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

Hu, H.-L.; Yeh, C.-W.

doi:10.1107/S1600536812046569

organic compounds

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Volume 68| Part 12| December 2012| Page o3372

doi:10.1107/S1600536812046569

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

Hui-Ling Hu ^a and Chun-Wei Yeh ^b,^a ^*

^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 π–π 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); Eshtiagh-Hosseini et al. (2010 ); Hu & Yeh (2012 ).

Experimental

Crystal data

C₆H₁₀N₃⁺·Cl⁻
M_r = 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 ) T_min = 0.869, T_max = 0.982
5044 measured reflections
1620 independent reflections
1008 reflections with I > 2σ(I)
R_int = 0.046

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.105
S = 0.90
1620 reflections
93 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −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	D⋯A	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—H5A⋯Cg1ⁱⁱⁱ	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 ); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT; 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.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812046569/gw2128sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812046569/gw2128Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812046569/gw2128Isup3.cml

checkCIF report

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.

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

	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.
	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⁺·Cl⁻	F(000) = 672
M_r = 159.62	D_x = 1.291 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 1118 reflections
a = 16.372 (4) Å	θ = 2.7–22.9°
b = 8.795 (2) Å	µ = 0.40 mm⁻¹
c = 12.007 (3) Å	T = 273 K
β = 108.133 (5)°	Block, yellow
V = 1642.9 (8) Å³	0.4 × 0.4 × 0.3 mm
Z = 8

Data collection top

Bruker APEXII CCD area-detector diffractometer	1620 independent reflections
Radiation source: fine-focus sealed tube	1008 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.046
phi and ω scans	θ_max = 26.0°, θ_min = 2.6°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −19→20
T_min = 0.869, T_max = 0.982	k = −10→10
5044 measured reflections	l = −14→11

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.105	H-atom parameters constrained
S = 0.90	w = 1/[σ²(F_o²) + (0.0545P)²] where P = (F_o² + 2F_c²)/3
1620 reflections	(Δ/σ)_max < 0.001
93 parameters	Δρ_max = 0.18 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₆H₁₀N₃⁺·Cl⁻	V = 1642.9 (8) Å³
M_r = 159.62	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 16.372 (4) Å	µ = 0.40 mm⁻¹
b = 8.795 (2) Å	T = 273 K
c = 12.007 (3) Å	0.4 × 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)
T_min = 0.869, T_max = 0.982	R_int = 0.046
5044 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.105	H-atom parameters constrained
S = 0.90	Δρ_max = 0.18 e Å⁻³
1620 reflections	Δρ_min = −0.17 e Å⁻³
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

	x	y	z	U_iso*/U_eq
Cl	0.06044 (4)	0.20186 (8)	0.63062 (5)	0.0635 (3)
C1	0.19281 (13)	0.0360 (3)	0.9384 (2)	0.0456 (6)
C2	0.28190 (14)	0.1835 (2)	0.8578 (2)	0.0476 (6)
C3	0.35098 (14)	0.1274 (3)	0.9429 (2)	0.0524 (6)
H3A	0.4063	0.1584	0.9477	0.063*
C4	0.33775 (13)	0.0227 (3)	1.0228 (2)	0.0490 (6)
C5	0.28542 (16)	0.2952 (3)	0.7666 (2)	0.0639 (7)
H5A	0.2522	0.3834	0.7718	0.096*
H5B	0.2623	0.2499	0.6905	0.096*
H5C	0.3440	0.3244	0.7785	0.096*
C6	0.41211 (15)	−0.0414 (3)	1.1175 (2)	0.0682 (8)
H6A	0.3997	−0.0390	1.1906	0.102*
H6B	0.4625	0.0183	1.1242	0.102*
H6C	0.4219	−0.1445	1.0987	0.102*
N1	0.11391 (11)	−0.0037 (2)	0.93458 (18)	0.0598 (6)
H1A	0.1063	−0.0665	0.9853	0.072*
H1B	0.0703	0.0334	0.8814	0.072*
N2	0.20317 (11)	0.1349 (2)	0.85719 (15)	0.0470 (5)
H2N	0.1585	0.1678	0.8037	0.056*
N3	0.25965 (11)	−0.0223 (2)	1.02128 (16)	0.0480 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl	0.0469 (4)	0.0883 (5)	0.0535 (4)	0.0071 (3)	0.0131 (3)	0.0016 (3)
C1	0.0433 (12)	0.0489 (13)	0.0451 (14)	−0.0002 (11)	0.0144 (11)	−0.0052 (11)
C2	0.0516 (13)	0.0483 (13)	0.0459 (13)	−0.0037 (11)	0.0193 (11)	−0.0071 (11)
C3	0.0415 (12)	0.0603 (15)	0.0579 (16)	−0.0074 (11)	0.0190 (11)	−0.0044 (13)
C4	0.0447 (13)	0.0536 (14)	0.0469 (14)	0.0019 (11)	0.0117 (11)	−0.0066 (11)
C5	0.0717 (16)	0.0674 (16)	0.0581 (16)	−0.0057 (14)	0.0280 (13)	0.0069 (14)
C6	0.0487 (13)	0.0823 (19)	0.0663 (19)	0.0064 (14)	0.0073 (13)	0.0103 (15)
N1	0.0407 (11)	0.0734 (15)	0.0629 (15)	−0.0037 (10)	0.0129 (10)	0.0083 (10)
N2	0.0434 (10)	0.0530 (11)	0.0428 (11)	0.0034 (9)	0.0107 (8)	0.0017 (9)
N3	0.0425 (10)	0.0528 (12)	0.0467 (12)	0.0015 (9)	0.0110 (9)	0.0027 (9)

Geometric parameters (Å, º) top

C1—N1	1.325 (3)	C5—H5A	0.9600
C1—N3	1.331 (3)	C5—H5B	0.9600
C1—N2	1.356 (3)	C5—H5C	0.9600
C2—N2	1.356 (3)	C6—H6A	0.9600
C2—C3	1.359 (3)	C6—H6B	0.9600
C2—C5	1.486 (3)	C6—H6C	0.9600
C3—C4	1.395 (3)	N1—H1A	0.8600
C3—H3A	0.9300	N1—H1B	0.8600
C4—N3	1.333 (3)	N2—H2N	0.8600
C4—C6	1.494 (3)

N1—C1—N3	119.3 (2)	H5A—C5—H5C	109.5
N1—C1—N2	118.9 (2)	H5B—C5—H5C	109.5
N3—C1—N2	121.8 (2)	C4—C6—H6A	109.5
N2—C2—C3	117.2 (2)	C4—C6—H6B	109.5
N2—C2—C5	117.3 (2)	H6A—C6—H6B	109.5
C3—C2—C5	125.4 (2)	C4—C6—H6C	109.5
C2—C3—C4	119.0 (2)	H6A—C6—H6C	109.5
C2—C3—H3A	120.5	H6B—C6—H6C	109.5
C4—C3—H3A	120.5	C1—N1—H1A	120.0
N3—C4—C3	122.7 (2)	C1—N1—H1B	120.0
N3—C4—C6	116.7 (2)	H1A—N1—H1B	120.0
C3—C4—C6	120.6 (2)	C2—N2—C1	121.99 (18)
C2—C5—H5A	109.5	C2—N2—H2N	119.0
C2—C5—H5B	109.5	C1—N2—H2N	119.0
H5A—C5—H5B	109.5	C1—N3—C4	117.2 (2)
C2—C5—H5C	109.5

Hydrogen-bond geometry (Å, º) top

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

D—H···A	D—H	H···A	D···A	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—H5A···Cg1ⁱⁱⁱ	0.96	3.00	3.446 (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 formula	C₆H₁₀N₃⁺·Cl⁻
M_r	159.62
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	273
a, b, c (Å)	16.372 (4), 8.795 (2), 12.007 (3)
β (°)	108.133 (5)
V (Å³)	1642.9 (8)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.40
Crystal size (mm)	0.4 × 0.4 × 0.3

Data collection
Diffractometer	Bruker APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2000)
T_min, T_max	0.869, 0.982
No. of measured, independent and observed [I > 2σ(I)] reflections	5044, 1620, 1008
R_int	0.046
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.105, 0.90
No. of reflections	1620
No. of parameters	93
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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—H5A···Cg1ⁱⁱⁱ	0.96	3.00	3.446 (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

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

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 68| Part 12| December 2012| Page o3372

doi:10.1107/S1600536812046569

Open

access