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Acta Crystallogr Sect E Struct Rep Online. 2010 July 1; 66(Pt 7): o1528.
Published online 2010 June 5. doi:  10.1107/S1600536810019896
PMCID: PMC3006899

2-Amino-4,6-dimethyl­pyrimidin-1-ium 1-oxo-2,6,7-trioxa-1λ5-phosphabicyclo­[2.2.2]octane-4-carboxyl­ate

Abstract

In the title compound, C6H10N3 +·C5H6O6P, the cation and anion are linked by pairs of N—H(...)O hydrogen bonds. There are additional inter­molecular N—H(...)N hydrogen bonds, which generate centrosymmetric tetramers of two cations and two anions.

Related literature

For the applications of caged bicyclic phosphates, see: Li et al. (2000 [triangle]). For related structures, see: Meng et al. (2009 [triangle]); Guo & Zang (2008 [triangle]); Thakur & Desiraju (2008 [triangle]); Wang et al. (2007 [triangle]).

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Object name is e-66-o1528-scheme1.jpg

Experimental

Crystal data

  • C6H10N3 +·C5H6O6P
  • M r = 317.24
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1528-efi1.jpg
  • a = 9.5080 (13) Å
  • b = 6.1870 (8) Å
  • c = 23.974 (2) Å
  • β = 99.611 (5)°
  • V = 1390.5 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.23 mm−1
  • T = 113 K
  • 0.24 × 0.22 × 0.14 mm

Data collection

  • Rigaku Saturn724 CCD diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009 [triangle]) T min = 0.947, T max = 0.969
  • 23989 measured reflections
  • 6532 independent reflections
  • 4883 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.107
  • S = 1.01
  • 6532 reflections
  • 204 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.54 e Å−3
  • Δρmin = −0.38 e Å−3

Data collection: CrystalClear-SM Expert (Rigaku/MSC, 2009 [triangle]); cell refinement: CrystalClear-SM Expert; data reduction: CrystalClear-SM Expert; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: CrystalStructure (Rigaku/MSC, 2009 [triangle]); software used to prepare material for publication: CrystalStructure.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810019896/fj2308sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810019896/fj2308Isup2.hkl

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

Acknowledgments

This work was supported by the Natural Science Foundation of Henan Province, China (grant No. 082300420110) and the Natural Science Foundation of Henan Province Education Department, China (grant No. 2007150036).

supplementary crystallographic information

Comment

Caged bicyclic phosphates are widely used as flame retardants or pesticides (Li et al. 2000). It can also serve as host–guest systems and have been studied in the context of hydrogen-bond patterns (Guo & Zang, 2008; Wang et al., 2007). Aminopyrimidine derivatives are biologically important compounds as they occur in nature as components of nucleic acids (Meng et al., 2009). The crystal structures of aminopyrimidine carboxylates have been reported (Thakur et al., 2008). We report here the crystal structure of a new bicyclic phosphate cage compound.

In the title compound, [C6H10N3]+ [C5H6O6P]-, The cation and anion in the asymmetric unit are linked by N—H···O hydrogen bonds. There is also addition intermolecular N—H···N hydrogen bonds. (Fig. 2).

Experimental

The title compound was obtained by reaction of 1-oxo-2,6,7-trioxa-1-phosphabicyclo[2.2.2]octane-4-carboxylic acid (0.39 g, 0.2 mmol) and 2-amino-4,6-dimethylpyrimidine(0.25 g, 0.2 mmol) in refluxing acetone (50 ml). The solvent was evaporated in vacuo. The title compound was recrystallized from ethanol and single crystals of (I) were obtained by slow evaporation.

Refinement

All H atoms were placed in calculated positions, with C—H = 0.98 Å or 0.99 Å, and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The asymmetric unit of the title compound, (I), with displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
The packing diagram of the title compound. Intermolecular hydrogen bonds are shown as dashed line.

Crystal data

C6H10N3+·C5H6O6PF(000) = 664
Mr = 317.24Dx = 1.515 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2ybcCell parameters from 5985 reflections
a = 9.5080 (13) Åθ = 2.2–36.3°
b = 6.1870 (8) ŵ = 0.23 mm1
c = 23.974 (2) ÅT = 113 K
β = 99.611 (5)°Prism, colorless
V = 1390.5 (3) Å30.24 × 0.22 × 0.14 mm
Z = 4

Data collection

Rigaku Saturn724 CCD diffractometer6532 independent reflections
Radiation source: rotating anode4883 reflections with I > 2σ(I)
multilayerRint = 0.035
Detector resolution: 14.222 pixels mm-1θmax = 36.5°, θmin = 1.7°
ω scansh = −15→14
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009)k = −10→10
Tmin = 0.947, Tmax = 0.969l = −36→39
23989 measured reflections

Refinement

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) = 0.107H atoms treated by a mixture of independent and constrained refinement
S = 1.01w = 1/[σ2(Fo2) + (0.0615P)2] where P = (Fo2 + 2Fc2)/3
6532 reflections(Δ/σ)max = 0.001
204 parametersΔρmax = 0.54 e Å3
0 restraintsΔρmin = −0.38 e Å3

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
P10.14090 (2)0.74372 (4)0.157866 (9)0.01584 (6)
O10.32415 (8)0.33013 (12)0.32735 (3)0.02813 (17)
O20.46621 (8)0.62093 (12)0.33500 (3)0.02544 (16)
O30.29862 (7)0.67033 (12)0.15596 (3)0.02097 (14)
O40.15812 (7)0.91396 (11)0.20765 (3)0.02023 (13)
O50.06923 (7)0.54214 (12)0.18168 (3)0.02421 (15)
O60.06557 (8)0.82445 (13)0.10419 (3)0.02619 (16)
N10.45629 (9)0.17785 (15)0.43177 (4)0.02312 (17)
N20.61028 (8)0.46847 (12)0.43466 (3)0.01702 (14)
N30.63811 (8)0.21010 (14)0.50821 (3)0.01949 (15)
C10.36366 (9)0.50774 (14)0.31115 (4)0.01674 (15)
C20.27993 (8)0.59650 (13)0.25498 (3)0.01332 (14)
C30.37600 (9)0.58891 (16)0.20974 (4)0.01990 (17)
H3A0.46210.67820.22190.024*
H3B0.40700.43830.20490.024*
C40.23414 (10)0.83103 (15)0.26188 (4)0.02018 (17)
H4A0.17110.83860.29080.024*
H4B0.31930.92140.27490.024*
C50.14789 (10)0.45860 (16)0.23533 (4)0.02254 (19)
H5A0.17690.30720.23020.027*
H5B0.08540.46050.26450.027*
C60.56840 (9)0.28450 (15)0.45830 (4)0.01698 (15)
C70.72567 (10)0.58213 (15)0.45997 (4)0.01896 (16)
C80.79892 (10)0.51036 (16)0.51086 (4)0.02109 (17)
H80.87920.58710.53000.025*
C90.75166 (10)0.32090 (16)0.53356 (4)0.01951 (17)
C100.76334 (12)0.77807 (16)0.42947 (5)0.0264 (2)
H10A0.80400.73420.39620.032*
H10B0.83340.86420.45470.032*
H10C0.67740.86470.41730.032*
C110.82793 (13)0.22887 (19)0.58813 (4)0.0295 (2)
H11A0.75810.18690.61200.035*
H11B0.89270.33790.60790.035*
H11C0.88280.10160.58030.035*
H10.4144 (16)0.231 (2)0.3998 (7)0.033 (4)*
H20.4287 (15)0.065 (2)0.4512 (6)0.039 (4)*
H30.5623 (16)0.511 (3)0.3965 (6)0.052 (4)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
P10.01665 (11)0.01722 (10)0.01235 (10)0.00168 (8)−0.00133 (7)0.00215 (7)
O10.0314 (4)0.0245 (3)0.0237 (3)−0.0074 (3)−0.0093 (3)0.0116 (3)
O20.0232 (3)0.0255 (3)0.0229 (3)−0.0060 (3)−0.0101 (3)0.0070 (3)
O30.0215 (3)0.0277 (3)0.0142 (3)0.0069 (3)0.0043 (2)0.0034 (2)
O40.0265 (3)0.0171 (3)0.0155 (3)0.0085 (2)−0.0013 (2)0.0013 (2)
O50.0211 (3)0.0261 (3)0.0213 (3)−0.0082 (3)−0.0087 (2)0.0080 (3)
O60.0282 (4)0.0310 (4)0.0167 (3)0.0031 (3)−0.0042 (3)0.0060 (3)
N10.0190 (4)0.0305 (4)0.0177 (4)−0.0039 (3)−0.0029 (3)0.0094 (3)
N20.0183 (3)0.0190 (3)0.0127 (3)0.0026 (3)−0.0005 (2)0.0021 (2)
N30.0171 (3)0.0277 (4)0.0127 (3)0.0015 (3)−0.0002 (3)0.0054 (3)
C10.0161 (4)0.0180 (4)0.0149 (4)0.0020 (3)−0.0012 (3)0.0028 (3)
C20.0126 (3)0.0130 (3)0.0134 (3)0.0002 (3)−0.0007 (3)0.0011 (3)
C30.0157 (4)0.0266 (4)0.0171 (4)0.0057 (3)0.0018 (3)0.0032 (3)
C40.0240 (4)0.0190 (4)0.0151 (4)0.0073 (3)−0.0040 (3)−0.0018 (3)
C50.0200 (4)0.0239 (4)0.0203 (4)−0.0077 (3)−0.0065 (3)0.0090 (3)
C60.0151 (4)0.0231 (4)0.0125 (3)0.0028 (3)0.0016 (3)0.0034 (3)
C70.0219 (4)0.0185 (4)0.0157 (4)0.0021 (3)0.0009 (3)−0.0016 (3)
C80.0231 (4)0.0231 (4)0.0154 (4)0.0002 (3)−0.0018 (3)−0.0015 (3)
C90.0187 (4)0.0273 (4)0.0116 (3)0.0031 (3)−0.0002 (3)0.0010 (3)
C100.0334 (5)0.0182 (4)0.0247 (5)−0.0026 (4)−0.0033 (4)0.0018 (3)
C110.0280 (5)0.0417 (6)0.0151 (4)−0.0023 (4)−0.0070 (4)0.0075 (4)

Geometric parameters (Å, °)

P1—O61.4529 (7)C2—C31.5310 (12)
P1—O51.5734 (7)C2—C41.5318 (12)
P1—O31.5748 (7)C3—H3A0.9900
P1—O41.5798 (7)C3—H3B0.9900
O1—C11.2443 (11)C4—H4A0.9900
O2—C11.2578 (11)C4—H4B0.9900
O3—C31.4631 (11)C5—H5A0.9900
O4—C41.4703 (10)C5—H5B0.9900
O5—C51.4694 (11)C7—C81.3737 (12)
N1—C61.3227 (12)C7—C101.4901 (14)
N1—H10.866 (15)C8—C91.3977 (14)
N1—H20.900 (14)C8—H80.9500
N2—C71.3580 (12)C9—C111.4983 (13)
N2—C61.3603 (12)C10—H10A0.9800
N2—H30.988 (15)C10—H10B0.9800
N3—C91.3363 (12)C10—H10C0.9800
N3—C61.3484 (11)C11—H11A0.9800
C1—C21.5460 (11)C11—H11B0.9800
C2—C51.5260 (12)C11—H11C0.9800
O6—P1—O5114.50 (4)O4—C4—H4B109.7
O6—P1—O3113.86 (4)C2—C4—H4B109.7
O5—P1—O3104.73 (4)H4A—C4—H4B108.2
O6—P1—O4114.43 (4)O5—C5—C2110.24 (7)
O5—P1—O4104.52 (4)O5—C5—H5A109.6
O3—P1—O4103.59 (4)C2—C5—H5A109.6
C3—O3—P1114.52 (5)O5—C5—H5B109.6
C4—O4—P1114.14 (5)C2—C5—H5B109.6
C5—O5—P1114.11 (5)H5A—C5—H5B108.1
C6—N1—H1116.8 (10)N1—C6—N3119.58 (8)
C6—N1—H2114.7 (9)N1—C6—N2119.05 (8)
H1—N1—H2128.2 (13)N3—C6—N2121.37 (8)
C7—N2—C6121.20 (7)N2—C7—C8118.78 (8)
C7—N2—H3119.3 (10)N2—C7—C10116.39 (8)
C6—N2—H3119.1 (10)C8—C7—C10124.83 (9)
C9—N3—C6117.95 (8)C7—C8—C9117.94 (8)
O1—C1—O2126.96 (8)C7—C8—H8121.0
O1—C1—C2116.56 (7)C9—C8—H8121.0
O2—C1—C2116.46 (7)N3—C9—C8122.75 (8)
C5—C2—C3108.75 (7)N3—C9—C11116.02 (9)
C5—C2—C4109.20 (7)C8—C9—C11121.23 (9)
C3—C2—C4108.63 (7)C7—C10—H10A109.5
C5—C2—C1110.36 (7)C7—C10—H10B109.5
C3—C2—C1108.95 (7)H10A—C10—H10B109.5
C4—C2—C1110.90 (7)C7—C10—H10C109.5
O3—C3—C2110.00 (7)H10A—C10—H10C109.5
O3—C3—H3A109.7H10B—C10—H10C109.5
C2—C3—H3A109.7C9—C11—H11A109.5
O3—C3—H3B109.7C9—C11—H11B109.5
C2—C3—H3B109.7H11A—C11—H11B109.5
H3A—C3—H3B108.2C9—C11—H11C109.5
O4—C4—C2109.99 (7)H11A—C11—H11C109.5
O4—C4—H4A109.7H11B—C11—H11C109.5
C2—C4—H4A109.7
O6—P1—O3—C3179.91 (6)C5—C2—C4—O4−59.68 (9)
O5—P1—O3—C3−54.29 (7)C3—C2—C4—O458.79 (9)
O4—P1—O3—C355.00 (7)C1—C2—C4—O4178.50 (7)
O6—P1—O4—C4179.86 (6)P1—O5—C5—C21.39 (11)
O5—P1—O4—C453.84 (7)C3—C2—C5—O5−60.03 (10)
O3—P1—O4—C4−55.60 (7)C4—C2—C5—O558.35 (10)
O6—P1—O5—C5178.68 (7)C1—C2—C5—O5−179.49 (7)
O3—P1—O5—C553.28 (8)C9—N3—C6—N1179.42 (9)
O4—P1—O5—C5−55.34 (8)C9—N3—C6—N2−1.06 (13)
O1—C1—C2—C58.87 (11)C7—N2—C6—N1−179.24 (9)
O2—C1—C2—C5−172.46 (9)C7—N2—C6—N31.24 (13)
O1—C1—C2—C3−110.46 (9)C6—N2—C7—C8−1.19 (13)
O2—C1—C2—C368.20 (10)C6—N2—C7—C10178.60 (8)
O1—C1—C2—C4130.02 (9)N2—C7—C8—C90.99 (13)
O2—C1—C2—C4−51.31 (11)C10—C7—C8—C9−178.78 (9)
P1—O3—C3—C20.12 (9)C6—N3—C9—C80.90 (14)
C5—C2—C3—O359.14 (9)C6—N3—C9—C11−178.44 (9)
C4—C2—C3—O3−59.61 (9)C7—C8—C9—N3−0.89 (14)
C1—C2—C3—O3179.47 (7)C7—C8—C9—C11178.42 (9)
P1—O4—C4—C21.10 (9)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O10.866 (15)1.907 (15)2.7719 (11)176.4 (14)
N1—H2···N3i0.900 (14)2.113 (15)3.0114 (12)176.3 (12)
N2—H3···O20.988 (15)1.738 (16)2.7170 (10)170.4 (15)

Symmetry codes: (i) −x+1, −y, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FJ2308).

References

  • Guo, M.-L. & Zang, H.-J. (2008). Acta Cryst. C64, m173–m175. [PubMed]
  • Li, X., Ou, Y.-X., Zhang, Y.-H. & Lian, D.-J. (2000). Chin. Chem. Lett.11, 887–890.
  • Meng, A.-L., Huang, J.-E., Zheng, B. & Li, Z.-J. (2009). Acta Cryst. E65, o1595. [PMC free article] [PubMed]
  • Rigaku/MSC (2009). CrystalClear-SM Expert and CrystalStructure Rigaku/MSC, The Woodlands, Texas, USA.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Thakur, T. S. & Desiraju, G. R. (2008). Cryst. Growth Des.8, 4031–4044.
  • Wang, Z., Zang, H.-J. & Guo, M.-L. (2007). Acta Cryst. E63, o3418.

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