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

Jeevaraj, M.; Edison, B.; Kavitha, S.J.; Thanikasalam, K.; Britto, S.; Balasubramani, K.

doi:10.1107/S2414314616010105

organic compounds

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ISSN: 2414-3146

Volume 1| Part 6| June 2016| x161010

doi:10.1107/S2414314616010105

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

Muthaiah Jeevaraj,^a Bellarmin Edison,^a Savaridasson Jose Kavitha,^b Kanagasabapathy Thanikasalam,^c Sebastian Britto ^d and Kasthuri Balasubramani ^a ^*

^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.

Keywords: crystal structure; molecular salt; pyridinium; N—H⋯O hydrogen bonds; C—H⋯O hydrogen bonds.

CCDC reference: 1486919

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 ). 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 ). 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 ). 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. 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 ). The cation is essentially planar, with a maximum deviation of 0.042 (3) Å for atom C5.

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

In the crystal, Fig. 2, 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), 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 ) and 2-amino-6-methylpyridinium 3-chlorobenzoate (Thanigaimani et al., 2013 ). These arrays are further interlinked with a neighboring array through a pair of C2—H2A⋯O1ⁱⁱ hydrogen bonds (Table 1 and Fig. 2), 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	D⋯A	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
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

) 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. 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⁻
M_r	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)
V (Å³)	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 )
T_min, T_max	0.946, 0.989
No. of measured, independent and observed [I > 2σ(I)] reflections	8256, 2467, 1674
R_int	0.060
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.40, −0.43
Computer programs: APEX2 and SAINT (Bruker, 2009), SHELXS97, SHELXL97 and SHELXTL (Sheldrick, 2008 ) and PLATON (Spek, 2009 ).

Structural data

CCDC reference: 1486919

Crystal structure: contains datablocks global, I. DOI: 10.1107/S2414314616010105/su4055sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2414314616010105/su4055Isup2.hkl

Supporting information file. DOI: 10.1107/S2414314616010105/su4055Isup3.cml

checkCIF report

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⁺·C₂F₃O₂⁻	Z = 2
M_r = 253.19	F(000) = 260
Triclinic, P1	D_x = 1.557 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 4.8087 (2) Å	Cell parameters from 2385 reflections
b = 11.0283 (5) Å	θ = 2.3–28.6°
c = 11.1135 (5) Å	µ = 0.15 mm⁻¹
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 tube	1674 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.060
φ and ω scans	θ_max = 27.5°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −6→6
T_min = 0.946, T_max = 0.989	k = −14→14
8256 measured reflections	l = −14→14

Refinement top

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)] = 0.065	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.245	H atoms treated by a mixture of independent and constrained refinement
S = 1.08	w = 1/[σ²(F_o²) + (0.1439P)² + 0.1968P] where P = (F_o² + 2F_c²)/3
2467 reflections	(Δ/σ)_max < 0.001
168 parameters	Δρ_max = 0.40 e Å⁻³
0 restraints	Δρ_min = −0.43 e Å⁻³

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

	x	y	z	U_iso*/U_eq
O1	1.4551 (4)	1.1091 (2)	0.17382 (19)	0.0228 (5)
N1	1.1022 (5)	1.0528 (2)	0.2807 (2)	0.0167 (5)
N2	0.7855 (5)	0.8428 (2)	0.1855 (2)	0.0163 (5)
N3	0.7455 (6)	0.9851 (3)	0.3832 (2)	0.0195 (6)
C1	1.2280 (6)	1.0222 (3)	0.1804 (3)	0.0158 (6)
C2	1.1430 (6)	0.9018 (3)	0.0739 (3)	0.0179 (6)
H2A	1.2385	0.8853	0.0017	0.021*
C3	0.9158 (6)	0.8112 (3)	0.0812 (3)	0.0171 (6)
C4	0.8787 (6)	0.9604 (3)	0.2842 (2)	0.0147 (6)
C5	1.5516 (7)	1.2318 (3)	0.2847 (3)	0.0251 (7)
H5A	1.7297	1.2834	0.2738	0.038*
H5B	1.5865	1.2115	0.3639	0.038*
H5C	1.4031	1.2825	0.2907	0.038*
C6	0.7968 (7)	0.6779 (3)	−0.0186 (3)	0.0230 (7)
H6A	0.5868	0.6619	−0.0380	0.035*
H6B	0.8501	0.6110	0.0140	0.035*
H6C	0.8753	0.6731	−0.0974	0.035*
F1	0.1552 (5)	0.49986 (19)	0.3587 (2)	0.0416 (6)
F2	−0.1411 (5)	0.6237 (2)	0.4158 (2)	0.0436 (6)
F3	−0.1740 (4)	0.50887 (18)	0.21656 (18)	0.0311 (5)
O2	0.3283 (4)	0.66321 (19)	0.20575 (18)	0.0214 (5)
O3	0.2727 (5)	0.8038 (2)	0.39445 (19)	0.0243 (5)
C7	0.0153 (7)	0.5820 (3)	0.3252 (3)	0.0223 (7)
C8	0.2262 (6)	0.6949 (3)	0.3065 (3)	0.0159 (6)
H1N3	0.807 (7)	1.059 (4)	0.446 (4)	0.022 (8)*
H2N3	0.592 (9)	0.925 (4)	0.385 (4)	0.035 (10)*
H1N2	0.628 (8)	0.792 (4)	0.197 (3)	0.023 (9)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0223 (11)	0.0158 (11)	0.0236 (11)	−0.0036 (8)	0.0021 (9)	0.0031 (9)
N1	0.0157 (12)	0.0118 (11)	0.0180 (11)	0.0001 (9)	−0.0016 (9)	0.0020 (9)
N2	0.0177 (13)	0.0098 (11)	0.0156 (11)	0.0005 (9)	−0.0003 (9)	−0.0010 (9)
N3	0.0196 (13)	0.0110 (12)	0.0194 (12)	−0.0012 (10)	0.0021 (10)	−0.0034 (10)
C1	0.0147 (14)	0.0122 (13)	0.0190 (13)	0.0029 (11)	−0.0009 (10)	0.0049 (11)
C2	0.0174 (14)	0.0161 (14)	0.0161 (13)	0.0017 (11)	−0.0003 (11)	0.0024 (11)
C3	0.0159 (14)	0.0160 (14)	0.0150 (12)	0.0021 (11)	−0.0024 (10)	0.0020 (11)
C4	0.0154 (13)	0.0111 (13)	0.0155 (12)	0.0035 (10)	−0.0015 (10)	0.0027 (10)
C5	0.0221 (16)	0.0120 (14)	0.0332 (16)	−0.0043 (11)	−0.0017 (13)	0.0039 (12)
C6	0.0294 (17)	0.0128 (14)	0.0177 (13)	0.0001 (12)	−0.0007 (12)	−0.0027 (11)
F1	0.0434 (13)	0.0260 (11)	0.0592 (14)	0.0030 (9)	−0.0028 (10)	0.0266 (10)
F2	0.0482 (14)	0.0313 (11)	0.0390 (12)	−0.0079 (10)	0.0241 (10)	0.0000 (9)
F3	0.0276 (11)	0.0195 (9)	0.0308 (10)	−0.0099 (8)	−0.0033 (8)	−0.0007 (8)
O2	0.0251 (12)	0.0133 (10)	0.0187 (10)	−0.0016 (8)	0.0035 (8)	−0.0006 (8)
O3	0.0291 (12)	0.0107 (10)	0.0226 (11)	−0.0026 (8)	0.0057 (9)	−0.0045 (8)
C7	0.0225 (15)	0.0172 (15)	0.0206 (14)	−0.0018 (12)	0.0019 (12)	0.0022 (12)
C8	0.0158 (14)	0.0085 (12)	0.0186 (13)	−0.0004 (10)	−0.0033 (10)	0.0019 (10)

Geometric parameters (Å, º) top

O1—C1	1.340 (3)	C3—C6	1.493 (4)
O1—C5	1.464 (4)	C5—H5A	0.9800
N1—C1	1.305 (3)	C5—H5B	0.9800
N1—C4	1.353 (3)	C5—H5C	0.9800
N2—C3	1.354 (3)	C6—H6A	0.9800
N2—C4	1.362 (3)	C6—H6B	0.9800
N2—H1N2	0.90 (4)	C6—H6C	0.9800
N3—C4	1.311 (3)	F1—C7	1.341 (4)
N3—H1N3	0.86 (4)	F2—C7	1.335 (3)
N3—H2N3	0.90 (4)	F3—C7	1.344 (3)
C1—C2	1.422 (4)	O2—C8	1.244 (3)
C2—C3	1.368 (4)	O3—C8	1.244 (3)
C2—H2A	0.9500	C7—C8	1.540 (4)

C1—O1—C5	116.5 (2)	O1—C5—H5B	109.5
C1—N1—C4	116.7 (2)	H5A—C5—H5B	109.5
C3—N2—C4	121.9 (2)	O1—C5—H5C	109.5
C3—N2—H1N2	125 (2)	H5A—C5—H5C	109.5
C4—N2—H1N2	113 (2)	H5B—C5—H5C	109.5
C4—N3—H1N3	119 (2)	C3—C6—H6A	109.5
C4—N3—H2N3	120 (2)	C3—C6—H6B	109.5
H1N3—N3—H2N3	121 (3)	H6A—C6—H6B	109.5
N1—C1—O1	119.1 (2)	C3—C6—H6C	109.5
N1—C1—C2	125.2 (3)	H6A—C6—H6C	109.5
O1—C1—C2	115.7 (2)	H6B—C6—H6C	109.5
C3—C2—C1	116.1 (2)	F2—C7—F1	107.4 (2)
C3—C2—H2A	121.9	F2—C7—F3	106.1 (2)
C1—C2—H2A	121.9	F1—C7—F3	106.5 (2)
N2—C3—C2	118.7 (2)	F2—C7—C8	113.2 (2)
N2—C3—C6	116.6 (2)	F1—C7—C8	111.1 (2)
C2—C3—C6	124.7 (2)	F3—C7—C8	112.1 (2)
N3—C4—N1	119.5 (2)	O2—C8—O3	129.4 (2)
N3—C4—N2	119.2 (3)	O2—C8—C7	114.8 (2)
N1—C4—N2	121.3 (2)	O3—C8—C7	115.8 (2)
O1—C5—H5A	109.5

C4—N1—C1—O1	−178.3 (2)	C1—N1—C4—N3	179.4 (3)
C4—N1—C1—C2	2.0 (4)	C1—N1—C4—N2	−1.9 (4)
C5—O1—C1—N1	2.3 (4)	C3—N2—C4—N3	−179.4 (3)
C5—O1—C1—C2	−178.0 (2)	C3—N2—C4—N1	1.8 (4)
N1—C1—C2—C3	−1.9 (4)	F2—C7—C8—O2	−164.9 (3)
O1—C1—C2—C3	178.4 (2)	F1—C7—C8—O2	74.2 (3)
C4—N2—C3—C2	−1.7 (4)	F3—C7—C8—O2	−44.9 (4)
C4—N2—C3—C6	178.6 (2)	F2—C7—C8—O3	16.0 (4)
C1—C2—C3—N2	1.6 (4)	F1—C7—C8—O3	−105.0 (3)
C1—C2—C3—C6	−178.7 (3)	F3—C7—C8—O3	135.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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.

Acknowledgements

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

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