2-Amino-4,6-dimethyl­pyrimidine–benzoic acid (1/1)

Meng, A.-L.; Huang, J.-E.; Zheng, B.; Li, Z.-J.

doi:10.1107/S1600536809020649

organic compounds

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ISSN: 2056-9890

Volume 65| Part 7| July 2009| Page o1595

doi:10.1107/S1600536809020649

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2-Amino-4,6-dimethylpyrimidine–benzoic acid (1/1)

A-Lan Meng,^a Jun-E Huang,^a Bin Zheng ^a and Zhen-Jiang Li ^a ^*

^aQingdao University of Science and Technology, Qingdao 266061, People's Republic of China
^*Correspondence e-mail: zjli126@126.com

(Received 11 May 2009; accepted 31 May 2009; online 17 June 2009)

The crystal of the title compound, C₆H₉N₃·C₇H₆O₂, contains tetrameric hydrogen-bonded units comprising a central pair of 2-aminopyrimidine molecules linked across a centre of inversion by N—H⋯N hydrogen bonds and two pendant benzoic acid molecules attached through N—H⋯O and O—H⋯N hydrogen bonds. These hydrogen-bonded units are arranged into layers in (002).

Related literature

For the biological activity of pyrimidine and aminopyrimidine derivatives, see: Hunt et al. (1980 ); Baker & Santi (1965 ). For related structures, see: Skovsgaard & Bond (2009 ); Fun et al. (2006 ); Wang et al. (2007 ); Schwalbe & Williams (1982 ); Hu et al. (2002 ); Chinnakali et al. (1999 ).

Experimental

Crystal data

C₆H₉N₃·C₇H₆O₂
M_r = 245.28
Monoclinic, P 2₁ /c
a = 6.7019 (9) Å
b = 7.6466 (10) Å
c = 25.285 (3) Å
β = 91.360 (2)°
V = 1295.4 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 295 K
0.18 × 0.15 × 0.10 mm

Data collection

Bruker SMART CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.985, T_max = 0.991
6594 measured reflections
2273 independent reflections
1228 reflections with I > 2σ(I)
R_int = 0.104

Refinement

R[F² > 2σ(F²)] = 0.053
wR(F²) = 0.137
S = 1.01
2273 reflections
167 parameters
H-atom parameters constrained
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯N1	0.82	1.82	2.606 (2)	160
N3—H3A⋯O2	0.86	2.16	3.003 (3)	168
N3—H3B⋯N2ⁱ	0.86	2.25	3.098 (3)	169
Symmetry code: (i) -x, -y+2, -z+1.

Data collection: SMART (Bruker, 2001 ); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; 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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809020649/bi2374sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809020649/bi2374Isup2.hkl

checkCIF report

Comment top

Pyrimidine and aminopyrimidine derivatives are biologically important compounds as they occur in nature as components of nucleic acids. Some aminopyrimidine derivatives are used as antifolate drugs (Hunt et al., 1980; Baker & Santi, 1965). The crystal structures of aminopyrimidine derivatives (Schwalbe & Williams, 1982), aminopyrimidine carboxylates (Hu et al., 2002) and co-crystal structures (Chinnakali et al., 1999; Skovsgaard & Bond, 2009) have been reported.

The title compound (Fig. 1) was obtained as the product of an attempted synthesis of benzoic acid and 2-amino-4,6-dimethylpyrimidine in acetone. The bond lengths and angles in the pyrimidine ring and phenyl ring are generally normal (Fun et al., 2006). The molecules associate through O—H···N, N—H···O and N—H···N hydrogen bonds into centrosymmetic tetrameric units. These units pack into stacked layers in the (002) planes (Fig. 2).

Related literature top

For the biological activity of pyrimidine and aminopyrimidine derivatives, see: Hunt et al. (1980); Baker & Santi (1965). For related structures, see: Skovsgaard & Bond (2009); Fun et al. (2006); Wang et al. (2007); Schwalbe & Williams (1982); Hu et al. (2002); Chinnakali et al. (1999).

Experimental top

Single crystals of the title compound were obtained by reaction of benzoic acid (0.2 mmol) and 2-amino-4,6-dimethylpyrimidine (0.2 mmol) in refluxing acetone (50 ml). Single crystals suitable for X-ray analysis were obtained by recrystallization from ethanol solution at room temperature.

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); 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).

Figures top

	Fig. 1. Molecular structure with displacement ellipsoids drawn at the 30% probability level for non-H atoms. Dashed lines denote hydrogen bonds.
	Fig. 2. Packing diagram showing one layer of molecules connected by N—H···O and O—H···N hydrogen bonds (dashed lines).

2-Amino-4,6-dimethylpyrimidine–benzoic acid (1/1) top

Crystal data top

C₆H₉N₃·C₇H₆O₂	F(000) = 520
M_r = 245.28	D_x = 1.258 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 167 reflections
a = 6.7019 (9) Å	θ = 1.6–25.0°
b = 7.6466 (10) Å	µ = 0.09 mm⁻¹
c = 25.285 (3) Å	T = 295 K
β = 91.360 (2)°	Block, colourless
V = 1295.4 (3) Å³	0.18 × 0.15 × 0.10 mm
Z = 4

Data collection top

Bruker SMART CCD diffractometer	2273 independent reflections
Radiation source: fine-focus sealed tube	1228 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.104
ϕ and ω scans	θ_max = 25.0°, θ_min = 1.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −7→7
T_min = 0.985, T_max = 0.991	k = −9→9
6594 measured reflections	l = −22→30

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.053	H-atom parameters constrained
wR(F²) = 0.137	w = 1/[σ²(F_o²) + (0.0352P)² + 0.012P] where P = (F_o² + 2F_c²)/3
S = 1.01	(Δ/σ)_max < 0.001
2273 reflections	Δρ_max = 0.22 e Å⁻³
167 parameters	Δρ_min = −0.19 e Å⁻³
0 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0077 (16)

Crystal data top

C₆H₉N₃·C₇H₆O₂	V = 1295.4 (3) Å³
M_r = 245.28	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.7019 (9) Å	µ = 0.09 mm⁻¹
b = 7.6466 (10) Å	T = 295 K
c = 25.285 (3) Å	0.18 × 0.15 × 0.10 mm
β = 91.360 (2)°

Data collection top

Bruker SMART CCD diffractometer	2273 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	1228 reflections with I > 2σ(I)
T_min = 0.985, T_max = 0.991	R_int = 0.104
6594 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.053	0 restraints
wR(F²) = 0.137	H-atom parameters constrained
S = 1.01	Δρ_max = 0.22 e Å⁻³
2273 reflections	Δρ_min = −0.19 e Å⁻³
167 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
O1	0.6583 (2)	0.6591 (2)	0.41923 (6)	0.0678 (5)
H1	0.5870	0.7100	0.4402	0.102*
O2	0.3940 (3)	0.6933 (3)	0.36625 (7)	0.0787 (6)
N1	0.4633 (3)	0.7645 (2)	0.50129 (7)	0.0482 (5)
N2	0.1976 (3)	0.9074 (2)	0.54612 (8)	0.0560 (6)
N3	0.1836 (3)	0.8632 (2)	0.45633 (8)	0.0646 (6)
H3A	0.2332	0.8250	0.4275	0.078*
H3B	0.0689	0.9137	0.4557	0.078*
C1	0.6891 (4)	0.5714 (3)	0.33125 (9)	0.0540 (6)
C2	0.8886 (4)	0.5334 (3)	0.34037 (10)	0.0662 (7)
H2	0.9484	0.5593	0.3730	0.079*
C3	0.9993 (5)	0.4573 (4)	0.30126 (13)	0.0813 (9)
H3	1.1337	0.4326	0.3075	0.098*
C4	0.9124 (6)	0.4184 (4)	0.25352 (13)	0.0892 (10)
H4	0.9866	0.3641	0.2276	0.107*
C5	0.7167 (6)	0.4587 (4)	0.24346 (11)	0.0931 (10)
H5	0.6586	0.4332	0.2106	0.112*
C6	0.6032 (4)	0.5382 (4)	0.28248 (10)	0.0754 (8)
H6	0.4708	0.5683	0.2754	0.090*
C7	0.5664 (4)	0.6473 (3)	0.37388 (10)	0.0542 (7)
C8	0.2837 (4)	0.8443 (3)	0.50166 (10)	0.0497 (6)
C9	0.5618 (3)	0.7431 (3)	0.54739 (9)	0.0522 (6)
C10	0.4805 (4)	0.8019 (3)	0.59401 (10)	0.0620 (7)
H10	0.5481	0.7868	0.6262	0.074*
C11	0.2973 (4)	0.8831 (3)	0.59146 (10)	0.0579 (7)
C12	0.7598 (4)	0.6537 (3)	0.54573 (11)	0.0699 (8)
H12A	0.7401	0.5309	0.5397	0.105*
H12B	0.8303	0.6706	0.5788	0.105*
H12C	0.8361	0.7022	0.5176	0.105*
C13	0.1975 (4)	0.9484 (3)	0.64045 (10)	0.0793 (9)
H13A	0.1886	1.0737	0.6393	0.119*
H13B	0.2743	0.9136	0.6712	0.119*
H13C	0.0658	0.8996	0.6421	0.119*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0593 (11)	0.0969 (15)	0.0473 (11)	0.0084 (10)	0.0053 (9)	−0.0141 (10)
O2	0.0568 (12)	0.1232 (16)	0.0564 (12)	0.0167 (11)	0.0055 (9)	−0.0012 (10)
N1	0.0425 (11)	0.0546 (12)	0.0480 (12)	−0.0031 (9)	0.0092 (9)	−0.0005 (9)
N2	0.0584 (13)	0.0594 (13)	0.0510 (13)	−0.0063 (10)	0.0179 (10)	−0.0042 (11)
N3	0.0552 (13)	0.0919 (16)	0.0472 (13)	0.0168 (11)	0.0084 (10)	−0.0057 (11)
C1	0.0620 (17)	0.0566 (15)	0.0439 (15)	−0.0070 (13)	0.0109 (12)	0.0003 (12)
C2	0.0670 (19)	0.0707 (18)	0.0617 (17)	−0.0002 (14)	0.0157 (14)	−0.0015 (14)
C3	0.081 (2)	0.085 (2)	0.080 (2)	0.0071 (17)	0.0337 (18)	−0.0012 (18)
C4	0.119 (3)	0.073 (2)	0.078 (2)	−0.003 (2)	0.056 (2)	−0.0027 (18)
C5	0.119 (3)	0.113 (3)	0.0486 (19)	−0.020 (2)	0.0181 (18)	−0.0134 (17)
C6	0.0767 (19)	0.098 (2)	0.0513 (17)	−0.0100 (16)	0.0084 (14)	−0.0062 (16)
C7	0.0529 (16)	0.0653 (17)	0.0448 (16)	−0.0014 (13)	0.0080 (13)	0.0025 (12)
C8	0.0524 (15)	0.0516 (14)	0.0456 (15)	−0.0068 (12)	0.0121 (12)	−0.0030 (12)
C9	0.0502 (15)	0.0550 (16)	0.0516 (16)	−0.0112 (12)	0.0041 (12)	0.0032 (12)
C10	0.0705 (19)	0.0703 (17)	0.0454 (16)	−0.0090 (15)	0.0058 (13)	0.0030 (13)
C11	0.0694 (18)	0.0566 (16)	0.0486 (16)	−0.0128 (14)	0.0196 (13)	−0.0031 (12)
C12	0.0561 (17)	0.0836 (18)	0.0700 (18)	0.0001 (14)	0.0004 (13)	0.0025 (15)
C13	0.100 (2)	0.0828 (19)	0.0562 (17)	−0.0108 (17)	0.0289 (15)	−0.0094 (15)

Geometric parameters (Å, º) top

O1—C7	1.292 (3)	C4—C5	1.365 (4)
O1—H1	0.820	C4—H4	0.930
O2—C7	1.218 (3)	C5—C6	1.399 (4)
N1—C9	1.336 (3)	C5—H5	0.930
N1—C8	1.350 (3)	C6—H6	0.930
N2—C11	1.326 (3)	C9—C10	1.385 (3)
N2—C8	1.364 (3)	C9—C12	1.494 (3)
N3—C8	1.322 (3)	C10—C11	1.376 (3)
N3—H3A	0.860	C10—H10	0.930
N3—H3B	0.860	C11—C13	1.507 (3)
C1—C6	1.372 (3)	C12—H12A	0.960
C1—C2	1.382 (3)	C12—H12B	0.960
C1—C7	1.489 (3)	C12—H12C	0.960
C2—C3	1.379 (4)	C13—H13A	0.960
C2—H2	0.930	C13—H13B	0.960
C3—C4	1.361 (4)	C13—H13C	0.960
C3—H3	0.930

C7—O1—H1	109.5	O1—C7—C1	114.2 (2)
C9—N1—C8	118.13 (19)	N3—C8—N1	118.5 (2)
C11—N2—C8	116.7 (2)	N3—C8—N2	117.4 (2)
C8—N3—H3A	120.0	N1—C8—N2	124.1 (2)
C8—N3—H3B	120.0	N1—C9—C10	120.4 (2)
H3A—N3—H3B	120.0	N1—C9—C12	116.9 (2)
C6—C1—C2	119.6 (2)	C10—C9—C12	122.7 (2)
C6—C1—C7	119.7 (2)	C11—C10—C9	118.4 (2)
C2—C1—C7	120.7 (2)	C11—C10—H10	120.8
C3—C2—C1	120.3 (3)	C9—C10—H10	120.8
C3—C2—H2	119.9	N2—C11—C10	122.3 (2)
C1—C2—H2	119.9	N2—C11—C13	116.1 (3)
C4—C3—C2	120.1 (3)	C10—C11—C13	121.6 (3)
C4—C3—H3	119.9	C9—C12—H12A	109.5
C2—C3—H3	119.9	C9—C12—H12B	109.5
C3—C4—C5	120.3 (3)	H12A—C12—H12B	109.5
C3—C4—H4	119.8	C9—C12—H12C	109.5
C5—C4—H4	119.8	H12A—C12—H12C	109.5
C4—C5—C6	120.2 (3)	H12B—C12—H12C	109.5
C4—C5—H5	119.9	C11—C13—H13A	109.5
C6—C5—H5	119.9	C11—C13—H13B	109.5
C1—C6—C5	119.4 (3)	H13A—C13—H13B	109.5
C1—C6—H6	120.3	C11—C13—H13C	109.5
C5—C6—H6	120.3	H13A—C13—H13C	109.5
O2—C7—O1	123.4 (2)	H13B—C13—H13C	109.5
O2—C7—C1	122.4 (2)

C6—C1—C2—C3	−2.1 (4)	C9—N1—C8—N3	−178.84 (19)
C7—C1—C2—C3	177.7 (2)	C9—N1—C8—N2	1.2 (3)
C1—C2—C3—C4	−0.3 (4)	C11—N2—C8—N3	178.20 (19)
C2—C3—C4—C5	1.8 (5)	C11—N2—C8—N1	−1.8 (3)
C3—C4—C5—C6	−0.9 (5)	C8—N1—C9—C10	−0.1 (3)
C2—C1—C6—C5	3.0 (4)	C8—N1—C9—C12	179.75 (19)
C7—C1—C6—C5	−176.8 (2)	N1—C9—C10—C11	−0.4 (3)
C4—C5—C6—C1	−1.5 (4)	C12—C9—C10—C11	179.9 (2)
C6—C1—C7—O2	−5.3 (4)	C8—N2—C11—C10	1.4 (3)
C2—C1—C7—O2	175.0 (2)	C8—N2—C11—C13	−178.11 (19)
C6—C1—C7—O1	174.4 (2)	C9—C10—C11—N2	−0.3 (4)
C2—C1—C7—O1	−5.3 (3)	C9—C10—C11—C13	179.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1	0.82	1.82	2.606 (2)	160
N3—H3A···O2	0.86	2.16	3.003 (3)	168
N3—H3B···N2ⁱ	0.86	2.25	3.098 (3)	169

Symmetry code: (i) −x, −y+2, −z+1.

Experimental details

Crystal data
Chemical formula	C₆H₉N₃·C₇H₆O₂
M_r	245.28
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	295
a, b, c (Å)	6.7019 (9), 7.6466 (10), 25.285 (3)
β (°)	91.360 (2)
V (Å³)	1295.4 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.18 × 0.15 × 0.10

Data collection
Diffractometer	Bruker SMART CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.985, 0.991
No. of measured, independent and observed [I > 2σ(I)] reflections	6594, 2273, 1228
R_int	0.104
(sin θ/λ)_max (Å⁻¹)	0.596

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.053, 0.137, 1.01
No. of reflections	2273
No. of parameters	167
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.19

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1	0.82	1.82	2.606 (2)	160
N3—H3A···O2	0.86	2.16	3.003 (3)	168
N3—H3B···N2ⁱ	0.86	2.25	3.098 (3)	169

Symmetry code: (i) −x, −y+2, −z+1.

Acknowledgements

The authors thank the Natural Science Foundation of China (grant No. 50572041) and the Science Item of Shandong Province (grant No. 2006 GG2203014).

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