supplementary materials


gk2582 scheme

Acta Cryst. (2013). E69, o1140    [ doi:10.1107/S1600536813016851 ]

2-{4-[(1,3-Benzodioxol-5-yl)methyl]piperazin-1-yl}pyrimidine

C. Wu, J. Li, H. Wei, Y. Hang and Y. Jiang

Abstract top

In the title compound, C16H18N4O2, known also as peribedil, the dihedral angle between the mean planes of the pyrimidine and benzene rings is 56.5 (8)°. The 1,3-dioxole fragment adopts an envelope conformation with the methylene C atom forming the flap; this atom deviates by 0.232 (3) Å from the plane defined by the remaining atoms of the 1,3-benzodioxole unit. In the crystal, C-H...[pi] interactions between c-glide-related molecules arrange them into columns extending along the c-axis direction. The columns related by a unit translation along the b axis are packed into (100) layers via another C-H...[pi] interaction involving the pyrimidine ring as an acceptor.

Comment top

Experimental investigation shows that the dopamine agonist, piribedil, is active in the treatment of Parkinson's disease, particularly with regard to tremor (Rondot et al., 1992). We report herein the synthesis (Hamid et al., 2007) and the crystal structure of the title compound. The benzene and pyrimidine rings subtend a dihedral angle of 56.5 (8)°. The benzo[1,3]dioxole fragments, the dihedral angle between O1—C16—O2 plane and the remaining 8 atoms of the bicyclic fragment (O1—C14—C13—C12—C11—C10—C15—O2) is 16.1 (1)°. Piperazine fragments, the dihedral angle between C5—C8 plane and C5—N3—C7 plane is 29.7 (3) °, C5—C8 plane and C6—N4—C8 plane is 23.9 (7) °. In the crystal, the molecules associate through C—H···π interactions (see table 1).

Related literature top

For details of the synthesis of piribedil, see: Duncton et al. (2006); Conroy & Denton (1953); Hamid et al. (2007). For the pharmacological activity of the title compound, see: Rondot et al. (1992).

Experimental top

The triethylamine catalyzed reaction of 5-chlorobenzo[d][1,3]dioxole (8.5 mmol) and 2-(piperazin-1-yl)pyrimidine (8.1 mmol) was carried out in isopropyl alcohol (10 mL). The reaction mixture was refluxed for 2 h to afford the title compound. Colorless blocks of the title compound were obtained by recrystallization from ethanol. Crystals suitable for X-ray analysis were grown from methyl alcohol-ethyl acetate solution at room temperature by slow evaporation over two weeks.

Refinement top

H atoms were placed in calculated positions and allowed to ride on their carriers with C—H distances 0.93–0.97 Å and Uiso(H)=1.2Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the compound, with 30% probability displacement ellipsoids for non-hydrogen atoms.
[Figure 2] Fig. 2. A view of the column along the c axis formed via C—H···π stacking interactions (symmetry code: A x,1.5 - y,z - 0.5; B x,1.5 - y,z + 0.5; D x,y,1 + z.).
2-{4-[(1,3-Benzodioxol-5-yl)methyl]piperazin-1-yl}pyrimidine top
Crystal data top
C16H18N4O2Dx = 1.334 Mg m3
Mr = 298.34Melting point = 370–372 K
Orthorhombic, PccnCu Kα radiation, λ = 1.5418 Å
a = 21.3085 (6) ÅCell parameters from 2402 reflections
b = 18.6249 (4) Åθ = 3.2–67.0°
c = 7.48851 (19) ŵ = 0.74 mm1
V = 2971.95 (12) Å3T = 291 K
Z = 8Block, colorless
F(000) = 12640.25 × 0.2 × 0.2 mm
Data collection top
Agilent Xcalibur (Eos, Gemini)
diffractometer
2635 independent reflections
Radiation source: Enhance (Cu) X-ray Source2186 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
Detector resolution: 16.2312 pixels mm-1θmax = 67.1°, θmin = 3.2°
ω scansh = 2524
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)'
k = 2219
Tmin = 0.910, Tmax = 1.000l = 78
6334 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.039H-atom parameters constrained
wR(F2) = 0.112 w = 1/[σ2(Fo2) + (0.0574P)2 + 0.4246P]
where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max < 0.001
2635 reflectionsΔρmax = 0.13 e Å3
200 parametersΔρmin = 0.14 e Å3
0 restraintsExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.00143 (18)
Crystal data top
C16H18N4O2V = 2971.95 (12) Å3
Mr = 298.34Z = 8
Orthorhombic, PccnCu Kα radiation
a = 21.3085 (6) ŵ = 0.74 mm1
b = 18.6249 (4) ÅT = 291 K
c = 7.48851 (19) Å0.25 × 0.2 × 0.2 mm
Data collection top
Agilent Xcalibur (Eos, Gemini)
diffractometer
2635 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)'
2186 reflections with I > 2σ(I)
Tmin = 0.910, Tmax = 1.000Rint = 0.019
6334 measured reflectionsθmax = 67.1°
Refinement top
R[F2 > 2σ(F2)] = 0.039H-atom parameters constrained
wR(F2) = 0.112Δρmax = 0.13 e Å3
S = 1.03Δρmin = 0.14 e Å3
2635 reflectionsAbsolute structure: ?
200 parametersAbsolute structure parameter: ?
0 restraintsRogers parameter: ?
Special details top

Experimental. 1H NMR (400 MHz, CDCl3, p.p.m.): 8.30 (d, J = 4.7 Hz, 1H), 6.90 (s, 1H), 6.76 (s, 1H), 6.47 (s, J = 4.7 Hz, 1H), 6.20 (dt, J = 10.6, 2.2 Hz, 1H), 5.95 (s, 1H), 3.89–3.66 (m, 2H), 3.46 (s, 1H), 2.58–2.27 (m, 2H); 13C NMR (101 MHz, CDCl3, p.p.m.): 161.67, 157.70, 147.68, 146.66, 131.91, 122.23 ,109.72, 109.50, 107.90, 100.91, 62.89, 52.85, 43.69; ESI–HRMS m/z: 299.1506 (calculated for C16H19N4O2 [M + 1]+: 299.1508).

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
O10.65086 (6)0.79907 (7)0.4624 (2)0.0734 (4)
O20.55046 (6)0.77275 (6)0.55466 (19)0.0663 (4)
N10.59429 (6)0.33262 (7)1.31759 (19)0.0498 (3)
N20.69678 (6)0.38529 (7)1.31927 (17)0.0476 (3)
N30.62385 (6)0.41598 (6)1.10454 (18)0.0457 (3)
N40.59232 (6)0.49704 (6)0.79397 (17)0.0440 (3)
C10.61119 (9)0.29307 (9)1.4583 (2)0.0557 (4)
H10.58190.26161.50700.067*
C20.66955 (9)0.29663 (9)1.5342 (2)0.0575 (4)
H20.68050.26851.63180.069*
C30.71099 (9)0.34407 (9)1.4582 (2)0.0545 (4)
H30.75110.34751.50660.065*
C40.63848 (7)0.37709 (7)1.2534 (2)0.0404 (3)
C50.65864 (8)0.48112 (8)1.0596 (2)0.0508 (4)
H5A0.70190.47621.09820.061*
H5B0.64040.52181.12190.061*
C60.65682 (7)0.49460 (8)0.8609 (2)0.0489 (4)
H6A0.67750.53980.83480.059*
H6B0.67960.45680.79980.059*
C70.56029 (8)0.41465 (9)1.0326 (2)0.0503 (4)
H7A0.53500.45091.09140.060*
H7B0.54140.36821.05520.060*
C80.56174 (8)0.42877 (8)0.8347 (2)0.0512 (4)
H8A0.58410.39020.77550.061*
H8B0.51920.42950.78900.061*
C90.59173 (9)0.51044 (9)0.6002 (2)0.0545 (4)
H9A0.55010.50060.55410.065*
H9B0.62080.47770.54260.065*
C100.56549 (8)0.64162 (9)0.5773 (2)0.0495 (4)
H100.52470.63190.61440.059*
C110.60958 (8)0.58649 (9)0.5536 (2)0.0491 (4)
C120.66915 (9)0.60274 (11)0.4929 (3)0.0619 (5)
H120.69750.56550.47460.074*
C130.68819 (9)0.67322 (11)0.4582 (3)0.0691 (5)
H130.72840.68370.41750.083*
C140.64478 (8)0.72593 (10)0.4871 (2)0.0567 (4)
C150.58497 (8)0.71057 (9)0.5435 (2)0.0494 (4)
C160.59495 (9)0.82922 (10)0.5360 (3)0.0644 (5)
H16A0.60370.85070.65130.077*
H16B0.57860.86620.45740.077*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0539 (8)0.0690 (8)0.0972 (11)0.0100 (7)0.0008 (7)0.0219 (8)
O20.0523 (7)0.0565 (7)0.0901 (9)0.0039 (6)0.0045 (7)0.0059 (6)
N10.0442 (7)0.0486 (7)0.0564 (8)0.0013 (6)0.0050 (6)0.0033 (6)
N20.0433 (7)0.0517 (7)0.0477 (7)0.0018 (6)0.0037 (6)0.0038 (6)
N30.0380 (7)0.0450 (6)0.0542 (7)0.0030 (5)0.0059 (6)0.0058 (6)
N40.0415 (7)0.0422 (6)0.0484 (7)0.0022 (5)0.0063 (5)0.0005 (5)
C10.0596 (11)0.0488 (8)0.0588 (10)0.0012 (8)0.0133 (8)0.0074 (8)
C20.0655 (11)0.0567 (9)0.0502 (9)0.0051 (9)0.0014 (8)0.0102 (8)
C30.0535 (10)0.0591 (9)0.0510 (9)0.0018 (8)0.0078 (8)0.0040 (8)
C40.0403 (7)0.0372 (7)0.0439 (8)0.0042 (6)0.0034 (6)0.0050 (6)
C50.0496 (9)0.0459 (8)0.0569 (9)0.0080 (7)0.0131 (7)0.0060 (7)
C60.0406 (8)0.0501 (8)0.0560 (9)0.0019 (7)0.0057 (7)0.0064 (7)
C70.0366 (8)0.0486 (8)0.0656 (10)0.0008 (7)0.0031 (7)0.0062 (8)
C80.0418 (8)0.0476 (8)0.0642 (10)0.0012 (7)0.0128 (7)0.0025 (8)
C90.0568 (10)0.0563 (9)0.0505 (9)0.0028 (8)0.0106 (8)0.0043 (8)
C100.0375 (8)0.0616 (9)0.0495 (9)0.0008 (7)0.0004 (7)0.0046 (7)
C110.0461 (9)0.0599 (9)0.0412 (8)0.0034 (7)0.0069 (6)0.0020 (7)
C120.0467 (10)0.0742 (11)0.0649 (11)0.0142 (9)0.0008 (8)0.0053 (9)
C130.0371 (9)0.0875 (13)0.0827 (13)0.0006 (9)0.0073 (9)0.0176 (11)
C140.0433 (9)0.0685 (10)0.0582 (9)0.0046 (8)0.0038 (7)0.0129 (8)
C150.0411 (8)0.0580 (9)0.0490 (8)0.0055 (7)0.0030 (7)0.0055 (7)
C160.0618 (12)0.0592 (10)0.0723 (12)0.0022 (9)0.0057 (9)0.0125 (9)
Geometric parameters (Å, º) top
O1—C141.381 (2)C6—H6A0.9700
O1—C161.428 (2)C6—H6B0.9700
O2—C151.374 (2)C7—H7A0.9700
O2—C161.423 (2)C7—H7B0.9700
N1—C11.335 (2)C7—C81.505 (2)
N1—C41.343 (2)C8—H8A0.9700
N2—C31.328 (2)C8—H8B0.9700
N2—C41.345 (2)C9—H9A0.9700
N3—C41.365 (2)C9—H9B0.9700
N3—C51.4611 (19)C9—C111.508 (2)
N3—C71.458 (2)C10—H100.9300
N4—C61.4636 (19)C10—C111.403 (2)
N4—C81.4610 (19)C10—C151.373 (2)
N4—C91.472 (2)C11—C121.382 (3)
C1—H10.9300C12—H120.9300
C1—C21.369 (3)C12—C131.398 (3)
C2—H20.9300C13—H130.9300
C2—C31.373 (3)C13—C141.366 (3)
C3—H30.9300C14—C151.373 (2)
C5—H5A0.9700C16—H16A0.9700
C5—H5B0.9700C16—H16B0.9700
C5—C61.510 (2)
C14—O1—C16104.96 (14)C8—C7—H7A109.7
C15—O2—C16105.09 (14)C8—C7—H7B109.7
C1—N1—C4115.70 (15)N4—C8—C7111.53 (13)
C3—N2—C4115.61 (14)N4—C8—H8A109.3
C4—N3—C5120.85 (13)N4—C8—H8B109.3
C4—N3—C7120.32 (13)C7—C8—H8A109.3
C7—N3—C5113.60 (12)C7—C8—H8B109.3
C6—N4—C9110.51 (13)H8A—C8—H8B108.0
C8—N4—C6108.67 (11)N4—C9—H9A109.1
C8—N4—C9110.47 (13)N4—C9—H9B109.1
N1—C1—H1118.5N4—C9—C11112.68 (13)
N1—C1—C2123.09 (16)H9A—C9—H9B107.8
C2—C1—H1118.5C11—C9—H9A109.1
C1—C2—H2121.8C11—C9—H9B109.1
C1—C2—C3116.33 (16)C11—C10—H10121.3
C3—C2—H2121.8C15—C10—H10121.3
N2—C3—C2123.37 (17)C15—C10—C11117.31 (15)
N2—C3—H3118.3C10—C11—C9119.30 (15)
C2—C3—H3118.3C12—C11—C9120.90 (16)
N1—C4—N2125.88 (14)C12—C11—C10119.77 (16)
N1—C4—N3117.34 (14)C11—C12—H12118.9
N2—C4—N3116.75 (13)C11—C12—C13122.22 (17)
N3—C5—H5A109.5C13—C12—H12118.9
N3—C5—H5B109.5C12—C13—H13121.7
N3—C5—C6110.62 (13)C14—C13—C12116.67 (17)
H5A—C5—H5B108.1C14—C13—H13121.7
C6—C5—H5A109.5C13—C14—O1128.63 (17)
C6—C5—H5B109.5C13—C14—C15121.84 (17)
N4—C6—C5111.51 (13)C15—C14—O1109.50 (16)
N4—C6—H6A109.3C10—C15—O2127.97 (15)
N4—C6—H6B109.3C14—C15—O2109.87 (15)
C5—C6—H6A109.3C14—C15—C10122.15 (16)
C5—C6—H6B109.3O1—C16—H16A110.2
H6A—C6—H6B108.0O1—C16—H16B110.2
N3—C7—H7A109.7O2—C16—O1107.65 (15)
N3—C7—H7B109.7O2—C16—H16A110.2
N3—C7—C8109.99 (14)O2—C16—H16B110.2
H7A—C7—H7B108.2H16A—C16—H16B108.5
O1—C14—C15—O20.8 (2)C7—N3—C5—C652.15 (18)
O1—C14—C15—C10179.46 (16)C8—N4—C6—C558.80 (17)
N1—C1—C2—C30.3 (3)C8—N4—C9—C11167.44 (13)
N3—C5—C6—N454.89 (18)C9—N4—C6—C5179.83 (13)
N3—C7—C8—N456.91 (17)C9—N4—C8—C7178.59 (14)
N4—C9—C11—C1076.79 (19)C9—C11—C12—C13176.31 (18)
N4—C9—C11—C12101.32 (19)C10—C11—C12—C131.8 (3)
C1—N1—C4—N20.8 (2)C11—C10—C15—O2178.97 (16)
C1—N1—C4—N3177.08 (13)C11—C10—C15—C140.6 (3)
C1—C2—C3—N20.3 (3)C11—C12—C13—C140.0 (3)
C3—N2—C4—N11.3 (2)C12—C13—C14—O1179.37 (19)
C3—N2—C4—N3176.54 (14)C12—C13—C14—C151.4 (3)
C4—N1—C1—C20.1 (2)C13—C14—C15—O2177.46 (18)
C4—N2—C3—C21.0 (2)C13—C14—C15—C101.2 (3)
C4—N3—C5—C6153.35 (14)C14—O1—C16—O216.4 (2)
C4—N3—C7—C8152.42 (14)C15—O2—C16—O116.9 (2)
C5—N3—C4—N1159.58 (14)C15—C10—C11—C9176.11 (14)
C5—N3—C4—N222.4 (2)C15—C10—C11—C122.0 (2)
C5—N3—C7—C852.93 (18)C16—O1—C14—C13172.2 (2)
C6—N4—C8—C760.01 (17)C16—O1—C14—C159.7 (2)
C6—N4—C9—C1172.26 (17)C16—O2—C15—C10170.46 (18)
C7—N3—C4—N16.8 (2)C16—O2—C15—C1411.0 (2)
C7—N3—C4—N2175.17 (13)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the pyrimidine ring and Cg2 is the centroid of the benzene ring.
D—H···AD—HH···AD···AD—H···A
C2—H2···Cg1i0.932.833.6771 (17)152
C9—H9B···Cg1ii0.972.923.8090 (18)152
C16—H16A···Cg2iii0.972.803.689 (2)153
Symmetry codes: (i) x, y1/2, z1/2; (ii) x, y, z1; (iii) x, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC16H18N4O2
Mr298.34
Crystal system, space groupOrthorhombic, Pccn
Temperature (K)291
a, b, c (Å)21.3085 (6), 18.6249 (4), 7.48851 (19)
V3)2971.95 (12)
Z8
Radiation typeCu Kα
µ (mm1)0.74
Crystal size (mm)0.25 × 0.2 × 0.2
Data collection
DiffractometerAgilent Xcalibur (Eos, Gemini)
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2012)'
Tmin, Tmax0.910, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
6334, 2635, 2186
Rint0.019
(sin θ/λ)max1)0.597
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.039, 0.112, 1.03
No. of reflections2635
No. of parameters200
No. of restraints0
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.13, 0.14

Computer programs: CrysAlis PRO (Agilent, 2012), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).

Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the pyrimidine ring and Cg2 is the centroid of the benzene ring.
D—H···AD—HH···AD···AD—H···A
C2—H2···Cg1i0.932.833.6771 (17)152
C9—H9B···Cg1ii0.972.923.8090 (18)152
C16—H16A···Cg2iii0.972.803.689 (2)153
Symmetry codes: (i) x, y1/2, z1/2; (ii) x, y, z1; (iii) x, y+1/2, z1/2.
Acknowledgements top

We thank Hongmin Liu (Zhengzhou University) for the analysis of the single-crystal data.

references
References top

Agilent (2012). CrysAlis PRO. Agilent Technologies, Yarnton, England.

Conroy, E. A. & Denton, J. J. (1953). J. Org. Chem. 18, 1489–1491.

Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.

Duncton, M. A. J., Roffey, J. R. A., Hamlyn, R. J. & Adams, D. R. (2006). Tetrahedron Lett. 47, 2549–2552.

Hamid, M. H. A. & Williams, J. M. J. (2007). Tetrahedron Lett., 48, 8263–8265.

Rondot, P. & Ziegler, M. (1992). J. Neurol. pp. S28–S34.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.