 | Acta Crystallographica Section E Acta Crystallographica Section E CRYSTALLOGRAPHIC COMMUNICATIONS |
journal menu
organic compounds
| CRYSTALLOGRAPHIC COMMUNICATIONS |
access2,4-Dioxo-1-(prop-2-ynyl)-1,2,3,4-tetrahydropyrimidine-5-carbaldehyde
aSchool of Chemistry and Environmental Science, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang, Henan 453007, People's Republic of China
*Correspondence e-mail: xyzh518@sohu.com
In the of the title compound, C8H6N2O3, the molecules are linked by a pairs of intermolecular N—H⋯O hydrogen bonds, forming inversion dimers. The aldehyde group is in the same plane as the pyrimidine ring [with a maximum deviation of 0.083 (2) Å for the O atom), and the linear propargyl group [C—C—C = 178.99 (19)°] makes a dihedral angle of 74.36 (13)° with the ring.
Related literature
For applications of acyclic pyrimidine see: De Clercq (2009![[De Clercq, E. (2009). Rev. Med. Virol. 19, 287-299.]](../../../../../../logos/arrows/e_arr.gif "De Clercq, E. (2009). Rev. Med. Virol. 19, 287-299.")
, 2010a,b); Fan et al. (2011).
![[Scheme 1]](is2760scheme1.gif)
Experimental
Crystal data
|
Refinement
|
| |||||||||||||||||
Data collection: SMART (Bruker, 1997); cell 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: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.
Supporting information
contains datablocks I, global. DOI: 10.1107/S1600536811032272/is2760sup1.cif
Structure factors: contains datablock I. DOI: 10.1107/S1600536811032272/is2760Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536811032272/is2760Isup3.cml
To a solution of K2S2O8 (16.5 mmol) and CuSO4 (3.2 mmol) in 30 ml H2O was added a CH3CN solution (25 ml) of 5-methyl-1-(prop-2-ynyl)pyrimidine-2,4(1H,3H)-dione (8 mmol) and 2,6-lutidine (3.2 ml). The mixture was stirred at 60 °C for 5 h. Upon completion, the mixture was concentrated to half of the initial volume, and the remaining solution was extracted with EtOAc. The organic layer was washed with H2O. The aqueous layers were combined and back-extracted with CHCl3. Then the organic layers were combined, dried over Na2SO4, and then concentrated. The residue was purified through silica gel with a mixture of methylene chloride-methanol (60:1, v/v) as to give 1,2,3,4-tetrahydro-2,4-dioxo-1-(prop-2-ynyl)- pyrimidine-5-carbaldehyde. Single crystals of the title compound were obtained by slow evaporation of the solvent from a methylene chloride-methanol (60:1 v/v) solution.
H atoms were positioned geometrically and refined using riding model, with C—H = 0.93 or 0.97 Å, and N—H = 0.86 Å, and with Uiso(H) = 1.2Ueq(C, N).
Data collection: SMART (Bruker, 1997); cell 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: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
![[Figure 1]](./is2760fig1thm.gif) | Fig. 1. Molecular structure of the title compound, with displacement ellipsoids drawn at the 30% probability level. |
![[Figure 2]](./is2760fig2thm.gif) | Fig. 2. Crystal packing of the title compound with view along the a axis. Intermolecular N—H···O hydrogen bonds are shown as dashed lines. |
| C8H6N2O3 | F(000) = 368 |
| Mr = 178.15 | Dx = 1.451 Mg m−3 |
| Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
| Hall symbol: -P 2yn | Cell parameters from 2188 reflections |
| a = 5.1756 (7) Å | θ = 2.6–26.7° |
| b = 8.4877 (12) Å | µ = 0.11 mm−1 |
| c = 18.565 (3) Å | T = 296 K |
| β = 90.611 (2)° | Block, colourless |
| V = 815.5 (2) Å3 | 0.41 × 0.37 × 0.25 mm |
| Z = 4 |
| Bruker SMART CCD area-detector diffractometer | 1520 independent reflections |
| Radiation source: fine-focus sealed tube | 1261 reflections with I > 2σ(I) |
| Graphite monochromator | Rint = 0.020 |
| phi and ω scans | θmax = 25.5°, θmin = 2.6° |
| Absorption correction: multi-scan (SADABS; Bruker, 1997) | h = −6→6 |
| Tmin = 0.955, Tmax = 0.972 | k = −10→10 |
| 5826 measured reflections | l = −22→21 |
| 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)] = 0.040 | Hydrogen site location: inferred from neighbouring sites |
| wR(F2) = 0.123 | H-atom parameters constrained |
| S = 1.08 | w = 1/[σ2(Fo2) + (0.0694P)2 + 0.1695P] where P = (Fo2 + 2Fc2)/3 |
| 1520 reflections | (Δ/σ)max < 0.001 |
| 118 parameters | Δρmax = 0.14 e Å−3 |
| 0 restraints | Δρmin = −0.23 e Å−3 |
| C8H6N2O3 | V = 815.5 (2) Å3 |
| Mr = 178.15 | Z = 4 |
| Monoclinic, P21/n | Mo Kα radiation |
| a = 5.1756 (7) Å | µ = 0.11 mm−1 |
| b = 8.4877 (12) Å | T = 296 K |
| c = 18.565 (3) Å | 0.41 × 0.37 × 0.25 mm |
| β = 90.611 (2)° |
| Bruker SMART CCD area-detector diffractometer | 1520 independent reflections |
| Absorption correction: multi-scan (SADABS; Bruker, 1997) | 1261 reflections with I > 2σ(I) |
| Tmin = 0.955, Tmax = 0.972 | Rint = 0.020 |
| 5826 measured reflections |
| R[F2 > 2σ(F2)] = 0.040 | 0 restraints |
| wR(F2) = 0.123 | H-atom parameters constrained |
| S = 1.08 | Δρmax = 0.14 e Å−3 |
| 1520 reflections | Δρmin = −0.23 e Å−3 |
| 118 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 | ||
| C1 | 0.7042 (3) | 0.8893 (2) | 0.44458 (8) | 0.0374 (4) | |
| C2 | 0.5046 (3) | 0.8128 (2) | 0.40196 (8) | 0.0376 (4) | |
| C3 | 0.4934 (3) | 0.84333 (19) | 0.33033 (8) | 0.0372 (4) | |
| H3 | 0.3631 | 0.7959 | 0.3031 | 0.045* | |
| C4 | 0.8652 (3) | 1.01190 (19) | 0.33360 (8) | 0.0368 (4) | |
| C5 | 0.3180 (4) | 0.7061 (2) | 0.43522 (10) | 0.0510 (5) | |
| H5 | 0.3435 | 0.6787 | 0.4833 | 0.061* | |
| C6 | 0.6377 (3) | 0.9724 (2) | 0.21870 (8) | 0.0432 (4) | |
| H6A | 0.4685 | 0.9390 | 0.2017 | 0.052* | |
| H6B | 0.6512 | 1.0851 | 0.2110 | 0.052* | |
| C7 | 0.8363 (4) | 0.8923 (2) | 0.17686 (9) | 0.0464 (5) | |
| C8 | 0.9931 (4) | 0.8282 (3) | 0.14242 (11) | 0.0612 (6) | |
| H8 | 1.1175 | 0.7773 | 0.1151 | 0.073* | |
| N1 | 0.6616 (2) | 0.93903 (17) | 0.29646 (7) | 0.0370 (4) | |
| N2 | 0.8664 (3) | 0.98582 (16) | 0.40649 (7) | 0.0398 (4) | |
| H2 | 0.9818 | 1.0356 | 0.4312 | 0.048* | |
| O1 | 0.7344 (2) | 0.87340 (16) | 0.51012 (6) | 0.0490 (4) | |
| O2 | 1.0262 (2) | 1.09061 (15) | 0.30334 (6) | 0.0472 (4) | |
| O3 | 0.1324 (3) | 0.65141 (19) | 0.40376 (8) | 0.0685 (5) |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| C1 | 0.0360 (8) | 0.0454 (9) | 0.0308 (8) | 0.0027 (7) | −0.0031 (6) | −0.0023 (7) |
| C2 | 0.0353 (8) | 0.0442 (9) | 0.0333 (8) | 0.0011 (7) | −0.0018 (6) | −0.0066 (7) |
| C3 | 0.0326 (8) | 0.0439 (9) | 0.0350 (8) | 0.0021 (7) | −0.0041 (6) | −0.0089 (7) |
| C4 | 0.0365 (8) | 0.0414 (9) | 0.0323 (8) | 0.0027 (7) | −0.0036 (7) | −0.0023 (7) |
| C5 | 0.0503 (10) | 0.0600 (11) | 0.0427 (10) | −0.0103 (9) | −0.0011 (8) | −0.0042 (8) |
| C6 | 0.0451 (10) | 0.0551 (10) | 0.0294 (8) | 0.0008 (8) | −0.0085 (7) | 0.0013 (7) |
| C7 | 0.0533 (11) | 0.0548 (11) | 0.0311 (8) | −0.0078 (9) | −0.0027 (8) | −0.0019 (8) |
| C8 | 0.0625 (13) | 0.0738 (14) | 0.0474 (11) | −0.0033 (11) | 0.0076 (10) | −0.0125 (10) |
| N1 | 0.0366 (7) | 0.0471 (8) | 0.0272 (7) | 0.0016 (6) | −0.0044 (5) | −0.0029 (6) |
| N2 | 0.0402 (8) | 0.0494 (8) | 0.0297 (7) | −0.0079 (6) | −0.0084 (5) | −0.0014 (6) |
| O1 | 0.0500 (7) | 0.0683 (8) | 0.0285 (6) | −0.0120 (6) | −0.0057 (5) | 0.0017 (5) |
| O2 | 0.0470 (7) | 0.0566 (8) | 0.0378 (7) | −0.0094 (6) | −0.0019 (5) | 0.0039 (5) |
| O3 | 0.0592 (9) | 0.0805 (11) | 0.0658 (10) | −0.0216 (7) | 0.0004 (7) | −0.0139 (8) |
| C1—O1 | 1.2325 (19) | C5—O3 | 1.211 (2) |
| C1—N2 | 1.374 (2) | C5—H5 | 0.9300 |
| C1—C2 | 1.449 (2) | C6—C7 | 1.462 (3) |
| C2—C3 | 1.356 (2) | C6—N1 | 1.475 (2) |
| C2—C5 | 1.465 (3) | C6—H6A | 0.9700 |
| C3—N1 | 1.351 (2) | C6—H6B | 0.9700 |
| C3—H3 | 0.9300 | C7—C8 | 1.173 (3) |
| C4—O2 | 1.211 (2) | C8—H8 | 0.9300 |
| C4—N2 | 1.371 (2) | N2—H2 | 0.8600 |
| C4—N1 | 1.397 (2) | ||
| O1—C1—N2 | 120.11 (14) | C7—C6—N1 | 112.24 (14) |
| O1—C1—C2 | 124.91 (15) | C7—C6—H6A | 109.2 |
| N2—C1—C2 | 114.98 (13) | N1—C6—H6A | 109.2 |
| C3—C2—C1 | 118.22 (15) | C7—C6—H6B | 109.2 |
| C3—C2—C5 | 120.68 (15) | N1—C6—H6B | 109.2 |
| C1—C2—C5 | 121.10 (15) | H6A—C6—H6B | 107.9 |
| N1—C3—C2 | 123.42 (14) | C8—C7—C6 | 178.99 (19) |
| N1—C3—H3 | 118.3 | C7—C8—H8 | 180.0 |
| C2—C3—H3 | 118.3 | C3—N1—C4 | 121.52 (13) |
| O2—C4—N2 | 123.44 (14) | C3—N1—C6 | 121.56 (13) |
| O2—C4—N1 | 122.30 (14) | C4—N1—C6 | 116.91 (14) |
| N2—C4—N1 | 114.26 (14) | C4—N2—C1 | 127.43 (13) |
| O3—C5—C2 | 123.80 (18) | C4—N2—H2 | 116.3 |
| O3—C5—H5 | 118.1 | C1—N2—H2 | 116.3 |
| C2—C5—H5 | 118.1 | ||
| O1—C1—C2—C3 | 179.16 (16) | O2—C4—N1—C3 | 175.63 (15) |
| N2—C1—C2—C3 | −0.7 (2) | N2—C4—N1—C3 | −4.1 (2) |
| O1—C1—C2—C5 | −0.4 (3) | O2—C4—N1—C6 | −4.8 (2) |
| N2—C1—C2—C5 | 179.81 (15) | N2—C4—N1—C6 | 175.44 (14) |
| C1—C2—C3—N1 | 1.3 (2) | C7—C6—N1—C3 | −106.92 (18) |
| C5—C2—C3—N1 | −179.19 (15) | C7—C6—N1—C4 | 73.53 (19) |
| C3—C2—C5—O3 | −7.1 (3) | O2—C4—N2—C1 | −174.72 (16) |
| C1—C2—C5—O3 | 172.38 (18) | N1—C4—N2—C1 | 5.0 (2) |
| C2—C3—N1—C4 | 1.3 (2) | O1—C1—N2—C4 | 177.47 (15) |
| C2—C3—N1—C6 | −178.27 (15) | C2—C1—N2—C4 | −2.7 (2) |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2···O1i | 0.86 | 1.98 | 2.8329 (18) | 174 |
| Symmetry code: (i) −x+2, −y+2, −z+1. |
Experimental details
| Crystal data | |
| Chemical formula | C8H6N2O3 |
| Mr | 178.15 |
| Crystal system, space group | Monoclinic, P21/n |
| Temperature (K) | 296 |
| a, b, c (Å) | 5.1756 (7), 8.4877 (12), 18.565 (3) |
| β (°) | 90.611 (2) |
| V (Å3) | 815.5 (2) |
| Z | 4 |
| Radiation type | Mo Kα |
| µ (mm−1) | 0.11 |
| Crystal size (mm) | 0.41 × 0.37 × 0.25 |
| Data collection | |
| Diffractometer | Bruker SMART CCD area-detector diffractometer |
| Absorption correction | Multi-scan (SADABS; Bruker, 1997) |
| Tmin, Tmax | 0.955, 0.972 |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 5826, 1520, 1261 |
| Rint | 0.020 |
| (sin θ/λ)max (Å−1) | 0.605 |
| Refinement | |
| R[F2 > 2σ(F2)], wR(F2), S | 0.040, 0.123, 1.08 |
| No. of reflections | 1520 |
| No. of parameters | 118 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.14, −0.23 |
Computer programs: SMART (Bruker, 1997), SAINT (Bruker, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2···O1i | 0.86 | 1.98 | 2.8329 (18) | 173.6 |
| Symmetry code: (i) −x+2, −y+2, −z+1. |
Acknowledgements
This work was supported by the National Natural Science Foundation of China (No. 20972042) and the Natural Science Foundation of Department of Education of Henan Province (No. 2008 A150013).
References
Bruker (1997). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
De Clercq, E. (2009). Rev. Med. Virol. 19, 287–299. Google Scholar
De Clercq, E. (2010a). J. Med. Chem. 53, 1438–1450. Google Scholar
De Clercq, E. (2010b). Antiviral Res. 85, 19–24. Google Scholar
Fan, X.-S., Wang, Y.-Y., Qu, Y.-Y., Xu, H.-Y., He, Y., Zhang, X.-Y. & Wang, J.-J. (2011). J. Org. Chem. 76, 982–985. Web of Science CSD CrossRef CAS PubMed Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
| CRYSTALLOGRAPHIC COMMUNICATIONS |
Acyclic pyrimidine nucleosides have drawn much attention because of their insteresting structures and broad utilizations as effective drugs for the treatment of diseases caused by herpes simplex virus (HSV) and varizella zoster (VZV) (De Clercq, 2009, 2010a,b). The title compound can be used as a powerful synthon for the preparation of acyclic pyrimidine nucleoside derivatives with potential biological activities due to the rich and extensive chemistry of the aldehyde carbonyl (Fan, 2011). Herein, we report the synthesis and crystal structure of the title compound.
In the title compound, C8H6N2O3, all the atoms in the pyrimidine ring, atoms connected directly with the pyrimidine ring and atoms in the aldehyde carbonyl group in the 5-position of the pyrimidine ring are in the same plane, which means there is a big conjugated system in the molecule. The linear structure of the propynyl group is connected with the big plane at an angle of 150.3°. In the crystal structure, the molecules are linked via intermolecular N—H···O hydrogen bond.