Crystal structure of 2-chloro-5-(3-hydroxy-3-methylbut-1-yn-1-yl)pyrimidine

The ethynylpyrimidine moiety displays an almost planar geometry. In the crystal, molecules are linked by O—H⋯N and C—Hpyrimidine⋯O hydrogen bonds, forming a three-dimensional supramolecular architecture.


Chemical context
The title compound, featuring a blocked acetylenic group and a chloro-substituted pyrimidine ring, is an interesting synthetic intermediate for the preparation of application-oriented solid materials including both porous coordination polymers (MacGillivray, 2010) and metal-organic frameworks (Noro & Kitagawa, 2010). Deprotection of the acetylenic functional group and transformation of the chloro substituent, e.g. into thiol or amino groups, should result in molecular building blocks for the formation of corresponding aggregate structures (Hü bscher et al., 2015;Gü nthel et al., 2015;Hü bscher et al., 2017). Aside from this experimental preparative relevance, substituted 3-hydroxyalkynes are also of considerable interest due to their structural capacity in supramolecular interactions, giving rise to particular modes of aggregation and behavior in the solid state (Toda et al., 1983(Toda et al., , 1985Bourne et al., 1994). In combination with heterocyclic nitrogen donors and chlorine substitution, as in the present title compound, a structural study involving competition aspects with regard to hydrogen bonding (Wang & Zheng, 2015) and potential halogen (Mukherjee et al., 2014) or -electron assisted (Tiekink & Zukerman-Schpector, 2012) interactions should be a promising field of inquiry for crystal engineering (Desiraju et al., 2012) being subject to the contacts emanating from a variety of functional groups. Thus, in this respect, the title compound could serve as a worthwhile test substance.

Structural commentary
A perspective view of the molecular structure of the title compound is depicted in Fig. 1. The ethynylpyrimidine moiety of the molecule is almost planar with the largest atomic distances from the mean plane being 0.015 (1) Å for atom C1 ISSN 2056-9890 and 0.013 (1) Å for atom C4. The OH group adopts a staggered arrangement with respect to the ethynyl unit and the methyl group C9, the C6-C7-O1-H1 torsion angle being 57.0 .

Supramolecular features
An O-HÁ Á Á C C hydrogen-bond type intermolecular interaction mode typical of 3-hydroxyalkyne structure units (Desiraju & Steiner, 1999) is not present here, apparently in favor of a stronger O-HÁ Á ÁN hydrogen bond involving the hydroxy group and a pyrimidine nitrogen atom (N2). Aside from this, C-H pyrimidine Á Á ÁO hydrogen bonds are found to yield a three-dimensional supramolecular architecture (Table 1, Fig. 2). No other types of directed intermolecular contacts, including those involving the Cl atom or -arene stacking, are observed. Hence, this shows that in the presence of a strong donor center such as a nitrogen atom, competing with the acetylenic moiety, the common O-HÁ Á Á C C hydrogen bonding is suppressed, which could be a useful finding in relation to aspects of crystal engineering.

Figure 2
Packing excerpt of the title compound. Hydrogen bonds are shown as dashed lines.

Figure 1
Perspective view of the molecular structure of the title compound including the atom-numbering scheme. Displacement parameters are drawn at the 50% probability level.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were included in calculated positions (C-H = 0.95, 0.98 Å ; O-H = 0.84 Å ) and allowed to ride on their parent atoms with U iso (H) = 1.5U eq (C,O) for methyl and hydroxy H atoms and 1.2U eq (C) for aryl H atoms.

2-Chloro-5-(3-hydroxy-3-methylbut-1-yn-1-yl)pyrimidine
Crystal data Special details Experimental. The melting point was measured using a microscope heating stage (Thermovar, Reichert-Jung). The NMR spectra were obtained on a Bruker Avance 500.1 ( 1 H) and 125.8 MHz ( 13 C) with TMS as internal standard (δ in ppm). The IR spectrum was determined on a Nicolet FT-IR 510 spectrometer as KBr pellet (wavenumber is given in cm -1 ). The mass spectrum was recorded on a Hewlett-Packard 5890 Series II/MS 5989A. Elemental analysis was carried out with a Hanau vario MICRO cube. 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 )
x y z U iso */U eq