organic compounds
2-Amino-4,6-dimethylpyrimidin-1-ium 1-oxo-2,6,7-trioxa-1λ5-phosphabicyclo[2.2.2]octane-4-carboxylate
aCollege of Chemistry and Chemical Engineering, Xuchang University, Xuchang, Henan Province 461000, People's Republic of China
*Correspondence e-mail: hxfst@yahoo.com.cn
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). For related structures, see: Meng et al. (2009); Guo & Zang (2008); Thakur & Desiraju (2008); Wang et al. (2007).
Experimental
Crystal data
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Refinement
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Data collection: CrystalClear-SM Expert (Rigaku/MSC, 2009); cell CrystalClear-SM Expert; data reduction: CrystalClear-SM Expert; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku/MSC, 2009); software used to prepare material for publication: CrystalStructure.
Supporting information
10.1107/S1600536810019896/fj2308sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536810019896/fj2308Isup2.hkl
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.
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
using a riding model, with Uiso(H) = 1.2Ueq(C).Data collection: CrystalClear-SM Expert (Rigaku/MSC, 2009); cell
CrystalClear-SM Expert (Rigaku/MSC, 2009); data reduction: CrystalClear-SM Expert (Rigaku/MSC, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku/MSC, 2009); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2009).C6H10N3+·C5H6O6P− | F(000) = 664 |
Mr = 317.24 | Dx = 1.515 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71075 Å |
Hall symbol: -P 2ybc | Cell parameters from 5985 reflections |
a = 9.5080 (13) Å | θ = 2.2–36.3° |
b = 6.1870 (8) Å | µ = 0.23 mm−1 |
c = 23.974 (2) Å | T = 113 K |
β = 99.611 (5)° | Prism, colorless |
V = 1390.5 (3) Å3 | 0.24 × 0.22 × 0.14 mm |
Z = 4 |
Rigaku Saturn724 CCD diffractometer | 6532 independent reflections |
Radiation source: rotating anode | 4883 reflections with I > 2σ(I) |
Multilayer monochromator | Rint = 0.035 |
Detector resolution: 14.222 pixels mm-1 | θmax = 36.5°, θmin = 1.7° |
ω scans | h = −15→14 |
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009) | k = −10→10 |
Tmin = 0.947, Tmax = 0.969 | l = −36→39 |
23989 measured reflections |
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) = 0.107 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | w = 1/[σ2(Fo2) + (0.0615P)2] where P = (Fo2 + 2Fc2)/3 |
6532 reflections | (Δ/σ)max = 0.001 |
204 parameters | Δρmax = 0.54 e Å−3 |
0 restraints | Δρmin = −0.38 e Å−3 |
C6H10N3+·C5H6O6P− | V = 1390.5 (3) Å3 |
Mr = 317.24 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.5080 (13) Å | µ = 0.23 mm−1 |
b = 6.1870 (8) Å | T = 113 K |
c = 23.974 (2) Å | 0.24 × 0.22 × 0.14 mm |
β = 99.611 (5)° |
Rigaku Saturn724 CCD diffractometer | 6532 independent reflections |
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009) | 4883 reflections with I > 2σ(I) |
Tmin = 0.947, Tmax = 0.969 | Rint = 0.035 |
23989 measured reflections |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.107 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.01 | Δρmax = 0.54 e Å−3 |
6532 reflections | Δρmin = −0.38 e Å−3 |
204 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
P1 | 0.14090 (2) | 0.74372 (4) | 0.157866 (9) | 0.01584 (6) | |
O1 | 0.32415 (8) | 0.33013 (12) | 0.32735 (3) | 0.02813 (17) | |
O2 | 0.46621 (8) | 0.62093 (12) | 0.33500 (3) | 0.02544 (16) | |
O3 | 0.29862 (7) | 0.67033 (12) | 0.15596 (3) | 0.02097 (14) | |
O4 | 0.15812 (7) | 0.91396 (11) | 0.20765 (3) | 0.02023 (13) | |
O5 | 0.06923 (7) | 0.54214 (12) | 0.18168 (3) | 0.02421 (15) | |
O6 | 0.06557 (8) | 0.82445 (13) | 0.10419 (3) | 0.02619 (16) | |
N1 | 0.45629 (9) | 0.17785 (15) | 0.43177 (4) | 0.02312 (17) | |
N2 | 0.61028 (8) | 0.46847 (12) | 0.43466 (3) | 0.01702 (14) | |
N3 | 0.63811 (8) | 0.21010 (14) | 0.50821 (3) | 0.01949 (15) | |
C1 | 0.36366 (9) | 0.50774 (14) | 0.31115 (4) | 0.01674 (15) | |
C2 | 0.27993 (8) | 0.59650 (13) | 0.25498 (3) | 0.01332 (14) | |
C3 | 0.37600 (9) | 0.58891 (16) | 0.20974 (4) | 0.01990 (17) | |
H3A | 0.4621 | 0.6782 | 0.2219 | 0.024* | |
H3B | 0.4070 | 0.4383 | 0.2049 | 0.024* | |
C4 | 0.23414 (10) | 0.83103 (15) | 0.26188 (4) | 0.02018 (17) | |
H4A | 0.1711 | 0.8386 | 0.2908 | 0.024* | |
H4B | 0.3193 | 0.9214 | 0.2749 | 0.024* | |
C5 | 0.14789 (10) | 0.45860 (16) | 0.23533 (4) | 0.02254 (19) | |
H5A | 0.1769 | 0.3072 | 0.2302 | 0.027* | |
H5B | 0.0854 | 0.4605 | 0.2645 | 0.027* | |
C6 | 0.56840 (9) | 0.28450 (15) | 0.45830 (4) | 0.01698 (15) | |
C7 | 0.72567 (10) | 0.58213 (15) | 0.45997 (4) | 0.01896 (16) | |
C8 | 0.79892 (10) | 0.51036 (16) | 0.51086 (4) | 0.02109 (17) | |
H8 | 0.8792 | 0.5871 | 0.5300 | 0.025* | |
C9 | 0.75166 (10) | 0.32090 (16) | 0.53356 (4) | 0.01951 (17) | |
C10 | 0.76334 (12) | 0.77807 (16) | 0.42947 (5) | 0.0264 (2) | |
H10A | 0.8040 | 0.7342 | 0.3962 | 0.032* | |
H10B | 0.8334 | 0.8642 | 0.4547 | 0.032* | |
H10C | 0.6774 | 0.8647 | 0.4173 | 0.032* | |
C11 | 0.82793 (13) | 0.22887 (19) | 0.58813 (4) | 0.0295 (2) | |
H11A | 0.7581 | 0.1869 | 0.6120 | 0.035* | |
H11B | 0.8927 | 0.3379 | 0.6079 | 0.035* | |
H11C | 0.8828 | 0.1016 | 0.5803 | 0.035* | |
H1 | 0.4144 (16) | 0.231 (2) | 0.3998 (7) | 0.033 (4)* | |
H2 | 0.4287 (15) | 0.065 (2) | 0.4512 (6) | 0.039 (4)* | |
H3 | 0.5623 (16) | 0.511 (3) | 0.3965 (6) | 0.052 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
P1 | 0.01665 (11) | 0.01722 (10) | 0.01235 (10) | 0.00168 (8) | −0.00133 (7) | 0.00215 (7) |
O1 | 0.0314 (4) | 0.0245 (3) | 0.0237 (3) | −0.0074 (3) | −0.0093 (3) | 0.0116 (3) |
O2 | 0.0232 (3) | 0.0255 (3) | 0.0229 (3) | −0.0060 (3) | −0.0101 (3) | 0.0070 (3) |
O3 | 0.0215 (3) | 0.0277 (3) | 0.0142 (3) | 0.0069 (3) | 0.0043 (2) | 0.0034 (2) |
O4 | 0.0265 (3) | 0.0171 (3) | 0.0155 (3) | 0.0085 (2) | −0.0013 (2) | 0.0013 (2) |
O5 | 0.0211 (3) | 0.0261 (3) | 0.0213 (3) | −0.0082 (3) | −0.0087 (2) | 0.0080 (3) |
O6 | 0.0282 (4) | 0.0310 (4) | 0.0167 (3) | 0.0031 (3) | −0.0042 (3) | 0.0060 (3) |
N1 | 0.0190 (4) | 0.0305 (4) | 0.0177 (4) | −0.0039 (3) | −0.0029 (3) | 0.0094 (3) |
N2 | 0.0183 (3) | 0.0190 (3) | 0.0127 (3) | 0.0026 (3) | −0.0005 (2) | 0.0021 (2) |
N3 | 0.0171 (3) | 0.0277 (4) | 0.0127 (3) | 0.0015 (3) | −0.0002 (3) | 0.0054 (3) |
C1 | 0.0161 (4) | 0.0180 (4) | 0.0149 (4) | 0.0020 (3) | −0.0012 (3) | 0.0028 (3) |
C2 | 0.0126 (3) | 0.0130 (3) | 0.0134 (3) | 0.0002 (3) | −0.0007 (3) | 0.0011 (3) |
C3 | 0.0157 (4) | 0.0266 (4) | 0.0171 (4) | 0.0057 (3) | 0.0018 (3) | 0.0032 (3) |
C4 | 0.0240 (4) | 0.0190 (4) | 0.0151 (4) | 0.0073 (3) | −0.0040 (3) | −0.0018 (3) |
C5 | 0.0200 (4) | 0.0239 (4) | 0.0203 (4) | −0.0077 (3) | −0.0065 (3) | 0.0090 (3) |
C6 | 0.0151 (4) | 0.0231 (4) | 0.0125 (3) | 0.0028 (3) | 0.0016 (3) | 0.0034 (3) |
C7 | 0.0219 (4) | 0.0185 (4) | 0.0157 (4) | 0.0021 (3) | 0.0009 (3) | −0.0016 (3) |
C8 | 0.0231 (4) | 0.0231 (4) | 0.0154 (4) | 0.0002 (3) | −0.0018 (3) | −0.0015 (3) |
C9 | 0.0187 (4) | 0.0273 (4) | 0.0116 (3) | 0.0031 (3) | −0.0002 (3) | 0.0010 (3) |
C10 | 0.0334 (5) | 0.0182 (4) | 0.0247 (5) | −0.0026 (4) | −0.0033 (4) | 0.0018 (3) |
C11 | 0.0280 (5) | 0.0417 (6) | 0.0151 (4) | −0.0023 (4) | −0.0070 (4) | 0.0075 (4) |
P1—O6 | 1.4529 (7) | C2—C3 | 1.5310 (12) |
P1—O5 | 1.5734 (7) | C2—C4 | 1.5318 (12) |
P1—O3 | 1.5748 (7) | C3—H3A | 0.9900 |
P1—O4 | 1.5798 (7) | C3—H3B | 0.9900 |
O1—C1 | 1.2443 (11) | C4—H4A | 0.9900 |
O2—C1 | 1.2578 (11) | C4—H4B | 0.9900 |
O3—C3 | 1.4631 (11) | C5—H5A | 0.9900 |
O4—C4 | 1.4703 (10) | C5—H5B | 0.9900 |
O5—C5 | 1.4694 (11) | C7—C8 | 1.3737 (12) |
N1—C6 | 1.3227 (12) | C7—C10 | 1.4901 (14) |
N1—H1 | 0.866 (15) | C8—C9 | 1.3977 (14) |
N1—H2 | 0.900 (14) | C8—H8 | 0.9500 |
N2—C7 | 1.3580 (12) | C9—C11 | 1.4983 (13) |
N2—C6 | 1.3603 (12) | C10—H10A | 0.9800 |
N2—H3 | 0.988 (15) | C10—H10B | 0.9800 |
N3—C9 | 1.3363 (12) | C10—H10C | 0.9800 |
N3—C6 | 1.3484 (11) | C11—H11A | 0.9800 |
C1—C2 | 1.5460 (11) | C11—H11B | 0.9800 |
C2—C5 | 1.5260 (12) | C11—H11C | 0.9800 |
O6—P1—O5 | 114.50 (4) | O4—C4—H4B | 109.7 |
O6—P1—O3 | 113.86 (4) | C2—C4—H4B | 109.7 |
O5—P1—O3 | 104.73 (4) | H4A—C4—H4B | 108.2 |
O6—P1—O4 | 114.43 (4) | O5—C5—C2 | 110.24 (7) |
O5—P1—O4 | 104.52 (4) | O5—C5—H5A | 109.6 |
O3—P1—O4 | 103.59 (4) | C2—C5—H5A | 109.6 |
C3—O3—P1 | 114.52 (5) | O5—C5—H5B | 109.6 |
C4—O4—P1 | 114.14 (5) | C2—C5—H5B | 109.6 |
C5—O5—P1 | 114.11 (5) | H5A—C5—H5B | 108.1 |
C6—N1—H1 | 116.8 (10) | N1—C6—N3 | 119.58 (8) |
C6—N1—H2 | 114.7 (9) | N1—C6—N2 | 119.05 (8) |
H1—N1—H2 | 128.2 (13) | N3—C6—N2 | 121.37 (8) |
C7—N2—C6 | 121.20 (7) | N2—C7—C8 | 118.78 (8) |
C7—N2—H3 | 119.3 (10) | N2—C7—C10 | 116.39 (8) |
C6—N2—H3 | 119.1 (10) | C8—C7—C10 | 124.83 (9) |
C9—N3—C6 | 117.95 (8) | C7—C8—C9 | 117.94 (8) |
O1—C1—O2 | 126.96 (8) | C7—C8—H8 | 121.0 |
O1—C1—C2 | 116.56 (7) | C9—C8—H8 | 121.0 |
O2—C1—C2 | 116.46 (7) | N3—C9—C8 | 122.75 (8) |
C5—C2—C3 | 108.75 (7) | N3—C9—C11 | 116.02 (9) |
C5—C2—C4 | 109.20 (7) | C8—C9—C11 | 121.23 (9) |
C3—C2—C4 | 108.63 (7) | C7—C10—H10A | 109.5 |
C5—C2—C1 | 110.36 (7) | C7—C10—H10B | 109.5 |
C3—C2—C1 | 108.95 (7) | H10A—C10—H10B | 109.5 |
C4—C2—C1 | 110.90 (7) | C7—C10—H10C | 109.5 |
O3—C3—C2 | 110.00 (7) | H10A—C10—H10C | 109.5 |
O3—C3—H3A | 109.7 | H10B—C10—H10C | 109.5 |
C2—C3—H3A | 109.7 | C9—C11—H11A | 109.5 |
O3—C3—H3B | 109.7 | C9—C11—H11B | 109.5 |
C2—C3—H3B | 109.7 | H11A—C11—H11B | 109.5 |
H3A—C3—H3B | 108.2 | C9—C11—H11C | 109.5 |
O4—C4—C2 | 109.99 (7) | H11A—C11—H11C | 109.5 |
O4—C4—H4A | 109.7 | H11B—C11—H11C | 109.5 |
C2—C4—H4A | 109.7 | ||
O6—P1—O3—C3 | 179.91 (6) | C5—C2—C4—O4 | −59.68 (9) |
O5—P1—O3—C3 | −54.29 (7) | C3—C2—C4—O4 | 58.79 (9) |
O4—P1—O3—C3 | 55.00 (7) | C1—C2—C4—O4 | 178.50 (7) |
O6—P1—O4—C4 | 179.86 (6) | P1—O5—C5—C2 | 1.39 (11) |
O5—P1—O4—C4 | 53.84 (7) | C3—C2—C5—O5 | −60.03 (10) |
O3—P1—O4—C4 | −55.60 (7) | C4—C2—C5—O5 | 58.35 (10) |
O6—P1—O5—C5 | 178.68 (7) | C1—C2—C5—O5 | −179.49 (7) |
O3—P1—O5—C5 | 53.28 (8) | C9—N3—C6—N1 | 179.42 (9) |
O4—P1—O5—C5 | −55.34 (8) | C9—N3—C6—N2 | −1.06 (13) |
O1—C1—C2—C5 | 8.87 (11) | C7—N2—C6—N1 | −179.24 (9) |
O2—C1—C2—C5 | −172.46 (9) | C7—N2—C6—N3 | 1.24 (13) |
O1—C1—C2—C3 | −110.46 (9) | C6—N2—C7—C8 | −1.19 (13) |
O2—C1—C2—C3 | 68.20 (10) | C6—N2—C7—C10 | 178.60 (8) |
O1—C1—C2—C4 | 130.02 (9) | N2—C7—C8—C9 | 0.99 (13) |
O2—C1—C2—C4 | −51.31 (11) | C10—C7—C8—C9 | −178.78 (9) |
P1—O3—C3—C2 | 0.12 (9) | C6—N3—C9—C8 | 0.90 (14) |
C5—C2—C3—O3 | 59.14 (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—O3 | 179.47 (7) | C7—C8—C9—C11 | 178.42 (9) |
P1—O4—C4—C2 | 1.10 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1 | 0.866 (15) | 1.907 (15) | 2.7719 (11) | 176.4 (14) |
N1—H2···N3i | 0.900 (14) | 2.113 (15) | 3.0114 (12) | 176.3 (12) |
N2—H3···O2 | 0.988 (15) | 1.738 (16) | 2.7170 (10) | 170.4 (15) |
Symmetry code: (i) −x+1, −y, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C6H10N3+·C5H6O6P− |
Mr | 317.24 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 113 |
a, b, c (Å) | 9.5080 (13), 6.1870 (8), 23.974 (2) |
β (°) | 99.611 (5) |
V (Å3) | 1390.5 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.23 |
Crystal size (mm) | 0.24 × 0.22 × 0.14 |
Data collection | |
Diffractometer | Rigaku Saturn724 CCD diffractometer |
Absorption correction | Multi-scan (CrystalClear; Rigaku/MSC, 2009) |
Tmin, Tmax | 0.947, 0.969 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23989, 6532, 4883 |
Rint | 0.035 |
(sin θ/λ)max (Å−1) | 0.836 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.107, 1.01 |
No. of reflections | 6532 |
No. of parameters | 204 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.54, −0.38 |
Computer programs: CrystalClear-SM Expert (Rigaku/MSC, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), CrystalStructure (Rigaku/MSC, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1 | 0.866 (15) | 1.907 (15) | 2.7719 (11) | 176.4 (14) |
N1—H2···N3i | 0.900 (14) | 2.113 (15) | 3.0114 (12) | 176.3 (12) |
N2—H3···O2 | 0.988 (15) | 1.738 (16) | 2.7170 (10) | 170.4 (15) |
Symmetry code: (i) −x+1, −y, −z+1. |
Acknowledgements
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).
References
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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).