2-Amino-4,6-dimethyl­pyrimidinium dihydrogenphosphate

Lin, C.-H.; Liu, N.-S.; Jian, F.-F.

doi:10.1107/S160053680903880X

organic compounds

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Volume 65| Part 11| November 2009| Page o2639

https://doi.org/10.1107/S160053680903880X

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2-Amino-4,6-dimethylpyrimidinium dihydrogenphosphate

Cui-Hua Lin,^a Nai-Sheng Liu ^b and Fang-Fang Jian ^c ^*

^aMicroscale Science Institute, Department of Chemistry and Chemical Engineering, Weifang University, Weifang 261061, People's Republic of China, ^bJournal Editorial Department, Weifang University, Weifang 261061, People's Republic of China, and ^cMicroscale Science Institute, Weifang University, Weifang 261061, People's Republic of China
^*Correspondence e-mail: ffjian2008@163.com

(Received 17 September 2009; accepted 25 September 2009; online 3 October 2009)

In the crystal structure of the title compound, C₆H₁₀N₃⁺·H₂PO₄⁻, the cations and anions are linked by intermolecular O—H⋯O and N—H⋯O hydrogen bonds, forming a two-dimensional network. Additional stabilization is provided by weak intermolecular C—H⋯O interactions. N—H⋯N interactions are also present.

Related literature

Five and six-membered heterocyclic compounds often exist in biologically active natural products and synthetic compounds of medicinal interest, see: Gilchrist (1998 ). For methylpyrimidines as precursors to potentially bioactive pyrimidine derivatives, see: Xue et al. (1993 ). For Ru complexes of pyrimidine with an –NH₂ substituent, see: Zhu et al. (2008 ). For bond-length data, see: Allen et al. (1987 ).

Experimental

Crystal data

C₆H₁₀N₃⁺·H₂PO₄⁻
M_r = 221.16
Monoclinic, P 2₁ /n
a = 11.743 (2) Å
b = 4.8266 (10) Å
c = 16.940 (3) Å
β = 95.55 (3)°
V = 955.6 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.28 mm⁻¹
T = 293 K
0.20 × 0.15 × 0.11 mm

Data collection

Bruker SMART CCD diffractometer
Absorption correction: none
8743 measured reflections
2193 independent reflections
1973 reflections with I > 2σ(I)
R_int = 0.021

Refinement

R[F² > 2σ(F²)] = 0.035
wR(F²) = 0.108
S = 1.08
2193 reflections
133 parameters
H-atom parameters constrained
Δρ_max = 0.40 e Å⁻³
Δρ_min = −0.41 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1	0.93	1.75	2.667 (2)	168
O2—H2A⋯O3ⁱ	0.87	1.70	2.560 (2)	171
N3—H3A⋯O3	0.82	2.02	2.831 (2)	170
N3—H3B⋯N2ⁱⁱ	0.93	2.07	3.004 (2)	178
O4—H4A⋯O1ⁱⁱⁱ	0.92	1.68	2.594 (2)	171
C3—H3D⋯O2^iv	0.93	2.40	3.319 (2)	171
Symmetry codes: (i) x, y+1, z; (ii) -x, -y-1, -z+2; (iii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iv) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 1997 ); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009 ); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S160053680903880X/lh2909sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053680903880X/lh2909Isup2.hkl

checkCIF report

Comment top

Five and six-membered heterocyclic compounds are important constituents that often exist in biologically active natural products and synthetic compounds of medicinal interest (Gilchrist, 1998). As useful precursors to potentially bioactive pyrimidine derivatives, methylpyrimidine has attracted considerable attention for many years (Xue et al., 1993). In recent years, Ru complexes of pyrimidine with an –NH2 substituent have been synthesized (Zhu et al., 2008). The title compound(I), was synthesized and we report herein its crystal structure.

The molecular structure of the title compound is shown in Fig. 1. There is one 2-Amino-4,6-dimethylpyrimidine cation and one dihydrogenphosphate anion in the asymmetric unit. All bond lengths are within the normal ranges (Allen et al., 1987). In the crystal structure, cations and anions are linked by intermolecular O-H···O and N-H···O hydrogen bonds to form a two-dimensional network. Additional stabilization is provided by weak intermolecular C—H···O interactions.

Related literature top

Five and six-membered heterocyclic compounds often exist in biologically active natural products and synthetic compounds of medicinal interest, see: Gilchrist (1998). For methylpyrimidines as precursors to potentially bioactive pyrimidine derivatives, see: Xue et al. (1993). For Ru complexes of pyrimidine with an –NH₂ substituent, see: Zhu et al. (2008). For bond-length data, see: Allen et al. (1987).

Experimental top

A mixture of guanidine hydrochloride (0.1 mol), acetyl acetone (0.2 mol), sodium carbonate (0.03 mol) and phosphoric acid (0.1 mol) was stirred with water (30 mL) for 5 h to afford the title compound (yield 78%). Single crystals suitable for X-ray measurements were obtained by recrystallization of the title compound from water at room temperature.

Structure description top

Five and six-membered heterocyclic compounds often exist in biologically active natural products and synthetic compounds of medicinal interest, see: Gilchrist (1998). For methylpyrimidines as precursors to potentially bioactive pyrimidine derivatives, see: Xue et al. (1993). For Ru complexes of pyrimidine with an –NH₂ substituent, see: Zhu et al. (2008). For bond-length data, see: Allen et al. (1987).

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

Fig. 1. The molecular structure of the title compound showing 30% probability displacement ellipsoids and the atom-numbering scheme.

2-Amino-4,6-dimethylpyrimidinium dihydrogenphosphate top

Crystal data top

C₆H₁₀N₃⁺·H₂PO₄⁻	F(000) = 464
M_r = 221.16	D_x = 1.537 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 1973 reflections
a = 11.743 (2) Å	θ = 3.5–27.5°
b = 4.8266 (10) Å	µ = 0.28 mm⁻¹
c = 16.940 (3) Å	T = 293 K
β = 95.55 (3)°	Block, colorless
V = 955.6 (3) Å³	0.20 × 0.15 × 0.11 mm
Z = 4

Data collection top

Bruker SMART CCD diffractometer	1973 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.021
Graphite monochromator	θ_max = 27.5°, θ_min = 3.5°
φ and ω scans	h = −15→15
8743 measured reflections	k = −6→5
2193 independent reflections	l = −21→21

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)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.108	H-atom parameters constrained
S = 1.08	w = 1/[σ²(F_o²) + (0.0686P)² + 0.3094P] where P = (F_o² + 2F_c²)/3
2193 reflections	(Δ/σ)_max = 0.001
133 parameters	Δρ_max = 0.40 e Å⁻³
0 restraints	Δρ_min = −0.41 e Å⁻³

Crystal data top

C₆H₁₀N₃⁺·H₂PO₄⁻	V = 955.6 (3) Å³
M_r = 221.16	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 11.743 (2) Å	µ = 0.28 mm⁻¹
b = 4.8266 (10) Å	T = 293 K
c = 16.940 (3) Å	0.20 × 0.15 × 0.11 mm
β = 95.55 (3)°

Data collection top

Bruker SMART CCD diffractometer	1973 reflections with I > 2σ(I)
8743 measured reflections	R_int = 0.021
2193 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	0 restraints
wR(F²) = 0.108	H-atom parameters constrained
S = 1.08	Δρ_max = 0.40 e Å⁻³
2193 reflections	Δρ_min = −0.41 e Å⁻³
133 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
P1	0.09666 (3)	0.22149 (8)	0.74781 (2)	0.02327 (14)
O1	0.17203 (9)	0.3129 (2)	0.82063 (6)	0.0302 (3)
O2	0.01084 (9)	0.4557 (2)	0.71860 (7)	0.0337 (3)
H2A	0.0243	0.6265	0.7326	0.085 (9)*
O3	0.02931 (10)	−0.0362 (2)	0.76133 (7)	0.0339 (3)
N1	0.20023 (11)	0.0034 (3)	0.95145 (7)	0.0270 (3)
H1A	0.1936	0.0900	0.9021	0.052 (6)*
O4	0.16964 (11)	0.1887 (3)	0.67571 (7)	0.0381 (3)
H4A	0.2241	0.0508	0.6822	0.084 (9)*
N3	0.02982 (11)	−0.2279 (3)	0.91928 (8)	0.0322 (3)
H3B	−0.0198	−0.3692	0.9308	0.032 (4)*
H3A	0.0243	−0.1573	0.8748	0.044 (6)*
C1	0.12099 (12)	−0.1846 (3)	0.96966 (8)	0.0252 (3)
N2	0.13194 (11)	−0.3247 (3)	1.03924 (7)	0.0282 (3)
C4	0.29458 (13)	0.0550 (3)	1.00208 (9)	0.0300 (3)
C2	0.22244 (14)	−0.2691 (3)	1.09017 (9)	0.0294 (3)
C3	0.30667 (13)	−0.0793 (4)	1.07340 (9)	0.0341 (3)
H3D	0.3695	−0.0453	1.1099	0.041*
C6	0.37991 (16)	0.2522 (4)	0.97449 (12)	0.0417 (4)
H6A	0.3427	0.4240	0.9594	0.063*
H6B	0.4128	0.1748	0.9297	0.063*
H6C	0.4391	0.2851	1.0166	0.063*
C5	0.23093 (16)	−0.4213 (4)	1.16774 (9)	0.0429 (4)
H5A	0.1664	−0.5429	1.1690	0.064*
H5B	0.2315	−0.2905	1.2105	0.064*
H5C	0.3002	−0.5280	1.1734	0.064*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
P1	0.0252 (2)	0.0188 (2)	0.0253 (2)	0.00191 (12)	−0.00052 (14)	0.00042 (12)
O1	0.0312 (6)	0.0308 (6)	0.0274 (5)	−0.0050 (4)	−0.0039 (4)	0.0044 (4)
O2	0.0333 (6)	0.0214 (5)	0.0437 (6)	0.0054 (4)	−0.0103 (4)	−0.0035 (4)
O3	0.0404 (6)	0.0207 (5)	0.0400 (6)	−0.0048 (4)	0.0005 (5)	0.0003 (4)
N1	0.0281 (6)	0.0277 (6)	0.0250 (6)	−0.0035 (5)	0.0012 (4)	0.0012 (5)
O4	0.0470 (7)	0.0380 (7)	0.0305 (6)	0.0135 (5)	0.0099 (5)	0.0051 (5)
N3	0.0327 (7)	0.0363 (7)	0.0263 (7)	−0.0087 (5)	−0.0031 (5)	0.0042 (5)
C1	0.0265 (7)	0.0256 (7)	0.0236 (7)	−0.0009 (5)	0.0026 (5)	−0.0008 (5)
N2	0.0303 (6)	0.0310 (7)	0.0233 (6)	−0.0038 (5)	0.0020 (5)	0.0020 (5)
C4	0.0277 (7)	0.0296 (7)	0.0322 (7)	−0.0034 (6)	0.0008 (5)	−0.0019 (6)
C2	0.0327 (8)	0.0313 (8)	0.0239 (7)	0.0003 (6)	0.0011 (5)	−0.0007 (5)
C3	0.0310 (8)	0.0391 (9)	0.0308 (7)	−0.0049 (7)	−0.0040 (6)	0.0005 (6)
C6	0.0346 (9)	0.0423 (10)	0.0475 (10)	−0.0125 (7)	−0.0002 (7)	0.0068 (7)
C5	0.0479 (10)	0.0532 (11)	0.0261 (7)	−0.0066 (8)	−0.0032 (6)	0.0089 (7)

Geometric parameters (Å, º) top

P1—O3	1.5033 (12)	N2—C2	1.330 (2)
P1—O1	1.5128 (12)	C4—C3	1.366 (2)
P1—O2	1.5626 (11)	C4—C6	1.490 (2)
P1—O4	1.5665 (12)	C2—C3	1.397 (2)
O2—H2A	0.8679	C2—C5	1.500 (2)
N1—C1	1.3566 (19)	C3—H3D	0.9300
N1—C4	1.3568 (19)	C6—H6A	0.9600
N1—H1A	0.9317	C6—H6B	0.9600
O4—H4A	0.9225	C6—H6C	0.9600
N3—C1	1.3195 (19)	C5—H5A	0.9600
N3—H3B	0.9302	C5—H5B	0.9600
N3—H3A	0.8243	C5—H5C	0.9600
C1—N2	1.3542 (19)

O3—P1—O1	113.08 (6)	C3—C4—C6	124.41 (15)
O3—P1—O2	108.30 (7)	N2—C2—C3	122.50 (14)
O1—P1—O2	110.84 (7)	N2—C2—C5	116.78 (14)
O3—P1—O4	111.77 (7)	C3—C2—C5	120.72 (15)
O1—P1—O4	110.13 (7)	C4—C3—C2	118.42 (14)
O2—P1—O4	102.18 (7)	C4—C3—H3D	120.8
P1—O2—H2A	120.4	C2—C3—H3D	120.8
C1—N1—C4	121.00 (13)	C4—C6—H6A	109.5
C1—N1—H1A	120.3	C4—C6—H6B	109.5
C4—N1—H1A	118.5	H6A—C6—H6B	109.5
P1—O4—H4A	113.9	C4—C6—H6C	109.5
C1—N3—H3B	117.8	H6A—C6—H6C	109.5
C1—N3—H3A	120.9	H6B—C6—H6C	109.5
H3B—N3—H3A	119.9	C2—C5—H5A	109.5
N3—C1—N2	119.12 (14)	C2—C5—H5B	109.5
N3—C1—N1	119.36 (13)	H5A—C5—H5B	109.5
N2—C1—N1	121.51 (13)	C2—C5—H5C	109.5
C2—N2—C1	117.81 (13)	H5A—C5—H5C	109.5
N1—C4—C3	118.72 (14)	H5B—C5—H5C	109.5
N1—C4—C6	116.85 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1	0.93	1.75	2.667 (2)	168
O2—H2A···O3ⁱ	0.87	1.70	2.560 (2)	171
N3—H3A···O3	0.82	2.02	2.831 (2)	170
N3—H3B···N2ⁱⁱ	0.93	2.07	3.004 (2)	178
O4—H4A···O1ⁱⁱⁱ	0.92	1.68	2.594 (2)	171
C3—H3D···O2^iv	0.93	2.40	3.319 (2)	171

Symmetry codes: (i) x, y+1, z; (ii) −x, −y−1, −z+2; (iii) −x+1/2, y−1/2, −z+3/2; (iv) x+1/2, −y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formula	C₆H₁₀N₃⁺·H₂PO₄⁻
M_r	221.16
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	293
a, b, c (Å)	11.743 (2), 4.8266 (10), 16.940 (3)
β (°)	95.55 (3)
V (Å³)	955.6 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.28
Crystal size (mm)	0.20 × 0.15 × 0.11

Data collection
Diffractometer	Bruker SMART CCD
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	8743, 2193, 1973
R_int	0.021
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.108, 1.08
No. of reflections	2193
No. of parameters	133
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.40, −0.41

Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1	0.93	1.75	2.667 (2)	168
O2—H2A···O3ⁱ	0.87	1.70	2.560 (2)	171
N3—H3A···O3	0.82	2.02	2.831 (2)	170
N3—H3B···N2ⁱⁱ	0.93	2.07	3.004 (2)	178
O4—H4A···O1ⁱⁱⁱ	0.92	1.68	2.594 (2)	171
C3—H3D···O2^iv	0.93	2.40	3.319 (2)	171

Symmetry codes: (i) x, y+1, z; (ii) −x, −y−1, −z+2; (iii) −x+1/2, y−1/2, −z+3/2; (iv) x+1/2, −y+1/2, z+1/2.

References

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. CSD CrossRef Web of Science Google Scholar
Bruker (1997). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Gilchrist, T. L. (1998). Heterocyclic Chemistry, 3rd ed. London: Addison-Wesley Longman Ltd. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
Xue, S. J., Zhang, A. D. & Wang, H. T. (1993). Chem. Reagents, 15, 181. Google Scholar
Zhu, W., Liu, X. & Wang, H. (2008). Acta Opt. Sin. 28, 1155–1160. CAS Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 65| Part 11| November 2009| Page o2639

https://doi.org/10.1107/S160053680903880X

Open

access