organic compounds
4-Methyl-2,6-bis(pyrrolidin-1-yl)pyrimidine
aDepartment of Studies and Research in Chemistry, Tumkur University, Tumkur, Karnataka 572 103, India, bDepartment of Studies and Research in Chemistry, U.C.S., Tumkur University, Tumkur, Karnataka 572 103, India, and cDepartment of Studies and Research in Physics, U.C.S., Tumkur University, Tumkur, Karnataka 572 103, India
*Correspondence e-mail: drsreenivasa@yahoo.co.in
In the crystal of the title compound, C13H20N4, the molecule is nearly planar, the dihedral angles between the pyrimidine and the two pyrrolidine rings being 4.71 (2) and 4.50 (2)°. The crystal features inversion-related dimers linked by pairs of C—H⋯N hydrogen bonds generating R22(16) patterns. The dimeric units are further linked into C(6) chains via an additional C—H⋯N hydrogen bond.
Related literature
For the synthesis and biological activity of pyrrolidine derivatives, see: Li et al. (2006); Lokhande et al. (2003); Imamura et al. (2004); Wyrzykiewicz, et al. (1993) and of pyrimidine derivatives, see: Holla et al. (2006); Zhao et al. (2007); Sondhi et al. (2005); Khalifa et al. (2005). For the graph-set description of hydrogen-bond motifs, see: Etter (1990); Bernstein et al. (1995).
Experimental
Crystal data
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Refinement
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Data collection: APEX2 (Bruker, 2009); cell APEX2 and SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012); software used to prepare material for publication: SHELXL97.
Supporting information
10.1107/S160053681204740X/bv2214sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S160053681204740X/bv2214Isup2.hkl
Supporting information file. DOI: 10.1107/S160053681204740X/bv2214Isup3.cml
2,4-Dichloro-6-methyl pyrimidine (3.11 mmol), pyrrolidine (6.83 mmol), and triethylamine (12.4 mmol) and 5 ml acetonitrile were taken in a microwave seal tube. The reaction mixture was irradiated with microwave for 90 min. The reaction was monitored by TLC with 30% ethyl acetate in petroleum ether. The solvent was removed and the residue dissolved in dichloromethane, purified by
and the collected fraction was concentrated under reduced pressure. Single crystals employed in X-ray diffraction studies were obtained from slow evaporation of the solvent from the solution of the compound in ethyl acetate-petroleum ether at room temperature.The H atoms were positioned with idealized geometry using a riding model with C—H = 0.93 - 0.97 Å. The isotropic displacement parameters for all H atoms were set to 1.2 times of the Ueq of the parent atom (1.5 times of the Ueq of the parent atom for CH3).
Data collection: APEX2 (Bruker, 2009); cell
APEX2 and SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).C13H20N4 | F(000) = 252 |
Mr = 232.33 | Colourless |
Triclinic, P1 | Dx = 1.177 Mg m−3 |
Hall symbol: -P 1 | Melting point: 446 K |
a = 6.344 (3) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 8.766 (4) Å | Cell parameters from 1600 reflections |
c = 12.056 (6) Å | θ = 25° |
α = 79.10 (3)° | µ = 0.07 mm−1 |
β = 86.05 (3)° | T = 296 K |
γ = 85.72 (3)° | Prism, colorless |
V = 655.6 (6) Å3 | 0.2 × 0.18 × 0.02 mm |
Z = 2 |
Bruker SMART X2S diffractometer | 2302 independent reflections |
Radiation source: fine-focus steel tube | 1600 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
Detector resolution: 1.03 pixels mm-1 | θmax = 25°, θmin = 1.7° |
phi and ω scans | h = −7→7 |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | k = −10→10 |
Tmin = 0.986, Tmax = 0.999 | l = −14→14 |
8712 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)] = 0.066 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.227 | H-atom parameters constrained |
S = 1.13 | w = 1/[σ2(Fo2) + (0.1307P)2 + 0.0781P] where P = (Fo2 + 2Fc2)/3 |
2302 reflections | (Δ/σ)max = 0.009 |
155 parameters | Δρmax = 0.24 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
0 constraints |
C13H20N4 | γ = 85.72 (3)° |
Mr = 232.33 | V = 655.6 (6) Å3 |
Triclinic, P1 | Z = 2 |
a = 6.344 (3) Å | Mo Kα radiation |
b = 8.766 (4) Å | µ = 0.07 mm−1 |
c = 12.056 (6) Å | T = 296 K |
α = 79.10 (3)° | 0.2 × 0.18 × 0.02 mm |
β = 86.05 (3)° |
Bruker SMART X2S diffractometer | 2302 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2009) | 1600 reflections with I > 2σ(I) |
Tmin = 0.986, Tmax = 0.999 | Rint = 0.022 |
8712 measured reflections |
R[F2 > 2σ(F2)] = 0.066 | 0 restraints |
wR(F2) = 0.227 | H-atom parameters constrained |
S = 1.13 | Δρmax = 0.24 e Å−3 |
2302 reflections | Δρmin = −0.20 e Å−3 |
155 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 | ||
N1 | 0.1352 (3) | 0.2849 (2) | 0.09361 (17) | 0.0628 (6) | |
N2 | 0.0463 (3) | 0.4541 (2) | 0.21449 (16) | 0.0540 (5) | |
N3 | −0.0420 (3) | 0.6226 (2) | 0.33585 (17) | 0.0645 (6) | |
N4 | −0.1692 (3) | 0.2415 (2) | 0.21113 (17) | 0.0642 (6) | |
C3 | 0.4251 (5) | 0.2730 (3) | −0.0331 (3) | 0.0869 (9) | |
H3A | 0.4825 | 0.3359 | −0.102 | 0.104* | |
H3B | 0.5404 | 0.2102 | 0.0052 | 0.104* | |
C4 | 0.3118 (4) | 0.3748 (3) | 0.0424 (2) | 0.0619 (7) | |
H4A | 0.4029 | 0.3928 | 0.0994 | 0.074* | |
H4B | 0.2625 | 0.4743 | −0.001 | 0.074* | |
C5 | 0.0014 (3) | 0.3283 (2) | 0.17442 (19) | 0.0535 (6) | |
C6 | −0.0892 (3) | 0.4968 (2) | 0.29357 (18) | 0.0534 (6) | |
C13 | −0.1759 (4) | 0.6913 (3) | 0.4170 (2) | 0.0730 (7) | |
H13A | −0.1876 | 0.6202 | 0.489 | 0.088* | |
H13B | −0.3164 | 0.72 | 0.3899 | 0.088* | |
C12 | −0.0658 (6) | 0.8320 (4) | 0.4279 (3) | 0.1077 (12) | |
H12A | −0.1492 | 0.9254 | 0.3963 | 0.129* | |
H12B | −0.0487 | 0.8332 | 0.507 | 0.129* | |
C2 | 0.2664 (5) | 0.1735 (3) | −0.0592 (3) | 0.0875 (9) | |
H2A | 0.3319 | 0.0727 | −0.0683 | 0.105* | |
H2B | 0.2005 | 0.2212 | −0.1287 | 0.105* | |
C1 | 0.1062 (5) | 0.1559 (3) | 0.0377 (2) | 0.0761 (8) | |
H1A | −0.0358 | 0.162 | 0.0114 | 0.091* | |
H1B | 0.1307 | 0.0571 | 0.0885 | 0.091* | |
C10 | 0.1473 (4) | 0.7058 (3) | 0.2981 (2) | 0.0695 (7) | |
H10A | 0.1459 | 0.7517 | 0.2183 | 0.083* | |
H10B | 0.2742 | 0.6376 | 0.3112 | 0.083* | |
C9 | −0.4898 (4) | 0.2017 (3) | 0.3329 (2) | 0.0803 (8) | |
H9A | −0.4633 | 0.1377 | 0.4051 | 0.121* | |
H9B | −0.5157 | 0.1369 | 0.28 | 0.121* | |
H9C | −0.6114 | 0.2717 | 0.3406 | 0.121* | |
C7 | −0.2678 (3) | 0.4204 (3) | 0.33417 (18) | 0.0538 (6) | |
H7 | −0.361 | 0.4543 | 0.3887 | 0.065* | |
C8 | −0.3015 (3) | 0.2932 (3) | 0.29089 (19) | 0.0567 (6) | |
C11 | 0.1343 (7) | 0.8278 (5) | 0.3691 (3) | 0.1257 (14) | |
H11A | 0.2446 | 0.8058 | 0.4228 | 0.151* | |
H11B | 0.156 | 0.9284 | 0.3216 | 0.151* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0602 (12) | 0.0608 (11) | 0.0737 (13) | −0.0221 (9) | 0.0104 (10) | −0.0268 (10) |
N2 | 0.0506 (10) | 0.0520 (10) | 0.0626 (11) | −0.0116 (8) | −0.0004 (8) | −0.0165 (8) |
N3 | 0.0629 (12) | 0.0625 (11) | 0.0740 (13) | −0.0178 (9) | 0.0070 (10) | −0.0262 (10) |
N4 | 0.0583 (12) | 0.0643 (12) | 0.0729 (13) | −0.0192 (9) | −0.0014 (10) | −0.0147 (10) |
C3 | 0.091 (2) | 0.0830 (18) | 0.0925 (19) | −0.0260 (15) | 0.0268 (16) | −0.0346 (15) |
C4 | 0.0580 (14) | 0.0593 (13) | 0.0705 (15) | −0.0163 (11) | 0.0054 (11) | −0.0156 (11) |
C5 | 0.0503 (12) | 0.0501 (12) | 0.0620 (13) | −0.0119 (9) | −0.0048 (10) | −0.0114 (10) |
C6 | 0.0514 (12) | 0.0509 (12) | 0.0585 (13) | −0.0055 (9) | −0.0055 (10) | −0.0101 (10) |
C13 | 0.0802 (17) | 0.0687 (15) | 0.0744 (16) | −0.0084 (13) | 0.0074 (13) | −0.0268 (13) |
C12 | 0.101 (2) | 0.089 (2) | 0.148 (3) | −0.0174 (17) | 0.020 (2) | −0.064 (2) |
C2 | 0.094 (2) | 0.0767 (18) | 0.101 (2) | −0.0113 (15) | 0.0081 (17) | −0.0419 (16) |
C1 | 0.0868 (18) | 0.0655 (15) | 0.0851 (17) | −0.0225 (13) | 0.0056 (15) | −0.0336 (13) |
C10 | 0.0694 (15) | 0.0633 (14) | 0.0805 (17) | −0.0199 (12) | −0.0011 (13) | −0.0202 (13) |
C9 | 0.0626 (15) | 0.0877 (18) | 0.0879 (18) | −0.0281 (13) | 0.0078 (13) | −0.0044 (15) |
C7 | 0.0492 (12) | 0.0566 (12) | 0.0560 (13) | −0.0066 (10) | 0.0063 (10) | −0.0135 (10) |
C8 | 0.0467 (12) | 0.0611 (13) | 0.0599 (13) | −0.0095 (10) | −0.0023 (10) | −0.0026 (11) |
C11 | 0.152 (3) | 0.120 (3) | 0.129 (3) | −0.076 (2) | 0.049 (3) | −0.077 (2) |
N1—C5 | 1.339 (3) | C12—C11 | 1.412 (5) |
N1—C1 | 1.451 (3) | C12—H12A | 0.97 |
N1—C4 | 1.452 (3) | C12—H12B | 0.97 |
N2—C6 | 1.328 (3) | C2—C1 | 1.488 (4) |
N2—C5 | 1.341 (3) | C2—H2A | 0.97 |
N3—C6 | 1.360 (3) | C2—H2B | 0.97 |
N3—C13 | 1.440 (3) | C1—H1A | 0.97 |
N3—C10 | 1.453 (3) | C1—H1B | 0.97 |
N4—C8 | 1.353 (3) | C10—C11 | 1.486 (4) |
N4—C5 | 1.369 (3) | C10—H10A | 0.97 |
C3—C2 | 1.467 (4) | C10—H10B | 0.97 |
C3—C4 | 1.505 (3) | C9—C8 | 1.494 (3) |
C3—H3A | 0.97 | C9—H9A | 0.96 |
C3—H3B | 0.97 | C9—H9B | 0.96 |
C4—H4A | 0.97 | C9—H9C | 0.96 |
C4—H4B | 0.97 | C7—C8 | 1.354 (3) |
C6—C7 | 1.373 (3) | C7—H7 | 0.93 |
C13—C12 | 1.492 (4) | C11—H11A | 0.97 |
C13—H13A | 0.97 | C11—H11B | 0.97 |
C13—H13B | 0.97 | ||
C5—N1—C1 | 124.27 (19) | H12A—C12—H12B | 108.3 |
C5—N1—C4 | 123.00 (19) | C3—C2—C1 | 106.7 (2) |
C1—N1—C4 | 112.31 (19) | C3—C2—H2A | 110.4 |
C6—N2—C5 | 116.30 (18) | C1—C2—H2A | 110.4 |
C6—N3—C13 | 124.4 (2) | C3—C2—H2B | 110.4 |
C6—N3—C10 | 122.3 (2) | C1—C2—H2B | 110.4 |
C13—N3—C10 | 113.3 (2) | H2A—C2—H2B | 108.6 |
C8—N4—C5 | 115.7 (2) | N1—C1—C2 | 104.37 (19) |
C2—C3—C4 | 106.1 (2) | N1—C1—H1A | 110.9 |
C2—C3—H3A | 110.5 | C2—C1—H1A | 110.9 |
C4—C3—H3A | 110.5 | N1—C1—H1B | 110.9 |
C2—C3—H3B | 110.5 | C2—C1—H1B | 110.9 |
C4—C3—H3B | 110.5 | H1A—C1—H1B | 108.9 |
H3A—C3—H3B | 108.7 | N3—C10—C11 | 102.9 (2) |
N1—C4—C3 | 103.21 (19) | N3—C10—H10A | 111.2 |
N1—C4—H4A | 111.1 | C11—C10—H10A | 111.2 |
C3—C4—H4A | 111.1 | N3—C10—H10B | 111.2 |
N1—C4—H4B | 111.1 | C11—C10—H10B | 111.2 |
C3—C4—H4B | 111.1 | H10A—C10—H10B | 109.1 |
H4A—C4—H4B | 109.1 | C8—C9—H9A | 109.5 |
N1—C5—N2 | 116.98 (19) | C8—C9—H9B | 109.5 |
N1—C5—N4 | 118.4 (2) | H9A—C9—H9B | 109.5 |
N2—C5—N4 | 124.6 (2) | C8—C9—H9C | 109.5 |
N2—C6—N3 | 116.4 (2) | H9A—C9—H9C | 109.5 |
N2—C6—C7 | 123.7 (2) | H9B—C9—H9C | 109.5 |
N3—C6—C7 | 119.8 (2) | C8—C7—C6 | 116.7 (2) |
N3—C13—C12 | 103.8 (2) | C8—C7—H7 | 121.7 |
N3—C13—H13A | 111 | C6—C7—H7 | 121.7 |
C12—C13—H13A | 111 | N4—C8—C7 | 123.0 (2) |
N3—C13—H13B | 111 | N4—C8—C9 | 117.2 (2) |
C12—C13—H13B | 111 | C7—C8—C9 | 119.8 (2) |
H13A—C13—H13B | 109 | C12—C11—C10 | 110.0 (3) |
C11—C12—C13 | 108.7 (3) | C12—C11—H11A | 109.7 |
C11—C12—H12A | 110 | C10—C11—H11A | 109.7 |
C13—C12—H12A | 110 | C12—C11—H11B | 109.7 |
C11—C12—H12B | 110 | C10—C11—H11B | 109.7 |
C13—C12—H12B | 110 | H11A—C11—H11B | 108.2 |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2B···N3i | 0.97 (1) | 2.82 | 3.793 (2) | 175 |
C9—H9C···N2ii | 0.96 (1) | 2.93 | 3.742 (2) | 143 |
Symmetry codes: (i) −x, −y+1, −z; (ii) x−1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C13H20N4 |
Mr | 232.33 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 296 |
a, b, c (Å) | 6.344 (3), 8.766 (4), 12.056 (6) |
α, β, γ (°) | 79.10 (3), 86.05 (3), 85.72 (3) |
V (Å3) | 655.6 (6) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.07 |
Crystal size (mm) | 0.2 × 0.18 × 0.02 |
Data collection | |
Diffractometer | Bruker SMART X2S diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2009) |
Tmin, Tmax | 0.986, 0.999 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8712, 2302, 1600 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.066, 0.227, 1.13 |
No. of reflections | 2302 |
No. of parameters | 155 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.24, −0.20 |
Computer programs: APEX2 (Bruker, 2009), APEX2 and SAINT (Bruker, 2009), SAINT (Bruker, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 2012).
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2B···N3i | 0.970 (0) | 2.82 | 3.793 (2) | 175 |
C9—H9C···N2ii | 0.960 (0) | 2.93 | 3.742 (2) | 143 |
Symmetry codes: (i) −x, −y+1, −z; (ii) x−1, y, z. |
Acknowledgements
The authors thank Dr S. C. Sharma, Vice Chancellor, Tumkur University, Tumkur, for his constant encouragement, Professor T. N. Guru Row and Vijithkumar, S. S. C. U., Indian Institute of Science, Bangalore, for their help in collecting single-crystal data. The authors also thank Dr H. C. Devaraje Gowda, Department of Physics Yuvarajas College (constituent), University of Mysore, for his support.
References
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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.
Organic compounds with the pyrrolidine ring system are known to display a wide range of biological activities such as antitumor (Li et al., 2006), antimicrobial (Lokhande et al., 2003), anti- HIV-1 (Imamura et al., 2004). Similarly pyrimidine derivatives exhibit a range of pharmacological activities such as antibacterial (Wyrzykiewicz et al., 1993), antifungal (Holla et al., 2006), anticancer (Zhao et al., 2007), anti inflammatory (Sondhi et al., 2005) and cardioprotective effects (Khalifa et al., 2005). In this view the title compound was synthesized to study its crystal structure.
The compound crystallizes in triclinic P-1 space group. In the crystal structure, the molecule is nearly planar, with the dihedral angles between the pyrimidine and the two pyrrolidine rings being 4.71 (2) and 4.50 (2)°. Further, the dihedral angle between the two pyrrolidine rings is 18.70 (2)°. The crystal structure features inversion-related dimers linked by pairs of C—H···N hydrogen bonds generating R22(16) patterns (Etter, 1990; Bernstein et al., 1995). The dimeric units are further linked into C(6) chains via an additional C—H···N hydrogen bond.