Crystal structure of 2-amino-4,6-di­meth­oxy­pyrimidinium thio­phene-2-carboxyl­ate

Ammaiyappan Rajam; PT Muthiah; Ray J Butcher; Jerry P Jasinski

doi:10.1107/S2056989015010907

. 2015 Jun 13;71(Pt 7):o479–o480. doi: 10.1107/S2056989015010907

Crystal structure of 2-amino-4,6-dimethoxypyrimidinium thiophene-2-carboxylate

Ammaiyappan Rajam ^a, PT Muthiah ^a,^*, Ray J Butcher ^b, Jerry P Jasinski ^c

PMCID: PMC4518905 PMID: 26279918

Abstract

In the title salt, C₆H₁₀N₃O₂ ⁺·C₅H₃O₂S⁻, the 2-amino-4,6-dimethoxypyrimidinium cation interacts with the carboxylate group of the thiophene-2-carboxylate anion through a pair of N—H⋯O hydrogen bonds, forming an R ₂ ²(8) ring motif. These motifs are centrosymmetrically paired via N—H⋯O hydrogen bonds, forming a complementary DDAA array. The separate DDAA arrays are linked by π–π stacking interactions between the pyrimidine rings, as well as by a number of weak C—H⋯O and N—H⋯O interactions. In the anion, the dihedral angle between the ring plane and the CO₂ group is 11.60 (3)°. In the cation, the C atoms of methoxy groups deviate from the ring plane by 0.433 (10) Å.

Keywords: crystal structure, crystal salts, hydrogen-bonding patterns, π–π stacking interactions

Related literature

For the role played by non-covalent interactions in molecular recognition porcesses, see: Desiraju (1989 ▸). For aminopryimidine–carboxylate interactions in protein–nucleic acid recognition and protein–drug binding inteactions, see: Hunt et al. (1980 ▸); Alkorta & Elguero (2003 ▸). For 1:1 salts between 2-aminopyrimidine and mono- and dicarboxylic acids, see: Etter & Adsmond (1990 ▸). For self-assembly of 2-aminopyrimidine compounds, see: Scheinbeim & Schempp (1976 ▸). For carboxylic acid and 2-amino heterocyclic ring system synthons, see: Lynch & Jones (2004 ▸). For crystal structures of related salts, see: Ebenezer et al. (2012 ▸); Jennifer & Muthiah (2014 ▸). DDAA arrays have been observed in trimethoprim hydrogen glutarate (Robert et al., 2001 ▸), trimethoprim formate (Umadevi et al., 2002 ▸), trimethoprim-m-chlorobenzoate (Raj et al., 2003 ▸), pyrimethaminium 3,5-dinitrobenzoate (Subashini et al., 2007 ▸) and 2-amino-4,6-dimethoxypyrimidinum-salicylate (Thanigaimani et al., 2007 ▸). graphic file with name e-71-0o479-scheme1.jpg

Experimental

Crystal data

C₆H₁₀N₃O₂ ⁺·C₅H₃O₂S⁻
M _r = 283.30
Monoclinic,
a = 6.7335 (3) Å
b = 7.6307 (4) Å
c = 25.0638 (10) Å
β = 93.928 (4)°
V = 1284.78 (10) Å³
Z = 4
Mo Kα radiation
μ = 0.27 mm⁻¹
T = 173 K
0.32 × 0.28 × 0.14 mm

Data collection

Agilent Eos Gemini diffractometer
Absorption correction: multi-scan (CrysAlis RED; Agilent, 2012 ▸) T _min = 0.789, T _max = 1.000
8844 measured reflections
4245 independent reflections
3071 reflections with I > 2σ(I)
R _int = 0.028

Refinement

R[F ² > 2σ(F ²)] = 0.062
wR(F ²) = 0.186
S = 1.05
4245 reflections
174 parameters
H-atom parameters constrained
Δρ_max = 0.79 e Å⁻³
Δρ_min = −0.55 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2012 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis RED (Agilent, 2012 ▸); program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007 ▸; Palatinus & van der Lee, 2008 ▸; Palatinus et al., 2012 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: OLEX2 (Dolomanov et al., 2009 ▸); software used to prepare material for publication: OLEX2.

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015010907/hg5442sup1.cif

e-71-0o479-sup1.cif^{(22.4KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015010907/hg5442Isup2.hkl

e-71-0o479-Isup2.hkl^{(232.9KB, hkl)}

Click here for additional data file.^{(5.2KB, cml)}

Supporting information file. DOI: 10.1107/S2056989015010907/hg5442Isup3.cml

Click here for additional data file.^{(1.2MB, tif)}

. DOI: 10.1107/S2056989015010907/hg5442fig1.tif

The asymmetric unit of the title compound, showing 30% probability displacement ellipsoids.

Click here for additional data file.^{(614KB, tif)}

b . DOI: 10.1107/S2056989015010907/hg5442fig2.tif

A view of DDAA array along the b axis formed by independent N—H⋯O hydrogen bonds. Symmetry codes are given in Table 1. Dashed lines represent hydrogen bonds.

Click here for additional data file.^{(1.3MB, tif)}

Cg Cg Cg . DOI: 10.1107/S2056989015010907/hg5442fig3.tif

A view of infinite number of DDAA arrays interconnected by π–π stacking interactions indicated by dotted lines. Cg1⋯Cg1 = 3.4689 (12) Å, where Cg1 represents the centroid of the ring N1/C1/N2/C2/C3/C4.

CCDC reference: 1405154

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
N1H1O2A ⁱ	0.88	1.76	2.637(2)	175
N3H3AO1A ⁱⁱ	0.88	2.04	2.826(2)	148
N3H3BO1A ⁱ	0.88	1.92	2.798(2)	173
C6H6BO1ⁱⁱⁱ	0.98	2.52	3.434(3)	155
C1AH1AO1^iv	0.95	2.60	3.365(3)	138
C1AH1AO2A ^v	0.95	2.60	3.383(3)	140

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) .

Acknowledgments

PTM is thankful to the UGC, New Delhi, for a UGC–BSR one-time grant to Faculty. JPJ acknowledges the NSF–MRI program (grant No. 1039027) for funds to purchase the X-ray diffractometer.

supplementary crystallographic information

S1. Structural commentary

The asymmetric unit of C₆H₁₀N₃O₂⁺ C₅H₃O₂S^-, (I), contains one 2-amino-4,6-dimethoxypyrimidinium cation and one thiophene-2-carboxylate anion (Fig 1). Protonation of the cation occurs at N1, providing a C1/N1/C2 angle of 119.39 (16)° compared to the C1/N2/C4 angle (115.99 (16)°) of the unprotonated N2 atom. The carboxylate group of the thiophene-2-carboxylate anion interacts with the protonated atom N1 and the 2-amino group of the pyrimidine moiety through a pair of N—H···O hydrogen bonds, forming an eight membered R²₂(8) ring motif. These motifs are centrosymmetrically paired via N—H···O hydrogen bonds to produce a DDAA (D = donor in hydrogen bonds, A = acceptor in hydrogen bonds) array of quadruple hydrogen bonds represented by the graph-set notation R²₂(8), R⁴₂(8) and R²₂(8) (Fig. 2). This type of array has also been identified in trimethoprim hydrogen glutarate (Robert et al., 2001), trimethoprim formate (Umadevi et al., 2002), trimethoprim- m-chlorobenzoate (Raj et al., 2003), pyrimethaminium 3,5-dinitrobenzoate (Subashini et al., 2007) and 2-amino-4,6-dimethoxypyrimidinum-salicylate (Thanigaimani et al., 2007). An infinite number of several such quadruple arrays are interconnected and stabilized by π—π stacking interactions between the pyrimidine ring of one array with a neighbouring array, with an observed interplanar distance of 3.356 Å, a centroid (Cg1)-to-centroid (Cg1) distance of 3.4689 (12) Å (where Cg1 equals the centroid of the ring N1/C1/N2/C2/C3/C4, Fig 3) and slip angle (the angle between the centroid vector and the normal to the plane) of 14.68°, which are typical aromatic stacking values (Hunter, 1994). In addition, a number of weak C—H···O and N—H···O intermolecular interactions are also observed which contribute to crystal packing stability (Table 2).

S2. Synthesis and crystallization

A hot methanolic solution of 2-amino-4,6-dimethoxy pyrimidine (38 mg, Aldrich) and thiophene-2-carboxylic acid (32 mg, Aldrich) was warmed for half an hour over a water bath. The mixture was cooled slowly and kept at room temperature. After a few days colourless crystals were obtained.

S3. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1. All of the H atoms were placed in their calculated positions andthen refined using the riding model with atom—H lengths of 0.95Å (CH), 0.98Å (CH₃)or 0.88Å (NH, NH₂). Isotropic displacement parameters for these atoms were set to 1.2 (CH, NH, NH₂) or 1.5 (CH₃) times Ueq of the parent atom. Idealised Me refined as rotating groups.