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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890

2-Amino-4,6-di­methyl­pyrimidin-1-ium chloride

aDepartment of Hospitality Management, Taoyuan Innovation Institute of Technology, Jhongli 32091, Taiwan, and bDepartment of Chemistry, Chung-Yuan Christian University, Jhongli 32023, Taiwan
*Correspondence e-mail: cwyeh@cycu.org.tw

(Received 13 October 2012; accepted 11 November 2012; online 17 November 2012)

In the title compound, C6H10N3+·Cl, the cation is essentially planar with an r.m.s. deviations of the fitted atoms of 0.008 Å. In the crystal, adjacent ions are linked by weak N—H⋯Cl hydrogen bonds involving the pyrimidine and amine N atoms, forming a three-dimensional network. C—H⋯π inter­actions between the methyl and pyrimidine groups and ππ stacking [centroid–centroid distance = 3.474 (1) Å] between parallel pyrimidine ring systems are also observed.

Related literature

For the crystal structures of 2-amino­pyrimidinium salts with other anions, see: Cheng et al. (2010)[Cheng, X.-L., Gao, S. & Ng, S. W. (2010). Acta Cryst. E66, o127.]; Eshtiagh-Hosseini et al. (2010[Eshtiagh-Hosseini, H., Mahjoobizadeh, M. & Mirzaei, M. (2010). Acta Cryst. E66, o2210.]); Hu & Yeh (2012[Hu, H.-L. & Yeh, C.-W. (2012). Acta Cryst. E68, o2925.]).

[Scheme 1]

Experimental

Crystal data
  • C6H10N3+·Cl

  • Mr = 159.62

  • Monoclinic, C 2/c

  • a = 16.372 (4) Å

  • b = 8.795 (2) Å

  • c = 12.007 (3) Å

  • β = 108.133 (5)°

  • V = 1642.9 (8) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.40 mm−1

  • T = 273 K

  • 0.4 × 0.4 × 0.3 mm

Data collection
  • Bruker APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.869, Tmax = 0.982

  • 5044 measured reflections

  • 1620 independent reflections

  • 1008 reflections with I > 2σ(I)

  • Rint = 0.046

Refinement
  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 0.105

  • S = 0.90

  • 1620 reflections

  • 93 parameters

  • H-atom parameters constrained

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.17 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C1–C4/N2/N3 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1A⋯Cli 0.86 2.42 3.260 (2) 167
N1—H1B⋯Clii 0.86 2.57 3.262 (2) 138
N2—H2N⋯Cl 0.86 2.22 3.042 (2) 161
C5—H5ACg1iii 0.96 3.00 3.446 (3) 110
Symmetry codes: (i) [x, -y, z+{\script{1\over 2}}]; (ii) [-x, y, -z+{\script{3\over 2}}]; (iii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}].

Data collection: APEX2 (Bruker, 2010[Bruker (2010). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2010[Bruker (2010). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008)[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008)[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]; molecular graphics: DIAMOND (Brandenburg, 2010[Brandenburg, K. (2010). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

There are several supramolecular structures containing 2-aminopyrimidinium cations with other anions constructed by hydrogen bonds (Cheng, et al. 2010; Eshtiagh-Hosseini, et al. 2010; Hu, et al. 2012). The asymmetric unit of the title molecule, C6H10N3+, Cl-, consists a mono-protonated 2-amino-4,6-dimethylpyrimidine and one chloride anion (Fig. 1). The protonated pyrimidine groups are flat and these carbon/nitrogen atoms of mean devition from plane are 0.008 Å. The cations and anions are interlinked through N—H···Cl hydrogen bonds which are found between the H atoms bound to the pyrimidine and amine N atoms and the chloride anions showing the three-dimensional net (Fig. 2, Tab. 1). In the crystal, the weak C—H···pi interactions between the methyl and pyrimidinyl groups and the pi···pi stacking between parallel pyrimidine ring systems are observed, respectively [3.474 (1) Å], while Cg1 is the centers of C1—C4/N2—N3.

Related literature top

For the crystal structures of 2-aminopyrimidinium salts with other anions, see: Cheng et al. (2010); Eshtiagh-Hosseini et al. (2010); Hu et al. (2012).

Experimental top

An aqueous solution (5.0 ml) of zinc chloride (1.0 mmol) was layered carefully over a methanolic solution (5.0 ml) of 2-amino-4,6-dimethylpyrimidine (2.0 mmol) in a tube. Yellow crystals were obtained after several weeks. These were washed with methanol and collected in 83.5% yield.

Refinement top

H atoms bound to C atoms were placed in idealized positions and constrained to ride on their parent atoms, with C—H = 0.93 - 0.96 Å and N—H = 0.86 Å, and with Uiso(H) = 1.2 or 1.5 Ueq(C/N).

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2010); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. An ORTEP view of the title compound with the atom-labelling scheme.Thermal ellipsoids are drawn at 30% probability level, and H atoms are represented by small spheres of arbitrary radii.
[Figure 2] Fig. 2. The packing diagram shows the N—H···Cl and C—H···pi hydrogen bonds and pi—pi stacking interactions forming the three-dimensional net.
2-Amino-4,6-dimethylpyrimidin-1-ium chloride top
Crystal data top
C6H10N3+·ClF(000) = 672
Mr = 159.62Dx = 1.291 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1118 reflections
a = 16.372 (4) Åθ = 2.7–22.9°
b = 8.795 (2) ŵ = 0.40 mm1
c = 12.007 (3) ÅT = 273 K
β = 108.133 (5)°Block, yellow
V = 1642.9 (8) Å30.4 × 0.4 × 0.3 mm
Z = 8
Data collection top
Bruker APEXII CCD area-detector
diffractometer
1620 independent reflections
Radiation source: fine-focus sealed tube1008 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
phi and ω scansθmax = 26.0°, θmin = 2.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
h = 1920
Tmin = 0.869, Tmax = 0.982k = 1010
5044 measured reflectionsl = 1411
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)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.105H-atom parameters constrained
S = 0.90 w = 1/[σ2(Fo2) + (0.0545P)2]
where P = (Fo2 + 2Fc2)/3
1620 reflections(Δ/σ)max < 0.001
93 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
C6H10N3+·ClV = 1642.9 (8) Å3
Mr = 159.62Z = 8
Monoclinic, C2/cMo Kα radiation
a = 16.372 (4) ŵ = 0.40 mm1
b = 8.795 (2) ÅT = 273 K
c = 12.007 (3) Å0.4 × 0.4 × 0.3 mm
β = 108.133 (5)°
Data collection top
Bruker APEXII CCD area-detector
diffractometer
1620 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)
1008 reflections with I > 2σ(I)
Tmin = 0.869, Tmax = 0.982Rint = 0.046
5044 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0390 restraints
wR(F2) = 0.105H-atom parameters constrained
S = 0.90Δρmax = 0.18 e Å3
1620 reflectionsΔρmin = 0.17 e Å3
93 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl0.06044 (4)0.20186 (8)0.63062 (5)0.0635 (3)
C10.19281 (13)0.0360 (3)0.9384 (2)0.0456 (6)
C20.28190 (14)0.1835 (2)0.8578 (2)0.0476 (6)
C30.35098 (14)0.1274 (3)0.9429 (2)0.0524 (6)
H3A0.40630.15840.94770.063*
C40.33775 (13)0.0227 (3)1.0228 (2)0.0490 (6)
C50.28542 (16)0.2952 (3)0.7666 (2)0.0639 (7)
H5A0.25220.38340.77180.096*
H5B0.26230.24990.69050.096*
H5C0.34400.32440.77850.096*
C60.41211 (15)0.0414 (3)1.1175 (2)0.0682 (8)
H6A0.39970.03901.19060.102*
H6B0.46250.01831.12420.102*
H6C0.42190.14451.09870.102*
N10.11391 (11)0.0037 (2)0.93458 (18)0.0598 (6)
H1A0.10630.06650.98530.072*
H1B0.07030.03340.88140.072*
N20.20317 (11)0.1349 (2)0.85719 (15)0.0470 (5)
H2N0.15850.16780.80370.056*
N30.25965 (11)0.0223 (2)1.02128 (16)0.0480 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl0.0469 (4)0.0883 (5)0.0535 (4)0.0071 (3)0.0131 (3)0.0016 (3)
C10.0433 (12)0.0489 (13)0.0451 (14)0.0002 (11)0.0144 (11)0.0052 (11)
C20.0516 (13)0.0483 (13)0.0459 (13)0.0037 (11)0.0193 (11)0.0071 (11)
C30.0415 (12)0.0603 (15)0.0579 (16)0.0074 (11)0.0190 (11)0.0044 (13)
C40.0447 (13)0.0536 (14)0.0469 (14)0.0019 (11)0.0117 (11)0.0066 (11)
C50.0717 (16)0.0674 (16)0.0581 (16)0.0057 (14)0.0280 (13)0.0069 (14)
C60.0487 (13)0.0823 (19)0.0663 (19)0.0064 (14)0.0073 (13)0.0103 (15)
N10.0407 (11)0.0734 (15)0.0629 (15)0.0037 (10)0.0129 (10)0.0083 (10)
N20.0434 (10)0.0530 (11)0.0428 (11)0.0034 (9)0.0107 (8)0.0017 (9)
N30.0425 (10)0.0528 (12)0.0467 (12)0.0015 (9)0.0110 (9)0.0027 (9)
Geometric parameters (Å, º) top
C1—N11.325 (3)C5—H5A0.9600
C1—N31.331 (3)C5—H5B0.9600
C1—N21.356 (3)C5—H5C0.9600
C2—N21.356 (3)C6—H6A0.9600
C2—C31.359 (3)C6—H6B0.9600
C2—C51.486 (3)C6—H6C0.9600
C3—C41.395 (3)N1—H1A0.8600
C3—H3A0.9300N1—H1B0.8600
C4—N31.333 (3)N2—H2N0.8600
C4—C61.494 (3)
N1—C1—N3119.3 (2)H5A—C5—H5C109.5
N1—C1—N2118.9 (2)H5B—C5—H5C109.5
N3—C1—N2121.8 (2)C4—C6—H6A109.5
N2—C2—C3117.2 (2)C4—C6—H6B109.5
N2—C2—C5117.3 (2)H6A—C6—H6B109.5
C3—C2—C5125.4 (2)C4—C6—H6C109.5
C2—C3—C4119.0 (2)H6A—C6—H6C109.5
C2—C3—H3A120.5H6B—C6—H6C109.5
C4—C3—H3A120.5C1—N1—H1A120.0
N3—C4—C3122.7 (2)C1—N1—H1B120.0
N3—C4—C6116.7 (2)H1A—N1—H1B120.0
C3—C4—C6120.6 (2)C2—N2—C1121.99 (18)
C2—C5—H5A109.5C2—N2—H2N119.0
C2—C5—H5B109.5C1—N2—H2N119.0
H5A—C5—H5B109.5C1—N3—C4117.2 (2)
C2—C5—H5C109.5
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C1–C4/N2/N3 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1A···Cli0.862.423.260 (2)167
N1—H1B···Clii0.862.573.262 (2)138
N2—H2N···Cl0.862.223.042 (2)161
C5—H5A···Cg1iii0.963.003.446 (3)110
Symmetry codes: (i) x, y, z+1/2; (ii) x, y, z+3/2; (iii) x+1/2, y+1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC6H10N3+·Cl
Mr159.62
Crystal system, space groupMonoclinic, C2/c
Temperature (K)273
a, b, c (Å)16.372 (4), 8.795 (2), 12.007 (3)
β (°) 108.133 (5)
V3)1642.9 (8)
Z8
Radiation typeMo Kα
µ (mm1)0.40
Crystal size (mm)0.4 × 0.4 × 0.3
Data collection
DiffractometerBruker APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.869, 0.982
No. of measured, independent and
observed [I > 2σ(I)] reflections
5044, 1620, 1008
Rint0.046
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.105, 0.90
No. of reflections1620
No. of parameters93
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.18, 0.17

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2010).

Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the C1–C4/N2/N3 ring.
D—H···AD—HH···AD···AD—H···A
N1—H1A···Cli0.862.423.260 (2)167
N1—H1B···Clii0.862.573.262 (2)138
N2—H2N···Cl0.862.223.042 (2)161
C5—H5A···Cg1iii0.963.003.446 (3)110
Symmetry codes: (i) x, y, z+1/2; (ii) x, y, z+3/2; (iii) x+1/2, y+1/2, z+3/2.
 

Acknowledgements

We are grateful to the National Science Council of the Republic of China and the Taoyuan Innovation Institute of Technology for support.

References

First citationBrandenburg, K. (2010). DIAMOND. Crystal Impact GbR, Bonn, Germany.
First citationBruker (2000). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationBruker (2010). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
First citationCheng, X.-L., Gao, S. & Ng, S. W. (2010). Acta Cryst. E66, o127.  Web of Science CSD CrossRef IUCr Journals
First citationEshtiagh-Hosseini, H., Mahjoobizadeh, M. & Mirzaei, M. (2010). Acta Cryst. E66, o2210.  Web of Science CSD CrossRef IUCr Journals
First citationHu, H.-L. & Yeh, C.-W. (2012). Acta Cryst. E68, o2925.  CSD CrossRef IUCr Journals
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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COMMUNICATIONS
ISSN: 2056-9890
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