organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

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

(Received 27 October 2012; accepted 19 November 2012; online 24 November 2012)

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[Li, X., Li, Y. & Xu, W. (2006). Bioorg. Med. Chem. 14, 1287-1293.]); Lokhande et al. (2003[Lokhande, T. N., Bobade, A. S. & Khadse, B. G. (2003). Indian Drugs, 40, 147-150.]); Imamura et al. (2004[Imamura, S., Ishihara, Y., Hattori, T., Kurasawa, O., Matsushita, Y. & Sugihara, Y. (2004). Chem. Pharm. Bull. 52, 63-73.]); Wyrzykiewicz, et al. (1993[Wyrzykiewicz, E., Bartkowiak, G. & Kedzia, B. (1993). Il Farmaco, 48, 979-988.]) and of pyrimidine derivatives, see: Holla et al. (2006[Holla, B. S., Mahalinga, M., Karthikeyan, M. S., Akberali, P. M. & Shetty, N. S. (2006). Bioorg. Med. Chem. 14, 2040-2047.]); Zhao et al. (2007[Zhao, X.-L., Zhao, Y.-F., Guo, S.-C., Song, H.-S., Wang, D. & Gong, P. (2007). Molecules, 12, 1136-1146.]); Sondhi et al. (2005[Sondhi, S. M., Singh, N., Johar, M. & Kumar, A. (2005). Bioorg. Med. Chem. 13, 6158-6166.]); Khalifa et al. (2005[Khalifa, N. M., Ismail, N. S. & Abdulla, M. M. (2005). Egypt. Pharm. J. 4, 277-288.]). For the graph-set description of hydrogen-bond motifs, see: Etter (1990[Etter, M. C. (1990). Acc. Chem. Res. 23, 120-126.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C13H20N4

  • Mr = 232.33

  • Triclinic, [P \overline 1]

  • a = 6.344 (3) Å

  • b = 8.766 (4) Å

  • c = 12.056 (6) Å

  • α = 79.10 (3)°

  • β = 86.05 (3)°

  • γ = 85.72 (3)°

  • V = 655.6 (6) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.07 mm−1

  • T = 296 K

  • 0.2 × 0.18 × 0.02 mm

Data collection
  • Bruker SMART X2S diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.986, Tmax = 0.999

  • 8712 measured reflections

  • 2302 independent reflections

  • 1600 reflections with I > 2σ(I)

  • Rint = 0.022

Refinement
  • R[F2 > 2σ(F2)] = 0.066

  • wR(F2) = 0.227

  • S = 1.13

  • 2302 reflections

  • 155 parameters

  • H-atom parameters constrained

  • Δρmax = 0.24 e Å−3

  • Δρmin = −0.20 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2 and SAINT (Bruker, 2009[Bruker (2009). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

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.

Related literature top

For literature related to the synthesis and biological activities of pyrrolidine derivatives, see: Li et al. (2006); Lokhande et al. (2003); Imamura et al. (2004); Wyrzykiewicz, et al. (1993). For literature related to the synthesis and biological activities of pyrimidine derivatives, see: Holla, et al. (2006); Zhao et al. (2007); Sondhi et al. (2005); Khalifa et al. (2005). For literature concerning the use of graph-set notation in designated hydrogen-bonding schemes, see: Etter (1990); Bernstein et al. (1995).

Experimental top

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 column chromatography, 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.

Refinement top

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).

Computing details top

Data collection: APEX2 (Bruker, 2009); cell refinement: 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).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Molecular packing in the title compound. Hydrogen bonds are shown as dashed lines.
4-Methyl-2,6-bis(pyrrolidin-1-yl)pyrimidine top
Crystal data top
C13H20N4F(000) = 252
Mr = 232.33Colourless
Triclinic, P1Dx = 1.177 Mg m3
Hall symbol: -P 1Melting point: 446 K
a = 6.344 (3) ÅMo Kα radiation, λ = 0.71073 Å
b = 8.766 (4) ÅCell parameters from 1600 reflections
c = 12.056 (6) Åθ = 25°
α = 79.10 (3)°µ = 0.07 mm1
β = 86.05 (3)°T = 296 K
γ = 85.72 (3)°Prism, colorless
V = 655.6 (6) Å30.2 × 0.18 × 0.02 mm
Z = 2
Data collection top
Bruker SMART X2S
diffractometer
2302 independent reflections
Radiation source: fine-focus steel tube1600 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
Detector resolution: 1.03 pixels mm-1θmax = 25°, θmin = 1.7°
phi and ω scansh = 77
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
k = 1010
Tmin = 0.986, Tmax = 0.999l = 1414
8712 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.066Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.227H-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 parametersΔρmax = 0.24 e Å3
0 restraintsΔρmin = 0.20 e Å3
0 constraints
Crystal data top
C13H20N4γ = 85.72 (3)°
Mr = 232.33V = 655.6 (6) Å3
Triclinic, P1Z = 2
a = 6.344 (3) ÅMo Kα radiation
b = 8.766 (4) ŵ = 0.07 mm1
c = 12.056 (6) ÅT = 296 K
α = 79.10 (3)°0.2 × 0.18 × 0.02 mm
β = 86.05 (3)°
Data collection top
Bruker SMART X2S
diffractometer
2302 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)
1600 reflections with I > 2σ(I)
Tmin = 0.986, Tmax = 0.999Rint = 0.022
8712 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0660 restraints
wR(F2) = 0.227H-atom parameters constrained
S = 1.13Δρmax = 0.24 e Å3
2302 reflectionsΔρmin = 0.20 e Å3
155 parameters
Special details top

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) top
xyzUiso*/Ueq
N10.1352 (3)0.2849 (2)0.09361 (17)0.0628 (6)
N20.0463 (3)0.4541 (2)0.21449 (16)0.0540 (5)
N30.0420 (3)0.6226 (2)0.33585 (17)0.0645 (6)
N40.1692 (3)0.2415 (2)0.21113 (17)0.0642 (6)
C30.4251 (5)0.2730 (3)0.0331 (3)0.0869 (9)
H3A0.48250.33590.1020.104*
H3B0.54040.21020.00520.104*
C40.3118 (4)0.3748 (3)0.0424 (2)0.0619 (7)
H4A0.40290.39280.09940.074*
H4B0.26250.47430.0010.074*
C50.0014 (3)0.3283 (2)0.17442 (19)0.0535 (6)
C60.0892 (3)0.4968 (2)0.29357 (18)0.0534 (6)
C130.1759 (4)0.6913 (3)0.4170 (2)0.0730 (7)
H13A0.18760.62020.4890.088*
H13B0.31640.720.38990.088*
C120.0658 (6)0.8320 (4)0.4279 (3)0.1077 (12)
H12A0.14920.92540.39630.129*
H12B0.04870.83320.5070.129*
C20.2664 (5)0.1735 (3)0.0592 (3)0.0875 (9)
H2A0.33190.07270.06830.105*
H2B0.20050.22120.12870.105*
C10.1062 (5)0.1559 (3)0.0377 (2)0.0761 (8)
H1A0.03580.1620.01140.091*
H1B0.13070.05710.08850.091*
C100.1473 (4)0.7058 (3)0.2981 (2)0.0695 (7)
H10A0.14590.75170.21830.083*
H10B0.27420.63760.31120.083*
C90.4898 (4)0.2017 (3)0.3329 (2)0.0803 (8)
H9A0.46330.13770.40510.121*
H9B0.51570.13690.280.121*
H9C0.61140.27170.34060.121*
C70.2678 (3)0.4204 (3)0.33417 (18)0.0538 (6)
H70.3610.45430.38870.065*
C80.3015 (3)0.2932 (3)0.29089 (19)0.0567 (6)
C110.1343 (7)0.8278 (5)0.3691 (3)0.1257 (14)
H11A0.24460.80580.42280.151*
H11B0.1560.92840.32160.151*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0602 (12)0.0608 (11)0.0737 (13)0.0221 (9)0.0104 (10)0.0268 (10)
N20.0506 (10)0.0520 (10)0.0626 (11)0.0116 (8)0.0004 (8)0.0165 (8)
N30.0629 (12)0.0625 (11)0.0740 (13)0.0178 (9)0.0070 (10)0.0262 (10)
N40.0583 (12)0.0643 (12)0.0729 (13)0.0192 (9)0.0014 (10)0.0147 (10)
C30.091 (2)0.0830 (18)0.0925 (19)0.0260 (15)0.0268 (16)0.0346 (15)
C40.0580 (14)0.0593 (13)0.0705 (15)0.0163 (11)0.0054 (11)0.0156 (11)
C50.0503 (12)0.0501 (12)0.0620 (13)0.0119 (9)0.0048 (10)0.0114 (10)
C60.0514 (12)0.0509 (12)0.0585 (13)0.0055 (9)0.0055 (10)0.0101 (10)
C130.0802 (17)0.0687 (15)0.0744 (16)0.0084 (13)0.0074 (13)0.0268 (13)
C120.101 (2)0.089 (2)0.148 (3)0.0174 (17)0.020 (2)0.064 (2)
C20.094 (2)0.0767 (18)0.101 (2)0.0113 (15)0.0081 (17)0.0419 (16)
C10.0868 (18)0.0655 (15)0.0851 (17)0.0225 (13)0.0056 (15)0.0336 (13)
C100.0694 (15)0.0633 (14)0.0805 (17)0.0199 (12)0.0011 (13)0.0202 (13)
C90.0626 (15)0.0877 (18)0.0879 (18)0.0281 (13)0.0078 (13)0.0044 (15)
C70.0492 (12)0.0566 (12)0.0560 (13)0.0066 (10)0.0063 (10)0.0135 (10)
C80.0467 (12)0.0611 (13)0.0599 (13)0.0095 (10)0.0023 (10)0.0026 (11)
C110.152 (3)0.120 (3)0.129 (3)0.076 (2)0.049 (3)0.077 (2)
Geometric parameters (Å, º) top
N1—C51.339 (3)C12—C111.412 (5)
N1—C11.451 (3)C12—H12A0.97
N1—C41.452 (3)C12—H12B0.97
N2—C61.328 (3)C2—C11.488 (4)
N2—C51.341 (3)C2—H2A0.97
N3—C61.360 (3)C2—H2B0.97
N3—C131.440 (3)C1—H1A0.97
N3—C101.453 (3)C1—H1B0.97
N4—C81.353 (3)C10—C111.486 (4)
N4—C51.369 (3)C10—H10A0.97
C3—C21.467 (4)C10—H10B0.97
C3—C41.505 (3)C9—C81.494 (3)
C3—H3A0.97C9—H9A0.96
C3—H3B0.97C9—H9B0.96
C4—H4A0.97C9—H9C0.96
C4—H4B0.97C7—C81.354 (3)
C6—C71.373 (3)C7—H70.93
C13—C121.492 (4)C11—H11A0.97
C13—H13A0.97C11—H11B0.97
C13—H13B0.97
C5—N1—C1124.27 (19)H12A—C12—H12B108.3
C5—N1—C4123.00 (19)C3—C2—C1106.7 (2)
C1—N1—C4112.31 (19)C3—C2—H2A110.4
C6—N2—C5116.30 (18)C1—C2—H2A110.4
C6—N3—C13124.4 (2)C3—C2—H2B110.4
C6—N3—C10122.3 (2)C1—C2—H2B110.4
C13—N3—C10113.3 (2)H2A—C2—H2B108.6
C8—N4—C5115.7 (2)N1—C1—C2104.37 (19)
C2—C3—C4106.1 (2)N1—C1—H1A110.9
C2—C3—H3A110.5C2—C1—H1A110.9
C4—C3—H3A110.5N1—C1—H1B110.9
C2—C3—H3B110.5C2—C1—H1B110.9
C4—C3—H3B110.5H1A—C1—H1B108.9
H3A—C3—H3B108.7N3—C10—C11102.9 (2)
N1—C4—C3103.21 (19)N3—C10—H10A111.2
N1—C4—H4A111.1C11—C10—H10A111.2
C3—C4—H4A111.1N3—C10—H10B111.2
N1—C4—H4B111.1C11—C10—H10B111.2
C3—C4—H4B111.1H10A—C10—H10B109.1
H4A—C4—H4B109.1C8—C9—H9A109.5
N1—C5—N2116.98 (19)C8—C9—H9B109.5
N1—C5—N4118.4 (2)H9A—C9—H9B109.5
N2—C5—N4124.6 (2)C8—C9—H9C109.5
N2—C6—N3116.4 (2)H9A—C9—H9C109.5
N2—C6—C7123.7 (2)H9B—C9—H9C109.5
N3—C6—C7119.8 (2)C8—C7—C6116.7 (2)
N3—C13—C12103.8 (2)C8—C7—H7121.7
N3—C13—H13A111C6—C7—H7121.7
C12—C13—H13A111N4—C8—C7123.0 (2)
N3—C13—H13B111N4—C8—C9117.2 (2)
C12—C13—H13B111C7—C8—C9119.8 (2)
H13A—C13—H13B109C12—C11—C10110.0 (3)
C11—C12—C13108.7 (3)C12—C11—H11A109.7
C11—C12—H12A110C10—C11—H11A109.7
C13—C12—H12A110C12—C11—H11B109.7
C11—C12—H12B110C10—C11—H11B109.7
C13—C12—H12B110H11A—C11—H11B108.2
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2B···N3i0.97 (1)2.823.793 (2)175
C9—H9C···N2ii0.96 (1)2.933.742 (2)143
Symmetry codes: (i) x, y+1, z; (ii) x1, y, z.

Experimental details

Crystal data
Chemical formulaC13H20N4
Mr232.33
Crystal system, space groupTriclinic, 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)
V3)655.6 (6)
Z2
Radiation typeMo Kα
µ (mm1)0.07
Crystal size (mm)0.2 × 0.18 × 0.02
Data collection
DiffractometerBruker SMART X2S
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.986, 0.999
No. of measured, independent and
observed [I > 2σ(I)] reflections
8712, 2302, 1600
Rint0.022
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.066, 0.227, 1.13
No. of reflections2302
No. of parameters155
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2B···N3i0.970 (0)2.823.793 (2)175
C9—H9C···N2ii0.960 (0)2.933.742 (2)143
Symmetry codes: (i) x, y+1, z; (ii) x1, 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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COMMUNICATIONS
ISSN: 2056-9890
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