) |
N3—H3···N1iii | 0.85 (2) | 2.15 (2) | 3.0014 (16) | 176 (2) |
N4—H4···O1iv | 0.78 (2) | 2.08 (2) | 2.8307 (16) | 161 (2) |
N4—H5···Cl1v | 0.77 (2) | 2.78 (2) | 3.3671 (13) | 135.0 (19) |
N4—H5···O2ii | 0.77 (2) | 2.56 (2) | 3.1458 (15) | 134.2 (19) |
C3—H3A···O2i | 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. |
Experimental details
Crystal data | |
Chemical formula | C4H6ClN4+·0.5C4H2O42− |
Mr | 202.61 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 100 |
a, b, c (Å) | 5.4478 (7), 10.5187 (14), 14.8171 (18) |
β (°) | 100.990 (4) |
V (Å3) | 833.50 (18) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.43 |
Crystal size (mm) | 0.71 × 0.31 × 0.17 |
Data collection | |
Diffractometer | Bruker SMART APEXII DUO CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.749, 0.931 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9206, 2984, 2708 |
Rint | 0.033 |
(sin θ/λ)max (Å−1) | 0.757 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.127, 1.08 |
No. of reflections | 2984 |
No. of parameters | 138 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.78, −0.78 |
Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H1···O2i | 0.862 (10) | 1.686 (12) | 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 | 0.9500 | 2.3900 | 3.3085 (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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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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.