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Acta Crystallogr Sect E Struct Rep Online. 2009 July 1; 65(Pt 7): o1595.
Published online 2009 June 17. doi:  10.1107/S1600536809020649
PMCID: PMC2969298

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

Abstract

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 [triangle]); Baker & Santi (1965 [triangle]). For related structures, see: Skovsgaard & Bond (2009 [triangle]); Fun et al. (2006 [triangle]); Wang et al. (2007 [triangle]); Schwalbe & Williams (1982 [triangle]); Hu et al. (2002 [triangle]); Chinnakali et al. (1999 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1595-scheme1.jpg

Experimental

Crystal data

  • C6H9N3·C7H6O2
  • M r = 245.28
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1595-efi1.jpg
  • 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 [triangle]) 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[F 2 > 2σ(F 2)] = 0.053
  • wR(F 2) = 0.137
  • S = 1.01
  • 2273 reflections
  • 167 parameters
  • H-atom parameters constrained
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT (Bruker, 2001 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

H atoms were fixed geometrically and allowed to ride on their attached atoms, with N—H = 0.86 Å, C—H = 0.93 or 0.96 Å, and with Uiso(H) = 1.5 Ueq(C) (for CH3) or 1.2 Ueq(C) (for CH2, aromatic CH and NH2).

Figures

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).

Crystal data

C6H9N3·C7H6O2F(000) = 520
Mr = 245.28Dx = 1.258 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 167 reflections
a = 6.7019 (9) Åθ = 1.6–25.0°
b = 7.6466 (10) ŵ = 0.09 mm1
c = 25.285 (3) ÅT = 295 K
β = 91.360 (2)°Block, colourless
V = 1295.4 (3) Å30.18 × 0.15 × 0.10 mm
Z = 4

Data collection

Bruker SMART CCD diffractometer2273 independent reflections
Radiation source: fine-focus sealed tube1228 reflections with I > 2σ(I)
graphiteRint = 0.104
[var phi] and ω scansθmax = 25.0°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −7→7
Tmin = 0.985, Tmax = 0.991k = −9→9
6594 measured reflectionsl = −22→30

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.053H-atom parameters constrained
wR(F2) = 0.137w = 1/[σ2(Fo2) + (0.0352P)2 + 0.012P] where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
2273 reflectionsΔρmax = 0.22 e Å3
167 parametersΔρmin = −0.19 e Å3
0 restraintsExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0077 (16)

Special details

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)

xyzUiso*/Ueq
O10.6583 (2)0.6591 (2)0.41923 (6)0.0678 (5)
H10.58700.71000.44020.102*
O20.3940 (3)0.6933 (3)0.36625 (7)0.0787 (6)
N10.4633 (3)0.7645 (2)0.50129 (7)0.0482 (5)
N20.1976 (3)0.9074 (2)0.54612 (8)0.0560 (6)
N30.1836 (3)0.8632 (2)0.45633 (8)0.0646 (6)
H3A0.23320.82500.42750.078*
H3B0.06890.91370.45570.078*
C10.6891 (4)0.5714 (3)0.33125 (9)0.0540 (6)
C20.8886 (4)0.5334 (3)0.34037 (10)0.0662 (7)
H20.94840.55930.37300.079*
C30.9993 (5)0.4573 (4)0.30126 (13)0.0813 (9)
H31.13370.43260.30750.098*
C40.9124 (6)0.4184 (4)0.25352 (13)0.0892 (10)
H40.98660.36410.22760.107*
C50.7167 (6)0.4587 (4)0.24346 (11)0.0931 (10)
H50.65860.43320.21060.112*
C60.6032 (4)0.5382 (4)0.28248 (10)0.0754 (8)
H60.47080.56830.27540.090*
C70.5664 (4)0.6473 (3)0.37388 (10)0.0542 (7)
C80.2837 (4)0.8443 (3)0.50166 (10)0.0497 (6)
C90.5618 (3)0.7431 (3)0.54739 (9)0.0522 (6)
C100.4805 (4)0.8019 (3)0.59401 (10)0.0620 (7)
H100.54810.78680.62620.074*
C110.2973 (4)0.8831 (3)0.59146 (10)0.0579 (7)
C120.7598 (4)0.6537 (3)0.54573 (11)0.0699 (8)
H12A0.74010.53090.53970.105*
H12B0.83030.67060.57880.105*
H12C0.83610.70220.51760.105*
C130.1975 (4)0.9484 (3)0.64045 (10)0.0793 (9)
H13A0.18861.07370.63930.119*
H13B0.27430.91360.67120.119*
H13C0.06580.89960.64210.119*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0593 (11)0.0969 (15)0.0473 (11)0.0084 (10)0.0053 (9)−0.0141 (10)
O20.0568 (12)0.1232 (16)0.0564 (12)0.0167 (11)0.0055 (9)−0.0012 (10)
N10.0425 (11)0.0546 (12)0.0480 (12)−0.0031 (9)0.0092 (9)−0.0005 (9)
N20.0584 (13)0.0594 (13)0.0510 (13)−0.0063 (10)0.0179 (10)−0.0042 (11)
N30.0552 (13)0.0919 (16)0.0472 (13)0.0168 (11)0.0084 (10)−0.0057 (11)
C10.0620 (17)0.0566 (15)0.0439 (15)−0.0070 (13)0.0109 (12)0.0003 (12)
C20.0670 (19)0.0707 (18)0.0617 (17)−0.0002 (14)0.0157 (14)−0.0015 (14)
C30.081 (2)0.085 (2)0.080 (2)0.0071 (17)0.0337 (18)−0.0012 (18)
C40.119 (3)0.073 (2)0.078 (2)−0.003 (2)0.056 (2)−0.0027 (18)
C50.119 (3)0.113 (3)0.0486 (19)−0.020 (2)0.0181 (18)−0.0134 (17)
C60.0767 (19)0.098 (2)0.0513 (17)−0.0100 (16)0.0084 (14)−0.0062 (16)
C70.0529 (16)0.0653 (17)0.0448 (16)−0.0014 (13)0.0080 (13)0.0025 (12)
C80.0524 (15)0.0516 (14)0.0456 (15)−0.0068 (12)0.0121 (12)−0.0030 (12)
C90.0502 (15)0.0550 (16)0.0516 (16)−0.0112 (12)0.0041 (12)0.0032 (12)
C100.0705 (19)0.0703 (17)0.0454 (16)−0.0090 (15)0.0058 (13)0.0030 (13)
C110.0694 (18)0.0566 (16)0.0486 (16)−0.0128 (14)0.0196 (13)−0.0031 (12)
C120.0561 (17)0.0836 (18)0.0700 (18)0.0001 (14)0.0004 (13)0.0025 (15)
C130.100 (2)0.0828 (19)0.0562 (17)−0.0108 (17)0.0289 (15)−0.0094 (15)

Geometric parameters (Å, °)

O1—C71.292 (3)C4—C51.365 (4)
O1—H10.820C4—H40.930
O2—C71.218 (3)C5—C61.399 (4)
N1—C91.336 (3)C5—H50.930
N1—C81.350 (3)C6—H60.930
N2—C111.326 (3)C9—C101.385 (3)
N2—C81.364 (3)C9—C121.494 (3)
N3—C81.322 (3)C10—C111.376 (3)
N3—H3A0.860C10—H100.930
N3—H3B0.860C11—C131.507 (3)
C1—C61.372 (3)C12—H12A0.960
C1—C21.382 (3)C12—H12B0.960
C1—C71.489 (3)C12—H12C0.960
C2—C31.379 (4)C13—H13A0.960
C2—H20.930C13—H13B0.960
C3—C41.361 (4)C13—H13C0.960
C3—H30.930
C7—O1—H1109.5O1—C7—C1114.2 (2)
C9—N1—C8118.13 (19)N3—C8—N1118.5 (2)
C11—N2—C8116.7 (2)N3—C8—N2117.4 (2)
C8—N3—H3A120.0N1—C8—N2124.1 (2)
C8—N3—H3B120.0N1—C9—C10120.4 (2)
H3A—N3—H3B120.0N1—C9—C12116.9 (2)
C6—C1—C2119.6 (2)C10—C9—C12122.7 (2)
C6—C1—C7119.7 (2)C11—C10—C9118.4 (2)
C2—C1—C7120.7 (2)C11—C10—H10120.8
C3—C2—C1120.3 (3)C9—C10—H10120.8
C3—C2—H2119.9N2—C11—C10122.3 (2)
C1—C2—H2119.9N2—C11—C13116.1 (3)
C4—C3—C2120.1 (3)C10—C11—C13121.6 (3)
C4—C3—H3119.9C9—C12—H12A109.5
C2—C3—H3119.9C9—C12—H12B109.5
C3—C4—C5120.3 (3)H12A—C12—H12B109.5
C3—C4—H4119.8C9—C12—H12C109.5
C5—C4—H4119.8H12A—C12—H12C109.5
C4—C5—C6120.2 (3)H12B—C12—H12C109.5
C4—C5—H5119.9C11—C13—H13A109.5
C6—C5—H5119.9C11—C13—H13B109.5
C1—C6—C5119.4 (3)H13A—C13—H13B109.5
C1—C6—H6120.3C11—C13—H13C109.5
C5—C6—H6120.3H13A—C13—H13C109.5
O2—C7—O1123.4 (2)H13B—C13—H13C109.5
O2—C7—C1122.4 (2)
C6—C1—C2—C3−2.1 (4)C9—N1—C8—N3−178.84 (19)
C7—C1—C2—C3177.7 (2)C9—N1—C8—N21.2 (3)
C1—C2—C3—C4−0.3 (4)C11—N2—C8—N3178.20 (19)
C2—C3—C4—C51.8 (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—C53.0 (4)C8—N1—C9—C12179.75 (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—C11179.9 (2)
C6—C1—C7—O2−5.3 (4)C8—N2—C11—C101.4 (3)
C2—C1—C7—O2175.0 (2)C8—N2—C11—C13−178.11 (19)
C6—C1—C7—O1174.4 (2)C9—C10—C11—N2−0.3 (4)
C2—C1—C7—O1−5.3 (3)C9—C10—C11—C13179.1 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1···N10.821.822.606 (2)160
N3—H3A···O20.862.163.003 (3)168
N3—H3B···N2i0.862.253.098 (3)169

Symmetry codes: (i) −x, −y+2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BI2374).

References

  • Baker, B. R. & Santi, D. V. (1965). J. Pharm. Sci.54, 1252–1257. [PubMed]
  • Bruker (2001). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Chinnakali, K., Fun, H.-K., Goswami, S., Mahapatra, A. K. & Nigam, G. D. (1999). Acta Cryst. C55, 399–401.
  • Fun, H.-K., Goswami, S., Jana, S. & Chantrapromma, S. (2006). Acta Cryst. E62, o5332–o5334.
  • Hu, M.-L., Ye, M.-D., Zain, S. M. & Ng, S. W. (2002). Acta Cryst. E58, o1005–o1007.
  • Hunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). J. Biochem.187, 533–536. [PubMed]
  • Schwalbe, C. H. & Williams, G. J. B. (1982). Acta Cryst. B38, 1840–1843.
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