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The 2-amino­pyrimidin-1-ium tri­chloro­acetate ion-pairs in the title compound, C4H6N3+·C2Cl3O2, are held together by two N—H...O hydrogen bonds [Namino...O = 2.733 (5); Npyrimidinium...O = 2.783 (6) Å], and adjacent ion-pairs are linked into a linear helical chain by a third and substantially weaker N—H...O hydrogen bond [N...O = 3.026 (3) Å]. The calculated structure of the ion-pair geometry, optimized at the PM3 level, shows good agreement with the experimental results.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S160053680201471X/ya6121sup1.cif
Contains datablocks I, ya6121

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S160053680201471X/ya6121Isup2.hkl
Contains datablock I

CCDC reference: 197474

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.008 Å
  • R factor = 0.058
  • wR factor = 0.181
  • Data-to-parameter ratio = 12.6

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


Amber Alert Alert Level B:
ABSTM_02 Alert B The ratio of Tmax/Tmin expected RT(exp) is > 1.20 Absorption corrections should be applied. Tmin and Tmax expected: 0.737 0.917 RT(exp) = 1.244 PLAT_731 Alert B Bond Calc 0.85(5), Rep 0.850(10) .... 5.00 s.u-Ratio N3 -H3N1 1.555 1.555 PLAT_735 Alert B D-H Calc 0.85(5), Rep 0.850(10) .... 5.00 s.u-Ratio N3 -H3N1 1.555 1.555
Yellow Alert Alert Level C:
PLAT_731 Alert C Bond Calc 0.84(3), Rep 0.850(10) .... 3.00 s.u-Ratio N3 -H3N2 1.555 1.555 PLAT_735 Alert C D-H Calc 0.85(4), Rep 0.850(10) .... 4.00 s.u-Ratio N1 -H1N1 1.555 1.555 PLAT_735 Alert C D-H Calc 0.84(3), Rep 0.850(10) .... 3.00 s.u-Ratio N3 -H3N2 1.555 1.555 PLAT_736 Alert C H...A Calc 1.89(4), Rep 1.890(10) .... 4.00 s.u-Ratio H1N1 -O1 1.555 1.555 PLAT_736 Alert C H...A Calc 1.95(5), Rep 1.95(2) .... 2.50 s.u-Ratio H3N1 -O2 1.555 1.555
0 Alert Level A = Potentially serious problem
3 Alert Level B = Potential problem
5 Alert Level C = Please check

Comment top

A number of carboxylic acids have been crystallographically documented as secondary-ammonium carboxylates; these compounds generally adopt dimeric hydrogen-bonded motifs (Ng et al., 2001). In the title 2-aminopyrimidin-1-ium carboxylate, the amino group forms a hydrogen bond with an oxygen atom of the carboxylate group, whose second oxygen atom is invoved in hydrogen bonding with the protonated nitrogen atom of the aromatic cation (Fig. 1). The ion-pairs are linked by a third, substantially weaker, hydrogen bond to furnish a helical chain that runs parallel to the b axis of the monoclinic cell (Fig. 2).

The calculated structure of the ion-pair that has been optimized at the PM3 level (Table 1) shows good agreement with the solid-state structure in the hydrogen-bonding interaction. However, the calculated structure has a delocalized carboxylate —COO group, whereas the geometry of this group in the experimental structure is indicative of at least partial localization of single and double carbon–oxygen bonds.

Experimental top

The organic salt was the crystalline compound that resulted from the reaction of europium perchlorate (0.45 g, 1 mmol), 2-aminopyrimidine (0.20 g, 2 mmol) and trichloroacetic acid (0.33 g, 2 mmol). 2-Aminopyrimidine dissolved in a small volume of ethanol was added to europium perchlorate dissolved in water to afford a precipitate. Trichloroacetic acid dissolved in water was then added to dissolve the precipitate; the clear solution was filtered and then set aside. Colorless crystals of the title compound separated from the solution after several days.

Refinement top

The nitrogen-bound H-atoms were located and refined, subject to N—H = 0.85±0.01 Å; the aromatic H-atoms were generated geometrically and were allowed to ride on their parent C-atoms, with U(H) = 1.2Ueq(C). A residual peak of 1 e Å−3 was found at 1.1 Å from the Cl3 atom.

For the geometry-optimization calculations, the initial structure was taken from the X-ray results. It was optimized in its lowest energy state (singlet spin state) using the semi-empirical quantum chemical PM3 Hamiltonian in HYPERCHEM (Hypercube, Inc., 2001). The unrestricted Hartree–Fock method was employed in the optimization.

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures top
[Figure 1] Fig. 1. ORTEPII (Johnson, 1976) plot of the hydrogen-bonded ion-pair at the 50% probability level. H atoms are drawn as spheres of arbitrary radii.
[Figure 2] Fig. 2. ORTEPII (Johnson, 1976) plot showing the ion-pairs linked by a weak N···O hydrogen bond [N3.·O1i = 3.026 (6) Å; N3—H.·Oi = 137 (5)°; symmetry code (i): 1 − x, 1/2 + y,1/2 − z] into a helical chain along the b axis.
2-Aminopyrimidin-1-ium trichloroacetate top
Crystal data top
C4H6N3+·C2Cl3O2F(000) = 520
Mr = 258.49Dx = 1.677 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 8.468 (2) ÅCell parameters from 1504 reflections
b = 11.297 (2) Åθ = 2.5–24.8°
c = 10.957 (2) ŵ = 0.87 mm1
β = 102.314 (3)°T = 298 K
V = 1024.1 (3) Å3Block, colorless
Z = 40.40 × 0.30 × 0.10 mm
Data collection top
Siemens CCD area-detector
diffractometer
1081 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.041
Graphite monochromatorθmax = 24.8°, θmin = 2.5°
ω scanh = 99
5155 measured reflectionsk = 1312
1748 independent reflectionsl = 1012
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)] = 0.058Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.181H atoms treated by a mixture of independent and constrained refinement
S = 1.04 w = 1/[σ2(Fo2) + (0.0924P)2 + 0.867P]
where P = (Fo2 + 2Fc2)/3
1748 reflections(Δ/σ)max < 0.001
139 parametersΔρmax = 1.04 e Å3
3 restraintsΔρmin = 0.51 e Å3
Crystal data top
C4H6N3+·C2Cl3O2V = 1024.1 (3) Å3
Mr = 258.49Z = 4
Monoclinic, P21/cMo Kα radiation
a = 8.468 (2) ŵ = 0.87 mm1
b = 11.297 (2) ÅT = 298 K
c = 10.957 (2) Å0.40 × 0.30 × 0.10 mm
β = 102.314 (3)°
Data collection top
Siemens CCD area-detector
diffractometer
1081 reflections with I > 2σ(I)
5155 measured reflectionsRint = 0.041
1748 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0583 restraints
wR(F2) = 0.181H atoms treated by a mixture of independent and constrained refinement
S = 1.04Δρmax = 1.04 e Å3
1748 reflectionsΔρmin = 0.51 e Å3
139 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl10.9403 (2)0.2646 (2)0.2322 (2)0.0722 (6)
Cl20.9414 (2)0.5017 (1)0.1497 (2)0.0728 (6)
Cl30.7626 (2)0.3246 (2)0.0119 (1)0.0752 (6)
O10.5992 (4)0.3078 (3)0.2269 (4)0.052 (1)
O20.6186 (6)0.5019 (3)0.1939 (5)0.078 (1)
N10.3828 (5)0.3477 (4)0.3752 (4)0.042 (1)
N20.2262 (6)0.4819 (4)0.4640 (4)0.054 (1)
N30.3827 (6)0.5467 (4)0.3302 (5)0.057 (1)
C10.6624 (6)0.3985 (5)0.1927 (5)0.047 (1)
C20.8195 (6)0.3754 (4)0.1431 (5)0.041 (1)
C30.3303 (6)0.4596 (4)0.3906 (5)0.043 (1)
C40.3369 (6)0.2561 (5)0.4378 (5)0.049 (1)
C50.2351 (7)0.2755 (5)0.5163 (5)0.054 (2)
C60.1814 (7)0.3907 (5)0.5242 (5)0.057 (2)
H40.37440.18010.42740.059*
H50.20290.21450.56260.065*
H60.10890.40480.57540.068*
H1n10.447 (5)0.336 (4)0.327 (4)0.04 (1)*
H3n10.441 (6)0.531 (5)0.278 (4)0.06 (2)*
H3n20.343 (7)0.615 (2)0.333 (6)0.07 (2)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.056 (1)0.070 (1)0.095 (1)0.013 (1)0.026 (1)0.027 (1)
Cl20.072 (1)0.049 (1)0.107 (1)0.023 (1)0.040 (1)0.009 (1)
Cl30.069 (1)0.109 (1)0.052 (1)0.016 (1)0.022 (1)0.022 (1)
O10.054 (2)0.038 (2)0.076 (3)0.006 (2)0.040 (2)0.003 (2)
O20.091 (3)0.042 (2)0.122 (4)0.021 (2)0.071 (3)0.023 (2)
N10.036 (2)0.040 (2)0.054 (3)0.004 (2)0.021 (2)0.004 (2)
N20.055 (3)0.047 (3)0.065 (3)0.006 (2)0.028 (2)0.005 (2)
N30.061 (3)0.040 (3)0.078 (4)0.014 (2)0.037 (3)0.010 (3)
C10.047 (3)0.049 (3)0.047 (3)0.001 (3)0.018 (2)0.000 (2)
C20.045 (3)0.033 (3)0.047 (3)0.003 (2)0.018 (2)0.001 (2)
C30.039 (3)0.041 (3)0.050 (3)0.005 (2)0.012 (2)0.005 (2)
C40.043 (3)0.040 (3)0.066 (4)0.002 (2)0.015 (3)0.000 (3)
C50.058 (4)0.051 (3)0.059 (4)0.001 (3)0.025 (3)0.006 (3)
C60.057 (4)0.063 (4)0.058 (4)0.004 (3)0.031 (3)0.005 (3)
Geometric parameters (Å, º) top
Cl1—C21.772 (5)C1—C21.563 (7)
Cl2—C21.753 (5)C4—C51.360 (7)
Cl3—C21.760 (5)C5—C61.387 (8)
O1—C11.250 (6)N1—H1n10.85 (1)
O2—C11.227 (6)N3—H3n10.85 (1)
N1—C41.344 (6)N3—H3n20.85 (1)
N1—C31.362 (6)C4—H40.930
N2—C61.321 (7)C5—H50.930
N2—C31.338 (6)C6—H60.930
N3—C31.315 (7)
C4—N1—C3120.9 (4)N1—C4—C5119.3 (5)
C6—N2—C3116.7 (4)C4—C5—C6116.8 (5)
O2—C1—O1128.8 (5)N2—C6—C5124.6 (5)
O2—C1—C2116.4 (5)C4—N1—H1n1119 (3)
O1—C1—C2114.7 (4)C3—N1—H1n1120 (3)
C1—C2—Cl2112.8 (3)C3—N3—H3n1119 (4)
C1—C2—Cl3108.2 (3)C3—N3—H3n2119 (4)
Cl2—C2—Cl3110.1 (3)H3n1—N3—H3n2121 (6)
C1—C2—Cl1111.1 (3)N1—C4—H4120.3
Cl2—C2—Cl1106.6 (3)C5—C4—H4120.3
Cl3—C2—Cl1108.0 (3)C4—C5—H5121.6
N3—C3—N2119.9 (5)C6—C5—H5121.6
N3—C3—N1118.5 (5)N2—C6—H6117.7
N2—C3—N1121.5 (5)C5—C6—H6117.7
O2—C1—C2—Cl221.1 (6)C6—N2—C3—N12.4 (8)
O1—C1—C2—Cl2158.4 (4)C4—N1—C3—N3177.9 (5)
O2—C1—C2—Cl3100.9 (5)C4—N1—C3—N22.9 (8)
O1—C1—C2—Cl379.6 (5)C3—N1—C4—C50.8 (8)
O2—C1—C2—Cl1140.7 (5)N1—C4—C5—C61.6 (8)
O1—C1—C2—Cl138.7 (6)C3—N2—C6—C50.1 (9)
C6—N2—C3—N3178.5 (5)C4—C5—C6—N22.1 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1n1···O10.85 (1)1.89 (1)2.733 (5)177 (5)
N3—H3n1···O20.85 (1)1.95 (2)2.783 (6)166 (5)
N3—H3n2···O1i0.85 (1)2.35 (4)3.026 (6)137 (5)
C4—H4···O2ii0.932.423.271 (6)152
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x+1, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC4H6N3+·C2Cl3O2
Mr258.49
Crystal system, space groupMonoclinic, P21/c
Temperature (K)298
a, b, c (Å)8.468 (2), 11.297 (2), 10.957 (2)
β (°) 102.314 (3)
V3)1024.1 (3)
Z4
Radiation typeMo Kα
µ (mm1)0.87
Crystal size (mm)0.40 × 0.30 × 0.10
Data collection
DiffractometerSiemens CCD area-detector
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
5155, 1748, 1081
Rint0.041
(sin θ/λ)max1)0.590
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.058, 0.181, 1.04
No. of reflections1748
No. of parameters139
No. of restraints3
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)1.04, 0.51

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1976).

Comparison of experimental and geometry-optimized bond dimensions. (Å, °) top
X-ray structureGeometry-optimized structure
Cl1-C21.772 (5)1.757
Cl2-C21.753 (5)1.754
Cl3-C21.760 (5)1.760
O1-C11.250 (6)1.263
O2-C11.227 (6)1.253
N1-C31.362 (6)1.404
N1-C41.344 (6)1.382
N2-C31.338 (6)1.402
N2-C61.321 (7)1.328
N3-C31.315 (7)1.351
C1-C21.563 (7)1.531
C4-C51.360 (7)1.374
C5-C61.387 (8)1.418
N1···O12.733 (5)2.704
N3···O22.783 (6)2.721
C4-N1-C3120.9 (4)118.5
C6-N2-C3116.7 (4)119.0
O1-C1-O2128.8 (5)121.1
O1-C1-C2114.7 (4)118.6
O2-C1-C2116.4 (5)120.3
C1-C2-Cl1111.1 (3)111.0
C1-C2-Cl2112.8 (3)113.5
C1-C2-Cl3108.2 (3)109.4
Cl1-C2-Cl2106.6 (3)107.8
Cl1-C2-Cl3108.0 (3)108.1
Cl2-C2-Cl3110.1 (3)107.9
N1-C3-N2121.5 (5)121.1
N1-C3-N3118.5 (5)120.2
N2-C3-N3119.9 (5)118.8
N1-C4-C5119.3 (5)120.7
C4-C5-C6116.8 (5)119.1
N2-C6-C5124.6 (5)121.7
N1-H···O1177 (5)180
N2-H···O2166 (5)168
 

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