The crystal structure of 1-(2-iodobenzoyl)-4-(pyrimidin-2-yl)piperazine: a three-dimensional hydrogen-bonded framework, augmented by π–π stacking interactions and I⋯N halogen bonds

Molecules of the title compound are linked into a complex three-dimensional network by a combination of C—H⋯O and C—H⋯π(arene) hydrogen bonds.


Supramolecular features
The supramolecular assembly of compound (I) is built from two C-HÁ Á ÁO hydrogen bonds, involving the aryl and pyrimidyl atoms C16 and C45 as the donors (Table 1), and one C-HÁ Á Á(arene) hydrogen bond: there is a further intermolecular C-HÁ Á ÁO contact, involving atom C13, but here the D-HÁ Á ÁA angle is less than 140 , and so this contact cannot be regarded as structurally significant (Wood et al., 2009). There are also present in the structure astacking interaction between pairs of pyrimidine rings and an IÁ Á ÁN halogen bond.
The hydrogen bonds give rise to a three-dimensional network structure of considerable complexity, but this is readily analysed in terms of three one-dimensional substructures (Ferguson et al., 1998a,b;Gregson et al., 2000). The action of the two C-HÁ Á ÁO hydrogen bonds in combination links molecules related by inversion and translation into a chain of edge-fused rings running parallel to the [001] direction (Fig. 2), in which R 2 2 (10) (Etter, 1990;Etter et al., 1990;Bernstein et al., 1995) rings centred at (0.5, 0.5, n + 0.5) alternate with R 2 4 (28) rings centred at (0.5, 0.5, n), where n represents an integer in each case.

Figure 2
Part of the crystal structure of compound (I) showing the formation of a hydrogen-bonded chain of edge-fused rings parallel to the [001] direction. Hydrogen bonds are drawn as dashed lines and, for the sake of clarity, the H atoms not involved in the motif shown have been omitted. The I atoms marked with an asterisk (*), a hash (#) or a dollar sign ($) are at the symmetry positions (1 À x, 1 À y, 1 À z), (x, y, 1 + z) and (1 À x, 1 À y, 2 À z), respectively.

Figure 1
The molecular structure of compound (I) showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.
use only one type of hydrogen bond, but the alternating action of the C-HÁ Á ÁO and C-HÁ Á Á(arene) hydrogen bonds involving atoms C16 and C46 as the donors (Table 1)  The formation of the hydrogen-bonded network is augmented by two further intermolecular interactions, each of which involves inversion related pairs of molecules. The pyrimidine rings of the molecules at (x, y, z) and (1 À x, 1 À y, 2 À z), which are components of the hydrogen-bonded chain along [001], are strictly parallel with an interplanar spacing of 3.4295 (10) Å and a ring-centroid separation of 3.4924 (6) Å , thus giving rise to astacking interaction (Fig. 5). Finally, we note a short intermolecular IÁ Á ÁN contact with geometrical parameters of I12Á Á ÁN41 i = 3.168 (2) Å and C12-I12Á Á ÁN41 i 174.83 (7) [symmetry code: (i) Àx, 1 À y, 1 À z], which can be regarded as a halogen bond (Gilday et al., 2015;Cavallo et al., 2016).

Database survey
It is of interest briefly to compare the structure of compound (I) reported here with those of some related structures which have been recently reported. In 2-{4-[(1,3-benzodioxol-5-yl)methyl]piperazin-1-yl}pyrimidine (II), the molecules are linked into sheets by a combination of C-HÁ Á Á(arene) and C-HÁ Á Á(pyrimidine) hydrogen bonds (Wu et al., 2013). N-(4-Chlorophenyl)-4-(pyrimidin-2-yl)piperazine-1-carboxamide (III) crystallizes with Z 0 = 2 in space group P2 1 /c (Li, 2011b), and the molecules are linked into chains by two independent N-HÁ Á ÁO hydrogen bonds: these chains, parallel to [100], are of the C 2 2 (8) type rather than of the C(4) type as originally reported. However, the original report overlooked the presence of C-HÁ Á ÁO hydrogen bonds which, in combination with the N-HÁ Á ÁO hydrogen bond within the selected asymmetric unit, generates a second chain, this time running parallel to the [010] direction ( Fig. 6), so that overall the supramolecular assembly takes the form of a sheet parallel to (001). In the simpler analogue N-(4-chlorophenyl)-4methylpiperidine-1-carboxamide (IV), the assembly was reported (Li, 2011a) as consisting of simple C(4) chains built from N-HÁ Á ÁO hydrogen bonds. However, the presence in (IV) of a C-HÁ Á ÁO hydrogen bond was overlooked, and the two hydrogen bonds together generate a complex sheet structure lying parallel to (100) (Fig. 7). Finally, we note also the structures of a number of salts of the 4-(pyrimidin-2yl)piperazin-1-ium cation, including the chloride and nitrate

Figure 3
Part of the crystal structure of compound (I) showing the formation of a hydrogen-bonded chain parallel to the [010] direction. Hydrogen bonds are drawn as dashed lines and, for the sake of clarity, the H atoms not involved in the motif shown have been omitted. The I atoms marked with an asterisk (*), a hash (#) or a dollar sign ($) are at the symmetry positions ( 1 2 À x, 1 2 + y, 3 2 À z), ( 1 2 À x, À 1 2 + y, 3 2 À z) and (x, 1 + y, z), respectively.

Synthesis and crystallization
1-(2-Pyrimidyl)piperazine was purchased from Sigma-Aldrich. For the synthesis of compound (I), 1-(3-dimethylaminopropyl)-3-ethylcarbodimide (52 mg, 0.6 mmol), 1-hydroxybenzotriazole (81 mg, 0.6 mmol) and triethylamine (0.5 ml, 1.8 mmol) were added to a solution of 2-iodobenzoic acid (0.6 mmol) in N,N-dimethylformamide (5 ml) and the resulting mixture stirred for 20 mins at 273 K. A solution of 1-(2-pyrimidyl)piperazine (100 mg, 0.6 mmol) in N,N-dimethylformamide (5 ml) was then added and stirring was continued overnight at ambient temperature. The reaction was confirmed to be complete using thin-layer chromatography, and the mixture was then quenched with water (10 ml) and extracted with ethyl acetate (20 ml). The organic layer was separated and washed successively with an aqueous hydrochloric acid solution (1 mol dm À3 ), a saturated solution of sodium hydrogencarbonate and then with brine. The organic phase was dried over anhydrous sodium sulfate and the solvent was removed under reduced pressure. Crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation, at ambient temperature and in the presence of air, of a solution in methanol; m. p. 450-452 K.   Part of the crystal structure of compound (IV) showing the formation of a hydrogen-bonded sheet parallel to (100). The original atomic coordinates (Li, 2011a) have been used and, for the sake of clarity, the H atoms not involved in the motif shown have been omitted.

Figure 5
Part of the crystal structure of compound (I) showing thestacking interaction between adjacent pyrimidine rings. For the sake of clarity, the unit-cell outline and the H atoms have been omitted. The I atom marked with an asterisk (*) is at the symmetry position (1 À x, 1 À y, 2 À z).

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were located in difference maps, and they were subsequently treated as riding atoms in geometrically idealized positions with C-H distances of 0.95 Å (aromatic) or 0.99 Å (CH 2 ), and with U iso (H) = 1.2U eq (C).

1-(2-Iodobenzoyl)-4-(pyrimidin-2-yl)piperazine
Crystal data Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å 2 )