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ISSN: 2414-3146

2-Amino-4-meth­­oxy-6-methyl­pyrimidin-1-ium tri­fluoro­acetate

aDepartment of Chemistry, Government Arts College (Autonomous), Thanthonimalai, Karur 639 005, Tamil Nadu, India, bDepartment of Chemistry, Mother Teresa Women's University, Kodaikanal 624 102, Tamil Nadu, India, cDepartment of Chemistry, Government Arts College, Tiruchirappalli 620 022, Tamil Nadu, India, and dDepartment of Chemistry, St. Joseph's College (Autonomous), Tiruchirappalli 620 002, Tamil Nadu, India
*Correspondence e-mail: manavaibala@gmail.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 19 June 2016; accepted 21 June 2016; online 24 June 2016)

In the title mol­ecular salt, C6H10N3O+·C2F3O2, the pyrimidinium cation is essentially planar, with a maximum deviation of 0.042 (3) Å for all non-H atoms. In the crystal, the cations and anions are linked via N—H⋯O hydrogen bonds, forming a centrosymmetric 2 + 2 aggregate with R22(8) and R42(8) ring motifs. These motifs are further linked through a pair of C—H⋯O hydrogen bonds into a supra­molecular tape along the [101] direction.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Pyrimidine and amino­pyrimidine derivatives are biologically very important compounds and they occur in nature as components of nucleic acids such as cytosine, uracil and thymine. Pyrimidine derivatives are very important mol­ecules in biology and have many applications in the areas of pesticide and pharmaceutical agents (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.]). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (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.]). Pyrimidine derivatives have also been developed as anti­viral agents, such as AZT, which is the most widely used anti-AIDS drug (Gilchrist, 1997[Gilchrist, T. L. (1997). Heterocycl. Chem. 3rd ed., pp. 261-276. Singapore: Addison Wesley Longman.]). Tri­fluoro­acetic acid is a very strong carb­oxy­lic acid, easily volatile and used for protein purification. An example of the crystal structure of a tri­fluoro­acetate salt has been reported (Rodrigues et al., 2001[Rodrigues, V. H., Paixão, J. A., Costa, M. M. R. R. & Matos Beja, A. (2001). Acta Cryst. C57, 761-763.]). In order to study potential hydrogen-bonding inter­actions, the crystal structure determination of the title compound was carried out.

The mol­ecular structure of the title mol­ecular salt is illustrated in Fig. 1[link]. The proton transfers from the one of the carboxyl group oxygen atoms (O2) to atom N2 of the cation resulted in the widening of C3—N2—C4 angle of the pyrimidinium ring to 121.9 (2)°, compared to the corresponding angle of 116.01 (18)° in neutral 2-amino-4-meth­oxy-6-methyl­pyrimidine (Glidewell et al., 2003[Glidewell, C., Low, J. N., Melguizo, M. & Quesada, A. (2003). Acta Cryst. C59, o9-o13.]). The cation is essentially planar, with a maximum deviation of 0.042 (3) Å for atom C5.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labelling and 50% probability displacement ellipsoids. The N—H⋯O hydrogen bonds are shown as dashed lines (see Table 1[link]).

In the crystal, Fig. 2[link], the protonated N2 atom and the 2-amino group (N3) are hydrogen bonded to the carboxyl­ate oxygen atoms (O2 and O3) via a pair of inter­molecular N2—H1N2⋯O2 and N3—H2N3⋯O3 hydrogen bonds, forming an [R_{2}^{2}](8) ring motif. These motifs are linked by pairs of N3—H1N3⋯O3i hydrogen bonds (Table 1[link]), to produce a DDAA array (where D is a hydrogen-bond donor and A is a hydrogen-bond acceptor) of four hydrogen bonds. This set of fused rings can be represented by the graph-set notations [R_{2}^{2}](8), [R_{4}^{2}](8) and [R_{2}^{2}](8). This type of motif has been reported in the crystal structures of trimethoprim hydrogen glutarate (Robert et al., 2001[Robert, J. J., Raj, S. B. & Muthiah, P. T. (2001). Acta Cryst. E57, o1206-o1208.]) and 2-amino-6-methyl­pyridinium 3-chloro­benzoate (Thanigaimani et al., 2013[Thanigaimani, K., Khalib, N. C., Arshad, S. & Razak, I. A. (2013). Acta Cryst. E69, o318.]). These arrays are further inter­linked with a neighboring array through a pair of C2—H2A⋯O1ii hydrogen bonds (Table 1[link] and Fig. 2[link]), leading to the formation of hydrogen-bonded supra­molecular tapes propagating along [101].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H1N3⋯O3i 0.86 (4) 2.05 (4) 2.822 (3) 148 (3)
N3—H2N3⋯O3 0.90 (4) 1.88 (5) 2.782 (4) 178 (5)
N2—H1N2⋯O2 0.90 (4) 1.86 (4) 2.758 (3) 170 (4)
C2—H2A⋯O1ii 0.95 2.58 3.514 (4) 168
Symmetry codes: (i) -x+1, -y+2, -z+1; (ii) -x+3, -y+2, -z.
[Figure 2]
Figure 2
The crystal packing of the title compound, viewed along the a axis. H atoms not involved in the hydrogen bonds (dashed lines; see Table 1[link]) have been omitted for clarity.

Synthesis and crystallization

To a hot methanol solution (20 ml) of 2-amino-4-meth­oxy-6-methyl­pyrimidine (69 mg, Aldrich) a few drops of tri­fluoro­acetic acid were added. The solution was 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

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The N-bound H atoms were located in a difference Fourier map and freely refined.

Table 2
Experimental details

Crystal data
Chemical formula C6H10N3O+·C2F3O2
Mr 253.19
Crystal system, space group Triclinic, P[\overline{1}]
Temperature (K) 100
a, b, c (Å) 4.8087 (2), 11.0283 (5), 11.1135 (5)
α, β, γ (°) 108.704 (3), 96.174 (3), 100.533 (3)
V3) 540.03 (4)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.15
Crystal size (mm) 0.37 × 0.21 × 0.07
 
Data collection
Diffractometer Bruker SMART APEXII CCD area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.946, 0.989
No. of measured, independent and observed [I > 2σ(I)] reflections 8256, 2467, 1674
Rint 0.060
(sin θ/λ)max−1) 0.649
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.065, 0.245, 1.08
No. of reflections 2467
No. of parameters 168
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.40, −0.43
Computer programs: APEX2 and SAINT (Bruker, 2009[Bruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS97, SHELXL97 and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

2-Amino-4-methoxy-6-methylpyrimidin-1-ium trifluoroacetate top
Crystal data top
C6H10N3O+·C2F3O2Z = 2
Mr = 253.19F(000) = 260
Triclinic, P1Dx = 1.557 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 4.8087 (2) ÅCell parameters from 2385 reflections
b = 11.0283 (5) Åθ = 2.3–28.6°
c = 11.1135 (5) ŵ = 0.15 mm1
α = 108.704 (3)°T = 100 K
β = 96.174 (3)°Plate, colourless
γ = 100.533 (3)°0.37 × 0.21 × 0.07 mm
V = 540.03 (4) Å3
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer
2467 independent reflections
Radiation source: fine-focus sealed tube1674 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.060
φ and ω scansθmax = 27.5°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
h = 66
Tmin = 0.946, Tmax = 0.989k = 1414
8256 measured reflectionsl = 1414
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)] = 0.065Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.245H atoms treated by a mixture of independent and constrained refinement
S = 1.08 w = 1/[σ2(Fo2) + (0.1439P)2 + 0.1968P]
where P = (Fo2 + 2Fc2)/3
2467 reflections(Δ/σ)max < 0.001
168 parametersΔρmax = 0.40 e Å3
0 restraintsΔρmin = 0.43 e Å3
Special details top

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat operating at 100.0 (1) K.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
O11.4551 (4)1.1091 (2)0.17382 (19)0.0228 (5)
N11.1022 (5)1.0528 (2)0.2807 (2)0.0167 (5)
N20.7855 (5)0.8428 (2)0.1855 (2)0.0163 (5)
N30.7455 (6)0.9851 (3)0.3832 (2)0.0195 (6)
C11.2280 (6)1.0222 (3)0.1804 (3)0.0158 (6)
C21.1430 (6)0.9018 (3)0.0739 (3)0.0179 (6)
H2A1.23850.88530.00170.021*
C30.9158 (6)0.8112 (3)0.0812 (3)0.0171 (6)
C40.8787 (6)0.9604 (3)0.2842 (2)0.0147 (6)
C51.5516 (7)1.2318 (3)0.2847 (3)0.0251 (7)
H5A1.72971.28340.27380.038*
H5B1.58651.21150.36390.038*
H5C1.40311.28250.29070.038*
C60.7968 (7)0.6779 (3)0.0186 (3)0.0230 (7)
H6A0.58680.66190.03800.035*
H6B0.85010.61100.01400.035*
H6C0.87530.67310.09740.035*
F10.1552 (5)0.49986 (19)0.3587 (2)0.0416 (6)
F20.1411 (5)0.6237 (2)0.4158 (2)0.0436 (6)
F30.1740 (4)0.50887 (18)0.21656 (18)0.0311 (5)
O20.3283 (4)0.66321 (19)0.20575 (18)0.0214 (5)
O30.2727 (5)0.8038 (2)0.39445 (19)0.0243 (5)
C70.0153 (7)0.5820 (3)0.3252 (3)0.0223 (7)
C80.2262 (6)0.6949 (3)0.3065 (3)0.0159 (6)
H1N30.807 (7)1.059 (4)0.446 (4)0.022 (8)*
H2N30.592 (9)0.925 (4)0.385 (4)0.035 (10)*
H1N20.628 (8)0.792 (4)0.197 (3)0.023 (9)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0223 (11)0.0158 (11)0.0236 (11)0.0036 (8)0.0021 (9)0.0031 (9)
N10.0157 (12)0.0118 (11)0.0180 (11)0.0001 (9)0.0016 (9)0.0020 (9)
N20.0177 (13)0.0098 (11)0.0156 (11)0.0005 (9)0.0003 (9)0.0010 (9)
N30.0196 (13)0.0110 (12)0.0194 (12)0.0012 (10)0.0021 (10)0.0034 (10)
C10.0147 (14)0.0122 (13)0.0190 (13)0.0029 (11)0.0009 (10)0.0049 (11)
C20.0174 (14)0.0161 (14)0.0161 (13)0.0017 (11)0.0003 (11)0.0024 (11)
C30.0159 (14)0.0160 (14)0.0150 (12)0.0021 (11)0.0024 (10)0.0020 (11)
C40.0154 (13)0.0111 (13)0.0155 (12)0.0035 (10)0.0015 (10)0.0027 (10)
C50.0221 (16)0.0120 (14)0.0332 (16)0.0043 (11)0.0017 (13)0.0039 (12)
C60.0294 (17)0.0128 (14)0.0177 (13)0.0001 (12)0.0007 (12)0.0027 (11)
F10.0434 (13)0.0260 (11)0.0592 (14)0.0030 (9)0.0028 (10)0.0266 (10)
F20.0482 (14)0.0313 (11)0.0390 (12)0.0079 (10)0.0241 (10)0.0000 (9)
F30.0276 (11)0.0195 (9)0.0308 (10)0.0099 (8)0.0033 (8)0.0007 (8)
O20.0251 (12)0.0133 (10)0.0187 (10)0.0016 (8)0.0035 (8)0.0006 (8)
O30.0291 (12)0.0107 (10)0.0226 (11)0.0026 (8)0.0057 (9)0.0045 (8)
C70.0225 (15)0.0172 (15)0.0206 (14)0.0018 (12)0.0019 (12)0.0022 (12)
C80.0158 (14)0.0085 (12)0.0186 (13)0.0004 (10)0.0033 (10)0.0019 (10)
Geometric parameters (Å, º) top
O1—C11.340 (3)C3—C61.493 (4)
O1—C51.464 (4)C5—H5A0.9800
N1—C11.305 (3)C5—H5B0.9800
N1—C41.353 (3)C5—H5C0.9800
N2—C31.354 (3)C6—H6A0.9800
N2—C41.362 (3)C6—H6B0.9800
N2—H1N20.90 (4)C6—H6C0.9800
N3—C41.311 (3)F1—C71.341 (4)
N3—H1N30.86 (4)F2—C71.335 (3)
N3—H2N30.90 (4)F3—C71.344 (3)
C1—C21.422 (4)O2—C81.244 (3)
C2—C31.368 (4)O3—C81.244 (3)
C2—H2A0.9500C7—C81.540 (4)
C1—O1—C5116.5 (2)O1—C5—H5B109.5
C1—N1—C4116.7 (2)H5A—C5—H5B109.5
C3—N2—C4121.9 (2)O1—C5—H5C109.5
C3—N2—H1N2125 (2)H5A—C5—H5C109.5
C4—N2—H1N2113 (2)H5B—C5—H5C109.5
C4—N3—H1N3119 (2)C3—C6—H6A109.5
C4—N3—H2N3120 (2)C3—C6—H6B109.5
H1N3—N3—H2N3121 (3)H6A—C6—H6B109.5
N1—C1—O1119.1 (2)C3—C6—H6C109.5
N1—C1—C2125.2 (3)H6A—C6—H6C109.5
O1—C1—C2115.7 (2)H6B—C6—H6C109.5
C3—C2—C1116.1 (2)F2—C7—F1107.4 (2)
C3—C2—H2A121.9F2—C7—F3106.1 (2)
C1—C2—H2A121.9F1—C7—F3106.5 (2)
N2—C3—C2118.7 (2)F2—C7—C8113.2 (2)
N2—C3—C6116.6 (2)F1—C7—C8111.1 (2)
C2—C3—C6124.7 (2)F3—C7—C8112.1 (2)
N3—C4—N1119.5 (2)O2—C8—O3129.4 (2)
N3—C4—N2119.2 (3)O2—C8—C7114.8 (2)
N1—C4—N2121.3 (2)O3—C8—C7115.8 (2)
O1—C5—H5A109.5
C4—N1—C1—O1178.3 (2)C1—N1—C4—N3179.4 (3)
C4—N1—C1—C22.0 (4)C1—N1—C4—N21.9 (4)
C5—O1—C1—N12.3 (4)C3—N2—C4—N3179.4 (3)
C5—O1—C1—C2178.0 (2)C3—N2—C4—N11.8 (4)
N1—C1—C2—C31.9 (4)F2—C7—C8—O2164.9 (3)
O1—C1—C2—C3178.4 (2)F1—C7—C8—O274.2 (3)
C4—N2—C3—C21.7 (4)F3—C7—C8—O244.9 (4)
C4—N2—C3—C6178.6 (2)F2—C7—C8—O316.0 (4)
C1—C2—C3—N21.6 (4)F1—C7—C8—O3105.0 (3)
C1—C2—C3—C6178.7 (3)F3—C7—C8—O3135.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H1N3···O3i0.86 (4)2.05 (4)2.822 (3)148 (3)
N3—H2N3···O30.90 (4)1.88 (5)2.782 (4)178 (5)
N2—H1N2···O20.90 (4)1.86 (4)2.758 (3)170 (4)
C2—H2A···O1ii0.952.583.514 (4)168
Symmetry codes: (i) x+1, y+2, z+1; (ii) x+3, y+2, z.
 

Acknowledgements

KB thanks the Department of Science and Technology (DST-SERB), New Delhi, India, for financial support (grant No. SB/FT/CS-058/2013).

References

First citationBruker (2009). SADABS, APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCondon, 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.  Google Scholar
First citationGilchrist, T. L. (1997). Heterocycl. Chem. 3rd ed., pp. 261–276. Singapore: Addison Wesley Longman.  Google Scholar
First citationGlidewell, C., Low, J. N., Melguizo, M. & Quesada, A. (2003). Acta Cryst. C59, o9–o13.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationMaeno, S., Miura, I., Masuda, K. & Nagata, T. (1990). Brighton Crop Protection Conference on Pests and Diseases, pp. 415–422 Alton, Hampshire, England: BCPC Publications.  Google Scholar
First citationRobert, J. J., Raj, S. B. & Muthiah, P. T. (2001). Acta Cryst. E57, o1206–o1208.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
First citationRodrigues, V. H., Paixão, J. A., Costa, M. M. R. R. & Matos Beja, A. (2001). Acta Cryst. C57, 761–763.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
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First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationThanigaimani, K., Khalib, N. C., Arshad, S. & Razak, I. A. (2013). Acta Cryst. E69, o318.  CSD CrossRef IUCr Journals Google Scholar

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